diff --git a/.config_files.xml b/.config_files.xml index 8e4868b94f..a1775b52ce 100644 --- a/.config_files.xml +++ b/.config_files.xml @@ -5,22 +5,24 @@ char unset - $SRCROOT - $CIMEROOT/src/components/data_comps/dlnd - $CIMEROOT/src/components/stub_comps/slnd - $CIMEROOT/src/components/xcpl_comps/xlnd + $SRCROOT + $SRCROOT + $CIMEROOT/src/components/data_comps_mct/dlnd + $CIMEROOT/src/components/cdeps/dlnd + $CIMEROOT/src/components/stub_comps_$COMP_INTERFACE/slnd + $CIMEROOT/src/components/xcpl_comps_$COMP_INTERFACE/xlnd case_comps env_case.xml diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000000..e9f0bd7694 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,6 @@ +*.svg filter=lfs diff=lfs merge=lfs -text +*.png filter=lfs diff=lfs merge=lfs -text +*.jpg filter=lfs diff=lfs merge=lfs -text +*.jpeg filter=lfs diff=lfs merge=lfs -text +*.gif filter=lfs diff=lfs merge=lfs -text +*.pdf filter=lfs diff=lfs merge=lfs -text diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 306ee7b1f3..4c8f6ca499 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -16,5 +16,7 @@ Testing performed, if any: (Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide) (aux_clm on cheyenne for intel/gnu and izumi for intel/gnu/nag/pgi is the standard for tags on master) -**NOTE: Be sure to check your Coding style against the standard:** -https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines +**NOTE: Be sure to check your coding style against the standard +(https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines) and review +the list of common problems to watch out for +(https://github.com/ESCOMP/CTSM/wiki/List-of-common-problems).** diff --git a/.gitignore b/.gitignore index 4a5672d970..26aca9549c 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,7 @@ manage_externals.log /tools/PTCLM/ /cime/ /components/ +/doc/doc-builder/ # ignore svn directories **/.svn/** @@ -17,6 +18,23 @@ manage_externals.log *.swp *~ +# vim files (from https://github.com/github/gitignore/blob/master/Global/Vim.gitignore) +# Swap +[._]*.s[a-v][a-z] +[._]*.sw[a-p] +[._]s[a-rt-v][a-z] +[._]ss[a-gi-z] +[._]sw[a-p] +# Session +Session.vim +# Temporary +.netrwhist +# (removed *~ because it is listed above) +# Auto-generated tag files +tags +# Persistent undo +[._]*.un~ + # mac files .DS_Store @@ -30,16 +48,6 @@ CMakeFiles/ # unit testing directories /src/unit_tests.* -# files generated by the unit test build -/src/dyn_subgrid/dynVarMod.F90 -/src/dyn_subgrid/dynVarTimeInterpMod.F90 -/src/dyn_subgrid/dynVarTimeUninterpMod.F90 -/src/utils/array_utils.F90 -/src/unit_test_stubs/utils/restUtilMod_stub.F90 -/src/unit_test_stubs/main/ncdio_pio_fake.F90 -/src/unit_test_stubs/main/ncdio_var.F90 -/src/unit_test_shr/unittestArrayMod.F90 - # cime_config buildnmlc @@ -55,6 +63,7 @@ buildnmlc /bld/unit_testers/drv_flds_in* /bld/unit_testers/temp_file.txt* /bld/unit_testers/user_nl_clm_real_parameters* +/bld/unit_testers/user_nl_ctsm_real_parameters* /bld/unit_testers/env_run.xml # tools testing output @@ -69,10 +78,13 @@ surfdata_*.namelist landuse.timeseries_*.namelist landuse.timeseries_*.log landuse_timeseries_*.txt -clm.input_data_list -clm.input_data_list.previous +ctsm.input_data_list +ctsm.input_data_list.previous *.stdout.txt.o* +# mksurfdata unit tests +unit_test_build + # Tools executables /tools/mksurfdata_map/mksurfdata_map /tools/mkprocdata_map/mkprocdata_map diff --git a/.lfsconfig b/.lfsconfig new file mode 100644 index 0000000000..3d2778fad3 --- /dev/null +++ b/.lfsconfig @@ -0,0 +1,2 @@ +[lfs] + fetchexclude = * diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000000..1982ce4917 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,7 @@ +{ + "creators": [ + { + "name": "CTSM Development Team" + } + ] +} diff --git a/Copyright b/Copyright deleted file mode 100644 index 21b9688874..0000000000 --- a/Copyright +++ /dev/null @@ -1,75 +0,0 @@ -CESM1.5: Copyright Notice and Disclaimer - -The Community Earth System Model (CESM was developed in cooperation with -the National Science Foundation, the Department of Energy, -the National Aeronautics and Space Administration, and -the University Corporation for Atmospheric Research National Center for Atmospheric Research. - -Except for the segregable components listed below, CESM is public domain software. -There may be other third party tools and libraries that are embedded, and -they may have their own copyright notices and terms. - -The following components are copyrighted and may only be used, modified, -or redistributed under the terms indicated below. - -Code Institution Copyright Terms of Use/Disclaimer ----- ----------- --------- ----------------------- -ESMF University of Copyright University of Illinois/NCSA Open Source License - Illinois/NCSA 2002-2009, - University of - Illinois/NCSA - Open Source - License - -POP,SCRIP,CICE Los Alamos National Copyright 2008 Los Alamos National Security, LLC - Laboratory Los Alamos - National - Security, LLC - -CISM NCAR/LANL/ORNL/SNL/ Copyright GNU Lesser General Public License v. 3 - LBNL/NYU/U. Bristol/ 2004-2018, CISM is free software: you can redistribute it - U. Edinburgh/ GNU Lesser and/or modify it under the terms of the GNU - U. Montana/U. Swansea General Public Lesser General Public License as published by the - License v. 3 Free Software Foundation, either version 3 of the - License, or (at your option) any later version. - -AER RRTMG Atmospheric Copyright AER RRTMG Copyright - and 2002-2010, - Environmental Atmospheric - Research, Inc. and - Environmental - Research, Inc. - -MCT Argonne Copyright 2000, MCT Copyright - National 2010, - Laboratory University of - Chicago. - -ICSSP N/A Copyright 2003, ISCCP Simulator Software - 2010, Steve - Klein and Mark - Webb - -XML/Lite Wadsack-Allen Copyright 2001, The documentation for the Perl XML-Lite - Digital Group 2010 module is no longer available on-line. - Wadsack-Allen - Digital Group - -Inf_NaN Lahey Copyright(c) Copies of this source code, or standalone compiled -_Detection Computer 2003, Lahey files derived from this source may not be sold -module Systems, Inc. Computer without permission from Lahey Computers Systems. - Systems, Inc. All or part of this module may be freely incorporated - into executable programs which are offered for sale. - Otherwise, distribution of all or part of this file is - permitted, provided this copyright notice and header - are included. - - -THIS SOFTWARE IS PROVIDED BY UCAR AND ANY CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, -INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -DISCLAIMED. IN NO EVENT SHALL UCAR OR ANY CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER -IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF -THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - diff --git a/Externals.cfg b/Externals.cfg index b15f54e496..8fdff0ac4b 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -7,33 +7,59 @@ required = True [cism] local_path = components/cism protocol = git -repo_url = https://github.com/ESCOMP/cism-wrapper -tag = cism2_1_68 +repo_url = https://github.com/ESCOMP/CISM-wrapper +tag = cism2_1_78 externals = Externals_CISM.cfg required = True [rtm] local_path = components/rtm protocol = git -repo_url = https://github.com/ESCOMP/rtm -tag = rtm1_0_70 +repo_url = https://github.com/ESCOMP/RTM +tag = rtm1_0_76 required = True [mosart] local_path = components/mosart protocol = git -repo_url = https://github.com/ESCOMP/mosart -tag = mosart1_0_35 +repo_url = https://github.com/ESCOMP/MOSART +tag = mosart1_0_42 +required = True + +[mizuRoute] +local_path = components/mizuRoute +protocol = git +repo_url = https://github.com/nmizukami/mizuRoute +hash = 34723c2 required = True [cime] local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = branch_tags/cime5.8.15_a01 -externals = ../Externals_cime.cfg +tag = branch_tags/cime5.8.42_a01 +required = True + +[cmeps] +local_path = cime/src/drivers/nuopc/ +protocol = git +repo_url = https://github.com/ESCOMP/CMEPS.git +tag = v0.9.0 required = True +[cdeps] +local_path = components/cdeps +protocol = git +repo_url = https://github.com/ESCOMP/CDEPS.git +tag = v0.6.0 +required = True + +[doc-builder] +local_path = doc/doc-builder +protocol = git +repo_url = https://github.com/ESMCI/doc-builder +tag = v1.0.5 +required = False + [externals_description] schema_version = 1.0.0 - diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 84b7d5ec33..4551c8a634 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,15 +1,15 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/NCAR/fates-release -tag = fates_s1.8.1_a3.0.0_rev2 +repo_url = https://github.com/NGEET/fates +tag = sci.1.45.0_api.15.0.0 required = True [PTCLM] local_path = tools/PTCLM protocol = git -repo_url = https://github.com/ESCOMP/ptclm -tag = PTCLM2_180611 +repo_url = https://github.com/ESCOMP/PTCLM +tag = PTCLM2_20200902 required = True [externals_description] diff --git a/Externals_cime.cfg b/Externals_cime.cfg deleted file mode 100644 index cbede7df52..0000000000 --- a/Externals_cime.cfg +++ /dev/null @@ -1,9 +0,0 @@ -[cmeps] -hash = 181ff1ed9dfb279e619e8a2173f43baf7bf1dce3 -protocol = git -repo_url = https://github.com/ESCOMP/CMEPS.git -local_path = src/drivers/nuopc/ -required = True - -[externals_description] -schema_version = 1.0.0 diff --git a/README b/README index 76c0a04982..e8db3de87f 100644 --- a/README +++ b/README @@ -135,6 +135,10 @@ tools/ncl_scripts ------------ Directory of NCL and perl scripts to do various tasks. Most notably to plot perturbation error growth testing and to extract regional information from global datasets for single-point/regional simulations. +tools/contrib ----------------- Miscellansous useful scripts for pre and post processing + as well as case management of CTSM. These scripts are + contributed by users and may not be as well tested or + supported as other tools. ============================================================================================= diff --git a/README.md b/README.md new file mode 100644 index 0000000000..766705ee69 --- /dev/null +++ b/README.md @@ -0,0 +1,58 @@ +# CTSM + +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3739617.svg)](https://doi.org/10.5281/zenodo.3739617) + +## Overview and resources + +The Community Terrestrial Systems Model. + +This includes the Community Land Model (CLM5.0 and CLM4.5) of the Community Earth System Model. + +For documentation, quick start, diagnostics, model output and +references, see + +http://www.cesm.ucar.edu/models/cesm2.0/land/ + +and + +https://escomp.github.io/ctsm-docs/ + +For help with how to work with CTSM in git, see + +https://github.com/ESCOMP/CTSM/wiki/Quick-start-to-CTSM-development-with-git + +and + +https://github.com/ESCOMP/ctsm/wiki/Recommended-git-setup + +For support with model use, troubleshooting, etc., please use the CTSM forum (or other +appropriate forum) here: + +https://xenforo.cgd.ucar.edu/cesm/ + +To get updates on CTSM tags and important notes on CTSM developments +join our low traffic email list: + +https://groups.google.com/a/ucar.edu/forum/#!forum/ctsm-dev + +(Send email to ctsm-software@ucar.edu if you have problems with any of this) + +## CTSM code management team + +CTSM code management is provided primarily by: + +Software engineering team: +- [Erik Kluzek](https://github.com/ekluzek) +- [Bill Sacks](https://github.com/billsacks) +- [Mariana Vertenstein](https://github.com/mvertens) +- [Negin Sobhani](https://github.com/negin513) +- [Sam Levis](https://github.com/slevisconsulting) + +Science team: +- [Dave Lawrence](https://github.com/dlawrenncar) +- [Will Wieder](https://github.com/wwieder) +- [Danica Lombardozzi](https://github.com/danicalombardozzi) +- [Keith Oleson](https://github.com/olyson) +- [Sean Swenson](https://github.com/swensosc) +- [Mike Barlage](https://github.com/barlage) +- [Rosie Fisher](https://github.com/rosiealice) diff --git a/README.rst b/README.rst deleted file mode 100644 index b7711d4026..0000000000 --- a/README.rst +++ /dev/null @@ -1,36 +0,0 @@ -==== -CTSM -==== - -The Community Terrestrial Systems Model. - -This includes the Community Land Model (CLM5.0 and CLM4.5) of the Community Earth System Model. - -For documentation, quick start, diagnostics, model output and -references, see - -http://www.cesm.ucar.edu/models/cesm2.0/land/ - -and - -https://escomp.github.io/ctsm-docs/ - -For help with how to work with CTSM in git, see - -https://github.com/ESCOMP/ctsm/wiki/Getting-started-with-CTSM-in-git - -and - -https://github.com/ESCOMP/ctsm/wiki/Recommended-git-setup - -For support with model use, troubleshooting, etc., please use the CTSM forum (or other -appropriate forum) here: - -https://xenforo.cgd.ucar.edu/cesm/ - -To get updates on CTSM tags and important notes on CTSM developments -join our low traffic email list: - -https://groups.google.com/a/ucar.edu/forum/#!forum/ctsm-dev - -(Send email to ctsm-software@ucar.edu if you have problems with any of this) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index ae58cbaf12..359909f94b 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -35,7 +35,7 @@ use File::Basename qw(dirname); use English; use Getopt::Long; use IO::File; -use File::Glob ':glob'; +use File::Glob ':bsd_glob'; #------------------------------------------------------------------------------- # @@ -78,7 +78,7 @@ REQUIRED OPTIONS "-res list" to list valid resolutions. (default: 0.9x1.25) -sim_year "year" Year to simulate for input datasets - (i.e. 1850, 2000, 1850-2000, 1850-2100) + (i.e. PtVg, 1850, 2000, 2010, 1850-2000, 1850-2100) "-sim_year list" to list valid simulation years (default 2000) -structure "structure" The overall structure being used [ standard | fast ] @@ -167,6 +167,7 @@ OPTIONS (Note: buildnml copies the file for use by the driver) -glc_nec Glacier number of elevation classes [0 | 3 | 5 | 10 | 36] (default is 0) (standard option with land-ice model is 10) + -glc_use_antarctica Set defaults appropriate for runs that include Antarctica -help [or -h] Print usage to STDOUT. -light_res Resolution of lightning dataset to use for CN fire (360x720 or 94x192) -ignore_ic_date Ignore the date on the initial condition files @@ -189,7 +190,6 @@ OPTIONS form \$CASEDIR/user_nl_clm/user_nl_clm_????) -inputdata "filepath" Writes out a list containing pathnames for required input datasets in file specified. - -l_ncpl "LND_NCPL" Number of CLM coupling time-steps in a day. -lnd_tuning_mode "value" Use the parameters tuned for the given configuration (CLM version and atmospheric forcing) -mask "landmask" Type of land-mask (default, navy, gx3v5, gx1v5 etc.) "-mask list" to list valid land masks. @@ -203,9 +203,10 @@ OPTIONS -[no-]note Add note to output namelist [do NOT add note] about the arguments to build-namelist. -output_reals Output real parameters to the given output file. - -rcp "value" Representative concentration pathway (rcp) to use for + -ssp_rcp "value" Shared Socioeconomic Pathway (SSP) and + Representative Concentration Pathway (RCP) combination to use for future scenarios. - "-rcp list" to list valid rcp settings. + "-ssp_rcp list" to list valid ssp_rcp settings. -s Turns on silent mode - only fatal messages issued. -test Enable checking that input datasets exist on local filesystem. -use_case "case" Specify a use case which will provide default values. @@ -253,12 +254,12 @@ sub process_commandline { clm_demand => "null", help => 0, glc_nec => "default", + glc_use_antarctica => 0, light_res => "default", - l_ncpl => undef, lnd_tuning_mode => "default", lnd_frac => undef, dir => "$cwd", - rcp => "default", + ssp_rcp => "default", sim_year => "default", structure => undef, clm_accelerated_spinup=> "default", @@ -298,6 +299,7 @@ sub process_commandline { "note!" => \$opts{'note'}, "megan!" => \$opts{'megan'}, "glc_nec=i" => \$opts{'glc_nec'}, + "glc_use_antarctica!" => \$opts{'glc_use_antarctica'}, "light_res=s" => \$opts{'light_res'}, "d:s" => \$opts{'dir'}, "h|help" => \$opts{'help'}, @@ -306,12 +308,11 @@ sub process_commandline { "infile=s" => \$opts{'infile'}, "lnd_frac=s" => \$opts{'lnd_frac'}, "lnd_tuning_mode=s" => \$opts{'lnd_tuning_mode'}, - "l_ncpl=i" => \$opts{'l_ncpl'}, "inputdata=s" => \$opts{'inputdata'}, "mask=s" => \$opts{'mask'}, "namelist=s" => \$opts{'namelist'}, "res=s" => \$opts{'res'}, - "rcp=s" => \$opts{'rcp'}, + "ssp_rcp=s" => \$opts{'ssp_rcp'}, "s|silent" => \$opts{'silent'}, "sim_year=s" => \$opts{'sim_year'}, "structure=s" => \$opts{'structure'}, @@ -476,7 +477,7 @@ sub read_envxml_case_files { my %envxml = (); if ( defined($opts->{'envxml_dir'}) ) { (-d $opts->{'envxml_dir'}) or $log->fatal_error( "envxml_dir is not a directory" ); - my @files = glob( $opts->{'envxml_dir'}."/env_*xml" ); + my @files = bsd_glob( $opts->{'envxml_dir'}."/env_*xml" ); ($#files >= 0) or $log->fatal_error( "there are no env_*xml files in the envxml_dir" ); foreach my $file (@files) { $log->verbose_message( "Open env.xml file: $file" ); @@ -623,7 +624,7 @@ sub process_namelist_commandline_options { # # First get the command-line specified overall values or their defaults # Obtain default values for the following build-namelist input arguments - # : res, mask, rcp, sim_year, sim_year_range, and clm_accelerated_spinup. + # : res, mask, ssp_rcp, sim_year, sim_year_range, and clm_accelerated_spinup. my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; @@ -637,7 +638,7 @@ sub process_namelist_commandline_options { setup_cmdl_crop($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_maxpft($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_glc_nec($opts, $nl_flags, $definition, $defaults, $nl); - setup_cmdl_rcp($opts, $nl_flags, $definition, $defaults, $nl); + setup_cmdl_ssp_rcp($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_simulation_year($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_dynamic_vegetation($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_fates_mode($opts, $nl_flags, $definition, $defaults, $nl); @@ -767,8 +768,9 @@ sub setup_cmdl_fates_mode { } } else { # dis-allow fates specific namelist items with non-fates runs - my @list = ( "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", - "use_fates_inventory_init", "fates_inventory_ctrl_filename","use_fates_logging" ); + my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", + "use_fates_cohort_age_tracking", + "use_fates_inventory_init","use_fates_fixed_biogeog", "fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode" ); foreach my $var ( @list ) { if ( defined($nl->get_value($var)) ) { $log->fatal_error("$var is being set, but can ONLY be set when -bgc fates option is used.\n"); @@ -909,52 +911,58 @@ sub setup_cmdl_fire_light_res { my $var = "light_res"; my $val = $opts->{$var}; if ( $val eq "default" ) { - $nl_flags->{$var} = remove_leading_and_trailing_quotes($defaults->get_value($var)); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, + 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, + 'fates_spitfire_mode'=>$nl->get_value('fates_spitfire_mode'), + 'use_fates'=>$nl_flags->{'use_fates'}, fire_method=>$nl->get_value('fire_method') ); + $val = remove_leading_and_trailing_quotes( $nl->get_value($var) ); + $nl_flags->{$var} = $val; } else { my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); if ( defined($fire_method) && $val ne "none" ) { if ( $fire_method eq "nofire" ) { $log->fatal_error("-$var option used with fire_method='nofire'. -$var can ONLY be used without the nofire option"); - } - } - my $stream_fldfilename_lightng = remove_leading_and_trailing_quotes( $nl->get_value('stream_fldfilename_lightng') ); - if ( defined($stream_fldfilename_lightng) && $val ne "none" ) { - $log->fatal_error("-$var option used while also explicitly setting stream_fldfilename_lightng filename which is a contradiction. Use one or the other not both."); - } - if ( ! &value_is_true($nl->get_value('use_cn')) ) { - $log->fatal_error("-$var option used CN is NOT on. -$var can only be used when CN is on (with bgc: cn or bgc)"); - } - if ( &value_is_true($nl->get_value('use_cn')) && $val eq "none" ) { - $log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction"); - } - $nl_flags->{$var} = $val; - } - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, quote_string($nl_flags->{$var}) ); - if ( ! $definition->is_valid_value( $var, $nl_flags->{$var}, 'noquotes'=>1 ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values"); - } - $log->verbose_message("Using $nl_flags->{$var} for $var."); - # - # Set flag if cn-fires are on or not - # - $var = "cnfireson"; - if ( &value_is_true($nl->get_value('use_cn')) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_method'); - } - my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); - if ( defined($fire_method) && ! &value_is_true($nl_flags->{'use_cn'}) ) { - $log->fatal_error("fire_method is being set even though bgc is NOT cn or bgc."); - } - if ( defined($fire_method) && $fire_method eq "nofire" ) { - $nl_flags->{$var} = ".false."; - } elsif ( &value_is_true($nl->get_value('use_cn')) ) { - $nl_flags->{$var} = ".true."; - } else { - $nl_flags->{$var} = ".false."; + } + } + my $stream_fldfilename_lightng = remove_leading_and_trailing_quotes( $nl->get_value('stream_fldfilename_lightng') ); + if ( defined($stream_fldfilename_lightng) && $val ne "none" ) { + $log->fatal_error("-$var option used while also explicitly setting stream_fldfilename_lightng filename which is a contradiction. Use one or the other not both."); + } + if ( ! &value_is_true($nl->get_value('use_cn')) ) { + $log->fatal_error("-$var option used CN is NOT on. -$var can only be used when CN is on (with bgc: cn or bgc)"); + } + if ( &value_is_true($nl->get_value('use_cn')) && $val eq "none" ) { + $log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction"); + } + $nl_flags->{$var} = $val; + } + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, quote_string($nl_flags->{$var}) ); + if ( ! $definition->is_valid_value( $var, $nl_flags->{$var}, 'noquotes'=>1 ) ) { + my @valid_values = $definition->get_valid_values( $var ); + $log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values"); + } + $log->verbose_message("Using $nl_flags->{$var} for $var."); + # + # Set flag if cn-fires are on or not + # + $var = "cnfireson"; + if ( &value_is_true($nl->get_value('use_cn')) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_method'); + } + my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); + if ( defined($fire_method) && ! &value_is_true($nl_flags->{'use_cn'}) && ! &value_is_true($nl_flags->{'use_fates'}) ) { + $log->fatal_error("fire_method is being set while use_cn and use_fates are both false."); + } + if ( defined($fire_method) && $fire_method eq "nofire" ) { + $nl_flags->{$var} = ".false."; +# } elsif ( &value_is_true($nl->get_value('use_cn')) || $nl_flags->{'fates_spitfire_mode'} > 1 ) { + } elsif ( &value_is_true($nl->get_value('use_cn')) || &value_is_true($nl->get_value('use_fates')) ) { + $nl_flags->{$var} = ".true."; + } else { + $nl_flags->{$var} = ".false."; + } } -} #------------------------------------------------------------------------------- @@ -1010,37 +1018,6 @@ sub setup_cmdl_maxpft { } $nl_flags->{'maxpft'} = $val; - if ( ($nl_flags->{'bgc_mode'} ne "sp") && ($nl_flags->{'maxpft'} != $maxpatchpft{$nl_flags->{'use_crop'}}) ) { - $log->fatal_error("** For CN or BGC mode you MUST set max patch PFT's to $maxpatchpft{$nl_flags->{'use_crop'}}\n" . - "**\n" . - "** When the crop model is on then it must be set to $maxpatchpft{'crop'} otherwise to $maxpatchpft{'nocrop'}\n" . - "** Set the bgc mode, crop and maxpft by the following means from highest to lowest precedence:\n" . - "** * by the command-line options -bgc, -crop and -maxpft\n" . - "** * by a default configuration file, specified by -defaults\n" . - "**"); - } - if ( $nl_flags->{'maxpft'} > $maxpatchpft{$nl_flags->{'use_crop'}} ) { - $log->fatal_error("** Max patch PFT's can NOT exceed $maxpatchpft{$nl_flags->{'use_crop'}}\n" . - "**\n" . - "** Set maxpft by the following means from highest to lowest precedence:\n" . - "** * by the command-line options -maxpft\n" . - "** * by a default configuration file, specified by -defaults\n" . - "**"); - } - if ( $nl_flags->{'maxpft'} != $maxpatchpft{$nl_flags->{'use_crop'}} ) { - $log->warning("running with maxpft NOT equal to $maxpatchpft{$nl_flags->{'use_crop'}} is " . - "NOT validated / scientifically supported." ); - } - $log->verbose_message("Using $nl_flags->{'maxpft'} for maxpft."); - - $var = "maxpatch_pft"; - $val = $nl_flags->{'maxpft'}; - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - if ( ! $definition->is_valid_value( $var, $val ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); - } } #------------------------------------------------------------------------------- @@ -1070,26 +1047,26 @@ sub setup_cmdl_glc_nec { #------------------------------------------------------------------------------- -sub setup_cmdl_rcp { - # representative concentration pathway +sub setup_cmdl_ssp_rcp { + # shared socioeconmic pathway and representative concentration pathway combination my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $val; - my $var = "rcp"; + my $var = "ssp_rcp"; if ( $opts->{$var} ne "default" ) { $val = $opts->{$var}; } else { - $val = $defaults->get_value($var); + $val = remove_leading_and_trailing_quotes( $defaults->get_value($var) ); } - $nl_flags->{'rcp'} = $val; - $opts->{'rcp'} = $nl_flags->{'rcp'}; + $nl_flags->{'ssp_rcp'} = $val; + $opts->{'ssp_rcp'} = $nl_flags->{'ssp_rcp'}; my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - if ( ! $definition->is_valid_value( $var, $val ) ) { + $nl->set_variable_value($group, $var, quote_string($val) ); + if ( ! $definition->is_valid_value( $var, $val, 'noquotes'=>1 ) ) { my @valid_values = $definition->get_valid_values( $var ); $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); } - $log->verbose_message("CLM future scenario representative concentration is $nl_flags->{'rcp'}"); + $log->verbose_message("CLM future scenario SSP-RCP combination is $nl_flags->{'ssp_rcp'}"); } #------------------------------------------------------------------------------- @@ -1115,21 +1092,30 @@ sub setup_cmdl_spinup { $log->fatal_error("$var has an invalid value ($val). Valid values are: @valid_values"); } $log->verbose_message("CLM accelerated spinup mode is $val"); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, - $defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{$var}, - use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'} ); - if ( $nl->get_value("spinup_state") ne 0 ) { - $nl_flags->{'bgc_spinup'} = "on"; - if ( $nl_flags->{'bgc_mode'} eq "sp" ) { - $log->fatal_error("spinup_state is accelerated (=1 or 2) which is for a BGC mode of CN or BGC," . - " but the BGC mode is Satellite Phenology, change one or the other"); - } - if ( $nl_flags->{'clm_accelerated_spinup'} eq "off" ) { - $log->fatal_error("spinup_state is accelerated, but clm_accelerated_spinup is off, change one or the other"); - } + if ( &value_is_true($nl_flags->{'use_cn'}) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, + $defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{$var}, + use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'} ); + if ( $nl->get_value("spinup_state") ne 0 ) { + $nl_flags->{'bgc_spinup'} = "on"; + if ( $nl_flags->{'clm_accelerated_spinup'} eq "off" ) { + $log->fatal_error("spinup_state is accelerated, but clm_accelerated_spinup is off, change one or the other"); + } + } else { + $nl_flags->{'bgc_spinup'} = "off"; + $val = $defaults->get_value($var); + } + # For AD spinup mode by default reseed dead plants + if ( $nl_flags->{$var} ne "off" ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, + $defaults, $nl, "reseed_dead_plants", clm_accelerated_spinup=>$nl_flags->{$var}, + use_cn=>$nl_flags->{'use_cn'} ); + } } else { - $nl_flags->{'bgc_spinup'} = "off"; - $val = $defaults->get_value($var); + if ( defined($nl->get_value("spinup_state")) ) { + $log->fatal_error("spinup_state is accelerated (=1 or 2) which is for a BGC mode of CN or BGC," . + " but the BGC mode is Satellite Phenology, change one or the other"); + } } $nl_flags->{$var} = $val; my $group = $definition->get_group_name($var); @@ -1166,19 +1152,19 @@ sub setup_cmdl_simulation_year { } $nl_flags->{'sim_year_range'} = $defaults->get_value("sim_year_range"); - $nl_flags->{'sim_year'} = $val; + $nl_flags->{'sim_year'} = &remove_leading_and_trailing_quotes($val); if ( $val =~ /([0-9]+)-([0-9]+)/ ) { $nl_flags->{'sim_year'} = $1; $nl_flags->{'sim_year_range'} = $val; } $val = $nl_flags->{'sim_year'}; my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val ); + $nl->set_variable_value($group, $var, "'$val'" ); if ( ! $definition->is_valid_value( $var, $val, 'noquotes'=>1 ) ) { my @valid_values = $definition->get_valid_values( $var ); $log->fatal_error("$var of $val is NOT valid. Valid values are: @valid_values"); } - $nl->set_variable_value($group, $var, $val ); + $nl->set_variable_value($group, $var, "'$val'" ); $log->verbose_message("CLM sim_year is $nl_flags->{'sim_year'}"); $var = "sim_year_range"; @@ -1204,19 +1190,34 @@ sub setup_cmdl_run_type { my $val; my $var = "clm_start_type"; + my $ic_date = $nl->get_value('start_ymd'); + my $st_year; + if ( defined($ic_date) ) { + $st_year = int( $ic_date / 10000); + } else { + $st_year = $nl_flags->{'sim_year'}; + $ic_date = $st_year *10000 + 101; + my $date = 'start_ymd'; + my $group = $definition->get_group_name($date); + $nl->set_variable_value($group, $date, $ic_date ); + } if (defined $opts->{$var}) { if ($opts->{$var} eq "default" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - 'use_cndv'=>$nl_flags->{'use_cndv'}, 'use_fates'=>$nl_flags->{'use_fates'} ); + 'use_cndv'=>$nl_flags->{'use_cndv'}, 'use_fates'=>$nl_flags->{'use_fates'}, + 'sim_year'=>$st_year, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, + 'bgc_spinup'=>$nl_flags->{'bgc_spinup'} ); } else { my $group = $definition->get_group_name($var); $nl->set_variable_value($group, $var, quote_string( $opts->{$var} ) ); } } else { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - 'use_cndv'=>$nl_flags->{'use_cndv'}, 'use_fates'=>$nl_flags->{'use_fates'} ); + 'use_cndv'=>$nl_flags->{'use_cndv'}, 'use_fates'=>$nl_flags->{'use_fates'}, + 'sim_year'=>$st_year ); } $nl_flags->{'clm_start_type'} = $nl->get_value($var); + $nl_flags->{'st_year'} = $st_year; } #------------------------------------------------------------------------------- @@ -1377,7 +1378,7 @@ sub process_namelist_commandline_clm_usr_name { my %settings; $settings{'mask'} = $nl_flags->{'mask'}; $settings{'sim_year'} = $nl_flags->{'sim_year'}; - $settings{'rcp'} = $nl_flags->{'rcp'}; + $settings{'ssp_rcp'} = $nl_flags->{'ssp_rcp'}; $settings{'sim_year_range'} = $nl_flags->{'sim_year_range'}; $settings{'clm_accelerated_spinup'} = $nl_flags->{'clm_accelerated_spinup'}; $settings{'clm_usr_name'} = $opts->{'clm_usr_name'}; @@ -1399,9 +1400,6 @@ sub process_namelist_commandline_clm_usr_name { $nvars++; } } - if ( $nvars == 0 ) { - $log->message("setting clm_usr_name -- but did NOT find any user datasets: $opts->{'clm_usr_name'}", $opts); - } # Go through all variables and expand any XML env settings in them expand_xml_variables_in_namelist( $nl_usrfile, $envxml_ref ); # Merge input values into namelist. Previously specified values have higher precedence @@ -1424,7 +1422,7 @@ sub process_namelist_commandline_use_case { my %settings; $settings{'res'} = $nl_flags->{'res'}; - $settings{'rcp'} = $nl_flags->{'rcp'}; + $settings{'ssp_rcp'} = $nl_flags->{'ssp_rcp'}; $settings{'mask'} = $nl_flags->{'mask'}; $settings{'sim_year'} = $nl_flags->{'sim_year'}; $settings{'sim_year_range'} = $nl_flags->{'sim_year_range'}; @@ -1443,7 +1441,7 @@ sub process_namelist_commandline_use_case { my $val = $uc_defaults->get_value($var, \%settings ); if ( defined($val) ) { - $log->message("CLM adding use_case $opts->{'use_case'} defaults for var '$var' with val '$val'"); + $log->verbose_message("CLM adding use_case $opts->{'use_case'} defaults for var '$var' with val '$val'"); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl_usecase, $var, 'val'=>$val); } @@ -1486,12 +1484,11 @@ sub process_namelist_inline_logic { ############################## # namelist group: clm_inparm # ############################## - setup_logic_site_specific($nl_flags, $definition, $nl); + setup_logic_site_specific($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_lnd_frac($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref); setup_logic_co2_type($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_start_type($opts, $nl_flags, $nl); - setup_logic_delta_time($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_decomp_performance($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_snow($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref); @@ -1515,6 +1512,7 @@ sub process_namelist_inline_logic { setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_snowpack($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_fates($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_misc($opts, $nl_flags, $definition, $defaults, $nl); ######################################### # namelist group: atm2lnd_inparm @@ -1572,6 +1570,11 @@ sub process_namelist_inline_logic { ################################# setup_logic_nitrif_params( $nl_flags, $definition, $defaults, $nl ); + ############################################# + # namelist group: mineral_nitrogen_dynamics # + ############################################# + setup_logic_mineral_nitrogen_dynamics( $opts, $nl_flags, $definition, $defaults, $nl ); + #################################### # namelist group: photosyns_inparm # #################################### @@ -1612,11 +1615,21 @@ sub process_namelist_inline_logic { ################################## setup_logic_lai_streams($opts, $nl_flags, $definition, $defaults, $nl); + ########################################## + # namelist group: soil_moisture_streams # + ########################################## + setup_logic_soilm_streams($opts, $nl_flags, $definition, $defaults, $nl, $physv); + ################################## # namelist group: bgc_shared ################################## setup_logic_bgc_shared($opts, $nl_flags, $definition, $defaults, $nl, $physv); + ################################## + # namelist group: cnphenology + ################################## + setup_logic_cnphenology($opts, $nl_flags, $definition, $defaults, $nl, $physv); + ############################################# # namelist group: soilwater_movement_inparm # ############################################# @@ -1637,6 +1650,10 @@ sub process_namelist_inline_logic { ################################################ setup_logic_century_soilbgcdecompcascade($opts, $nl_flags, $definition, $defaults, $nl); + ############################# + # namelist group: cngeneral # + ############################# + setup_logic_cngeneral($opts, $nl_flags, $definition, $defaults, $nl); #################################### # namelist group: cnvegcarbonstate # #################################### @@ -1702,7 +1719,7 @@ sub process_namelist_inline_logic { sub setup_logic_site_specific { # site specific requirements - my ($nl_flags, $definition, $nl) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; # res check prevents polluting the namelist with an unnecessary # false variable for every run @@ -1733,6 +1750,9 @@ sub setup_logic_site_specific { $log->fatal_error("1x1_numaIA grids must use a compset with CN and CROP turned on."); } } + # Set compname + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'compname', + 'phys'=>$nl_flags->{'phys'} ); } #------------------------------------------------------------------------------- @@ -1810,7 +1830,8 @@ sub setup_logic_co2_type { my $group = $definition->get_group_name($var); $nl->set_variable_value($group, $var, $opts->{$var}); } else { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'sim_year'=>$nl_flags->{'sim_year'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'sim_year'=>$nl_flags->{'sim_year'}, + 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} ); } } } @@ -1821,7 +1842,8 @@ sub setup_logic_irrigate { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'irrigate', - 'use_crop'=>$nl_flags->{'use_crop'}, 'use_cndv'=>$nl_flags->{'use_cndv'} ); + 'use_crop'=>$nl_flags->{'use_crop'}, 'use_cndv'=>$nl_flags->{'use_cndv'}, + 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, ); if ( &value_is_true($nl->get_value('irrigate') ) ) { $nl_flags->{'irrigate'} = ".true." } else { @@ -1842,6 +1864,12 @@ sub setup_logic_start_type { if (not defined $nl->get_value('nrevsn')) { $log->fatal_error("nrevsn is required for a branch type."); } + if (defined $nl->get_value('use_init_interp')) { + if ( &value_is_true($nl->get_value('use_init_interp') ) ) { + # Always print this warning, but don't stop if it happens + print "\nWARNING: use_init_interp will NOT happen for a branch case.\n\n"; + } + } } else { if (defined $nl->get_value('nrevsn')) { $log->fatal_error("nrevsn should ONLY be set for a branch type."); @@ -1851,28 +1879,6 @@ sub setup_logic_start_type { #------------------------------------------------------------------------------- -sub setup_logic_delta_time { - my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - - if ( defined($opts->{'l_ncpl'}) ) { - my $l_ncpl = $opts->{'l_ncpl'}; - if ( $l_ncpl <= 0 ) { - $log->fatal_error("bad value for -l_ncpl option."); - } - my $val = ( 3600 * 24 ) / $l_ncpl; - my $dtime = $nl->get_value('dtime'); - if ( ! defined($dtime) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dtime', 'val'=>$val); - } elsif ( $dtime ne $val ) { - $log->fatal_error("can NOT set both -l_ncpl option (via LND_NCPL env variable) AND dtime namelist variable."); - } - } else { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dtime', 'hgrid'=>$nl_flags->{'res'}); - } -} - -#------------------------------------------------------------------------------- - sub setup_logic_decomp_performance { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; @@ -1910,7 +1916,7 @@ sub setup_logic_glacier { $log->fatal_error("glc_do_dynglacier can only be set via the env variable $clm_upvar: it can NOT be set in user_nl_clm"); } - my $var = "maxpatch_glcmec"; + my $var = "maxpatch_glc"; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'val'=>$nl_flags->{'glc_nec'} ); my $val = $nl->get_value($var); @@ -1925,7 +1931,8 @@ sub setup_logic_glacier { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glc_snow_persistence_max_days'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'albice'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_behavior'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_behavior', + 'glc_use_antarctica'=>$opts->{'glc_use_antarctica'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_melt_behavior'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'glacier_region_ice_runoff_behavior'); } @@ -1985,7 +1992,8 @@ sub setup_logic_cnfire { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my @fire_consts = ( "rh_low", "rh_hgh", "bt_min", "bt_max", "cli_scale", "boreal_peatfire_c", "non_boreal_peatfire_c", - "pot_hmn_ign_counts_alpha", "cropfire_a1", "occur_hi_gdp_tree", "lfuel", "ufuel", "cmb_cmplt_fact" ); + "pot_hmn_ign_counts_alpha", "cropfire_a1", "occur_hi_gdp_tree", "lfuel", "ufuel", + "cmb_cmplt_fact_litter", "cmb_cmplt_fact_cwd" ); if ( &value_is_true($nl->get_value('use_cn')) ) { foreach my $item ( @fire_consts ) { if ( ! &value_is_true($nl_flags->{'cnfireson'} ) ) { @@ -2077,7 +2085,6 @@ sub error_if_set { } } - #------------------------------------------------------------------------------- sub setup_logic_soilstate { @@ -2125,7 +2132,7 @@ sub setup_logic_demand { $settings{'sim_year_range'} = $nl_flags->{'sim_year_range'}; $settings{'mask'} = $nl_flags->{'mask'}; $settings{'crop'} = $nl_flags->{'crop'}; - $settings{'rcp'} = $nl_flags->{'rcp'}; + $settings{'ssp_rcp'} = $nl_flags->{'ssp_rcp'}; $settings{'glc_nec'} = $nl_flags->{'glc_nec'}; # necessary for demand to be set correctly (flanduse_timeseries requires # use_crop, maybe other options require other flags?)! @@ -2191,11 +2198,8 @@ sub setup_logic_surface_dataset { if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_cndv'}) ) { $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with dynamic vegetation (use_cndv=.true)." ); } - if ($flanduse_timeseries ne "null" && &value_is_true($nl_flags->{'use_fates'}) ) { - $log->fatal_error( "dynamic PFT's (setting flanduse_timeseries) are incompatible with ecosystem dynamics (use_fates=.true)." ); - } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsurdat', - 'hgrid'=>$nl_flags->{'res'}, + 'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'}, 'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'}); } @@ -2236,7 +2240,7 @@ sub setup_logic_initial_conditions { if (not defined $finidat ) { my $ic_date = $nl->get_value('start_ymd'); - my $st_year = int( $ic_date / 10000); + my $st_year = $nl_flags->{'st_year'}; my $nofail = 1; my %settings; $settings{'hgrid'} = $nl_flags->{'res'}; @@ -2252,11 +2256,11 @@ sub setup_logic_initial_conditions { $settings{'sim_year'} = $nl_flags->{'sim_year'}; $opts->{'ignore_ic_year'} = 1; } else { - delete( $settings{'sim_year'} ); + $settings{'sim_year'} = $st_year; } foreach my $item ( "mask", "maxpft", "irrigate", "glc_nec", "use_crop", "use_cn", "use_cndv", "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp", "use_fates", - "lnd_tuning_mode" + "lnd_tuning_mode", ) { $settings{$item} = $nl_flags->{$item}; } @@ -2275,10 +2279,11 @@ sub setup_logic_initial_conditions { my $try = 0; my $done = 2; my $use_init_interp_default = $nl->get_value($useinitvar); + $settings{$useinitvar} = $use_init_interp_default; if ( string_is_undef_or_empty( $use_init_interp_default ) ) { - $use_init_interp_default = ".false."; + $use_init_interp_default = $defaults->get_value($useinitvar, \%settings); + $settings{$useinitvar} = ".false."; } - $settings{$useinitvar} = $use_init_interp_default; do { $try++; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, %settings ); @@ -2293,39 +2298,65 @@ sub setup_logic_initial_conditions { #} add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_sim_years" ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_how_close" ); - foreach my $sim_yr ( split( /,/, $nl->get_value("init_interp_sim_years") )) { - if ( abs($st_year - $sim_yr) < $nl->get_value("init_interp_how_close") ) { + # + # Figure out which sim_year has a usable finidat file that is closest to the desired one + # + my $close = $nl->get_value("init_interp_how_close"); + my $closest_sim_year = undef; + my @sim_years = split( /,/, $nl->get_value("init_interp_sim_years") ); +SIMYR: foreach my $sim_yr ( @sim_years ) { + my $how_close = undef; + if ( $nl_flags->{'sim_year'} eq "PtVg" ) { + $how_close = abs(1850 - $sim_yr); + } elsif ( $nl_flags->{'flanduse_timeseries'} eq "null" ) { + $how_close = abs($nl_flags->{'sim_year'} - $sim_yr); + } else { + $how_close = abs($st_year - $sim_yr); + } + if ( ($sim_yr == $sim_years[-1]) || (($how_close < $nl->get_value("init_interp_how_close")) && ($how_close < $close)) ) { + my $group = $definition->get_group_name($useinitvar); $settings{'sim_year'} = $sim_yr; + $settings{$useinitvar} = $defaults->get_value($useinitvar, \%settings); + if ( ! defined($settings{$useinitvar}) ) { + $settings{$useinitvar} = $use_init_interp_default; + } + if ( &value_is_true($settings{$useinitvar}) ) { + + if ( ($how_close < $nl->get_value("init_interp_how_close")) && ($how_close < $close) ) { + $close = $how_close; + $closest_sim_year = $sim_yr; + } + } } - } + } # SIMYR: + $settings{'sim_year'} = $closest_sim_year; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $useinitvar, - 'use_cndv'=>$nl_flags->{'use_cndv'}, 'phys'=>$physv->as_string(), - 'sim_year'=>$settings{'sim_year'}, 'nofail'=>1, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, - 'use_fates'=>$nl_flags->{'use_fates'} ); + 'use_cndv'=>$nl_flags->{'use_cndv'}, 'phys'=>$physv->as_string(), 'hgrid'=>$nl_flags->{'res'}, + 'sim_year'=>$settings{'sim_year'}, 'nofail'=>1, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'use_fates'=>$nl_flags->{'use_fates'} ); $settings{$useinitvar} = $nl->get_value($useinitvar); - if ( $try > 1 ) { - my $group = $definition->get_group_name($useinitvar); - $nl->set_variable_value($group, $useinitvar, $use_init_interp_default ); - } - if ( &value_is_true($nl->get_value($useinitvar) ) ) { - - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_attributes", - 'sim_year'=>$settings{'sim_year'}, 'use_cndv'=>$nl_flags->{'use_cndv'}, - 'glc_nec'=>$nl_flags->{'glc_nec'}, 'use_fates'=>$nl_flags->{'use_fates'}, - 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'},'nofail'=>1 ); - my $attributes_string = remove_leading_and_trailing_quotes($nl->get_value("init_interp_attributes")); + if ( ! &value_is_true($nl->get_value($useinitvar) ) ) { + if ( $nl_flags->{'clm_start_type'} =~ /startup/ ) { + $log->fatal_error("clm_start_type is startup so an initial conditions ($var) file is required, but can't find one without $useinitvar being set to true"); + } + } else { + my $stat = add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_attributes", + 'sim_year'=>$settings{'sim_year'}, 'use_cndv'=>$nl_flags->{'use_cndv'}, + 'glc_nec'=>$nl_flags->{'glc_nec'}, 'use_fates'=>$nl_flags->{'use_fates'}, + 'hgrid'=>$nl_flags->{'res'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'nofail'=>1 ); + if ( $stat ) { + $log->fatal_error("$useinitvar is NOT synchronized with init_interp_attributes"); + } + my $attributes = $nl->get_value("init_interp_attributes"); + my $attributes_string = remove_leading_and_trailing_quotes($attributes); foreach my $pair ( split( /\s/, $attributes_string) ) { - if ( $pair =~ /^([a-z_]+)=([a-z._0-9]+)$/ ) { + if ( $pair =~ /^([a-z_]+)=([a-zA-Z._0-9]+)$/ ) { $settings{$1} = $2; } else { - $log->fatal_error("Problem interpreting init_interp_attributes"); + $log->fatal_error("Problem interpreting init_interp_attributes: $pair"); } } - } else { - if ( $nl_flags->{'clm_start_type'} =~ /startup/ ) { - $log->fatal_error("clm_start_type is startup so an initial conditions ($var) file is required, but can't find one without $useinitvar being set to true"); - } - $try = $done; } } else { $try = $done @@ -2352,6 +2383,7 @@ sub setup_logic_dynamic_subgrid { setup_logic_do_transient_pfts($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_do_transient_crops($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_do_transient_lakes($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_do_harvest($opts, $nl_flags, $definition, $defaults, $nl); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_dynbal_baselines'); @@ -2517,6 +2549,69 @@ sub setup_logic_do_transient_crops { } } +sub setup_logic_do_transient_lakes { + # + # Set do_transient_lakes default value, and perform error checking on do_transient_lakes + # + # Assumes the following are already set in the namelist (although it's okay + # for them to be unset if that will be their final state): + # - flanduse_timeseries + # + # NOTE(wjs, 2020-08-23) I based this function on setup_logic_do_transient_crops. I'm + # not sure if all of the checks here are truly important for transient lakes (in + # particular, my guess is that collapse_urban could probably be done with transient + # lakes - as well as transient pfts and transient crops for that matter), but some of + # the checks probably are needed, and it seems best to keep transient lakes consistent + # with other transient areas in this respect. + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + my $var = 'do_transient_lakes'; + + # cannot_be_true will be set to a non-empty string in any case where + # do_transient_lakes should not be true; if it turns out that + # do_transient_lakes IS true in any of these cases, a fatal error will be + # generated + my $cannot_be_true = ""; + + my $n_dom_pfts = $nl->get_value( 'n_dom_pfts' ); + my $n_dom_landunits = $nl->get_value( 'n_dom_landunits' ); + my $toosmall_soil = $nl->get_value( 'toosmall_soil' ); + my $toosmall_crop = $nl->get_value( 'toosmall_crop' ); + my $toosmall_glacier = $nl->get_value( 'toosmall_glacier' ); + my $toosmall_lake = $nl->get_value( 'toosmall_lake' ); + my $toosmall_wetland = $nl->get_value( 'toosmall_wetland' ); + my $toosmall_urban = $nl->get_value( 'toosmall_urban' ); + + if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { + $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; + } + + if (!$cannot_be_true) { + # Note that, if the variable cannot be true, we don't call add_default + # - so that we don't clutter up the namelist with variables that don't + # matter for this case + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var); + } + + # Make sure the value is false when it needs to be false - i.e., that the + # user hasn't tried to set a true value at an inappropriate time. + + if (&value_is_true($nl->get_value($var)) && $cannot_be_true) { + $log->fatal_error($cannot_be_true); + } + + # if do_transient_lakes is .true. and any of these (n_dom_* or toosmall_*) + # are > 0 or collapse_urban = .true., then give fatal error + if (&value_is_true($nl->get_value($var))) { + if (&value_is_true($nl->get_value('collapse_urban'))) { + $log->fatal_error("$var cannot be combined with collapse_urban"); + } + if ($n_dom_pfts > 0 || $n_dom_landunits > 0 || $toosmall_soil > 0 || $toosmall_crop > 0 || $toosmall_glacier > 0 || $toosmall_lake > 0 || $toosmall_wetland > 0 || $toosmall_urban > 0) { + $log->fatal_error("$var cannot be combined with any of the of the following > 0: n_dom_pfts > 0, n_dom_landunit > 0, toosmall_soil > 0._r8, toosmall_crop > 0._r8, toosmall_glacier > 0._r8, toosmall_lake > 0._r8, toosmall_wetland > 0._r8, toosmall_urban > 0._r8"); + } + } +} + sub setup_logic_do_harvest { # # Set do_harvest default value, and perform error checking on do_harvest @@ -2543,17 +2638,17 @@ sub setup_logic_do_harvest { # in any of these cases, a fatal error will be generated my $cannot_be_true = ""; - if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { - $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; - } elsif (!&value_is_true($nl->get_value('use_cn'))) { - $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)"; - } elsif (&value_is_true($nl->get_value('use_fates'))) { - $cannot_be_true = "$var currently doesn't work with ED"; - } + if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { + $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; + } - if ($cannot_be_true) { - $default_val = ".false."; - } + elsif (!&value_is_true($nl->get_value('use_cn')) && !&value_is_true($nl->get_value('use_fates'))) { + $cannot_be_true = "$var can only be set to true when running with either CN or FATES"; + } + + if ($cannot_be_true) { + $default_val = ".false."; + } if (!$cannot_be_true) { # Note that, if the variable cannot be true, we don't call add_default @@ -2605,6 +2700,24 @@ sub setup_logic_bgc_shared { #------------------------------------------------------------------------------- +sub setup_logic_cnphenology { + my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + + my @list = ( "onset_thresh_depends_on_veg", "min_crtical_dayl_depends_on_lat" ); + foreach my $var ( @list ) { + if ( &value_is_true($nl_flags->{'use_cn'}) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, + 'phys'=>$physv->as_string(), 'use_cn'=>$nl_flags->{'use_cn'} ); + } else { + if ( defined($nl->get_value($var)) ) { + $log->fatal_error("$var should only be set if use_cn is on"); + } + } + } +} + +#------------------------------------------------------------------------------- + sub setup_logic_supplemental_nitrogen { # # Supplemental Nitrogen for prognostic crop cases @@ -2629,7 +2742,7 @@ sub setup_logic_supplemental_nitrogen { } if ( $suplnitro =~ /ALL/i ) { - if ( $nl_flags->{'bgc_spinup'} ne "off" ) { + if ( $nl_flags->{'bgc_spinup'} eq "on" ) { $log->warning("There is no need to use a bgc_spinup mode when supplemental Nitrogen is on for all PFT's, as these modes spinup Nitrogen" ); } } @@ -2720,8 +2833,7 @@ sub setup_logic_nitrif_params { my ($nl_flags, $definition, $defaults, $nl) = @_; if ( ! &value_is_true($nl_flags->{'use_nitrif_denitrif'}) ) { - my @vars = ( "k_nitr_max", "denitrif_respiration_coefficient", "denitrif_respiration_exponent", - "denitrif_nitrateconc_coefficient", "denitrif_nitrateconc_exponent" ); + my @vars = ( "k_nitr_max", "denitrif_respiration_coefficient", "denitrif_respiration_exponent"); foreach my $var ( @vars ) { if ( defined($nl->get_value( $var ) ) ) { $log->fatal_error("$var is only used when use_nitrif_denitrif is turned on"); @@ -2730,6 +2842,30 @@ sub setup_logic_nitrif_params { } } +#------------------------------------------------------------------------------- + +sub setup_logic_mineral_nitrogen_dynamics { + # + # Logic for mineral_nitrogen_dynamics + # + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + my @vars = ( "freelivfix_slope_wet", "freelivfix_intercept" ); + if ( &value_is_true($nl_flags->{'use_cn'}) && &value_is_true($nl->get_value('use_fun')) ) { + foreach my $var ( @vars ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, + 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fun'=>$nl->get_value('use_fun') ); + } + } else { + foreach my $var ( @vars ) { + if ( defined($nl->get_value( $var ) ) ) { + $log->fatal_error("$var is only used when use_cn and use_fun are both turned on"); + } + } + } +} + + #------------------------------------------------------------------------------- sub setup_logic_hydrology_switches { @@ -2793,13 +2929,11 @@ sub setup_logic_methane { # Get resolution to read streams file for # my $finundation_method = remove_leading_and_trailing_quotes($nl->get_value('finundation_method' )); - if ( $finundation_method eq "TWS_inversion" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'finundation_res', - 'finundation_method'=>$finundation_method ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ch4finundated', - 'finundation_method'=>$finundation_method, - 'finundation_res'=>$nl->get_value('finundation_res') ); - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'finundation_res', + 'finundation_method'=>$finundation_method ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ch4finundated', + 'finundation_method'=>$finundation_method, + 'finundation_res'=>$nl->get_value('finundation_res') ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_aereoxid_prog', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_fates'=>$nl_flags->{'use_fates'} ); # @@ -3027,7 +3161,8 @@ sub setup_logic_c_isotope { my $use_c14_bombspike = $nl->get_value('use_c14_bombspike'); if ( defined($use_c14_bombspike) && &value_is_true($use_c14_bombspike) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename', - 'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike') ); + 'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'), + 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} ); } } else { if ( defined($nl->get_value('use_c14_bombspike')) || @@ -3046,7 +3181,8 @@ sub setup_logic_c_isotope { my $use_c13_timeseries = $nl->get_value('use_c13_timeseries'); if ( defined($use_c13_timeseries) && &value_is_true($use_c13_timeseries) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename', - 'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries') ); + 'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'), + 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} ); } } else { if ( defined($nl->get_value('use_c13_timeseries')) || @@ -3085,16 +3221,12 @@ sub setup_logic_nitrogen_deposition { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); - if ( defined($opts->{'use_case'}) ) { - if ( ($nl_flags->{'lnd_tuning_mode'} =~ /clm5_0_cam/) && ($opts->{'use_case'} eq "1850_control") ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_taxmode', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_varlist', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); - } - } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_taxmode', 'phys'=>$nl_flags->{'phys'}, + 'use_cn'=>$nl_flags->{'use_cn'}, + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_varlist', 'phys'=>$nl_flags->{'phys'}, + 'use_cn'=>$nl_flags->{'use_cn'}, + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_ndep', 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); @@ -3107,9 +3239,21 @@ sub setup_logic_nitrogen_deposition { 'sim_year_range'=>$nl_flags->{'sim_year_range'}); } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, 'rcp'=>$nl_flags->{'rcp'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, - 'hgrid'=>"1.9x2.5" ); + 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'hgrid'=>"0.9x1.25", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); + if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) { + # Also check at f19 resolution + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); + # If not found report an error + if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) { + $log->warning("Did NOT find the Nitrogen-deposition forcing file (stream_fldfilename_ndep) for this ssp_rcp\n" . + "One way to get around this is to point to a file for another existing ssp_rcp in your user_nl_clm file.\n" . + "If you are running with CAM and WACCM chemistry Nitrogen deposition will come through the coupler.\n" . + "This file won't be used, so it doesn't matter what it points to -- but it's required to point to something.\n" ) + } + } } else { # If bgc is NOT CN/CNDV then make sure none of the ndep settings are set! if ( defined($nl->get_value('stream_year_first_ndep')) || @@ -3218,15 +3362,16 @@ sub setup_logic_popd_streams { 'sim_year_range'=>$nl_flags->{'sim_year_range'}, 'cnfireson'=>$nl_flags->{'cnfireson'}); } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_popdens', 'phys'=>$nl_flags->{'phys'}, - 'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>"0.5x0.5" ); + 'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>"0.5x0.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} ); } else { # If bgc is NOT CN/CNDV or fire_method==nofire then make sure none of the popdens settings are set if ( defined($nl->get_value('stream_year_first_popdens')) || defined($nl->get_value('stream_year_last_popdens')) || defined($nl->get_value('model_year_align_popdens')) || + defined($nl->get_value('popdens_tintalgo' )) || defined($nl->get_value('stream_fldfilename_popdens')) ) { $log->fatal_error("When bgc is SP (NOT CN or BGC) or fire_method==nofire none of: stream_year_first_popdens,\n" . - "stream_year_last_popdens, model_year_align_popdens, nor\n" . + "stream_year_last_popdens, model_year_align_popdens, popdens_tintalgo nor\n" . "stream_fldfilename_popdens can be set!"); } } @@ -3262,32 +3407,33 @@ sub setup_logic_lightning_streams { # lightning streams require CN/BGC my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( &value_is_true($nl_flags->{'cnfireson'}) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lightngmapalgo', 'use_cn'=>$nl_flags->{'use_cn'}, - 'hgrid'=>$nl_flags->{'res'}, - 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lightng', 'use_cn'=>$nl_flags->{'use_cn'}, - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lightng', 'use_cn'=>$nl_flags->{'use_cn'}, - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - # Set align year, if first and last years are different - if ( $nl->get_value('stream_year_first_lightng') != - $nl->get_value('stream_year_last_lightng') ) { + if ( $nl_flags->{'light_res'} ne "none" ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lightngmapalgo', + 'hgrid'=>$nl_flags->{'res'}, + 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lightng', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lightng', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different + if ( $nl->get_value('stream_year_first_lightng') != + $nl->get_value('stream_year_last_lightng') ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'model_year_align_lightng', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lightng', 'use_cn'=>$nl_flags->{'use_cn'}, + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lightng', 'hgrid'=>$nl_flags->{'light_res'} ); } else { # If bgc is NOT CN/CNDV then make sure none of the Lightng settings are set if ( defined($nl->get_value('stream_year_first_lightng')) || defined($nl->get_value('stream_year_last_lightng')) || defined($nl->get_value('model_year_align_lightng')) || + defined($nl->get_value('lightng_tintalgo' )) || defined($nl->get_value('stream_fldfilename_lightng')) ) { - $log->fatal_error("When bgc is SP (NOT CN or BGC) or fire_method==nofire none of: stream_year_first_lightng,\n" . - "stream_year_last_lightng, model_year_align_lightng, nor\n" . + $log->fatal_error("When bgc is SP (NOT CN or BGC or FATES) or fire is turned off none of: stream_year_first_lightng,\n" . + "stream_year_last_lightng, model_year_align_lightng, lightng_tintalgo nor\n" . "stream_fldfilename_lightng can be set!"); } } @@ -3360,40 +3506,92 @@ sub setup_logic_megan { #------------------------------------------------------------------------------- +sub setup_logic_soilm_streams { + # prescribed soil moisture streams require clm4_5/clm5_0/clm5_1 + my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_soil_moisture_streams'); + if ( &value_is_true( $nl->get_value('use_soil_moisture_streams') ) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soilm_tintalgo', + 'hgrid'=>$nl_flags->{'res'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'soilm_offset', + 'hgrid'=>$nl_flags->{'res'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_soilm', 'phys'=>$nl_flags->{'phys'}, + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_soilm', 'phys'=>$nl_flags->{'phys'}, + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different + if ( $nl->get_value('stream_year_first_soilm') != + $nl->get_value('stream_year_last_soilm') ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'model_year_align_soilm', 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_soilm', 'phys'=>$nl_flags->{'phys'}, + 'hgrid'=>$nl_flags->{'res'} ); + if ( ($opts->{'use_case'} =~ /_transient$/) && + (remove_leading_and_trailing_quotes($nl->get_value("soilm_tintalgo")) eq "linear") ) { + $log->warning("For a transient case, soil moisture streams, should NOT use soilm_tintalgo='linear'" . + " since vegetated areas could go from missing to not missing or vice versa" ); + } + } else { + if ( defined($nl->get_value('stream_year_first_soilm')) || + defined($nl->get_value('model_year_align_soilm')) || + defined($nl->get_value('stream_fldfilename_soilm')) || + defined($nl->get_value('soilm_tintalgo')) || + defined($nl->get_value('soilm_offset')) || + defined($nl->get_value('stream_year_last_soilm')) ) { + $log->fatal_error("One of the soilm streams namelist items (stream_year_first_soilm, " . + " model_year_align_soilm, stream_fldfilename_soilm, stream_fldfilename_soilm)" . + " soilm_tintalgo soilm_offset" . + " is defined, but use_soil_moisture_streams option NOT set to true"); + } + } +} + +#------------------------------------------------------------------------------- + sub setup_logic_lai_streams { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl_flags->{'use_lai_streams'}) ) { - $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); + + if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { + $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } if ( $nl_flags->{'bgc_mode'} eq "sp" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo', - 'hgrid'=>$nl_flags->{'res'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lai', - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lai', - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - # Set align year, if first and last years are different - if ( $nl->get_value('stream_year_first_lai') != - $nl->get_value('stream_year_last_lai') ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, - 'model_year_align_lai', 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + if ( &value_is_true($nl->get_value('use_lai_streams')) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo', + 'hgrid'=>$nl_flags->{'res'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_lai', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_lai', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different + if ( $nl->get_value('stream_year_first_lai') != + $nl->get_value('stream_year_last_lai') ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'model_year_align_lai', 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lai', + 'hgrid'=>"360x720cru" ); } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_lai', - 'hgrid'=>"360x720cru" ); } else { # If bgc is CN/CNDV then make sure none of the LAI settings are set if ( defined($nl->get_value('stream_year_first_lai')) || defined($nl->get_value('stream_year_last_lai')) || defined($nl->get_value('model_year_align_lai')) || + defined($nl->get_value('lai_tintalgo' )) || defined($nl->get_value('stream_fldfilename_lai')) ) { $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" . - "stream_year_last_lai, model_year_align_lai, nor\n" . + "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" . "stream_fldfilename_lai (eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); } } @@ -3454,6 +3652,32 @@ sub setup_logic_cnvegcarbonstate { #------------------------------------------------------------------------------- +sub setup_logic_cngeneral { + # Must be set after setup_logic_co2_type + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + if ( &value_is_true($nl->get_value('use_cn')) ) { + if ( &value_is_true($nl->get_value('use_crop')) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'dribble_crophrv_xsmrpool_2atm', + 'co2_type' => remove_leading_and_trailing_quotes($nl->get_value('co2_type')), + 'use_crop' => $nl->get_value('use_crop') ); + } else { + if ( defined($nl->get_value('dribble_crophrv_xsmrpool_2atm')) ) { + $log->fatal_error("When CROP is NOT on dribble_crophrv_xsmrpool_2atm can NOT be set\n" ); + } + } + } else { + if ( defined($nl->get_value('reseed_dead_plants')) || + defined($nl->get_value('dribble_crophrv_xsmrpool_2atm')) ) { + $log->fatal_error("When CN is not on none of the following can be set: ,\n" . + "dribble_crophrv_xsmrpool_2atm nor reseed_dead_plantsr\n" . + "(eg. don't use these options with SP mode)."); + } + } +} + +#------------------------------------------------------------------------------- + sub setup_logic_rooting_profile { # my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; @@ -3488,6 +3712,11 @@ sub setup_logic_canopyfluxes { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_undercanopy_stability' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'itmax_canopy_fluxes', 'structure'=>$nl_flags->{'structure'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_biomass_heat_storage', + 'use_fates'=>$nl_flags->{'use_fates'}, 'phys'=>$nl_flags->{'phys'} ); + if ( &value_is_true($nl->get_value('use_biomass_heat_storage') ) && &value_is_true( $nl_flags->{'use_fates'}) ) { + $log->fatal_error('use_biomass_heat_storage can NOT be set to true when fates is on'); + } } #------------------------------------------------------------------------------- @@ -3674,8 +3903,8 @@ sub setup_logic_fates { if (&value_is_true( $nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); - my @list = ( "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", - "use_fates_inventory_init", "use_fates_logging" ); + my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", + "use_fates_inventory_init","use_fates_fixed_biogeog", "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking" ); foreach my $var ( @list ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'} ); } @@ -3683,10 +3912,11 @@ sub setup_logic_fates { if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { $var = "fates_inventory_ctrl_filename"; + my $fname = substr $nl->get_value($var), 1, -1; # ignore first and last positions of string because those are quote characters if ( ! defined($nl->get_value($var)) ) { $log->fatal_error("$var is required when use_fates_inventory_init is set" ); - } elsif ( ! -f "$nl->get_value($var)" ) { - $log->fatal_error("$var does NOT point to a valid filename" ); + } elsif ( ! -f "$fname" ) { + $log->fatal_error("$fname does NOT point to a valid filename" ); } } } @@ -3695,6 +3925,18 @@ sub setup_logic_fates { #------------------------------------------------------------------------------- +sub setup_logic_misc { + # + # Set some misc options + # + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_run_ncdiopio_tests'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_master_list_file'); +} + +#------------------------------------------------------------------------------- + sub write_output_files { my ($opts, $nl_flags, $defaults, $nl) = @_; @@ -3713,7 +3955,7 @@ sub write_output_files { # CLM component my @groups; @groups = qw(clm_inparm ndepdyn_nml popd_streams urbantv_streams light_streams - lai_streams atm2lnd_inparm lnd2atm_inparm clm_canopyhydrology_inparm cnphenology + soil_moisture_streams lai_streams atm2lnd_inparm lnd2atm_inparm clm_canopyhydrology_inparm cnphenology clm_soilhydrology_inparm dynamic_subgrid cnvegcarbonstate finidat_consistency_checks dynpft_consistency_checks clm_initinterp_inparm century_soilbgcdecompcascade @@ -3873,7 +4115,7 @@ sub add_default { } } else { - return; + return( 1 ); } } @@ -3908,6 +4150,7 @@ sub add_default { # set the value in the namelist $nl->set_variable_value($group, $var, $val); } + return( 0 ); } @@ -4054,10 +4297,10 @@ sub check_use_case_name { my $diestring = "bad use_case name $use_case, follow the conventions " . "in namelist_files/use_cases/README\n"; my $desc = "[a-zA-Z0-9]*"; - my $rcp = "rcp[0-9\.]+"; - if ( $use_case =~ /^[0-9]+-[0-9]+([a-zA-Z0-9_\.]*)_transient$/ ) { + my $ssp_rcp = "SSP[0-9]-[0-9\.]+"; + if ( $use_case =~ /^[0-9]+-[0-9]+([a-zA-Z0-9_\.-]*)_transient$/ ) { my $string = $1; - if ( $string =~ /^_($rcp)_*($desc)$/ ) { + if ( $string =~ /^_($ssp_rcp)_*($desc)$/ ) { # valid name } elsif ( $string =~ /^_*($desc)$/ ) { # valid name @@ -4066,7 +4309,7 @@ sub check_use_case_name { } } elsif ( $use_case =~ /^20thC([a-zA-Z0-9_\.]*)_transient$/ ) { my $string = $1; - if ( $string =~ /^_($rcp)_*($desc)$/ ) { + if ( $string =~ /^_($ssp_rcp)_*($desc)$/ ) { # valid name } elsif ( $string =~ /^_*($desc)$/ ) { # valid name @@ -4102,7 +4345,7 @@ sub validate_options { # create the @expect array by listing the files in $use_case_dir # and strip off the ".xml" part of the filename @expect = (); - my @files = glob("$opts->{'use_case_dir'}/*.xml"); + my @files = bsd_glob("$opts->{'use_case_dir'}/*.xml"); foreach my $file (@files) { $file =~ m{.*/(.*)\.xml}; &check_use_case_name( $1 ); @@ -4116,7 +4359,7 @@ sub validate_options { } else { print "Use cases are:...\n\n"; my @ucases; - foreach my $file( sort( glob($opts->{'use_case_dir'}."/*.xml") ) ) { + foreach my $file( sort( bsd_glob($opts->{'use_case_dir'}."/*.xml") ) ) { my $use_case; if ( $file =~ /\/([^\/]+)\.xml$/ ) { &check_use_case_name( $1 ); @@ -4142,9 +4385,9 @@ sub list_options { my ($opts_cmdl, $definition, $defaults) = @_; # options to list values that are in the defaults files - my @opts_list = ( "res", "mask", "sim_year", "rcp" ); + my @opts_list = ( "res", "mask", "sim_year", "ssp_rcp" ); my %opts_local; - foreach my $var ( "res", "mask", "sim_year", "rcp" ) { + foreach my $var ( "res", "mask", "sim_year", "ssp_rcp" ) { my $val; if ( $opts_cmdl->{$var} eq "list" ) { $val = "default"; diff --git a/bld/config_files/clm_phys_vers.pm b/bld/config_files/clm_phys_vers.pm index 32124491a8..3e4de9c610 100755 --- a/bld/config_files/clm_phys_vers.pm +++ b/bld/config_files/clm_phys_vers.pm @@ -28,7 +28,7 @@ use bigint; #use warnings; #use diagnostics; -my @version_strings = ("clm4_5", "clm5_0"); +my @version_strings = ("clm4_5", "clm5_0", "clm5_1"); #------------------------------------------------------------------------------- @@ -83,12 +83,12 @@ if ( ! defined(caller) && $#ARGV == -1 ) { require Test::More; Test::More->import( ); - plan( tests=>2 ); + plan( tests=>3 ); sub testit { print "unit tester\n"; my %lastv; - my @vers_list = ( "clm4_5", "clm5_0" ); + my @vers_list = ( "clm4_5", "clm5_0", "clm5_1" ); foreach my $vers ( @vers_list ) { my $phys = config_files::clm_phys_vers->new($vers); isa_ok($phys, "config_files::clm_phys_vers", "created clm_phys_vers object"); diff --git a/bld/config_files/config_definition_ctsm.xml b/bld/config_files/config_definition_ctsm.xml index b02510ed64..06263c6d19 100644 --- a/bld/config_files/config_definition_ctsm.xml +++ b/bld/config_files/config_definition_ctsm.xml @@ -5,10 +5,10 @@ -Specifies either clm4_5 or clm5_0 physics +Specifies either clm4_5, clm5_0, or clm5_1 physics new($config_cachefile, '>') or die "can't open file: $config_cachefile"; + print $fh < + + +Specifies clm physics + +EOF + $fh->close(); +} + #----------------------------------------------------------------------------------------------- sub GetListofNeededFiles { @@ -191,14 +205,12 @@ sub GetListofNeededFiles { "$cfgdir/namelist_files/namelist_definition_ctsm.xml" ); $inputopts{'nldef_files'} = \@nl_definition_files; - $inputopts{'empty_cfg_file'} = "$cfgdir/config_files/config_definition_ctsm.xml"; + $inputopts{'empty_cfg_file'} = "config_cache.xml"; my $definition = Build::NamelistDefinition->new( $nl_definition_files[0] ); foreach my $nl_defin_file ( @nl_definition_files ) { $definition->add( "$nl_defin_file" ); } - my $cfg = Build::Config->new( $inputopts{'empty_cfg_file'} ); - # Resolutions... my @resolutions; if ( $opts{'res'} eq "all" ) { @@ -208,6 +220,7 @@ sub GetListofNeededFiles { } # Input options + &make_config_cache( "clm5_0", $inputopts{'empty_cfg_file'} ); push @nl_defaults_files, "$cfgdir/namelist_files/namelist_defaults_ctsm.xml"; if ( defined($opts{'usrdat'}) ) { push @nl_defaults_files, "$cfgdir/namelist_files/namelist_defaults_usr_files.xml"; @@ -248,14 +261,14 @@ sub GetListofNeededFiles { # Loop over all possible simulation year: 1890, 2000, 2100 etc. # $settings{'sim_year_range'} = "constant"; - my @rcps = $definition->get_valid_values( "rcp", 'noquotes'=>1 ); - $settings{'rcp'} = $rcps[0]; + my @ssp_rcps = $definition->get_valid_values( "ssp_rcp", 'noquotes'=>1 ); + $settings{'ssp_rcp'} = $ssp_rcps[0]; YEAR: foreach my $sim_year ( $definition->get_valid_values( "sim_year", 'noquotes'=>1 ) ) { print "sim_year = $sim_year\n" if $printing; $settings{'sim_year'} = $sim_year; if ( $sim_year ne 1850 && $sim_year ne 2000 && $sim_year > 1800 ) { next YEAR; } - my @bgcsettings = $cfg->get_valid_values( "bgc" ); + my @bgcsettings = $definition->get_valid_values( "bgc_mode", 'noquotes'=>1 ); print "bgc=@bgcsettings\n" if $printing; # # Loop over all possible BGC settings @@ -298,11 +311,11 @@ sub GetListofNeededFiles { $settings{'sim_year'} = $1; } # - # Loop over all possible rcp's + # Loop over all possible ssp_rcp's # - print "sim_year_range=$sim_year_range rcp=@rcps\n" if $printing; - foreach my $rcp ( @rcps ) { - $settings{'rcp'} = $rcp; + print "sim_year_range=$sim_year_range ssp_rcp=@ssp_rcps\n" if $printing; + foreach my $ssp_rcp ( @ssp_rcps ) { + $settings{'ssp_rcp'} = $ssp_rcp; &GetListofNeededFiles( \%inputopts, \%settings, \%files ); if ( $printTimes >= 1 ) { $inputopts{'printing'} = 0; diff --git a/bld/namelist_files/createMkSrfEntry.py b/bld/namelist_files/createMkSrfEntry.py index ee1175c9b1..b76e83af4d 100755 --- a/bld/namelist_files/createMkSrfEntry.py +++ b/bld/namelist_files/createMkSrfEntry.py @@ -5,12 +5,12 @@ class mksrfDataEntry_prog: # Class data - year_start = 2016 - year_end = 2100 - ssp_rcp = "SSP5-8.5" - subdir = "pftcftdynharv.0.25x0.25.SSP5-8.5.simyr2016-2100.c171005" - cdate = 171005 - desc = "SSP5RCP85_clm5" + year_start = 850 + year_end = 1849 + ssp_rcp = "hist" + subdir = "pftcftdynharv.0.25x0.25.LUH2.histsimyr0850-1849.c171012" + cdate = 171012 + desc = "histclm50_LUH2" def parse_cmdline_args( self ): "Parse the command line arguments for create data entry list" diff --git a/bld/namelist_files/namelist_defaults.xsl b/bld/namelist_files/namelist_defaults.xsl index 20a8c4a8ad..6960cfbef9 100644 --- a/bld/namelist_files/namelist_defaults.xsl +++ b/bld/namelist_files/namelist_defaults.xsl @@ -28,7 +28,7 @@
  • Site specific point name (sitespf_pt)
  • Crop model (crop)
  • Data model forcing source (forcing)
    • -
  • Representative concentration pathway for future scenarios (rcp)
    • +
  • Representative concentration pathway for future scenarios (SSP-rcp)
  • New good wood harvest (newwoodharv)
  • CN Spin-up mode (spinup)
  • Type of file (type)
    • diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index a32c807f16..d805f11dee 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -19,13 +19,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 2000 - -1800 - 379.0 +336.6 379.0 +388.8 +397.5 284.7 +284.7 constant @@ -33,19 +34,38 @@ attributes from the config_cache.xml file (with keys converted to upper-case). sp -clm4_5_CRUv7 -clm5_0_cam6.0 +clm4_5_CRUv7 +clm5_0_cam6.0 +clm5_1_GSWP3v1 + + +clm2 +clm2 +clm2 off +2 2 1 +2 +2 +2 2 1 0 + +.true. +.false. + +.false. + + +.false. + .true. 20 -.false. -.false. - - -.true. -.false. +.false. +.false. +.false. -.true. +.true. +.true. +.false. -2 -1 -0 +2 +2 +1 +0 +.true. .true. .false. -Medlyn2011 -Ball-Berry1987 -Ball-Berry1987 +Medlyn2011 +Ball-Berry1987 +Medlyn2011 +Ball-Berry1987 +Ball-Berry1987 -lnd/clm2/isotopes/atm_delta_C13_CMIP6_1850-2015_yearly_v2.0_c190528.nc -lnd/clm2/isotopes/atm_delta_C14_CMIP6_3x1_global_1850-2015_yearly_v2.0_c190528.nc +lnd/clm2/isotopes/atm_delta_C13_CMIP6_1850-2015_yearly_v2.0_c190528.nc +lnd/clm2/isotopes/atm_delta_C13_CMIP6_SSP119_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C13_CMIP6_SSP126_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C13_CMIP6_SSP245_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C13_CMIP6_SSP3B_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C13_CMIP6_SSP534os_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C13_CMIP6_SSP5B_1850-2100_yearly_c181209.nc + +lnd/clm2/isotopes/atm_delta_C14_CMIP6_3x1_global_1850-2015_yearly_v2.0_c190528.nc +lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP119_3x1_global_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP126_3x1_global_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP245_3x1_global_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP3B_3x1_global_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP534os_3x1_global_1850-2100_yearly_c181209.nc +lnd/clm2/isotopes/atm_delta_C14_CMIP6_SSP5B_3x1_global_1850-2100_yearly_c181209.nc +.true. +.false. +.true. +.false. +.false. + .false. .true. + .false. @@ -105,18 +148,22 @@ attributes from the config_cache.xml file (with keys converted to upper-case). NONE -0.50,0.30 -0.60,0.40 +0.50,0.30 +0.50,0.30 +0.60,0.40 +ON_WASTEHEAT ON_WASTEHEAT ON -1 -0 +1 +1 +0 -FAST -NONE +FAST +FAST +NONE .false. @@ -124,41 +171,52 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .true. .false. +.false. 4SL_2m -20SL_8.5m -10SL_3.5m - -.false. -.false. -.true. -.false. - +20SL_8.5m +20SL_8.5m +10SL_3.5m + +.false. +.false. +.true. +.false. +.false. +.true. +.false. -1 -0 +1 +1 +0 -1 -1 +1 +1 +1 -1 -0 +1 +1 +0 -1.d-2 -0.001d00 -1.d-2 -1.d-2 +1.d-2 +0.001d00 +1.d-2 +0.001d00 +1.d-2 +1.d-2 -2.0d00 -0.5d00 +2.0d00 +0.5d00 +0.5d00 -.true. -.false. +.true. +.true. +.false. .true. @@ -173,24 +231,29 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 0. 2. -0. -2. +0. +2. --2. -0. +-2. +0. + +-2. +0. -.false. -.true. +.false. +.true. +.true. -li2016crufrc -li2014qianfrc +li2021gswpfrc +li2016crufrc +li2014qianfrc 30.0d00 80.0d00 @@ -204,7 +267,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 0.39d00 75.d00 1050.d00 -0.5d00, 0.25d00 +0.5d00 +0.25d00 30.0d00 @@ -228,30 +292,57 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 0.33d00 105.d00 1050.d00 -0.5d00, 0.28d00 +0.5d00 +0.28d00 + +30.0d00 +80.0d00 +0.85d00 +0.98d00 +0.025d00 +0.09d-4 +0.010d00 +0.17d-3 +1.6d-4 +0.33d00 +75.d00 +1050.d00 +0.5d00 +0.28d00 -.false. -.true. +.false. +.false. +.true. + +.true. +.false. +.false. 40 3 -.true. -1.0 -0.05 +.true. +1.0 +0.05 -.false. -0.25 -1.0 +.true. +1.0 +0.05 + +.false. +0.25 +1.0 -0 -1 +0 +1 +1 1 1 +1 4 2 @@ -272,13 +363,15 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 14400 -3400. 0.6 -1.0 -0.5 +1.0 +1.0 +0.5 0.1 -.false. -.false. +.false. +.false. +.false. .false. @@ -288,15 +381,19 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .true. -12 -5 -5 +12 +5 +12 +5 +5 -10000.0 -5000.0 -1000.0 +10000.0 +5000.0 +10000.0 +5000.0 +1000.0 0.010d00 0.015d00 @@ -305,27 +402,34 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 0.02d00 0.05d00 -2000. +2000. +2000. -1.e30 +1.e30 -10.0d00 -10.0 +10.0d00 +10.0d00 +10.0 +.true. .true. .false. -'Vionnet2012' -'Anderson1976' +'Vionnet2012' +'Vionnet2012' +'Anderson1976' -'Slater2017' -'TruncatedAnderson1976' +'Slater2017' +'Slater2017' +'TruncatedAnderson1976' -100.d00 -175.d00 +100.d00 +175.d00 +175.d00 -54.526d00 -204.526d00 +54.526d00 +204.526d00 +204.526d00 0.08d00 @@ -342,8 +446,14 @@ attributes from the config_cache.xml file (with keys converted to upper-case). Mountain glaciers: single_at_atm_topo Greenland - inside CISM grid but outside Greenland itself: virtual Greenland itself: virtual - Antarctica: multiple --> -'single_at_atm_topo','virtual','virtual','multiple' + Antarctica: multiple + + If CISM is running over Antarctica, then we change the Antarctica + behavior to virtual. Note that the Greenland behavior is always + virtual, even if Greenland isn't included in this run. +--> +'single_at_atm_topo','virtual','virtual','multiple' +'single_at_atm_topo','virtual','virtual','virtual' +0 0 7300 @@ -372,25 +483,30 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/clm5_params.c190829.nc -lnd/clm2/paramdata/clm_params.c190829.nc +lnd/clm2/paramdata/ctsm51_params.c210305.nc +lnd/clm2/paramdata/clm50_params.c210217.nc +lnd/clm2/paramdata/clm45_params.c210217.nc -lnd/clm2/paramdata/fates_params_2troppftclones.c171018.nc +lnd/clm2/paramdata/fates_params_api.14.0.0_12pft_c200921.nc -.true. -.false. -.false. +.true. +.false. +.true. +.false. +.false. +.true. +.false. .true. -.false. +.false. .false. @@ -418,58 +534,84 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. .false. -.true. -.true. +.true. +.true. +.true. -0.093563 +0.17 +0.17 .false. -.false. -.true. +.false. +.true. +.true. -constant -varytropicsbylat -12.0d00 -0.4d00 - -3.d00 -1.d00 - +constant +varytropicsbylat +12.0d00 +0.4d00 +varytropicsbylat +12.0d00 +0.4d00 + +3.d00 +3.d00 +1.d00 + + +.true. +.true. +.false. +.false. -0.5 -10.0 +0.5 +10.0 +10.0 -.false. -.true. +.false. +.true. +.true. .true. -.false. -.false. -.false. -.false. -.false. +.false. +.false. +.false. +.false. +.false. +.false. -.false. -.false. -.true. - -1.d-9 -1.d-8 --6.d+1 --6.d+0 --6.d+2 --6.d+1 +.false. +.false. +.true. +.false. +.true. + +1.d-9 +1.d-9 +1.d-8 +-6.d+1 +-6.d+0 +-6.d+1 +-6.d+0 +-6.d+2 +-6.d+1 -.false. -.true. +.false. +.true. +.true. + + + +.true. + -75 +61 -1850,2000 +1850,1979,2000,2003,2013 - -.true. -.true. -.false. + + + + +.true. + + +.true. +.true. +.true. +.true. + +.true. + + +.true. + +.true. +.true. + +.true. +.true. +.true. + +.false. + + +hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_nitrif_denitrif=.false. use_vertsoilc=.false. use_crop=.false. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10 + + + +hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_nitrif_denitrif=.false. use_vertsoilc=.false. use_crop=.false. irrigate=.true. glc_nec=10 + + +hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + +hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + + + + +hgrid=ne120np4.pg3 maxpft=79 mask=tx0.1v3 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + + + +hgrid=0.9x1.25 maxpft=17 mask=gx1v7 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+2101 +2015 + +2010 +2010 + 2000 2000 @@ -997,26 +1480,51 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc2000 2000 -1850 -2015 - -1850 -2100 - -2000 -2100 - -lnd/clm2/ndepdata/fndep_clm_hist_simyr1849-2006_1.9x2.5_c100428.nc -lnd/clm2/ndepdata/fndep_clm_rcp8.5_simyr1849-2106_1.9x2.5_c100428.nc -lnd/clm2/ndepdata/fndep_clm_rcp6.0_simyr1849-2106_1.9x2.5_c100810.nc -lnd/clm2/ndepdata/fndep_clm_rcp4.5_simyr1849-2106_1.9x2.5_c100428.nc -lnd/clm2/ndepdata/fndep_clm_rcp2.6_simyr1849-2106_1.9x2.5_c100428.nc - -extend - -NDEP_year - -bilinear +lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc +lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc +lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc + + +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP2-4.5-WACCM_1849-2101_monthly_c191007.nc +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_1849-2101_monthly_c191007.nc + +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP2-4.5-WACCM_1849-2101_monthly_c191007.nc +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_1849-2101_monthly_c191007.nc + +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc +lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_1849-2101_monthly_c191007.nc + +cycle +NDEP_month +limit + +cycle +NDEP_month +limit + +cycle +NDEP_month +limit + +bilinear nn nn @@ -1026,6 +1534,18 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.ncnn nn + + +.false. +1997 +1997 +1997 + +lnd/clm2/prescribed_data/LFMIP-pdLC-SST.H2OSOI.0.9x1.25.20levsoi.natveg.climo1980-2014.MONS_c190709.nc + +linear +0 + .false. 2001 @@ -1057,24 +1577,46 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.ncnone 94x192 94x192 +360x720 +none +none +none +360x720 +360x720 +360x720 + +0001 +0001 + +atm/datm7/NASA_LIS/clmforc.Li_2012_climo1995-2011.T62.lnfm_Total_c140423.nc +atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_c160825.nc + +bilinear + +nn +nn +nn +nn +nn +nn +nn -0001 -0001 + +2015 +2100 +2015 -atm/datm7/NASA_LIS/clmforc.Li_2012_climo1995-2011.T62.lnfm_Total_c140423.nc -atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_c160825.nc +2015 +2100 +2015 -bilinear +2015 +2100 +2015 -nn -nn -nn -nn -nn -nn -nn +2010 +2010 - 2000 2000 @@ -1090,16 +1632,59 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc2000 2000 -1850 -2016 +2010 +2010 + +2000 +2000 + +1850 +1850 -1850 -2016 +2000 +2000 -1850 -2016 +2000 +2000 + +2000 +2000 lnd/clm2/firedata/clmforc.Li_2017_HYDEv3.2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2016_c180202.nc +lnd/clm2/firedata/clmforc.Li_2018_SSP1_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP1_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP3_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP4_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP4_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP5_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP5_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + + +lnd/clm2/firedata/clmforc.Li_2017_HYDEv3.2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2016_c180202.nc +lnd/clm2/firedata/clmforc.Li_2018_SSP1_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP1_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP3_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP4_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP4_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP5_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + +lnd/clm2/firedata/clmforc.Li_2018_SSP5_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc + bilinear @@ -1111,7 +1696,29 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.ncnn nn +bilinear + +nn +nn +nn +nn +nn +nn +nn + +2015 +2106 +2015 + +2015 +2106 +2015 + +2015 +2106 +2015 + 2000 2000 @@ -1130,16 +1737,13 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc1850 2106 -1850 -2106 - -1850 -2106 +lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc -lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc -lnd/clm2/urbandata/CLM45_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc nn @@ -1242,6 +1846,8 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nclnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_10x10min_nomask_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_3x3min_MODIS_to_1x1_asphaltjungleNJ_nomask_aave_da_c120717.nc +lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_3x3min_MODISv2_to_1x1_asphaltjungleNJ_nomask_aave_da_c190507.nc lnd/clm2/mappingdata/maps/1x1_asphaltjungleNJ/map_3x3min_MODIS-wCsp_to_1x1_asphaltjungleNJ_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/1x1_brazil/map_10x10min_nomask_to_1x1_brazil_nomask_aave_da_c120717.nc lnd/clm2/mappingdata/maps/1x1_brazil/map_3x3min_MODIS_to_1x1_brazil_nomask_aave_da_c120717.nc +lnd/clm2/mappingdata/maps/1x1_brazil/map_3x3min_MODISv2_to_1x1_brazil_nomask_aave_da_c190507.nc lnd/clm2/mappingdata/maps/1x1_brazil/map_3x3min_MODIS-wCsp_to_1x1_brazil_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_10x10min_nomask_to_1x1_camdenNJ_nomask_aave_da_c120717.nc lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_3x3min_MODIS_to_1x1_camdenNJ_nomask_aave_da_c120717.nc +lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_3x3min_MODISv2_to_1x1_camdenNJ_nomask_aave_da_c190506.nc lnd/clm2/mappingdata/maps/1x1_camdenNJ/map_3x3min_MODIS-wCsp_to_1x1_camdenNJ_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_10x10min_nomask_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_MODIS_to_1x1_mexicocityMEX_nomask_aave_da_c120717.nc +lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_MODISv2_to_1x1_mexicocityMEX_nomask_aave_da_c190507.nc lnd/clm2/mappingdata/maps/1x1_mexicocityMEX/map_3x3min_MODIS-wCsp_to_1x1_mexicocityMEX_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/1x1_numaIA/map_10x10min_nomask_to_1x1_numaIA_nomask_aave_da_c120717.nc lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_MODIS_to_1x1_numaIA_nomask_aave_da_c120717.nc +lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_MODISv2_to_1x1_numaIA_nomask_aave_da_c190507.nc lnd/clm2/mappingdata/maps/1x1_numaIA/map_3x3min_MODIS-wCsp_to_1x1_numaIA_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_10x10min_nomask_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_MODIS_to_1x1_smallvilleIA_nomask_aave_da_c120717.nc +lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_MODISv2_to_1x1_smallvilleIA_nomask_aave_da_c190507.nc lnd/clm2/mappingdata/maps/1x1_smallvilleIA/map_3x3min_MODIS-wCsp_to_1x1_smallvilleIA_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_10x10min_nomask_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_MODIS_to_1x1_urbanc_alpha_nomask_aave_da_c120717.nc +lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_MODISv2_to_1x1_urbanc_alpha_nomask_aave_da_c190507.nc lnd/clm2/mappingdata/maps/1x1_urbanc_alpha/map_3x3min_MODIS-wCsp_to_1x1_urbanc_alpha_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_10x10min_nomask_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_MODIS_to_1x1_vancouverCAN_nomask_aave_da_c120717.nc +lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_MODISv2_to_1x1_vancouverCAN_nomask_aave_da_c190506.nc lnd/clm2/mappingdata/maps/1x1_vancouverCAN/map_3x3min_MODIS-wCsp_to_1x1_vancouverCAN_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/0.47x0.63/map_3x3min_GLOBE-Gardner_to_0.47x0.63_nomask_aave_da_c170914.nc lnd/clm2/mappingdata/maps/0.47x0.63/map_3x3min_LandScan2004_to_0.47x0.63_nomask_aave_da_c170914.nc +lnd/clm2/mappingdata/maps/0.47x0.63/map_3x3min_MODISv2_to_0.47x0.63_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/0.47x0.63/map_3x3min_MODIS-wCsp_to_0.47x0.63_nomask_aave_da_c170914.nc lnd/clm2/mappingdata/maps/0.9x1.25/map_5x5min_ORNL-Soil_to_0.9x1.25_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_MODIS_to_0.9x1.25_nomask_aave_da_c120523.nc +lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_MODISv2_to_0.9x1.25_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/0.9x1.25/map_3x3min_MODIS-wCsp_to_0.9x1.25_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/1.9x2.5/map_5x5min_ORNL-Soil_to_1.9x2.5_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_MODIS_to_1.9x2.5_nomask_aave_da_c111111.nc +lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_MODISv2_to_1.9x2.5_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/1.9x2.5/map_3x3min_MODIS-wCsp_to_1.9x2.5_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/10x15/map_5x5min_ORNL-Soil_to_10x15_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/10x15/map_3x3min_MODIS_to_10x15_nomask_aave_da_c111111.nc +lnd/clm2/mappingdata/maps/10x15/map_3x3min_MODISv2_to_10x15_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/10x15/map_3x3min_MODIS-wCsp_to_10x15_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/360x720/map_5x5min_ORNL-Soil_to_360x720cru_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/360x720/map_3x3min_MODIS_to_360x720_nomask_aave_da_c120830.nc +lnd/clm2/mappingdata/maps/360x720/map_3x3min_MODISv2_to_360x720cru_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/360x720/map_3x3min_MODIS-wCsp_to_360x720cru_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/512x1024/map_5x5min_ORNL-Soil_to_512x1024_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/512x1024/map_3x3min_MODIS_to_512x1024_nomask_aave_da_c111111.nc +lnd/clm2/mappingdata/maps/512x1024/map_3x3min_MODISv2_to_512x1024_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/512x1024/map_3x3min_MODIS-wCsp_to_512x1024_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/128x256/map_5x5min_ORNL-Soil_to_128x256_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/128x256/map_3x3min_MODIS_to_128x256_nomask_aave_da_c111111.nc +lnd/clm2/mappingdata/maps/128x256/map_3x3min_MODISv2_to_128x256_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/128x256/map_3x3min_MODIS-wCsp_to_128x256_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/64x128/map_5x5min_ORNL-Soil_to_64x128_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/64x128/map_3x3min_MODIS_to_64x128_nomask_aave_da_c111111.nc +lnd/clm2/mappingdata/maps/64x128/map_3x3min_MODISv2_to_64x128_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/64x128/map_3x3min_MODIS-wCsp_to_64x128_nomask_aave_da_c160428.nc lnd/clm2/mappingdata/maps/48x96/map_5x5min_ORNL-Soil_to_48x96_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/48x96/map_3x3min_MODIS_to_48x96_nomask_aave_da_c111111.nc +lnd/clm2/mappingdata/maps/48x96/map_3x3min_MODISv2_to_48x96_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/48x96/map_3x3min_MODIS-wCsp_to_48x96_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/48x96/map_1km-merge-10min_HYDRO1K-merge-nomask_to_48x96_nomask_aave_da_c130405.nc -lnd/clm2/mappingdata/maps/32x64/map_0.5x0.5_MODIS_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_0.25x0.25_MODIS_to_32x64_nomask_aave_da_c170321.nc -lnd/clm2/mappingdata/maps/32x64/map_0.5x0.5_AVHRR_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_10x10min_nomask_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_5x5min_IGBP-GSDP_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_5x5min_nomask_to_32x64_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/32x64/map_5x5min_ISRIC-WISE_to_32x64_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/32x64/map_5x5min_ORNL-Soil_to_32x64_nomask_aave_da_c170706.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_MODIS_to_32x64_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_MODIS-wCsp_to_32x64_nomask_aave_da_c160425.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_USGS_to_32x64_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_LandScan2004_to_32x64_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_GLOBE-Gardner_to_32x64_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/32x64/map_3x3min_GLOBE-Gardner-mergeGIS_to_32x64_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/32x64/map_0.9x1.25_GRDC_to_32x64_nomask_aave_da_c130308.nc -lnd/clm2/mappingdata/maps/32x64/map_360x720_cruncep_to_32x64_nomask_aave_da_c130326.nc -lnd/clm2/mappingdata/maps/32x64/map_1km-merge-10min_HYDRO1K-merge-nomask_to_32x64_nomask_aave_da_c130405.nc - -lnd/clm2/mappingdata/maps/8x16/map_0.5x0.5_MODIS_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_0.25x0.25_MODIS_to_8x16_nomask_aave_da_c170321.nc -lnd/clm2/mappingdata/maps/8x16/map_0.5x0.5_AVHRR_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_10x10min_nomask_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_5x5min_IGBP-GSDP_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_5x5min_nomask_to_8x16_nomask_aave_da_c110920.nc -lnd/clm2/mappingdata/maps/8x16/map_5x5min_ISRIC-WISE_to_8x16_nomask_aave_da_c111115.nc -lnd/clm2/mappingdata/maps/8x16/map_5x5min_ORNL-Soil_to_8x16_nomask_aave_da_c170706.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_MODIS_to_8x16_nomask_aave_da_c111111.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_MODIS-wCsp_to_8x16_nomask_aave_da_c160425.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_USGS_to_8x16_nomask_aave_da_c120926.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_LandScan2004_to_8x16_nomask_aave_da_c120518.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_GLOBE-Gardner_to_8x16_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/8x16/map_3x3min_GLOBE-Gardner-mergeGIS_to_8x16_nomask_aave_da_c120923.nc -lnd/clm2/mappingdata/maps/8x16/map_0.9x1.25_GRDC_to_8x16_nomask_aave_da_c130308.nc -lnd/clm2/mappingdata/maps/8x16/map_360x720_cruncep_to_8x16_nomask_aave_da_c130326.nc -lnd/clm2/mappingdata/maps/8x16/map_1km-merge-10min_HYDRO1K-merge-nomask_to_8x16_nomask_aave_da_c130411.nc - lnd/clm2/mappingdata/maps/4x5/map_0.5x0.5_MODIS_to_4x5_nomask_aave_da_c110822.nc lnd/clm2/mappingdata/maps/4x5/map_5x5min_ORNL-Soil_to_4x5_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/4x5/map_3x3min_MODIS_to_4x5_nomask_aave_da_c111111.nc +lnd/clm2/mappingdata/maps/4x5/map_3x3min_MODISv2_to_4x5_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/4x5/map_3x3min_MODIS-wCsp_to_4x5_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/0.23x0.31/map_5x5min_ORNL-Soil_to_0.23x0.31_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/0.23x0.31/map_3x3min_MODIS_to_0.23x0.31_nomask_aave_da_c110930.nc +lnd/clm2/mappingdata/maps/0.23x0.31/map_3x3min_MODISv2_to_0.23x0.31_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/0.23x0.31/map_3x3min_MODIS-wCsp_to_0.23x0.31_nomask_aave_da_c160425.nc lnd/clm2/mappingdata/maps/2.5x3.33/map_5x5min_ORNL-Soil_to_2.5x3.33_nomask_aave_da_c170706.nc lnd/clm2/mappingdata/maps/2.5x3.33/map_3x3min_MODIS_to_2.5x3.33_nomask_aave_da_c111111.nc +lnd/clm2/mappingdata/maps/2.5x3.33/map_3x3min_MODISv2_to_2.5x3.33_nomask_aave_da_c190505.nc lnd/clm2/mappingdata/maps/2.5x3.33/map_3x3min_MODIS-wCsp_to_2.5x3.33_nomask_aave_da_c160425.nc + +lnd/clm2/mappingdata/maps/C24/map_0.5x0.5_TO_C24_aave.181018.nc +lnd/clm2/mappingdata/maps/C24/map_0.5x0.5_MODIS_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_0.25x0.25_MODIS_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_0.5x0.5_AVHRR_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_10x10min_nomask_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_5x5min_IGBP-GSDP_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_5x5min_nomask_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_5x5min_ISRIC-WISE_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_5x5min_ORNL-Soil_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_3x3min_MODIS-wCsp_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_3x3min_USGS_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_3x3min_LandScan2004_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_3x3min_GLOBE-Gardner_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_3x3min_GLOBE-Gardner-mergeGIS_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_0.9x1.25_GRDC_to_C24_nomask_aave_da_c181018.nc +lnd/clm2/mappingdata/maps/C24/map_360x720cru_cruncep_to_C24_nomask_aave_da_c181018.nc 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+lnd/clm2/mappingdata/maps/ne120np4.pg3/map_5x5min_IGBP-GSDP_to_ne120np4.pg3_nomask_aave_da_c200426.nc +lnd/clm2/mappingdata/maps/ne120np4.pg3/map_5x5min_ISRIC-WISE_to_ne120np4.pg3_nomask_aave_da_c200426.nc +lnd/clm2/mappingdata/maps/ne120np4.pg3/map_5x5min_nomask_to_ne120np4.pg3_nomask_aave_da_c200426.nc +lnd/clm2/mappingdata/maps/ne120np4.pg3/map_3x3min_MODISv2_to_ne120np4.pg3_nomask_aave_da_c200426.nc + + @@ -2477,15 +3606,19 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc -TWS_inversion -ZWT_inversion +TWS_inversion +TWS_inversion +ZWT_inversion .true. .true. 1.9x2.5 +1.9x2.5 lnd/clm2/paramdata/finundated_inversiondata_0.9x1.25_c170706.nc +lnd/clm2/paramdata/finundated_inversiondata_0.9x1.25_c170706.nc @@ -2512,18 +3645,22 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc.false. -.false. +0 .false. +.false. .false. .false. .false. .false. +.false. +1 +.false. .false. diff --git a/bld/namelist_files/namelist_defaults_ctsm_tools.xml b/bld/namelist_files/namelist_defaults_ctsm_tools.xml index 9fa7b11d33..78ab368110 100644 --- a/bld/namelist_files/namelist_defaults_ctsm_tools.xml +++ b/bld/namelist_files/namelist_defaults_ctsm_tools.xml @@ -38,13 +38,29 @@ attributes from the config_cache.xml file (with keys converted to upper-case). lnd/clm2/mappingdata/grids/SCRIPgrid_32x64_nomask_c110308.nc lnd/clm2/mappingdata/grids/SCRIPgrid_8x16_nomask_c110308.nc + +atm/cam/coords/C384_SCRIP_desc.181018.nc +atm/cam/coords/C192_SCRIP_desc.181018.nc +atm/cam/coords/C96_SCRIP_desc.181018.nc +atm/cam/coords/C48_SCRIP_desc.181018.nc +atm/cam/coords/C24_SCRIP_desc.181018.nc + -lnd/clm2/mappingdata/grids/SCRIPgrid_ne240np4_nomask_c091227.nc -lnd/clm2/mappingdata/grids/SCRIPgrid_ne120np4_nomask_c101123.nc -lnd/clm2/mappingdata/grids/SCRIPgrid_ne60np4_nomask_c100408.nc -lnd/clm2/mappingdata/grids/SCRIPgrid_ne30np4_nomask_c101123.nc -lnd/clm2/mappingdata/grids/SCRIPgrid_ne16np4_nomask_c110512.nc -lnd/clm2/mappingdata/grids/SCRIPgrid_ne4np4_nomask_c110808.nc +lnd/clm2/mappingdata/grids/SCRIPgrid_ne240np4_nomask_c091227.nc +lnd/clm2/mappingdata/grids/SCRIPgrid_ne120np4_nomask_c101123.nc +lnd/clm2/mappingdata/grids/SCRIPgrid_ne60np4_nomask_c100408.nc +lnd/clm2/mappingdata/grids/SCRIPgrid_ne30np4_nomask_c101123.nc +lnd/clm2/mappingdata/grids/SCRIPgrid_ne16np4_nomask_c110512.nc + +atm/cam/coords/ne30pg2_scrip_c170608.nc +atm/cam/coords/ne30pg3_scrip_170604.nc +atm/cam/coords/ne120pg2_scrip_c170629.nc +atm/cam/coords/ne120pg3_scrip_c170628.nc + + +atm/cam/coords/ne0CONUSne30x8_scrip_c200107.nc +atm/cam/coords/ne0ARCTICGRISne30x8_scrip_c191209.nc +atm/cam/coords/ne0ARCTICne30x4_scrip_c191212.nc lnd/clm2/mappingdata/grids/SCRIPgrid_10x10min_IGBPmergeICESatGIS_c110818.nc lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_MODIS_c110915.nc +lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_MODISv2_c190503.nc lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_MODISwcspsea_c151020.nc 64bit_offset +64bit_offset 64bit_offset lnd/clm2/mappingdata/grids/SCRIPgrid_3x3_USGS_c120912.nc @@ -131,11 +150,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case). AVHRR AVHRR MODIS +MODISv2 MODIS -MODIS +MODISv2 MODIS LandScan2004 MODIS +MODISv2 ISRIC-WISE GLOBE-Gardner GLOBE-Gardner-mergeGIS @@ -157,11 +178,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 0.5x0.5 0.5x0.5 0.25x0.25 +3x3min 0.25x0.25 3x3min 0.25x0.25 3x3min 0.25x0.25 +3x3min 5x5min 3x3min 10x10min @@ -205,6 +228,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case). +lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190116/mksrf_lai_histclm52deg005_earthstatmirca_2005.c190119.nc + + lnd/clm2/rawdata/pftcftlandusedynharv.0.25x0.25.MODIS.simyr1850-2015.c170412/mksrf_lai_78pfts_simyr2005.c170413.nc @@ -216,6 +243,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case). lnd/clm2/rawdata/mksrf_soitex.10level.c010119.nc +lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190116/mksrf_soilcolor_histclm52deg005_earthstatmirca_2005.c190116.nc + + lnd/clm2/rawdata/pftcftlandusedynharv.0.25x0.25.MODIS.simyr1850-2015.c170412/mksrf_soilcolor_CMIP6_simyr2005.c170623.nc @@ -240,6 +271,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). lnd/clm2/rawdata/mksrf_urban_0.05x0.05_simyr2000.c120621.nc +lnd/clm2/rawdata/mksrf_urban_0.05x0.05_zerourbanpct.c181014.nc + lnd/clm2/rawdata/mksrf_gdp_0.5x0.5_AVHRR_simyr2000.c130228.nc +lnd/clm2/rawdata/mksrf_gdp_0.5x0_zerogdp.c200413.nc lnd/clm2/rawdata/mksrf_peatf_0.5x0.5_AVHRR_simyr2000.c130228.nc @@ -278,6 +314,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). lnd/clm2/rawdata/mksrf_abm_0.5x0.5_AVHRR_simyr2000.c130201.nc +lnd/clm2/rawdata/mksrf_abm_0.5x0.5_missingabm.c200413.nc + lnd/clm2/rawdata/mksrf_topostats_1km-merge-10min_HYDRO1K-merge-nomask_simyr2000.c130402.nc @@ -290,340 +329,6755 @@ attributes from the config_cache.xml file (with keys converted to upper-case). - -lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c170629/mksrf_landuse_histclm50_LUH2_1850.c170629.nc + +lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190116/mksrf_landuse_clm52deg005_histLUH2_1850.c190119.nc -lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c170629/mksrf_landuse_histclm50_LUH2_1851.c170629.nc +lnd/clm2/rawdata/pftcftdynharv.0.05x0.05.LUH2.histsimyr2005.c190116/mksrf_landuse_clm52deg005_histLUH2_2005.c190119.nc -lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c170629/mksrf_landuse_histclm50_LUH2_1852.c170629.nc + + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr0850-1849.c171012/mksrf_landuse_histclm50_LUH2_850.c171012.nc -lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c170629/mksrf_landuse_histclm50_LUH2_1853.c170629.nc + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr0850-1849.c171012/mksrf_landuse_histclm50_LUH2_851.c171012.nc 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+lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2060.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2061.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2062.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2063.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2064.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2065.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2066.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2067.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2068.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2069.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2070.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2071.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2072.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2073.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2074.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2075.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2076.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2077.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2078.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2079.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2080.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2081.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2082.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2083.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2084.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2085.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2086.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2087.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2088.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2089.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2090.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2091.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2092.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2093.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2094.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2095.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2096.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2097.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2098.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2099.c181217.nc + + +lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP4-6.0.simyr2016-2100.c181217/mksrf_landuse_SSP4RCP60_clm5_2100.c181217.nc + + + + + lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.SSP5-8.5.simyr2016-2100.c171005/mksrf_landuse_SSP5RCP85_clm5_2016.c171005.nc @@ -966,7 +7420,25 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -atm/waccm/lb/LBC_17500116-20150116_CMIP6_0p5degLat_c180905.nc -/gpfs/fs1/p/acom/acom-climate/cesm2/inputdata/atm/waccm/lb/LBC_1750-2015_CMIP6_GlobAnnAvg_c180905.nc +atm/waccm/lb/LBC_17500116-20150116_CMIP6_0p5degLat_c180905.nc +atm/waccm/lb/LBC_1750-2015_CMIP6_GlobAnnAvg_c180926.nc + +atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP119_0p5degLat_c190514.nc +atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP126_0p5degLat_c180905.nc +atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP245_0p5degLat_c180905.nc +atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP370_0p5degLat_c180905.nc +atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP119_0p5degLat_c190514.nc +atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP460_0p5degLat_c180905.nc +atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP534os_0p5degLat_c180905.nc +atm/waccm/lb/LBC_20140116-25001216_CMIP6_SSP585_0p5degLat_c180905.nc + +atm/waccm/lb/LBC_2014-2500_CMIP6_SSP119_0p5degLat_GlobAnnAvg_c190514.nc +atm/waccm/lb/LBC_2014-2500_CMIP6_SSP126_0p5degLat_GlobAnnAvg_c190301.nc +atm/waccm/lb/LBC_2014-2500_CMIP6_SSP245_0p5degLat_GlobAnnAvg_c190301.nc +atm/waccm/lb/LBC_2014-2500_CMIP6_SSP370_0p5degLat_GlobAnnAvg_c190301.nc +atm/waccm/lb/LBC_2014-2500_CMIP6_SSP434_0p5degLat_GlobAnnAvg_c190514.nc +atm/waccm/lb/LBC_2014-2500_CMIP6_SSP460_0p5degLat_GlobAnnAvg_c190301.nc +atm/waccm/lb/LBC_2014-2500_CMIP6_SSP534os_0p5degLat_GlobAnnAvg_c190301.nc +atm/waccm/lb/LBC_2014-2500_CMIP6_SSP585_0p5degLat_GlobAnnAvg_c190301.nc diff --git a/bld/namelist_files/namelist_defaults_drydep.xml b/bld/namelist_files/namelist_defaults_drydep.xml index e73f2987c2..25094e4ea8 100644 --- a/bld/namelist_files/namelist_defaults_drydep.xml +++ b/bld/namelist_files/namelist_defaults_drydep.xml @@ -23,6 +23,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 'ISOP = isoprene', 'C10H16 = pinene_a + carene_3 + thujene_a', 'CH3OH = methanol', 'C2H5OH = ethanol', 'CH2O = formaldehyde', 'CH3CHO = acetaldehyde', 'CH3COOH = acetic_acid', 'CH3COCH3 = acetone' +atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc diff --git a/bld/namelist_files/namelist_defaults_overall.xml b/bld/namelist_files/namelist_defaults_overall.xml index f7f2d041c2..f0c7f3c0ff 100644 --- a/bld/namelist_files/namelist_defaults_overall.xml +++ b/bld/namelist_files/namelist_defaults_overall.xml @@ -12,14 +12,41 @@ in a namelist, but they are default values that will help determine default values for namelists. --> - -startup -startup -arb_ic -arb_ic -arb_ic -arb_ic -cold + + +arb_ic +arb_ic +arb_ic +arb_ic +arb_ic +arb_ic +startup +startup +startup +startup +startup +startup +arb_ic +arb_ic +arb_ic +arb_ic +cold + +arb_ic + + + +flanduse_timeseries +flanduse_timeseries + /fs/cgd/csm/inputdata @@ -42,32 +69,31 @@ determine default values for namelists. constant - -1 -0 + +0 1 0 - --999.9 + +hist gx1v6 gx1v6 -gx1v6 -gx1v6 +gx1v7 +gx1v7 gx3v7 gx3v7 -USGS +gx3v7 cruncep -USGS -USGS +gx1v7 +gx1v7 gx3v7 -USGS -USGS +gx3v7 +gx3v7 T62 @@ -85,7 +111,7 @@ determine default values for namelists. test navy test -gx1v6 +gx1v7 diff --git a/bld/namelist_files/namelist_defaults_usr_files.xml b/bld/namelist_files/namelist_defaults_usr_files.xml index 8ef06f8014..41e6dcd47b 100644 --- a/bld/namelist_files/namelist_defaults_usr_files.xml +++ b/bld/namelist_files/namelist_defaults_usr_files.xml @@ -23,13 +23,14 @@ provided they are in the valid list expressed above. lnd/clm2/initdata/clmi.${clm_usr_name}_${mask}_simyr${sim_year}.nc +lnd/clm2/surfdata/surfdata_${clm_usr_name}_simyr${sim_year}.nc lnd/clm2/surfdata_map/surfdata_${clm_usr_name}_simyr${sim_year}.nc -null -lnd/clm2/surfdata/landuse.timeseries_${clm_usr_name}_simyr${sim_year_range}.nc -lnd/clm2/surfdata/landuse.timeseries_${clm_usr_name}_simyr1849-2006.nc -lnd/clm2/surfdata/landuse.timeseries_rcp${rcp}_${clm_usr_name}_simyr${sim_year_range}.nc -lnd/clm2/surfdata/landuse.timeseries_rcp${rcp}_${clm_usr_name}_simyr1849-2006.nc +null +lnd/clm2/surfdata/landuse.timeseries_${clm_usr_name}_simyr${sim_year_range}.nc +lnd/clm2/surfdata/landuse.timeseries_${clm_usr_name}_simyr1849-2006.nc +lnd/clm2/surfdata/landuse.timeseries_${ssp_rcp}_${clm_usr_name}_simyr${sim_year_range}.nc +lnd/clm2/surfdata/landuse.timeseries_${ssp_rcp}_${clm_usr_name}_simyr1849-2006.nc diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 83502c5f32..d74989889c 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -49,6 +49,15 @@ Full pathname of master restart file for a branch run. (only used if RUN_TYPE=br (Set with RUN_REFCASE and RUN_REFDATE)     + +Component name to use in history and restart files + + + group="cnfire_inparm" valid_values="nofire,li2014qianfrc,li2016crufrc,li2021gswpfrc" > The method type to use for CNFire nofire: Turn fire effects off li2014qianfrc: Reference paper Li, et. al.(2014) tuned with QIAN atmospheric forcing li2016crufrc: Reference paper Li, et. al.(2016) tuned with CRU-NCEP atmospheric forcing +li2021gswpfrc: Reference paper Li, et. al.(2021?) tuned with GSWP3 atmospheric forcing - -Combustion completeness factor (for litter and CWD[Course Woody Debris]) (unitless) +Combustion completeness factor for litter (unitless) + + + +Combustion completeness factor for CWD[Course Woody Debris] (unitless) + +If TRUE, include biomass heat storage in canopy energy balance. + Max number of iterations used in subr. CanopyFluxes. For many years, 40 was the hardwired default value. @@ -482,7 +501,7 @@ If TRUE, irrigation will be active. If TRUE, fsat will be set to zero for crop columns. - Number of multiple elevation classes over glacier points. @@ -619,54 +638,78 @@ The maximum value to use for zeta under stable conditions baseline proportion of nitrogen allocated for electron transport (J) - -Time step (seconds) - - Toggle to turn on the FATES model -(use_fates= '.true.' is EXPERIMENTAL NOT SUPPORTED!) +Functionally Assembled Terrestrial Ecosystem Simulator (FATES) - -Toggle to turn on spitfire module for modeling fire (only relevant if FATES is being used). + +Switch deciding which nutrient model to use in FATES. +(Only relevant if FATES is on) + + + +Turn on spitfire module to simulate fire by setting fates_spitfire_mode > 0. +Allowed values are: + 0 : Simulations of fire are off + 1 : use a global constant lightning rate found in fates_params. + 2 : use an external lightning dataset. + 3 : use an external confirmed ignitions dataset (not available through standard CSEM dataset collection). + 4 : use external lightning and population datasets to simulate both natural and anthropogenic +ignitions. +(Only relevant if FATES is on) + + + +Toggle to turn on fixed biogeography mode +(Only relevant if FATES is on) -Toggle to turn on the logging module (only relevant if FATES is being used). +Toggle to turn on the logging module +(Only relevant if FATES is on) -Toggle to turn on plant hydraulics (only relevant if FATES is on). -(use_fates_planthydro=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!) + group="clm_inparm" valid_values="" value=".false."> +Toggle to turn on plant hydraulics +(Only relevant if FATES is on) + + + +Toggle to turn on cohort age tracking (by default FATES only tracks age of patches) +(Only relevant if FATES is on). Toggle to turn on Static Stand Structure Mode (only relevant if FATES is being used). -(use_fates_ed_st3=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!) +(Only relevant if FATES is on). -Toggle to turn on prescribed physiology (only relevant if FATES is being used). +Toggle to turn on prescribed physiology +(Only relevant if FATES is on). -Toggle to turn on inventory initialization to startup FATES (only relevant if FATES is being used). -(use_fates_inventory_init=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!) +Toggle to turn on inventory initialization to startup FATES +(Only relevant if FATES is on). Full pathname to the inventory initialization control file. (Required, if use_fates_inventory_init=T) +(Only relevant if FATES is on). Full pathname datafile with fates parameters +(Only relevant if FATES is on). + +If TRUE, write master field list to separate file for documentation purposes + + Per file averaging flag. @@ -926,6 +975,12 @@ Whether to use subgrid fluxes for snow Whether snow on the vegetation canopy affects the radiation/albedo calculations + +Whether to run some tests of ncdio_pio as part of the model run. This is +typically only used in automated tests. + + @@ -971,18 +1026,6 @@ Exponent power for heterotrophic respiration for max denitrification rates (ONLY used if use_nitrif_denitrif is enabled) - -Multiplier for nitrate concentration for max denitrification rates -(ONLY used if use_nitrif_denitrif is enabled) - - - -Exponent power for nitrate concentrationfor max denitrification rates -(ONLY used if use_nitrif_denitrif is enabled) - - Maximum nitrification rate constant (1/s) @@ -1053,6 +1096,18 @@ Initial seed Carbon to use at planting (only used when CN is on as well as crop) + +Phenology onset depends on the vegetation type +(only used when CN is on) + + + +The minimum critical day length for onset depends on latitude +(only used when CN is on) + + Toggle to turn on ozone stress @@ -1079,11 +1134,6 @@ Toggle for vancouver specific logic. Toggle for mexico city specific logic. - -Max number of plant functional types in naturally vegetated landunit. - - @@ -1105,37 +1155,37 @@ If true, this directs the model to collapse the urban landunits to the dominant Percentage threshold above which the model keeps the soil landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the crop landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the glacier landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the lake landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the wetland landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the urban landunits. Selecting the value 0 means DO NOTHING. If collapse_urban = .false., the same threshold will apply to all three urban landunits if they are present. If collapse_urban = .true., this threshold will apply to the single collapsed urban landunit if presnet. Default: 0 @@ -1499,7 +1549,7 @@ If TRUE, repartition rain/snow from atmosphere based on temperature. -If TRUE, downscale longwave radiation over glc_mec landunits. +If TRUE, downscale longwave radiation over glacier landunits. This downscaling is conservative. Default: .true. @@ -1594,6 +1644,11 @@ Time interpolation mode to determine how to handle data before and after the tim limit = Only use the data within the times available -- abort if the model tries to go outside it + +Time interpolation method to use for Nitrogen Deposition + + Colon delimited list of variables to read from the streams file for nitrogen deposition @@ -1612,7 +1667,7 @@ Mapping method from Nitrogen deposition input file to the model resolution - + + + +Toggle to turn on use of input prescribed soil moisture streams rather than have CLM prognose it (EXPERIMENTAL) + + + +First year to loop over for prescribed soil moisture streams data + + + +Last year to loop over for prescribed soil moisture streams data + + + +Simulation year that aligns with stream_year_first_soilm value + + + +Filename of input stream data for prescribed soil moisture streams data + + + +Time interpolation method to use for prescribed soil moisture streams data + + + +Offset in time coordinate for soil moisture streams (sec) + + + +If false will abort if using soil moisture streams and find a point where the model shows H2OSOI_VOL +should be set because it's vegetated, but the input soilm streams dataset shows that point is missing. +If true, will ignore the prescribed soilm data for that point and let the model run for that point without +prescribed data. + + @@ -1652,6 +1751,11 @@ Simulation year that aligns with stream_year_first_lai value Filename of input stream data for LAI + +Time interpolation method to use with LAI streams + + Mapping method from LAI input file to the model resolution @@ -1688,6 +1792,11 @@ Simulation year that aligns with stream_year_first_lightng value Filename of input stream data for Lightning + +Time interpolation method to use with Lightning streams + + Mapping method from Lightning input file to the model resolution @@ -1725,6 +1834,11 @@ Simulation year that aligns with stream_year_first_popdens value Filename of input stream data for human population density + +Time interpolation method to use with human population density streams + + Mapping method from human population density input file to the model resolution @@ -1762,6 +1876,11 @@ Simulation year that aligns with stream_year_first_urbantv value Filename of input stream data for urban time varying + +Time interpolation method to use with urban time varying streams + + Mapping method from urban time varying input file to the model resolution @@ -1848,36 +1967,30 @@ CLM run type. + valid_values="512x1024,360x720cru,128x256,64x128,48x96,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,0.125nldas2,5x5_amazon,1x1_camdenNJ,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ,1x1_brazil,1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA,0.1x0.1,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne4np4,ne16np4,ne30np4.pg2,ne30np4.pg3,ne30np4,ne60np4,ne120np4,ne120np4.pg2,ne120np4.pg3,ne0np4CONUS.ne30x8,ne0np4.ARCTIC.ne30x4,ne0np4.ARCTICGRIS.ne30x8,ne240np4,1km-merge-10min,C24,C48,C96,C192,C384"> Horizontal resolutions -Note: 0.1x0.1, 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min and 0.33x0.33 are only used for CLM tools +Note: 0.1x0.1, 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min, 1km-merge-10min and 0.33x0.33 are only used for CLM toolsI - -Representative concentration pathway for future scenarios [radiative forcing at peak or 2100 in W/m^2] --999.9 means do NOT use a future scenario, just use historical data. - - - -Shared Socioeconomic Pathway and Representative Concentration Pathway combination for future scenarios + valid_values="hist,SSP1-2.6,SSP3-7.0,SSP5-3.4,SSP2-4.5,SSP1-1.9,SSP4-3.4,SSP4-6.0,SSP5-8.5"> +Shared Socioeconomic Pathway (SSP) and Representative Concentration Pathway (RCP) combination for future scenarios The form is SSPn-m.m Where n is the SSP number and m.m is RCP radiative forcing at peak or 2100 in W/m^2 +n is just the whole number of the specific SSP scenario. The lower numbers have higher mitigation +- the higher numbers less mitigation, more than one SSP can result in the same RCP forcing hist means do NOT use a future scenario, just use historical data. + valid_values="USGS,gx3v7,gx1v6,gx1v7,navy,test,tx0.1v2,tx0.1v3,tx1v1,T62,cruncep,nldas2"> Land mask description + valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm5_0_cam6.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1"> General configuration of model version and atmospheric forcing to tune the model to run under. This sets the model to run with constants and initial conditions that were set to run well under the configuration of model version and atmospheric forcing. To run well constants would need to be changed @@ -1889,19 +2002,20 @@ to run with a different type of atmospheric forcing. If 1, turn on the MEGAN model for BVOC's (Biogenic Volitile Organic Compounds) - +"PtVg,1000,850,1100,1350,1600,1850,1855,1865,1875,1885,1895,1905,1915,1925,1935,1945,1955,1965,1975,1979,1980,1982,1985,1995,2000,2005,2010,2013,2015,2025,2035,2045,2055,2065,2075,2085,2095,2105"> Year to simulate and to provide datasets for (such as surface datasets, initial conditions, aerosol-deposition, Nitrogen deposition rates etc.) A sim_year of 1000 corresponds to data used for testing only, NOT corresponding to any real datasets. -A sim_year greater than 2005 corresponds to rcp scenario data +A sim_year greater than 2015 corresponds to ssp_rcp scenario data +A sim_year of PtVg refers to the Potential Vegetation dataset, that doesn't include human influences Most years are only used for clm_tools and there aren't CLM datasets that correspond to them. CLM datasets exist for years: 1000 (for testing), 1850, and 2000 +"constant,1000-1002,1000-1004,850-1850,1850-1855,1850-2000,1850-2005,1850-2100,1980-2015,2000-2025,2000-2100"> Range of years to simulate transitory datasets for (such as dynamic: land-use datasets, aerosol-deposition, Nitrogen deposition rates etc.) Constant means simulation will be held at a constant year given in sim_year. A sim_year_range of 1000-1002 or 1000-1004 corresponds to data used for testing only, NOT corresponding to any real datasets. @@ -1928,8 +2042,8 @@ Attributes to use when looking for an initial condition file (finidat) if interp How close in years to use when looking for an initial condition file (finidat) if interpolation is turned on (use_init_interp is .true.) - + Simulation years you can look for in initial condition files (finidat) if interpolation is turned on (use_init_interp is .true.) @@ -2032,6 +2146,11 @@ Number of days over which to use exponential relaxation of NPP in N fixation cal Flag to reseed any dead plants on startup from reading the initial conditions file + +Harvest the XSMR pool at crop harvest time to the atmosphere slowly at an exponential rate + + @@ -2321,6 +2440,12 @@ If TRUE, apply transient crops from flanduse_timeseries file. (Only valid for transient runs, where there is a flanduse_timeseries file.) + +If TRUE, apply transient lakes from flanduse_timeseries file. +(Only valid for transient runs, where there is a flanduse_timeseries file.) + + If TRUE, apply harvest from flanduse_timeseries file. diff --git a/bld/namelist_files/use_cases/1850-2100_SSP1-1.9_transient.xml b/bld/namelist_files/use_cases/1850-2100_SSP1-1.9_transient.xml new file mode 100644 index 0000000000..93e5e24372 --- /dev/null +++ b/bld/namelist_files/use_cases/1850-2100_SSP1-1.9_transient.xml @@ -0,0 +1,17 @@ + + + + +Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP1-1.9 scenario +Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP1-1.9 scenario + + + +1850 + +1850-2100 + +SSP1-1.9 + + diff --git a/bld/namelist_files/use_cases/1850-2100_SSP1-2.6_transient.xml b/bld/namelist_files/use_cases/1850-2100_SSP1-2.6_transient.xml new file mode 100644 index 0000000000..d10ef6d45f --- /dev/null +++ b/bld/namelist_files/use_cases/1850-2100_SSP1-2.6_transient.xml @@ -0,0 +1,17 @@ + + + + +Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP1-2.6 scenario +Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP1-2.6 scenario + + + +1850 + +1850-2100 + +SSP1-2.6 + + diff --git a/bld/namelist_files/use_cases/1850-2100_SSP2-4.5_transient.xml b/bld/namelist_files/use_cases/1850-2100_SSP2-4.5_transient.xml new file mode 100644 index 0000000000..85859517f1 --- /dev/null +++ b/bld/namelist_files/use_cases/1850-2100_SSP2-4.5_transient.xml @@ -0,0 +1,17 @@ + + + + +Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP2-4.5 scenario +Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP2-4.5 scenario + + + +1850 + +1850-2100 + +SSP2-4.5 + + diff --git a/bld/namelist_files/use_cases/1850-2100_SSP3-7.0_transient.xml b/bld/namelist_files/use_cases/1850-2100_SSP3-7.0_transient.xml new file mode 100644 index 0000000000..317ca3fbcd --- /dev/null +++ b/bld/namelist_files/use_cases/1850-2100_SSP3-7.0_transient.xml @@ -0,0 +1,17 @@ + + + + +Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP3-7.0 scenario +Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP3-7.0 scenario + + + +1850 + +1850-2100 + +SSP3-7.0 + + diff --git a/bld/namelist_files/use_cases/1850-2100_SSP4-3.4_transient.xml b/bld/namelist_files/use_cases/1850-2100_SSP4-3.4_transient.xml new file mode 100644 index 0000000000..0e42bbd724 --- /dev/null +++ b/bld/namelist_files/use_cases/1850-2100_SSP4-3.4_transient.xml @@ -0,0 +1,17 @@ + + + + +Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP4-3.4 scenario +Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP4-3.4 scenario + + + +1850 + +1850-2100 + +SSP4-3.4 + + diff --git a/bld/namelist_files/use_cases/1850-2100_SSP4-6.0_transient.xml b/bld/namelist_files/use_cases/1850-2100_SSP4-6.0_transient.xml new file mode 100644 index 0000000000..b2b67a4d5b --- /dev/null +++ b/bld/namelist_files/use_cases/1850-2100_SSP4-6.0_transient.xml @@ -0,0 +1,17 @@ + + + + +Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP4-6.0 scenario +Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP4-6.0 scenario + + + +1850 + +1850-2100 + +SSP4-6.0 + + diff --git a/bld/namelist_files/use_cases/1850-2100_SSP5-3.4_transient.xml b/bld/namelist_files/use_cases/1850-2100_SSP5-3.4_transient.xml new file mode 100644 index 0000000000..e4ae71ca94 --- /dev/null +++ b/bld/namelist_files/use_cases/1850-2100_SSP5-3.4_transient.xml @@ -0,0 +1,17 @@ + + + + +Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-3.4 scenario +Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-3.4 scenario + + + +1850 + +1850-2100 + +SSP5-3.4 + + diff --git a/bld/namelist_files/use_cases/1850-2100_SSP5-8.5_transient.xml b/bld/namelist_files/use_cases/1850-2100_SSP5-8.5_transient.xml new file mode 100644 index 0000000000..fbb8af4d10 --- /dev/null +++ b/bld/namelist_files/use_cases/1850-2100_SSP5-8.5_transient.xml @@ -0,0 +1,17 @@ + + + + +Simulate transient land-use, and aerosol deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-8.5 scenario +Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP5-8.5 scenario + + + +1850 + +1850-2100 + +SSP5-8.5 + + diff --git a/bld/namelist_files/use_cases/1850-2100_rcp2.6_transient.xml b/bld/namelist_files/use_cases/1850-2100_rcp2.6_transient.xml deleted file mode 100644 index 4252c1e64f..0000000000 --- a/bld/namelist_files/use_cases/1850-2100_rcp2.6_transient.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - -Simulate transient land-use, and aerosol deposition changes with historical data from 1850 to 2005 and then with the RCP2.6 scenario from IMAGE - -Simulate transient land-use, aerosol and Nitrogen deposition changes with historical data from 1850 to 2005 and then with the RCP2.6 scenario from IMAGE - - -Simulate transient land-use, aerosol and Nitrogen deposition changes with historical data from 1850 to 2005 and then with the RCP2.6 scenario from IMAGE - - -1850 - -1850-2100 - -2.6 - -flanduse_timeseries - -.true. -.false. -.false. - -arb_ic - -1850 -2100 -1850 - -1850 -2100 -1850 - -1850 -2010 -1850 - -1850 -2010 -1850 - -1850 -2100 -1850 - -1850 -2100 -1850 - - - diff --git a/bld/namelist_files/use_cases/1850-2100_rcp4.5_transient.xml b/bld/namelist_files/use_cases/1850-2100_rcp4.5_transient.xml deleted file mode 100644 index 09541a7b86..0000000000 --- a/bld/namelist_files/use_cases/1850-2100_rcp4.5_transient.xml +++ /dev/null @@ -1,51 +0,0 @@ - - - - -Simulate transient land-use, and aerosol deposition changes with historical data from 1850 to 2005 and then with the RCP4.5 scenario from MINICAM - -Simulate transient land-use, aerosol and Nitrogen deposition changes with historical data from 1850 to 2005 and then with the RCP4.5 scenario from MINICAM - - -Simulate transient land-use, aerosol and Nitrogen deposition changes with historical data from 1850 to 2005 and then with the RCP4.5 scenario from MINICAM - - -1850 - -1850-2100 - -4.5 - -flanduse_timeseries - -arb_ic - -.true. -.false. -.false. - -1850 -2100 -1850 - -1850 -2100 -1850 - -1850 -2010 -1850 - -1850 -2010 -1850 - -1850 -2100 -1850 - -1850 -2100 -1850 - - diff --git a/bld/namelist_files/use_cases/1850-2100_rcp6_transient.xml b/bld/namelist_files/use_cases/1850-2100_rcp6_transient.xml deleted file mode 100644 index 4ee8db473e..0000000000 --- a/bld/namelist_files/use_cases/1850-2100_rcp6_transient.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - -Simulate transient land-use, and aerosol deposition changes with historical data from 1850 to 2005 and then with the RCP6 scenario from AIM - - -Simulate transient land-use, aerosol and Nitrogen deposition changes with historical data from 1850 to 2005 and then with the RCP6 scenario from AIM - - -Simulate transient land-use, aerosol and Nitrogen deposition changes with historical data from 1850 to 2005 and then with the RCP6 scenario from AIM - - -1850 - -1850-2100 - -6 - -.true. -.false. -.false. - -flanduse_timeseries - -arb_ic - -1850 -2100 -1850 - -1850 -2100 -1850 - -1850 -2010 -1850 - -1850 -2010 -1850 - -1850 -2100 -1850 - -1850 -2100 -1850 - - diff --git a/bld/namelist_files/use_cases/1850-2100_rcp8.5_transient.xml b/bld/namelist_files/use_cases/1850-2100_rcp8.5_transient.xml deleted file mode 100644 index c649101306..0000000000 --- a/bld/namelist_files/use_cases/1850-2100_rcp8.5_transient.xml +++ /dev/null @@ -1,51 +0,0 @@ - - - - -Simulate transient land-use, and aerosol deposition changes with historical data from 1850 to 2005 and then with the RCP8.5 scenario from MESSAGE - -Simulate transient land-use, aerosol and Nitrogen deposition changes with historical data from 1850 to 2005 and then with the RCP8.5 scenario from MESSAGE - - -Simulate transient land-use, aerosol and Nitrogen deposition changes with historical data from 1850 to 2005 and then with the RCP8.5 scenario from MESSAGE - - -1850 - -1850-2100 - -8.5 - -.true. -.false. -.false. - -flanduse_timeseries - -arb_ic - -1850 -2100 -1850 - -1850 -2100 -1850 - -1850 -2010 -1850 - -1850 -2010 -1850 - -1850 -2100 -1850 - -1850 -2100 -1850 - - diff --git a/bld/namelist_files/use_cases/1850_control.xml b/bld/namelist_files/use_cases/1850_control.xml index bafb1e2774..94ee8c5d0d 100644 --- a/bld/namelist_files/use_cases/1850_control.xml +++ b/bld/namelist_files/use_cases/1850_control.xml @@ -8,6 +8,7 @@ constant +.false. .false. .false. @@ -17,23 +18,37 @@ 1850 1850 +1850 +1850 + 1850 1850 1850 1850 +1850 +1850 + 1850 -1850 +1850 1850 1850 +1850 +1850 + +lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc + lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc -cycle - -NDEP_month +lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc + +cycle +cycle diff --git a/bld/namelist_files/use_cases/1850_noanthro_control.xml b/bld/namelist_files/use_cases/1850_noanthro_control.xml new file mode 100644 index 0000000000..c998d97608 --- /dev/null +++ b/bld/namelist_files/use_cases/1850_noanthro_control.xml @@ -0,0 +1,59 @@ + + + + +Simulate current conditions without ANY anthropogenic influnces + +PtVg + +constant + +.false. + +1850 +1850 + +1850 +1850 + +1850 +1850 + +cycle +cycle + +1925 +1925 + +1925 +1925 + +1925 +1925 + + +lnd/clm2/firedata/clmforc.no_anthro_zero_hdm_1x1_simyr1925_181113.nc +nn + +1850 +1850 + +1850 +1850 + +1850 +1850 + + +NONE + + +OFF +.false. + + +0.0 +0.0 + + diff --git a/bld/namelist_files/use_cases/2000-2100_rcp8.5_transient.xml b/bld/namelist_files/use_cases/2000-2100_rcp8.5_transient.xml deleted file mode 100644 index bff9ef7f0f..0000000000 --- a/bld/namelist_files/use_cases/2000-2100_rcp8.5_transient.xml +++ /dev/null @@ -1,50 +0,0 @@ - - - - -Simulate transient land-use, and aerosol deposition changes with historical data from 2000 to 2005 and then with the RCP8.5 scenario from MESSAGE - -Simulate transient land-use, aerosol and Nitrogen deposition changes with historical data from 2000 to 2005 and then with the RCP8.5 scenario from MESSAGE - - -20050101 - -1850 - -2000-2100 - -8.5 - -.true. -.false. -.false. - -flanduse_timeseries - -arb_ic - -2000 -2100 -2000 - -2000 -2100 -2000 - -2000 -2010 -2000 - -2000 -2010 -2000 - -2000 -2100 -2000 - -2000 -2100 -2000 - - diff --git a/bld/namelist_files/use_cases/2000_control.xml b/bld/namelist_files/use_cases/2000_control.xml index f829e97772..f3c4980fc8 100644 --- a/bld/namelist_files/use_cases/2000_control.xml +++ b/bld/namelist_files/use_cases/2000_control.xml @@ -8,9 +8,11 @@ constant -.true. -.false. -.false. +.true. +.false. +.true. +.false. +.false. 2000 2000 @@ -18,16 +20,25 @@ 2000 2000 +2000 +2000 + 2000 2000 2000 2000 +2000 +2000 + 2000 2000 2000 2000 +2000 +2000 + diff --git a/bld/namelist_files/use_cases/2010_control.xml b/bld/namelist_files/use_cases/2010_control.xml new file mode 100644 index 0000000000..9316ecfb7f --- /dev/null +++ b/bld/namelist_files/use_cases/2010_control.xml @@ -0,0 +1,51 @@ + + + + +Conditions to simulate 2010 land-use + +2000 + +constant + +.true. +.true. +.false. +.true. +.false. +.false. + +2010 +2010 + +2010 +2010 + +2010 +2010 + +2010 +2010 + +2010 +2010 + +2010 +2010 + +2010 +2010 + +2010 +2010 + +2010 +2010 + +2010 +2010 + +2010 +2010 + + diff --git a/bld/namelist_files/use_cases/20thC_transient.xml b/bld/namelist_files/use_cases/20thC_transient.xml index 8dfa8fc1a6..faf0534f34 100644 --- a/bld/namelist_files/use_cases/20thC_transient.xml +++ b/bld/namelist_files/use_cases/20thC_transient.xml @@ -14,18 +14,24 @@ flanduse_timeseries -.true. -.false. -.false. +.true. +.false. +.true. +.false. +.false. 1850 -2005 +2015 1850 1850 -2005 +2015 1850 +1850 +2015 +1850 + 1850 2016 1850 @@ -34,6 +40,10 @@ 2016 1850 +1850 +2016 +1850 + 1850 2106 1850 @@ -42,4 +52,8 @@ 2106 1850 +1850 +2106 +1850 + diff --git a/bld/namelist_files/use_cases/README b/bld/namelist_files/use_cases/README index 40b992332b..4ccaf00bdc 100644 --- a/bld/namelist_files/use_cases/README +++ b/bld/namelist_files/use_cases/README @@ -11,7 +11,7 @@ Ending suffix requires one of these endings: _transient, _control or _pd Transient cases: - yyyy-yyyy_$rcp$desc_transient (for example 1850-2100_rcp8.5_transient) + yyyy-yyyy_$ssp_rcp$desc_transient (for example 1850-2100_SSP5-8.5_transient) or @@ -30,9 +30,9 @@ Where yyyy = Simulation year (such as 1850 or 2000). yyyy-yyyy = Range of simulation years to run over (i.e.. 1850-2000). -$rcp = Representative concentration pathway (rcp) description string +$ssp_rcp = Shared Socieconomic Pathway (SSP) Representative concentration pathway (RCP) description string for future scenarios: - rcp#.# (for example: rcp8.5, rcp6, rcp4.5, rcp2.6) + SSP#-#.# (for example: SSP5-8.5, SSP1-2.6, SSP4-6.0 [can be blank for historical cases]. $desc = Description of anything else -- alpha-numeric. Should start with an underscore ("_") if not by itself diff --git a/bld/namelist_files/use_cases/stdurbpt_pd.xml b/bld/namelist_files/use_cases/stdurbpt_pd.xml index 9114742e66..65786f32ae 100644 --- a/bld/namelist_files/use_cases/stdurbpt_pd.xml +++ b/bld/namelist_files/use_cases/stdurbpt_pd.xml @@ -10,7 +10,7 @@ 'TBUILD','BUILDHEAT','TRAFFICFLUX','WASTEHEAT','SWup','LWup','Rnet','Qh','Qle','Qstor','Qtau','Qanth','Wind','Qair','Tair','PSurf','Rainf','SWdown','LWdown','COSZEN' -'TG','TBOT','FIRE','FIRA','FLDS','FSDS','FSR','FSA','FGEV','FSH','FGR','TSOI','ERRSOI','BUILDHEAT','SABV','SABG','FSDSVD','FSDSND','FSDSVI','FSDSNI','FSRVD','FSRND','FSRVI','FSRNI','TSA','FCTR','FCEV','QBOT','Q2M','H2OSOI','H2OSNO','SOILLIQ','SOILICE','SWup','LWup','Rnet','Qh','Qle','Qstor','Qtau','Qanth','Wind','Qair','Tair','PSurf','Rainf','SWdown','LWdown','SoilAlpha_U','ZWT','WA' +'TG','TBOT','FIRE','FIRA','FLDS','FSDS','FSR','FSA','FGEV','FSH','FGR','TSOI','ERRSOI','BUILDHEAT','SABV','SABG','FSDSVD','FSDSND','FSDSVI','FSDSNI','FSRVD','FSRND','FSRVI','FSRNI','TSA','FCTR','FCEV','QBOT','Q2M','H2OSOI','H2OSNO','SOILLIQ','SOILICE','SWup','LWup','Rnet','Qh','Qle','Qstor','Qtau','Qanth','Wind','Qair','Tair','PSurf','Rainf','SWdown','LWdown','SoilAlpha_U','ZWT' 'SWup','LWup','Rnet','Qh','Qle','Qstor','Qtau','Qanth','Wind','Qair','Tair','PSurf','Rainf','SWdown','LWdown','FSA','FIRA','TG','COSZEN','SoilAlpha_U','TBUILD','BUILDHEAT' @@ -18,8 +18,10 @@ 'OFF' -.true. -.false. -.false. +.true. +.false. +.true. +.false. +.false. diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 77ea34f13c..c12b0b211f 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -29,7 +29,7 @@ sub usage { -compare Compare namelists for this version to namelists created by another version. -generate Leave the namelists in place to do a later compare. - -test Use the -test option to make sure datasets exist. + -no-test Do NOT Use the -test option to make sure datasets exist. -csmdata "dir" Root directory of CESM input data. EOF @@ -78,7 +78,7 @@ sub make_config_cache { -Specifies clm physics +Specifies clm physics EOF $fh->close(); @@ -89,7 +89,7 @@ sub make_config_cache { # my %opts = ( help => 0, generate => 0, - test => 0, + test => 1, compare => undef, csmdata => undef, ); @@ -98,7 +98,7 @@ sub make_config_cache { "h|help" => \$opts{'help'}, "compare=s" => \$opts{'compare'}, "generate" => \$opts{'generate'}, - "test" => \$opts{'test'}, + "test!" => \$opts{'test'}, "csmdata=s" => \$opts{'csmdata'}, ) or usage(); @@ -138,9 +138,9 @@ sub make_config_cache { # # Figure out number of tests that will run # -my $ntests = 927; +my $ntests = 1552; if ( defined($opts{'compare'}) ) { - $ntests += 588; + $ntests += 1044; } plan( tests=>$ntests ); @@ -164,7 +164,7 @@ sub make_config_cache { &make_config_cache($phys); my $DOMFILE = "$inputdata_rootdir/atm/datm7/domain.lnd.T31_gx3v7.090928.nc"; -my $real_par_file = "user_nl_clm_real_parameters"; +my $real_par_file = "user_nl_ctsm_real_parameters"; my $bldnml = "../build-namelist -verbose -csmdata $inputdata_rootdir -lnd_frac $DOMFILE -configuration clm -structure standard -glc_nec 10 -no-note -output_reals $real_par_file"; if ( $opts{'test'} ) { $bldnml .= " -test"; @@ -211,7 +211,7 @@ sub make_config_cache { $cfiles->copyfiles( "default", $mode ); &cleanup(); # Simple test -- run all the list options -foreach my $options ( "clm_demand", "rcp", "res", +foreach my $options ( "clm_demand", "ssp_rcp", "res", "sim_year", "use_case" ) { &make_env_run(); eval{ system( "$bldnml -${options} list > $tempfile 2>&1 " ); }; @@ -234,7 +234,7 @@ sub make_config_cache { # Exercise a bunch of options my $options = "-co2_ppmv 250 "; - $options .= " -res 0.9x1.25 -rcp 2.6 -envxml_dir ."; + $options .= " -res 0.9x1.25 -ssp_rcp SSP1-2.6 -envxml_dir ."; &make_env_run(); eval{ system( "$bldnml $options > $tempfile 2>&1 " ); }; @@ -287,31 +287,29 @@ sub make_config_cache { &make_config_cache($phys); print "\n===============================================================================\n"; -print "Test configuration, structure, irrigate, verbose, clm_demand, rcp, test, sim_year, use_case, l_ncpl\n"; +print "Test configuration, structure, irrigate, verbose, clm_demand, ssp_rcp, test, sim_year, use_case\n"; print "=================================================================================\n"; -# configuration, structure, irrigate, verbose, clm_demand, rcp, test, sim_year, use_case, l_ncpl +# configuration, structure, irrigate, verbose, clm_demand, ssp_rcp, test, sim_year, use_case my $startfile = "clmrun.clm2.r.1964-05-27-00000.nc"; foreach my $options ( "-configuration nwp", "-structure fast", - "-namelist '&a irrigate=.true./'", "-verbose", "-rcp 2.6", "-test", "-sim_year 1850", - "-use_case 1850_control", "-l_ncpl 1", + "-namelist '&a irrigate=.true./'", "-verbose", "-ssp_rcp SSP1-2.6", "-test", "-sim_year 1850", + "-use_case 1850_control", "-clm_start_type startup", "-namelist '&a irrigate=.false./' -crop -bgc bgc", "-envxml_dir . -infile myuser_nl_clm", "-ignore_ic_date -clm_start_type branch -namelist '&a nrevsn=\"thing.nc\"/' -bgc bgc -crop", + "-clm_start_type branch -namelist '&a nrevsn=\"thing.nc\",use_init_interp=T/'", "-ignore_ic_date -clm_start_type startup -namelist '&a finidat=\"thing.nc\"/' -bgc bgc -crop", ) { my $file = $startfile; &make_env_run(); - eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); }; + eval{ system( "$bldnml -res 0.9x1.25 -envxml_dir . $options > $tempfile 2>&1 " ); }; is( $@, '', "options: $options" ); $cfiles->checkfilesexist( "$options", $mode ); $cfiles->shownmldiff( "default", $mode ); my $finidat = `grep finidat lnd_in`; - if ( $options eq "-l_ncpl 1" ) { - my $dtime = `grep dtime lnd_in`; - like( $dtime, "/ 86400\$/", "$options" ); - } elsif ( $options =~ /myuser_nl_clm/ ) { + if ( $options =~ /myuser_nl_clm/ ) { my $fsurdat = `grep fsurdat lnd_in`; like( $fsurdat, "/MYDINLOCROOT/lnd/clm2/PTCLMmydatafiles/1x1pt_US-UMB/surfdata_1x1pt_US-UMB_simyr2000_clm4_5_c131122.nc/", "$options" ); } @@ -325,6 +323,44 @@ sub make_config_cache { } &cleanup(); } + +print "\n===============================================================================\n"; +print "Test some CAM specific setups for special grids \n"; +print "=================================================================================\n"; +foreach my $phys ( "clm4_5", "clm5_0" ) { + $mode = "-phys $phys"; + &make_config_cache($phys); + foreach my $options ( + "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res ne0np4.ARCTICGRIS.ne30x8 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res 0.9x1.25 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res 0.9x1.25 -bgc bgc -crop -use_case 20thC_transient -namelist '&a start_ymd=19500101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res ne0np4CONUS.ne30x8 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=20030101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res 1.9x2.5 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res 1x1_brazil -bgc fates -no-megan -use_case 2000_control -lnd_tuning_mode ${phys}_CRUv7", + "-res C192 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam6.0", + ) { + &make_env_run(); + eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); }; + is( $@, '', "options: $options" ); + $cfiles->checkfilesexist( "$options", $mode ); + $cfiles->shownmldiff( "default", $mode ); + if ( defined($opts{'compare'}) ) { + $cfiles->doNOTdodiffonfile( "$tempfile", "$options", $mode ); + $cfiles->dodiffonfile( "lnd_in", "$options", $mode ); + $cfiles->dodiffonfile( "$real_par_file", "$options", $mode ); + $cfiles->comparefiles( "$options", $mode, $opts{'compare'} ); + } + if ( defined($opts{'generate'}) ) { + $cfiles->copyfiles( "$options", $mode ); + } + &cleanup(); + } +} + print "\n==============================================================\n"; print "Test several use_cases and specific configurations for clm5_0\n"; print "==============================================================\n"; @@ -332,12 +368,14 @@ sub make_config_cache { $mode = "-phys $phys"; &make_config_cache($phys); foreach my $options ( - "-bgc bgc -use_case 1850-2100_rcp2.6_transient -namelist '&a start_ymd=20100101/'", - "-bgc sp -use_case 1850-2100_rcp4.5_transient -namelist '&a start_ymd=18501223/'", - "-bgc bgc -use_case 1850-2100_rcp6_transient -namelist '&a start_ymd=20701029/'", + "-bgc bgc -use_case 1850-2100_SSP1-2.6_transient -namelist '&a start_ymd=20100101/'", + "-bgc sp -use_case 1850-2100_SSP2-4.5_transient -namelist '&a start_ymd=18501223/'", + "-bgc bgc -use_case 1850-2100_SSP3-7.0_transient -namelist '&a start_ymd=20701029/'", "-bgc fates -use_case 2000_control -no-megan", - "-bgc cn -use_case 1850-2100_rcp8.5_transient -namelist '&a start_ymd=19201023/'", + "-bgc sp -use_case 2000_control -res 0.9x1.25 -namelist '&a use_soil_moisture_streams = T/'", + "-bgc cn -use_case 1850-2100_SSP5-8.5_transient -namelist '&a start_ymd=19101023/'", "-bgc bgc -use_case 2000_control -namelist \"&a fire_method='nofire'/\" -crop", + "-res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control -drydep -fire_emis -light_res 360x720", ) { my $file = $startfile; &make_env_run(); @@ -388,28 +426,38 @@ sub make_config_cache { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "l_ncpl is zero" =>{ options=>"-l_ncpl 0 -envxml_dir .", - namelst=>"", + "use_crop without -crop" =>{ options=>" -envxml_dir .", + namelst=>"use_crop=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm4_5", + }, + "soilm_stream wo use" =>{ options=>"-res 0.9x1.25 -envxml_dir .", + namelst=>"use_soil_moisture_streams = .false.,stream_fldfilename_soilm='missing_file'", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "l_ncpl not integer" =>{ options=>"-l_ncpl 1.0 -envxml_dir .", + "clm50CNDVwtransient" =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "both l_ncpl and dtime" =>{ options=>"-l_ncpl 24 -envxml_dir .", - namelst=>"dtime=1800", + "reseed without CN" =>{ options=>" -envxml_dir . -bgc sp", + namelst=>"reseed_dead_plants=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "use_crop without -crop" =>{ options=>" -envxml_dir .", - namelst=>"use_crop=.true.", + "onset_threh w SP" =>{ options=>" -envxml_dir . -bgc sp", + namelst=>"onset_thresh_depends_on_veg=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm4_5", + phys=>"clm5_1", }, - "clm50CNDVwtransient" =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings", - namelst=>"", + "dribble_crphrv w/o CN" =>{ options=>" -envxml_dir . -bgc sp", + namelst=>"dribble_crophrv_xsmrpool_2atm=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "dribble_crphrv w/o crop" =>{ options=>" -envxml_dir . -bgc cn -no-crop", + namelst=>"dribble_crophrv_xsmrpool_2atm=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, @@ -594,6 +642,11 @@ sub make_config_cache { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, + "freeliv wo fun" =>{ options=>"-bgc bgc -envxml_dir .", + namelst=>"freelivfix_intercept=9.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm4_5", + }, "use_cn=false bgc=cn" =>{ options=>"-bgc cn -envxml_dir .", namelst=>"use_cn=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", @@ -755,7 +808,7 @@ sub make_config_cache { phys=>"clm5_0", }, "glc_nec inconsistent" =>{ options=>"-envxml_dir .", - namelst=>"maxpatch_glcmec=5", + namelst=>"maxpatch_glc=5", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, @@ -789,18 +842,28 @@ sub make_config_cache { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "createcropFalse" =>{ options=>"-bgc bgc -envxml_dir . -no-megan", - namelst=>"create_crop_landunit=.false.", + "useFATESWbMH" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + namelst=>"use_biomass_heat_storage=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm5_0", + phys=>"clm5_1", }, - "useFATESWTransient" =>{ options=>"-bgc fates -use_case 20thC_transient -envxml_dir . -no-megan -res 10x15", - namelst=>"", + "FireNoneButFATESfireon" =>{ options=>"-bgc fates -envxml_dir . -no-megan -light_res none", + namelst=>"fates_spitfire_mode=4", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_1", + }, + "FireNoneButBGCfireon" =>{ options=>"-bgc bgc -envxml_dir . -light_res none", + namelst=>"fire_method='li2021gswpfrc'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_1", + }, + "createcropFalse" =>{ options=>"-bgc bgc -envxml_dir . -no-megan", + namelst=>"create_crop_landunit=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, "usespitfireButNOTFATES" =>{ options=>"-envxml_dir . -no-megan", - namelst=>"use_fates_spitfire=.true.", + namelst=>"fates_spitfire_mode>0", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, @@ -844,6 +907,16 @@ sub make_config_cache { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, + "noanthro_w_crop" =>{ options=>"-envxml_dir . -res 0.9x1.25 -bgc bgc -crop -use_case 1850_noanthro_control", + namelst=>"", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "noanthro_w_irrig" =>{ options=>"-envxml_dir . -res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control", + namelst=>"irrigate=T", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, "spdotransconflict" =>{ options=>"-envxml_dir . -bgc sp -use_case 20thC_transient", namelst=>"do_transient_pfts=T,do_transient_crops=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", @@ -914,16 +987,6 @@ sub make_config_cache { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "nitrcoefWOnitrif" =>{ options=>"-envxml_dir . -bgc bgc", - namelst=>"use_nitrif_denitrif=.false., denitrif_nitrateconc_coefficient=1.0", - GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm5_0", - }, - "nitrexpWOnitrif" =>{ options=>"-envxml_dir . -bgc bgc", - namelst=>"use_nitrif_denitrif=.false., denitrif_nitrateconc_exponent=1.0", - GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm5_0", - }, "lunaWSPandlnctrue" =>{ options=>"-envxml_dir . -bgc sp", namelst=>"use_luna=.true., lnc_opt=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", @@ -980,13 +1043,18 @@ sub make_config_cache { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "use_c14_wo_bgc" =>{ options=>"-envxml_dir . -bgc cndv", + "use_c14_wo_bgc" =>{ options=>"-envxml_dir . -bgc cn", namelst=>"use_c14=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "maxpft_wrong" =>{ options=>"-envxml_dir . -bgc cndv", - namelst=>"maxpatch_pft=19", + "soilm_stream w transient" =>{ options=>"-res 0.9x1.25 -envxml_dir . -use_case 20thC_transient", + namelst=>"use_soil_moisture_streams=T,soilm_tintalgo='linear'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "missing_ndep_file" =>{ options=>"-envxml_dir . -bgc bgc -ssp_rcp SSP5-3.4", + namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, @@ -1008,19 +1076,23 @@ sub make_config_cache { # Now run with -ignore_warnings and make sure it works $options .= " -ignore_warnings"; eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); }; + is( $?, 0, $key ); is( $@, '', "$options" ); system( "cat $tempfile" ); } +# +# Loop over all physics versions +# +foreach my $phys ( "clm4_5", "clm5_0", "clm5_1" ) { +$mode = "-phys $phys"; +&make_config_cache($phys); print "\n==================================================\n"; -print "Test ALL resolutions with CLM5.0 and SP \n"; +print "Test ALL resolutions with SP\n"; print "==================================================\n"; # Check for ALL resolutions with CLM50SP -$phys = "clm5_0"; -$mode = "-phys $phys"; -&make_config_cache($phys); my $reslist = `../queryDefaultNamelist.pl -res list -s`; my @resolutions = split( / /, $reslist ); my @regional; @@ -1050,12 +1122,18 @@ sub make_config_cache { $res eq "ne4np4" || $res eq "2.5x3.33" || $res eq "0.23x0.31" || + $res eq "0.47x0.63" || $res eq "94x192" || $res eq "8x16" || $res eq "32x64" || $res eq "128x256" || + $res eq "360x720cru" || $res eq "512x1024" ) { next; + # Resolutions not supported on release branch + } elsif ( $res eq "ne120np4" || + $res eq "conus_30_x8" ) { + next; } &make_env_run(); @@ -1078,16 +1156,13 @@ sub make_config_cache { } print "\n==================================================\n"; -print " Test important resolutions for CLM4.5 and BGC\n"; +print " Test important resolutions for BGC\n"; print "==================================================\n"; -$phys = "clm4_5"; -$mode = "-phys $phys"; -&make_config_cache($phys); -my @resolutions = ( "4x5", "10x15", "ne30np4", "ne120np4", "ne16np4", "1.9x2.5", "0.9x1.25" ); +my @resolutions = ( "4x5", "10x15", "ne30np4", "ne16np4", "1.9x2.5", "0.9x1.25" ); my @regional; my $nlbgcmode = "bgc"; -my $mode = "clm45-$nlbgcmode"; +my $mode = "$phys-$nlbgcmode"; foreach my $res ( @resolutions ) { chomp($res); print "=== Test $res === \n"; @@ -1145,10 +1220,7 @@ sub make_config_cache { print "==================================================\n"; # Check for crop resolutions -$phys = "clm5_0"; -$mode = "-phys $phys"; -&make_config_cache($phys); -my @crop_res = ( "1x1_numaIA", "1x1_smallvilleIA", "4x5", "10x15", "0.9x1.25", "1.9x2.5", "ne30np4", "ne120np4" ); +my @crop_res = ( "1x1_numaIA", "1x1_smallvilleIA", "4x5", "10x15", "0.9x1.25", "1.9x2.5", "ne30np4" ); foreach my $res ( @crop_res ) { $options = "-bgc bgc -crop -res $res -envxml_dir ."; &make_env_run(); @@ -1181,21 +1253,29 @@ sub make_config_cache { # use cases, but I've kept these pointing to the equivalent normal use # cases; I'm not sure if it's actually important to test this with all # of the different use cases. -$phys = "clm4_5"; -$mode = "-phys $phys"; -&make_config_cache($phys); -my @glc_res = ( "48x96", "0.9x1.25", "1.9x2.5" ); -my @use_cases = ( "1850-2100_rcp2.6_transient", - "1850-2100_rcp4.5_transient", - "1850-2100_rcp6_transient", - "1850-2100_rcp8.5_transient", +my @glc_res = ( "0.9x1.25", "1.9x2.5" ); +my @use_cases = ( "1850-2100_SSP1-2.6_transient", + "1850-2100_SSP2-4.5_transient", + "1850-2100_SSP3-7.0_transient", + "1850-2100_SSP5-8.5_transient", "1850_control", "2000_control", + "2010_control", "20thC_transient", ); foreach my $res ( @glc_res ) { foreach my $usecase ( @usecases ) { - $options = "-bgc bgc -res $res -use_case $usecase -envxml_dir . "; + my $startymd = undef; + if ( ($usecase eq "1850_control") || ($usecase eq "20thC_transient") ) { + $startymd = 18500101; + } elsif ( $usecase eq "2000_control") { + $startymd = 20000101; + } elsif ( $usecase eq "2010_control") { + $startymd = 20100101; + } else { + $startymd = 20150101; + } + $options = "-bgc bgc -res $res -use_case $usecase -envxml_dir . -namelist '&a start_ymd=$startymd/'"; &make_env_run(); eval{ system( "$bldnml $options > $tempfile 2>&1 " ); }; is( $@, '', "$options" ); @@ -1212,14 +1292,11 @@ sub make_config_cache { } } # Transient 20th Century simulations -$phys = "clm5_0"; -$mode = "-phys $phys"; -&make_config_cache($phys); -my @tran_res = ( "48x96", "0.9x1.25", "1.9x2.5", "ne30np4", "ne120np4", "10x15" ); +my @tran_res = ( "0.9x1.25", "1.9x2.5", "ne30np4", "10x15" ); my $usecase = "20thC_transient"; my $GLC_NEC = 10; foreach my $res ( @tran_res ) { - $options = "-res $res -use_case $usecase -envxml_dir . "; + $options = "-res $res -use_case $usecase -envxml_dir . -namelist '&a start_ymd=18500101/'"; &make_env_run(); eval{ system( "$bldnml $options > $tempfile 2>&1 " ); }; is( $@, '', "$options" ); @@ -1235,14 +1312,18 @@ sub make_config_cache { } &cleanup(); } -# Transient rcp scenarios -$phys = "clm5_0"; -$mode = "-phys $phys"; -&make_config_cache($phys); -my @tran_res = ( "48x96", "0.9x1.25", "1.9x2.5", "ne30np4", "10x15" ); -foreach my $usecase ( "1850_control", "1850-2100_rcp2.6_transient", "1850-2100_rcp4.5_transient", "1850-2100_rcp6_transient", "1850-2100_rcp8.5_transient" ) { +# Transient ssp_rcp scenarios that work +my @tran_res = ( "0.9x1.25", "1.9x2.5", "10x15" ); +foreach my $usecase ( "1850_control", "1850-2100_SSP5-8.5_transient", "1850-2100_SSP1-2.6_transient", "1850-2100_SSP3-7.0_transient", + "1850-2100_SSP2-4.5_transient" ) { + my $startymd = undef; + if ( $usecase eq "1850_control") { + $startymd = 18500101; + } else { + $startymd = 20150101; + } foreach my $res ( @tran_res ) { - $options = "-res $res -bgc bgc -crop -use_case $usecase -envxml_dir . "; + $options = "-res $res -bgc bgc -crop -use_case $usecase -envxml_dir . -namelist '&a start_ymd=$startymd/'"; &make_env_run(); eval{ system( "$bldnml $options > $tempfile 2>&1 " ); }; is( $@, '', "$options" ); @@ -1259,19 +1340,38 @@ sub make_config_cache { &cleanup(); } } +} # End loop over all physics versions +# +# End loop over versions +# + +# The SSP's that fail... +$phys = "clm5_0"; +$mode = "-phys $phys"; +&make_config_cache($phys); +my $res = "0.9x1.25"; +foreach my $usecase ( "1850-2100_SSP4-3.4_transient", "1850-2100_SSP5-3.4_transient", "1850-2100_SSP1-1.9_transient", + "1850-2100_SSP4-6.0_transient" ) { + $options = "-res $res -bgc bgc -crop -use_case $usecase -envxml_dir . -namelist '&a start_ymd=20150101/'"; + &make_env_run(); + eval{ system( "$bldnml $options > $tempfile 2>&1 " ); }; + isnt( $?, 0, $usecase ); + system( "cat $tempfile" ); +} print "\n==================================================\n"; -print "Test clm4.5/clm5.0 resolutions \n"; +print "Test clm4.5/clm5.0/clm5_1 resolutions \n"; print "==================================================\n"; -foreach my $phys ( "clm4_5", 'clm5_0' ) { +foreach my $phys ( "clm4_5", 'clm5_0', 'clm5_1' ) { my $mode = "-phys $phys"; &make_config_cache($phys); my @clmoptions = ( "-bgc bgc -envxml_dir .", "-bgc bgc -envxml_dir . -clm_accelerated_spinup=on", "-bgc bgc -envxml_dir . -light_res 360x720", - "-bgc sp -envxml_dir . -vichydro", "-bgc bgc -dynamic_vegetation -ignore_warnings", "-bgc bgc -clm_demand flanduse_timeseries -sim_year 1850-2000", + "-bgc sp -envxml_dir . -vichydro", "-bgc bgc -dynamic_vegetation -ignore_warnings", + "-bgc bgc -clm_demand flanduse_timeseries -sim_year 1850-2000 -namelist '&a start_ymd=18500101/'", "-bgc bgc -envxml_dir . -namelist '&a use_c13=.true.,use_c14=.true.,use_c14_bombspike=.true./'" ); foreach my $clmopts ( @clmoptions ) { - my @clmres = ( "ne120np4", "10x15", "0.9x1.25", "1.9x2.5" ); + my @clmres = ( "10x15", "0.9x1.25", "1.9x2.5" ); foreach my $res ( @clmres ) { $options = "-res $res -envxml_dir . "; &make_env_run( ); @@ -1292,7 +1392,7 @@ sub make_config_cache { my @clmoptions = ( "-bgc bgc -envxml_dir .", "-bgc sp -envxml_dir .", ); foreach my $clmopts ( @clmoptions ) { - my @clmres = ( "ne16np4", "360x720cru" ); + my @clmres = ( "ne16np4" ); foreach my $res ( @clmres ) { $options = "-res $res -envxml_dir . "; &make_env_run( ); @@ -1328,22 +1428,30 @@ sub make_config_cache { &cleanup(); # Run FATES mode for several resolutions and configurations my $clmoptions = "-bgc fates -envxml_dir . -no-megan"; - my @clmres = ( "1x1_brazil", "5x5_amazon", "10x15", "1.9x2.5" ); + my @clmres = ( "1x1_brazil", "5x5_amazon", "4x5", "1.9x2.5" ); foreach my $res ( @clmres ) { - $options = "-res $res"; - my @edoptions = ( "-use_case 2000_control", "", "-namelist \"&a use_lch4=.true.,use_nitrif_denitrif=.true./\"", "-clm_accelerated_spinup on" ); + $options = "-res $res -clm_start_type cold"; + my @edoptions = ( "-use_case 2000_control", + "-use_case 1850_control", + "", + "-namelist \"&a use_lch4=.true.,use_nitrif_denitrif=.true./\"", + "-clm_accelerated_spinup on" + ); foreach my $edop (@edoptions ) { + if ( $res eq "5x5_amazon" && ($edop =~ /1850_control/) ) { + next; + } &make_env_run( ); eval{ system( "$bldnml $options $clmoptions $edop > $tempfile 2>&1 " ); }; is( $@, '', "$options $edop" ); - $cfiles->checkfilesexist( "$options $edop", $mode ); + $cfiles->checkfilesexist( "$options $clmoptions $edop", $mode ); $cfiles->shownmldiff( "default", "standard" ); if ( defined($opts{'compare'}) ) { - $cfiles->doNOTdodiffonfile( "$tempfile", "$options $edop", $mode ); - $cfiles->comparefiles( "$options $edop", $mode, $opts{'compare'} ); + $cfiles->doNOTdodiffonfile( "$tempfile", "$options $clmoptions $edop", $mode ); + $cfiles->comparefiles( "$options $clmoptions $edop", $mode, $opts{'compare'} ); } if ( defined($opts{'generate'}) ) { - $cfiles->copyfiles( "$options $edop", $mode ); + $cfiles->copyfiles( "$options $clmoptions $edop", $mode ); } &cleanup(); } @@ -1355,10 +1463,16 @@ sub make_config_cache { my $res = "0.9x1.25"; my $mask = "gx1v6"; my $simyr = "1850"; -foreach my $phys ( "clm4_5", 'clm5_0' ) { +foreach my $phys ( "clm4_5", 'clm5_0', 'clm5_1' ) { my $mode = "-phys $phys"; &make_config_cache($phys); - foreach my $forc ( "CRUv7", "GSWP3v1", "cam6.0" ) { + my @forclist = (); + if ( $phys == "clm5_1" ) { + @forclist = ( "GSWP3v1" ); + } else { + @forclist = ( "CRUv7", "GSWP3v1", "cam6.0" ); + } + foreach my $forc ( @forclist ) { foreach my $bgc ( "sp", "bgc" ) { my $lndtuningmode = "${phys}_${forc}"; my $clmoptions = "-res $res -mask $mask -sim_year $simyr -envxml_dir . -lnd_tuning_mod $lndtuningmode -bgc $bgc"; @@ -1403,7 +1517,7 @@ sub cleanup { system( "/bin/rm env_run.xml $real_par_file" ); if ( defined($type) ) { if ( $type eq "config" ) { - system( "/bin/rm Filepath config_cache.xml CESM_cppdefs" ); + system( "/bin/rm config_cache.xml" ); } } else { system( "/bin/rm $tempfile *_in" ); diff --git a/bld/unit_testers/xFail/expectedFail.pm b/bld/unit_testers/xFail/expectedFail.pm index 877d4a71ae..9feaa3e38b 100755 --- a/bld/unit_testers/xFail/expectedFail.pm +++ b/bld/unit_testers/xFail/expectedFail.pm @@ -428,7 +428,7 @@ sub _readXml # Add $cfgdir to the list of paths that Perl searches for modules my @dirs = ( $cfgdir, "$cfgdir/perl5lib", "$cfgdir/../../cime/utils/perl5lib", - "$cfgdir/../../../cime/utils/perl5lib" + "$cfgdir/../../../../cime/utils/perl5lib" ); unshift @INC, @dirs; my $result = eval "require XML::Lite"; diff --git a/cime_config/SystemTests/lciso.py b/cime_config/SystemTests/lciso.py index e79af2886b..12a74d5d5c 100644 --- a/cime_config/SystemTests/lciso.py +++ b/cime_config/SystemTests/lciso.py @@ -17,6 +17,7 @@ class LCISO(SystemTestsCompareTwo): def __init__(self, case): + self.comp = case.get_value("COMP_LND") SystemTestsCompareTwo.__init__(self, case, separate_builds = False, run_two_suffix = 'cisoallon', @@ -26,11 +27,11 @@ def __init__(self, case): def _case_one_setup(self): append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", + component = self.comp, contents = "use_c13=F, use_c14=F") def _case_two_setup(self): append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", + component = self.comp, contents = "use_c13=.true.,use_c14=.true.,use_c13_timeseries=.true.,use_c14_bombspike=.true." ) diff --git a/cime_config/SystemTests/lii.py b/cime_config/SystemTests/lii.py index 0bf371ee9a..d89bd0aa09 100644 --- a/cime_config/SystemTests/lii.py +++ b/cime_config/SystemTests/lii.py @@ -1,5 +1,4 @@ -""" -Implementation of the CIME LII test. +"""Implementation of the CIME LII test. This is a CLM specific test: Verifies that interpolation of initial conditions onto an identical @@ -23,10 +22,11 @@ (2) Copy the finidat_interp_dest.nc file from the 'base' case to the inputdata space. Rename this to be similar to the name of the file pointed to in this -test's user_nl_clm file, but with a new creation date. +test's user_nl_ctsm file, but with a new creation date. -(3) Update this test's user_nl_clm file (in the appropriate testmods directory) -to point to the new finidat file. +(3) Update this test's user_nl_ctsm file (in the appropriate testmods directory, or in +namelist_defaults if the test is using an out-of-the-box initial conditions file and it is +acceptable to update that file) to point to the new finidat file. """ from CIME.SystemTests.system_tests_compare_two import SystemTestsCompareTwo diff --git a/cime_config/SystemTests/lii2finidatareas.py b/cime_config/SystemTests/lii2finidatareas.py index 21ba082fff..f7a0a2f10e 100644 --- a/cime_config/SystemTests/lii2finidatareas.py +++ b/cime_config/SystemTests/lii2finidatareas.py @@ -1,17 +1,11 @@ -""" -Implementation of the LII2FINIDATAREAS test. +"""Implementation of the LII2FINIDATAREAS test. This is similar to the LII test, but tests init_interp with mode 'use_finidat_areas'. -As with the standard LII test, this must be used in a configuration for -which we have a compatible out-of-the-box finidat file (so that the run -with use_init_interp = .false. runs successfully). In constrast to our -standard LII test (which uses glcMEC_spunup_1way), this one can use a -standard CISM2%NOEVOLVE configuration: we do *not* need to set -GLC_TWO_WAY_COUPLING=FALSE; in fact, it's a better test if we have -GLC_TWO_WAY_COUPLING=TRUE: with this mode of operation, areas should -match between the two runs. +As with the standard LII test, this must be used in a configuration for which we have a +compatible out-of-the-box finidat file (so that the run with use_init_interp = +.false. runs successfully). It may not be totally necessary to have a system test covering this init_interp_method: between unit tests and inline checks, we have quite @@ -41,7 +35,7 @@ (3) Update namelist defaults to point to the new finidat file. If updating the out-of-the-box file is not desired, then you could instead -point to this new finidat file with a user_nl_clm file in this testmod. +point to this new finidat file with a user_nl_ctsm file in this testmod. """ from CIME.XML.standard_module_setup import * diff --git a/cime_config/SystemTests/lilacsmoke.py b/cime_config/SystemTests/lilacsmoke.py new file mode 100644 index 0000000000..2a566feb60 --- /dev/null +++ b/cime_config/SystemTests/lilacsmoke.py @@ -0,0 +1,380 @@ +""" +Implementation of the CIME LILACSMOKE (LILAC smoke) test. + +This is a CTSM-specific test. It tests the building and running of CTSM via LILAC. Compset +is ignored, but grid is important. Also, it's important that this test use the nuopc +driver, both for the sake of the build and for extracting some runtime settings. This test +should also use the lilac testmod (or a testmod that derives from it) in order to +establish the user_nl_ctsm file correctly. + +Important directories under CASEROOT are: +- lilac_build: this contains the build and the runtime inputs for the lilac run +- lilac_atm_driver: this contains the build of the test driver as well as the run + directory in which the test is actually run + +Note that namelists for this test are generated in the build phase; they are NOT +regenerated when the test is submitted / run. This means that, if you have made any +changes that will impact namelists, you will need to rebuild this test. +""" + +import glob +import os +import shutil + +from CIME.SystemTests.system_tests_common import SystemTestsCommon +from CIME.utils import run_cmd, run_cmd_no_fail, symlink_force, new_lid, safe_copy, append_testlog +from CIME.build import post_build +from CIME.test_status import NAMELIST_PHASE, GENERATE_PHASE, BASELINE_PHASE, TEST_PASS_STATUS, TEST_FAIL_STATUS +from CIME.XML.standard_module_setup import * + +logger = logging.getLogger(__name__) + +_LILAC_RUNTIME_FILES = ['lnd_in', 'lnd_modelio.nml', 'lilac_in'] + +class LILACSMOKE(SystemTestsCommon): + + def __init__(self, case): + SystemTestsCommon.__init__(self, case) + + def build_phase(self, sharedlib_only=False, model_only=False): + if not sharedlib_only: + caseroot = self._case.get_value('CASEROOT') + lndroot = self._case.get_value('COMP_ROOT_DIR_LND') + exeroot = self._case.get_value('EXEROOT') + build_dir = os.path.join(caseroot, 'lilac_build') + script_path = os.path.abspath(os.path.join(lndroot, 'lilac', 'build_ctsm')) + + # We only run the initial build command if the build_dir doesn't exist + # yet. This is to support rebuilding the test case. (The first time through, + # the build_dir won't exist yet; subsequent times, it will already exist, so + # we skip to the rebuild command.) + if not os.path.isdir(build_dir): + machine = self._case.get_value('MACH') + compiler = self._case.get_value('COMPILER') + debug = self._case.get_value('DEBUG') + # It would be possible to do this testing via the python interface rather + # than through a separate subprocess. However, we do it through a + # subprocess in order to test the full build_ctsm script, including + # command-line parsing. + cmd = '{script_path} {build_dir} --machine {machine} --compiler {compiler}'.format( + script_path=script_path, + build_dir=build_dir, + machine=machine, + compiler=compiler) + # It isn't straightforward to determine if pnetcdf is available on a + # machine. To keep things simple, always run without pnetcdf. + cmd += ' --no-pnetcdf' + if debug: + cmd += ' --build-debug' + self._run_build_cmd(cmd, exeroot, 'build_ctsm.bldlog') + + # We call the build script with --rebuild even for an initial build. This is + # so we make sure to test the code path for --rebuild. (This is also needed if + # the user rebuilds the test case, in which case this will be the only command + # run, since the build_dir will already exist.) + cmd = '{script_path} {build_dir} --rebuild'.format( + script_path=script_path, + build_dir=build_dir) + self._run_build_cmd(cmd, exeroot, 'rebuild_ctsm.bldlog') + + self._build_atm_driver() + + self._create_link_to_atm_driver() + + self._create_runtime_inputs() + + self._setup_atm_driver_rundir() + + self._cmpgen_namelists() + + # Setting logs=[] implies that we don't bother gzipping any of the build log + # files; that seems fine for these purposes (and it keeps the above code + # simpler). + post_build(self._case, logs=[], build_complete=True) + + def _build_atm_driver(self): + caseroot = self._case.get_value('CASEROOT') + lndroot = self._case.get_value('COMP_ROOT_DIR_LND') + blddir = os.path.join(caseroot, 'lilac_atm_driver', 'bld') + + if not os.path.exists(blddir): + os.makedirs(blddir) + symlink_force(os.path.join(lndroot, 'lilac', 'atm_driver', 'Makefile'), + os.path.join(blddir, 'Makefile')) + symlink_force(os.path.join(lndroot, 'lilac', 'atm_driver', 'atm_driver.F90'), + os.path.join(blddir, 'atm_driver.F90')) + symlink_force(os.path.join(caseroot, 'Macros.make'), + os.path.join(blddir, 'Macros.make')) + + makevars = 'COMPILER={compiler} DEBUG={debug} CTSM_MKFILE={ctsm_mkfile}'.format( + compiler=self._case.get_value('COMPILER'), + debug=str(self._case.get_value('DEBUG')).upper(), + ctsm_mkfile=os.path.join(caseroot, 'lilac_build', 'ctsm.mk')) + makecmd = 'make {makevars} atm_driver'.format(makevars=makevars) + + # Normally the user will source either ctsm_build_environment.sh or + # ctsm_build_environment.csh before building the atmosphere model. In the context + # of this test case, case.load_env does the equivalent. + self._case.load_env() + + self._run_build_cmd(makecmd, blddir, 'atm_driver.bldlog') + + def _create_link_to_atm_driver(self): + caseroot = self._case.get_value('CASEROOT') + run_exe = (self._case.get_value('run_exe')).strip() + + # Make a symlink to the atm_driver executable so that the case's run command finds + # it in the expected location + symlink_force(os.path.join(caseroot, 'lilac_atm_driver', 'bld', 'atm_driver.exe'), + run_exe) + + def _create_runtime_inputs(self): + caseroot = self._case.get_value('CASEROOT') + runtime_inputs = self._runtime_inputs_dir() + lnd_domain_file = os.path.join(self._case.get_value('LND_DOMAIN_PATH'), + self._case.get_value('LND_DOMAIN_FILE')) + + # Cheat a bit here: Get the fsurdat file from the already-generated lnd_in file in + # the host test case - i.e., from the standard cime-based preview_namelists. But + # this isn't really a morally-objectionable cheat, because in the real workflow, + # we expect the user to identify fsurdat manually; in this testing situation, we + # need to come up with some way to replace this manual identification, so cheating + # feels acceptable. + self._case.create_namelists(component='lnd') + fsurdat = self._extract_var_from_namelist( + nl_filename=os.path.join(caseroot, 'CaseDocs', 'lnd_in'), + varname='fsurdat') + + self._fill_in_variables_in_file(filepath=os.path.join(runtime_inputs, 'ctsm.cfg'), + replacements={'lnd_domain_file':lnd_domain_file, + 'fsurdat':fsurdat}) + + # The user_nl_ctsm in the case directory is set up based on the standard testmods + # mechanism. We use that one in place of the standard user_nl_ctsm, since the one + # in the case directory may contain test-specific modifications. + shutil.copyfile(src=os.path.join(caseroot, 'user_nl_ctsm'), + dst=os.path.join(runtime_inputs, 'user_nl_ctsm')) + + script_to_run = os.path.join(runtime_inputs, 'make_runtime_inputs') + self._run_build_cmd('{} --rundir {}'.format(script_to_run, runtime_inputs), + runtime_inputs, + 'make_runtime_inputs.log') + + # In lilac_in, we intentionally use the land mesh file for both atm_mesh_filename + # and lnd_mesh_filename + lnd_mesh = self._case.get_value('LND_DOMAIN_MESH') + casename = self._case.get_value('CASE') + self._fill_in_variables_in_file(filepath=os.path.join(runtime_inputs, 'lilac_in'), + replacements={'caseid':casename, + 'atm_mesh_filename':lnd_mesh, + 'lnd_mesh_filename':lnd_mesh, + 'lilac_histfreq_option':'ndays'}, + placeholders={'caseid':'ctsm_lilac', + 'lilac_histfreq_option':'never'}) + + # We run download_input_data partly because it may be needed and partly to test + # this script. + script_to_run = os.path.join(runtime_inputs, 'download_input_data') + self._run_build_cmd('{} --rundir {}'.format(script_to_run, runtime_inputs), + runtime_inputs, + 'download_input_data.log') + + def _setup_atm_driver_rundir(self): + """Set up the directory from which we will actually do the run""" + lndroot = self._case.get_value('COMP_ROOT_DIR_LND') + rundir = self._atm_driver_rundir() + + if not os.path.exists(rundir): + os.makedirs(rundir) + shutil.copyfile(src=os.path.join(lndroot, 'lilac', 'atm_driver', 'atm_driver_in'), + dst=os.path.join(rundir, 'atm_driver_in')) + + # As elsewhere: assume the land variables also apply to the atmosphere + lnd_mesh = self._case.get_value('LND_DOMAIN_MESH') + lnd_nx = self._case.get_value('LND_NX') + lnd_ny = self._case.get_value('LND_NY') + expect(self._case.get_value('STOP_OPTION') == 'ndays', + 'LILAC testing currently assumes STOP_OPTION of ndays, not {}'.format( + self._case.get_value('STOP_OPTION'))) + stop_n = self._case.get_value('STOP_N') + casename = self._case.get_value('CASE') + self._fill_in_variables_in_file(filepath=os.path.join(rundir, 'atm_driver_in'), + replacements={'caseid':casename, + 'atm_mesh_file':lnd_mesh, + 'atm_global_nx':str(lnd_nx), + 'atm_global_ny':str(lnd_ny), + 'atm_stop_day':str(stop_n+1), + 'atm_ndays_all_segs':str(stop_n)}) + + for file_to_link in _LILAC_RUNTIME_FILES: + symlink_force(os.path.join(self._runtime_inputs_dir(), file_to_link), + os.path.join(rundir, file_to_link)) + + def _cmpgen_namelists(self): + """Redoes the namelist comparison & generation with appropriate namelists + + The standard namelist comparison & generation is done with the CaseDocs directory + from the test case. That isn't appropriate here, because those namelists aren't + actually used in this test. Instead, we want to compare & generate the namelists + used by the atm_driver-lilac-ctsm execution. Here, we do some file copies and then + re-call the namelist comparison & generation script in order to accomplish + this. This will overwrite the namelists generated earlier in the test, and will + also replace the results of the NLCOMP phase. + + Note that we expect a failure in the NLCOMP phase that is run earlier in the test, + because that one will have compared the test's standard CaseDocs with the files + generated from here - and those two sets of namelists can be quite different. + """ + caseroot = self._case.get_value('CASEROOT') + casedocs = os.path.join(caseroot, 'CaseDocs') + if os.path.exists(casedocs): + shutil.rmtree(casedocs) + os.makedirs(casedocs) + + # case_cmpgen_namelists uses the existence of drv_in to decide whether namelists + # need to be regenerated. We do NOT want it to regenerate namelists, so we give it + # the file it wants. + with open(os.path.join(casedocs, 'drv_in'), 'a') as drv_in: + pass + + for onefile in _LILAC_RUNTIME_FILES + ['atm_driver_in']: + safe_copy(os.path.join(self._atm_driver_rundir(), onefile), + os.path.join(casedocs, onefile)) + + success = self._case.case_cmpgen_namelists() + # The setting of the NLCOMP phase status in case_cmpgen_namelists doesn't work + # here (probably because the test object has a saved version of the test status + # and so, when it goes to write the status of the build phase, it ends up + # overwriting whatever was set by case_cmpgen_namelists). So we need to set it + # here. + with self._test_status: + self._test_status.set_status(NAMELIST_PHASE, TEST_PASS_STATUS if success else TEST_FAIL_STATUS, + comments="(used lilac namelists)") + + def _extract_var_from_namelist(self, nl_filename, varname): + """Tries to find a variable named varname in the given file; returns its value + + If not found, aborts + """ + with open(nl_filename) as nl_file: + for line in nl_file: + match = re.search(r'^ *{} *= *[\'"]([^\'"]+)'.format(varname), line) + if match: + return match.group(1) + expect(False, '{} not found in {}'.format(varname, nl_filename)) + + def _fill_in_variables_in_file(self, filepath, replacements, placeholders=None): + """For the given file, make the given replacements + + replacements should be a dictionary mapping variable names to their values + + If placeholders is given, it should be a dictionary mapping some subset of + variable names to their placeholders. Anything not given here uses a placeholder + of 'FILL_THIS_IN'. + """ + if placeholders is None: + placeholders = {} + + orig_filepath = '{}.orig'.format(filepath) + if not os.path.exists(orig_filepath): + shutil.copyfile(src=filepath, + dst=orig_filepath) + os.remove(filepath) + + counts = dict.fromkeys(replacements, 0) + with open(orig_filepath) as orig_file: + with open(filepath, 'w') as new_file: + for orig_line in orig_file: + line = orig_line + for varname in replacements: + if varname in placeholders: + this_placeholder = placeholders[varname] + else: + this_placeholder = 'FILL_THIS_IN' + line, replacement_done = self._fill_in_variable( + line=line, + varname=varname, + value=replacements[varname], + placeholder=this_placeholder) + if replacement_done: + counts[varname] += 1 + break + new_file.write(line) + + for varname in counts: + expect(counts[varname] > 0, + 'Did not find any instances of <{}> to replace in {}'.format(varname, filepath)) + + def _fill_in_variable(self, line, varname, value, placeholder): + """Fill in a placeholder variable in a config or namelist file + + Returns a tuple: (newline, replacement_done) + - newline is the line with the given placeholder replaced with the given value if this + line is for varname; otherwise returns line unchanged + - replacement_done is True if the replacement was done, otherwise False + """ + if re.search(r'^ *{} *='.format(varname), line): + expect(placeholder in line, + 'Placeholder to replace ({}) not found in <{}>'.format(placeholder, line.strip())) + newline = line.replace(placeholder, value) + replacement_done = True + else: + newline = line + replacement_done = False + return (newline, replacement_done) + + def _runtime_inputs_dir(self): + return os.path.join(self._case.get_value('CASEROOT'), 'lilac_build', 'runtime_inputs') + + def _atm_driver_rundir(self): + return os.path.join(self._case.get_value('CASEROOT'), 'lilac_atm_driver', 'run') + + @staticmethod + def _run_build_cmd(cmd, exeroot, logfile): + """ + Runs the given build command, with output to the given logfile + + Args: + cmd: str (command to run) + exeroot: str (path to exeroot) + logfile: str (path to logfile) + """ + append_testlog(cmd) + run_cmd_no_fail(cmd, arg_stdout=logfile, combine_output=True, from_dir=exeroot) + with open(os.path.join(exeroot, logfile)) as lf: + append_testlog(lf.read()) + + def run_phase(self): + # This mimics a bit of what's done in the typical case.run. Note that + # case.get_mpirun_cmd creates a command that runs the executable given by + # case.run_exe. So it's important that (elsewhere in this test script) we create a + # link pointing from that to the atm_driver.exe executable. + lid = new_lid() + os.environ["OMP_NUM_THREADS"] = str(self._case.thread_count) + cmd = self._case.get_mpirun_cmd(allow_unresolved_envvars=False) + run_cmd_no_fail(cmd, from_dir=self._atm_driver_rundir()) + + self._link_to_output_files() + + def _link_to_output_files(self): + """Make links to the output files so that they appear in the directory expected by the test case + + Note: We do the run from a different directory in order to ensure that the run + isn't using any of the files that are staged by the test case in the standard run + directory. But then we need to create these links afterwards for the sake of + baseline generation / comparison. + """ + casename = self._case.get_value('CASE') + rundir = self._case.get_value('RUNDIR') + pattern = '{}*.nc'.format(casename) + + # First remove any old files from the run directory + old_files = glob.glob(os.path.join(rundir, pattern)) + for one_file in old_files: + os.remove(one_file) + + # Now link to new files + output_files = glob.glob(os.path.join(self._atm_driver_rundir(), pattern)) + for one_file in output_files: + file_basename = os.path.basename(one_file) + symlink_force(one_file, os.path.join(rundir, file_basename)) diff --git a/cime_config/SystemTests/soilstructud.py b/cime_config/SystemTests/soilstructud.py index c59ab8b4f6..b454695f6e 100644 --- a/cime_config/SystemTests/soilstructud.py +++ b/cime_config/SystemTests/soilstructud.py @@ -2,10 +2,10 @@ Implementation of the CIME SOILSTRUCTUD test. This is a CLM specific test: -Verifies that a simulation that points to user_nl_clm containing +Verifies that a simulation that points to user_nl_ctsm containing soil_layerstruct_userdefined_nlevsoi = 4 soil_layerstruct_userdefined = 0.1d0,0.3d0,0.6d0,1.0d0,1.0d0 -gives bfb same results as one that points to user_nl_clm containing +gives bfb same results as one that points to user_nl_ctsm containing soil_layerstruct_predefined = '4SL_2m' """ diff --git a/cime_config/SystemTests/ssp.py b/cime_config/SystemTests/ssp.py index 4aad37274a..26337d323d 100644 --- a/cime_config/SystemTests/ssp.py +++ b/cime_config/SystemTests/ssp.py @@ -45,7 +45,7 @@ def run_phase(self): # determine run lengths needed below stop_nf = self._case.get_value("STOP_N") - stop_n1 = stop_nf / 2 + stop_n1 = int(stop_nf / 2) stop_n2 = stop_nf - stop_n1 #------------------------------------------------------------------- @@ -83,7 +83,14 @@ def run_phase(self): rest_path = os.path.join(dout_sr, "rest", "{}-{}".format(refdate, refsec)) for item in glob.glob("{}/*{}*".format(rest_path, refdate)): - os.symlink(item, os.path.join(rundir, os.path.basename(item))) + link_name = os.path.join(rundir, os.path.basename(item)) + if os.path.islink(link_name) and os.readlink(link_name) == item: + # Link is already set up correctly: do nothing + # (os.symlink raises an exception if you try to replace an + # existing file) + pass + else: + os.symlink(item, link_name) for item in glob.glob("{}/*rpointer*".format(rest_path)): shutil.copy(item, rundir) diff --git a/cime_config/buildlib b/cime_config/buildlib index fabf2e8d45..55c47be4e9 100755 --- a/cime_config/buildlib +++ b/cime_config/buildlib @@ -1,7 +1,7 @@ #!/usr/bin/env python """ -build clm library +build ctsm library """ import sys, os @@ -20,6 +20,65 @@ from CIME.utils import run_cmd, expect logger = logging.getLogger(__name__) +############################################################################### +def _write_ctsm_mk(gmake, gmake_opts, makefile, exeroot, libroot): + """Writes a ctsm.mk file in exeroot. + + This file can be included by atmosphere model builds outside of cime. + """ + + cime_output_file = os.path.join(exeroot, 'cime_variables.mk') + # Set MODEL=driver because some link flags are set differently when MODEL=driver, and + # those are the ones we want here. + cmd = ("{gmake} write_include_and_link_flags OUTPUT_FILE={cime_output_file} " + "MODEL=driver {gmake_opts} -f {makefile} ").format( + gmake=gmake, cime_output_file=cime_output_file, gmake_opts=gmake_opts, makefile=makefile) + rc, out, err = run_cmd(cmd) + logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n"%(cmd,out,err)) + expect(rc == 0, "Command %s failed with rc=%s" % (cmd, rc)) + + ctsm_mk_path = os.path.join(exeroot, 'ctsm.mk') + with open(ctsm_mk_path, 'w') as ctsm_mk: + ctsm_mk.write(""" +# ====================================================================== +# Include this file to get makefile variables needed to include / link +# LILAC/CTSM in an atmosphere model's build +# +# Variables of interest are: +# - CTSM_INCLUDES: add this to the compilation line +# - CTSM_LIBS: add this to the link line +# ====================================================================== + +# ====================================================================== +# The following CIME variables are meant for internal use, and generally +# should not be included directly in an atmosphere model's build. +# ====================================================================== + +""") + with open(cime_output_file) as infile: + ctsm_mk.write(infile.read()) + + ctsm_bld_dir = os.path.abspath(os.path.join(libroot, os.pardir)) + with open(ctsm_mk_path, 'a') as ctsm_mk: + ctsm_mk.write(""" +# ====================================================================== +# The following settings are meant for internal use, and generally +# should not be included directly in an atmosphere model's build. +# NOTE: clm library name and subdirectory will eventually need to +# be updated to ctsm. +# ====================================================================== + +CTSM_BLD_DIR = {ctsm_bld_dir} +CTSM_INC = $(CTSM_BLD_DIR)/clm/obj + +# ====================================================================== +# The following settings should be included in an atmosphere model's build. +# ====================================================================== + +CTSM_INCLUDES = $(CIME_ESMF_F90COMPILEPATHS) -I$(CIME_CSM_SHR_INCLUDE) -I$(CTSM_INC) +CTSM_LIBS = -L$(CTSM_BLD_DIR)/lib -lclm $(CIME_ULIBS) $(CIME_SLIBS) $(CIME_MLIBS) $(CIME_F90_LDFLAGS) +""".format(ctsm_bld_dir=ctsm_bld_dir)) + ############################################################################### def _main_func(): ############################################################################### @@ -29,32 +88,54 @@ def _main_func(): with Case(caseroot) as case: casetools = case.get_value("CASETOOLS") + makefile = os.path.join(casetools, "Makefile") lnd_root = case.get_value("COMP_ROOT_DIR_LND") gmake_j = case.get_value("GMAKE_J") gmake = case.get_value("GMAKE") + gmake_opts = get_standard_makefile_args(case) driver = case.get_value("COMP_INTERFACE").lower() + lilac_mode = case.get_value("LILAC_MODE") + + if lilac_mode == 'on': + driver = "lilac" #------------------------------------------------------- # create Filepath file #------------------------------------------------------- + compname = case.get_value("COMP_LND") filepath_file = os.path.join(bldroot,"Filepath") if not os.path.isfile(filepath_file): caseroot = case.get_value("CASEROOT") - paths = [os.path.join(caseroot,"SourceMods","src.clm"), + expect( ((compname == "clm") or (compname == "ctsm")), "Unexpected COMP_LND name: %s" % (compname)) + + paths = [os.path.join(caseroot,"SourceMods","src."+compname), + os.path.join(lnd_root,"src","cpl",driver), os.path.join(lnd_root,"src","main"), os.path.join(lnd_root,"src","biogeophys"), os.path.join(lnd_root,"src","biogeochem"), os.path.join(lnd_root,"src","soilbiogeochem"), os.path.join(lnd_root,"src","dyn_subgrid"), os.path.join(lnd_root,"src","init_interp"), + os.path.join(lnd_root,"src","self_tests"), os.path.join(lnd_root,"src","fates"), os.path.join(lnd_root,"src","fates","main"), os.path.join(lnd_root,"src","fates","biogeophys"), os.path.join(lnd_root,"src","fates","biogeochem"), os.path.join(lnd_root,"src","fates","fire"), + os.path.join(lnd_root,"src","fates","parteh"), os.path.join(lnd_root,"src","utils"), os.path.join(lnd_root,"src","cpl"), - os.path.join(lnd_root,"src","cpl",driver)] + os.path.join(lnd_root,"src","cpl","utils")] + + if lilac_mode == 'on': + paths.append(os.path.join(lnd_root,"lilac","src")) + # If we want to build with a real river model (e.g., MOSART), we'll need + # to use its directories in place of stub_rof + paths.append(os.path.join(lnd_root,"lilac","stub_rof")) + + if (driver == 'lilac' or driver == 'nuopc'): + paths.append(os.path.join(lnd_root,"src","cpl","share_esmf")) + with open(filepath_file, "w") as filepath: filepath.write("\n".join(paths)) filepath.write("\n") @@ -63,16 +144,26 @@ def _main_func(): # create the library in libroot #------------------------------------------------------- - complib = os.path.join(libroot,"libclm.a") - makefile = os.path.join(casetools, "Makefile") + complib = os.path.join(libroot,"lib%s.a"%(compname)) - cmd = "{} complib -j {} MODEL=clm COMPLIB={} -f {} {}" \ - .format(gmake, gmake_j, complib, makefile, get_standard_makefile_args(case)) + cmd = "{} complib -j {} MODEL={} COMPLIB={} -f {} {}" \ + .format(gmake, gmake_j, compname, complib, makefile, gmake_opts) rc, out, err = run_cmd(cmd) logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n"%(cmd,out,err)) expect(rc == 0, "Command %s failed with rc=%s" % (cmd, rc)) + # ------------------------------------------------------------------------ + # for lilac usage, we need a file containing some Makefile variables (for the atmosphere model's build) + # ------------------------------------------------------------------------ + + if lilac_mode == 'on': + _write_ctsm_mk(gmake=gmake, + gmake_opts=gmake_opts, + makefile=makefile, + exeroot=case.get_value("EXEROOT"), + libroot=libroot) + ############################################################################### if __name__ == "__main__": diff --git a/cime_config/buildnml b/cime_config/buildnml index 9940de97a3..725f636642 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -1,7 +1,7 @@ #!/usr/bin/env python """ -CLM namelist creator +CTSM namelist creator """ import sys, os, shutil @@ -23,17 +23,17 @@ _config_cache_template = """ -Specifies clm physics +Specifies CTSM physics """ ############################################################################### def buildnml(case, caseroot, compname): ############################################################################### - """Build the clm namelist """ + """Build the CTSM namelist """ # Build the component namelist - if compname != "clm": + if compname != "ctsm" and compname != "clm": raise AttributeError lnd_root = case.get_value("COMP_ROOT_DIR_LND") @@ -50,7 +50,6 @@ def buildnml(case, caseroot, compname): clm_accelerated_spinup = case.get_value("CLM_ACCELERATED_SPINUP") comp_atm = case.get_value("COMP_ATM") lnd_grid = case.get_value("LND_GRID") - lnd_ncpl = case.get_value("LND_NCPL") lnd_domain_path = case.get_value("LND_DOMAIN_PATH") lnd_domain_file = case.get_value("LND_DOMAIN_FILE") ninst_lnd = case.get_value("NINST_LND") @@ -61,15 +60,16 @@ def buildnml(case, caseroot, compname): run_refdate = case.get_value("RUN_REFDATE") run_reftod = case.get_value("RUN_REFTOD") glc_nec = case.get_value("GLC_NEC") + cism_use_antarctica = case.get_value("CISM_USE_ANTARCTICA") mask = case.get_value("MASK_GRID") # ----------------------------------------------------- - # Set clmconf + # Set ctsmconf # ----------------------------------------------------- - clmconf = os.path.join(caseroot, "Buildconf", "clmconf") - if not os.path.isdir(clmconf): - os.makedirs(clmconf) + ctsmconf = os.path.join(caseroot, "Buildconf", compname+"conf") + if not os.path.isdir(ctsmconf): + os.makedirs(ctsmconf) # ----------------------------------------------------- # Create config_cache.xml file @@ -81,7 +81,7 @@ def buildnml(case, caseroot, compname): clm_phys = case.get_value("CLM_PHYSICS_VERSION") config_cache_text = _config_cache_template.format(clm_phys=clm_phys) - config_cache_path = os.path.join(caseroot, "Buildconf", "clmconf", "config_cache.xml") + config_cache_path = os.path.join(caseroot, "Buildconf", compname+"conf", "config_cache.xml") with open(config_cache_path, 'w') as config_cache_file: config_cache_file.write(config_cache_text) @@ -128,6 +128,18 @@ def buildnml(case, caseroot, compname): else: nomeg = "" + if cism_use_antarctica is None: + # This is the case for compsets without CISM, where the CISM_USE_ANTARCTICA xml + # variable isn't defined + glc_use_antarctica_flag = "" + elif isinstance(cism_use_antarctica, bool): + if cism_use_antarctica: + glc_use_antarctica_flag = "-glc_use_antarctica" + else: + glc_use_antarctica_flag = "" + else: + expect(False, "Unexpected value for CISM_USE_ANTARCTICA: {}".format(cism_use_antarctica)) + if clm_nml_use_case != "UNSET": usecase = "-use_case %s" %clm_nml_use_case else: @@ -149,13 +161,13 @@ def buildnml(case, caseroot, compname): spinup = "-clm_accelerated_spinup %s "%clm_accelerated_spinup - infile = os.path.join(clmconf, "namelist") + infile = os.path.join(ctsmconf, "namelist") - inputdata_file = os.path.join(caseroot,"Buildconf","clm.input_data_list") + inputdata_file = os.path.join(caseroot,"Buildconf","ctsm.input_data_list") lndfrac_file = os.path.join(lnd_domain_path,lnd_domain_file) - config_cache_file = os.path.join(caseroot,"Buildconf","clmconf","config_cache.xml") + config_cache_file = os.path.join(caseroot,"Buildconf", compname+"conf","config_cache.xml") # ----------------------------------------------------- # Clear out old data @@ -189,11 +201,19 @@ def buildnml(case, caseroot, compname): # ----------------------------------------------------- if run_type == "hybrid" or run_type == "branch": - clm_startfile = "%s.clm2%s.r.%s-%s.nc"%(run_refcase,inst_string,run_refdate,run_reftod) - if not os.path.exists(os.path.join(rundir, clm_startfile)): - clm_startfile = "%s.clm2.r.%s-%s.nc"%(run_refcase,run_refdate,run_reftod) - logger.warning( "WARNING: the start file being used for a multi-instance case is a single instance: "+clm_startfile ) + compnames = [ "clm4", "clm5", "clm2" ] + for comp in compnames: + clm_startfile = "%s.%s%s.r.%s-%s.nc"%(run_refcase,comp,inst_string,run_refdate,run_reftod) + if os.path.exists(os.path.join(rundir, clm_startfile)): + break + else: + clm_startfile = "%s.%s.r.%s-%s.nc"%(run_refcase,comp,run_refdate,run_reftod) + if os.path.exists(os.path.join(rundir, clm_startfile)): + logger.warning( "WARNING: the start file being used for a multi-instance case is a single instance: "+clm_startfile ) + break + if not os.path.exists(os.path.join(rundir, clm_startfile)): + logger.warning( "WARNING: Could NOT find a start file to use using"+clm_startfile ) clm_icfile = "%s = \'%s\'"%(startfile_type, clm_startfile) else: clm_icfile = "" @@ -202,24 +222,24 @@ def buildnml(case, caseroot, compname): infile_lines.append(clm_icfile) user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string) - namelist_infile = os.path.join(clmconf, "namelist") + namelist_infile = os.path.join(ctsmconf, "namelist") create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines)) cmd = os.path.join(lnd_root,"bld","build-namelist") command = ("%s -cimeroot %s -infile %s -csmdata %s -inputdata %s %s -namelist \"&clm_inparm start_ymd=%s %s/ \" " - "%s %s -res %s %s -clm_start_type %s -envxml_dir %s -l_ncpl %s " + "%s %s -res %s %s -clm_start_type %s -envxml_dir %s " "-configuration %s -structure %s " - "-lnd_frac %s -glc_nec %s -co2_ppmv %s -co2_type %s -config %s " + "-lnd_frac %s -glc_nec %s %s -co2_ppmv %s -co2_type %s -config %s " "%s %s %s %s" %(cmd, _CIMEROOT, infile, din_loc_root, inputdata_file, ignore, start_ymd, clm_namelist_opts, - nomeg, usecase, lnd_grid, clmusr, start_type, caseroot, lnd_ncpl, + nomeg, usecase, lnd_grid, clmusr, start_type, caseroot, configuration, structure, - lndfrac_file, glc_nec, ccsm_co2_ppmv, clm_co2_type, config_cache_file, + lndfrac_file, glc_nec, glc_use_antarctica_flag, ccsm_co2_ppmv, clm_co2_type, config_cache_file, clm_bldnml_opts, spinup, tuning, gridmask)) - rc, out, err = run_cmd(command, from_dir=clmconf) + rc, out, err = run_cmd(command, from_dir=ctsmconf) expect(rc==0,"Command %s failed rc=%d\nout=%s\nerr=%s"%(cmd,rc,out,err)) if out is not None: logger.debug(" %s"%out) @@ -231,11 +251,11 @@ def buildnml(case, caseroot, compname): # ----------------------------------------------------- if os.path.isdir(rundir): - file1 = os.path.join(clmconf, "lnd_in") + file1 = os.path.join(ctsmconf, "lnd_in") file2 = os.path.join(rundir, "lnd_in") if ninst > 1: file2 += inst_string - logger.debug("CLM namelist copy: file1 %s file2 %s " %(file1, file2)) + logger.debug("CTSM namelist copy: file1 %s file2 %s " %(file1, file2)) shutil.copy(file1,file2) ############################################################################### @@ -243,7 +263,8 @@ def _main_func(): caseroot = parse_input(sys.argv) with Case(caseroot) as case: - buildnml(case, caseroot, "clm") + compname = case.get_value("COMP_LND") + buildnml(case, caseroot, compname) if __name__ == "__main__": _main_func() diff --git a/cime_config/config_archive.xml b/cime_config/config_archive.xml index 4c2412a0e3..c219a1d1ef 100644 --- a/cime_config/config_archive.xml +++ b/cime_config/config_archive.xml @@ -3,6 +3,8 @@ r rh\d? h\d*.*\.nc$ + lilac_hi.*\.nc$ + lilac_atm_driver_h\d*.*\.nc$ e locfnh @@ -15,10 +17,33 @@ casename.clm2.r.1976-01-01-00000.nc casename.clm2.rh4.1976-01-01-00000.nc casename.clm2.h0.1976-01-01-00000.nc + casename.clm2.lilac_hi.1976-01-01-00000.nc + casename.clm2.lilac_atm_driver_h0.0001-01.nc casename.clm2.h0.1976-01-01-00000.nc.base casename.clm2_0002.e.postassim.1976-01-01-00000.nc casename.clm2_0002.e.preassim.1976-01-01-00000.nc anothercasename.clm2.i.1976-01-01-00000.nc + + r + rh\d? + h\d*.*\.nc$ + e + locfnh + + rpointer.lnd$NINST_STRING + ./$CASE.ctsm$NINST_STRING.r.$DATENAME.nc + + + rpointer.lnd + rpointer.lnd_9999 + casename.ctsm.r.1976-01-01-00000.nc + casename.ctsm.rh4.1976-01-01-00000.nc + casename.ctsm.h0.1976-01-01-00000.nc + casename.ctsm.h0.1976-01-01-00000.nc.base + casename.ctsm_0002.e.postassim.1976-01-01-00000.nc + casename.ctsm_0002.e.preassim.1976-01-01-00000.nc + + diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index f9eeca8b7c..51f8e4bd96 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -15,7 +15,8 @@ clm4.5: - clm5.0: + clm5.0: + clm5.1: Satellite phenology: CN: Carbon Nitrogen model CNDV: CN with Dynamic Vegetation (deprecated) @@ -23,8 +24,10 @@ CNDV with prognostic crop: (deprecated) Satellite phenology with VIC hydrology: + Satellite phenology without anthropomorphic influences BGC (vert. resol. CN and methane): BGC (vert. resol. CN and methane) with prognostic crop: + BGC (vert. resol. CN and methane) without anthropomorphic influences: FATES (Functionally Assembled Terrestrial Ecosystem Simulator) Ecosystem Demography model: (experimental) BGC (vert. resol. CN and methane) with dynamic vegetation: BGC (vert. resol. CN and methane) with dynamic vegetation and prognostic crop: @@ -34,24 +37,36 @@ NWP configuration with satellite phenology: NWP configuration with BGC and CROP: - char - clm - clm + clm,ctsm + UNSET + + clm + ctsm + case_comp env_case.xml Name of land component + + char + on,off + off + build_component_ctsm + env_build.xml + Flag to enable building the LILAC cap and coupling code + + char - run_component_clm + run_component_ctsm env_run.xml Tuning parameters and initial conditions should be optimized for what CLM model version and what meteorlogical forcing combination? UNSET - clm5_0_cam6.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0 + clm5_0_cam6.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm5_1_GSWP3v1 clm4_5_CRUv7 clm4_5_CRUv7 @@ -61,22 +76,24 @@ clm5_0_CRUv7 clm5_0_GSWP3v1 clm5_0_cam6.0 + clm5_1_GSWP3v1 char - clm4_5,clm5_0 + clm4_5,clm5_0,clm5_1 UNSET - clm4_5 - clm5_0 + clm4_5 + clm5_0 + clm5_1 - run_component_clm + run_component_ctsm env_run.xml Overall physics version to use. This sets the default values for many different namelist options. @@ -90,7 +107,7 @@ nwp - run_component_clm + run_component_ctsm env_run.xml Sets CLM default namelist options related to model configuration. clm: Configuration used for climate applications (CLM) @@ -105,7 +122,7 @@ fast - run_component_clm + run_component_ctsm env_run.xml Sets CLM default namelist options related to model structure. standard: Standard model structure, allowing for more subgrid heterogeneity, @@ -119,18 +136,25 @@ char UNSET - - 2000_control - 1850_control - 20thC_transient - 1850-2100_rcp6_transient - 1850-2100_rcp4.5_transient - 1850-2100_rcp2.6_transient - 1850-2100_rcp8.5_transient - 20thC_transient - 1850-2100_rcp4.5_transient + + 2010_control + 2000_control + 1850_control + 1850_noanthro_control + 20thC_transient + 1850-2100_SSP5-8.5_transient + 1850-2100_SSP1-2.6_transient + 1850-2100_SSP3-7.0_transient + 1850-2100_SSP5-3.4_transient + 1850-2100_SSP2-4.5_transient + 1850-2100_SSP1-1.9_transient + 1850-2100_SSP4-3.4_transient + 1850-2100_SSP4-6.0_transient + 1850-2100_SSP5-8.5_transient + 20thC_transient + 1850-2100_SSP5-8.5_transient - run_component_clm + run_component_ctsm env_run.xml CLM namelist use_case. Determines the use-case that will be sent to the CLM build-namelist utility. @@ -167,8 +191,13 @@ -bgc bgc -dynamic_vegetation -crop -bgc sp -vichydro -bgc fates -no-megan + + -bgc sp + -bgc bgc + -bgc bgc -crop + -bgc fates -no-megan - run_component_clm + run_component_ctsm env_run.xml CLM build-namelist options @@ -178,13 +207,13 @@ constant,diagnostic,prognostic constant - diagnostic + diagnostic diagnostic prognostic diagnostic - diagnostic + diagnostic - run_component_clm + run_component_ctsm env_run.xml Determines how CLM will determine where CO2 is set. If value is constant, it will be set to CCSM_CO2_PPMV, @@ -199,7 +228,7 @@ char - run_component_clm + run_component_ctsm env_run.xml CLM-specific namelist settings for -namelist option in the CLM build-namelist. CLM_NAMELIST_OPTS is normally set as a compset variable @@ -214,7 +243,7 @@ char on,off off - run_component_clm + run_component_ctsm env_run.xml Turn on any settings for accellerating the model spinup. @@ -223,7 +252,7 @@ char UNSET - run_component_clm + run_component_ctsm env_run.xml Dataset name for user-created datasets. This is used as the argument in Buildconf/clm.buildnml to build-namelist -clm_usr_name. An example of @@ -235,13 +264,13 @@ char on,off off - run_component_clm + run_component_ctsm env_run.xml Flag to the CLM build-namelist command to force CLM to do a cold start (finidat will be set to blanks). A value of on forces the model to spin up from a cold-start (arbitrary initial conditions). Setting this value in the xml file will take - precedence over any settings for finidat in the $CASEROOT/user_clm_clm file. + precedence over any settings for finidat in the $CASEROOT/user_nl_ctsm file. @@ -249,10 +278,12 @@ - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck - run_component_clm + run_component_ctsm env_case.xml User mods to apply to specific compset matches. diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml index a1954b5dde..3c7e196178 100644 --- a/cime_config/config_compsets.xml +++ b/cime_config/config_compsets.xml @@ -12,13 +12,13 @@ The notation for the compset longname is TIME_ATM[%phys]_LND[%phys]_ICE[%phys]_OCN[%phys]_ROF[%phys]_GLC[%phys]_WAV[%phys][_BGC%phys] Where for the CAM specific compsets below the following is supported - TIME = Time period (e.g. 2000, HIST, RCP8...) + TIME = Time period (e.g. 2000, HIST, SSP585...) ATM = [CAM40, CAM50, CAM55] - LND = [CLM45, CLM50, SLND] + LND = [CLM45, CLM50, CLM51, SLND] ICE = [CICE, DICE, SICE] OCN = [DOCN, ,AQUAP, SOCN] ROF = [RTM, SROF] - GLC = [CISM1, CISM2] + GLC = [CISM2, SGLC] WAV = [SWAV] BGC = optional BGC scenario @@ -37,249 +37,375 @@ - I1PtClm50SpGs - 2000_DATM%1PT_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV + I1PtClm51SpRs + 2000_DATM%1PT_CLM51%SP_SICE_SOCN_SROF_SGLC_SWAV - I1PtClm45SpGs - 2000_DATM%1PT_CLM45%SP_SICE_SOCN_RTM_SGLC_SWAV + I1PtClm50SpRs + 2000_DATM%1PT_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV + + + + I1PtClm45SpRs + 2000_DATM%1PT_CLM45%SP_SICE_SOCN_SROF_SGLC_SWAV I2000Clm50Sp - 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV - I2000Clm50SpRsGs + I2000Clm50SpRs 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV + + I2000Clm51Sp + 2000_DATM%GSWP3v1_CLM51%SP_SICE_SOCN_MOSART_SGLC_SWAV + + + + + I2000Clm51SpRs + 2000_DATM%GSWP3v1_CLM51%SP_SICE_SOCN_SROF_SGLC_SWAV + + - I2000Clm50SpRtmGs + I2000Clm50SpRtm 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_RTM_SGLC_SWAV + + I2000Clm50SpMizGs + 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MIZUROUTE_SGLC_SWAV + + + + I2010Clm50Sp + 2010_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV + + I2000Clm50BgcCru - 2000_DATM%CRUv7_CLM50%BGC_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 2000_DATM%CRUv7_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV I2000Clm50BgcCropRtm - 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_RTM_SGLC_SWAV I2000Clm50BgcCrop - 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + + I2000Clm51BgcCrop + 2000_DATM%GSWP3v1_CLM51%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + + I2000Clm51Bgc + 2000_DATM%GSWP3v1_CLM51%BGC_SICE_SOCN_MOSART_SGLC_SWAV I2000Clm50Cn - 2000_DATM%GSWP3v1_CLM50%CN_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM50%CN_SICE_SOCN_MOSART_SGLC_SWAV I1850Clm50Sp - 1850_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 1850_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV I1850Clm50SpCru - 1850_DATM%CRUv7_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 1850_DATM%CRUv7_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV I1850Clm50BgcCrop - 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV - - I1850Clm50BgcCropCmip6 - 1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + I1850Clm51BgcCrop + 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV - - I1850Clm50BgcCropCmip6waccm - 1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + I1850Clm51Sp + 1850_DATM%GSWP3v1_CLM51%SP_SICE_SOCN_MOSART_SGLC_SWAV - I1850Clm50BgcCropCru - 1850_DATM%CRUv7_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV - - + I1850Clm51Bgc + 1850_DATM%GSWP3v1_CLM51%BGC_SICE_SOCN_MOSART_SGLC_SWAV + + - I2000Clm50SpGs - 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV + I1850Clm50BgcCropCmip6 + 1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6DECK_SICE_SOCN_MOSART_SGLC_SWAV - + - I2000Clm50BgcCropGs - 2000_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + I1850Clm50BgcCropCmip6waccm + 1850_DATM%GSWP3v1_CLM50%BGC-CROP-CMIP6WACCMDECK_SICE_SOCN_MOSART_SGLC_SWAV - - I2000Clm50BgcCropQianGs - 2000_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + I1850Clm50BgcCropCru + 1850_DATM%CRUv7_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + atm forcing to speed up datm, SROF to speed up build and run --> - I2000Clm50BgcCropQianRsGs + I2000Clm50BgcCropQianRs 2000_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV - I2000Clm45BgcCropQianRsGs + I2000Clm45BgcCropQianRs 2000_DATM%QIA_CLM45%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV - I2000Clm50BgcCruGs - 2000_DATM%CRUv7_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV + I2000Clm50BgcCruRs + 2000_DATM%CRUv7_CLM50%BGC_SICE_SOCN_SROF_SGLC_SWAV I2000Clm50SpRtmFl - 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_RTM%FLOOD_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_RTM%FLOOD_SGLC_SWAV + + I2000Clm51Fates + 2000_DATM%GSWP3v1_CLM51%FATES_SICE_SOCN_MOSART_SGLC_SWAV + I2000Clm50Fates - 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV + + + I2000Clm50FatesCruRsGs + 2000_DATM%CRUv7_CLM50%FATES_SICE_SOCN_SROF_SGLC_SWAV - I2000Clm50FatesCruGs + I2000Clm50FatesCru 2000_DATM%CRUv7_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV - - I2000Clm50FatesGs - 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV + I2000Clm50FatesRs + 2000_DATM%GSWP3v1_CLM50%FATES_SICE_SOCN_SROF_SGLC_SWAV I1850Clm50Bgc - 1850_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 1850_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV + + + + I1850Clm50BgcNoAnthro + 1850_DATM%GSWP3v1_CLM50%BGC-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV + + + + I1850Clm50SpNoAnthro + 1850_DATM%GSWP3v1_CLM50%SP-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV IHistClm50BgcCrop - HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + I1850Clm51Bgc + 1850_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV + + + + + I1850Clm51SpNoAnthro + 1850_DATM%GSWP3v1_CLM51%SP-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV + + + + IHistClm51Sp + HIST_DATM%GSWP3v1_CLM51%SP_SICE_SOCN_MOSART_SGLC_SWAV + + + + IHistClm51Bgc + HIST_DATM%GSWP3v1_CLM51%BGC_SICE_SOCN_MOSART_SGLC_SWAV + + + + IHistClm51BgcCrop + HIST_DATM%GSWP3v1_CLM51%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + IHistClm50Sp - HIST_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + HIST_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV + + + + + + IHistClm50SpCru + HIST_DATM%CRUv7_CLM50%SP_SICE_SOCN_MOSART_SGLC_SWAV IHistClm50Bgc - HIST_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + HIST_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV - + - IHistClm50BgcQianGs + IHistClm50BgcQian HIST_DATM%QIA_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV - - IHistClm50BgcCropGs - HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + IHistClm50BgcQianRs + HIST_DATM%QIA_CLM50%BGC_SICE_SOCN_SROF_SGLC_SWAV + + + + + ISSP585Clm50BgcCrop + SSP585_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + + ISSP126Clm50BgcCrop + SSP126_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + + ISSP119Clm50BgcCrop + SSP119_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV - - IHistClm50BgcCropQianGs - HIST_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + ISSP245Clm50BgcCrop + SSP245_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + + ISSP370Clm50BgcCrop + SSP370_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + + ISSP434Clm50BgcCrop + SSP434_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + + ISSP460Clm50BgcCrop + SSP460_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + + ISSP534Clm50BgcCrop + SSP534_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + + + + + + IHistClm50BgcCropQianRs + HIST_DATM%QIA_CLM50%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV + + + + + IHistClm50BgcCropRs + HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV I2000Clm50BgcDvCrop - 2000_DATM%GSWP3v1_CLM50%BGCDV-CROP_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM50%BGCDV-CROP_SICE_SOCN_MOSART_SGLC_SWAV - I2000Clm50BgcDvCropQianGs - 2000_DATM%QIA_CLM50%BGCDV-CROP_SICE_SOCN_MOSART_SGLC_SWAV + I2000Clm50BgcDvCropQianRs + 2000_DATM%QIA_CLM50%BGCDV-CROP_SICE_SOCN_SROF_SGLC_SWAV I1850Clm50BgcSpinup - 1850_DATM%CPLHIST_CLM50%BGC_SICE_SOCN_MOSART_CISM2%NOEVOLVE_SWAV + 1850_DATM%CPLHIST_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV - I2000Ctsm50NwpSpGswpGs + I2000Ctsm50NwpSpGswp 2000_DATM%GSWP3v1_CLM50%NWP-SP_SICE_SOCN_MOSART_SGLC_SWAV - I2000Ctsm50NwpBgcCropGswpGs + I2000Ctsm50NwpBgcCropGswp 2000_DATM%GSWP3v1_CLM50%NWP-BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV - I2000Ctsm50NwpSpNldasGs + I2000Ctsm50NwpSpNldas 2000_DATM%NLDAS2_CLM50%NWP-SP_SICE_SOCN_MOSART_SGLC_SWAV - I2000Ctsm50NwpSpNldasRsGs + I2000Ctsm50NwpSpNldasRs 2000_DATM%NLDAS2_CLM50%NWP-SP_SICE_SOCN_SROF_SGLC_SWAV @@ -287,11 +413,11 @@ I1850Clm45BgcCrop - 1850_DATM%GSWP3v1_CLM45%BGC-CROP_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + 1850_DATM%GSWP3v1_CLM45%BGC-CROP_SICE_SOCN_RTM_SGLC_SWAV - I1850Clm45BgcCruGs + I1850Clm45BgcCru 1850_DATM%CRUv7_CLM45%BGC_SICE_SOCN_RTM_SGLC_SWAV @@ -300,75 +426,67 @@ IHistClm45BgcCrop - HIST_DATM%GSWP3v1_CLM45%BGC-CROP_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + HIST_DATM%GSWP3v1_CLM45%BGC-CROP_SICE_SOCN_RTM_SGLC_SWAV - IHistClm45BgcCropQianGs - HIST_DATM%QIA_CLM45%BGC-CROP_SICE_SOCN_RTM_SGLC_SWAV + IHistClm45BgcCropQianRs + HIST_DATM%QIA_CLM45%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV I2000Clm45Sp - 2000_DATM%GSWP3v1_CLM45%SP_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM45%SP_SICE_SOCN_RTM_SGLC_SWAV I2000Clm45BgcCrop - 2000_DATM%GSWP3v1_CLM45%BGC-CROP_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM45%BGC-CROP_SICE_SOCN_RTM_SGLC_SWAV I2000Clm45Fates - 2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_RTM_SGLC_SWAV - + - I2000Clm45FatesGs - 2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_RTM_SGLC_SWAV + I2000Clm45FatesRs + 2000_DATM%GSWP3v1_CLM45%FATES_SICE_SOCN_SROF_SGLC_SWAV I1850Clm45Cn - 1850_DATM%GSWP3v1_CLM45%CN_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + 1850_DATM%GSWP3v1_CLM45%CN_SICE_SOCN_RTM_SGLC_SWAV I1850Clm45Bgc - 1850_DATM%GSWP3v1_CLM45%BGC_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV - - - - I1850Clm45BgcGs 1850_DATM%GSWP3v1_CLM45%BGC_SICE_SOCN_RTM_SGLC_SWAV - - I1850Clm45BgcCru - 1850_DATM%CRUv7_CLM45%BGC_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV - - IHistClm45Bgc - HIST_DATM%GSWP3v1_CLM45%BGC_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + HIST_DATM%GSWP3v1_CLM45%BGC_SICE_SOCN_RTM_SGLC_SWAV + + - IHistClm45BgcGs - HIST_DATM%GSWP3v1_CLM45%BGC_SICE_SOCN_RTM_SGLC_SWAV + IHistClm45BgcCru + HIST_DATM%CRUv7_CLM45%BGC_SICE_SOCN_RTM_SGLC_SWAV - IHistClm45BgcCruGs - HIST_DATM%CRUv7_CLM45%BGC_SICE_SOCN_RTM_SGLC_SWAV + IHistClm45Sp + HIST_DATM%GSWP3v1_CLM45%SP_SICE_SOCN_RTM_SGLC_SWAV @@ -376,33 +494,45 @@ I2000Clm50Vic - 2000_DATM%GSWP3v1_CLM50%SP-VIC_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + 2000_DATM%GSWP3v1_CLM50%SP-VIC_SICE_SOCN_RTM_SGLC_SWAV I2000Clm45VicCru - 2000_DATM%CRUv7_CLM45%SP-VIC_SICE_SOCN_RTM_CISM2%NOEVOLVE_SWAV + 2000_DATM%CRUv7_CLM45%SP-VIC_SICE_SOCN_RTM_SGLC_SWAV I1850Clm50SpG - 1850_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%EVOLVE_SWAV + 1850_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV IHistClm50SpG - HIST_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%EVOLVE_SWAV + HIST_DATM%GSWP3v1_CLM50%SP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV I1850Clm50BgcCropG - 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%EVOLVE_SWAV + 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV IHistClm50BgcCropG - HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%EVOLVE_SWAV + HIST_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_CISM2%GRIS-EVOLVE_SWAV + + + + + I2000Ctsm50NwpSpAsRs + 2000_SATM_CLM50%NWP-SP_SICE_SOCN_SROF_SGLC_SWAV @@ -413,6 +543,7 @@ 1850-01-01 2000-01-01 2010-01-01 + 2015-01-01 1980-01-15 1997-12-31 1993-12-01 diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index 9467994e62..bf141781ec 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -409,6 +409,228 @@ + + + + none + + -12 + -12 + -12 + -12 + -12 + -12 + -12 + -12 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + + + + + none + + -1 + -70 + -70 + -70 + -70 + -70 + -70 + -70 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + + + + + none + + -12 + -12 + -12 + -12 + -12 + -12 + -12 + -12 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + + + + + none + + -1 + -70 + -70 + -70 + -70 + -70 + -70 + -70 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + + + + + none + + -12 + -12 + -12 + -12 + -12 + -12 + -12 + -12 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + + + + + none + + -1 + -70 + -70 + -70 + -70 + -70 + -70 + -70 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + @@ -483,6 +705,228 @@ + + + + none + + -12 + -12 + -12 + -12 + -12 + -12 + -12 + -12 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + + + + + none + + -1 + -48 + -48 + -48 + -48 + -48 + -48 + -48 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + + + + + none + + -24 + -24 + -24 + -24 + -24 + -24 + -24 + -24 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + + + + + none + + -1 + -48 + -48 + -48 + -48 + -48 + -48 + -48 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + + + + + none + + -48 + -48 + -48 + -48 + -48 + -48 + -48 + -48 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + + + + + none + + -1 + -96 + -96 + -96 + -96 + -96 + -96 + -96 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + @@ -746,19 +1190,4 @@ - - - - - - 1 - - - 1 - - - - - - diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml index 8a40ea9183..8a933581cf 100644 --- a/cime_config/config_tests.xml +++ b/cime_config/config_tests.xml @@ -1,19 +1,7 @@ @@ -47,6 +35,16 @@ SSP smoke CLM spinup test (only valid for CLM compsets with CLM45) $STOP_N + + CTSM test: Smoke test of building and running CTSM via LILAC. Grid and compset (and most case settings) are ignored. + + 1 + ndays + 11 + FALSE + FALSE + + CLM test: Verify that adding virtual glacier columns doesn't change answers 1 @@ -85,6 +83,14 @@ SSP smoke CLM spinup test (only valid for CLM compsets with CLM45) $STOP_N + + smoke CLM spinup test 1 diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index d12defc385..0de093b7c4 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -30,17 +30,73 @@ - + + + FAIL + #1117 + + + + FAIL - #158 + ESCOMP/CMEPS#175 - - + + + FAIL + ESMCI/cime#3905 + + + + + + FAIL + ESMCI/cime#3905 + + + + + + FAIL + ESMCI/cime#3915 + + + + + + FAIL + ESMCI/cime#3915 + + + + + + FAIL + #1317 + + + + + + FAIL + #1317 + + + + + FAIL - #550 + ESMCI/cime#3496 + + + + + + FAIL + ESMCI/cime#3496 @@ -81,6 +137,27 @@ + + + FAIL + NGEET/fates#510 + + + + + + FAIL + NGEET/fates#508 + + + + + + FAIL + NGEET/fates#508 + + + FAIL @@ -109,4 +186,25 @@ + + + FAIL + #667 + + + + + + FAIL + #667 + + + + + + FAIL + #667 + + + diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 36b083427a..f7f2e3391e 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1,6 +1,6 @@ - + @@ -8,24 +8,45 @@ - + + - + - + + + + + + + + + + + + + + + + + + + + + - + - + @@ -34,7 +55,16 @@ - + + + + + + + + + + @@ -59,18 +89,70 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - + + @@ -84,12 +166,21 @@ - + + + + + + + + + + @@ -100,15 +191,38 @@ - + + + + + + + + + + + + + + + + + + + + + - + @@ -116,7 +230,7 @@ - + @@ -124,7 +238,7 @@ - + @@ -132,7 +246,7 @@ - + @@ -141,7 +255,7 @@ - + @@ -149,7 +263,7 @@ - + @@ -157,15 +271,15 @@ - + - + - + @@ -174,7 +288,7 @@ - + @@ -183,23 +297,36 @@ - + - + + - + - + + + + + + + + + + + + + - + @@ -207,7 +334,36 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -216,7 +372,7 @@ - + @@ -224,7 +380,7 @@ - + @@ -232,7 +388,7 @@ - + @@ -240,7 +396,7 @@ - + @@ -248,41 +404,42 @@ - + + - + - - + + - + + - + - - + @@ -290,23 +447,45 @@ - + + - + + - + + + + + + + + + + + + + + + + + + + + + @@ -314,17 +493,25 @@ - + - - + + + + + + + + + + @@ -332,7 +519,7 @@ - + @@ -348,7 +535,7 @@ - + @@ -359,7 +546,7 @@ - + @@ -367,7 +554,7 @@ - + @@ -375,7 +562,7 @@ - + @@ -383,7 +570,7 @@ - + @@ -391,7 +578,7 @@ - + @@ -400,7 +587,7 @@ - + @@ -409,7 +596,7 @@ - + @@ -418,7 +605,7 @@ - + @@ -427,24 +614,36 @@ - + + - + - + + + + + + + + + + + + - + @@ -452,7 +651,7 @@ - + @@ -460,7 +659,7 @@ - + @@ -477,7 +676,7 @@ - + @@ -487,8 +686,9 @@ - + + @@ -502,7 +702,7 @@ - + @@ -510,7 +710,7 @@ - + @@ -526,23 +726,27 @@ - + - + + + - + - + + + - + @@ -550,7 +754,7 @@ - + @@ -558,7 +762,7 @@ - + @@ -566,7 +770,7 @@ - + @@ -575,33 +779,45 @@ - + - + + - + - + + + + + + + + + + + - + - + + - + @@ -609,7 +825,7 @@ - + @@ -617,17 +833,16 @@ - + - - + @@ -637,16 +852,84 @@ - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -667,6 +950,7 @@ + @@ -685,12 +969,21 @@ + + + + + + + + + - + @@ -699,7 +992,7 @@ - + @@ -709,7 +1002,7 @@ - + @@ -717,7 +1010,7 @@ - + @@ -726,7 +1019,7 @@ - + @@ -736,17 +1029,27 @@ - + - + - + + + + + + + + + + + @@ -754,7 +1057,7 @@ - + @@ -763,7 +1066,16 @@ - + + + + + + + + + + @@ -772,7 +1084,7 @@ - + @@ -781,7 +1093,7 @@ - + @@ -790,15 +1102,16 @@ - + + - + @@ -809,15 +1122,17 @@ - + + + - + @@ -826,7 +1141,7 @@ - + @@ -834,7 +1149,7 @@ - + @@ -842,7 +1157,7 @@ - + @@ -850,7 +1165,7 @@ - + @@ -859,7 +1174,7 @@ - + @@ -876,40 +1191,42 @@ - + + - + - + - + - + - + + - + - - + + - + @@ -918,7 +1235,7 @@ - + @@ -927,7 +1244,7 @@ - + @@ -937,7 +1254,7 @@ - + @@ -946,7 +1263,7 @@ - + @@ -955,7 +1272,7 @@ - + @@ -964,15 +1281,16 @@ - + - + - + + - + @@ -981,7 +1299,7 @@ - + @@ -990,7 +1308,7 @@ - + @@ -1000,13 +1318,13 @@ - + - + @@ -1018,7 +1336,7 @@ - + @@ -1027,51 +1345,46 @@ - + + - - - - - - - - - + + - + + - + + - + - @@ -1079,7 +1392,7 @@ - + @@ -1097,6 +1410,89 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1106,7 +1502,7 @@ - + @@ -1125,7 +1521,7 @@ - + @@ -1133,7 +1529,7 @@ - + @@ -1141,7 +1537,7 @@ - + @@ -1151,7 +1547,7 @@ - + @@ -1164,7 +1560,17 @@ - + + + + + + + + + + + @@ -1172,7 +1578,7 @@ - + @@ -1182,7 +1588,7 @@ - + @@ -1190,26 +1596,37 @@ - + + + + + + + + + + + - + + - + @@ -1217,15 +1634,26 @@ - + + - + + + + + + + + + + + @@ -1234,16 +1662,17 @@ - + + - + @@ -1253,7 +1682,17 @@ - + + + + + + + + + + + @@ -1262,7 +1701,7 @@ - + @@ -1271,16 +1710,27 @@ - + + + + + + + + + + + + - + @@ -1288,10 +1738,9 @@ - + - @@ -1305,7 +1754,7 @@ - + @@ -1313,17 +1762,16 @@ - + - - + @@ -1331,7 +1779,7 @@ - + @@ -1339,7 +1787,7 @@ - + @@ -1366,7 +1814,7 @@ - + @@ -1374,7 +1822,7 @@ - + @@ -1382,24 +1830,53 @@ - + + + - + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + @@ -1408,24 +1885,26 @@ - + + - + + - + @@ -1434,7 +1913,7 @@ - + @@ -1443,7 +1922,16 @@ - + + + + + + + + + + @@ -1468,7 +1956,7 @@ - + @@ -1477,17 +1965,26 @@ - + + - + + + + + + + + + @@ -1496,7 +1993,7 @@ - + @@ -1505,7 +2002,7 @@ - + @@ -1514,7 +2011,7 @@ - + @@ -1523,7 +2020,7 @@ - + @@ -1531,7 +2028,7 @@ - + @@ -1541,7 +2038,16 @@ - + + + + + + + + + + @@ -1549,7 +2055,7 @@ - + @@ -1567,22 +2073,24 @@ - + + - + + @@ -1596,6 +2104,7 @@ + @@ -1609,7 +2118,7 @@ - + @@ -1625,7 +2134,7 @@ - + @@ -1642,231 +2151,324 @@ - + - + - + - + - + - + - + - + - + - + - + - - + + - + - - + + - + + - + + - + + + + - + - + + - + - + + - + + - + + + - + + - + + + - + - + + - + + + - + - + + - + + + - + + + - + + - + + + + + + + + + + + + + + - + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + + + - + + + - + + + + + + + + + + + @@ -1876,7 +2478,7 @@ - + @@ -1886,7 +2488,7 @@ - + @@ -1896,31 +2498,48 @@ - + - - + + + + - + + - - + + + + + + + + + + + + + + + - + + - + diff --git a/cime_config/testdefs/testmods_dirs/clm/cropColdStart/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ADspinup/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/cropColdStart/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/ADspinup/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/ADspinup/shell_commands b/cime_config/testdefs/testmods_dirs/clm/ADspinup/shell_commands new file mode 100644 index 0000000000..771777c92a --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ADspinup/shell_commands @@ -0,0 +1,4 @@ +#!/bin/bash + +./xmlchange CLM_ACCELERATED_SPINUP="on" + diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands index 41a2342a51..fe7182b67f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands @@ -1,2 +1,3 @@ ./xmlchange CLM_BLDNML_OPTS="-no-megan" --append ./xmlchange BFBFLAG="TRUE" +./xmlchange CLM_FORCE_COLDSTART="on" diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm index 487ad09863..90a188bdb1 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm @@ -1,11 +1,13 @@ -!!finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_map/iclm45fates-finit-s1.4.0-a3.0.0-1x1br.clm2.r.0111-01-01-00000.nc' +!! USES THE DEFAULT INITIALIZATION FILE SPECIFIED IN bld/namelist_files/namelist_defaults_ctsm.xml hist_mfilt = 365 hist_nhtfrq = -24 hist_empty_htapes = .true. -use_fates_spitfire= .true. -hist_fincl1 = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT', - 'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef', - 'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass', +fates_spitfire_mode = 1 +hist_fincl1 = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN_ELEM','LITTER_OUT_ELEM', + 'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','FIRE_FUEL_MEF', + 'FIRE_FUEL_BULKD','FIRE_FUEL_SAV','FIRE_NESTEROV_INDEX','PFTbiomass', 'PFTleafbiomass','FIRE_ROS','WIND','AREA_TREES','AREA_PLANT', - 'TOTSOMC','TOTLITC','T_SCALAR','NEP','NBP','HR','TOTECOSYSC','NPLANT_SCAG','NPLANT_SCPF', - 'BA_SCLS','NPP_BY_AGE','CWD_AG_CWDSC','PARSUN_Z_CNLF','PARSUN_Z_CNLFPFT','PARSHA_Z_CAN' + 'TOTSOMC','TOTLITC','T_SCALAR','NEP','HR','NPLANT_SCAG','NPLANT_SCPF', + 'BA_SCLS','NPP_BY_AGE','CWD_AG_CWDSC','PARSUN_Z_CNLF','PARSUN_Z_CNLFPFT','PARSHA_Z_CAN', + 'LITTER_FINES_AG_ELEM','LITTER_FINES_BG_ELEM','LITTER_CWD_AG_ELEM','LITTER_CWD_BG_ELEM', + 'SEED_BANK' diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesAllVars/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesAllVars/include_user_mods index 4c7aa0f2b4..1f2c03aebe 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesAllVars/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesAllVars/include_user_mods @@ -1 +1 @@ -../Fates +../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesAllVars/user_nl_clm index a869310636..cd1daa4eea 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesAllVars/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesAllVars/user_nl_clm @@ -2,30 +2,44 @@ hist_mfilt = 365 hist_nhtfrq = -24 hist_empty_htapes = .false. -use_fates_spitfire= .true. -hist_fincl1 = 'NCL_BY_AGE','NPATCH_BY_AGE','BIOMASS_BY_AGE','NPP_BY_AGE','GPP_BY_AGE','PARSUN_Z_CNLF','PARSHA_Z_CNLF','PARSUN_Z_CNLFPFT', - 'PARSHA_Z_CNLFPFT','PARSUN_Z_CAN','PARSHA_Z_CAN','LAISUN_Z_CNLF','LAISHA_Z_CNLF','LAISUN_Z_CNLFPFT','LAISHA_Z_CNLFPFT', - 'LAISUN_TOP_CAN','LAISHA_TOP_CAN','FABD_SUN_CNLFPFT','FABD_SHA_CNLFPFT','FABI_SUN_CNLFPFT','FABI_SHA_CNLFPFT', - 'FABD_SUN_CNLF','FABD_SHA_CNLF','FABI_SUN_CNLF','FABI_SHA_CNLF','FABD_SUN_TOPLF_BYCANLAYER','FABD_SHA_TOPLF_BYCANLAYER', - 'FABI_SUN_TOPLF_BYCANLAYER','FABI_SHA_TOPLF_BYCANLAYER','TS_NET_UPTAKE_CNLF','YEAR_NET_UPTAKE_CNLF','CROWNAREA_CNLF', - 'MORTALITY_CARBONFLUX_CANOPY','MORTALITY_CARBONFLUX_UNDERSTORY','NPLANT_SCAG','NPLANT_CANOPY_SCAG','NPLANT_UNDERSTORY_SCAG', - 'DDBH_CANOPY_SCAG','DDBH_UNDERSTORY_SCAG','MORTALITY_CANOPY_SCAG','MORTALITY_UNDERSTORY_SCAG','GPP_SCPF','GPP_CANOPY_SCPF', - 'AR_CANOPY_SCPF','GPP_UNDERSTORY_SCPF','AR_UNDERSTORY_SCPF','NPP_SCPF','NPP_LEAF_SCPF','NPP_SEED_SCPF','NPP_FNRT_SCPF', - 'NPP_BGSW_SCPF','NPP_BGDW_SCPF','NPP_AGSW_SCPF','NPP_AGDW_SCPF','NPP_STOR_SCPF','DDBH_SCPF','DDBH_CANOPY_SCPF', - 'DDBH_UNDERSTORY_SCPF','BA_SCPF','NPLANT_SCPF','M1_SCPF','M2_SCPF','M3_SCPF','M4_SCPF','M5_SCPF','M6_SCPF','M7_SCPF', - 'MORTALITY_CANOPY_SCPF','BSTOR_CANOPY_SCPF','BLEAF_CANOPY_SCPF','NPLANT_CANOPY_SCPF','MORTALITY_UNDERSTORY_SCPF', - 'BSTOR_UNDERSTORY_SCPF','BLEAF_UNDERSTORY_SCPF','NPLANT_UNDERSTORY_SCPF','CWD_AG_CWDSC','CWD_BG_CWDSC','CWD_AG_IN_CWDSC', - 'CWD_BG_IN_CWDSC','CWD_AG_OUT_CWDSC','CWD_BG_OUT_CWDSC','AR_SCPF','AR_GROW_SCPF','AR_MAINT_SCPF','AR_DARKM_SCPF','AR_AGSAPM_SCPF', - 'AR_CROOTM_SCPF','AR_FROOTM_SCPF','DDBH_CANOPY_SCLS','DDBH_UNDERSTORY_SCLS','YESTERDAYCANLEV_CANOPY_SCLS', - 'YESTERDAYCANLEV_UNDERSTORY_SCLS','BA_SCLS','DEMOTION_RATE_SCLS','PROMOTION_RATE_SCLS','NPLANT_CANOPY_SCLS', - 'MORTALITY_CANOPY_SCLS','NPLANT_UNDERSTORY_SCLS','MORTALITY_UNDERSTORY_SCLS','TRIMMING_CANOPY_SCLS','TRIMMING_UNDERSTORY_SCLS', - 'CROWN_AREA_CANOPY_SCLS','CROWN_AREA_UNDERSTORY_SCLS','LEAF_MD_CANOPY_SCLS','ROOT_MD_CANOPY_SCLS','CARBON_BALANCE_CANOPY_SCLS', - 'SEED_PROD_CANOPY_SCLS','DBALIVEDT_CANOPY_SCLS','DBDEADDT_CANOPY_SCLS','DBSTOREDT_CANOPY_SCLS','STORAGE_FLUX_CANOPY_SCLS', - 'NPP_LEAF_CANOPY_SCLS','NPP_FROOT_CANOPY_SCLS','NPP_BSW_CANOPY_SCLS','NPP_BDEAD_CANOPY_SCLS','NPP_BSEED_CANOPY_SCLS', - 'NPP_STORE_CANOPY_SCLS','RDARK_CANOPY_SCLS','LIVESTEM_MR_CANOPY_SCLS','LIVECROOT_MR_CANOPY_SCLS','FROOT_MR_CANOPY_SCLS', - 'RESP_G_CANOPY_SCLS','RESP_M_CANOPY_SCLS','LEAF_MD_UNDERSTORY_SCLS','ROOT_MD_UNDERSTORY_SCLS','CARBON_BALANCE_UNDERSTORY_SCLS', - 'SEED_PROD_UNDERSTORY_SCLS','DBALIVEDT_UNDERSTORY_SCLS','DBDEADDT_UNDERSTORY_SCLS','DBSTOREDT_UNDERSTORY_SCLS', - 'STORAGE_FLUX_UNDERSTORY_SCLS','NPP_LEAF_UNDERSTORY_SCLS','NPP_FROOT_UNDERSTORY_SCLS','NPP_BSW_UNDERSTORY_SCLS', - 'NPP_BDEAD_UNDERSTORY_SCLS','NPP_BSEED_UNDERSTORY_SCLS','NPP_STORE_UNDERSTORY_SCLS','RDARK_UNDERSTORY_SCLS', - 'LIVESTEM_MR_UNDERSTORY_SCLS','LIVECROOT_MR_UNDERSTORY_SCLS','FROOT_MR_UNDERSTORY_SCLS','RESP_G_UNDERSTORY_SCLS', - 'RESP_M_UNDERSTORY_SCLS' +fates_spitfire_mode = 1 +hist_fincl1 = 'PFTcrownarea','PFTcanopycrownarea','NCL_BY_AGE','NPATCH_BY_AGE', +'BIOMASS_BY_AGE','SECONDARY_FOREST_FRACTION','WOOD_PRODUCT','SECONDARY_FOREST_BIOMASS', +'SECONDARY_AREA_AGE_ANTHRO_DIST','SECONDARY_AREA_PATCH_AGE_DIST','C_STOMATA_BY_AGE','C_LBLAYER_BY_AGE', +'NPP_BY_AGE','GPP_BY_AGE','PARSUN_Z_CNLF','PARSHA_Z_CNLF', +'PARSUN_Z_CNLFPFT','PARSHA_Z_CNLFPFT','PARSUN_Z_CAN','PARSHA_Z_CAN', +'LAISUN_Z_CNLF','LAISHA_Z_CNLF','LAISUN_Z_CNLFPFT','LAISHA_Z_CNLFPFT', +'LAISUN_TOP_CAN','LAISHA_TOP_CAN','FABD_SUN_CNLFPFT','FABD_SHA_CNLFPFT', +'FABI_SUN_CNLFPFT','FABI_SHA_CNLFPFT','FABD_SUN_CNLF','FABD_SHA_CNLF', +'FABI_SUN_CNLF','FABI_SHA_CNLF','PARPROF_DIR_CNLFPFT','PARPROF_DIF_CNLFPFT', +'PARPROF_DIR_CNLF','PARPROF_DIF_CNLF','FABD_SUN_TOPLF_BYCANLAYER', +'FABD_SHA_TOPLF_BYCANLAYER','FABI_SUN_TOPLF_BYCANLAYER','FABI_SHA_TOPLF_BYCANLAYER', +'NET_C_UPTAKE_CNLF','CROWNAREA_CNLF','NPLANT_CANOPY_SCAG','NPLANT_UNDERSTORY_SCAG', +'DDBH_CANOPY_SCAG','DDBH_UNDERSTORY_SCAG','MORTALITY_CANOPY_SCAG','MORTALITY_UNDERSTORY_SCAG', +'NPLANT_SCAGPFT','NPP_AGEPFT','BIOMASS_AGEPFT','GPP_SCPF','GPP_CANOPY_SCPF', +'AR_CANOPY_SCPF','GPP_UNDERSTORY_SCPF','AR_UNDERSTORY_SCPF','NPP_SCPF', +'NPP_LEAF_SCPF','NPP_SEED_SCPF','NPP_FNRT_SCPF','NPP_BGSW_SCPF','NPP_BGDW_SCPF','NPP_AGSW_SCPF', +'NPP_AGDW_SCPF','NPP_STOR_SCPF','DDBH_SCPF','GROWTHFLUX_SCPF','GROWTHFLUX_FUSION_SCPF', +'DDBH_CANOPY_SCPF','DDBH_UNDERSTORY_SCPF','BA_SCPF','AGB_SCPF','NPLANT_SCPF', +'NPLANT_CAPF','M1_SCPF','M2_SCPF','M3_SCPF','M4_SCPF','M5_SCPF','CROWNFIREMORT_SCPF','CAMBIALFIREMORT_SCPF', +'M6_SCPF','M7_SCPF','M8_SCPF','M9_SCPF','M10_SCPF', +'M10_CAPF','MORTALITY_CANOPY_SCPF','BSTOR_CANOPY_SCPF','BLEAF_CANOPY_SCPF', +'NPLANT_CANOPY_SCPF','MORTALITY_UNDERSTORY_SCPF','BSTOR_UNDERSTORY_SCPF','BLEAF_UNDERSTORY_SCPF', +'NPLANT_UNDERSTORY_SCPF','CWD_AG_CWDSC','CWD_BG_CWDSC','CWD_AG_IN_CWDSC', +'CWD_BG_IN_CWDSC','CWD_AG_OUT_CWDSC','CWD_BG_OUT_CWDSC','AR_SCPF','AR_GROW_SCPF', +'AR_MAINT_SCPF','AR_DARKM_SCPF','AR_AGSAPM_SCPF','AR_CROOTM_SCPF','AR_FROOTM_SCPF', +'YESTERDAYCANLEV_CANOPY_SCLS','YESTERDAYCANLEV_UNDERSTORY_SCLS', +'BIOMASS_SCLS','DEMOTION_RATE_SCLS','PROMOTION_RATE_SCLS','SAI_CANOPY_SCLS','SAI_UNDERSTORY_SCLS', +'CARBON_BALANCE_CANOPY_SCLS','CARBON_BALANCE_UNDERSTORY_SCLS','TRIMMING_CANOPY_SCLS', +'TRIMMING_UNDERSTORY_SCLS','CROWN_AREA_CANOPY_SCLS','CROWN_AREA_UNDERSTORY_SCLS', +'LEAF_MD_CANOPY_SCLS','ROOT_MD_CANOPY_SCLS','BSTORE_MD_CANOPY_SCLS','BDEAD_MD_CANOPY_SCLS', +'BSW_MD_CANOPY_SCLS','SEED_PROD_CANOPY_SCLS','NPP_LEAF_CANOPY_SCLS','NPP_FROOT_CANOPY_SCLS', +'NPP_BSW_CANOPY_SCLS','NPP_BDEAD_CANOPY_SCLS','NPP_BSEED_CANOPY_SCLS', +'NPP_STORE_CANOPY_SCLS','RDARK_CANOPY_SCLS', +'LIVESTEM_MR_CANOPY_SCLS','LIVECROOT_MR_CANOPY_SCLS','FROOT_MR_CANOPY_SCLS','RESP_G_CANOPY_SCLS', +'RESP_M_CANOPY_SCLS','LEAF_MD_UNDERSTORY_SCLS','ROOT_MD_UNDERSTORY_SCLS','BSTORE_MD_UNDERSTORY_SCLS', +'BDEAD_MD_UNDERSTORY_SCLS','BSW_MD_UNDERSTORY_SCLS','SEED_PROD_UNDERSTORY_SCLS','NPP_LEAF_UNDERSTORY_SCLS', +'NPP_FROOT_UNDERSTORY_SCLS','NPP_BSW_UNDERSTORY_SCLS','NPP_BDEAD_UNDERSTORY_SCLS','NPP_BSEED_UNDERSTORY_SCLS', +'NPP_STORE_UNDERSTORY_SCLS','RDARK_UNDERSTORY_SCLS','LIVESTEM_MR_UNDERSTORY_SCLS','LIVECROOT_MR_UNDERSTORY_SCLS', +'FROOT_MR_UNDERSTORY_SCLS','RESP_G_UNDERSTORY_SCLS','RESP_M_UNDERSTORY_SCLS','TOTVEGC_SCPF', +'LEAFC_SCPF','FNRTC_SCPF','SAPWC_SCPF','STOREC_SCPF','REPROC_SCPF','CEFFLUX_SCPF' diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDef/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDef/user_nl_clm index 144569c412..c092059cea 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDef/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDef/user_nl_clm @@ -1,6 +1,10 @@ +hist_mfilt = 365 +hist_nhtfrq = -24 +hist_empty_htapes = .true. +fates_spitfire_mode = 1 hist_fincl1 = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT', - 'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef', - 'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass', + 'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','FIRE_FUEL_MEF', + 'FIRE_FUEL_BULKD','FIRE_FUEL_SAV','FIRE_NESTEROV_INDEX','PFTbiomass', 'PFTleafbiomass','FIRE_ROS','WIND','AREA_TREES','AREA_PLANT', - 'TOTSOMC','TOTLITC','T_SCALAR','NEP','NBP','HR','TOTECOSYSC','NPLANT_SCAG','NPLANT_SCPF', + 'TOTSOMC','TOTLITC','T_SCALAR','NEP','HR','NPLANT_SCAG','NPLANT_SCPF', 'BA_SCLS','NPP_BY_AGE','CWD_AG_CWDSC','PARSUN_Z_CNLF','PARSUN_Z_CNLFPFT','PARSHA_Z_CAN' diff --git a/cime_config/testdefs/testmods_dirs/clm/cropColdStart/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesHydro/shell_commands old mode 100755 new mode 100644 similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/cropColdStart/shell_commands rename to cime_config/testdefs/testmods_dirs/clm/FatesHydro/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesHydro/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesHydro/user_nl_clm new file mode 100644 index 0000000000..bd4ddb8b3e --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesHydro/user_nl_clm @@ -0,0 +1,11 @@ +hist_mfilt = 365 +hist_nhtfrq = -24 +hist_empty_htapes = .true. +use_fates_planthydro= .true. +hist_fincl1 = 'FATES_ERRH2O_SCPF','FATES_TRAN_SCPF', +'FATES_SAPFLOW_SCPF','FATES_ITERH1_SCPF','FATES_ATH_SCPF','FATES_TTH_SCPF', +'FATES_STH_SCPF','FATES_LTH_SCPF','FATES_AWP_SCPF','FATES_BTRAN_SCPF', +'FATES_ROOTWGT_SOILVWC_SI','FATES_ROOTWGT_SOILVWCSAT_SI', +'FATES_ROOTWGT_SOILMATPOT_SI','FATES_SOILMATPOT_SL','FATES_SOILVWC_SL','FATES_SOILVWCSAT_SL', +'FATES_ROOTUPTAKE_SI','FATES_ROOTUPTAKE_SL','FATES_ROOTUPTAKE0_SCPF','FATES_ROOTUPTAKE10_SCPF', +'FATES_ROOTUPTAKE50_SCPF','FATES_ROOTUPTAKE100_SCPF' diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLogging/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesLogging/include_user_mods index 4c7aa0f2b4..1f2c03aebe 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesLogging/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesLogging/include_user_mods @@ -1 +1 @@ -../Fates +../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesNoFire/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesNoFire/include_user_mods index 4c7aa0f2b4..1f2c03aebe 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesNoFire/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesNoFire/include_user_mods @@ -1 +1 @@ -../Fates +../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesNoFire/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesNoFire/user_nl_clm index dfdb775ec5..8fc4951e6a 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesNoFire/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesNoFire/user_nl_clm @@ -1 +1 @@ -use_fates_spitfire= .false. +fates_spitfire_mode = 0 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesPPhys/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesPPhys/include_user_mods index 4c7aa0f2b4..1f2c03aebe 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesPPhys/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesPPhys/include_user_mods @@ -1 +1 @@ -../Fates +../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesPRT2/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesPRT2/include_user_mods new file mode 100644 index 0000000000..4c7aa0f2b4 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesPRT2/include_user_mods @@ -0,0 +1 @@ +../Fates diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesPRT2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesPRT2/user_nl_clm new file mode 100644 index 0000000000..400fa7cfd4 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesPRT2/user_nl_clm @@ -0,0 +1,5 @@ +hist_mfilt = 365 +hist_nhtfrq = -24 +hist_empty_htapes = .false. +fates_parteh_mode = 2 +fates_spitfire_mode = 1 \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexFixedBiogeo/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexFixedBiogeo/include_user_mods new file mode 100644 index 0000000000..1f2c03aebe --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexFixedBiogeo/include_user_mods @@ -0,0 +1 @@ +../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexFixedBiogeo/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexFixedBiogeo/user_nl_clm new file mode 100644 index 0000000000..d3349780e0 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesReducedComplexFixedBiogeo/user_nl_clm @@ -0,0 +1 @@ +use_fates_fixed_biogeog=.true. \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesST3/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesST3/include_user_mods index 4c7aa0f2b4..1f2c03aebe 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesST3/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesST3/include_user_mods @@ -1 +1 @@ -../Fates +../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesShortList/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesShortList/user_nl_clm index f9d31eecbb..1790bb86c8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesShortList/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesShortList/user_nl_clm @@ -1,5 +1,5 @@ hist_fincl1 = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT', - 'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef', - 'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass', + 'FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','FIRE_FUEL_MEF', + 'FIRE_FUEL_BULKD','FIRE_FUEL_SAV','FIRE_NESTEROV_INDEX','PFTbiomass', 'PFTleafbiomass','FIRE_ROS','WIND','AREA_TREES','AREA_PLANT', - 'TOTSOMC','TOTLITC','T_SCALAR','NEP','NBP','HR','TOTECOSYSC' + 'TOTSOMC','TOTLITC','T_SCALAR','NEP','HR' diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/include_user_mods new file mode 100644 index 0000000000..1f2c03aebe --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/include_user_mods @@ -0,0 +1 @@ +../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/user_nl_clm new file mode 100644 index 0000000000..cb7cc262fe --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesSizeAgeMort/user_nl_clm @@ -0,0 +1,3 @@ +hist_empty_htapes = .true. +use_fates_cohort_age_tracking=.true. +hist_fincl1 = 'M9_SCPF','M10_SCPF','M10_CAPF','NPLANT_CACLS','NPLANT_CAPF', 'M9_SCLS','M10_SCLS','M10_CACLS' diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates_nat_and_anthro_ignitions/README b/cime_config/testdefs/testmods_dirs/clm/Fates_nat_and_anthro_ignitions/README new file mode 100644 index 0000000000..3bd8c7dd62 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/Fates_nat_and_anthro_ignitions/README @@ -0,0 +1,26 @@ +Testing capability to read/use lightning frequency & population density +datasets. Calculates lightning ignitions using the SPITFIRE +formulation and anthropogenic ignitions using the Li et al. 2012 formulation +based on human population density implemented in CTSM-CN's fire model. + +Testing does not include a separate test for reading/using a successful +ignitions dataset which uses the same format and units so handling +is the same until you're in subroutine area_burnt_intensity where for +"successful ignitions" the model selects +currentSite%FDI = 1.0_r8 +cloud_to_ground_strikes = 1.0_r8 +while for lightning the model can use values < 1 for both. + +Lara Kueppers (UC-Berkeley) has access to a "successful ignitions" +dataset for California that has not been placed in the repository of +CTSM datasets as of 2020/6/6. That dataset can be used with the +following settings: + +fire_method = 'spitfire' +fates_spitfire_mode = 3 +stream_fldfilename_lightng = '.../data_UCB/observed/CA_monthly_ignition_number_1980-2016/ignition_1980_to_2016_monthly_20190801.nc' +stream_year_first_lightng = 1980 +stream_year_last_lightng = 2016 +model_year_align_lightng = 1980 + +where {...} = /fs/cgd/data0/slevis on izumi and /glade/work/slevis on cheyenne. diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates_nat_and_anthro_ignitions/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates_nat_and_anthro_ignitions/user_nl_clm new file mode 100644 index 0000000000..7915bb63eb --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/Fates_nat_and_anthro_ignitions/user_nl_clm @@ -0,0 +1,3 @@ +fates_spitfire_mode = 4 +hist_nhtfrq = 0 +hist_mfilt = 1 diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_dec2050Start/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ciso_dec2050Start/include_user_mods new file mode 100644 index 0000000000..c9053f7b07 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_dec2050Start/include_user_mods @@ -0,0 +1,2 @@ +../ciso +../decStart diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_dec2050Start/shell_commands b/cime_config/testdefs/testmods_dirs/clm/ciso_dec2050Start/shell_commands new file mode 100755 index 0000000000..8bd67a0031 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_dec2050Start/shell_commands @@ -0,0 +1 @@ +./xmlchange RUN_STARTDATE=2050-12-30 diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_dec2050Start/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_dec2050Start/user_nl_clm new file mode 100644 index 0000000000..f5f43b3aff --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_dec2050Start/user_nl_clm @@ -0,0 +1,3 @@ +! Initial condition file from a coupled run at 2015 that will work with this setup.. + finidat = "$DIN_LOC_ROOT/cesm2_init/b.e21.BHIST.f09_g17.CMIP6-historical.010/2015-01-01/b.e21.BHIST.f09_g17.CMIP6-historical.010.clm2.r.2015-01-01-00000.nc" + use_init_interp = T diff --git a/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/shell_commands b/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/shell_commands new file mode 100644 index 0000000000..bc72045eeb --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm45cam6LndTuningMode/shell_commands @@ -0,0 +1,4 @@ +#!/bin/bash + +./xmlchange LND_TUNING_MODE="clm4_5_cam6.0" + diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode/shell_commands b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode/shell_commands new file mode 100644 index 0000000000..0ed374e279 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode/shell_commands @@ -0,0 +1,5 @@ +#!/bin/bash + +./xmlchange LND_TUNING_MODE="clm5_0_cam6.0" +./xmlchange ROF_NCPL='$ATM_NCPL' + diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_1979Start/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_1979Start/include_user_mods new file mode 100644 index 0000000000..1c3eece35d --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_1979Start/include_user_mods @@ -0,0 +1 @@ +../clm50cam6LndTuningMode diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_1979Start/shell_commands b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_1979Start/shell_commands new file mode 100644 index 0000000000..2aafcc1186 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_1979Start/shell_commands @@ -0,0 +1 @@ +./xmlchange RUN_STARTDATE=1979-01-01 diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_2013Start/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_2013Start/include_user_mods new file mode 100644 index 0000000000..1c3eece35d --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_2013Start/include_user_mods @@ -0,0 +1 @@ +../clm50cam6LndTuningMode diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_2013Start/shell_commands b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_2013Start/shell_commands new file mode 100644 index 0000000000..035842f982 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm50cam6LndTuningMode_2013Start/shell_commands @@ -0,0 +1 @@ +./xmlchange RUN_STARTDATE=2013-01-01 diff --git a/cime_config/testdefs/testmods_dirs/clm/decStart/user_nl_cism b/cime_config/testdefs/testmods_dirs/clm/decStart/user_nl_cism deleted file mode 100644 index 85f5789000..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/decStart/user_nl_cism +++ /dev/null @@ -1,9 +0,0 @@ -! The need for this is subtle. The problem is that this decStart testmod is used in short -! (multi-day) ERP tests, whose length is such that the end of the year occurs in the -! initial run but not in the restart run. Without setting history_option = 'coupler', this -! would mean that CISM outputs a history file in the initial run but not in the restart -! run, which causes the test to fail because the test system requires any component's -! final history file in one case to have a counterpart in the other case. Setting -! history_option = 'coupler' forces CISM to output a history file only at the end of the -! run. -history_option = 'coupler' diff --git a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README index 83fad7964a..03bc956b6f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README +++ b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README @@ -1 +1,4 @@ This test mod turns on extra diagnostic fields + +It also outputs an optional text file containing a table of the +history fields master list diff --git a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm index 512a426909..6d1167fc39 100644 --- a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm @@ -1 +1,2 @@ calc_human_stress_indices = 'ALL' +hist_master_list_file = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/fatesFire/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/fatesFire/user_nl_clm index e3a3b76d71..265f4c5406 100644 --- a/cime_config/testdefs/testmods_dirs/clm/fatesFire/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/fatesFire/user_nl_clm @@ -1,2 +1,2 @@ -use_fates_spitfire = .true. +fates_spitfire_mode = 1 diff --git a/cime_config/testdefs/testmods_dirs/clm/fire_emis/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/fire_emis/user_nl_clm index 3f5749e61f..027b17630e 100644 --- a/cime_config/testdefs/testmods_dirs/clm/fire_emis/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/fire_emis/user_nl_clm @@ -7,12 +7,11 @@ ! ! EXCEPTIONS: ! Set co2_ppmv with CCSM_CO2_PPMV option -! Set dtime with L_NCPL option ! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options ! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases ! (includes $inst_string for multi-ensemble cases) ! Set glc_grid with CISM_GRID option -! Set maxpatch_glcmec with GLC_NEC option +! Set maxpatch_glc with GLC_NEC option !---------------------------------------------------------------------------------- hist_mfilt = 1,30 diff --git a/cime_config/testdefs/testmods_dirs/clm/glcMEC_changeFlags/README b/cime_config/testdefs/testmods_dirs/clm/glcMEC_changeFlags/README index 2e8fcfc52e..5afac87d62 100644 --- a/cime_config/testdefs/testmods_dirs/clm/glcMEC_changeFlags/README +++ b/cime_config/testdefs/testmods_dirs/clm/glcMEC_changeFlags/README @@ -1,4 +1,10 @@ This testmods directory switches some glc_mec-related flags in CLM, in order to test different branches than are tested with the default options. -It also turns off the feedback from CISM to CLM, to test that option. +It also turns off the feedback from CISM to CLM, to test that +option. For this piece of the test to be useful, it should be used in a +test that uses CISM rather than SGLC, and ideally should be in a test +where CISM's glacier areas change within the test (though that last +piece may not be strictly necessary, since the relevant logic will still +be exercised in the first time step of the run even with a non-evolving +CISM). diff --git a/cime_config/testdefs/testmods_dirs/clm/glcMEC_changeFlags/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/glcMEC_changeFlags/include_user_mods index 1730b6b7cf..f076fe1cf5 100644 --- a/cime_config/testdefs/testmods_dirs/clm/glcMEC_changeFlags/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/glcMEC_changeFlags/include_user_mods @@ -1 +1 @@ -../glcMEC +../glcMEC_increase diff --git a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/README b/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/README deleted file mode 100644 index ec74e38b4c..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/README +++ /dev/null @@ -1,34 +0,0 @@ -This testmods directory is for running LII tests which compare the answers for a case where -initial condition interpolation is on (use_init_interp=T) to a case with it's off and ensures -they are exact. For the interpolated result to match uninterpolation, it needs to be a case that -essentially needs no interpolation so it's at the same resolution as the initial condition -file (finidat file). When surface datasets are changed, or the land-mask is changed, or an -important change is made to model physics (for example where new fields are added to the restart -file) -- you'll need to update the initial conditions file in this test (finidat file in -the user_nl_clm file). - -This testmods also turns off the glc two-way coupling. This is done so that -glacier areas are taken from the restart file rather than from -CISM. This is partly so that changes in CISM don't affect the test -results, but more importantly so that LII tests can pass even if CISM -changes. (GLC two-way coupling was off in the generation of the -initial conditions file used here, too.) (4-24-18: I *think* we'll be -able to turn two-way coupling on once -https://github.com/ESCOMP/ctsm/issues/340 is resolved, though I'm not -positive about that. However, if -https://github.com/ESMCI/cime/issues/2484 is done, then we'd need this -testmods to turn off comparison of cpl initial hist files if we have -two-way coupling on, since areas will differ in initialization between -the two cases.) - -To update the initial conditions (finidat) file for this test: - -(1) Run the LII test; the 'base' case should run to completion even if the -no_interp test fails. - -(2) Copy the finidat_interp_dest.nc file from the 'base' case to the inputdata -space. Rename this to be similar to the name of the file pointed to in this -test's user_nl_clm file, but with a new creation date. - -(3) Update this the user_nl_clm file in this directory to point to the new -finidat file. diff --git a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/include_user_mods deleted file mode 100644 index 1730b6b7cf..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../glcMEC diff --git a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/shell_commands b/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/shell_commands deleted file mode 100755 index 404b22b006..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/shell_commands +++ /dev/null @@ -1 +0,0 @@ -./xmlchange GLC_TWO_WAY_COUPLING=FALSE diff --git a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/user_nl_clm deleted file mode 100644 index c269a24911..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/glcMEC_spunup_1way/user_nl_clm +++ /dev/null @@ -1,5 +0,0 @@ -! See more notes in the README file in this directory and in the comments in the test list. -! -! Initial condition file at the desired configuration to run, so can verify that interpolating from it gives the same result -! Note that this was generated with GLC_TWO_WAY_COUPLING=FALSE -finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_map/clmi.I2000Clm50BgcCrop.2000-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c180306.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/ignor_warn_cropMonthOutputColdStart/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ignor_warn_cropMonthOutputColdStart/include_user_mods new file mode 100644 index 0000000000..5c73adaa4a --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ignor_warn_cropMonthOutputColdStart/include_user_mods @@ -0,0 +1,3 @@ +../_includes/ignore_warnings +../coldStart +../cropMonthOutput diff --git a/cime_config/testdefs/testmods_dirs/clm/lilac/README b/cime_config/testdefs/testmods_dirs/clm/lilac/README new file mode 100644 index 0000000000..049407e30b --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/lilac/README @@ -0,0 +1,4 @@ +This testmods directory inherits from the directory containing the +user_nl_ctsm file that is staged for users by the build_ctsm +script. Thus, tests using this testmod will include the settings that +users get by default in LILAC configurations. diff --git a/cime_config/testdefs/testmods_dirs/clm/lilac/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/lilac/include_user_mods new file mode 100644 index 0000000000..7b5f17cf20 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/lilac/include_user_mods @@ -0,0 +1 @@ +../../../../usermods_dirs/lilac diff --git a/cime_config/testdefs/testmods_dirs/clm/lilac/user_nl_ctsm b/cime_config/testdefs/testmods_dirs/clm/lilac/user_nl_ctsm new file mode 100644 index 0000000000..740014baa9 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/lilac/user_nl_ctsm @@ -0,0 +1,3 @@ + hist_ndens = 1,1,1,1,1,1 + hist_nhtfrq(1) = -24 + hist_mfilt(1) = 1 diff --git a/cime_config/testdefs/testmods_dirs/clm/nlevgrnd_small/README b/cime_config/testdefs/testmods_dirs/clm/nlevgrnd_small/README new file mode 100644 index 0000000000..3be0d15bfc --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/nlevgrnd_small/README @@ -0,0 +1,13 @@ +The main point of this testmod is to exercise the case where nlevgrnd < +nlevurb (connected with +https://github.com/ESCOMP/CTSM/issues/674). If/when we have an +out-of-the-box configuration with nlevgrnd < nlevurb (such as the NWP +configuration once nlevurb = 10 is the standard) then we can remove this +test. + +A secondary consideration is having a test that interpolates from a +configuration with nlevgrnd > nlevurb onto one with lower nlevgrnd and +nlevgrnd < nlevurb. But I don't think it's critical to maintain this +test just for that purpose - e.g., if we start having an out-of-the-box +configuration with nlevgrnd < nlevurb but where the finidat file also +has nlevgrnd < nlevurb, then I feel it will be okay to remove this test. diff --git a/cime_config/testdefs/testmods_dirs/clm/nlevgrnd_small/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/nlevgrnd_small/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/nlevgrnd_small/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/nlevgrnd_small/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/nlevgrnd_small/user_nl_clm new file mode 100644 index 0000000000..d7e1f9bbc2 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/nlevgrnd_small/user_nl_clm @@ -0,0 +1,8 @@ +! The following results in nlevsoi = 3, nlevgrnd = 4; together with the standard setting +! of nlevurb = 5, this results in nlevgrnd < nlevurb, which is what we particularly want +! to test here. +soil_layerstruct_userdefined = 0.2, 0.4, 0.8, 1.6 +soil_layerstruct_userdefined_nlevsoi = 3 + +! Need to make sure interpolation is on because of the change in nlevgrnd relative to finidat +use_init_interp = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/prescribed/README b/cime_config/testdefs/testmods_dirs/clm/prescribed/README new file mode 100644 index 0000000000..4c0c56bb8c --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/prescribed/README @@ -0,0 +1,7 @@ +This test-mods turns on using the prescribed moisture streams file +(rather than prognosing it in the model). And it turns on the lai streams +to test that's working as well. + +The only resolution we currently have data for is f09, so this must be done +at 0.9x1.25 resolution. And it makes the most sense for present day and +Satellite Phenology (Sp). diff --git a/cime_config/testdefs/testmods_dirs/clm/prescribed/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/prescribed/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/prescribed/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/prescribed/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/prescribed/user_nl_clm new file mode 100644 index 0000000000..c2290397dd --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/prescribed/user_nl_clm @@ -0,0 +1,6 @@ + use_soil_moisture_streams = .true. + use_lai_streams = .true. + hist_fincl1 += 'H2OSOI_PRESCRIBED_GRC' + soilm_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare to input dataset + lai_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare more directly to input dataset + soilm_ignore_data_if_missing = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/pts/shell_commands b/cime_config/testdefs/testmods_dirs/clm/pts/shell_commands index ad140e45e1..1613d28b25 100644 --- a/cime_config/testdefs/testmods_dirs/clm/pts/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/pts/shell_commands @@ -22,3 +22,5 @@ ./xmlchange NTASKS_ROF=1 ./xmlchange NTASKS_WAV=1 ./xmlchange NTASKS_ESP=1 +./xmlchange MOSART_MODE=NULL +./xmlchange RTM_MODE=NULL diff --git a/cime_config/testdefs/testmods_dirs/clm/run_self_tests/README b/cime_config/testdefs/testmods_dirs/clm/run_self_tests/README new file mode 100644 index 0000000000..938dffbe6f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/run_self_tests/README @@ -0,0 +1,5 @@ +The purpose of this testmod directory is to trigger the runtime +self-tests. This runs a suite of unit/integration tests. + +We use cold start so that we can get through initialization faster, +since how we initialize the model is unimportant for these self-tests. diff --git a/cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands b/cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands new file mode 100644 index 0000000000..a66f52f6fd --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands @@ -0,0 +1,3 @@ +#!/bin/bash +./xmlchange CLM_FORCE_COLDSTART="on" + diff --git a/cime_config/testdefs/testmods_dirs/clm/run_self_tests/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/run_self_tests/user_nl_clm new file mode 100644 index 0000000000..6187386336 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/run_self_tests/user_nl_clm @@ -0,0 +1 @@ +for_testing_run_ncdiopio_tests = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/snowlayers_3_monthly/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/snowlayers_3_monthly/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm new file mode 100644 index 0000000000..b85d0ba6c1 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/smallville_dynlakes_monthly/user_nl_clm @@ -0,0 +1,12 @@ +do_transient_lakes = .true. + +! This file was created with the following command: +! ncap2 -s 'PCT_LAKE=array(0.0,0.0,PCT_CROP); PCT_LAKE={0.,50.,25.,25.,25.,25.}; HASLAKE=array(1.,1.,AREA); PCT_CROP=array(0.0,0.0,PCT_LAKE); PCT_CROP={0.,25.,12.,12.,12.,12.}' landuse.timeseries_1x1_smallvilleIA_hist_78pfts_simyr1850-1855_c160127.nc landuse.timeseries_1x1_smallvilleIA_hist_78pfts_simyr1850-1855_dynLakes_c200928.nc +! Key points are that lake area starts as 0, increases after the first year, then decreases after the second year. +! PCT_CROP is also changed so that PCT_LAKE + PCT_CROP <= 100. (Here, PCT_CROP increases and decreases at the same time as PCT_LAKE in order to exercise the simultaneous increase or decrease of two landunits, but that isn't a critical part of this test.) +! Note that the use of this file means that this testmod can only be used with the 1x1_smallvilleIA grid. +flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/landuse.timeseries_1x1_smallvilleIA_hist_78pfts_simyr1850-1855_dynLakes_c200928.nc' + +! BUG(wjs, 2020-09-25, ESCOMP/CTSM#43) Dynamic lakes don't work when methane is active, +! so for now disable methane for this test. +use_lch4 = .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/snowlayers_3_monthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/snowlayers_3_monthly/user_nl_clm deleted file mode 100644 index e7500fff58..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/snowlayers_3_monthly/user_nl_clm +++ /dev/null @@ -1,4 +0,0 @@ -nlevsno = 3 - -! Need to set use_init_interp because initial conditions file has 5 snow layers -use_init_interp = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/shell_commands b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/shell_commands index 09dc866921..5e9068895c 100755 --- a/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline/shell_commands @@ -1,2 +1,5 @@ -./xmlchange USE_ESMF_LIB=TRUE,ATM_NCPL=288,CALENDAR=GREGORIAN +./xmlchange USE_ESMF_LIB=TRUE,ATM_NCPL=288,CALENDAR=GREGORIAN,ROF_NCPL='$ATM_NCPL',LND_TUNING_MODE="clm5_0_cam6.0" +./xmlchange CLM_BLDNML_OPTS="-megan -drydep" --append +./xmlchange RUN_STARTDATE=1979-01-01 +./xmlchange ROF_NCPL='$ATM_NCPL' diff --git a/cime_config/testdefs/testmods_dirs/clm/waccmx_offline2005Start/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline2005Start/include_user_mods new file mode 100644 index 0000000000..e46fc10b2e --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline2005Start/include_user_mods @@ -0,0 +1 @@ +../waccmx_offline diff --git a/cime_config/testdefs/testmods_dirs/clm/waccmx_offline2005Start/shell_commands b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline2005Start/shell_commands new file mode 100755 index 0000000000..b926b0dbb1 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/waccmx_offline2005Start/shell_commands @@ -0,0 +1 @@ +./xmlchange RUN_STARTDATE=2005-01-01 diff --git a/cime_config/user_nl_clm b/cime_config/user_nl_clm index cfc5c71308..47865671a2 100644 --- a/cime_config/user_nl_clm +++ b/cime_config/user_nl_clm @@ -9,13 +9,12 @@ ! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting ! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting ! Set co2_ppmv with CCSM_CO2_PPMV option -! Set dtime with L_NCPL option ! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options ! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases ! (includes $inst_string for multi-ensemble cases) ! or with CLM_FORCE_COLDSTART to do a cold start ! or set it with an explicit filename here. -! Set maxpatch_glcmec with GLC_NEC option +! Set maxpatch_glc with GLC_NEC option ! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable !---------------------------------------------------------------------------------- diff --git a/cime_config/usermods_dirs/_includes/output_base/user_nl_clm b/cime_config/usermods_dirs/_includes/output_base/user_nl_clm index 52254161ef..509e0436d3 100644 --- a/cime_config/usermods_dirs/_includes/output_base/user_nl_clm +++ b/cime_config/usermods_dirs/_includes/output_base/user_nl_clm @@ -9,11 +9,10 @@ ! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting ! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting ! Set co2_ppmv with CCSM_CO2_PPMV option -! Set dtime with L_NCPL option ! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options ! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases ! (includes $inst_string for multi-ensemble cases) -! Set maxpatch_glcmec with GLC_NEC option +! Set maxpatch_glc with GLC_NEC option ! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable !---------------------------------------------------------------------------------- diff --git a/cime_config/usermods_dirs/cmip6_waccm_deck/shell_commands b/cime_config/usermods_dirs/cmip6_waccm_deck/shell_commands new file mode 100755 index 0000000000..5b872fb7bc --- /dev/null +++ b/cime_config/usermods_dirs/cmip6_waccm_deck/shell_commands @@ -0,0 +1,3 @@ +#!/bin/bash +# Turn ignore-warnings on, so won't abort on missing ndep file, as WACCM should provide it +./xmlchange --append CLM_BLDNML_OPTS="--ignore_warnings" diff --git a/cime_config/usermods_dirs/cmip6_waccm_nociso_deck/README b/cime_config/usermods_dirs/cmip6_waccm_nociso_deck/README new file mode 100644 index 0000000000..79cbbeefe8 --- /dev/null +++ b/cime_config/usermods_dirs/cmip6_waccm_nociso_deck/README @@ -0,0 +1,17 @@ +WACCM DECK runs should be configured similarly to CAM DECK runs, but +without virtual elevation classes over Antarctica. At 2-degree we ++also decided to NOT turn on Carbon isotopes. + +(2018-10-22) In discussions between Bill Sacks and Bill Lipscomb: We +have decided NOT to turn on virtual Antarctica columns for any of the +WACCM simulations (DECK or ScenarioMIP): these weren't turned on in the +WACCM PI-Control or historical runs (either by accident or +intentionally: I'm not sure which, and can't find emails describing this +decision). Since this setting needs to be compatible with the REFCASE, +it's simpler if we keep it consistent for all WACCM runs, and there +seems to be only limited value in turning on virtual Antarctica columns +in the remaining WACCM runs (1% CO2, 4xCO2 and ScenarioMIP) when they +weren't on in the WACCM PI-Control or Historical runs. And Mike Mills +says that there won't be any more sharing of initial conditions between +CAM and WACCM CMIP6 runs, so it's fine if the two sets remain different +in this respect. diff --git a/cime_config/usermods_dirs/cmip6_waccm_nociso_deck/include_user_mods b/cime_config/usermods_dirs/cmip6_waccm_nociso_deck/include_user_mods new file mode 100644 index 0000000000..64c3f6f670 --- /dev/null +++ b/cime_config/usermods_dirs/cmip6_waccm_nociso_deck/include_user_mods @@ -0,0 +1,2 @@ +../_includes/cmip6_glaciers_cplhist +../output_crop diff --git a/cime_config/usermods_dirs/lilac/README b/cime_config/usermods_dirs/lilac/README new file mode 100644 index 0000000000..c87aee3af4 --- /dev/null +++ b/cime_config/usermods_dirs/lilac/README @@ -0,0 +1,2 @@ +The user_nl_ctsm file in this directory is copied to the runtime_inputs +directory when setting up a LILAC build using build_ctsm. diff --git a/cime_config/usermods_dirs/lilac/user_nl_ctsm b/cime_config/usermods_dirs/lilac/user_nl_ctsm new file mode 100644 index 0000000000..5ff40dbff8 --- /dev/null +++ b/cime_config/usermods_dirs/lilac/user_nl_ctsm @@ -0,0 +1,17 @@ +!---------------------------------------------------------------------------------- +! Users should add all user specific namelist changes below in the form of +! namelist_var = new_namelist_value +! +! (Exceptions are settings that are set in ctsm.cfg.) +!---------------------------------------------------------------------------------- + +! The following hist options set up three output streams from CTSM. The first (h0 files) +! is monthly and contains all of CTSM's default output variables. The second (h1 files) is +! daily, with a small list of fields given by hist_fincl2. The third (h2 files) is hourly, +! with a small list of fields given by hist_fincl3. You can change these settings however +! you'd like. +hist_mfilt = 1,1,24 +hist_nhtfrq = 0,-24,-1 +hist_fincl2 = 'SNO_LIQH2O','SNO_ICE','SNOTTOPL','SNOW_DEPTH','TSA','RAIN','SNOW','Q2M','RH2M','FSH','FCTR','FCEV','FGEV','FSDS','FSR','FIRA','BTRAN','SOILWATER_10CM','TSOI_10CM','H2OSOI','TSOI' +hist_fincl3 = 'SNO_LIQH2O','SNO_ICE','SNOTTOPL','SNOW_DEPTH','TSA','RAIN','SNOW','Q2M','RH2M','FSH','FCTR','FCEV','FGEV','FSDS','FSR','FIRA','BTRAN','SOILWATER_10CM','TSOI_10CM','H2OSOI','TSOI' + diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template index f5474f33a8..f72764d0f4 100644 --- a/doc/.ChangeLog_template +++ b/doc/.ChangeLog_template @@ -4,23 +4,12 @@ Originator(s): Date: One-line Summary: -Purpose of changes ------------------- +Purpose and description of changes +---------------------------------- [Fill this in with details] -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): [If none, remove this line] -CIME Issues fixed (include issue #): [If none, remove this line] - -Known bugs introduced in this tag (include github issue ID): [If none, remove this line] - -Known bugs found since the previous tag (include github issue ID): [If none, remove this line] - - Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -29,14 +18,31 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 [ ] ctsm5_0-nwp [ ] clm4_5 + +Bugs fixed or introduced +------------------------ +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +Issues fixed (include CTSM Issue #): + +CIME Issues fixed (include issue #): + +Known bugs introduced in this tag (include issue #): + +Known bugs found since the previous tag (include issue #): + + Notes of particular relevance for users --------------------------------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] Caveats for users (e.g., need to interpolate initial conditions): @@ -46,55 +52,78 @@ Changes made to namelist defaults (e.g., changed parameter values): Changes to the datasets (e.g., parameter, surface or initial files): -Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] +Substantial timing or memory changes: +[For timing changes, you should at least check the PFS test in the test + suite, whether or not you expect timing changes: ensure that its run + time has not increased significantly relative to the baseline.] + -Notes of particular relevance for developers: (including Code reviews and testing) +Notes of particular relevance for developers: --------------------------------------------- NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +[Remove any lines that don't apply. Remove entire section if nothing applies.] Caveats for developers (e.g., code that is duplicated that requires double maintenance): Changes to tests or testing: -Code reviewed by: +Testing summary: +---------------- +[... Remove before making master tag. -CTSM testing: +Nearly all CTSM tags should undergo 'regular' (aux_clm) testing. +However, it occasionally makes sense to do more or less system testing; +here is guidance on different available levels of system testing: + a) no system testing (for use when the only changes are ones that + have absolutely no impact on system runs; this + includes documentation-only tags, tags that + just change the tools or some python code that + does not impact system runs, etc.) + b) minimal (for use in rare cases where only a small change with + known behavior is added ... eg. a minor bug fix. This + might be to just run the "short" test list, or to run + a single test. Whatever makes sense for the particular case.) + c) regular (regular tests on normal machines if CTSM source is modified) + d) release (regular tests plus the fates, ctsm_sci, mosart and rtm test lists + and normally all of the ancillary tests (build-namelist, python, ptclm, etc.) + would be run as well) -[... Remove before making master tag. Available test levels: +In addition, various other tests of the tools, python and perl +infrastructure should be run when appropriate, as described below. - a) regular (must be run before handing off a tag to SEs and must be run - before committing a tag) - b) build_namelist (if namelists and/or build_system changed)) - c) tools (only if tools are modified and no CTSM source is modified) - d) short (for use during development and in rare cases where only a small - change with known behavior is added ... eg. a minor bug fix) - e) doc (no source testing required) +...] -... ] +[Remove any lines that don't apply.] - [PASS means all tests PASS and OK means tests PASS other than expected fails.] + [PASS means all tests PASS; OK means tests PASS other than expected fails.] - build-namelist tests: + build-namelist tests (if CLMBuildNamelist.pm has changed): cheyenne - - tools-tests (test/tools): + tools-tests (test/tools) (if tools have been changed): cheyenne - - PTCLM testing (tools/shared/PTCLM/test): + PTCLM testing (tools/shared/PTCLM/test): (if cime or cime_config are changed) + (PTCLM is being deprecated, so we only expect this to be done on occasion) cheyenne - - python testing (see instructions in python/README.md; document testing done): + python testing (if python code has changed; see instructions in python/README.md; document testing done): (any machine) - - regular tests (aux_clm): + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): cheyenne ---- izumi ------- + + fates tests: + cheyenne ---- + + any other testing (give details below): If the tag used for baseline comparisons was NOT the previous tag, note that here: @@ -104,8 +133,9 @@ Answer changes Changes answers relative to baseline: - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): + [ If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section). + And always remove these three lines and parts that don't apply. ] Summarize any changes to answers, i.e., - what code configurations: @@ -122,8 +152,9 @@ Changes answers relative to baseline: URL for LMWG diagnostics output used to validate new climate: -Detailed list of changes ------------------------- +Other details +------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): diff --git a/doc/.release-ChangeLog_template b/doc/.release-ChangeLog_template new file mode 100644 index 0000000000..aca4c9440c --- /dev/null +++ b/doc/.release-ChangeLog_template @@ -0,0 +1,101 @@ +=============================================================== +Tag name: +Originator(s): +Date: +One-line Summary: + +Purpose of this version: +------------------------ + +[Fill this in with details] + + +CTSM Master Tag This Corresponds To: + +Summary of changes: +------------------- + +Issues fixed (include CTSM Issue #): [If none, remove this line] +CIME Issues fixed (include issue #): [If none, remove this line] + +Science changes since: + +Software changes since: + +Changes to User Interface since: + +Testing: +-------- + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + unit-tests (components/clm/src): + + cheyenne - + izumi ---- + + tools-tests (components/clm/test/tools): + + cheyenne - + izumi ---- + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - + izumi ---- + + regular tests (aux_clm): + + cheyenne_intel ---- + cheyenne_gnu ------ + izumi_nag --------- + izumi_pgi --------- + izumi_intel ------- + + regular tests (prealpha): + + cheyenne_intel - + cheyenne_gnu --- + izumi_nag ------ + + regular tests (prebeta): + + cheyenne_intel - + cheyenne_gnu --- + izumi_nag ------ + +Summary of Answer changes: +------------------------- + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + +Changes answers relative to baseline: + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + + Summarize any changes to answers, i.e., + - what code configurations: + - what platforms/compilers: + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + URL for LMWG diagnostics output for new climate: + + Will new REFCASES need to be made for cesm and/or CAM?: No + (This will likely be true if the LII tests failed) + +Detailed list of changes: +------------------------ + +Externals being used: + +CTSM Tag versions pulled over from master development branch: + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== diff --git a/doc/ChangeLog b/doc/ChangeLog index 431d21a68d..fbdd413d1e 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,96 +1,93 @@ =============================================================== -Tag name: ctsm1.0.dev082 -Originator(s): oleson (Keith Oleson) -Date: Sat Feb 1 09:28:41 MST 2020 -One-line Summary: Rename variables to avoid confusion; fix QSNOEVAP diagnostic - -Purpose of changes ------------------- - -Renamed variables as discussed in ESCOMP/ctsm#118 throughout the code. - -Also made a couple of minor changes to fix a couple of potential -problems with these variables as described in the branch commit logs. - -Tested for bfb before changing the history field variables -themselves. These changes are all bfb (with the exception of QSNOEVAP) -for a 1 month global 2deg simulation, but may not be bfb under all -conditions. QSNOEVAP is not bfb because I've added in qflx_ev_snow for -lakes. - -Also, update cime slightly with a fix for izumi machine updates +Tag name: ctsm5.1.dev038 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Tue Apr 27 23:51:04 MDT 2021 +One-line Summary: Bring in minor changes from the cesm2.2.0 release tag -Bugs fixed or introduced ------------------------- +Purpose and description of changes +---------------------------------- -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#118 +Bring in the changes that went in the cesm2.2.0 release tag. +Get the CLM offline tools working as well as the tools testing. +Remove the finidat file for FATES as it was shown to be problematic +in the release testing. Significant changes to scientifically-supported configurations -------------------------------------------------------------- -Does this tag change answers significantly for any of the following physics configurations? +Does this tag change answers significantly for any of the following physics configurations? No (Details of any changes will be given in the "Answer changes" section below.) [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 [ ] ctsm5_0-nwp [ ] clm4_5 -Notes of particular relevance for users ---------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): none +Bugs fixed or introduced +------------------------ -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none +Issues fixed (include CTSM Issue #): + Fixes #1134 mkmapdata.sh is not working + Fixes #1128 missing compset -Changes made to namelist defaults (e.g., changed parameter values): none +Known bugs found since the previous tag (include issue #): + #1358 -- C isotope fields can have garbage values starting in ctsm5.1.dev008 + #1357 -- No output values in large lake gridcells in 0.5° resolution (hcru_hcru) -Changes to the datasets (e.g., parameter, surface or initial files): none -Substantial timing or memory changes: none expected (not checked) +Notes of particular relevance for users +--------------------------------------- -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + Add a new compset alias: I2000Clm50FatesCruRsGs -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none +Changes to the datasets (e.g., parameter, surface or initial files): + Remove finidat file setting for FATES becaues it sometimes caused problems. -Changes to tests or testing: none +Notes of particular relevance for developers: +--------------------------------------------- -Code reviewed by: Bill Sacks +Changes to tests or testing: + A couple of the tools tests were changed -CTSM testing: +Testing summary: regular +---------------- - [PASS means all tests PASS and OK means tests PASS other than expected fails.] + [PASS means all tests PASS; OK means tests PASS other than expected fails.] - build-namelist tests: + build-namelist tests (if CLMBuildNamelist.pm has changed): - cheyenne - not run + cheyenne - PASS - tools-tests (test/tools): + tools-tests (test/tools) (if tools have been changed): - cheyenne - not run + cheyenne - PASS - PTCLM testing (tools/shared/PTCLM/test): + PTCLM testing (tools/shared/PTCLM/test): (if cime or cime_config are changed) + (PTCLM is being deprecated, so we only expect this to be done on occasion) - cheyenne - not run + cheyenne - OK - python testing (see instructions in python/README.md; document testing done): + python testing (if python code has changed; see instructions in python/README.md; document testing done): - (any machine) - not run + cheyenne -- PASS - regular tests (aux_clm): + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- ok - izumi ------- ok + cheyenne ---- OK + izumi ------- OK + + any other testing (give details below): - ok: tests pass, answer changes in QSNOEVAP but nothing else (as expected) + Ran mkmapdata.sh for 1-deg maps If the tag used for baseline comparisons was NOT the previous tag, note that here: @@ -98,60 +95,33 @@ If the tag used for baseline comparisons was NOT the previous tag, note that her Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - Larger than roundoff, but only in the diagnostic field QSNOEVAP - - Possibility of other answer changes in rare circumstances, not - observed in testing. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A +Changes answers relative to baseline: No bit-for-bit - URL for LMWG diagnostics output used to validate new climate: N/A - +Other details +------------- -Detailed list of changes ------------------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): PTCLM + PTCLM to PTCLM2_20200902 -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- cime: cime5.8.15 -> branch_tags/cime5.8.15_a01 - Minor update for izumi machine changes +Pull Requests that document the changes (include PR ids): #1179 +(https://github.com/ESCOMP/ctsm/pull) -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/CTSM/pull/893 + #1179 -- Bring in changes from release-cesm2.2.01 to main-development =============================================================== =============================================================== -Tag name: ctsm1.0.dev081 -Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) -Date: Mon Jan 13 15:37:07 MST 2020 -One-line Summary: Speed up restart writes - -Purpose of changes ------------------- - - E3SM#3163 made some changes to speed up restart writes. I use E3SM#3163 - function GetGlobalIndexArray in place of GetGlobalIndex so as to get - global indices by array rather than looping over every element. +Tag name: ctsm5.1.dev037 +Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310) +Date: Fri Apr 23 10:06:32 MDT 2021 +One-line Summary: Correct vertical interpolation in init_interp when soil thicknesses change +Purpose and description of changes +---------------------------------- -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #801 + To correct how init_interp handles soil variables with units of kg/m2 or mm + or mm/s (generally speaking so-called extensive properties), we now add DZSOI + and a scale_by_thickness flag to restart files. In init_interp we use these to + scale the vertical interpolation by soil layer thickness. Significant changes to scientifically-supported configurations @@ -162,105 +132,103 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: Limited testing did not show substantial timing changes +[X] clm5_1 -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none +[X] clm5_0 -Changes to tests or testing: none +[X] ctsm5_0-nwp -Code reviewed by: - @billsacks - @bishtgautam +[X] clm4_5 -CTSM testing: - [PASS means all tests PASS and OK means tests PASS other than expected fails.] +Bugs fixed or introduced +------------------------ +[Remove any lines that don't apply. Remove entire section if nothing applies.] - build-namelist tests: +Issues fixed (include CTSM Issue #): #1298 - cheyenne - +Notes of particular relevance for users +--------------------------------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] - tools-tests (test/tools): +Caveats for users (e.g., need to interpolate initial conditions): + For H2OSOI_LIQ, H2OSOI_ICE, SMP, and HK, from now on init_interp interpolates + from the soil profile in finidat to the soil profile in the model by + scaling these variables by dzsoi (layer thickness). This makes the vertical + interpolation of these variables more accurate. Users need not do anything. - cheyenne - +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): - PTCLM testing (tools/shared/PTCLM/test): +Changes to the datasets (e.g., parameter, surface or initial files): + From now on newly generated finidat files will contain the scale_by_thickness + flag and DZSOI for use by the new code. For backwards compatibility, the code + handles preexisting finidat files by deriving dzsoi from the node depths for + the four variables listed above. - cheyenne - +Notes of particular relevance for developers: +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +[Remove any lines that don't apply. Remove entire section if nothing applies.] - python testing (see instructions in python/README.md; document testing done): +Changes to tests or testing: + Added two unit tests to confirm that the modified vertical interpolation + behaves as expected. - (any machine) - - regular tests (aux_clm): +Testing summary: +---------------- +[Remove any lines that don't apply.] - cheyenne ---- OK - izumi ------- PASS + [PASS means all tests PASS; OK means tests PASS other than expected fails.] -If the tag used for baseline comparisons was NOT the previous tag, note that here: + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + cheyenne ---- OK + izumi ------- OK + + any other testing (give details below): + Unit tests PASS Answer changes -------------- -Changes answers relative to baseline: - No +Changes answers relative to baseline: Yes - @billsacks recommended running a global test in the branch vs. in master (i.e. - with vs. without the code mods) to compare restart files because the test suite - does not compare restart files and an error in the subgrid indices on the - restart file might go undetected. I ran this test: - ERS_D_Ld6.f10_f10_musgs.I1850Clm45BgcCrop.cheyenne_intel.clm-clm50CMIP6frc - and got identical values for all variables in the two restart files. + [ If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section). + And always remove these three lines and parts that don't apply. ] -Detailed list of changes ------------------------- + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change: larger than roundoff/same climate -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + scale_by_thickness=.true. for the four variables that require it (listed + above). This causes answers to change for all tests in the test suite that + interpolate from the soil profile found in finidat to a differing soil profile + used by the model. + +Other details +------------- Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/ctsm/pull/880 + https://github.com/ESCOMP/CTSM/pull/1301 =============================================================== =============================================================== -Tag name: ctsm1.0.dev080 -Originator(s): sacks (Bill Sacks) -Date: Mon Dec 2 12:23:22 MST 2019 -One-line Summary: Update externals, minor fixes to work with latest cime, get nuopc cap working - -Purpose of changes ------------------- +Tag name: ctsm5.1.dev036 +Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049) +Date: Wed Apr 21 14:50:19 MDT 2021 +One-line Summary: FATES tag update and snow occlusion of LAI fix -(1) Update to latest version of externals. This includes a significant - cime update. - -(2) Minor fixes to get things working with the latest version of cime. - -(3) Fix from Mariana Vertenstein to get NUOPC cap working, fixes to - externals cfg files to allow running NUOPC cases out of the box, and - add a NUOPC test. +Purpose and description of changes +---------------------------------- +This tag updates the way in which fates is called during restarts to appropriately +handle the fates-side snow occlusion code. Additionally, this update points to the +most recent fates tag, which includes a number of fates science updates (including +the snow occlusion fix) and fates-side bug fixes (see below for list of issues +addressed). Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -270,133 +238,118 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 [ ] ctsm5_0-nwp [ ] clm4_5 -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): -CIME update brings in some changes, e.g., in mapping files; otherwise, none. - -Substantial timing or memory changes: not investigated - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: -- Added NUOPC test: - SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default - -Code reviewed by: self - - -CTSM testing: - [PASS means all tests PASS and OK means tests PASS other than expected fails.] +Bugs fixed or introduced +------------------------ - build-namelist tests: +Issues fixed (include CTSM Issue #): + #1293 -- Update FATES on CTSM main-dev + NGEET/fates#359 -- ground snow is not occluding lai profile + NGEET/fates#709 -- Error Check issue in EDPatchDynamicsMod.F90: spawn_patches() causes problem with logging module + NGEET/fates#725 -- declaration of the prt pointer + NGEET/fates#713 -- Changes associated with patch fraction burnt + NGEET/fates#473 -- Update FIRE_AREA long name units + NGEET/fates#575 -- Clean up NaN and zeroing of fire variables in Patch and Cohort Dynamics - cheyenne - not run +Known bugs found since the previous tag (include issue #): + #1338 -- Floating point exception in fates gnu compiler regression test with ctsm5.1.dev027 - tools-tests (test/tools): +Testing summary: regular +---------------- - cheyenne - not run + [PASS means all tests PASS; OK means tests PASS other than expected fails.] - PTCLM testing (tools/shared/PTCLM/test): + build-namelist tests (if CLMBuildNamelist.pm has changed): - cheyenne - not run + cheyenne - PASS - python testing (see instructions in python/README.md; document testing done): + python testing (if python code has changed; see instructions in python/README.md; document testing done): - (any machine) - not run + cheyenne - PASS - regular tests (aux_clm): + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): cheyenne ---- ok izumi ------- ok + + ok: All non-fates testmods PASS b4b. Fates testmods have DIFF as expected due to update of fates science tag. - ok means tests passed, some baseline comparisons failed as expected - - Note: Most testing was done on ad1ad752; then, from the latest - version, I ran a 2-test test list of: - - SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default - - SMS_D.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default - - In addition to verifying that the above tests passed, I also - inspected the sharedlib build area to verify that separate builds of - the clm library were done for mct and nuopc. + fates tests: + cheyenne ---- ok -If the tag used for baseline comparisons was NOT the previous tag, note that here: -- cheyenne tests compared against ctsm1.0.dev078, since cheyenne testing -was not run on ctsm1.0.dev079. + ok: NLCOMP failures due to clm50_param file update relative to ctsm tag used on the last fates baseline. + fates baseline: fates-sci.1.44.1_api.14.2.0-ctsm5.1.dev033-C30ca1849-F6065b9a2 Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): +Changes answers relative to baseline: Yes, only for fates Summarize any changes to answers, i.e., - - what code configurations: Cases at f10 resolution + - what code configurations: all fates - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Larger than roundoff, but probably same climate - - Answer changes are due to https://github.com/esmci/cime/pull/3186 + - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A + than roundoff? + - fates-side review of expected differences for all PRs that changed answers (2 science updates + and 2 bug fixes) -Detailed list of changes ------------------------- +Other details +------------- List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- cime: branch_tags/cime5.8.3_chint17-05 -> cime5.8.15 -- rtm: rtm1_0_68 -> rtm1_0_70 -- mosart: mosart1_0_34 -> mosart1_0_35 -- cmeps: 471ac52 -> 181ff1ed9dfb279e619e8a2173f43baf7bf1dce3 - Also, note that cmeps is now checked out automatically + fates: sci.1.43.2_api.14.2.0 -> sci.1.45.0_api.15.0.0 Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/CTSM/pull/845 +(https://github.com/ESCOMP/ctsm/pull) + - https://github.com/ESCOMP/CTSM/pull/1324 + - https://github.com/NGEET/fates/pull/734 + =============================================================== =============================================================== -Tag name: ctsm1.0.dev079 +Tag name: ctsm5.1.dev035 Originator(s): sacks (Bill Sacks) -Date: Mon Nov 4 14:41:41 MST 2019 -One-line Summary: Change a few uses of shr_kind +Date: Tue Apr 20 10:45:25 MDT 2021 +One-line Summary: Misc bfb enhancements and fixes -Purpose of changes ------------------- +Purpose and description of changes +---------------------------------- + +(1) If CISM is running over Antarctica, use virtual glacier columns over + Antarctica + +(2) Remove "mec" from some glacier/ice variable names (it is misleading + to have "mec" in variable names when the ice landunit can actually + have multiple columns *or* a single column) (ESCOMP/CTSM#1294) + +(3) Add history file metadata on each variable's l2g_scale_type (adds a + landunit_mask attribute) (ESCOMP/CTSM#1343) + +(4) Use python3 in more shebang lines - needed to run python unit tests + on cheyenne -Change a few uses of shr_kind to work with latest cime. These changes -are from Mariana Vertenstein. +(5) New compset naming for IG compsets (ESCOMP/CTSM#1289) +(6) Remove calculation of fun_cost_fix that is overwritten + (ESCOMP/CTSM#1115) + +(7) Bypass grid-level water mass check when fates hydro is active + (ESCOMP/CTSM#1334) + +(8) Remove some dead code (ESCOMP/CTSM#1333) Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -406,122 +359,89 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 [ ] ctsm5_0-nwp [ ] clm4_5 + +Bugs fixed or introduced +------------------------ +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1115 (overwrite fun_cost_fix) +- Resolves ESCOMP/CTSM#1289 (After updating to cism2_1_76 or later, + change compsets involving CISM) +- Resolves ESCOMP/CTSM#1294 (Replace istice_mec with istice) +- Resolves ESCOMP/CTSM#1333 (Remove some dead code) +- Resolves ESCOMP/CTSM#1343 (Add landunit_mask (formerly l2g_scale_type) + metadata to history file) + Notes of particular relevance for users --------------------------------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] -Caveats for users (e.g., need to interpolate initial conditions): none +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- Renamed maxpatch_glcmec to maxpatch_glc -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none +Substantial timing or memory changes: +- Increase in land initialization time in the PFS test + (PFS_Ld20.f09_g17.I2000Clm50BgcCrop.cheyenne_intel); this is probably + due to machine variability because I don't think any of the changes in + this tag would have any significant impact on model initialization + time. -Changes made to namelist defaults (e.g., changed parameter values): none -Changes to the datasets (e.g., parameter, surface or initial files): none +Testing summary: +---------------- -Substantial timing or memory changes: none + build-namelist tests (if CLMBuildNamelist.pm has changed): -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + cheyenne - ok (tests pass, namelists differ as expected) -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + python testing (if python code has changed; see instructions in python/README.md; document testing done): -Changes to tests or testing: none + (any machine) - pass (ran 'make test' on cheyenne and 'make all' on my Mac) -Code reviewed by: Bill Sacks + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + cheyenne ---- ok + izumi ------- ok -CTSM testing: +Answer changes +-------------- - [PASS means all tests PASS and OK means tests PASS other than expected fails.] +Changes answers relative to baseline: NO - build-namelist tests: +Other details +------------- - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- NOT RUN! - izumi ------- pass - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none +Pull Requests that document the changes (include PR ids): +- One small piece is documented in https://github.com/ESCOMP/CTSM/pull/1334 =============================================================== =============================================================== -Tag name: ctsm1.0.dev078 -Originator(s): oleson (Keith Oleson) -Date: Thu Oct 31 12:30:00 MDT 2019 -One-line Summary: Fix rootr calculation with use_hydrstress true - -Purpose of changes ------------------- - -In cases with use_hydrstress=.true., both rootr_patch and rootr_col had -problems. This affected the diagnostic fields ROOTR and ROOTR_COLUMN, -and (in BGC cases) fed back on other parts of the system via affecting -the methane code. See https://github.com/ESCOMP/CTSM/issues/812 for more -details. - -This tag fixes this issue via these specific changes: - -1. Calculate btran in SoilMoistStressMod.F90 regardless of - use_hydrstress - -2. Comment on the applicability of this calculation and that of rootr in - SoilMoistStressMod.F90 - -3. Add the following comment to uses of rootr and rootr_col throughout - the code: "SMS method only" - -4. Allow ROOTR_COL history field only if use_hydrstress = .false. - -5. Remove the calculation of rootr_col in subroutine - Compute_EffecRootFrac_And_VertTranSink_HydStress within module - SoilWaterPlantSinkMod.F90 since that calculation is invalid for PHS. - -6. Normalize root resistances for pervious road over nlevgrnd, not - nlevsoi - -Note that the rootr calculation is done using the non-PHS (i.e., SMS) -method. So rootr is not really consistent with PHS; this is something -that should probably be revisited later. +Tag name: ctsm5.1.dev034 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Mon Apr 19 16:02:29 MDT 2021 +One-line Summary: Bring in Arctic changes to LUNA from Leah Birch +Purpose and description of changes +---------------------------------- -Bugs fixed or introduced ------------------------- +This is @lmbirch89 branch from #947 with the exception that Kattge is used in place of +Leuning in LUNA. Also the startup initial values in the luna bug fix branch #961 is +used in place of the updated values by @lmbirch89. The LUNA bug fixes have already come +in, so these are some changes to improve arctic plants. -Issues fixed (include CTSM Issue #): -- Fixes ESCOMP/ctsm#812 (Problems with rootr when use_hydrstress=.true.) +We have addressed the issues in phenology and photosynthesis in the high latitudes. +Development was focused on PFT specific differences and we used observations to inform +model development. GPP is improved now such that the tundra is realistically less +productive than the boreal forest. Significant changes to scientifically-supported configurations @@ -532,313 +452,112 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[x] clm5_1 + [ ] clm5_0 [ ] ctsm5_0-nwp [ ] clm4_5 -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: not checked; none expected - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: Bill Sacks - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - izumi ------- ok - - ok means tests pass, answers change as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: Clm50Bgc (cases with both use_hydrstress=.true. and methane active) - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - larger than roundoff / same climate - - For details on differences, see - https://github.com/ESCOMP/CTSM/issues/812#issuecomment-547924289 - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: - http://webext.cgd.ucar.edu/I20TR/clm50_ctsm10d074_2deg_GSWP3V1_rootr_hist/lnd/clm50_ctsm10d074_2deg_GSWP3V1_rootr_hist.1995_2014-clm50_ctsm10d074_2deg_GSWP3V1_hist.1995_2014/setsIndex.html - -Detailed list of changes +Bugs fixed or introduced ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev077 -Originator(s): sacks (Bill Sacks) -Date: Sun Oct 27 16:23:39 MDT 2019 -One-line Summary: Consistently use frac_sno_eff rather than frac_sno in qg calculations - -Purpose of changes ------------------- - -Consistently use frac_sno_eff rather than frac_sno in qg calculations - -The change here only changes answers for (1) urban pervious road, and -(2) more broadly with use_subgrid_fluxes = .false. - -Previously, code in CalculateSurfaceHumidity was inconsistent regarding -the use of frac_sno vs. frac_sno_eff. I wanted to make this consistent -to facilitate upcoming cleanup of CalculateSurfaceHumidity. I went back -and forth as to which one we should use here. (See also -https://github.com/ESCOMP/CTSM/issues/822). - -Argument for frac_sno_eff: This is consistent with the use of -frac_sno_eff elsewhere in the calculation of surface fluxes. - -Argument for frac_sno: Even in CLM4.0 (prior to the introduction of -frac_sno_eff and frac_h2osfc), frac_sno was used to calculate surface -relative humidity. That makes me think that the parameterizations were -improved by using frac_sno here, even though frac_sno at that point was -mainly just used for albedo / radiation calculations. So sticking with -frac_sno would be more consistent with what has been done for a long -time, and would presumably be a bit better scientifically. - -However, when I tried changing this to use frac_sno rather than -frac_sno_eff: - - qg(c) = frac_sno_eff(c)*qg_snow(c) + (1._r8 - frac_sno_eff(c) - frac_h2osfc(c))*qg_soil(c) & - + frac_h2osfc(c) * qg_h2osfc(c) - -I got a crash with use_subgrid_fluxes false (test -SMS_D_Ld1_P4x1.f10_f10_musgs.I2000Clm45BgcCropQianRsGs.bishorn_gnu.clm-no_subgrid_fluxes), -due to a check I put in relatively recently to ensure that the top-layer -soil liquid never goes significantly negative: - -WJS 218: frac_sno, frac_sno_eff, frac_h2osfc, snl = 6.6447358408778726E-005 1.0000000000000000 0.0000000000000000 -1 - qg_snow, qg_soil, qg_h2osfc, qg = 3.8414454029812475E-003 3.6634834595404343E-003 3.6635176705822736E-003 3.6634952846414733E-003 - ERROR: In UpdateState_TopLayerFluxes, h2osoi_liq has gone significantly negative - Bulk/tracer name = bulk - c, lev_top(c) = 218 0 - h2osoi_liq_top_orig = 6.6448689668604415E-004 - h2osoi_liq = -2.6754040213948407E-004 - frac_sno_eff = 1.0000000000000000 - qflx_liq_grnd*dtime = 0.0000000000000000 - qflx_dew_grnd*dtime = 0.0000000000000000 - qflx_evap_grnd*dtime = 9.3202729882552822E-004 - ENDRUN: - ERROR: In UpdateState_TopLayerFluxes, h2osoi_liq has gone significantly negative - -What seems to be going on is: With a little bit of snow present, when I -use frac_sno rather than frac_sno_eff, we end up with a qg value very -close to that of soil. But I think the later evaporation happens from -the snow, at which point I guess the dryer air above leads to there -being too large evaporation from the snow. - -So in the end, I decided to consistently use frac_sno_eff, even though -this might be a small step backwards in terms of the accuracy of surface -humidity for urban pervious road and with use_subgrid_fluxes = .false. - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp +Issues fixed (include CTSM Issue #): + Fixes #807 -- Revisit PFT optical properties per Majasalmi and Bright (2019) + Fixes #1307 -- Turn on reseed_dead_plants when you start AD spinup mode -[ ] clm4_5 +Known bugs introduced in this tag (include issue #): + #1346 -- Use of floating point flag onset_thresh is confusing in CNPhenologyMod Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New namelist items: onset_thresh_depends_on_veg and min_crtical_dayl_depends_on_lat -Changes to the datasets (e.g., parameter, surface or initial files): none +Changes made to namelist defaults (e.g., changed parameter values): + reseed_dead_plants turned on when AD spinup mode turned on + onset_thresh_depends_on_veg and min_crtical_dayl_depends_on_lat turned on for clm5_1 physics -Substantial timing or memory changes: none +Changes to the datasets (e.g., parameter, surface or initial files): + New parameter file (same as start used in PPE work) also has additional fields on it -Notes of particular relevance for developers: (including Code reviews and testing) +Notes of particular relevance for developers: --------------------------------------------- NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +[Remove any lines that don't apply. Remove entire section if nothing applies.] -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self (but approved conceptually by Sean Swenson and -Keith Oleson) - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + As noted in #1346 some of the logic in CNPhenology in CNSeasonDecidPhenology is a bit confusing. + The soil layer used was put in CNSharedParameters and needed it's own subroutine to prevent circular dependencies. + There are new accumulator variables added that area always turned on even when not needed. Doing this + in a reasonable manner (without having lots of CNPhenology logic spilled into base types) would require + a refactoring of a better way to figure this out. - python testing (see instructions in python/README.md; document testing done): +Testing summary: regular +---------------- - (any machine) - not run + [PASS means all tests PASS; OK means tests PASS other than expected fails.] - regular tests (aux_clm): + build-namelist tests (if CLMBuildNamelist.pm has changed): - cheyenne ---- ok - izumi ------- ok + cheyenne - PASS - ok means tests pass, answers change as expected + python testing (if python code has changed; see instructions in python/README.md; document testing done): -If the tag used for baseline comparisons was NOT the previous tag, note that here: + cheyenne - PASS + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + cheyenne ---- OK + izumi ------- OK + Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): +Changes answers relative to baseline: Yes for clm5_1 physics Summarize any changes to answers, i.e., - - what code configurations: all + - what code configurations: clm5_1 - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Expected to be larger than roundoff/same climate, but not - investigated carefully - - For the default configuration with use_subgrid_fluxes = .true., - differences are restricted to urban pervious road. I spot-checked - a few tests to ensure that we only saw differences in FSH for - urban landunits; this was generally true, with the exception of - ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput, - which also had differences over crop and natural veg - landunits. This spillover effect seems to be related to the - non-local interactions that arise from methane's dependence on - TWS, though I don't understand why I only saw this in a transient - case, and not in similar non-transient cases. See - https://github.com/ESCOMP/CTSM/issues/658#issuecomment-546740771 - for more details. - - For the non-default use_subgrid_fluxes = .false., there - differences in the natural vegetation and crop landunits, too. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A + - nature of change: new climate If this tag changes climate describe the run(s) done to evaluate the new climate (put details of the simulations in the experiment database) - - casename: N/A + oleson -- clm50_ctsm10d089_2deg_GSWP3V1_lmbirch_wkattge_jmaxb1-0.17_slatopA_1850AD - URL for LMWG diagnostics output used to validate new climate: N/A + URL for LMWG diagnostics output used to validate new climate: + http://webext.cgd.ucar.edu/I1850/clm50_ctsm10d089_2deg_GSWP3V1_lmbirch_wkattge_jmaxb1-0.17_slatopA_1850AD/ -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +Other details +------------- +Pull Requests that document the changes (include PR ids): #990 +(https://github.com/ESCOMP/ctsm/pull) -Pull Requests that document the changes (include PR ids): none + #990 -- Arctic changes branch with Kattge in place of Leuning in LUNA =============================================================== =============================================================== -Tag name: ctsm1.0.dev076 -Originator(s): sacks (Bill Sacks) -Date: Fri Oct 25 16:04:20 MDT 2019 -One-line Summary: Set frac_sno_eff=0 if frac_sno is 0; avoid unnecessary calls to QSat - -Purpose of changes ------------------- +Tag name: ctsm5.1.dev033 +Originator(s): mvertens (Mariana Vertenstein), sacks (Bill Sacks) +Date: Sat Apr 10 16:42:06 MDT 2021 +One-line Summary: Remove unnecessary settings of nextsw_cday -Two changes that are bit-for-bit except for changes in the FSNO_EFF -diagnostic field, both with an eye towards cleaning up -SurfaceHumidityMod in preparation for adding water tracers to that -module: +Purpose and description of changes +---------------------------------- -(1) Set frac_sno_eff to 0 if frac_sno is 0. Previously, for cases where - frac_sno_eff was a binary 0/1 rather than being set equal to - frac_sno, frac_sno_eff was always being set to 1, even if there was - no snow. Sean Swenson thinks that didn't matter, but I found it - confusing, and it could be more problematic with some upcoming - changes I plan to make (where I'm going to use frac_sno_eff as a - weighting factor in calculating qg terms, including for landunits - that use a binary 0/1 frac_sno_eff.) +Remove setting of nextsw_cday in initialization: this hasn't been needed +ever since we stopped calculating albedos in initialization. -(2) Avoid unnecessary calls to QSat, since this function is relatively - expensive. +Also remove nextsw_cday from clm_time_manager: this was being set but +was never referenced from here: instead, nextsw_cday was being passed as +an argument to clm_drv. +Also, updates cime to a branch tag where I have fixed the --retry option +to create_test. Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -848,6523 +567,61 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 [ ] ctsm5_0-nwp [ ] clm4_5 -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: No substantial changes; from a -single run of PFS_Ld20.f09_g17.I2000Clm50BgcCrop.cheyenne_intel, max -timing of the main changed section (bgp1) decreased by about 10%; this -may be within machine variability, though. - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self +Bugs fixed or introduced +------------------------ -CTSM testing: +CIME Issues fixed (include issue #): +- ESMCI/cime#3912 (create_test --retry fails if the test is doing + baseline generation) - [PASS means all tests PASS and OK means tests PASS other than expected fails.] +Testing summary: +---------------- + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - build-namelist tests: + cheyenne ---- OK + izumi ------- OK - cheyenne - not run +Answer changes +-------------- - tools-tests (test/tools): +Changes answers relative to baseline: NO - cheyenne - not run +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.8.42 -> branch_tags/cime5.8.42_a01 - PTCLM testing (tools/shared/PTCLM/test): +Pull Requests that document the changes (include PR ids): +- Second part of https://github.com/ESCOMP/CTSM/pull/1330 - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - izumi ------- ok - - ok means tests pass, answer changes as expected just for FSNO_EFF - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES, but just for the diagnostic field FSNO_EFF - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - diagnostic only: just changes FSNO_EFF - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev075 -Originator(s): sacks (Bill Sacks) -Date: Fri Oct 25 15:44:52 MDT 2019 -One-line Summary: Lakes: Adjust frac_sno after updating 0-layer snow pack for dew & sublimation - -Purpose of changes ------------------- - -Main change is: for lakes, possibly adjust frac_sno after updating -0-layer snow pack for dew & sub, ensuring that zero vs. non-zero values -of frac_sno agree with whether the snow pack has zero or non-zero -amounts of snow. The main motivation for this is to ensure that, if we -have any snow, then frac_sno should be non-zero. Along with this, I'm -also ensuring that, if we go down to 0 snow, then we also go down to 0 -frac_sno. - -A related change was to move the code ensuring that h2osno_no_layers -doesn't go negative: I have moved this to before h2osno_no_layers is -referenced, to assure we don't get a slightly negative snow depth. (I -haven't noticed any problems due to the old placement, but it seems -safer to put the limiting before the reference to h2osno_no_layers.) - -Also, an unrelated change in run_sys_tests: Add option for rerunning -existing failed tests. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#827 (Lake frac_sno can remain 0 even when there - is some snow addition from frost) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: None expected - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - pass (on my mac: 'make test' with python2 & python3 and 'make lint') - - regular tests (aux_clm): - - cheyenne ---- ok - izumi ------- ok - - ok means tests pass, answers change as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Expected to be larger than roundoff/same climate - - Changes are introduced only over lake columns, and these changes - should be small, since they only relate to the setting of frac_sno - when there is dew or sublimation on a very thin snow - pack. - - Although the direct changes should only affect lakes, I did - observe changes in crop columns in a transient test that I - spot-checked - (ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput) - - maybe due to some of the non-local interactions in - https://github.com/ESCOMP/CTSM/wiki/Parameterizations-that-can-cause-nonlocal-interactions, - or maybe due to some other non-local interaction, either known or - buggy. (In non-transient tests that I spot checked - (ERP_P72x2_Lm36.f10_f10_musgs.I2000Clm50BgcCrop.cheyenne_intel.clm-clm50cropIrrigMonth_interp - and - SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput): - diffs in FSH in h1 file are just over lake landunits, as - expected.) - - Update: it seems that these changes in crop columns arise from - the nonlocal interactions caused by the dependence of methane - on TWS, though I don't understand why I only saw this in a - transient case, and not in similar non-transient cases. See - https://github.com/ESCOMP/CTSM/issues/658#issuecomment-546740771 - for more details. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev074 -Originator(s): sacks (Bill Sacks) -Date: Wed Oct 23 19:25:21 MDT 2019 -One-line Summary: For lakes: when reading finidat, set frac_sno=1 if h2osno_total > 0 - -Purpose of changes ------------------- - -Due to ESCOMP/ctsm#783, frac_sno used to be 0 for all lake points. That -was mostly fixed, but the issue is still present on initial conditions -files that were generated prior to that fix (which includes most or all -of our out-of-the-box restart files). This causes frac_sno to be 0 for -lake points at the start of the simulation, even if there is a snow pack -present. Currently this doesn't cause significant problems, but I'd like -to change the calculation of frac_sno_eff so that it is 0 if frac_sno is -0 - and then this frac_sno problem becomes an issue (causing divide by 0 -in at least one place). - -However, further problems were introduced if I tried to always apply -this correction: It appears that sometimes the restart file legitimately -has frac_sno == 0 for lake columns with non-zero snow cover. To avoid -changing answers for newer restart files, I am writing metadata to the -restart file documenting whether the fix has already been applied on -that restart file, and if so, we avoid reapplying the fix. - -Getting this restart metadata correct was tricky, especially when -running init_interp. I have introduced a new module to encapsulate this -complexity. This can be used in general for writing / reading metadata -on which issues have been fixed on a given restart file. - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): [If none, remove this line] -- Resolves ESCOMP/ctsm#783 - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): -- The setting of initial lake frac_sno to 1 isn't exactly correct, but - it's better than the old value of 0. - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none -- I didn't check the PFS test, but the only change that could have - likely led to performance changes was the addition of a metadata copy - in init_interp. I checked the timing of this piece, and found it to be - a negligible portion of the total init_interp time - (https://github.com/ESCOMP/CTSM/pull/825#issuecomment-545219601). - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: Erik Kluzek gave this an initial look and gave general -approval for the restart file metadata mechanism I have added. He may -give it a more careful look, possibly accompanied by a further cleanup -tag addressing any issues he finds. - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - izumi ------- ok - - ok means tests passed, baselines fail as expected. - - Note that the FUNIT test failed initially; I got it passing on my - Mac, but didn't rerun it on cheyenne. - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Larger than roundoff/same climate - - The only change is in initial lake frac_sno. This should only - affect the start of the simulation, and only over lake points. I - verified that changes are only over lake points via: For both - SMS_D_Ld1.f09_g17.I1850Clm50Sp.cheyenne_intel.clm-default (which - doesn't use init_interp) and - SMS_D_Ld3.f10_f10_musgs.I2000Clm50BgcCruGs.cheyenne_gnu.clm-default - (which uses init_interp): I checked which points have differences - in FSH in the h1 (vector) history file. Diffs were only over lake - points. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/CTSM/pull/825 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev073 -Originator(s): sacks (Bill Sacks) -Date: Tue Oct 22 06:14:24 MDT 2019 -One-line Summary: Fix bug in calculation of dqgdT - -Purpose of changes ------------------- - -The calculation of dqgdT, which gives the derivative, d(qg)/dT, was -incorrect for soil/crop landunits when there is no snow. This tag fixes -that bug. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/CTSM#824 (dqgdT incorrect when there is no snow) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: not checked, but none expected - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: Sean Swenson reviewed and approved my plan, though not the final code - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - izumi ------- ok - - ok means tests pass, answers change as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Larger than roundoff/same climate - - I checked the impact from one-day averages in test - SMS_D_Ld1_P4x1.f10_f10_musgs.I2000Clm50BgcCropQianRsGs.bishorn_gnu.clm-default, - by looking at differences in EFLX_LH_TOT. The impact is small: - daily-average differences in that variable are typically 0.01 W - m-2 or less; most grid cells have significantly less difference - than that; only one or a few f10 grid cells have significantly - greater differences, with the biggest difference being about 0.1 W - m-2. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev072 -Originator(s): mvertens (Mariana Vertenstein) -Date: Tue Oct 15 09:41:50 MDT 2019 -One-line Summary: Add NUOPC cap - -Purpose of changes ------------------- - -Add NUOPC cap in order to run with the new NUOPC driver/mediator. There -was some code movement / refactoring of existing code to support this, -with the biggest change being the introduction of a new subdirectory -under src/cpl. - -Most changes are from Mariana Vertenstein and Jim Edwards. - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none expected (not checked) - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): -- NUOPC cap currently does not have any tests in the aux_clm test suite -- There are currently no tests ensuring that the nuopc and mct caps give - bit-for-bit answers, though the nuopc_cap_bfb testmod could be used to - support such a test - -Changes to tests or testing: none - -Code reviewed by: Bill Sacks - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- pass - izumi ------- pass - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- mosart: mosart1_0_33 -> mosart1_0_34 (supports nuopc cap) - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev071 -Originator(s): sacks (Bill Sacks) -Date: Fri Oct 11 07:03:40 MDT 2019 -One-line Summary: Split CanopyTemperature into separate pieces - -Purpose of changes ------------------- - -CanopyTemperature was doing a few unrelated things, none of which -actually had anything to do with calculating canopy temperature. At the -driver level, I have split CanopyTemperature into BiogeophysPreFluxCalcs -and CalculateSurfaceHumidity. BiogeophysPreFluxCalcs calls out to a -number of separate routines, some in that same module and some -elsewhere, including a new routine in FrictionVelocityMod. - -Also some minor related cleanup, including - -- Made FrictionVelocityMod object-oriented - -- A bit of rework of how qflx_evap_veg and qflx_tran_veg are set. This - changes answers for the (default inactive) QFLX_EVAP_VEG history field - (see also ESCOMP/ctsm#816). - -- Removed qsat conditionals that should never be invoked - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Fixes ESCOMP/ctsm#816 (QFLX_EVAP_VEG should be 0 over lakes) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- pass - izumi ------- pass - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES, but only for the -(default-inactive) field QFLX_EVAP_VEG - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - larger than roundoff, but only for the default-inactive field QFLX_EVAP_VEG - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev070 -Originator(s): sacks (Bill Sacks) -Date: Wed Oct 9 06:16:39 MDT 2019 -One-line Summary: Fix for writing 0-d variables with PIO2 - -Purpose of changes ------------------- - -Previously, there were problems when writing 0-d (scalar) variables with -PIO2 in DEBUG mode. This change fixes that issue. - -Jim Edwards put in place an initial fix; I put in place the final fix -based on changes Mariana Vertenstein made in MOSART. I have not tested -this with PIO2, but am hopeful that it fixes the PIO2 problem since the -similar MOSART changes fixed that problem. - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self; earlier version reviewed by Erik Kluzek and Mariana Vertenstein - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- pass - izumi ------- pass - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/CTSM/pull/810 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev069 -Originator(s): sacks (Bill Sacks) -Date: Mon Oct 7 10:22:22 MDT 2019 -One-line Summary: Misc. code cleanup and minor bug fixes - -Purpose of changes ------------------- - -Resolve a variety of "simple bfb" issues. Note that some of these result -in answer changes for select diagnostic fields. See specific notes below -for details, under "Issues fixed" and answer changes. - -The fix for ESCOMP/ctsm#27 changes answers for some diagnostic fields, -as noted below. - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#27 (BTRAN should be spval over all special - landunits) - - Also fixed some related fields, as noted below, under answer changes - -- Resolves ESCOMP/ctsm#31 (some CLM history fields don't restart - properly) - - This was mostly resolved previously; here I just did some final - cleanup and fixing of NFIRE - -- Resolves ESCOMP/ctsm#48 (code for initializing some isotope carbon - state variables looks wrong) - - Removed the incorrect code, which was never being exercised - -- Resolves ESCOMP/ctsm#58 (Change SHR_ASSERT calls to avoid using - errMsg) - - Purpose was to speed up DEBUG runs on some machines/compilers - -- Resolves ESCOMP/ctsm#111 (Precision of constants in - SoilTemperature.F90 is not double) - - No answer changes, because 1 (single prec) = 1 (double prec) - -- Resolves ESCOMP/ctsm#334 (Introduce a new activelayer_type) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: potentially speeds up debug runs on some machines/compilers - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - izumi ------- ok - - ok means tests pass, some baseline comparisons fail as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES, but just for select diagnostic fields - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: ALL - - what platforms/compilers: ALL - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Greater than roundoff, but only in select diagnostic field - no impact on climate - - There were changes in the following diagnostic fields, which are - now averaged over only vegetated landunits (see ESCOMP/ctsm#27): - - BTRAN - - BTRANMN - - RSSHA - - RSSUN - - ROOTR (inactive by default) - - ROOTR_COLUMN (inactive by default) - - RRESIS (inactive by default) - - Changes are also possible in rare circumstances for the NFIRE - diagnostic field, in transient cases, although no differences were - observed for this field in the test suite (see ESCOMP/ctsm#31). - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev068 -Originator(s): sacks (Bill Sacks) -Date: Mon Sep 30 09:57:04 MDT 2019 -One-line Summary: Add water tracers to CombineSnowLayers, DivideSnowLayers, ZeroEmptySnowLayers - -Purpose of changes ------------------- - -Add water tracers to CombineSnowLayers, DivideSnowLayers and -ZeroEmptySnowLayers. This completes the tracerization of the core snow -code: most or all of the code in SnowHydrologyMod is now tracerized. - -In contrast to most routines that I have tracerized, the tracerization -of these routines is done by embedding loops over tracers inside -existing code structures, rather than splitting out separate routines -that operate on bulk or tracer quantities. This is because (1) it didn't -make sense to introduce explicit fluxes for the state updates done here, -so we didn't have the extra need of having separate routines for flux -calculations vs. state updates; (2) the state updates were embedded in -loops over levels and conditionals in a way that would have been awkward -and messy to try to separately update bulk-and-tracer quantities -(h2osoi_liq, h2osoi_ice, etc.) from bulk-only quantities (dz, etc.). - -Also, a bit of reordering of LakeHydrologyMod in order to keep the snow -code more together. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#778 (Implement water tracers for combining and - dividing snow layers) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: I don't think so - Based on the changes introduced, I expect *very* small increases in - runtime of the modified routines (which would show up in the - hydro_without_drainage timer), even for cases without water tracers, - but I wouldn't expect this to have a significant impact. From PFS - test, and specifically looking at the timing of - hydro_without_drainage in that test, I see a possible small increase - (a few percent) in the timing of that section, though the differences - are within typical machine variability, so don't seem necessarily - significant. - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- pass - izumi ------- pass - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev067 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Thu Sep 26 15:02:39 MDT 2019 -One-line Summary: Add config_archive.xml to CTSM cime_config -- no testing - -Purpose of changes ------------------- - -Add config_archive.xml to cime_config for CTSM. Update the CODE_OF_CONDUCT -to the August/2019 UCAR version. - -No testing done. - -Bugs fixed or introduced ------------------------- - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None - -Changes made to namelist defaults (e.g., changed parameter values): None - -Changes to the datasets (e.g., parameter, surface or initial files): None - -Substantial timing or memory changes: None - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None - -Changes to tests or testing: None - -Code reviewed by: self - - -CTSM testing: doc (no standard testing done) - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - src unit-tests: - - cheyenne - PASS - - regular tests (aux_clm): None - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - - -Answer changes --------------- - -Changes answers relative to baseline: No! - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None - -Pull Requests that document the changes (include PR ids): None -(https://github.com/ESCOMP/ctsm/pull) - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev066 -Originator(s): sacks (Bill Sacks) -Date: Fri Sep 20 09:07:23 MDT 2019 -One-line Summary: Add water tracers to SnowCapping - -Purpose of changes ------------------- - -Update water tracer terms in SnowCapping. As I have done elsewhere, this -has involved splitting each piece of SnowCapping into its own subroutine, -which operates either on bulk, tracers, or bulk + tracers. - -This is supported by calls to ResetCheckedTracers prior to the call to -SnowCapping, since some intervening code is not yet tracerized. - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#777 (Implement water tracers for SnowCapping) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - Small increase in total runtime of PFS test, but the relevant timing - section, hydro_without_drainage, took slightly *less* time compared - with the last tag. - - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- pass - izumi ------- pass - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev065 -Originator(s): sacks (Bill Sacks) -Date: Sat Sep 14 12:52:42 MDT 2019 -One-line Summary: Add water tracers to SnowWater - -Purpose of changes ------------------- - -Update water tracer terms in SnowWater. As I have done elsewhere, this -has involved splitting each piece of SnowWater into its own subroutine, -which operates either on bulk, tracers, or bulk + tracers. - -This is supported by calls to ResetCheckedTracers prior to the call to -SnowWater, since some intervening code is not yet tracerized. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#776 (Implement water tracers for SnowWater) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - izumi ------- ok - - ok means tests pass, baselines fail as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - Roundoff level: answer changes just arise because I have made - qflx_snow_percolation_col a true flux, with units of - per-unit-time; this involved dividing by dtime, and later - multiplying by dtime when it is applied to states. Previously, the - corresponding variable (qout / qin) was not per-unit-time. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - - I ran comparisons against a version off of master that had the - minimal changes to exhibit these roundoff-level changes. Diffs for - this are below. My branch is bit-for-bit with this version. - - diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 - index cad47e28..0abcc49f 100644 - --- a/src/biogeophys/SnowHydrologyMod.F90 - +++ b/src/biogeophys/SnowHydrologyMod.F90 - @@ -1140,17 +1140,17 @@ subroutine SnowWater(bounds, & - c = filter_snowc(fc) - if (j >= snl(c)+1) then - - - h2osoi_liq(c,j) = h2osoi_liq(c,j) + qin(c) - + h2osoi_liq(c,j) = h2osoi_liq(c,j) + qin(c)*dtime - - - mss_bcphi(c,j) = mss_bcphi(c,j) + qin_bc_phi(c) - - mss_bcpho(c,j) = mss_bcpho(c,j) + qin_bc_pho(c) - - mss_ocphi(c,j) = mss_ocphi(c,j) + qin_oc_phi(c) - - mss_ocpho(c,j) = mss_ocpho(c,j) + qin_oc_pho(c) - + mss_bcphi(c,j) = mss_bcphi(c,j) + qin_bc_phi(c)*dtime - + mss_bcpho(c,j) = mss_bcpho(c,j) + qin_bc_pho(c)*dtime - + mss_ocphi(c,j) = mss_ocphi(c,j) + qin_oc_phi(c)*dtime - + mss_ocpho(c,j) = mss_ocpho(c,j) + qin_oc_pho(c)*dtime - - - mss_dst1(c,j) = mss_dst1(c,j) + qin_dst1(c) - - mss_dst2(c,j) = mss_dst2(c,j) + qin_dst2(c) - - mss_dst3(c,j) = mss_dst3(c,j) + qin_dst3(c) - - mss_dst4(c,j) = mss_dst4(c,j) + qin_dst4(c) - + mss_dst1(c,j) = mss_dst1(c,j) + qin_dst1(c)*dtime - + mss_dst2(c,j) = mss_dst2(c,j) + qin_dst2(c)*dtime - + mss_dst3(c,j) = mss_dst3(c,j) + qin_dst3(c)*dtime - + mss_dst4(c,j) = mss_dst4(c,j) + qin_dst4(c)*dtime - - if (j <= -1) then - ! No runoff over snow surface, just ponding on surface - @@ -1167,8 +1167,8 @@ subroutine SnowWater(bounds, & - qout(c) = max(0._r8,(vol_liq(c,j) & - - ssi*eff_porosity(c,j))*dz(c,j)*frac_sno_eff(c)) - end if - - qout(c) = qout(c)*1000._r8 - - h2osoi_liq(c,j) = h2osoi_liq(c,j) - qout(c) - + qout(c) = (qout(c)*1000._r8)/dtime - + h2osoi_liq(c,j) = h2osoi_liq(c,j) - qout(c)*dtime - qin(c) = qout(c) - - ! mass of ice+water: in extremely rare circumstances, this can - @@ -1187,7 +1187,7 @@ subroutine SnowWater(bounds, & - if (qout_bc_phi(c) > mss_bcphi(c,j)) then - qout_bc_phi(c) = mss_bcphi(c,j) - endif - - mss_bcphi(c,j) = mss_bcphi(c,j) - qout_bc_phi(c) - + mss_bcphi(c,j) = mss_bcphi(c,j) - qout_bc_phi(c)*dtime - qin_bc_phi(c) = qout_bc_phi(c) - - ! BCPHO: - @@ -1196,7 +1196,7 @@ subroutine SnowWater(bounds, & - if (qout_bc_pho(c) > mss_bcpho(c,j)) then - qout_bc_pho(c) = mss_bcpho(c,j) - endif - - mss_bcpho(c,j) = mss_bcpho(c,j) - qout_bc_pho(c) - + mss_bcpho(c,j) = mss_bcpho(c,j) - qout_bc_pho(c)*dtime - qin_bc_pho(c) = qout_bc_pho(c) - - ! OCPHI: - @@ -1205,7 +1205,7 @@ subroutine SnowWater(bounds, & - if (qout_oc_phi(c) > mss_ocphi(c,j)) then - qout_oc_phi(c) = mss_ocphi(c,j) - endif - - mss_ocphi(c,j) = mss_ocphi(c,j) - qout_oc_phi(c) - + mss_ocphi(c,j) = mss_ocphi(c,j) - qout_oc_phi(c)*dtime - qin_oc_phi(c) = qout_oc_phi(c) - - ! OCPHO: - @@ -1214,7 +1214,7 @@ subroutine SnowWater(bounds, & - if (qout_oc_pho(c) > mss_ocpho(c,j)) then - qout_oc_pho(c) = mss_ocpho(c,j) - endif - - mss_ocpho(c,j) = mss_ocpho(c,j) - qout_oc_pho(c) - + mss_ocpho(c,j) = mss_ocpho(c,j) - qout_oc_pho(c)*dtime - qin_oc_pho(c) = qout_oc_pho(c) - - ! DUST 1: - @@ -1223,7 +1223,7 @@ subroutine SnowWater(bounds, & - if (qout_dst1(c) > mss_dst1(c,j)) then - qout_dst1(c) = mss_dst1(c,j) - endif - - mss_dst1(c,j) = mss_dst1(c,j) - qout_dst1(c) - + mss_dst1(c,j) = mss_dst1(c,j) - qout_dst1(c)*dtime - qin_dst1(c) = qout_dst1(c) - - ! DUST 2: - @@ -1232,7 +1232,7 @@ subroutine SnowWater(bounds, & - if (qout_dst2(c) > mss_dst2(c,j)) then - qout_dst2(c) = mss_dst2(c,j) - endif - - mss_dst2(c,j) = mss_dst2(c,j) - qout_dst2(c) - + mss_dst2(c,j) = mss_dst2(c,j) - qout_dst2(c)*dtime - qin_dst2(c) = qout_dst2(c) - - ! DUST 3: - @@ -1241,7 +1241,7 @@ subroutine SnowWater(bounds, & - if (qout_dst3(c) > mss_dst3(c,j)) then - qout_dst3(c) = mss_dst3(c,j) - endif - - mss_dst3(c,j) = mss_dst3(c,j) - qout_dst3(c) - + mss_dst3(c,j) = mss_dst3(c,j) - qout_dst3(c)*dtime - qin_dst3(c) = qout_dst3(c) - - ! DUST 4: - @@ -1250,7 +1250,7 @@ subroutine SnowWater(bounds, & - if (qout_dst4(c) > mss_dst4(c,j)) then - qout_dst4(c) = mss_dst4(c,j) - endif - - mss_dst4(c,j) = mss_dst4(c,j) - qout_dst4(c) - + mss_dst4(c,j) = mss_dst4(c,j) - qout_dst4(c)*dtime - qin_dst4(c) = qout_dst4(c) - - end if - @@ -1280,9 +1280,9 @@ subroutine SnowWater(bounds, & - do fc = 1, num_snowc - c = filter_snowc(fc) - ! Qout from snow bottom - - qflx_snow_drain(c) = qflx_snow_drain(c) + (qout(c) / dtime) - + qflx_snow_drain(c) = qflx_snow_drain(c) + qout(c) - - - qflx_rain_plus_snomelt(c) = (qout(c) / dtime) & - + qflx_rain_plus_snomelt(c) = qout(c) & - + (1.0_r8 - frac_sno_eff(c)) * qflx_liq_grnd(c) - int_snow(c) = int_snow(c) + frac_sno_eff(c) & - * (qflx_dew_snow(c) + qflx_dew_grnd(c) + qflx_liq_grnd(c)) * dtime - - - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev064 -Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) -Date: Mon Sep 9 13:14:51 MDT 2019 -One-line Summary: User defined top-two snow layers - -Purpose of changes ------------------- - - Instead of hardcoding, we now set: - - dzmin(1) = snow_dzmin_1 - dzmax_l(1) = snow_dzmax_l_1 - dzmax_u(1) = snow_dzmax_u_1 - dzmin(2) = snow_dzmin_2 - dzmax_l(2) = snow_dzmax_l_2 - dzmax_u(2) = snow_dzmax_u_2 - - where the right-hand-side variables get namelist-defined values and the - model calculates dzmin and dzmax_* for the remaining snow layers using - recursive formulas. The calculation is intended to match the previously - hardcoded values, except for the bottom snow layer when nlevsno < 12. - The bottom layer now always gets dzmax_* = huge(1._r8). The formulas - appear in a document titled "A firn model for CLM" that is linked to - #729. - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #729 - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): - New namelist parameters for specifying the top-two snow layers: - snow_dzmin_1, snow_dzmax_l_1, snow_dzmax_u_1 - snow_dzmin_2, snow_dzmax_l_2, snow_dzmax_u_2 - -Changes made to namelist defaults (e.g., changed parameter values): - Introduced default values for the new parameters so as to maintain - same answers to within roundoff - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: @billsacks - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - - - tools-tests (test/tools): - - cheyenne - - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - - - regular tests (aux_clm): - - cheyenne ---- OK - izumi ------- OK - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change: roundoff - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - Introduced temporary code to overwrite dzmin(j), dzmax_l(j), and - dzmax_u(j) with their original values when different by less than - 1e-13 from their original values for all but the bottom snow layer. - The bottom layer was left as dzmax_l = dzmax_u(j) = huge(1._8), i.e. - the new value. The test resulted in bit-for-bit same answers. - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/ctsm/pull/792 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev063 -Originator(s): erik (Erik Kluzek) -Date: Thu Sep 5 21:28:02 MDT 2019 -One-line Summary: Two answer changing fixes (fire, DWT_SLASH) and fix for urban streams for Clm45 - -Purpose of changes ------------------- - -Fire bug fix and DWT_SLASH change and fix urban stream years for clm4_5. -The latitude used in an expression for Bgc-Fire model Li2016 (used in Clm50) -had latitude in degrees rather than in radians as it should have been. The -term is used for ignition and the cosine was being taken in degrees rather -than radians, hence the spatial pattern for ignition with latitude was incorrect. - -The history field DWT_SLASH_CFLUX was being calculated on the column, but -really should have been a patch level variable. In the same way other fields -were handled we made DWT_SLASH_CFLUX a grid-cell variable, and added -DWT_SLASH_CFLUX_PATCH on the patch level that could be added to output. The same -is true of the C13_ and C14_ versions of it. - -Clm45 was setting urbantv to year 2000, rather than 1850 or historical as it should -have. The urbantv file for Clm45 doesn't actually change, so this doesn't actually -make a difference. But, it does make the namelist look wrong. - -Note, that SP cases, Vic cases and Fates cases do NOT change answers. Or if fire is -off, or certain single-point cases. Some cold-start cases don't seem to be sensitive -to it either. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #175, #787, #780 - fixes #175 urban stream years for clm4_5 - fixes #787 DWT_SLASH field - fixes #780 Bug in CN Fire Li 2016 which used latitude in degrees rather than radians - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[X] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None - -Changes made to namelist defaults (e.g., changed parameter values): Defaults for urbantv for clm4_5 - -Changes to the datasets (e.g., parameter, surface or initial files): None - -Substantial timing or memory changes: None - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None - -Changes to tests or testing: None - -Code reviewed by: self, @olywon - - -CTSM testing: regular - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS (62 compare fail due to namelist changes) - - regular tests (aux_clm): - - cheyenne ---- OK - izumi ------- OK - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - - -Answer changes --------------- - -Changes answers relative to baseline: Yes! - - Summarize any changes to answers, i.e., - - what code configurations: Clm50Bgc and some Clm45Bgc cases - - what platforms/compilers: All - - nature of change: similar climate (but fire ignition pattern changes by latitude) - DWT_SLASH_* history fields change because moved to gridcell quantity (so change is relatively minor) - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: - oleson/clm50_cesm20R_2deg_GSWP3V1_issue780_hist (for the fire change) - - URL for LMWG diagnostics output used to validate new climate: -http://webext.cgd.ucar.edu/I20TR/clm50_cesm20R_2deg_GSWP3V1_issue780_hist/lnd/clm50_cesm20R_2deg_GSWP3V1_issue780_hist.1995_2014-clm50_cesm20R_2deg_GSWP3V1_hist.1995_2014/setsIndex.html - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None - -Pull Requests that document the changes (include PR ids): #802 -(https://github.com/ESCOMP/ctsm/pull) - #802 -- Three answer changing fixes (fire, DWT_SLASH, urban streams for clm4_5) - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev062 -Originator(s): sacks (Bill Sacks) -Date: Tue Sep 3 16:04:28 MDT 2019 -One-line Summary: Move hobart tests to izumi - -Purpose of changes ------------------- - -Move all hobart testing to izumi. - - -Bugs fixed or introduced ------------------------- - -Known bugs introduced in this tag (include github issue ID): -- Recurrence of ESCOMP/ctsm#174 (ne30 case fails on hobart_nag due to floating overflow) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): -- Testing should now be run on izumi, not hobart - -Changes to tests or testing: -- All hobart tests moved to izumi - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- not run - izumi ------- pass - - Also ran prealpha and prebeta tests that I moved from hobart to izumi. These passed except: - - ERP_D_Ld5.ne30_g16.I1850Clm50BgcCrop.izumi_nag.clm-default (#174) - - ERP_Ld5.f19_g17.I2000Clm50SpRtmFl.izumi_pgi.clm-default - - SMS_D_Ld1.f19_g17.I1850Clm45Cn.izumi_pgi.clm-default - - The last two failed with errors like: - - i011.unified.ucar.edu.44619hfi_userinit: mmap of status page (dabbad0008040000) failed: Operation not permitted - - I wonder if the issue is that multi-node pgi cases don't work on izumi? - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- cime: cime5.8.3_chint17-04 -> cime5.8.3_chint17-05 - Minor change on izumi to allow using run_sys_tests - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev061 -Originator(s): erik (Erik Kluzek) -Date: Sun Sep 1 22:37:07 MDT 2019 -One-line Summary: Simple b4b fixes: new params file, remove override_nsrest/anoxia_wtsat, DV deprecated - -Purpose of changes ------------------- - -New clm5 paramsfile that has the bad date of 631 changed to 701. Along with some simple bit for -bit changes. Removing some problematic options. Making Dynamic Vegetation a deprecated option -that requires you to use -ignore_warnings with it. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #463 #79 #97 #98 #104 #122 #173 #794 #795 #796 - - Fixes #463 bad date on params file that didn't allow using ESMF library with Crop - Fixes #79 correct documentation of qflx_evap_tot - Fixes #97 remove override_nsrest - Fixes #98 add warning when using single instance of a startup file for multi-instance cases - Fixes #104 use get_step_size_real when putting into a real variable - Fixes #122 decomp pool arrays should not start at 0 but 1 - Fixes #173 remove psi_soil_ref as not used - Fixes #794 remove anoxia_wtsat - Fixes #795 Correct documentation of -light_res - Fixes #796 Deprecate Dynamic Vegetation - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): Remove namelist items - Remove namelist items: anoxia_wtsat, override_nsrest - Turning dynamic Vegetation on, now displays a warning, and requires using -ignore_warnings in CLM_BLDNML_OPTS - -Changes made to namelist defaults (e.g., changed parameter values): New paramdata files - -Changes to the datasets (e.g., parameter, surface or initial files): - clm5 paramdata file has correct date for crop of 701 (rather than incorrect 631) - clm5 and clm4_5 paramdata file removed an unused variable - -Substantial timing or memory changes: None - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None - -Changes to tests or testing: DV tests removed or changed - -Code reviewed by: self - -CTSM testing: regular - - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS (compare shows changes becausse of paramdata files) - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - -An additional fail is ERP_P36x2_D_Ld5.f10_f10_musgs.I2000Clm50Cn.cheyenne_gnu.clm-default, because -of #798. Because it's an issue with cime, I'm not marking it as an expected error. - -If the tag used for baseline comparisons was NOT the previous tag, note that here: previous - - -Answer changes --------------- - -Changes answers relative to baseline: No bit-for-bit - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None - -Pull Requests that document the changes (include PR ids): #797 -(https://github.com/ESCOMP/ctsm/pull) - - #797 -- Simple b4b fixes: new params file, remove override_nsrest/anoxia_wtsat, DV deprecated - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev060 -Originator(s): sacks (Bill Sacks) -Date: Thu Aug 29 11:18:20 MDT 2019 -One-line Summary: In SnowWater, truncate small h2osoi residuals - -Purpose of changes ------------------- - -Previously, in the handling of sublimation and evaporation from the snow -pack, if these fluxes led to negative h2osoi_ice or h2osoi_liq, these -negative values would be passed down the snow pack until they found a -layer with a large enough positive state to absorb them. This logic was -going to be a challenge for adding water tracers. - -I have done some tests to verify that these negative values never exceed -roundoff-level in either an absolute or relative sense (with tolerance -of 1.e-13). Specifically, I ran the full aux_clm test suite with the -diffs below and verified that the endrun calls were never triggered. - -So here, I simplify this logic: After truncating any near-zero states to -exactly zero, I check to confirm that the states are never negative. I -then removed the code that passed these negative values down the snow -pack: if they are only roundoff-level negative, then it seems safe to -just throw them away rather than trying to handle them. - -Here were the diffs used to verify that the negative values are never -greater than roundoff-level; these endrun calls were never triggered in -a run of the full aux_clm test suite: - - diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 - index 3dd555cc..07776123 100644 - --- a/src/biogeophys/SnowHydrologyMod.F90 - +++ b/src/biogeophys/SnowHydrologyMod.F90 - @@ -970,6 +970,8 @@ subroutine SnowWater(bounds, & - real(r8) :: vol_ice(bounds%begc:bounds%endc,-nlevsno+1:0) ! partial volume of ice lens in layer - real(r8) :: eff_porosity(bounds%begc:bounds%endc,-nlevsno+1:0) ! effective porosity = porosity - vol_ice - real(r8) :: mss_liqice(bounds%begc:bounds%endc,-nlevsno+1:0) ! mass of liquid+ice in a layer - + real(r8) :: h2osoi_ice_orig - + real(r8) :: h2osoi_liq_orig - !----------------------------------------------------------------------- - - associate( & - @@ -1017,10 +1019,23 @@ subroutine SnowWater(bounds, & - c = filter_snowc(fc) - l=col%landunit(c) - - + h2osoi_ice_orig = h2osoi_ice(c,snl(c)+1) - + h2osoi_liq_orig = h2osoi_liq(c,snl(c)+1) - + - wgdif = h2osoi_ice(c,snl(c)+1) & - + frac_sno_eff(c) * (qflx_dew_snow(c) - qflx_sub_snow(c)) * dtime - h2osoi_ice(c,snl(c)+1) = wgdif - if (wgdif < 0._r8) then - + if (wgdif < -1.e-13_r8) then - + write(iulog,*) 'WJS: big abs wgdif ice: ', c, wgdif, h2osoi_ice_orig - + call endrun('WJS: big abs wgdif ice') - + end if - + if (h2osoi_ice_orig > 0._r8) then - + if (abs(wgdif / h2osoi_ice_orig) > 1.e-13_r8) then - + write(iulog,*) 'WJS: big rel wgdif ice: ', c, wgdif, h2osoi_ice_orig - + call endrun('WJS: big rel wgdif ice') - + end if - + end if - h2osoi_ice(c,snl(c)+1) = 0._r8 - h2osoi_liq(c,snl(c)+1) = h2osoi_liq(c,snl(c)+1) + wgdif - end if - @@ -1030,6 +1045,16 @@ subroutine SnowWater(bounds, & - - ! if negative, reduce deeper layer's liquid water content sequentially - if(h2osoi_liq(c,snl(c)+1) < 0._r8) then - + if (h2osoi_liq(c,snl(c)+1) < -1.e-13_r8) then - + write(iulog,*) 'WJS: big abs wgdif liq: ', c, h2osoi_liq(c,snl(c)+1), h2osoi_liq_orig - + call endrun('WJS: big abs wgdif liq') - + end if - + if (h2osoi_liq_orig > 0._r8) then - + if (abs(h2osoi_liq(c,snl(c)+1) / h2osoi_liq_orig) > 1.e-13_r8) then - + write(iulog,*) 'WJS: big rel wgdif liq: ', c, h2osoi_liq(c,snl(c)+1), h2osoi_liq_orig - + call endrun('WJS: big rel wgdif liq') - + end if - + end if - do j = snl(c)+1, 1 - wgdif=h2osoi_liq(c,j) - if (wgdif >= 0._r8) exit - -Bugs fixed or introduced ------------------------- - -None - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): -- It's possible that the extra error checks I have added (to ensure we - don't have greater-than-roundoff-level negative residuals) will be - triggered in rare circumstances in a production run, even though they - were never triggered in the test suite. - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none -Although there was a very small increase in total lnd run time, the -timing of hydro_without_drainage actually decreased slightly in the PFS -test relative to the last tag. - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): -- It's possible that the extra error checks I have added (to ensure we - don't have greater-than-roundoff-level negative residuals) will be - triggered in rare circumstances in a production run, even though they - were never triggered in the test suite. - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests passed, some answer changes as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: potentially all, though only show up in - a few tests - - what platforms/compilers: potentially all, though only show up in - a few tests - - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - - First, I did some preliminary analyses as documented above, to - ensure that any negative residuals were no greater than roundoff. - - Second, note that the use of truncate_small_values can only - introduce roundoff-level changes (by truncating values that are - roundoff-level different from zero to exactly zero). - - Third, only a few tests showed answer changes, and these were only - in limited fields, and were fairly small RMS differences: - - ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput - ERS_Ly3.f10_f10_musgs.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic - ERS_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCropG.cheyenne_intel.clm-cropMonthOutput - ERS_Ly5_P144x1.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput - - I actually expected more tests to show differences, but most tests - were bit-for-bit. I'm guessing this is because the code added a - roundoff-level term to a larger term, and this ended up not - changing the larger term. - - Finally, as an extra precaution, I ran the test suite twice, on - two different implementations of the truncation: the final one - (which uses truncate_small_values), and one in which I did the - truncation using custom, inline code (commit 0d21ccb5). These two - were bit-for-bit with each other, giving me more confidence that I - didn't make a mistake with either implementation. - - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev059 -Originator(s): sacks (Bill Sacks) -Date: Sat Aug 24 15:14:06 MDT 2019 -One-line Summary: Continue adding water tracers to LakeHydrology - -Purpose of changes ------------------- - -Finish implementing water tracers for initial snow-related code in -LakeHydrology. This involved refactoring code in order to reuse existing -code in SnowHydrology rather than having near-duplicates of that code in -LakeHydrology. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#775 (Implement water tracers for initial - snow-related code in LakeHydrology) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none -Many tests took longer, including the PFS test. However, by looking at -more detailed timing numbers in the PFS test, the main increases in time -were in initialization and atm run: lnd run only showed a very small -increase. This suggests that glade slowness was probably primarily -responsible for the increased time. - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: Increased allowed wallclock time for a few tests -These tests took longer, likely due to machine variability. Increasing -their wallclock time to prevent them from timing out. - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- pass - hobart ------ pass - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev058 -Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) -Date: Thu Aug 22 10:02:49 MDT 2019 -One-line Summary: Soil texture interpolation bug-fix - -Purpose of changes ------------------- - - When assigning soil texture values from dataset soil levels to model - soil levels, we should be comparing zsoi (NOT zisoi) in the model with - zisoi on the file, i.e. we should be asking whether the node - center (NOT interface) of a given model level falls between two - interface depths on the file. - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #772 - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[X] clm5_0 - -[X] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: - Unexpected failure of test - SMS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.hobart_nag.clm-tracer_consistency - Bill Sacks did some follow-up testing and concluded that this may be a - compiler-specific issue, so he changed the test from "nag" to "intel" - and generated the new test's corresponding baseline - -Code reviewed by: @billsacks - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - - - tools-tests (test/tools): - - cheyenne - - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: - - Summarize any changes to answers, i.e., - - what code configurations: not clm45 - - what platforms/compilers: all - - nature of change: larger than roundoff/same climate - based on the assumption that shifting soil texture assignments by - one level in model soil levels below the top-most level should not - generate climate-changing differences. - -Detailed list of changes ------------------------- - 1. Changed zisoi to zsoi as described in the Purpose section above. - This caused the larger than roundoff changes. Before the fix some - model soil levels were getting assigned soil textures from a deeper - soil level in the dataset than they should. - 2. In the same section of code I completed the if-block to address all - zsoi vs. zisoifl comparisons. This ensures explicit assignment of - soil textures for all model soil levels and avoids leaving some - model soil levels with the texture assignment of the previous model - soil level. - -Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull/788) - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev057 -Originator(s): sacks (Bill Sacks) -Date: Tue Aug 20 13:17:39 MDT 2019 -One-line Summary: Fix frac_sno bugs - -Purpose of changes ------------------- - -Two bug fixes related to frac_sno, and a third change involving -replacing a frac_sno calculation with a simpler equation that is -algebraically equivalent: - -(1) Fix lake frac_sno always being 0 - (https://github.com/ESCOMP/ctsm/issues/783). This fixes the albedo - calculation (and possibly others) over snow-covered lake surfaces. - -(2) Fix threshold for explicit snow pack initiation to use frac_sno_eff, - not frac_sno (https://github.com/ESCOMP/ctsm/issues/785). For - standard runs (which have use_subgrid_fluxes = .true.), this just - changes answers for urban columns. This also changes answers more - widely for runs with use_subgrid_fluxes = .false. - -(3) Rewrite Swenson & Lawrence 2012 frac_sno equation to be more - straightforward and less sensitive to roundoff errors - (https://github.com/ESCOMP/ctsm/issues/784) - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#783 (frac_sno is always 0 for lake points) -- Resolves ESCOMP/ctsm#785 (Threshold for explicit snow pack initiation - should use frac_sno_eff, not frac_sno) -- Resolves ESCOMP/ctsm#784 (Suggested algebraic rework of frac_sno - calculation) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[X] clm5_0 - -[X] ctsm5_0-nwp - -[X] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, answers change as expected - - Ran most testing on 95dad328 (before 8f1263a7, which removes a - temporary endrun error check). Just reran - SMS_Ld5_D_P48x1.f10_f10_musgs.IHistClm50Bgc.hobart_nag.clm-decStart - on the final version. - - There was a memleak for this test: - - FAIL SMS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.hobart_nag.clm-tracer_consistency MEMLEAK memleak detected, memory went from 1250.830000 to 1518.500000 in 8 days - - I have had memleak issues for this test before - (https://github.com/ESCOMP/ctsm/issues/763), which I have chalked up - to a compiler-specific issue. I have simply increased the tolerance - for memleaks for this test moving forward. - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Larger than roundoff; expected to be same climate in general, - because the only impacts are on urban and lake points, which - represent a small fraction of most grid cells. However, this needs - further investigation. - - See above (under "Purpose of changes") for a description of the - different answer changes in this tag. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - - I verified that change (3) is no greater than roundoff by - temporarily putting in an endrun if the new frac_sno differs from - the old by more than 1e-13; this was not triggered for any test in - the aux_clm test suite. - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A (Keith Oleson will run this) - - URL for LMWG diagnostics output used to validate new climate: N/A (Keith Oleson will run this) - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev056 -Originator(s): sacks (Bill Sacks) -Date: Fri Aug 16 11:44:43 MDT 2019 -One-line Summary: Start adding water tracers to LakeHydrology, and related refactoring - -Purpose of changes ------------------- - -Start adding water tracers to LakeHydrology, beginning with some initial -things done for snow. - -This also includes some significant refactoring to allow LakeHydrology -to reuse some of the same snow code used for non-lake columns. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Partially addresses ESCOMP/ctsm#775 (Implement water tracers for - initial snow-related code in LakeHydrology) - -Known bugs found since the previous tag (include github issue ID): -The following will be fixed in an upcoming tag: -- ESCOMP/ctsm#783 (frac_sno is always 0 for lake points) -- ESCOMP/ctsm#784 (Suggested algebraic rework of frac_sno calculation) -- ESCOMP/ctsm#785 (Threshold for explicit snow pack initiation should - use frac_sno_eff, not frac_sno) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, answers change as expected - - Note: Did most testing on 054dc95b (before the small change in - 7e4e52a9); just ran - LWISO_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_gnu.clm-coldStart - on the final commit - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff - - There are two answer-changes here: - - (1) Roundoff-level changes due to changing some order of operations - for the updating of snow_depth and dz for lakes: The previous - code effectively used (qflx_snow_grnd(c)/bifall(c))*dtime, - whereas the new code uses (qflx_snow_grnd(c)*dtime)/bifall(c); - similarly, the dz update differs. - - (2) A change in FSNO_EFF for lakes: previously, this was set to 0 - when there was no snow. Now this is set consistently with other - landunits, for which it is 1 even if there is no snow. Note that - this only affects the FSNO_EFF diagnostic field, and nothing - else. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - - I confirmed that the order-of-operations change is the only - answer-changing part of this tag by comparing against a one-off - from master with the following diffs; this comparison was - bit-for-bit except for changes in the FSNO_EFF diagnostic field: - - diff --git a/src/biogeophys/LakeHydrologyMod.F90 b/src/biogeophys/LakeHydrologyMod.F90 - index 91ddfc79..9711dad7 100644 - --- a/src/biogeophys/LakeHydrologyMod.F90 - +++ b/src/biogeophys/LakeHydrologyMod.F90 - @@ -126,6 +126,8 @@ subroutine LakeHydrology(bounds, & - real(r8) :: heatsum(bounds%begc:bounds%endc) ! used in case above [J/m^2] - real(r8) :: snowmass ! liquid+ice snow mass in a layer [kg/m2] - real(r8) :: snowcap_scl_fct ! temporary factor used to correct for snow capping - + real(r8) :: temp_snow_depth - + real(r8) :: newsnow - real(r8), parameter :: snow_bd = 250._r8 ! assumed snow bulk density (for lakes w/out resolved snow layers) [kg/m^3] - ! Should only be used for frost below. - !----------------------------------------------------------------------- - @@ -246,8 +248,10 @@ subroutine LakeHydrology(bounds, & - ! U.S.Department of Agriculture Forest Service, Project F, - ! Progress Rep. 1, Alta Avalanche Study Center:Snow Layer Densification. - - - dz_snowf = qflx_snow_grnd(c)/bifall(c) - - snow_depth(c) = snow_depth(c) + dz_snowf*dtime - + temp_snow_depth = snow_depth(c) - + newsnow = qflx_snow_grnd(c)*dtime - + snow_depth(c) = snow_depth(c) + newsnow/bifall(c) - + dz_snowf = (snow_depth(c) - temp_snow_depth)/dtime - if (snl(c) == 0) then - h2osno_no_layers(c) = h2osno_no_layers(c) + qflx_snow_grnd(c)*dtime ! snow water equivalent (mm) - else - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev055 -Originator(s): sacks (Bill Sacks) -Date: Tue Aug 6 14:06:50 MDT 2019 -One-line Summary: Modularize snow cover fraction method - -Purpose of changes ------------------- - -This tag moves the calculation of frac_sno - and the related updates of -snow_depth - into a new set of classes, with one class for each -parameterization (Niu & Yang 2007 and Swenson & Lawrence 2012). - -Previously, the code always calculated frac_sno the new way, but then -possibly overwrote it if using the older Niu & Yang method. The new code -cleans this up, only doing the calculations that are needed for each -method. - -In addition, other code that is specific to one of the two methods is -now moved to a home that makes this dependence on method explicit. This -includes the addition of newsnow to int_snow: previously, int_snow was -always updated using an equation specific to the newer CLM5 -parameterization of frac_sno, which was not appropriate if using the Niu -& Yang parameterization; this doesn't make a difference currently, since -int_snow is only referenced if using the Swenson & Lawrence -parameterization, but this clears up some confusion. Also, time-constant -parameters read from namelist or the netCDF parameter file now reside in -the appropriate class rather than being more global. - -This tag also renames two namelist options to increase clarity: -- subgridflag is renamed to use_subgrid_fluxes, and is now a logical -- oldfflag is renamed to snow_cover_fraction_method, and is now a string - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#502 (oldfflag can NOT be used with - subgridflag==1, and rename subgridflag) -- Resolves ESCOMP/ctsm#503 (Clean up CanopyHydrology) - - This tag does the last piece of cleanup called for in that issue -- Resolves ESCOMP/ctsm#571 (Add a system test: turning on water isotopes - shouldn't change answers) - - This is unrelated to the other changes in this tag - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -This tag renames two namelist options to increase clarity: -- subgridflag is renamed to use_subgrid_fluxes, and is now a logical -- oldfflag is renamed to snow_cover_fraction_method, and is now a string - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: -- Added a LWISO test, which confirms that turning on water isotopes - doesn't change answers for bulk -- Added a test with the newer snow cover fraction method but - use_subgrid_fluxes false (testmod no_subgrid_fluxes) - -Code reviewed by: Sean Swenson, Erik Kluzek - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - ok - - Tests pass; baseline comparisons not done (baseline comparisons - expected to differ) - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- pass - hobart ------ pass - - Additional tests: Compared both of these against ctsm1.0.dev052 (which - should be bit-for-bit with ctsm1.0.dev054): Both were bit-for-bit: - - ERP_D_P36x2_Ld3.f10_f10_musgs.I2000Clm45BgcCrop.cheyenne_gnu.clm-no_subgrid_fluxes - This is a new test, so did not have baselines; I created baselines - from ctsm1.0.dev052 and compared against those - SMS_Ly3.f10_f10_musgs.I2000Clm45BgcCrop.cheyenne_intel.clm-oldhyd_monthly - This was a temporary test for the sake of running a longer test with - the oldhyd testmod. This testmod was created as a one-off by - changing the current oldhyd testmod to inherit from monthly rather - than default. I ran baselines like this from ctsm1.0.dev052 then ran - this test from this branch and compared against those baselines. - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/769 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev054 -Originator(s): sacks (Bill Sacks) -Date: Fri Aug 2 07:57:51 MDT 2019 -One-line Summary: Fix interpolation of surfdat soil layers so we can use interpolation for 10SL case - -Purpose of changes ------------------- - -Previously, on master, there was special-purpose code for the 10SL case -that avoided doing interpolation from the surface dataset to the soil -variables in the model. It would be cleaner - especially now that we -allow user-defined soil layer structures - if we could use the general -interpolation code always, rather than sometimes having special-purpose -code that avoids doing the interpolation. - -This tag accomplishes that generality. In order to preserve answers for -clm45 cases, I needed to make three changes: - -1. The constant 0.025 needed an _r8 appended to it; otherwise, zisoifl - could differ by roundoff from zisoi. - -2. I changed which level is used when zisoi(lev) is exactly equal to - zisoifl(j) for some j: I changed the conditional in the following: - - if (zisoi(lev) >= zisoifl(j) .AND. zisoi(lev) < zisoifl(j+1)) then - clay = clay3d(g,j+1) - sand = sand3d(g,j+1) - om_frac = organic3d(g,j+1)/organic_max - endif - - to: - - if (zisoi(lev) > zisoifl(j) .AND. zisoi(lev) <= zisoifl(j+1)) then - - Previously, when the zisoi values in the model exactly lined up with - the zisoi values in the file, we would set clay in model level j - equal to the value from level j+1 from the surface dataset (and - similarly for sand and om_frac); in the new code, we use level j from - the surface dataset for model level j in this case. - -3. I changed the way zisoifl is calculated for the lowest layer, so that - it matches zisoi(nlevsoi) when running with 10SL_3.5m. Previously, we - had: - - zisoi(10) = 0.38018819123227207690E+01 - zisoifl(10) = 0.34330930154359391437E+01 - - This tag changes zisoifl(10) to match zisoi(10). - -Bugs fixed or introduced ------------------------- - -Known bugs found since the previous tag (include github issue ID): -- #772: Interpolation of clay, sand and om_frac can use the wrong layer - (points out more fundamental issues with this interpolation of layers - from the surface dataset) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: Sam Levis - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- pass - hobart ------ pass - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO (but see note below) - - In principle, the changes in this tag could change answers for some - soil layer structures, but there were no answer changes for any of - the cases covered by the test suite. - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/771 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev053 -Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) -Date: Thu Aug 1 16:56:09 MDT 2019 -One-line Summary: Soil layer definition clean-up and user-defined option - -Purpose of changes ------------------- - - Code clean-up clarifes that there are two types of soil layer - definition: the node-based and the thickness-based. - - User-defined option allows user to specify a soil layer profile in the - form of a dzsoi vector (values in meters) in the thickness-based - approach. - - Default nlevsoi for NWP configurations had to change from 5 to 4 for - consistency with the new error check described in known bugs below. - - Other code clean-up removes a couple of sections of repeating code. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #279 #728 - -Known bugs found since the previous tag (include github issue ID): - #759 (this PR) bug causes model to abort when nlevsoi = nlevgrnd; - bug has been corrected with an error check - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[X] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): - if neither soil_layerstruct_predefined nor soil_layerstruct_userdefined - get specified in the namelist, then the model sets - soil_layerstruct_predefined to the old default setting for - soil_layerstruct (clm5: 20SL_8.5m, clm4.5: 10SL_3.5m) - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): - renamed soil_layerstruct to soil_layerstruct_predefined and added - soil_layerstruct_userdefined - -Changes made to namelist defaults (e.g., changed parameter values): - Default nlevsoi for NWP configurations had to change from 5 to 4 for - consistency with the new error check described in known bugs below - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers --------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: - 1) New test... - ERP_P36x2_D_Ld5.f10_f10_musgs.I2000Ctsm50NwpBgcCropGswpGs.cheyenne_intel.clm-default - replaces existing test - ERS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-rm_indiv_lunits_and_collapse_to_dom - to check the correction described in known bugs above; the new test - together with existing unit tests cover what the old test was testing - - 2) New test and new test type... - SOILSTRUCTUD_Ld5.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-default - ensures that soil_layerstruct_userdefined gives bfb same answers as - soil_layerstruct_predefined = '4SL_2m' when set with the same dzsoi - values. The new test type was put together by: - - listing the test in (1) testlist_clm.xml (as all tests) and (2) config_tests.xml - - creating the file .../cime_config/SystemTests/soilstructud.py named after the test in lower case - -Code reviewed by: @billsacks - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - - - tools-tests (test/tools): - - cheyenne - - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES (just for NWP configurations) - - Summarize any changes to answers, i.e., - - what code configurations: nwp - - what platforms/compilers: all - - nature of change: larger than roundoff/same climate - This is due to the change of nlevsoi from 5 to 4 (more info above). - I confirmed that nwp does return bfb same answers when I revert this - change. - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/ctsm/pull/759 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev052 -Originator(s): sacks (Bill Sacks) -Date: Mon Jul 22 14:02:43 MDT 2019 -One-line Summary: Fix rare soil color bug in mksurfdata_map - -Purpose of changes ------------------- - -Under rare conditions, mksurfdata_map could put the default soil color -in an output cell where there is actually more information. This tag -fixes that issue. None of the out-of-the-box surface datasets are -impacted by this bug, so I have not recreated any surface datasets. (I -checked all out-of-the-box surface datasets except for -surfdata_0.125x0.125_mp24_simyr2000_c150114.nc, because it doesn't get -remade cleanly out of the box.) - -Also: - -- Add some unit tests for the creation of soil color in mksurfdata_map - -- Point to correct (existing) surface dataset for year-1850 at f05 - resolution - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#4 (Minor bug in creation of soil color in - mksurfdata_map: points can be given the default soil color, when they - should have a real color) -- Resolves ESCOMP/ctsm#765 (Year-1850 f05 surface dataset missing from - inputdata repository) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): -- Year-1850 f05 surface dataset now points to a file that actually exists - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - ok - - Most tests pass, including baseline comparisons. The following tests fail, but also failed for me on master: - - 019 smiS4 TSMscript_tools.sh ncl_scripts getregional_datasets.pl getregional ....................\c - rc=6 FAIL - 020 bliS4 TBLscript_tools.sh ncl_scripts getregional_datasets.pl getregional ....................\c - rc=4 FAIL - 027 smf84 TSMscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_clm4_5^buildtools ....................\c - rc=6 FAIL - 028 blf84 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_clm4_5^buildtools ....................\c - rc=4 FAIL - 029 smfc4 TSMscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Cycle_clm4_5^buildtools ..............\c - rc=6 FAIL - 030 blfc4 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Cycle_clm4_5^buildtools ..............\c - rc=4 FAIL - 031 smfg4 TSMscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Global_clm4_5^buildtools .............\c - rc=6 FAIL - 032 blfg4 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Global_clm4_5^buildtools .............\c - rc=4 FAIL - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- not run - hobart ------ not run - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev051 -Originator(s): sacks (Bill Sacks) -Date: Fri Jul 19 13:26:25 MDT 2019 -One-line Summary: Update water tracers for remainder of first stage of hydrology - -Purpose of changes ------------------- - -Main change is to do tracer updates for final pieces of first stage of -hydrology: HandleNewSnow and UpdateFracH2oSfc. Along with this, I have -introduced greater modularity into these routines (breaking the -operations down into more granular steps). - -Other changes included here (somewhat related to the main changes) are: - -- Added a routine that resets checked tracers to bulk*ratio to allow - running the tracer consistency check for more than one time step; we - now run it for 10 days - -- Change logic for rain-snow conversion terms: Use rain diff in rain to - snow, snow diff in snow to rain. This is less sensitive to roundoff - errors, and was needed in order to get the 10-day tracer consistency - test to pass. - -- Setting of qflx_snow_h2osfc moved to CanopyInterceptionAndThroughfall - -- Add col%lun_itype. col%lun_itype(ci) is the same as - lun%itype(col%landunit(ci)), but is often a more convenient way to - access this type. I got tired of having to get the landunit index just - for the sake of getting the landunit's type of a given column. I have - NOT gone through the code and replaced lun%itype(l) with - col%lun_itype(c) where applicable, but this will be useful for the - future. - -- Removed unnecessary code for backwards compatibility of FH2OSFC from - restart files - -- Point to slightly modified initial conditions files for two CLm45 - initial conditions files. These two had FH2OSFC > 0 for some glc_mec - points. I'm not sure how that came to be, but Sean Swenson and I think - that shouldn't be the case. This caused soil balance errors in these - tests: - - ERS_Ly5_P72x1.f10_f10_musgs.IHistClm45BgcCrop.cheyenne_intel.clm-cropMonthOutput - SMS_D_Ld1.f09_g17.I1850Clm45BgcCruGs.cheyenne_intel.clm-default - - I'm fixing the problem by pointing to updated files with FH2OSFC set - to 0 for special landunits, using the following python: - - ctypel = dat.variables['cols1d_ityplun'][:] - dat.variables['FH2OSFC'][ctypel > 2] = 0 - -- Small cime update to fix the SHAREDLIBBUILD phase of - ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#718 (Implement water tracers for HandleNewSnow - and FracH2oSfc) -- Resolves ESCOMP/ctsm#498 (Do tracer consistency checks every time - step, not just first) - -CIME Issues fixed (include issue #): -- ESCMI/cime#3717 (Cheyenne ESMF missing for WACCM X) - -Known bugs introduced in this tag (include github issue ID): -- ESCOMP/ctsm#762 (Water tracers: Make sure calls to ResetCheckedTracers - are removed) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): -- If you have an initial conditions file with non-zero FH2OSFC for - glacier (this was the case for some out-of-the-box clm45 files, which - are now fixed), may run into soil balance errors. To fix this, set - FH2OSFC to 0 in your restart file for all special landunits. - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): -- Point to slightly modified initial conditions files for two CLm45 - initial conditions files: see above for details. - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: -- Changed tracer consistency test to 10 days rather than a single time step - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, some roundoff-level diffs in baseline - comparisons, as noted below - - Also, in order to have a more powerful test of the changes in - SurfaceWaterMod (since the relevant code isn't triggered very often), - I introduced the following diffs: - - diff --git a/src/biogeophys/SurfaceWaterMod.F90 b/src/biogeophys/SurfaceWaterMod.F90 - index 1bc03cae..be656a15 100644 - --- a/src/biogeophys/SurfaceWaterMod.F90 - +++ b/src/biogeophys/SurfaceWaterMod.F90 - @@ -12,6 +12,7 @@ module SurfaceWaterMod - use shr_spfn_mod , only : erf => shr_spfn_erf - use clm_varcon , only : denh2o, denice, roverg, wimp, tfrz, pc, mu, rpi - use clm_varpar , only : nlevsno, nlevgrnd - + use clm_varctl , only : iulog - use clm_time_manager , only : get_step_size - use column_varcon , only : icol_roof, icol_road_imperv, icol_sunwall, icol_shadewall, icol_road_perv - use decompMod , only : bounds_type - @@ -201,7 +202,7 @@ subroutine BulkDiag_FracH2oSfc(bounds, num_soilc, filter_soilc, & - SHR_ASSERT_FL((ubound(qflx_too_small_h2osfc_to_soil, 1) == bounds%endc), sourcefile, __LINE__) - - ! arbitrary lower limit on h2osfc for safer numerics... - - min_h2osfc=1.e-8_r8 - + min_h2osfc=1.e0_r8 - - do f = 1, num_soilc - c = filter_soilc(f) - @@ -230,6 +231,9 @@ subroutine BulkDiag_FracH2oSfc(bounds, num_soilc, filter_soilc, & - - else - frac_h2osfc(c) = 0._r8 - + if (h2osfc(c) > 0._r8) then - + write(iulog,*) 'WJS: in else' - + end if - qflx_too_small_h2osfc_to_soil(c) = h2osfc(c) / dtime - ! The update of h2osfc is deferred to later, keeping with our standard - ! separation of flux calculations from state updates, and because the state - - With those diffs, I ran the tracer consistency test; it passed. In - addition, I ran - SMS_D_Ld1_P4x1.f10_f10_musgs.I2000Clm50BgcCropQianRsGs.bishorn_gnu.clm-default - with comparison against master, with the following diffs on master - (the first change changes behavior to force the relevant code to be - triggered, and is the same on master and on the branch; the second - change on master divides then multiplies by dtime to avoid - roundoff-level diffs): - - diff --git a/src/biogeophys/SurfaceWaterMod.F90 b/src/biogeophys/SurfaceWaterMod.F90 - index 959d539b..4a4a4824 100644 - --- a/src/biogeophys/SurfaceWaterMod.F90 - +++ b/src/biogeophys/SurfaceWaterMod.F90 - @@ -77,7 +77,7 @@ subroutine FracH2oSfc(bounds, num_nolakec, filter_nolakec, & - ) - - ! arbitrary lower limit on h2osfc for safer numerics... - - min_h2osfc=1.e-8_r8 - + min_h2osfc=1.e0_r8 - - call waterstatebulk_inst%CalculateTotalH2osno(bounds, num_nolakec, filter_nolakec, & - caller = 'FracH2oSfc', & - @@ -112,7 +112,7 @@ subroutine FracH2oSfc(bounds, num_nolakec, filter_nolakec, & - - else - frac_h2osfc(c) = 0._r8 - - h2osoi_liq(c,1) = h2osoi_liq(c,1) + h2osfc(c) - + h2osoi_liq(c,1) = h2osoi_liq(c,1) + (h2osfc(c) / get_step_size()) * get_step_size() - h2osfc(c)=0._r8 - endif - - This test passed and was bit-for-bit with master with the above changes. - - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: Many/all - - what platforms/compilers: All - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Roundoff: just roundoff-level changes in FSH_PRECIP_CONVERSION, - FSH_TO_COUPLER, l2x_Fall_sen due to refactored calculation of - FSH_PRECIP_CONVERSION - - If bitwise differences were observed, how did you show they were no worse - than roundoff? via summarize_cprnc_diffs - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- cime: branch_tags/cime5.8.3_chint17-03 -> branch_tags/cime5.8.3_chint17-04 - Fixes ESMCI/cime#3171 - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev050 -Originator(s): slevis (Samuel Levis,SLevisConsulting LLC,303-665-1310) -Date: Mon Jul 15 11:40:09 MDT 2019 -One-line Summary: dz --> dz_lake bug-fix in LakeTemperatureMod.F90 line 960 - -Purpose of changes ------------------- - - Bug-fix to prevent the model from aborting when running with fewer soil - layers than lake layers; not to imply that this was not a bug when the - model wasn't aborting. It was. - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #760 - -Known bugs found since the previous tag (include github issue ID): #759 bug causing model to abort when nlevsoi = nlevgrnd - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers --------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: @dlawrenncar @billsacks - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - - - tools-tests (test/tools): - - cheyenne - - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: - - Summarize any changes to answers, i.e., - - what code configurations: use_lch4 = .true. - - what platforms/compilers: all - - nature of change: diagnostic variable WTGQ only - Confirmed this on cheynne and hobart by running - ./summarize_cprnc_diffs -baseline .../tests_0712... -testid '*' - and inspecting the file cprnc.summary.*.by_varname - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/ctsm/pull/761 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev049 -Originator(s): erik (Erik Kluzek) -Date: Sun Jun 23 20:56:55 MDT 2019 -One-line Summary: Update mosart and intel to intel-19 on cheyenne - -Purpose of changes ------------------- - -Update mosart to trunk tag (that has a roundoff change to history file -output). And update intel compiler on cheyenne to intel-19. - -Bugs fixed or introduced None ------------------------- - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None - -Changes made to namelist defaults (e.g., changed parameter values): None - -Changes to the datasets (e.g., parameter, surface or initial files): None - -Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] None - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None - -Changes to tests or testing: None - -Code reviewed by: self - -CTSM testing: regular - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: Yes - - Summarize any changes to answers, i.e., - - what code configurations: some compsets with mosart - - what platforms/compilers: cheyenne/intel - - nature of change: roundoff - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, and mosart - mosart to mosart1_0_33 - cime to branch_tags/cime5.8.3_chint17-03 - -Pull Requests that document the changes (include PR ids): #753 -(https://github.com/ESCOMP/ctsm/pull) - #753 -- Update cheyenne to intel/19 and update mosart - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev048 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Sun Jun 23 15:16:01 MDT 2019 -One-line Summary: Updates for buildlib changes and cime and externals updates - -Purpose of changes ------------------- - -Update of most externals: cime, mosart, rtm, cism. The cime update also includes a required CESM-wide -change in buildlib. Uses a function to get the Macros filename "get_standard_makefile_args". -The cime update brought in some answer chagnes, with an update of the intel compiler (but we backed those -out by using a cime branch). There is also a roundoff change by going to the trunk version of RTM. - -Bugs fixed or introduced None ------------------------- - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None - -Changes made to namelist defaults (e.g., changed parameter values): None - -Changes to the datasets (e.g., parameter, surface or initial files): None - -Substantial timing or memory changes: None - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None - -Changes to tests or testing: None - -Code reviewed by: @jedwards, self - - -CTSM testing: regular - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - tools-tests (test/tools): - - cheyenne - PASS - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - PASS - - python testing (see instructions in python/README.md; document testing done): - - cheyenne - PASS (for python3) - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: Yes, but only for a few cases (compsets with RTM) - - Summarize any changes to answers, i.e., - - what code configurations: With RTM - - what platforms/compilers: All - - nature of change: roundoff - fieldlist is different for CISM in some cases - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, mosart, rtm, cism - cime to branch_tags/cime5.8.3_chint17-02 - cism to cism2_0_68 - rtm to rtm1_0_68 - mosart to nldas-grid.n02_mosart1_0_31 - -Pull Requests that document the changes (include PR ids): #752 -(https://github.com/ESCOMP/ctsm/pull) - - #752 -- buildlib, cime and externals update - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev047 -Originator(s): sacks (Bill Sacks) -Date: Sun Jun 16 13:04:38 MDT 2019 -One-line Summary: Fix negative snow compaction during snow melt - -Purpose of changes ------------------- - -Fix an issue reported by @kjetilaas: In the presence of surface water, -the old and new snow cover fractions are inconsistently calculated in -subroutine "SnowCompaction". This can result in significant negative -compaction (snow depth increase) during snow melt. - -More details from @kjetilaas (copied from -https://github.com/escomp/ctsm/issues/573): - -There is an inconsistency in the calculation of snow cover fraction -(FSNO) in the SnowCompaction subroutine when there is surface water -present. The actual snow cover is limited to 0.99 when surface water is -present (and the surface water fraction is set to 0.01). However, -SnowCompaction recalculates the old FSNO without accounting for this -limitation. This results in an apparent decrease in FSNO, and -corresponding negative snow compaction from snow melt (ddz3). - -This can result in substantial, artificial increase in snow depth during -summer (can be more than 0.5 m during a single season). - -The problem might be masked in monthly output, but could be significant -whenever snow cover is close to 1 and surface water present. Snow mass -is indirectly affected by this as radiation and temperature fluxes in -the snow pack will be affected by artificially thick snow layers. - -This tag fixes this issue. The fix was implemented and tested by -@swensosc (Sean Swenson). - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#573 (Snow depth increase due to inconsistent snow - cover fraction calculation) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[X] clm5_0 - -[X] ctsm5_0-nwp - -[X] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: Sean Swenson, @kjetilaas, Bill Sacks - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, answers change as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Larger than roundoff/same climate - - Sean Swenson ran the LMWG diagnostics package and looked at the - results with Keith Oleson. Their main findings were: - - - Snow depth is a bit smaller over Greenland and polar regions on - average, as expected (up to 5-10% decrease in average snow depth - averaged over the Canadian Arctic) - - - There is a small increase in h2osno over Greenland: about 30 mm - averaged over Greenland; it looks like the main changes are - around the coasts (which makes sense given that this bug only - affects vegetated landunits) - - - There are small changes in runoff over Greenland - - - Changes in snow cover fraction are tiny - - - Overall, this doesn't look climate changing, but could - potentially have a significant impact on select grid cells, and - on some variables in polar regions - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev046 -Originator(s): sacks (Bill Sacks) -Date: Sat Jun 15 15:54:44 MDT 2019 -One-line Summary: Separate the two uses of h2osno - -Purpose of changes ------------------- - -Until now, h2osno has been used in two ways: - -1. When there are explicit snow layers, h2osno is the sum of snow - (liquid + ice) in all layers - -2. When there is a little bit of snow, but not enough to create a snow - layer, h2osno gives the amount of this very thin snow pack (assumed - to be all ice) - -This is confusing and complicates the addition of water tracers to the -code. This tag separates h2osno into two different variables: - -1. h2osno_no_layers is a fundamental state variable that gives the - amount of snow in the case where we don't have explicit snow layers - -2. h2osno_total is purely a diagnostic variable that is the sum of snow - in all explicit layers, plus h2osno_unresolved. This exists in - waterdiagnosticbulk_type, but the version there is just set once at - the end of the time step, so that version is only meant for - diagnostic (history) output. Code that needs the current sum of - h2osno at a given point now computes it locally, via a new method on - waterstate_type: CalculateTotalH2osno. If running in debug mode, that - routine also performs some consistency checks. - -Also, an unrelated change to prevent user from trying to interpolate a -file onto itself. - -Also, add a compset for testing, which is good for use on my mac. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#733 (Make h2osno purely a diagnostic variable) -- Resolves ESCOMP/ctsm#749 (h2osno inconsistent when interpolating from - initial conditions with different snow layers) -- Resolves ESCOMP/ctsm#750 (Prevent user from trying to use the same - filename for init_interp source and destination files) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none (possibly a small improvement -in timing based on PFS run time) - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: self - - -CTSM testing: - - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass; baseline comparisons fail as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Mostly roundoff; greater than roundoff/same climate for cases for - which number of snow layers is less in the case than in its - initial conditions file, due to fixing #749 - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - - There was one point where h2osno_total differed from the old h2osno - by roundoff, as verified by a run of the test suite (where I verified - that (a) it only differed by 1e-11 or less, and (b) if I reset it, - there were just roundoff-level changes in a few diagnostic - fields). That one place with roundoff-level diffs can lead to - propagation of diffs, causing differences in many fields in the final - run of the test suite. In particular: I ran the test suite on - 69823de4 (which had this temporary check and reset of h2osno_total - vs. old h2osno). For nearly all tests, there were only roundoff-level - changes in a few diagnostic fields. I then removed the temporary - check and reset and ran the test suite on the result - (4353cc90). Finally, I ran the test suite on the final, cleaned-up - code, with comparison against 4353cc90 and verified bfb. - - In my testing on 69823de4: There were a few tests with greater than - roundoff-level changes due just to differences in the initial value - of h2osno_total (which was incorrect in the old due to #749). I - verified that these only had roundoff-level changes in a few - diagnostic fields if I used the following diffs in both the baseline - and my branch, indicating that the diffs just arose due to the fix of - #749: - - diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 - index 793b36ac..f10ee5e1 100644 - --- a/src/main/clm_initializeMod.F90 - +++ b/src/main/clm_initializeMod.F90 - @@ -762,6 +762,18 @@ subroutine initialize2( ) - !$OMP END PARALLEL DO - end if - + do c = bounds_proc%begc, bounds_proc%endc - + if (col%snl(c) < 0) then - + water_inst%waterstatebulk_inst%h2osno_col(c) = 0._r8 - + do j = col%snl(c)+1, 0 - + water_inst%waterstatebulk_inst%h2osno_col(c) = & - + water_inst%waterstatebulk_inst%h2osno_col(c) + & - + water_inst%waterstatebulk_inst%h2osoi_ice_col(c,j) + & - + water_inst%waterstatebulk_inst%h2osoi_liq_col(c,j) - + end do - + end if - + end do - + - end subroutine initialize2 - end module clm_initializeMod - - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: n/a - - URL for LMWG diagnostics output used to validate new climate: n/a - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev045 -Originator(s): sacks (Bill Sacks) -Date: Thu Jun 6 12:26:57 MDT 2019 -One-line Summary: Recalculate h2osno for the sake of SnowCapping - -Purpose of changes ------------------- - -SnowCapping decides whether to remove excess snow based on -h2osno. However, at the point where this is called,h2osno is out of sync -with (h2osoi_liq + h2osoi_ice): Those variables can be changed slightly -in SnowWater (which is called before SnowCapping), yet h2osno isn't -recalculated based on those changes. - -I don't think this causes a big problem in practice, but it seems like -it would improve code understandability if we had the general rule that -any code that references h2osno is using a version of h2osno that is in -sync with (h2osoi_liq + h2osoi_ice). This is also needed to prevent -answer changes in an upcoming major refactor. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#736 - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: Sean Swenson signed off on the change, but didn't -review the final code - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, answers change as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Larger than roundoff/same climate - - Answer changes are expected to be small, since this should just - change the timing of snow capping a bit, but I haven't looked - closely at the magnitude of the answer changes. - - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev044 -Originator(s): sacks (Bill Sacks) -Date: Thu Jun 6 12:14:39 MDT 2019 -One-line Summary: Make wetland snow resetting behavior more explicit - -Purpose of changes ------------------- - -There is some code that zeroes out h2osno over thawed wetlands. It seems -like the intended behavior here is to zero out the entire snow -pack. Currently, however, this only zeros out a very thin (zero-layer) -snow pack. For now, I'm adding an snl==0 conditional to make this -behavior explicit; long-term, we'd like to change this to actually zero -out the whole snow pack. (At that time, this code block should probably -be moved to a more appropriate home, as noted in comments in issue -ESCOMP/ctsm#735.) - -Also, unrelated change in run_sys_tests: support machine-specific -baseline directory, in order to support new default location for CTSM -baselines on cheyenne. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Partially addresses, but does NOT fix, ESCOMP/ctsm#735 - -Known bugs introduced in this tag (include github issue ID): -- Partially addresses, but does NOT fix, ESCOMP/ctsm#735 - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: Sean Swenson and Keith Oleson approved this change, -though didn't actually review the final code. - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - python testing (see instructions in python/README.md; document testing done): - - (any machine) - pass on cgdm-bishorn - make python=python2 test - make pyhton=python3 test - make lint - - regular tests (aux_clm): - - cheyenne ---- pass - hobart ------ pass - - Also ran SMS_Ly1.f09_g17.I2000Clm50SpGs.cheyenne_intel.clm-monthly - with comparison against baselines: passed and bit-for-bit. - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: NO (but see notes below) - - It seems theoretically possible for this to change answers, but no - answer changes were observed in the aux_clm test suite or - SMS_Ly1.f09_g17.I2000Clm50SpGs.cheyenne_intel.clm-monthly. - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev043 -Originator(s): erik (Erik Kluzek) -Date: Wed Jun 5 10:17:06 MDT 2019 -One-line Summary: Fix FUN bug (frac_ideal_C_use was backwards in regard to delta_CN), and replace Ball-Berry mbbopt with the CLM4.5 version - -Purpose of changes ------------------- - -Carbon allocation to uptake responds to CN(uptake-cost) and CN(actual). The intended implementation is: For C:N -less than the target C:N, C allocation is reduced with cost. For C:N greater than the target C:N, C allocation -is increased with high C:N. However, the actual implementation is reversed. This change fixes that problem. - -Also the Ball-Berry mbbopt values had been changed in the creation of CLM5.0, as part of the tuning, but the new -values don't work well (as our final tuning uses Medlyn photosynshesis rather than Ball-Berry). This brings the values -for Ball-Berry for CLM5.0 back to the CLM4.5 values. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #704 #705 - - Fixes #705 -- Ball-Berry parameters in CLM5.0 should go back to the previous values in CLM4.5 - Fixes #704 -- FUN code logic to reduce or increase carbon allocation used for uptake is reversed - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[X] clm5_0 - -[X] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None - -Changes made to namelist defaults (e.g., changed parameter values): New clm5.0 paramdata file - -Changes to the datasets (e.g., parameter, surface or initial files): mbbopt now use the clm4_5 values - rather than the pretuned clm5_0 values (before Medlyn was being used) - -Substantial timing or memory changes: None - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None - -Changes to tests or testing: None - -Code reviewed by: self, olyson - - -CTSM testing: regular - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS (134 tests are different from baseline as expected) - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: Yes! - - Summarize any changes to answers, i.e., - - what code configurations: Anything with use_FUN=T (so Clm50Bgc compsets) - Also with Clm5.0 and Ball-Berry (stomatalcond_method='Ball-Berry1987') (so Clm50Nwp compsets) - - what platforms/compilers: All - - nature of change: climate is similar - - "Our assessment is that the impact is relatively small, but would affect climate; - however it doesn’t appear to strongly affect transient C response." - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - Experiments were done on the release branch - - casename: oleson/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_1850 - oleson/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_hist - - URL for LMWG diagnostics output used to validate new climate: - -http://webext.cgd.ucar.edu/I1850/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_1850/lnd/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_1850.21_40-clm50_release-clm5.0.15_2deg_GSWP3V1_1850.21_40/setsIndex.html - -We've also completed a historical run. Diagnostics are here: - -http://webext.cgd.ucar.edu/I20TR/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_hist/lnd/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_hist.1995_2014-clm50_release-clm5.0.15_2deg_GSWP3V1_hist.1995_2014/setsIndex.html - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None - -Pull Requests that document the changes (include PR ids): #727 -(https://github.com/ESCOMP/ctsm/pull) - - #727 -- Fix the FUN bug, where an if statement was backwards - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev042 -Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) -Date: Tue May 21 23:29:31 MDT 2019 -One-line Summary: Rename, correct, and simplify parameters dewmx and sno_stor_max - -Purpose of changes ------------------- - - To rename - dewmx to liq_canopy_storage_scalar - sno_stor_max to sno_canopy_storage_scalar - in the code and in the clm45 and clm50 param files. - - To change snocanmx, liqcanmx, and fcansno to... - snocanmx = params_inst%snow_canopy_storage_scalar(p) * (elai(p) + esai(p)) - liqcanmx = params_inst%liq_canopy_storage_scalar(p) * (elai(p) + esai(p)) - fcansno(p) = (snocan(p) / (vegt * params_inst%sno_stor_max))**0.15_r8 - - Rewrote fwet(p) to follow the same format as fcansno(p). - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #710 - Fixes #710 -- rename dewmx - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None - -Changes made to namelist defaults (e.g., changed parameter values): New default parameter file - -Changes to the datasets (e.g., parameter, surface or initial files): - Pointing to new clm45 and clm50 param files containing the two renamed - parameters listed above. - -Substantial timing or memory changes: None - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None - -Changes to tests or testing: None - -Code reviewed by: - @billsacks - -CTSM testing: regular - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS (196 different because of new param file) - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - Roundoff changes were expected. - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: Yes! - - Summarize any changes to answers, i.e., - - what code configurations: ALL - - what platforms/compilers: ALL - - nature of change: roundoff - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - The code modifications causing the change were of the order-of-calculations - type in two lines of code. - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None - -Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/ctsm/pull/719 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev041 -Originator(s): sacks (Bill Sacks) -Date: Fri May 17 06:02:38 MDT 2019 -One-line Summary: Add water tracers to CanopyHydrologyMod - -Purpose of changes ------------------- - -Major overhaul of CanopyHydrologyMod in order to support water tracers. - -The part of CanopyHydrology that was actually dealing with canopy -hydrology has now been broken out into a number of small routines in -order to separate flux calculations from state updates. This is needed -in order to calculate tracer versions of the relevant variables, which -is now done here. - -The parts of CanopyHydrology that were NOT dealing with canopy hydrology -have been moved to more appropriate homes. They have not yet been -tracerized, but will be soon. - -This also makes some minor changes to diagnostic fields related to -canopy hydrology. Of particular note: QDRIP now has a different meaning: -it now corresponds to the excess liquid water that runs off from the -canopy (and is inactive by default). - -The design of this broken-out code was developed in consultation with -Mike Barlage, Erik Kluzek, Negin Sobhani, Sean Swenson and Mariana -Vertenstein. We plan to apply this design moving forward to other parts -of the code that need tracerization. See also -. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#360 - Implement water isotopes for - CanopyHydrology -- Resolves ESCOMP/ctsm#709 - QDRIP diagnostic field misleadingly named -- Partially addresses ESCOMP/ctsm#503 - Clean up CanopyHydrology - (We still need to clean up / tracerize the parts that have now been - moved elsewhere.) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): -- Changed meaning of QDRIP diagnostic field: it now corresponds to - qflx_liqcanfall rather than qflx_prec_grnd_patch, and is default - inactive. (There is no longer a diagnostic field corresponding to - qflx_prec_grnd_patch, but there are separate diagnostic fields for the - rain and snow portions of this, both default inactive.) - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none -- checked timing of hydro1 timer vs. previous canhydro timer from my - dev039 testing: differences are negligible - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: -- Design reviewed by Mike Barlage, Erik Kluzek, Negin Sobhani, Sean - Swenson and Mariana Vertenstein -- Final code reviewed only by self - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, baseline comparisons fail as expected - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - roundoff - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - - Ensured no-greater-than-roundoff-level by: - - First, generated baselines using code with these diffs (note extra - parentheses in multiplication): - - diff --git a/src/biogeophys/CanopyHydrologyMod.F90 b/src/biogeophys/CanopyHydrologyMod.F90 - index f848f520..31c8c550 100644 - --- a/src/biogeophys/CanopyHydrologyMod.F90 - +++ b/src/biogeophys/CanopyHydrologyMod.F90 - @@ -338,8 +338,8 @@ subroutine CanopyHydrology(bounds, & - ! Intercepted precipitation [mm/s] - qflx_prec_intr(p) = forc_snow(c)*fpisnow + qflx_liq_above_canopy(p)*fpi - ! storage of intercepted snowfall, rain, and dew - - snocan(p) = max(0._r8, snocan(p) + dtime*forc_snow(c)*fpisnow) - - liqcan(p) = max(0._r8, liqcan(p) + dtime*qflx_liq_above_canopy(p)*fpi) - + snocan(p) = max(0._r8, snocan(p) + dtime*(forc_snow(c)*fpisnow)) - + liqcan(p) = max(0._r8, liqcan(p) + dtime*(qflx_liq_above_canopy(p)*fpi)) - - ! Initialize rate of canopy runoff and snow falling off canopy - qflx_snocanfall(p) = 0._r8 - - - Then ran test suite on 1cc9d38a. This is very close to the final - branch, but had a few small tweaks in place to get bit-for-bit: - - 1. Under some conditions, the final branch code resets slightly - negative snocan and liqcan to 0, where master did not. This - commit puts in place temporary code to maintain the slightly - negative values under these conditions, along with a check to - ensure that the values are really always only slightly negative - in this situation. - - 2. When snocan > snocanmx, master reset snocan to exactly snocanmx, - whereas the final branch code can result in snocan being - roundoff-level different from snocanmx, and similar for - liqcan. This commit puts in place temporary code to set snocan - to snocanmx under appropriate circumstances, and liqcan to - liqcanmx, along with a check to ensure that this is only leading - to roundoff-level changes in these state variables. - - 3. Multiplies then divides a flux by dtime in one place - - 4. Has parentheses around a partial sum to ensure same order of - operations as before - - This was bfb with the baselines generated with the diff noted - above, except for roundoff-level changes in SNOCAN in one grid cell - in just one test - (SMS_D_Ld1.f19_g17.I1850Clm45Cn.hobart_gnu.clm-default; old: - -8.15e-322, new: -2e-323). - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): -None. But see -https://github.com/billsacks/prototypes-ctsm-canopyhydrology_tracers, -which was the source of our design discussions and contains notes from -these discussions. - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev040 -Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) -Date: Fri May 03 10:34:46 MDT 2019 -One-line Summary: Move some hard-coded parameters from code to params.nc file - -Purpose of changes ------------------- - - Reduce the number of parameters that get hardwired directly in the code - by placing in the params.nc file where they become visible and easier - to modify. - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #680 - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users: - None - -Changes to CTSM's user interface: - Parameters that were hardwired in the code can now be seen and changed - in the params.nc file. - -Changes made to namelist defaults (e.g., changed parameter values): - None - -Changes to the datasets (e.g., parameter, surface or initial files): - Various parameters have moved out of the code and into the params.nc file. - -Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] - -Notes of particular relevance for developers: - None ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): - None - -Changes to tests or testing: - None - -Code reviewed by: - @ekluzek - @billsacks - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - - - tools-tests (test/tools): - - cheyenne - - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - Answers change as expected. - -CTSM tag used for the baseline comparisons: - ctsm1.0.dev039 - -Answer changes --------------- - -Changes answers relative to baseline: YES - Summarize any changes to answers, i.e., - - what code configurations: ALL - - what platforms/compilers: ALL - - nature of change: single-precision roundoff - Changes are due to four parameters: - accum_factor - ko25_coef - kc25_coef - frac_sat_soil_dsl_init - that were not declared "_r8" when hardwired in the code, - while now they are declared "double" in the params.nc files. I - showed that the change was no greater than single-precision roundoff - by writing the new and old values to the lnd and cesm log files and - confirming differences smaller than 1.e-6. - -Detailed list of changes ------------------------- - - - Updated the clm5 and clm4.5 params.nc files to contain the previously - hard-coded parameters that Katie Dagon recommended moving out of the - code (listed here: https://docs.google.com/spreadsheets/d/1cRmcB0xz7CjVP6ljUoCehJx49Usxsore5ma4mWcvQwM/edit#gid=0) - - Now read the parameters in the modules that use them - -Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/ctsm/pull/684 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev039 -Originator(s): sacks (Bill Sacks) -Date: Wed May 1 11:12:34 MDT 2019 -One-line Summary: Remove excess canopy liquid/snow regardless of temperature - -Purpose of changes ------------------- - -Previously: if it was above freezing, snow was allowed to accumulate on -the canopy beyond the specified capacity, and if it was below freezing, -liquid was allowed to accumulate beyond the specified capacity. Sean -Swenson, Keith Oleson and Dave Lawrence agreed that this seems wrong. - -This tag changes the behavior so that both liquid and snow canopy -capacities are enforced regardless of temperature. - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#699 (Canopy liquid and snow capacities not - enforced consistently?) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[X] clm5_0 - -[X] ctsm5_0-nwp - -[X] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: Keith Oleson - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, answers change as expected - -CTSM tag used for the baseline comparisons: ctsm1.0.dev038 - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - larger than roundoff; likely same climate, but this still requires - investigation - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A (Keith Oleson will run this soon) - - URL for LMWG diagnostics output used to validate new climate: N/A - (Keith Oleson will run this soon) - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/703 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev038 -Originator(s): sacks (Bill Sacks) -Date: Wed May 1 10:53:02 MDT 2019 -One-line Summary: Support for NWP configuration, NLDAS grid and NLDAS datm forcing - -Purpose of changes ------------------- - -This tag includes a set of changes that, together, provide support for -running an initial Numerical Weather Prediction version of CTSM over the -Continental U.S. - -(1) NWP configuration: The changes in this configuration relative to the - climate (CLM5) configuration mainly target decreasing runtime by - removing features that are expensive and not as important for NWP - time scales (days to months rather than many years) and space scales - (high resolution): - - - Single dominant landunit; if vegetated, single dominant PFT - - - Only 5 soil layers, down to 3 m - - - Only 5 snow layers - - - Plant hydraulic stress off - - - Ball-Berry rather than Medlyn stomatal conductance method (this is - a side-effect of turning plant hydraulic stress off, and is not - itself a critical aspect of the NWP configuration) - - - Maximum of 3 iterations to compute canopy fluxes - - - MEGAN is off - - Note that the NWP compset triggers changes in two new xml variables: - CLM_CONFIGURATION ('clm' vs. 'nwp'; this controls things of a more - scientific nature, like whether plant hydraulic stress is on or - off), and CLM_STRUCTURE ('standard' vs. 'fast'; this controls - structural things like the maximum number of landunits per grid cell - and the soil layer structure). Thus, you can create a case that is a - hybrid between the CLM and NWP configurations by changing these two - xml variables independently. - -(2) NLDAS2 regional grid: 0.125 deg grid over the Continental U.S. - -(3) Updated version of MOSART with support for the same NLDAS2 regional - grid - -(4) NLDAS2 data atmosphere forcing: over the same regional grid; forcing - data are available from 1980 - 2018. (We have excluded 1979 because - a small amount of data were missing for that year, and we didn't - have a good way to handle those missing data.) - -These changes can be used independently or all together. However, note -that you will get garbage if you try to use the new NLDAS2 datm forcing -for a run that extends beyond the boundaries of the NLDAS2 domain. - -There are three new NWP compsets: -- I2000Ctsm50NwpSpGswpGs: GSWP3 datm forcing; meant for global runs or - regional runs outside the NLDAS domain -- I2000Ctsm50NwpSpNldasGs: NLDAS2 datm forcing; meant for regional runs - over the NLDAS domain or some portion of it -- I2000Ctsm50NwpSpNldasRsGs: Same as above, but with a stub runoff model - in place of MOSART, for runs that aren't interested in having a runoff - model and for which you want improved throughput - -The alias for the new grid is: nldas2_rnldas2_mnldas2 (indicating that -we're using the nldas2 grid for land/atmosphere, runoff ('r') and the -ocean mask ('m'). - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#451 (Add NWP physics option) -- Resolves ESCOMP/ctsm#452 (Add an NWP compset) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): -- The NWP configuration is still a work in progress -- The NLDAS surface data set is still a work in progress (will soon - update this to use high-res PFTs) - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -- New xml variables: - - CLM_CONFIGURATION (will eventually be renamed to CTSM_CONFIGURATION) - - CLM_STRUCTURE (will eventually be renamed to CTSM_STRUCTURE) -- New namelist variable: - - itmax_canopy_fluxes - -Changes made to namelist defaults (e.g., changed parameter values): -No changes for existing CLM compsets; new defaults for NWP compsets - -Changes to the datasets (e.g., parameter, surface or initial files): -No changes for existing grids; new surface dataset for nldas2 grid - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: -- New tests covering NWP compsets, nldas grid and nldas datm forcing - -Code reviewed by: Mike Barlage, Erik Kluzek - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - ok - - tests pass; namelists change as expected - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - regular tests (aux_clm): - - cheyenne ---- pass - hobart ------ pass - -CTSM tag used for the baseline comparisons: ctsm1.0.dev037 - - -Answer changes --------------- - -Changes answers relative to baseline: NO - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- MOSART: release-cesm2.0.00 -> nldas-grid.n01_mosart1_0_31 -- CIME: ctsm/ctsm1.0/cime5.7.9/n04 -> ctsm/ctsm1.0/cime5.7.9/n05 - -Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/682 -- https://github.com/ESCOMP/ctsm/pull/685 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev037 -Originator(s): sacks (Bill Sacks) -Date: Mon Apr 29 16:11:47 MDT 2019 -One-line Summary: Change year alignment for present-day I compsets - -Purpose of changes ------------------- - -Change year alignment for present-day I compsets (typically, these -compsets have aliases beginning with "I2000"), in order to work better -for cases that are meant to replicate particular years. - -(1) Start the model in year 2000 rather than year 1 - -(2) Change datm's year alignment so that model year 2000 uses -observations from year 2000, model year 2001 uses observations from year -2001, etc. - -(This change was requested by Sean Swenson and supported by Dave -Lawrence.) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): -- Year-2000 compsets now start in model year 2000 rather than 1 - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: cime changes reviewed by Erik Kluzek and others - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, year-2000 cases change answers as expected - -CTSM tag used for the baseline comparisons: ctsm1.0.dev036 - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: Present-day compsets (I2000, I1Pt; also I2010 once those compsets are added) - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - larger than roundoff/same climate - - This changes the year alignment of datm. Climatological averages - should be the same as before, but the alignment of model year to - datm year changes. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- cime: ctsm/ctsm1.0/cime5.7.9/n03 -> ctsm/ctsm1.0/cime5.7.9/n04 - -Pull Requests that document the changes (include PR ids): -- cime changes documented in https://github.com/ESMCI/cime/pull/3093 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev036 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Fri Apr 26 01:20:57 MDT 2019 -One-line Summary: Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change - -Purpose of changes ------------------- - -We currently have a bug so that for transient land-use change cases answers are different starting in soil -carbon when Carbon isotopes (use_c13, or use_c14) are on versus off. Answers are identical if there is no -land-use change. The bug does cause bulk Carbon (C12) to be slightly different, but qualitatively the same. -There is a significant impact to the Carbon isotope simulation however. The bug was causing changes in isotopic -pools to be directed to the bulk Carbon. Because, isotopes are so much smaller than bulk Carbon, this doesn't -cause a marked difference in the bulk Carbon simulation. But, the lack of the change in the isotopic pool -does have a meaningful impact on the simulation of the Carbon isotopic fields. - -Also added a general test for this and specific one to catch this case. And did some updates on documentation -files, and a small bug fix for run_sys_tests. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #692 #675 #686 - #675 -- Answers differ when carbon isotopes are on under transient cases - #686 -- Add a system test to make sure turning on carbon isotopes doesn't change answers - #692 -- run_sys_test issue - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[X] clm5_0 - -[X] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None - -Changes made to namelist defaults (e.g., changed parameter values): None - -Changes to the datasets (e.g., parameter, surface or initial files): None - -Substantial timing or memory changes: None - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None - -Changes to tests or testing: Added LCISO test type and a 13 month Hist test to make sure carbon isotopes - don't cause a change to answers - -Code reviewed by: dlawren, billsacks, klindsey, bishtgautum - -CTSM testing: regular - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS - - tools-tests (test/tools): - - cheyenne - PASS - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - PASS (compare tests fail, because of namelist updates) - - regular tests (aux_clm): - - cheyenne ---- OK - hobart ------ OK - -CTSM tag used for the baseline comparisons: ctsm1.0.dev035 - - -Answer changes --------------- - -Changes answers relative to baseline: Only for Carbon isotopes on under transient land-use change! - - Summarize any changes to answers, i.e., - - what code configurations: Bgc with use_c13 or use_c14 T and with a transient land-use change after each year boundary - - what platforms/compilers: All - - nature of change: same climate for bulk Carbon, isotopic Carbon is quite different for regions with land-use change - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: - - URL for LMWG diagnostics output used to validate new climate: - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime - cime from -- ctsm/ctsm1.0/cime5.7.9/n01 to ctsm/ctsm1.0/cime5.7.9/n03 - cime update allows the new test to work and starts adding NLDAS grid in - -Pull Requests that document the changes (include PR ids): #696 #694 -(https://github.com/ESCOMP/ctsm/pull) - #696 -- run_sys_test small fix - #694 -- Carbon isotope fix - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev035 -Originator(s): sacks (Bill Sacks) -Date: Mon Apr 22 20:17:40 MDT 2019 -One-line Summary: Change h2ocan to a purely diagnostic variable - -Purpose of changes ------------------- - -Previously, h2ocan_patch was maintained through the driver loop as the -sum of liqcan_patch and snocan_patch. However, there were places where -it was updated separately (though consistently) - i.e., it was not -simply a matter of 'h2ocan = liqcan + snocan'. This made the code -more complex, especially for the upcoming addition of water tracers. - -This tag changes h2ocan_patch to be a purely diagnostic variable, set -once at the end of the driver loop. Prognostic equations that used to -use h2ocan now use liqcan and snocan, either directly or indirectly via -a temporary variable set equal to the current value of liqcan+snocan. - -This tag also completely removes support for snowveg_flag = 'OFF' in -order to clean up the code. - -In addition, this tag renames the namelist variable snowveg_flag to -snowveg_affects_radiation (now a logical). - -Finally, this tag includes a minor change to always compute fcansno, -even if snowveg_affects_radiation is false, in order to simplify the -code. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#199 - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -- snowveg_flag renamed to snowveg_affects_radiation, and changed to a - logical flag - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none - -Code reviewed by: -- Answer-changing portion of these changes reviewed by Keith Oleson and - (at least to some extent) Sean Swenson - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, answers change as expected - -CTSM tag used for the baseline comparisons: ctsm1.0.dev034 - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: all - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - roundoff - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - - I split these changes into two pieces: (1) an answer-changing piece - where I made minimal changes to replace uses of h2ocan_patch with - liqcan+snocan (via temporary h2ocan variables holding this sum), - and (2) non-answer-changing code cleanup. (1) consisted of the - first two commits on this branch (461cafea and f195c105). With the - changes in (1), I added checks near each change to ensure that the - new expression differed by no more than roundoff from the old - (using an absolute cutoff of 1e-13). I ran the full test suite with - these checks in place, and generated new baselines. I then compared - the changes in (2) with the baselines from (1); this cleanup step - was bit-for-bit except for roundoff-level changes in the - now-diagnostic-only field H2OCAN. - - As noted in ESCOMP/ctsm#689, the changes in (1) were larger than I - expected, presumably because initially roundoff-level differences - can lead to divergent code behavior. The most obvious example of - this is in the check of h2ocan > 0 in subroutine FracWet. I have - found that, due to roundoff errors, it is possible for h2ocan_patch - > 0 by roundoff, while (liqcan_patch + snocan_patch) <= 0 by - roundoff. (Presumably the reverse could also be true, though I - haven't seen that – but I haven't spent much time looking for it.) - - Soon, we plan to do a more rigorous test to double check that this - change is not climate-changing. - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): -- First part of changes in https://github.com/ESCOMP/ctsm/pull/689 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev034 -Originator(s): sacks (Bill Sacks) -Date: Sat Apr 20 06:11:23 MDT 2019 -One-line Summary: Change clm4_5: Use Justin Perket snow on vegetation - -Purpose of changes ------------------- - -This tag changes the behavior of clm4_5, making it now use Justin -Perket's snow on vegetation parameterization. This parameterization was -originally introduced in clm4_5_1_r112. At the time it was only used for -clm5_0 cases. This tag uses that parameterization for clm4_5 cases, too, -so that (like clm5_0) they use snowveg_flag = 'ON_RAD' (i.e., vegetation -snow canopy on with albedo influence). - -This changes climate for clm4_5, mainly through albedo changes, -particularly in the shoulder seasons. - -The reason for this change is to allow an upcoming cleanup of the -relationship between h2ocan, snocan and liqcan. (See -https://github.com/escomp/ctsm/issues/199 for details.) - -This tag also no longer allows snowveg_flag = 'OFF'. However, code -cleanup is deferred to a follow-on tag, in order to separate the answer -changes in this tag from the no-greater-than-roundoff-level changes in -the follow-on tag. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- First step towards addressing ESCOMP/ctsm#199 (Clean up relationship - between h2ocan, snocan and liqcan) - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[X] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): -- Changes the scientific configuration of clm4_5 cases, as noted above - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): -- For clm4_5: snowveg_flag = 'ON_RAD' rather than 'OFF' - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): -- Need to clean up code involving snowveg_flag, liqcan, snocan and - h2ocan. I will do this in a follow-on tag. - -Changes to tests or testing: -- Added a test with snowveg_flag = 'ON'. (At least some of the code - paths triggered by this setting were previously covered by clm45 - cases. Now that both clm45 and clm50 use snowveg_flag = 'ON_RAD', - there was some uncovered code. This new test covers this code.) -- Changed long single-point tests to use Qian forcing: With the default - GSWP3 forcing, the vast majority of the runtime was being spent in - datm. In addition, I was getting repeated failures of - ERS_Lm54_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropGs.cheyenne_intel.clm-cropMonthOutput, - I think due to memory issues; I'm hopeful that changing the datm - forcing will help with that. - -Code reviewed by: self - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass; NLCOMP and BASELINE failures for Clm45 cases, - as expected - -CTSM tag used for the baseline comparisons: ctsm1.0.dev033 - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: Clm45 compsets - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - New climate (as in clm4_5_1_r112 for clm5_0); the main impact is - through albedo changes, particularly in the shoulder seasons. - - Changes in clm4_5 cases are due to: - - (1) Using snowveg_flag = 'ON_RAD' rather than 'OFF' - - (2) Changed initial conditions for canopy water: Rather than using - H2OCAN, which is the meaningful state variable on previous - clm4_5 initial conditions files, now we use LIQCAN and - SNOCAN. These may be 0, although at least some clm4_5 initial - conditions files (including the two non-Fates out-of-the-box - clm4_5 initial conditions files) have non-zero (though still - reasonable) LIQCAN for reasons I can't understand. - - (Also changes answers for - ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline, - which uses a clm45 initial file.) - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - -Pull Requests that document the changes (include PR ids): none - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev033 -Originator(s): slevis (Samuel Levis, SLevis Consulting LLC, 303-665-1310) -Date: Thu Apr 11 10:51:29 MDT 2019 -One-line Summary: Limit landunit presence with thresholds set in the namelist - -Purpose of changes ------------------- - - Faster simulations. Motivated by NWP applications: - - Introduce user-defined namelist parameters to use as thresholds - above which landunit areas are kept and - below which landunit areas are removed. - - Introduce user-defined logical namelist parameter to collapse the up to - three urban landunits to the dominant urban landunit. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): #581 - Fixes #581 -- Allow zeroing out special landunits if their area is below some threshold - - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? No - -Notes of particular relevance for users ---------------------------------------- - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): - - New namelist variables with valid real values from 0._r8 to 100._r8, where - 0 means "do nothing" and other values determine the threshold above - which to keep the landunit in a gridcell. The new variables are: - toosmall_soil - toosmall_crop - toosmall_glacier - toosmall_lake - toosmall_wetland - toosmall_urban - - New logical namelist variable collapse_urban. If .true. then the up to - three urban landunits collapse to the dominant urban landunit. - ---------------------------------------------- -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): - There's a typo in the name for n_dom_landunits (missing the s) in bld/CLMBuildNamelist.pm - build-namelist doesn't check for toosmall_* below 0 or above 100, but the code does - -Changes to tests or testing: Yes - New unit tests subroutine test_collapse_individual_lunits and - test_collapse_all_lunit_opts_active in test_surfrdUtils.pf - Modified standard suite test - ERS_D_Ld10.f10_f10_musgs.IHistClm50BgcCropGs.cheyenne_intel.clm-collapse_to_dominant_decStart - to - ERS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-rm_indiv_lunits_and_collapse_to_dom - and introduced fatal error message when namelist parameters toosmall_* > 0 or - n_dom_* > 0 in transient simulations - -Code reviewed by: Erik Kluzek, Bill Sacks - -CTSM testing: regular - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - PASS (384 differences because of new namelist items) - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - -CTSM tag used for the baseline comparisons: - cheyenne ctsm1.0.dev031 - hobart ctsm1.0.dev032 - - -Answer changes --------------- - -Changes answers relative to baseline: No - Note: Comparison to baseline gives NLCOMP failures because the new namelist - parameters always appear in the namelist now, even when they have not been - changed from their default value by the user. - -Detailed list of changes ------------------------- - - Introduced call to new subroutine collapse_individual_lunits that uses - the user-defined namelist variables listed above to determine whether - a landunit gets kept or removed from a gridcell. - - Introduced new call to collapse_to_dominant for when collapse_urban = .true. - - Introduced error checks that do not allow coexistence of transient - simulations and the toosmall_* variables OR the n_dom_pfts/n_dom_landunits - variables OR the collapse_urban parameter. - -Pull Requests that document the changes (include PR ids): #641 - https://github.com/ESCOMP/ctsm/pull/641 - #641 -- Ability to remove individual landunits for faster runs - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev032 -Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) -Date: Mon Apr 8 08:26:57 MDT 2019 -One-line Summary: Fixing the balance check to check for possible errors over all columns/patches - -Purpose of changes ------------------- -Up until now, the BalanceCheckMod code in biogeophysics did not check all -the possible errors over all columns or patches with the error threshold for -aborting clm and it merely compared the last column/patch found (where -warning threshold is met) with the error threshold. -Therefore, there was always a possibility that the abort is not triggered -when it should have been. This issue was first mentioned in ctsm issue #55 -for soil energy balance check, but a similar issue is also present for -other balance checks in BalanceCheckMod.F90 . - -Below is the list of the balance checks with a similar issue: -1. Water balance check -2. Snow balance check -3. Solar radiation energy balance check -4. Longwave radiation energy balance check -5. Surface energy balance check -6. Soil energy balance check (Issue #55) - -For remediating this issue, we used MAXVAL and MAXLOC Fortran intrinsic functions -to compare the largest error with the warning and error thresholds instead -of checking the last column or looping over all columns. - - -In addition, this PR also makes slight changes to ./run_sys_tests outputi/case -directory structure. Previously for each case in a test suite, there were -two set of directories created by run_sys_tests as follows: - * one directory which included run/ and bld/ and named as $SCRATCH/[case-name].... - * The case directory which included logs , timings, CaseDocs/, and misc. scripts - for ./case.build, ./case.submit... under $SCRATCH/tests-[testID]/[case-name].... - -This made debugging confusing and populated many folders in user's scratch. -Now, for every case in a test, all directories related to that case -including bld/ and run/ directories are nested under the case directory under $SCRATCH/tests-[testID]/[case-name].... -This is now similar to ./create_test output folder structure. - - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm issue#55 - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_0 - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None - -Changes made to namelist defaults (e.g., changed parameter values): None - -Changes to the datasets (e.g., parameter, surface or initial files): None - -Substantial timing or memory changes: None - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): - -Changes to tests or testing: - - ./run_sys_test is changed so that it nests bld/ and run/ directories under the case directory as $SCRATCH/tests-[testID]/[case-name]... - The output folder structure now is similar to ./create_test for each case in a test. - -Code reviewed by: Bill Sacks - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - -CTSM tag used for the baseline comparisons: ctsm1.0.dev031 - - -Answer changes --------------- - -Changes answers relative to baseline: No - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None - -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/670 - -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev031 -Originator(s): sacks (Bill Sacks) -Date: Wed Mar 13 15:03:42 MDT 2019 -One-line Summary: Subtract virtual states to reduce dynbal fluxes for transient glaciers - -Purpose of changes ------------------- - -Up until now, when computing the dynbal correction (conservation) fluxes -for transient glacier columns, we have been (1) counting the mass and -energy in the ice column as if that is a real state, but on the other -hand (2) NOT accounting for the fact that glacier columns don't -represent the soil under glacier. These two issues work in opposite -directions, but (1) dominates, because there is much more ice (and -energy, I think) in the roughly 50 m of glacial ice than there is in a -typical 50 m soil column. - -In discussing this issue with Bill Lipscomb, we came up with the idea of -subtracting some baseline value from each glacier column. I think that, -as long as we subtract the same baseline value throughout an entire -simulation for a given column, we will still conserve mass and energy -through dynamic landunit transitions. - -So, here we subtract baseline values from glacier columns, accounting -for the two issues mentioned above: (1) we subtract the water and energy -in the glacier ice, because this is a virtual state in CTSM, and (2) we -add the water and energy from the vegetated column(s), to account for -the fact that we don't have an explicit representation of -soil-under-glacier (this carries the assumption that the -soil-under-glacier has the same state as the initial vegetated state in -that grid cell). We set these baselines in initialization, so they begin -equal to the cold start state. Water and ice in the glacial ice stay -fixed over the course of a simulation, so the cold start values should -be the same as the current values at any point in time. The heat content -of the glacial ice does change over time, but by subtracting this -baseline value, we can potentially reduce the dynbal sensible heat -fluxes (however, note that it's also possible that these sensible heat -fluxes could increase when subtracting the cold start value, if ice -temperatures are closer to 0 deg C than to the cold start value, -currently 250 K). - -In addition, this introduces a new namelist flag, -reset_dynbal_baselines, which allows the user to reset these baselines -at some desired point in the simulation. I think that, in general, this -resetting would break conservation. But as long as it is done before the -onset of transient glaciers, I think this should be okay. In this way, -the user can minimize dynbal fluxes even further, by resetting the -baselines after the system has spun up. If the states haven't changed -much from this point to the point when glacier dynamics occur, then the -dynbal fluxes should now be very small. (See the documentation of this -flag in namelist_definition_ctsm.xml for more details.) - -Without this change, dynbal fluxes for a grid cell that undergoes 100% -glaciation / deglaciation in a single year are around 50 m ice, 1 m -liquid water, and a few tens of W m-2 (where those quantities of ice and -water are dribbled throughout the year, so we end up with an ice flux of -about 1.5e-6 mm/s throughout the year; and the energy flux is applied -evenly throughout the year - i.e., tens of W m-2 every time step for a -year). With this change, and with reset_dynbal_baselines set at an -appropriate time, these fluxes can be reduced to close to zero. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Partially addresses ESCOMP/ctsm#274 (Dynamic landunits: improve water - and energy conservation) - -CIME Issues fixed (include issue #): -- Fixes three issues related to inputdata checksum: - - ESCMI/cime#3033 - - ESCMI/cime#3034 - - ESCMI/cime#3036 - -Known bugs introduced in this tag (include github issue ID): -- ESCOMP/ctsm#659 (Subtract dynbal baselines from begwb and endwb) - - This can't be fixed until we're okay having this answer change on - master - -Known bugs found since the previous tag (include github issue ID): -- ESCOMP/ctsm#658 (Methane should not depend on gridcell-level TWS) - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[X] clm5_0 - -[X] clm4_5 - -Significant answer changes for runs with transient glaciers. - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): -- For runs with transient glaciers, careful thought should be given to - when to set reset_dynbal_baselines -- Inconsistency between begwb/endwb and liq1/liq2/ice1/ice2 (see ESCOMP/ctsm#659) - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -- New namelist variable: reset_dynbal_baselines - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): -- Inconsistency between begwb/endwb and liq1/liq2/ice1/ice2 (see ESCOMP/ctsm#659) - -Changes to tests or testing: -- Tweaked a test with transient glacier areas, including adding this new - flag to the test - -Code reviewed by: Bill Lipscomb reviewed the conceptual ideas, but -nobody has reviewed the actual code - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - regular tests (aux_clm): - - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, answers change as expected - -CTSM tag used for the baseline comparisons: ctsm1.0.dev030 - - -Answer changes --------------- - -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: ALL, but different configurations show - different levels of changes, as noted below - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - new climate (at least regionally) for some configurations; - roundoff for others: see below - - There are three levels of changes here: - - (1) For runs with transient glaciers, there are large answer changes - in regions with changing glacier area. These answer changes are - in the various dynbal fluxes - for liquid water and ice runoff, - and for the dynbal sensible heat flux. - - (2) For runs with transient vegetation (Hist, Dv and Fates), there - are roundoff-level changes in the dynbal fluxes. For liquid - water and ice, these changes appear to only occur in grid cells - where there is some glacier area (because now both the before - and after gridcell water contents have changed by the same fixed - amount, which changes the difference at the roundoff level). For - heat, there are roundoff-level changes everywhere (because of - changes in the order of operations). - - (3) All runs have large changes in the diagnostic variables, - ICE_CONTENT1, LIQUID_CONTENT1 and HEAT_CONTENT1, over grid cells - containing some glacier area. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- cime: cime5.7.9 -> ctsm/ctsm1.0/cime5.7.9/n01 - - Fixes issues related to inputdata checksum - -Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/650 - -=============================================================== =============================================================== -Tag name: ctsm1.0.dev030 -Originator(s): sacks (Bill Sacks) -Date: Fri Mar 8 15:08:34 MST 2019 -One-line Summary: Update CIME; hookup expected test fails - -Purpose of changes ------------------- - -Two main changes: - -(1) Update to latest cime (from ctsm/ctsm1.0/cime5.7.5/n01 to - cime5.7.9). Some of the important changes are: - - Fix for recent cheyenne system changes - - New domain file for f19_g17 (changes answers at the roundoff - level) - - New domain file for T31_g37 (changes answers by greater than - roundoff) - -(2) In system tests: Annotate cs.status output with expected failures - -Bugs fixed or introduced ------------------------- +=============================================================== +Tag name: ctsm5.1.dev032 +Originator(s): mvertens (Mariana Vertenstein), sacks (Bill Sacks) +Date: Sat Apr 10 09:47:25 MDT 2021 +One-line Summary: Fix bugs in co2 from atmosphere -Issues fixed (include CTSM Issue #): -- Fixes ESCOMP/ctsm#654 +Purpose and description of changes +---------------------------------- -CIME Issues fixed (include issue #): (Many) +ctsm5.1.dev002 introduced bugs when receiving co2 from the atmosphere, +both for mct and nuopc: +- For mct, with spatially-varying co2 from atmosphere, all grid cells on + a given processor were given the co2 value from the last grid cell on + that processor +- For nuopc, co2 from atmosphere was ignored and overridden with a + constant co2 value +This tag fixes both of those bugs. Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -7374,242 +631,287 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 +[X] clm5_1 -[ ] clm4_5 +[X] clm5_0 -Notes of particular relevance for users ---------------------------------------- +[X] ctsm5_0-nwp -Caveats for users (e.g., need to interpolate initial conditions): none +[X] clm4_5 -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none -Changes made to namelist defaults (e.g., changed parameter values): none +Bugs fixed or introduced +------------------------ +[Remove any lines that don't apply. Remove entire section if nothing applies.] -Changes to the datasets (e.g., parameter, surface or initial files): none +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1327 (When using co2 from atmosphere with mct, it + looks like values are taken just from the last gridcell on each proc) -Substantial timing or memory changes: none? - The PFS test showed a significant speedup (170s in the previous tag, - 124s in this tag). However, some other tests showed either a slowdown - or not much change. So I'm not sure there is a consistent pattern of - speedup in this tag. +Testing summary: +---------------- -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + cheyenne ---- OK + izumi ------- OK -Changes to tests or testing: none +Answer changes +-------------- -Code reviewed by: Erik Kluzek +Changes answers relative to baseline: YES + Summarize any changes to answers, i.e., + - what code configurations: Cases where CTSM receives CO2 from atmosphere + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + potentially new climate -CTSM testing: + Answer changes due to fixing these issues: + - For mct, with spatially-varying co2 from atmosphere, all grid cells on + a given processor were given the co2 value from the last grid cell on + that processor + - For nuopc, co2 from atmosphere was ignored and overridden with a + constant co2 value - [PASS means all tests PASS and OK means tests PASS other than expected fails.] + In the test suite, this leads to changes in: + - ERP_D_Ld10_P36x2_Vnuopc.f10_f10_mg37.IHistClm51BgcCrop.cheyenne_intel.clm-ciso_decStart + - ERS_Ly3_P72x2_Vnuopc.f10_f10_mg37.IHistClm50BgcCropG.cheyenne_intel.clm-cropMonthOutput + - SMS_D_Ln9_P480x1_Vnuopc.f19_g17.IHistClm50Sp.cheyenne_intel.clm-waccmx_offline - build-namelist tests: + But more widespread changes are expected - including for mct - if + coupled runs can generate spatially-varying co2 from atm - cheyenne - not run +Other details +------------- +Pull Requests that document the changes (include PR ids): +- Merges the first part of the changes in + https://github.com/ESCOMP/CTSM/pull/1330 - tools-tests (test/tools): +=============================================================== +=============================================================== +Tag name: ctsm5.1.dev031 +Originator(s): jedwards (Jim Edwards), sacks (Bill Sacks) +Date: Sat Apr 10 07:33:49 MDT 2021 +One-line Summary: Update externals and fixes for nuopc threading - cheyenne - not run +Purpose and description of changes +---------------------------------- - PTCLM testing (tools/shared/PTCLM/test): +(1) Some fixes for threading with the nuopc/cmeps driver. (However, + threading with nuopc/cmeps still doesn't work completely: see + https://github.com/ESCOMP/CTSM/issues/1331.) - cheyenne - not run +(2) Updates externals to versions needed for these nuopc threading changes - regular tests (aux_clm): +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- - cheyenne ---- ok - hobart ------ ok +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] - ok means tests pass, some baselines failed as noted below +[ ] clm5_1 - Most testing done with cime at eb2eb704f - excluded PR #3030, which - updated support for CAM-SE grids (but the changes in this PR were - very limited). Ran SSP tests with the final version of cime (so I'd - have a few tests covering the latest cime). +[ ] clm5_0 -CTSM tag used for the baseline comparisons: ctsm1.0.dev029 +[ ] ctsm5_0-nwp +[ ] clm4_5 -Answer changes --------------- -Changes answers relative to baseline: YES +Bugs fixed or introduced +------------------------ +Known bugs introduced in this tag (include issue #): +- https://github.com/ESCOMP/CTSM/issues/1331 Some runs with NUOPC driver + with multiple threads can hang - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: +- Temporarily changed + SMS_D_Ln9_P480x3_Vnuopc.f19_g17.IHistClm50Sp.cheyenne_intel.clm-waccmx_offline + to use a 480x1 layout so that it will pass reliably (see + https://github.com/ESCOMP/CTSM/issues/1331) - Summarize any changes to answers, i.e., - - what code configurations: f19_g17, T31_g37 - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): +Testing summary: +---------------- + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - - f19_g17: roundoff-level, presumably due to new domain file (some - diffs grew to greater than roundoff-level: some methane - variables in a long test - - SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput; - and many variables in test with flooding - - ERP_P180x2_D.f19_g17.I2000Clm50SpRtmFl.cheyenne_intel.clm-default) + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: - - T31_g37: greater than roundoff-level, presumably due to new - domain file from cime commit 4fcf592ee +Answer changes +-------------- - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A +Changes answers relative to baseline: YES (but very limited) - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A + Summarize any changes to answers, i.e., + - what code configurations: NUOPC driver with CISM + - what platforms/compilers: cheyenne_intel; maybe others + - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff - URL for LMWG diagnostics output used to validate new climate: N/A - + For an unknown reason, the new externals lead to small differences + in global sums in the CMEPS driver/mediator. For what we assume is + the same reason, lnd -> glc fields can change by roundoff (probably + due to the global renormalization). -Detailed list of changes ------------------------- + The only test in the aux_clm test suite where this shows up is + ERS_Ly3_P72x2_Vnuopc.f10_f10_mg37.IHistClm50BgcCropG.cheyenne_intel.clm-cropMonthOutput + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + Inspection of cpl hist files + +Other details +------------- List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- cime: ctsm/ctsm1.0/cime5.7.5/n01 -> cime5.7.9 +- cism: cism2_1_75 -> cism_1_78 +- rtm: rtm1_0_75 -> rtm1_0_76 +- mosart: mosart1_0_41 -> mosart1_0_42 +- cime: cime5.8.39 -> cime5.8.42 +- cmeps: v0.5.0 -> v0.9.0 +- cdeps: v0.5.0 -> v0.6.0 Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/602 +- https://github.com/ESCOMP/CTSM/pull/1319 =============================================================== =============================================================== -Tag name: ctsm1.0.dev029 -Originator(s): slevis (Samuel Levis, SLevis Consulting LLC, 303-665-1310) -Date: Tue Feb 26 23:42:39 MST 2019 -One-line Summary: Collapse landunits to the N most dominant - -Purpose of changes ------------------- +Tag name: ctsm5.1.dev030 +Originator(s): mvertens / erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Wed Mar 31 16:46:04 MDT 2021 +One-line Summary: New single column functionality for the NUOPC cap - Allows the collapse to fewer landunits using the concept of - N most dominant for the purpose of faster runs, eg in the context - of NWP (Numerical Weather Prediction). +Purpose and description of changes +---------------------------------- -Bugs fixed or introduced ------------------------- +Implemented new nuopc/cmeps single column functionality. -Issues fixed (include CTSM Issue #): #581 +In config/cesm/config_files.xml - single point domains are only used +for mct/cpl7. For cmeps single point meshes are now generated on the +fly and component domains files are no longer needed. +env_run.xml variables PTS_LAT, PTS_LON and PTS_DOMAINFILE are used +to determine if there is a single point or single column run. +If PTS_LAT and PTS_LON are not -999 and PTS_DOMAINFILE is UNSET, +then you have a single point run and the exact values of PTS_LAT +and PTS_LON are used. If PTS_LAT and PTS_LON are not -999 and +PTS_DOMAINFILE is not UNSET, then then the cmeps driver will recognize the nearest neighbor +values of PTS_LAT and PTS_LON in PTS_DOMAINFILE as the single column lat and lon to use. Significant changes to scientifically-supported configurations -------------------------------------------------------------- -Does this tag change answers significantly for any of the following physics configurations? No +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 +[ ] ctsm5_0-nwp + [ ] clm4_5 -Notes of particular relevance for users ---------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): None +Bugs fixed or introduced +------------------------ -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): - New namelist variable n_dom_landunits with valid integer values from 0 to - max_lunit currently equal to 9, where 0 means “do nothing†and other - values determine the number of active landunits when running the model. +Issues fixed (include CTSM Issue #): + Fixes #1312 -- Add NUOPC tests + Fixes #1302 -- Setup to allow landuse.timeseries file for high resolution cases for 2000-2025 + Fixes #1183 -- mkmapdata needs input option for large file support, current defaults unsuitable for high res grids. -Changes made to namelist defaults (e.g., changed parameter values): None +Known bugs introduced in this tag (include issue #): -Changes to the datasets (e.g., parameter, surface or initial files): None +Known bugs found since the previous tag (include issue #): + #1317 -- MPI timeout for some izumi_nag tests reading in datm forcing files in NUOPC cap + #1314 -- Send unset value for scol_lat/lon from driver -Substantial timing or memory changes: None +Notes of particular relevance for users +--------------------------------------- -Notes of particular relevance for developers: (including Code reviews and testing) +Notes of particular relevance for developers: --------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +[Remove any lines that don't apply. Remove entire section if nothing applies.] Caveats for developers (e.g., code that is duplicated that requires double maintenance): - There is a question left in on whether the collapse call needs to also - be moved to inside dynamic landunits reading. - -Changes to tests or testing: Yes - ERS_D_Ld10.f10_f10_musgs.IHistClm50BgcCropGs.cheyenne_intel.clm-collapse_to_dominant_decStart - now replaces (by combining with) this test introduced in ctsm1.0.dev026 - ERS_D_Ld10.f10_f10_musgs.IHistClm50BgcCropGs.cheyenne_intel.clm-collapse_nat_pfts_decStart - I added subroutine test_collapse_to_dom_landunits to test_surfrdUtils.pf - to include new Unit Tests. In same file I renamed - subroutine test_collapse_nat_pfts to test_collapse_to_dom_pfts - to accurately describe the contents of the subroutine. + Nine step tests changed so that they have ROF run at same frequency as ATM (like the similar CAM tests) + as these will fail with NUOPC since it doesn't allow you to end not on an even time-step for all components. + One of these tests changed to a CAM type test from decStart -Code reviewed by: Erik Kluzek +Changes to tests or testing: Add more NUOPC tests to test list -CTSM testing: - [PASS means all tests PASS and OK means tests PASS other than expected fails.] +Testing summary: regular +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] - build-namelist tests: + build-namelist tests (if CLMBuildNamelist.pm has changed): cheyenne - PASS - regular tests (aux_clm): + tools-tests (test/tools) (if tools have been changed): + + cheyenne - OK + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + cheyenne -- FAIL + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): cheyenne ---- OK - hobart ------ OK + izumi ------- OK + + any other testing (give details below): Ran full izumi test list for nuopc driver (failed tests appear above) -CTSM tag used for the baseline comparisons: - ctsm1.0.dev028 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- Changes answers relative to baseline: No + (List of fields change though) + -Detailed list of changes ------------------------- - - Replaced existing subroutine collapse_nat_pfts with - subroutine collapse_to_dominant which can collapse to the - N dominant landunits or N dominant pfts by performing the - same actions on the data. +Other details +------------- -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, CDEPS, CMEPS + cime to cime5.8.39 + CDEPS to v0.5.0 + CMEPS to v0.5.0 -Pull Requests that document the changes (include PR ids): #639 - https://github.com/ESCOMP/ctsm/pull/639 +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + #1309 -- New single column functionality for NUOPC/CMEPS + #1310 -- run_sys_tests: add --retry option on izumi =============================================================== =============================================================== -Tag name: ctsm1.0.dev028 -Originator(s): sacks (Bill Sacks) -Date: Tue Feb 26 14:35:01 MST 2019 -One-line Summary: Interpolate out-of-the-box initial conditions and remove expensive tests - -Purpose of changes ------------------- - -Two main changes (plus some small additional changes): - -1. Removed / reworked some expensive tests +Tag name: ctsm5.1.dev029 +Originator(s): mvertens (Mariana Vertenstein), sacks (Bill Sacks) +Date: Thu Mar 18 21:21:21 MDT 2021 +One-line Summary: Rework domain initialization for nuopc -2. Interpolated all out-of-the-box initial conditions, so that the - out-of-the-box version is now compatible with our current - configuration. The changes from before were (a) our standard - configuration now uses the gx1v7 rather than gx1v6 land mask; (b) - many inactive points are now absent in memory. +Purpose and description of changes +---------------------------------- -See https://github.com/ESCOMP/ctsm/pull/622 for details. - - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#312 -- Partially addresses ESCOMP/ctsm#275 (just a bit) +Total rework of land domain initialization - no longer need domain files +to be created with NUOPC cap. +Also, significant performance improvements with the NUOPC cap. Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -7619,184 +921,83 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- +[ ] clm5_1 -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none +[ ] clm5_0 -Changes made to namelist defaults (e.g., changed parameter values): none +[ ] ctsm5_0-nwp -Changes to the datasets (e.g., parameter, surface or initial files): -- New finidat files +[ ] clm4_5 -Substantial timing or memory changes: -- Faster initialization times for cases that no longer need to interpolate initial conditions -Notes of particular relevance for developers: (including Code reviews and testing) +Notes of particular relevance for developers: --------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: -- Removed or reworked expensive tests: see details in https://github.com/ESCOMP/ctsm/pull/622 - -Code reviewed by: Erik Kluzek - - -CTSM testing: - - [PASS means all tests PASS and OK means tests PASS other than expected fails.] - - build-namelist tests: - - cheyenne - not run - - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): - - cheyenne - not run - - regular tests (aux_clm): +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- We still need to figure out how to apply this to LILAC: for now, LILAC + is still using the old method (as is MCT): reading domain information + from fatmlndfrac - cheyenne ---- ok - hobart ------ ok - ok: tests pass, baselines fail as expected +Testing summary: +---------------- -CTSM tag used for the baseline comparisons: ctsm1.0.dev027 + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + cheyenne ---- OK + izumi ------- PASS Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): +Changes answers relative to baseline: YES, but just for NUOPC and +limited changes for LILAC Summarize any changes to answers, i.e., - - what code configurations: all configurations that still need use_init_interp = .true. + - what code configurations: NUOPC, and limited changes for LILAC - what platforms/compilers: all - nature of change (roundoff; larger than roundoff/same climate; new climate): - Not investigated carefully, but expected to be larger than roundoff/same climate - - Answers change for cases that still need to do interpolation from - these out-of-the-box finidat files. - - I first confirmed that the new finidat files are good via: - - - Compared `ncdump -h` of old vs. new initial conditions files - - - Ran the following tests, with comparison against master; verified that - these all pass and are bit-for-bit, that they use the new initial - conditions files, and that they now have `use_init_interp` unset - (whereas they used to have `use_init_interp` set to `.true.`); note - that these cover 6 of the 7 new initial conditions files: - - ``` - SMS_Ld1.f09_g17.I1850Clm45BgcGs.cheyenne_intel.clm-default - SMS_Ld1.f09_g17.I1850Clm45BgcCruGs.cheyenne_intel.clm-default - SMS_Ld1.f09_g17.I1850Clm50Sp.cheyenne_intel.clm-default - SMS_Ld1.f09_g17.I1850Clm50BgcCrop.cheyenne_intel.clm-ciso - SMS_Ld1.f09_g17.I1850Clm50BgcCropCru.cheyenne_intel.clm-ciso - SMS_Ld1.f09_g17.I1850Clm50SpCru.cheyenne_intel.clm-default - ``` - - - To cover the last new initial conditions file, ran the following test - (with the same checks as above: passes and bit-for-bit, checked - finidat, and checked `use_init_interp`), with `./xmlchange - LND_TUNING_MODE=clm5_0_cam6.0` (for the baseline for this test, I set - `init_interp_method = 'use_finidat_areas'`, which I also used in - interpolating this initial conditions file): - - ``` - SMS_Ld1.f09_g17.I1850Clm50BgcCrop.cheyenne_intel - ``` - - Details on answer changes: - - As noted above, these changes are bit-for-bit for configurations - that can now use the out-of-the-box initial conditions without - interpolation. However, answers change for configurations that still - require interpolation of the out-of-the-box initial conditions - (e.g., because they are at a different resolution than the finidat - file). - - I expected these answer changes around the Caspian Sea, due to the - fact that we are now effectively interpolating twice from the - original file: once to produce the new out-of-the-box file (which - includes an interpolation from `gx1v6` to `gx1v7`, and so - interpolates onto the Caspian Sea region) and once to go from - `f09_g17` to the target resolution (rather than interpolating - directly from `f09_g16` to the target resolution). - - However, when I ran a test with comparison to baselines - - `ERP_Ld5.f19_g17.I1850Clm50Bgc.cheyenne_intel.clm-default` - I saw - changes in regions further afield than simply around the Caspian - Sea. See images in https://github.com/ESCOMP/ctsm/pull/622 for - details. It's possible that the other differences are also due to - the Caspian Sea change, but it's also possible that there is some - other cause here that I don't understand. But Erik Kluzek and I - agreed that it isn't worth trying to understand these other - (isolated) differences. - - Also note: While most f09_g17 tests are bit-for-bit with the earlier - tag (because now use_init_interp is .false. for those tests), - `SMS_Ld2_D.f09_g17.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic_interp` - differs in some glc forcing fields for a few grid cells in - Antarctica. This is perhaps not surprising, since this test needs to - use interpolation to get fields for the Antarctica virtual columns; - so, while I don't completely understand the cause of these answer - changes, I suspect the root cause is similar to the isolated answer - changes I saw sprinkled around the world for - `ERP_Ld5.f19_g17.I1850Clm50Bgc.cheyenne_intel.clm-default`. + roundoff + For nuopc: changes in area (relatively large differences in the + f10 test in the test suite, but Mariana saw only very small + changes in an f09 case), landfrac; these influence l2r fields, + which in turn influence TWS and methane fields. + + For lilac: just changes in area + If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - + than roundoff? Examination of cprnc diffs. -Detailed list of changes ------------------------- +Other details +------------- -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- rtm: rtm1_0_74 -> rtm1_0_75 +- mosart: branch_tag/pio2.n01_mosart1_0_38 -> mosart1_0_41 Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/622 +- https://github.com/ESCOMP/CTSM/pull/1258 +- https://github.com/ESCOMP/CTSM/pull/1236 (closed and replaced by 1258) =============================================================== =============================================================== -Tag name: ctsm1.0.dev027 -Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) -Date: Tue Feb 19 12:57:12 MST 2019 -One-line Summary: Non-constant time initialization for soil hydrology types are moved to SoilHydrologyType.F90. - -Purpose of changes ------------------- +Tag name: ctsm5.1.dev028 +Originator(s): swensosc (Sean Swenson) +Date: Wed Mar 17 20:08:51 MDT 2021 +One-line Summary: Change limitation of top layer evaporation/sublimation -Initalization of time-varying `zwt`, `zwt_perched`, and `frost_table` are moved to `InitCold` in `SoilHydrologyType.F90`. +Purpose and description of changes +---------------------------------- -Previously, `zwt`, `zwt_perched`, and `frost_table` were initialized in `SoilHydrologyInitTimeConstMod.F90`, which caused confusions. +Sublimation from top soil layer and evaporation/sublimation from top +snow layer needs to be limited to ensure moisture states do not become +negative. The original formulation did not always work, so we added a +new limitation to SoilFluxesMod. -Bugs fixed or introduced ------------------------- -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#575 ("Some variables initialized in SoilHydrologyInitTimeConstMod are not time-constant") +Also removes a limitation in SoilHydrologyMod that seemed not to +conserve energy and should no longer be necessary with the reworked +limitation in SoilFluxesMod. Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -7806,95 +1007,86 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none - -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: Updated a test. The test added in previous tag included decStart with transient glaciers, which would not work. Hence, this test is modified so the compset does not include G. -Test IHistClm50SpG is updated to IHistClm50Sp. +[ ] clm5_1 -Code reviewed by: -Bill Sacks -Erik Kluzek - -CTSM testing: +[ ] clm5_0 +[ ] ctsm5_0-nwp - build-namelist tests: +[ ] clm4_5 - cheyenne - not run - tools-tests (test/tools): +Bugs fixed or introduced +------------------------ - cheyenne - not run +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1253 (h2osoi_ice can go significantly negative) - PTCLM testing (tools/shared/PTCLM/test): - cheyenne - not run +Notes of particular relevance for users +--------------------------------------- - regular tests (aux_clm): +Caveats for users (e.g., need to interpolate initial conditions): +- The old flux limitation in SoilHydrologyMod has been replaced by a + truncation of roundoff-level values followed by a check that the final + state is non-negative. Although this check hasn't been triggered in + any of our testing, it's possible that we'll run into situations where + we need to relax the tolerance for this check. - cheyenne ---- ok - hobart ------ ok +Testing summary: +---------------- - ok means tests pass, except for the expected failures. + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): -CTSM tag used for the baseline comparisons: -ctsm1.0.dev026 + cheyenne ---- OK + izumi ------- OK Answer changes -------------- - -Changes answers relative to baseline: no +-------------- +Changes answers relative to baseline: YES -Detailed list of changes ------------------------- + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Not investigated carefully, but expected to be larger than + roundoff/same climate + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +Other details +------------- Pull Requests that document the changes (include PR ids): -PR #631 Soil hydrology initialization of time-constant variables moved to SoilHydrologyType -https://github.com/ESCOMP/ctsm/pull/631 - +https://github.com/ESCOMP/CTSM/pull/1282 =============================================================== =============================================================== -Tag name: ctsm1.0.dev026 -Originator(s): slevis (Samuel Levis, SLevis Consulting LLC, 303-665-1310) -Date: Tue Feb 5 17:08:48 MST 2019 -One-line Summary: Collapse unmanaged PFTs to the N most dominant - -Purpose of changes ------------------- +Tag name: ctsm5.1.dev027 +Originator(s): sacks (Bill Sacks) +Date: Mon Mar 15 14:05:20 MDT 2021 +One-line Summary: Update cime and other externals; includes switch to pio2 -To run simulations fast for applications such as NWP (Numerical Weather -Prediction), allow collapsing natural PFT's to the number the user wants. +Purpose and description of changes +---------------------------------- +Updates cime and other externals to version in cesm2_3_alpha02b (with +some minor changes to cime on top of that). This includes substantial +changes to cime, including switching to PIO2 rather than PIO1. -Bugs fixed or introduced ------------------------- +Also: -Issues fixed (include CTSM Issue #): 457 +- For LILAC, changes default pio_rearranger now that we're using PIO2 by + default +- In run_sys_tests, adds '-k oed' to qsub command on cheyenne; this is + useful now that qpeek is disabled on cheyenne (this puts the job's + stdout and stderr files directly in their final location from the + beginning, rather than keeping them in some temporary location on the + compute node until the job completes) Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -7904,117 +1096,98 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -New namelist parameter n_dom_pfts with valid integer values from 0 to -14, where 0 means “do nothing†and other values determine the number -of active pfts when running the model +[ ] clm5_1 -Changes made to namelist defaults (e.g., changed parameter values): None +[ ] clm5_0 -Changes to the datasets (e.g., parameter, surface or initial files): None +[ ] ctsm5_0-nwp -Substantial timing or memory changes: None (unless new option invoked) +[ ] clm4_5 -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none +Bugs fixed or introduced +------------------------ -Changes to tests or testing: updated tests, added new test -Updated standard testing test to include decStart -(December start). Confirmed that answers were bit-for-bit same with -baseline before introducing the change. -Added standard testing test to test n_dom_pfts = 2 in a -transient vegetation case with December start. -Added subroutine test_collapse_nat_pfts to test_surfrdUtils.pf to -include new Unit Tests. - -Code reviewed by: -Erik Kluzek -Bill Sacks +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1175 (Once there is a cime tag with pio2 as the + default, update to it) +- Resolves ESCOMP/CTSM#1194 (Once we switch to pio2 by default, change + the default rearranger used in LILAC) -CTSM testing: +Notes of particular relevance for users +--------------------------------------- - [PASS means all tests PASS and OK means tests PASS other than expected fails.] +Caveats for users (e.g., need to interpolate initial conditions): +- PIO2 is now the default. This has been tested extensively, but let us + know if you run into any I/O related issues. Also, from testing we've + done, I/O performance looks better than with PIO1 in many cases, but + also let us know if you see a substantial degradation in I/O + performance. - build-namelist tests: +Changes made to namelist defaults (e.g., changed parameter values): +- Some I/O-related defaults change with the use of PIO2 rather than PIO1 - cheyenne - PASS +Substantial timing or memory changes: +- Various changes due to the change to PIO2, some of them large. For the + most part, timing improves with PIO2, particularly for production + resolutions. +- The PFS test and many others show a substantial improvement in timing. + This is especially noticeable in initialization time. For example, the + initialization time of + PFS_Ld20.f09_g17.I2000Clm50BgcCrop.cheyenne_intel dropped from 111 sec + to 34 sec. (These tests were run a couple of weeks apart, before and + after a cheyenne upgrade, so there may be some machine variability in + these numbers, but I saw a big improvement a few months ago with a + more objective comparison.) + +Testing summary: +---------------- + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - regular tests (aux_clm): + cheyenne ---- ok + izumi ------- pass - cheyenne ---- OK - hobart ------ OK +If the tag used for baseline comparisons was NOT the previous tag, note that here: -CTSM tag used for the baseline comparisons: -ctsm1.0.dev025 Answer changes -------------- -Changes answers relative to baseline: No (bit-for-bit) +Changes answers relative to baseline: YES, but just for nuopc -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + Summarize any changes to answers, i.e., + - what code configurations: Just with nuopc driver + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Not investigated -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/588 -- NWP collapse pfts to the N most dominant -https://github.com/ESCOMP/ctsm/pull/583 -- Add routine to find indices of max k values in data + The only test that changes answers is + SMS_D_Ld5_Vnuopc.f10_f10_mg37.I2000Clm50BgcCrop.cheyenne_intel.clm-default -Added new subroutines collapse_nat_pfts and collapse_crop_var and called -them from surfrdMod.F90. The second of these subroutines is not needed -when collapsing unmanaged PFTs; however, I created it early in the PR -and decided to keep it for use soon with crop-related variables like -irrigation water and fertilizer. + (There are NLCOMP failures in all tests, though, due to the update to pio2.) -Bill Sacks made changes to include subroutine find_k_max_indices for the -benefit of this PR (#583) +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- CISM: cism2_1_69 -> cism2_1_75 +- RTM: rtm1_0_73 -> rtm1_0_74 +- MOSART: mosart1_0_38 -> branch_tag/pio2.n01_mosart1_0_38 +- CIME: branch_tags/cime5.8.32_a02 -> branch_tags/cime5.8.37_a02 +- CMEPS: 7654038 -> c4acaa8 +- CDEPS: 45b7a85 -> 1f02a73 =============================================================== =============================================================== -Tag name: ctsm1.0.dev025 -Originator(s): Keith Oleson, Bill Sacks -Date: Wed Jan 23 10:48:01 MST 2019 -One-line Summary: History fields for vertically-resolved sums of soil C and N, and minor fixes - -Purpose of changes ------------------- - -Main change is from Keith Oleson: Add history fields for -vertically-resolved sums of SOIL1C, SOIL2C, and SOIL3C for C12, C13, -C14, and similarly for N. New fields are SOILC_vr, C13_SOILC_vr, and -C14_SOILC_vr, and SOILN_vr. For runs that use the output_bgc usermods, -including cmip6 runs, we no longer output 'SOIL1C_vr', 'SOIL1N_vr', -'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr'; instead we output -'SOILC_vr', 'SOILN_vr', and similarly for C isotopes. - -Also minor fixes: -- Output cpl hist files in SSP test (resolves ESCOMP/ctsm#61) -- Remove FATES-related commented-out code in OzoneMod (this has been - moved to https://github.com/ESCOMP/ctsm/issues/618) -- Minor tweak to run_sys_tests +Tag name: ctsm5.1.dev026 +Originator(s): sacks (Bill Sacks) +Date: Mon Mar 8 13:20:33 MST 2021 +One-line Summary: Change f10 tests to use mg37 mask -Bugs fixed or introduced ------------------------- +Purpose and description of changes +---------------------------------- -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#61 +The musgs mask will soon be dropped, and has already been dropped for +nuopc Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -8024,58 +1197,100 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 +[ ] ctsm5_0-nwp + [ ] clm4_5 -Notes of particular relevance for users ---------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): none +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: All f10_f10_musgs tests changed to f10_f10_mg37 -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none -Changes made to namelist defaults (e.g., changed parameter values): -- For runs that use the output_bgc usermods, including cmip6 runs, we no - longer output 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', - 'SOIL3C_vr', 'SOIL3N_vr'; instead we output 'SOILC_vr', 'SOILN_vr', - and similarly for C isotopes. +Testing summary: +---------------- + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): -Changes to the datasets (e.g., parameter, surface or initial files): none + cheyenne ---- pass + izumi ------- pass -Substantial timing or memory changes: none +Answer changes +-------------- -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide +Changes answers relative to baseline: NO -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + BFAIL results for all f10 tests because the tests have changed, but + no answer changes -Changes to tests or testing: none +=============================================================== +=============================================================== +Tag name: ctsm5.1.dev025 +Originator(s): sacks (Bill Sacks) +Date: Tue Feb 23 11:20:17 MST 2021 +One-line Summary: Refactor ozone code, and misc. small fixes -Code reviewed by: Bill Sacks; Erik Kluzek reviewed the changes to the SSP test +Purpose and description of changes +---------------------------------- +(1) Restructure ozone code (https://github.com/ESCOMP/CTSM/pull/1276) in + preparation for new ozone parameterization. -CTSM testing: +(2) Fix non-standard hexadecimal constant + (https://github.com/ESCOMP/CTSM/pull/1271), needed for gfortran 10 - build-namelist tests: +(3) Remove support for CISM1 (https://github.com/ESCOMP/CTSM/pull/1226) - cheyenne - not run +(4) Move final WaterGridcellBalance call out to clm_driver (resolves + ESCOMP/CTSM#1286) - tools-tests (test/tools): +(5) Only add WA and QCHARGE history fields if use_aquifer_layer is true + (resolves ESCOMP/CTSM#1281) - cheyenne - not run +(6) Consolidate conditional structures for VIC initialization (resolves + ESCOMP/CTSM#1287) - PTCLM testing (tools/shared/PTCLM/test): +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- - cheyenne - not run +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) - regular tests (aux_clm): + [Put an [X] in the box for any configuration with significant answer changes.] - cheyenne ---- pass - hobart ------ pass +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1286 (Move call to WaterGridcellBalance out to + the driver) +- Resolves ESCOMP/CTSM#1281 (Remove deprecated history output) +- Resolves ESCOMP/CTSM#1287 (Inconsistent logic for VIC initialization + can cause crash in debug mode) +- Resolves ESCOMP/CTSM#1270 (Hexadecimal constants use non-standard + Fortran) + + +Testing summary: +---------------- + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK -CTSM tag used for the baseline comparisons: ctsm1.0.dev024 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes @@ -8083,33 +1298,35 @@ Answer changes Changes answers relative to baseline: NO + Field lists differ for Clm50 / Clm51 / Ctsm50 tests; otherwise + bit-for-bit -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - +Other details +------------- Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/551 +- https://github.com/ESCOMP/CTSM/pull/1276 (Restructure ozone code) +- https://github.com/ESCOMP/CTSM/pull/1271 (Fix non-standard hexadecimal constant) +- https://github.com/ESCOMP/CTSM/pull/1226 (Remove support for CISM1) =============================================================== =============================================================== -Tag name: ctsm1.0.dev024 -Originator(s): slevis (Samuel Levis,SLevis Consulting, LLC, 303-665-1310) -Date: Mon Jan 14 11:07:04 MST 2019 -One-line Summary: Remove unnecessary restart variables +Tag name: ctsm5.1.dev024 +Originator(s): slevis (Samuel Levis,303-665-1310) +Date: Sat Feb 20 14:42:33 MST 2021 +One-line Summary: Grid cell-level error check for H2O Purpose of changes ------------------ -Remove unnecessary restart variables to conserve on computing resources -and disk space + For more robust mass balance error checking, introduced + grid cell-level error check for H2O following the approach + of pull requests #984 and #1022 Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): 285 +Issues fixed (include CTSM Issue #): #201 Significant changes to scientifically-supported configurations @@ -8120,86 +1337,108 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 +[ ] ctsm5_0-nwp + [ ] clm4_5 Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): + None Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + None Changes made to namelist defaults (e.g., changed parameter values): + None Changes to the datasets (e.g., parameter, surface or initial files): + None -Substantial timing or memory changes: +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] + None -Notes of particular relevance for developers: -Code reviewed by Bill Sacks. -Standard testing (cheyenne and hobart) OK -Unit testing PASS +Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): + None Changes to tests or testing: - -Code reviewed by: Bill Sacks + None CTSM testing: -Regular testing (cheyenne and hobart) OK -Unit testing PASS -CTSM tag used for the baseline comparisons: -ctsm1.0.dev023 + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK (comparisons to baseline fail as expected) + izumi ------- OK (comparisons to baseline fail as expected) + +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: NO (bfb) +Changes answers relative to baseline: YES + + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change: ROUNDOFF + + Explanation: Moving call BalanceCheck to after the call lnd2glc in + subroutine clm_drv causes a change in order of operations that leads to + roundoff change in ERRH2O. Confirmed by running ./summarize_cprnc_diffs Detailed list of changes ------------------------ List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + None Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/598 - -Variables removed from restart: -plant_nalloc -pot_f_nit_vr* -f_nit_vr* -root_depth -qflx_floodg -snounload -qflx_snofrz_lyr -sminn_to_plant_fun_patch + https://github.com/ESCOMP/ctsm/pull/1228 =============================================================== =============================================================== -Tag name: ctsm1.0.dev023 -Originator(s): sacks (Bill Sacks) -Date: Thu Jan 10 13:00:42 MST 2019 -One-line Summary: Remove CLM4.0 - -Purpose of changes ------------------- +Tag name: ctsm5.1.dev023 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Thu Feb 11 00:14:03 MST 2021 +One-line Summary: Calculate leaf biomass for non-woody PFTS, and a few other small answer changes -Remove CLM4.0. This consists of removing code and other files that are -specific to CLM4.0, and doing some resulting cleanup of code that was -shared between CLM4.0 and later versions (primarily in build-namelist). +Purpose and description of changes +---------------------------------- -Bugs fixed or introduced ------------------------- +Replace hard code constant 0.25 for leaf mass per area with calculation based on parameter slatop (specific leaf area, top of +canopy). Also move num_iter into loop over patches; currently it sits outside a loop, so p index is incorrect. -Issues fixed (include CTSM Issue #): -- Resolves #455 (Remove CLM4.0) +Also do some small answer changes in terms of new parameter files, and some other existing issues that have mild answer changes. Significant changes to scientifically-supported configurations @@ -8210,152 +1449,111 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 - -[ ] clm4_5 - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users (e.g., need to interpolate initial conditions): -- Can no longer run CLM4.0 cases +[X] clm5_1 -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -- CLM4.0 compsets no longer supported +[ ] clm5_0 -Changes made to namelist defaults (e.g., changed parameter values): none +[ ] ctsm5_0-nwp -Changes to the datasets (e.g., parameter, surface or initial files): none +[ ] clm4_5 -Substantial timing or memory changes: none -Notes of particular relevance for developers: (including Code reviews and testing) ---------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide +Bugs fixed or introduced +------------------------ +Issues fixed (include CTSM Issue #): + Fixes #1256 -- num_iter incorrect + Fixes #1268 -- Leaf biomass not updated for + Fixes #1262 -- pconv should be 1 for crops + Fixes #1261 -- Restarts fail in AD-spinup mode + Fixes #1255 -- mkmapdata crashes because of modules + Fixes #1252 -- New urban dataset for fsurdat fails when used with new model + Fixes #1184 -- slatop for generic crop + Fixes #932 --- Diagnostic variables are incorrect + Fixes #478 --- Bare soil g1 should be zero -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none +Known bugs found since the previous tag (include issue #): + #1274 -- Dead PFTs in PPE2_BHSon simulations -Changes to tests or testing: Removed CLM4.0 tests -Code reviewed by: Erik Kluzek +Notes of particular relevance for users +--------------------------------------- +Changes made to namelist defaults (e.g., changed parameter values): + Parameter files are updated -CTSM testing: +Changes to the datasets (e.g., parameter, surface or initial files): - build-namelist tests: +Notes of particular relevance for developers: +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide - cheyenne - pass +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Leaf biomass should still be completely moved outside of CanopyFluxes - tools-tests (test/tools): +Changes to tests or testing: Add ADspinup test + Add an ADspinup restart test that would've detected one of the bugs fixed here - cheyenne - pass - PTCLM testing (tools/shared/PTCLM/test): +Testing summary: regular tools +---------------- - cheyenne - ok + [PASS means all tests PASS; OK means tests PASS other than expected fails.] - Total number of tests = 52 - Number of tests that PASS = 51 - Number of tests that Fail = 1 - Number of compare tests that PASS = 37 - Number of compare tests that Fail = 4 - Number of tests without compare = 11 + build-namelist tests (if CLMBuildNamelist.pm has changed): - The one failing test is: - FAIL fail-no_towerdata.-d+/glade/p/cesmdata/cseg/inputdata++-s+RF-Bra+--debug+--pftgrid+--soilgrid. + cheyenne - PASS (348 tests are different because of parameter file update) - These same failures occurred in ctsm1.0.dev022 (including the - compare tests that Fail). Erik Kluzek says these failures are - okay. + tools-tests (test/tools) (if tools have been changed): - regular tests (aux_clm): + cheyenne - PASS - cheyenne ---- pass - hobart ------ pass + python testing (if python code has changed; see instructions in python/README.md; document testing done): - Notes on testing: + cheyenne - PASS - - Most testing done on b5380c7e8. Since then, updated to a version of - cime that fixes cime's configure tool (but this isn't invoked in - system tests, so I didn't rerun the system tests) and pointed cime - to a tag rather than a hash. + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - - For tools tests: In baseline, cherry-picked commit 148bc2158 into - cime + cheyenne ---- PASS + izumi ------- PASS + + any other testing (give details below): -CTSM tag used for the baseline comparisons: ctsm1.0.dev022 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: NO - -Detailed list of changes ------------------------- - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- cime: points to branch tag off of cime5.7.5 - (ctsm/ctsm1.0/cime5.7.5/n01), with changes for: - (1) Removal of support for CLM4.0 (equivalent to the changes in - https://github.com/ESMCI/cime/pull/2968) +Changes answers relative to baseline: Yes, clm51, clm50-non-crop, clm45 two diagnostics - (2) Fix for cime configure (cherry-picked 148bc2158) + Summarize any changes to answers, i.e., + - what code configurations: clm5_1 for all, clm50 for non-crop (Sp and Bgc), clm4_5 two diagnostics + - what platforms/compilers: All + - nature of change: clm51--BGC climate, others similar climate +Other details +------------- Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/609 (Remove CLM4.0) -- https://github.com/ESCOMP/ctsm/pull/601 (Print git status and related - info when running run_sys_tests) +(https://github.com/ESCOMP/ctsm/pull) + #1254 -- replace constant leaf mass per area (lma) =============================================================== =============================================================== -Tag name: ctsm1.0.dev022 -Originator(s): sacks (Bill Sacks) -Date: Tue Jan 8 11:01:38 MST 2019 -One-line Summary: Set tracer version of irrigation fluxes - -Purpose of changes ------------------- - -Set tracer version of irrigation fluxes. - -This required a substantial rewrite of ApplyIrrigation (now renamed to -CalcIrrigationFluxes). The problem was that the code was written to -compute the total irrigation withdrawal from groundwater, then use this -to compute the application fluxes (drip/sprinkler), then later divide -this total withdrawal by layer. But for tracer fluxes to be computed -correctly, we needed to reorder this, so that the per-layer withdrawals -are determined before determining the application fluxes. This is -because the application flux needs to know the tracer concentrations of -the source, which requires knowing which layers the source is drawing -from. This was made more challenging because of the mix of patch-level -and column-level variables at play: irrigation demand is patch-level, -groundwater availability and extraction is column-level, but application -is back to patch-level. - -In a somewhat-related change, I also reworked the passing of information -between soil hydrology (groundwater availability) and irrigation: -Previously, there was some near-duplicate code in -CalcAvailableUnconfinedAquifer (which was called prior to -ApplyIrrigation) and WithdrawGroundwaterIrrigation (which was called -after ApplyIrrigation). I have reworked the code to remove this -duplication, calling the new CalcIrrigWithdrawals in the midst of -CalcIrrigationFluxes. In doing so, I reconciled an accidental -discrepancy between the two original routines (see -https://github.com/escomp/ctsm/issues/595). +Tag name: ctsm5.1.dev022 +Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049) +Date: Fri Feb 5 00:03:28 MST 2021 +One-line Summary: Merge fates_main_api into ctsm master +Purpose and description of changes +---------------------------------- -Bugs fixed or introduced ------------------------- +This brings fates_main_api into and up-to-date with ctsm master. +At the point of merge, fates_main_api was parallel with ctsm5.1.dev020, +only one tag behind ctsm master's head. -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#521 (Set tracer versions of fluxes set by - ApplyIrrigation) -- Resolves ESCOMP/ctsm#593 (Generalize groundwater irrigation availability to - handle multiple patches per column) -- Resolves ESCOMP/ctsm#595 (Inconsistency between CalcAvailableUnconfinedAquifer - and WithdrawGroundwaterIrrigation) +The purpose of this merge is to make all future updates to fates +on the ctsm master branch instead of on the fates_main_api branch. Significant changes to scientifically-supported configurations @@ -8366,173 +1564,154 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): + Fixes #1128 -- missing compset for FATES tests + Fixes #1002 -- allow transient land-use files when FATES is on? + Some work was done on #1272 -- namelist refactor for FATES + +Known bugs introduced in this tag (include issue #): + #1265 -- Diversifying fates testmods included in `aux_clm` test suite + #1266 - Add test for successful_ignitions mode for FATES-SPITFIRE -[ ] clm4_0 +Known bugs found since the previous tag (include issue #): + #1269 -- GSWP3V1 atmospheric forcing for 2011-2014 is "bad" over Antarctica Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none +Changes made to namelist defaults (e.g., changed parameter values): + - fates_spitfire_mode updated with multiple modes that use external datasets + - use_fates_cohort_age_tracking added to enable size and age dependent mortality + - fates_parteh_mode option 2 added for fates CNP mode -Changes made to namelist defaults (e.g., changed parameter values): none +Changes to the datasets (e.g., parameter, surface or initial files): + fates_paramfile updated to fates_params_api.14.0.0_12pft_c200921.nc -Changes to the datasets (e.g., parameter, surface or initial files): none +Substantial timing or memory changes: + Only the fates testmod FatesAllVars failed the MEMCOMP test due to the increase in the number of variables included -Substantial timing or memory changes: none -Notes of particular relevance for developers: (including Code reviews and testing) +Notes of particular relevance for developers: --------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + There are a couple of issues we plan to address later (#1265, and #1272) + Note also that NAG compiler production tests started failing because of a compiler error + Since, we only care about NAG for DEBUG testing we removed those tests. Hopefully, a compiler + update will allow that to work in the future. -Code reviewed by: +Changes to tests or testing: + - Added FatesPRT2 testmod test which activates fates CNP mode + - Added FatesReducedComplexFixedBiogeo testmod which activates fates fixed biogeography mode + - Added FatesSizeAgeMort testmod which activates tracking of size and age dependent mortality in fates + - Added Fates_nat_and_anthro_ignitions testmod to activate use of external lightning and population datasets + - Non-debug mode nag tests replaced in izumi test list with debug versions due to internal compiler error. -- Sean Swenson reviewed the initial parts of the rework of - ApplyIrrigation and the passing of information between soil hydrology - and irrigation -CTSM testing: +Testing summary: regular +---------------- - build-namelist tests: + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + build-namelist tests (if CLMBuildNamelist.pm has changed): - cheyenne - not run + cheyenne - PASS (61 namelists are different because of fates changes) - tools-tests (test/tools): + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne - not run + cheyenne ---- PASS (fates testmods DIFFs are expected) + izumi ------- OK - PTCLM testing (tools/shared/PTCLM/test): + ok: All non-fates testmods PASS. Fates testmods have DIFF as expected due to update of fates tag. + BFAILs expected due to changing non-debug nag test to debug. See #1264 comments for discussion. - cheyenne - not run + fates tests: + cheyenne ---- OK - regular tests (aux_clm): + ok: expected failures on COMPARE_base_rest for FatesHydro + and Fates_nat_and_anthro_ignitions. All else B4B. - cheyenne ---- ok - hobart ------ ok - - ok means tests pass, expected baseline failures as noted below - - Additional manual testing: - - - Out of the box, the one-timestep tracer consistency test - (SMS_D_Ln1.f10_f10_musgs.I2000Clm50BgcCropGs.hobart_nag.clm-tracer_consistency) - passed when the new check was inserted after the irrigation call, - even without the changes in this tag. Presumably this is because no - irrigation was being done in the first time step of this test. To - confirm that the changes here were both necessary and effective, I - hacked the code to force irrigation of all types (surface and - groundwater) on the first time step (see - https://github.com/billsacks/ctsm/commit/d28a03145). I confirmed - that this test, with those code hacks, failed before the changes in - this tag, and passed with these changes in place. - - - I used a multi-step process to confirm that these changes are only - roundoff-level different for groundwater irrigation (because - feedbacks in the system result in - SMS_D_Ld5.f10_f10_musgs.I2000Clm50BgcCrop.hobart_nag.clm-irrig_alternate - looking greater-than-roundoff-level different from the baseline): - - (1) Confirmed that e507fe603 is only roundoff-level different from - baseline using cprnc output from this test. - - (2) Confirmed that a4a1a626c is only roundoff-level different from - e507fe603. This was the tricky part. I did this by introducing - some temporary code that (a) computed some fluxes in both the - old and new ways, (b) compared the old and new methods for each - point and time step, confirming that they were no more than - roundoff-level different, then (c) set the fluxes to the old - method. I confirmed that this was bit-for-bit with e507fe603, - and the checks for greater-than-roundoff-level differences - between the old and new methods were never triggered. (See - https://github.com/billsacks/ctsm/commit/7d23e9e and the earlier - commits on that branch.) - - (3) Confirmed that remaining changes an the branch are bit-for-bit - with a4a1a626c. - -CTSM tag used for the baseline comparisons: ctsm1.0.dev021 + fates baseline: fates-sci.1.43.2_api.14.2.0-ctsm5.1.dev020-C5f348cac-F5534a940 + + any other testing (give details below): +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): +Changes answers relative to baseline: Yes, only for fates Summarize any changes to answers, i.e., - - what code configurations: - - - Small answer changes when groundwater irrigation is enabled. In - principle, could change answers by greater than roundoff due to - fix of #595, but I didn't see any answer changes in my 7-month - test due to that change. Other than that, just roundoff-level - changes. - - - Answer changes when tracers are enabled. - - - Roundoff-level changes in the diagnostic field, - QIRRIG_FROM_SURFACE, for many tests - + - what code configurations: all fates - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - See notes under "what code configurations" for details. + - nature of change (roundoff; larger than roundoff/same climate; new + climate): larger than roundoff - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A + Comparison made using fates suite between fates_main_api (at ctsm5.1.dev020) + and ctsm5.1.dev022. All tests PASS, except for two expected failures and + expected NLCOMP failure due to ctsm5.1.dev021 update to paramfile. - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - URL for LMWG diagnostics output used to validate new climate: N/A - +Other details +------------- -Detailed list of changes ------------------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +fates -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + fates: sci.1.30.0_api.8.0.0 -> sci.1.43.2_api.14.2.0 Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/600 +(https://github.com/ESCOMP/ctsm/pull) + #1264 -- Merge fates_main_api into master =============================================================== =============================================================== -Tag name: ctsm1.0.dev021 -Originator(s): mvr (Mathew Rothstein,UCAR/CSEG,303-497-1304) -Date: Wed Dec 26 16:29:06 MST 2018 -One-line Summary: Added tracer ratio capability and included it in consistency checks +Tag name: ctsm5.1.dev021 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Tue Jan 12 20:21:52 MST 2021 +One-line Summary: Add option for biomass heat storage (BHS) to clm5_1 physics Purpose of changes ------------------ -These changes are needed to support the implementation of water isotopes by ensuring -that isotope-related variables are being updated consistently throughout the model. -The consistency checks include the testing of a bulk tracer that should always be -equal to the bulk, and also test tracers that maintain a fixed ratio (other than -one) to the bulk. This commit includes fixes to the cold start initialization for -the water tracers with ratios other than one. +Add heat stored in biomass (for trees and shrubs) to the surface energy balance calculation. Add +a switch for it and turn it on by default for clm5_1 physics. It's turned off for clm4_5, clm5_0 +physics and when FATES is turned on. Those cases are identical to before, answers only change +when it's turned on. + +Papers describing BHS simulations: +R. Meier, Davin, E., Swenson, S., Lawrence, D., and Schwaab, Jo. (2019). Biomass heat +storage dampens diurnal temperature variations +in forests. Environmental Research Letters. 14. 084026. 10.1088/1748-9326/ab2b4e. + +S.C. Swenson, Burns, S. P., and Lawrence, D. M. ( 2019). The impact of biomass heat storage +on the canopy energy balance and atmospheric stability in the community land model, Journal +of Advances in Modeling Earth Systems, 11, 83– 98. +https://doi.org/10.1029/2018MS001476 Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): [If none, remove this line] -#541 Only do water tracer consistency checks on tracers that are - supposed to maintain a fixed ratio -#459 Fix cold start initialization of water tracers -#508 Remove unused variables in new Water types -#357 Put in place Water isotope consistency checks - +Issues fixed (include CTSM Issue #): + #342 --- set medlynslope to C4 appropriate value for millet and sorghum + (had already been done for miscanthus and switchgrass) + #1246 -- Make spinup_factor_deadwood a variable rather than hardcoded constant +Known bugs introduced in this tag (include github issue ID): + #1247 -- FATES doesn't work with BHS Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -8542,134 +1721,111 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[X] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none +Caveats for users (e.g., need to interpolate initial conditions): + New variables are added on the restart files (stem/leaf biomass and stem Temp) + Testing didn't show this as a problem, but theoretically could require + updating initial conditions + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): New compsets, new hist fields + I1850Clm51BgcCrop + I1850Clm51Bgc + History fields: AGSB, AGLB, FSH_STEM, DHDT_CANOPY, RAH1, RAH2, RAW1, RAW2, USTAR, UM, UAF, UM, UAF, + TAF, QAF, OBU, ZETA, VPD, num_iter, RB, TSTEM + DHSDT_CANOPY, TSTEM are default active + +Changes made to namelist defaults (e.g., changed parameter values): New use_biomass_heat_storage + New namelist item: use_biomass_heat_storage to turn on or off (by default only on for clm5_1 + physics for both SP and BGC modes) + +Changes to the datasets (e.g., parameter, surface or initial files): New parameter datasets + All of the params files were updated. New terms were BHS parameters and taper + stocking is now set as "nstem" on the parameter file + taper is now on the parameter file + +Substantial timing or memory changes: Doesn't seem to + Only one short test failed the TPUTCOMP test + Longer tests were not significantly different Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: added unit tests +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Code reviewed by: bill sacks +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Setting of leaf/stem biomass should be refactored and removed from CanopyFluxes (as described in #1247) + There's a change in CNGapMortality that could change for DV when AD mode is on + Stability cap (zera) is different for BHS on than off +Changes to tests or testing: New CLM51 FATES test -CTSM testing: +CTSM testing: regular + [PASS means all tests PASS and OK means tests PASS other than expected fails.] build-namelist tests: - cheyenne - not run + cheyenne - OK (462 comparisons fail because of new namelist and params files) - tools-tests (test/tools): - - cheyenne - not run - - PTCLM testing (tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + cheyenne -- PASS regular tests (aux_clm): - cheyenne ---- PASS - hobart ------ PASS + cheyenne ---- OK + izumi ------- OK -CTSM tag used for the baseline comparisons: ctsm1.0.dev020 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: no, b4b - +Changes answers relative to baseline: Yes! + Summarize any changes to answers, i.e., + - what code configurations: clm5_1 + - what platforms/compilers: all + - nature of change: new climate for tree and shrubs Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none -Pull Requests that document the changes (include PR ids): #599 Adding isotope - tracer ratios +Pull Requests that document the changes (include PR ids): (https://github.com/ESCOMP/ctsm/pull) + #1016 -- Heat Storage biomass =============================================================== =============================================================== -Tag name: ctsm1.0.dev020 -Originator(s): Sean Swenson, Bill Sacks -Date: Mon Dec 3 11:51:24 MST 2018 -One-line Summary: New options for irrigation and crop fsat +Tag name: ctsm5.1.dev020 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Wed Dec 30 00:42:16 MST 2020 +One-line Summary: Potential roundoff changes in preparation for bio-mass heat storage option Purpose of changes ------------------ -Introduce three new options: - -(1) Ability to withdraw irrigation water from groundwater if not enough - water is available from rivers. This is controlled via new namelist - flag, use_groundwater_irrigation. Water can be withdrawn from both - the unconfined (from the soil column) and confined (from wa) - aquifers. - -(2) Irrigation method: sprinkler (above canopy) vs. drip (below - canopy). This can be set on a per-crop and per-gridcell basis on the - surface dataset, but out-of-the-box support for creating the - necessary surface dataset field is not yet in place (see - ESCOMP/ctsm#565). For now, it can be controlled globally via a new - namelist flag, irrig_method_default. The default is drip, which was - what we were previously using implicitly. - -(3) Set crop fsat to zero. This is controlled by a new namelist option, - crop_fsat_equals_zero. - -Default behavior is the same as before for all three options. - -Also: - -- If use_aquifer_layer is false (which is the default for CLM50), no - longer reset wa_col every time step +This adds in some changes that may be roundoff different in preparation for bringing in the changes +that allow turning on the bio-mass heat storage option. There's a few zeroed terms added to some calculations +in CanopyFluxes. The new terms are identical to what will come in for BHS except the zeroed terms are +not arrays here but scalars. I showed the new terms are only off by roundoff with a previous commit that added +explicit tests for the terms and verified it for two tests. -- Adds indices to vector history files giving column, landunit and - gridcell indices for each patch, etc. (Resolves ESCOMP/ctsm#81: - "Restart files are different for CLM when run over different number of - tasks" (issue name is a misnomer of the remaining to-dos in that - issue.) - -- Writes 3d time-constant fields on first history file for all tapes, - not just the first - -- Small performance improvements to irrigation Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): -- Resolves ESCOMP/ctsm#81 ("Restart files are different for CLM when run - over different number of tasks", but that name was a misnomer for the - remaining work needed on the issue) - -Known bugs introduced in this tag (include github issue ID): -- ESCOMP/ctsm#565: Surface dataset enhancements needed for irrigation method - - Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -8678,181 +1834,108 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): none - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -- New namelist variables: - - use_groundwater_irrigation - - irrig_method_default - - crop_fsat_equals_zero -- Partial support for new surface dataset field: irrigation_method - -Changes made to namelist defaults (e.g., changed parameter values): none - -Changes to the datasets (e.g., parameter, surface or initial files): none - -Substantial timing or memory changes: none +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): Added new Clm51 compsets + I1PtClm51SpRs + I2000Clm51Sp + I2000Clm51SpRs + I1850Clm51Sp + I2000Clm51Fates + I1850Clm51SpNoAnthro + IHistClm51Sp Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Here I set some terms to zero that will be non-zero even when BHS is off + Earlier commits show the smaller set of changes that are needed. -Changes to tests or testing: -- Added two tests of the new irrigation options -- Added an _includes directory to hold things that should be included by - testmods (not used directly) - - -Code reviewed by: Bill Sacks and Sean Swenson reviewed each other's code +Changes to tests or testing: Switched one Clm50Sp test to Clm51Sp and added one HistClm51Sp test - -CTSM testing: +CTSM testing: regular [PASS means all tests PASS and OK means tests PASS other than expected fails.] build-namelist tests: - cheyenne - ok - - Tests pass, namelists differ as expected - - tools-tests (test/tools): - - cheyenne - not run + cheyenne - PASS - PTCLM testing (tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + cheyenne - PASS regular tests (aux_clm): - cheyenne ---- ok - hobart ------ pass - - ok: tests pass, some answers change as noted below + cheyenne ---- OK + izumi ------- OK -CTSM tag used for the baseline comparisons: ctsm1.0.dev019 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): +Changes answers relative to baseline: Summarize any changes to answers, i.e., - - what code configurations: Some CLM50 cases that are either cold start - or (unusually) use a CLM45 initial conditions file; it's possible - that non-cold-start configurations would see differences rarely. - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Larger than roundoff, same climate - - Differences arise due to no longer resetting wa_col to - aquifer_water_baseline every time step in BeginWaterBalanceSingle - if use_aquifer_layer is false (which is the default for - CLM50). (This change is needed to conserve water properly with the - new groundwater-based irrigation.) For the most part, wa_col - wasn't being changed when use_aquifer_layer is false (so no longer - resetting it has no effect if groundwater irrigation isn't being - used), but the one exception is the "work around of the negative - liquid water" added by Jinyun Tang in subroutine SoilWater (dated - Jan 14, 2015), which can be exercised when use_flexibleCN is - true. Sean Swenson did some experimentation, and found that the - code that updates wa_col is only exercised in the first time step - of a cold start run, and that finding is borne out in the test - suite results. However, it's possible that there are rare cases - when this is exercised later in a run. - - I have confirmed that this branch is bit-for-bit with the baseline - if I revert the addition of the use_aquifer_layer conditional - around the wa_col resetting in - BeginWaterBalanceSingle. Alternatively, nearly all tests are - bit-for-bit with the baseline if I remove the one line updating - wa_col in subroutine SoilWater (and also remove the endrun for - water balance errors from BalanceCheck); the one exception is the - waccmx_offline test, which uses a CLM45 initial conditions file in - a CLM50 configuration. - - The following tests had baseline failures: - - Cold start tests: - - ERP_D_Ld5.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-allActive - ERP_D_P36x2_Ld3.f10_f10_musgs.I2000Clm50BgcCrop.cheyenne_intel.clm-cropColdStart - ERP_P180x2_D_Ld5.f19_g17.I2000Clm50BgcDvCrop.cheyenne_intel.clm-crop - ERP_P36x2_Lm25.f10_f10_musgs.I2000Clm50BgcDvCrop.cheyenne_intel.clm-monthly - ERP_P72x2_Lm25.f10_f10_musgs.I2000Clm50BgcDvCrop.cheyenne_intel.clm-monthly - - Test that uses a CLM45 initial conditions file in a CLM50 - configuration: - - ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline + - what code configurations: all + - what platforms/compilers: izumi-PGI + - nature of change: roundoff If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A + than roundoff? - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A + Earlier commit tested the new terms versus the old and showed they were + order e-11 for absolute difference and e-14 relative difference. - URL for LMWG diagnostics output used to validate new climate: N/A - + Tests that change from baseline.... + + ERS_Ly5_P144x1.f10_f10_musgs.IHistClm51BgcCrop.cheyenne_intel.clm-cropMonthOutput + SMS.f10_f10_musgs.I2000Clm50BgcCrop.izumi_pgi.clm-crop + SMS_D.f10_f10_musgs.I2000Clm51BgcCrop.izumi_pgi.clm-crop Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +Pull Requests that document the changes (include PR ids): #1241 +(https://github.com/ESCOMP/ctsm/pull) -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/523 + #1241 -- Small answer changes in preparation for adding option for bio-mass heat storage =============================================================== =============================================================== -Tag name: ctsm1.0.dev019 +Tag name: ctsm5.1.dev019 Originator(s): sacks (Bill Sacks) -Date: Fri Nov 30 13:36:57 MST 2018 -One-line Summary: Rework cold start initialization of wa and zwt +Date: Sat Dec 19 06:55:46 MST 2020 +One-line Summary: Fix ndep from coupler Purpose of changes ------------------ -Rework cold start initialization of wa and zwt when use_aquifer_layer is -false to reduce answer changes in upcoming groundwater_irrigation -branch. - -In the groundwater_irrigation branch -(https://github.com/ESCOMP/ctsm/pull/523), Sean Swenson has stopped -resetting wa_col each time step if use_aquifer_layer is false. However, -this leads to having a substantially different value of wa_col when -use_aquifer_layer is false: previously, it was reset to -aquifer_water_baseline each time step, but with Sean's changes, it stays -close to its initial values, which have been 4000 in most places. This -tag changes the initial values to match the value it was being reset to, -so it simply starts at aquifer_water_baseline - so the -every-time-step-resetting to aquifer_water_baseline can be removed -without massively changing the value of wa_col. - -In addition to changing the cold start initialization of wa_col, we are -also changing the cold start initialization of zwt in this case where -use_aquifer_layer is false: The old initialization of zwt wouldn't work -as intended now that we have changed the initial value of wa_col; Sean -Swenson suggested this new initialization method instead. This -initialization to zi(c,nbedrock(c)) is correct if there are no saturated -layers, and close enough for a decent cold start even if there are. +There was a bug in ndep forcing (forc_ndep_grc) when receiving ndep from +CAM (ndep_from_cpl true). This first appeared in ctsm5.1.dev002. NDEP +forcings have been garbage since then when receiving ndep from CAM. + +This tag fixes that issue. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1233 (ndep forcing incorrect when receiving ndep + from CAM (starting with ctsm5.1.dev002)) Significant changes to scientifically-supported configurations @@ -8863,11 +1946,13 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- @@ -8880,19 +1965,16 @@ Changes made to namelist defaults (e.g., changed parameter values): none Changes to the datasets (e.g., parameter, surface or initial files): none -Substantial timing or memory changes: none +Substantial timing or memory changes: none expected (not checked) Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): none Changes to tests or testing: none -Code reviewed by: Sean Swenson - - CTSM testing: [PASS means all tests PASS and OK means tests PASS other than expected fails.] @@ -8907,37 +1989,40 @@ CTSM testing: PTCLM testing (tools/shared/PTCLM/test): - cheyenne - not run + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run regular tests (aux_clm): - cheyenne ---- ok - hobart ------ ok + cheyenne ---- pass + izumi ------- pass - ok means tests pass, answers change as expected for some cases + izumi testing: baseline generation failed due to running out of disk + space. I have sym linked the ctsm5.1.dev018 baselines to + ctsm5.1.dev019, because answers are bit-for-bit between the two tags + as far as aux_clm testing is concerned. -CTSM tag used for the baseline comparisons: ctsm1.0.dev018 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: YES +Changes answers relative to baseline: YES, but just in select coupled configurations - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): + [ If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section). + And always remove these three lines and parts that don't apply. ] Summarize any changes to answers, i.e., - - what code configurations: CLM50 cold start or transient (Hist) cases + - what code configurations: Coupled configurations where CTSM + receives NDEP from CAM - what platforms/compilers: all - nature of change (roundoff; larger than roundoff/same climate; new climate): - - Larger than roundoff, same climate (not investigated completely - rigorously through long simulations, but Sean Swenson and Bill - Sacks are both pretty confident that the resulting changes will be - small, partly based on difference statistics from the test suite, - and partly based on the fact that the only change in this tag is - in cold start initialization of some values). + potentially new climate If bitwise differences were observed, how did you show they were no worse than roundoff? N/A @@ -8954,44 +2039,25 @@ Detailed list of changes List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none -Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/577 +Pull Requests that document the changes (include PR ids): none =============================================================== =============================================================== -Tag name: ctsm1.0.dev018 -Originator(s): sacks (Bill Sacks) -Date: Thu Nov 29 16:03:50 MST 2018 -One-line Summary: Water tracer updates for initial things in driver loop +Tag name: ctsm5.1.dev018 +Originator(s): slevis (Samuel Levis,,303-665-1310) +Date: Tue Dec 8 11:19:02 MST 2020 +One-line Summary: Add ACTIVE (T/F) column to master hist fields table and alphabetize Purpose of changes ------------------ -Update water tracers for initial stuff done in driver loop. This includes -atm2lnd forcings (non-downscaled and downscaled), balance check initialization, -and dyn subgrid updates. - -Broadly speaking, the changes here are: - -(1) Reworked WaterType to make it easier / more robust for other code to loop - over tracers or bulk+tracers - -(2) The most interesting changes are probably the code to update the atm2lnd - water tracers (in Wateratm2lndType.F90 and WaterTracerUtils.F90) - -(3) In various other places, do some infrastructurey stuff (initializing water - balance, doing dyn subgrid stuff) for tracers as well as bulk - -(4) Supporting unit tests and unit test infrastructure - + For convenience, added an ACTIVE column to the master fields table and + alphabetized. Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): -Resolves ESCOMP/ctsm#487 -Resolves ESCOMP/ctsm#488 -Resolves ESCOMP/ctsm#489 +Issues fixed (include CTSM Issue #): #941 Significant changes to scientifically-supported configurations @@ -9002,44 +2068,41 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): none +Caveats for users (e.g., need to interpolate initial conditions): + None -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + None -Changes made to namelist defaults (e.g., changed parameter values): none +Changes made to namelist defaults (e.g., changed parameter values): + None -Changes to the datasets (e.g., parameter, surface or initial files): none +Changes to the datasets (e.g., parameter, surface or initial files): + None -Substantial timing or memory changes: none +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] + None Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): -- We have chosen not to set all water tracers as soon as possible, but instead - to do these tracer settings later in the driver loop. This keeps the driver - loop cleaner, but means that you cannot arbitrarily sprinkle calls to - TracerConsistencyCheck throughout the driver. Specifically for this tag: the - non-downscaled, gridcell-level atm2lnd water tracers are not updated until - after the call to downscale_forcings, so tracer consistency checks before that - point would fail. + None Changes to tests or testing: -- Added a PFS test - -Code reviewed by: Portions of the design (and possibly code) have been reviewed -by Mat Rothstein, David Noone and Mariana Vertenstein - + None CTSM testing: @@ -9047,84 +2110,65 @@ CTSM testing: build-namelist tests: - cheyenne - not run + cheyenne - tools-tests (test/tools): - cheyenne - not run + cheyenne - PTCLM testing (tools/shared/PTCLM/test): - cheyenne - not run + cheyenne - - regular tests (aux_clm): + python testing (see instructions in python/README.md; document testing done): - cheyenne ---- ok - hobart ------ ok + (any machine) - + + regular tests (aux_clm): - ok means tests pass, some answers change as expected + cheyenne ---- PASS + izumi ------- PASS -CTSM tag used for the baseline comparisons: ctsm1.0.dev017 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: many - - what platforms/compilers: all - - nature of change (roundoff; larger than roundoff/same climate; new climate): - roundoff-level changes in sensible heat flux from precip conversion due to - refactoring this calculation; everything else bit-for-bit - - If bitwise differences were observed, how did you show they were no worse - than roundoff? via summarize_cprnc_diffs to see differences in the test suite - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - +Changes answers relative to baseline: + No Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + None Pull Requests that document the changes (include PR ids): -https://github.com/ESCOMP/ctsm/pull/572 + https://github.com/ESCOMP/CTSM/pull/1222 =============================================================== =============================================================== -Tag name: ctsm1.0.dev017 -Originator(s): slevis (Samuel Levis, Slevis Consulting LLC,303-665-1310) -Date: Wed Nov 28 14:27:50 MST 2018 -One-line Summary: Merge the collapse2gencrop branch +Tag name: ctsm5.1.dev017 +Originator(s): slevis (Samuel Levis,303-665-1310) +Date: Tue Nov 17 18:19:20 MST 2020 +One-line Summary: Write history fields master list to separate optional file Purpose of changes ------------------ -These changes allow the model to not need to read 16-pft -datasets and rather read 78-pft datasets. The 78-pft datasets were -developed for use with prognostic crops originally. The current changes -allow the model to use the 78-pft datasets in 16-pft runs by -collapsing the crop pfts (cfts) from specific types to the model's -generic crop types. The changes are generic so that the model may still -read 16-pft datasets for 16-pft runs. Ultimately these changes will -permit users to run with any number of pfts, while the ctsm group -maintains a single set of input pft data. + User can choose to write the history fields master list in a separate + text file by setting hist_master_list_file = .true. in CTSM's namelist. + + File contents follow recommended reStructuredText "simple table" + formatting (see + https://docutils.sourceforge.io/docs/user/rst/quickref.html#tables) + for use in CTSM documentation in the sphinx environment. Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): Fixes #509 (partial) - #509 -- irrigate in 1850 is off for runs with use_crop but on for those without +Issues fixed (include CTSM Issue #): #34 #941 Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -9132,121 +2176,119 @@ Significant changes to scientifically-supported configurations Does this tag change answers significantly for any of the following physics configurations? (Details of any changes will be given in the "Answer changes" section below.) + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- +Caveats for users (e.g., need to interpolate initial conditions): + None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New namelist option hist_master_list_file. Setting to true generates a + new text output file containing the history fields master list. + Changes made to namelist defaults (e.g., changed parameter values): -- maxpatch_pft made obsolete -- nnegcrit was increased because of failure in the TRENDY simulations. -This was done in the source, rather than the namelist but does have an -effect on user behavior. + Default for hist_master_list_file = .false. -Substantial timing or memory changes: No +Changes to the datasets (e.g., parameter, surface or initial files): + None + +Substantial timing or memory changes: + No Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): + None - The "irrigate" attribute should now be removed from all fsurdat files for namelist generation. - Thus irrigate on or off is now an option for non-crop cases. +Changes to tests or testing: + Introduced testing for the new namelist option within the existing test + ERP_P36x2_D_Ld3.f10_f10_musgs.I1850Clm50BgcCrop.cheyenne_gnu.clm-extra_outputs + by adding hist_master_list_file = .true. to the test's user_nl_clm +CTSM testing: -Renamed parameters: -maxpatch_pft is obsolete; remove from namelist-related scripts in future PR -numpft + 1 ---> maxsoil_patches -maxpatch_pft ---> maxsoil_patches in CNDV -numpft ---> maxveg -numpft_ed ---> maxveg_fates +[... Remove before making master tag. Available test levels: -Several modules were made default private. The list of variables in them -that are public are explicitly listed now: -LakeCon.F90 -clm_initializeMod.F90 -clm_instMod.F90 -clm_varpar.F90 -pftconMod.F90 -subgridAveMod.F90 + a) regular (must be run before handing off a tag to SEs and must be run + before committing a tag) + b) build_namelist (if namelists and/or build_system changed)) + c) tools (only if tools are modified and no CTSM source is modified) + d) short (for use during development and in rare cases where only a small + change with known behavior is added ... eg. a minor bug fix) + e) doc (no source testing required) -Changes to tests or testing: -New test -New unit tests in test_surfrdUtils.pf, all containing the prefix -test_collapse_crop_types_* +... ] -Code reviewed by: -Erik Kluzek and Bill Sacks + [PASS means all tests PASS and OK means tests PASS other than expected fails.] -CTSM testing: -Regular + build-namelist tests: - [PASS means all tests PASS and OK means tests PASS other than expected fails.] + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - regular tests (aux_clm): - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- PASS - hobart_pgi -------- OK - hobart_intel ------ PASS + cheyenne ---- OK (NLCOMP tests fail as expected) + izumi ------- OK (NLCOMP tests fail as expected) + +If the tag used for baseline comparisons was NOT the previous tag, note that here: -CTSM tag used for the baseline comparisons: ctsm1.0.dev016 Answer changes -------------- -Changes answers relative to baseline: NO - +Changes answers relative to baseline: + No Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None - -Pull Requests that document the changes (include PR ids): #483 + Added section to subr. hist_printflds (called by subr. initialize2). + The new section runs when hist_master_list_file = .true. -Sam Levis cloned Erik Kluzek's collapse2gencrop branch and then -tested, corrected errors, resolved conflicts, added unit tests, while -updating to newer tags as needed. +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + None +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/CTSM/pull/1209 =============================================================== =============================================================== -Tag name: ctsm1.0.dev016 -Originator(s): sacks (Bill Sacks) -Date: Thu Nov 1 07:27:48 MDT 2018 -One-line Summary: Update cime, fix FATES DEBUG token, add script to easily run system tests +Tag name: ctsm5.1.dev016 +Originator(s): mvertens (Mariana Vertenstein), jedwards (Jim Edwards), + sacks (Bill Sacks), erik (Erik Kluzek) +Date: Tue Nov 17 10:49:40 MST 2020 +One-line Summary: Updates for nuopc Purpose of changes ------------------ -(1) Update to latest version of cime master - -(2) Update FATES with a minor change: change DEBUG to debug, to allow - working with a preprocessor-defined DEBUG token - -(3) Add a script (run_sys_tests) that allows easily running all system - tests (see - https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide#running-test-suites-with-the-run-sys-tests-wrapper - for details) - -(4) As part of (3), start work on a CTSM python library and associated - test infrastructure. - -Bugs fixed or introduced ------------------------- - -Issues fixed (include CTSM Issue #): -- Fixes ESCOMP/ctsm#535 (Run Fortran unit tests as part of create_test) +Various updates needed for NUOPC. -CIME Issues fixed (include issue #): -- Various - see CIME ChangeLog for details +Also adds mizuRoute as an external component. Significant changes to scientifically-supported configurations @@ -9257,11 +2299,13 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[X] clm5_0 +[ ] clm5_1 -[X] clm4_5 +[ ] clm5_0 + +[ ] ctsm5_0-nwp -[X] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- @@ -9278,16 +2322,16 @@ Substantial timing or memory changes: none Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: -- New run_sys_tests wrapper -- Fortran unit tests now run as part of aux_clm +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Code reviewed by: Erik Kluzek +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- SoilMoistureStreamMod now is duplicated: the version used with mct is + still in src/biogeochem, but there is a new version used with nuopc + and the CDEPS data models in src/cpl/nuopc. The latter has just been + introduced for testing purposes. Eventually, once we switch everything + to use CDEPS, we'll remove this duplicated version. +Changes to tests or testing: none CTSM testing: @@ -9303,114 +2347,66 @@ CTSM testing: PTCLM testing (tools/shared/PTCLM/test): - cheyenne - not run + cheyenne - not run - regular tests (aux_clm): + python testing (see instructions in python/README.md; document testing done): - cheyenne ---- ok - hobart ------ ok + (any machine) - not run + + regular tests (aux_clm): - ok means tests pass, baselines fail as expected + cheyenne ---- pass + izumi ------- pass -CTSM tag used for the baseline comparisons: ctsm1.0.dev015 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: All I compsets (except spinup test that uses cplhist datm forcing) - - what platforms/compilers: All - - nature of change (roundoff; larger than roundoff/same climate; new climate): - Potentially new climate - - Changes answers for I compsets due to datm update as part of the cime - update: new presaero and CO2 datasets - (https://github.com/esmci/cime/pull/2828) - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - +Changes answers relative to baseline: NO Detailed list of changes ------------------------ List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -- cime: cime5.7.3 -> cime5.7.5 -- fates: fates_s1.8.1_a3.0.0 -> fates_s1.8.1_a3.0.0_rev2 +- Added mizuRoute (at 34723c2) +- cime: branch_tags/cime5.8.32_a01 -> branch_tags/cime5.8.32_a02 +- (Some other rearrangement of Externals files, but versions stayed the + same) -Pull Requests that document the changes (include PR ids): -- https://github.com/escomp/ctsm/pull/493 (Wrapper to system tests, and - start of a ctsm python library) +Pull Requests that document the changes (include PR ids): none =============================================================== =============================================================== -Tag name: ctsm1.0.dev015 +Tag name: ctsm5.1.dev015 Originator(s): sacks (Bill Sacks) -Date: Sun Oct 28 14:29:30 MDT 2018 -One-line Summary: CMIP6 compset modifiers, usermods for typical output, and other output enhancements +Date: Fri Nov 13 11:52:34 MST 2020 +One-line Summary: A few small fixes Purpose of changes ------------------ -(1) Support %BGC-CROP-CMIP6DECK and %BGC-CROP-CMIP6WACCMDECK compset - modifiers, so that we can turn on the necessary options - (output-related and others) via new CMIP6-specific compsets. - -(2) Turn on carbon isotopes in CMIP6 runs (from Erik Kluzek) - -(3) Remove setting of CCSM_BGC=CO2A in the cmip6 usermods - -(4) Add usermods directories for getting typical extra output that's - wanted in many cases: output_crop, output_crop_highfreq, output_bgc, - output_bgc_highfreq, output_sp, and output_sp_highfreq. These can be - enabled by adding something like '--user-mods-dir output_crop' on - the create_newcase line (that short-hand works for an I compset; for - F or B compsets, you need to provide the full path to the usermod - directory). +(1) Fixes needed for PIO2 when running in pts/scam mode (from Jim + Edwards and Bill Sacks) -(4) Allow holes in the number of history tapes. Holes are cases where, - for example, we have h0, h1 and h3 tapes, but no h2 tape (because - there are no fields on the h2 tape). (This is needed for (3).) +(2) Fix mpi broadcast of hist_avgflag_pertape so that this namelist + variable is applied properly (from Sunniva Indrehus, Keith Oleson + and Bill Sacks) -(5) Fix reading and writing of 1-d logical global arrays. This fixes - ESCOMP/ctsm#24 for real (rather than just preventing an attempt to - read/write 1-d logical arrays, as was done in the previous 'fix'). +(3) Fix invalid xml in namelist_definition_ctsm.xml -(6) Add C13_NBP and C14_NBP diagnostic fields (from Keith Oleson) - -(7) Make a bunch of carbon isotope diagnostic fields inactive by default - -(8) Don't allow interpolation (use_init_interp) from a case without - carbon isotopes to a case with carbon isotopes: Due to - https://github.com/ESCOMP/ctsm/issues/67, interpolation from a case - without carbon isotopes to a case with carbon isotopes yields - incorrect initialization values for the carbon isotopes. Now that - we're turning carbon isotopes on via some semi-out-of-the-box - usermods (for cmip6), it is becoming more important to check to make - sure someone doesn't shoot themselves in the foot this way. - -(9) Add tests of the new output usermods as well as of the CMIP6 compset - modifiers +(4) Add point of interest code for debugging Bugs fixed or introduced ------------------------ Issues fixed (include CTSM Issue #): -- Fixes #24 for real (ncd_io_1d_log_glob is broken) -- Fixes #529 (Organize usermods_dirs to facilitate running cases with - the right output) +- Resolves ESCOMP/CTSM#1191 (hist_avgflag_pertape doesn't always produce + desired averaging type for some history file streams) +- Resolves ESCOMP/CTSM#1159 (Invalid xml in + namelist_definition_ctsm.xml) +- Resolves ESCOMP/CTSM#1210 (Add "point of interest" code) Significant changes to scientifically-supported configurations @@ -9421,48 +2417,34 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): none -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -- New namelist variable, just for testing purposes: - for_testing_allow_interp_non_ciso_to_ciso. This bypasses an error - check, and should only be used in tests. +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none Changes made to namelist defaults (e.g., changed parameter values): none Changes to the datasets (e.g., parameter, surface or initial files): none -Substantial timing or memory changes: none +Substantial timing or memory changes: none expected (not checked) Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): none -Changes to tests or testing: -- Reworked tests of cmip6_deck usermods to use the new - %BGC-CROP-CMIP6DECK compset modifier, and changed f09_g16 to f09_g17 -- Added a test of the %BGC-CROP-CMIP6WACCMDECK compset modifier -- Added tests of output_crop_highfreq, output_bgc_highfreq and - output_sp_highfreq usermods directories -- Note that there are NO tests covering the cmip6_evolving_icesheet - usermods: this usermod directory adds very little beyond cmip6_deck, - so it didn't seem worth its own test - -Code reviewed by: Erik Kluzek - - -CTSM testing: +Changes to tests or testing: none [PASS means all tests PASS and OK means tests PASS other than expected fails.] @@ -9470,42 +2452,24 @@ CTSM testing: cheyenne - not run - unit-tests (components/clm/src): + tools-tests (test/tools): - cheyenne - pass + cheyenne - not run - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): cheyenne - not run - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- pass - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass - - ERI_D_Ld9.T31_g37.I2000Clm50Sp.cheyenne_intel.clm-SNICARFRC - initially failed COMPARE_base_hybrid, COMPARE_base_rest and BASELINE - comparisons. I reran it and it passed. - - Manually compared all history files from - ERS_Ly3.f10_f10_musgs.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic - with baseline - ERS_Ly3.f10_f10_musgs.I1850Clm50BgcCrop.cheyenne_intel.clm-cmip6. They - were all identical. Also compared all history files from - SMS_Ld5_D.f09_g17.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic - with baseline - SMS_Ld5_D.f09_g17.I1850Clm50BgcCrop.cheyenne_intel.clm-cmip6. They - were all identical (but note that this basically just compared the - cpl.hi file: the test was too short to produce monthly files.) + cheyenne ---- pass + izumi ------- pass -CTSM tag used for the baseline comparisons: ctsm1.0.dev014 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes @@ -9513,55 +2477,57 @@ Answer changes Changes answers relative to baseline: NO - Detailed list of changes ------------------------ List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/536 - Allow holes in the number of - history tapes and reorganize cmip6 usermods (main PR containing all of - these changes) -- https://github.com/ESCOMP/ctsm/pull/527 - Add carbon_isotope user-mod - directory to turn on c13 and c14 -- https://github.com/ESCOMP/ctsm/pull/539 - Support a %CMIP6DECK compset - modifier +https://github.com/ESCOMP/CTSM/pull/1214 =============================================================== =============================================================== -Tag name: ctsm1.0.dev014 -Originator(s): sacks (Bill Sacks) -Date: Fri Oct 26 06:20:34 MDT 2018 -One-line Summary: Miscellaneous minor, bit-for-bit bug fixes +Tag name: ctsm5.1.dev014 +Originator(s): dll (Danica Lombardozzi) / oleson (Keith Oleson) / sacks (Bill Sacks) +Date: Sat Nov 7 12:19:14 MST 2020 +One-line Summary: Grass/crop snow burial fraction fix, and some other fixes Purpose of changes ------------------ -Four miscellaneous minor, bit-for-bit bug fixes: +(1) Crop/grass snow burial changed based on height and lodging (Danica + Lombardozzi) - resolves ESCOMP/CTSM#516. Updates grass and crop snow + burial ('fb' in SatellitePhenologyMod.F90) from being 0.2m to change + with PFT height and accounts for 20% lodging (falling over). -(1) Py3 pylint check and address cime issue ESMCI/cime#2822 (from Jim - Edwards: ESCOMP/ctsm#526) +(2) In BGC code, make elai and esai depend on frac_sno (Danica + Lombardozzi, Keith Oleson & Bill Sacks) - resolves ESCOMP/CTSM#1116 -(2) Change uppercase DEBUG variables to lowercase debug (requested by - Jim Edwards to avoid conflicting with the DEBUG CPP token) - (Fixes ESCOMP/ctsm#534) +(3) Fix to quadratic solution error bug caused by negative shaded + photosynthesis (Danica Lombardozzi & Keith Oleson) - resolves + ESCOMP/CTSM#756 -(3) Remove unnecessary line of code in LunaMod.F90 that was causing - problems with some compilers due to an uninitialized variable - (Fixes ESCOMP/ctsm#322) - -(4) Add r8 to 0 constant to fix build issue with XLF compiler (from Jim - Edwards: ESCOMP/ctsm#531) +(4) Point to cime branch tag that avoids building CDEPS with LILAC, to + avoid dependence on unreleased ESMF code (Bill Sacks) - resolves + ESCOMP/CTSM#1203 +(5) Some tweaks to documentation and how the documentation is built + (Bill Sacks) Bugs fixed or introduced ------------------------ Issues fixed (include CTSM Issue #): -- Fixes ESCOMP/ctsm#322 (ERS_D_Ld5.f19_g16.I2000Clm50BgcCruGs run FAIL (intel)) -- Fixes ESCOMP/ctsm#534 (Rename DEBUG to debug in a few places) +- Resolves ESCOMP/CTSM#516 (crop and grass snow burial) +- Resolves ESCOMP/CTSM#1116 (elai and esai for non-SP runs should use + frac_sno) +- Resolves ESCOMP/CTSM#756 (Quadratic solution error) +- Resolves ESCOMP/CTSM#1203 (Rework LILAC build to avoid dependence on + unreleased ESMF code) +CIME Issues fixed (include issue #): +- https://github.com/ESMCI/cime/issues/3769 (Avoid building CDEPS with + CTSM's LILAC) Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -9571,11 +2537,13 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 +[X] clm5_1 -[ ] clm4_5 +[X] clm5_0 + +[X] ctsm5_0-nwp -[ ] clm4_0 +[X] clm4_5 Notes of particular relevance for users --------------------------------------- @@ -9592,15 +2560,12 @@ Substantial timing or memory changes: none Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Caveats for developers (e.g., code that is duplicated that requires double maintenance): +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none Changes to tests or testing: none -Code reviewed by: different pieces reviewed by different people - - CTSM testing: [PASS means all tests PASS and OK means tests PASS other than expected fails.] @@ -9609,90 +2574,95 @@ CTSM testing: cheyenne - not run - unit-tests (components/clm/src): + tools-tests (test/tools): - cheyenne - pass + cheyenne - not run - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): cheyenne - not run - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- ok - cheyenne_gnu ------ ok - hobart_nag -------- ok - hobart_pgi -------- ok - hobart_intel ------ ok - - ok means tests and baseline comparisons pass. There were unexpected - NLCOMP diffs. From spot-checking a few tests, I see the following: + cheyenne ---- ok + izumi ------- ok - - (1) On both cheyenne and hobart: Diffs in logfile. This looks like a - problem in cime: it says: + ok: tests pass, baselines fail as expected - BASE: logfile = 'rof.log.136342.hobart.cgd.ucar.edu - COMP: logfile = 'rof.log +If the tag used for baseline comparisons was NOT the previous tag, note that here: - (2) On hobart: Diffs in pio_typename: netcdf vs. pnetcdf (says that - new uses pnetcdf): but when I compare files by hand, they look - the same in this respect (both baseline and new use netcdf), so - maybe this is due to a problem in the timing of when nlcomp is - run? - Since these both look like problems in the comparison script rather - than in the tag, I'm letting these go, but will open a cime issue if - we see this again. +Answer changes +-------------- +Changes answers relative to baseline: YES -CTSM tag used for the baseline comparisons: ctsm1.0.dev013 + Summarize any changes to answers, i.e., + - what code configurations: all (or at least most) + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + new climate, at least to some extent + Changes arise from (1) & (2) (large changes) and from (3) (small + changes). The change in snow burial parameterizations results in + changes to albedo and water & energy fluxes. -Answer changes --------------- + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A -Changes answers relative to baseline: NO + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + URL for LMWG diagnostics output used to validate new climate: + For analysis of diffs, see + https://github.com/danicalombardozzi/ctsm_py/blob/7543b0f3b413bae9974c11b467fdbc0413c3b7fa/notebooks/SnowBurial.ipynb Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.8.32 -> branch_tags/cime5.8.32_a01 +- doc-builder: v1.0.2 -> v1.0.4 Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/531 (fix build issue with xlf compiler) -- https://github.com/ESCOMP/ctsm/pull/526 (fix cime issue 2822 and pylint chk) +https://github.com/ESCOMP/CTSM/pull/1112 =============================================================== =============================================================== -Tag name: ctsm1.0.dev013 -Originator(s): erik (Erik Kluzek)/slevisconsulting -Date: Thu Oct 25 18:09:47 MDT 2018 -One-line Summary: Fix the fact that transient Bgc and SP cases had constant crop area in time +Tag name: ctsm5.1.dev013 +Originator(s): jedwards (Jim Edwards) / sacks (Bill Sacks) +Date: Wed Nov 4 14:24:55 MST 2020 +One-line Summary: Allow pnetcdf for vector history files Purpose of changes ------------------ -Fix transient non-crop cases that had constant crop area so that crop area will change in time -(and hence natural veg area will also change corresponding to it). - -Also bring in changes to update mksurfdata_map to handle SSP-RCP future scenarios. Right now -it can handle SSP5-8.5 out of the box. Also add a new test for that. +Ever since clm4_5_1_r091, we had been avoiding the use of pnetcdf for +vector history files (i.e., history files with dov2xy = .false.). This +was to workaround an issue that was found on the old yellowstone +supercomputer (bugzilla 1730). However, I cannot reproduce this issue on +cheyenne, either with PIO1 or with PIO2. Moreover, the workaround was +leading to very slow performance with PIO2, at least for some +tests. This tag removes that old workaround. -Bugs fixed or introduced ------------------------- +See https://github.com/ESCOMP/CTSM/issues/33 for details. -Issues fixed (include CTSM Issue #): #538 - #538 -- In transient pft simulations with use_crop=.false., %crop does not advance from 1850 values +Also change PE layouts for C96 and C192. The main motivation for this is +to get the aux_clm C96 test through the queue faster (the current test +sometimes waits for multiple hours in the queue): -Known bugs found since the previous tag (include github issue ID): #545 - #545 -- Antarctica ice shelves are being treated as wetlands rather than glaciers +(1) Make the out-of-the-box PE counts unthreaded, as is standard for I + compsets +(2) In the aux_clm test for C92, use a 360x2 PE layout: Use a PE layout + that (a) has threading, because CAM uses threading at this + resolution; and (b) has a smaller-than-standard task count in order + to get through the queue faster. Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -9702,138 +2672,118 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[X] clm5_0 +[ ] clm5_1 -[X] clm4_5 +[ ] clm5_0 + +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): A few more namelist checks - Added a check to make sure do_transient_pfts was the same as do_transient_crops - Don't allow use_fertilizer for non-crop case - namelist checks that create_crop_landunit=T except for FATES +Caveats for users (e.g., need to interpolate initial conditions): none -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): - New -ssp_rcp option to mksurfdata.pl +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none -Changes made to namelist defaults (e.g., changed parameter values): None +Changes made to namelist defaults (e.g., changed parameter values): none -Changes to the datasets (e.g., parameter, surface or initial files): New mksrfpft datasets in XML for SSP5-8.5 +Changes to the datasets (e.g., parameter, surface or initial files): none -Substantial timing or memory changes: None +Substantial timing or memory changes: + + Timing changes seem small, though not investigated carefully. No + timing changes are expected to show up in the PFS test (because it + doesn't do history output), but I looked at a few other non-debug f09 + cases: ERP_Ld5.f09_g17.I2000Clm50Vic.cheyenne_intel.clm-vrtlay, + ERP_Ld3.f09_g17.I1850Clm50BgcCropCru.cheyenne_intel.clm-ciso, + ERS_Ld3.f09_g17.I1850Clm50BgcCrop.cheyenne_intel.clm-rad_hrly_light_res_half, + ERS_Ld3.f09_g17.I2000Clm50Fates.cheyenne_intel.clm-FatesColdDef. Total + runtime of these increased in some tests and decreased in others + relative to the baseline, but on average, there was little change + relative to the baseline. I have more carefully investigated this + change in the context of pio2, which will soon become the default: + with pio2, this change is important to get good performance. + Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): - Now, do_transient_pfts and do_transient_crops only work in unison, and hence - should be simplified to one logical called do_transient_veg +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Changes to tests or testing: Add new SSP5-8.5 mksurf test +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none -Code reviewed by: self, slevisconsulting, billsacks +Changes to tests or testing: Changed PE layout for C96 test -CTSM testing: regular, tools +CTSM testing: [PASS means all tests PASS and OK means tests PASS other than expected fails.] build-namelist tests: - cheyenne - PASS (18 of the transient test namelists are different to baseline as expected) + cheyenne - not run + + tools-tests (test/tools): - unit-tests (components/clm/src): + cheyenne - not run - cheyenne - PASS + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run - tools-tests (components/clm/test/tools): + python testing (see instructions in python/README.md; document testing done): - cheyenne - OK (PTCLM tests fail) + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK + cheyenne ---- pass + izumi ------- pass + + Note: testing was done on 13c693d88, which was before the PE layout + change for C96 and C192. I then ran the new C96 test manually. -CTSM tag used for the baseline comparisons: ctsm1.0.dev012 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: Yes! - - Summarize any changes to answers, i.e., - - what code configurations: clm4_5/clm5_0 transient simulations without Crop (either Bgc or SP) - - what platforms/compilers: All - - nature of change: crop areas increase in time and impact simulations - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: dll/clm50_r267_1deg_GSWP3V1_iso_hist_nocrop_transientfix +Changes answers relative to baseline: NO Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None - -Pull Requests that document the changes (include PR ids): #546, #540 -(https://github.com/ESCOMP/ctsm/pull) +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - #546 -- Add in ability for mksurfdata_map to handle ssp_rcp scenarios and specifically SSP5-8.5 - $540 -- Transient PFT issue +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1190 =============================================================== =============================================================== -Tag name: ctsm1.0.dev012 -Originator(s): erik (Erik Kluzek) -Date: Sat Sep 29 11:49:35 MDT 2018 -One-line Summary: Add snow-free fields for snowmip, fix several issues +Tag name: ctsm5.1.dev012 +Originator(s): oleson (Keith Oleson) / sacks (Bill Sacks) +Date: Tue Nov 3 09:31:41 MST 2020 +One-line Summary: Allow nlevgrnd < nlevurb Purpose of changes ------------------ -Bring in new diagnostic fields added by Justin Perket, Sean Swenson and Mark Flanner -for Snow-MIP. Most of those are fields that represent "Snow Free" data. +Allow nlevgrnd < nlevurb. This will become more important soon, when +nlevurb is increased to 10, yet we want to allow simple soil layer +structures, e.g., for NWP applications. -Also bring in fixes for a list of issues. Add handling of the new CO2 which includes -both latitude-band and global average versions. Add some changes to make it easier -for input data processing including NOT doing the slow 1km map file creation. Have -the number of steps that are skipped at startup dependent on the time-step size. Add -a test for some requirements of WACCMX (time-step and use of ESMF). Calculations of -local time are now done in a global subroutine, that can handle negative longitudes. -Fix how FFIX_TO_SMINN is handled for history output. The namelist logical "calc_human_stress_indices" -changed from logical to a character string of three values: FAST, NONE, ALL. FAST -is the default so the less expensive ones are output, NONE turns them all off, and ] -ALL does all of them including the expensive ones. +Also some additions to ncdio-related utilities to support this, +including extending find_var_on_file to support dimensions as well as +variables. +Also add levsoi coordinate variable on history files. Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): #428, #474, #475, #476, #450, #482, #481, #491 - Fix #428 -- Update getco2_historical.ncl to handle latitude varying CO2 - Fix #474 -- Add ability to send GRIDFILE to regridbatch.sh script - Fix #475 -- Have number of steps to skip balance-check based on time - Fix #476 -- Add a test for WACCMX standalone - Fix #450 -- Add option to use global average of terrain standard deviation on surfdata files - (partial fix with simplest option) - Fix #482 -- Add extra field on CO2 streams file for global/time-averaged data - Fix #481 -- FFIX_TO_SMINN needs to be output when FUN is on - Fix #491 -- Calculations of local noon assume that longitude is 0 to 360 rather than -180 to 180 - -Known bugs introduced in this tag (include github issue ID): cime#2801 - cime#2801 -- Problem building with ESMF_LIB - -Known bugs found since the previous tag (include github issue ID): #507, #505 - #507 -- Albedo's are bad at night with negative longitudes - #505 -- CTSM input data-set tools can only work on 0-360 grids, and require monotone increasing longitude +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#674 (Allow nlevgrnd less than nlevurb) Significant changes to scientifically-supported configurations @@ -9844,142 +2794,140 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): None - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +Caveats for users (e.g., need to interpolate initial conditions): none - New namelist: - use_ssre -- Turn on show free fields needed for SnowMIP - - Changed namelist: - calc_human_stress_indices changed from logical to character with options: ALL, FAST, NONE - - New history fields: - Mostly added Snow Free (SF) fields - ALBDSF - ALBISF - FSRSF - FSRSFND - FSRSFNDLN - FSRSFNI - FSRSFVD - FSRSFVDLN - FSRSFVI - SSRE_FSR - SSRE_FSRND - SSRE_FSRNDLN - SSRE_FSRNI - SSRE_FSRVD - SSRE_FSRVDLN - SSRE_FSRVI +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none -Changes made to namelist defaults (e.g., changed parameter values): - calc_human_stress_indices = 'FAST' is now the default +Changes made to namelist defaults (e.g., changed parameter values): none -Changes to the datasets (e.g., parameter, surface or initial files): - mkghg_bndtvghg -- Update with new CO2 files, both monthly, lat-bands and yearly, global +Changes to the datasets (e.g., parameter, surface or initial files): none -Substantial timing or memory changes: None +Substantial timing or memory changes: none Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Caveats for developers (e.g., code that is duplicated that requires double maintenance): - I was able to reduce the duplication in SurfaceAlbedoMod where the original implementation added a cut - and paste copy of code. But, there is still a lot of duplication in this file that could be improved, by - making smaller functions/subroutines to do sections of code that are essentially repeated many times. - There's a bit of an increase in complexity to reduce the duplication, but reducing the duplication was worth it. +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none Changes to tests or testing: - Add a new waccmx_offline test mods and test with it - New test expected fail because of cime issue: ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline - Turn use_ssre on for most tests, off for reducedOutput - And set calc_human_stress_indices=NONE for reducedOutput, FAST for most, and ALL for KitchenSink and KSMOut tests +- Removed the no-longer-useful snowlayers_3_monthly test +- Added a test with nlevgrnd < nlevurb + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] -Code reviewed by: self, @olyson, @billsacks + build-namelist tests: + cheyenne - not run -CTSM testing: regular + tools-tests (test/tools): - [PASS means all tests PASS and OK means tests PASS other than expected fails.] + cheyenne - not run - build-namelist tests: + PTCLM testing (tools/shared/PTCLM/test): - cheyenne - PASS + cheyenne - not run - unit-tests (components/clm/src): + python testing (see instructions in python/README.md; document testing done): - cheyenne - PASS + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK + cheyenne ---- pass + izumi ------- pass -CTSM tag used for the baseline comparisons: ctsm1.0.dev011 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: no bit-for-bit +Changes answers relative to baseline: NO Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): No - -Pull Requests that document the changes (include PR ids): #462 #449 -(https://github.com/ESCOMP/ctsm/pull) +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none - #462 -- Add namelist item to calculate all heat stress indices only if requested; to speed up model - #449 -- Bring in snowmip diagnostic fields +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1195 =============================================================== =============================================================== -Tag name: ctsm1.0.dev011 -Originator(s): sacks (Bill Sacks), mvr (Mathew Rothstein) -Date: Wed Sep 12 10:50:31 MDT 2018 -One-line Summary: Add water tracer consistency checks, and other water tracer work +Tag name: ctsm5.1.dev011 +Originator(s): sacks (Bill Sacks) +Date: Mon Nov 2 10:28:35 MST 2020 +One-line Summary: Change CISM2%NOEVOLVE compsets to use SGLC; documentation updates Purpose of changes ------------------ -1. Add water tracer consistency checks - -2. Add infrastructure for looping over all water tracers - currently - just used for the tracer consistency checks - -3. Breakout of atm2lnd and lnd2atm water variables, needed for water tracers - -4. Add some namelist control over the addition of water tracers +(1) Change CISM2%NOEVOLVE compsets to use SGLC. + +The use of CISM2%NOEVOLVE adds complexity and (perhaps most importantly) +increases the turnaround time of CTSM software testing, while adding +only marginal scientific value. Therefore, we are changing I compsets to +use a stub glacier (SGLC) rather than CISM2%NOEVOLVE for now. Within the +next year, we'd like to have these use a data glc model, but that will +most likely wait until we switch to using NUOPC by default (so we can +use a data glc in CDEPS: ESCOMP/CDEPS#25). + +This tag changes the meaning of compset aliases that previously had +neither a Gs (for stub glacier) or G (for CISM2%EVOLVE), so that they +now use a stub glacier (SGLC) rather than CISM2%NOEVOLVE. Compset +aliases that previously had Gs (so were already using a stub glacier) +have been changed so that there is no longer a Gs in the alias: stub +glacier is now the implied default. + +This change reduces our test build time to 40% of what it previously +was! When I ran the test suite for ctsm5.1.dev010, the cheyenne-intel +test suite (by far the largest of our test suites) took 5 hours, 8 min +to build. In yesterday's run of the test suite with this change in +place, the cheyenne-intel test suite took only 2 hours, 6 min to build! +The final test in this test suite finished running just 2 hours, 29 min +after I started the test suite. This may not be a completely fair +comparison, because the machine may have been relatively lightly loaded +during this Sunday afternoon run, but I wouldn't expect the test suite +build time (which is what I'm reporting here) to be hugely impacted by +that. + +Changes due to using SGLC in place of CISM2%NOEVOLVE are documented +here: +. + +(2) Documentation updates + +Brings in a new optional external, doc-builder, to assist with building +the documentation, specifically with a new Docker-based workflow +documented here +. + +Also updates LILAC documentation and a bit more. -5. Add a system test that exercises the water tracer consistency checks - -6. Add a 'ratio' variable for each water tracer - -7. Add some unit tests of the new water tracer infrastructure Bugs fixed or introduced ------------------------ Issues fixed (include CTSM Issue #): -- Partially addresses #357 -- Resolves #479 -- Resolves #492 +- Resolves ESCOMP/CTSM#1135 (Replace CISM2%NOEVOLVE compsets with SGLC) + +Known bugs introduced in this tag (include github issue ID): +- See ESCOMP/CTSM#1136 (Use data glc model where we used to use CISM2%NOEVOLVE) + Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -9989,23 +2937,26 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 +[X] clm5_1 -[ ] clm4_5 +[X] clm5_0 -[ ] clm4_0 +[X] ctsm5_0-nwp + +[X] clm4_5 Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): -- Don't be fooled by the new namelist variable, enable_water_isotopes: - This is just a place-holder for now, not implying that water isotopes - are actually working. +- This tag changes the meaning of compset aliases that previously had + neither a Gs (for stub glacier) or G (for CISM2%EVOLVE), so that they + now use a stub glacier (SGLC) rather than CISM2%NOEVOLVE. Compset + aliases that previously had Gs (so were already using a stub glacier) + have been changed so that there is no longer a Gs in the alias: stub + glacier is now the implied default. -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -- New namelist variables: enable_water_tracer_consistency_checks and - enable_water_isotopes. The latter is just a place-holder for now. +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none Changes made to namelist defaults (e.g., changed parameter values): none @@ -10015,16 +2966,19 @@ Substantial timing or memory changes: none Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): none -Changes to tests or testing: New test that runs the water tracer consistency check - I ran this test on cheyenne_gnu and cheyenne_intel along with the - out-of-the-box hobart_nag version - -Code reviewed by: Mat Rothstein and I have worked together on many of -these changes, but not all code has been reviewed by the other. +Changes to tests or testing: +- Changed compsets used in testing according to the above notes. In + particular, this involved removing the 'Gs' from compset names in + tests. +- No longer need a specific testmod for the LII test (see commit + f75335a45) +- Changed the glcMEC_changeFlags test to be more useful (see commit + e350beced) +- Removed _gl4 from resolution in tests that no longer use CISM CTSM testing: @@ -10032,68 +2986,110 @@ CTSM testing: build-namelist tests: - cheyenne - ok (tests pass, clm4_5 and clm5_0 namelists differ from - baseline as expected) + cheyenne - not run - unit-tests (components/clm/src): + tools-tests (test/tools): - cheyenne - pass + cheyenne - not run - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): cheyenne - not run - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- pass - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass + cheyenne ---- ok + izumi ------- ok + + ok: tests pass, baselines fail as expected -CTSM tag used for the baseline comparisons: ctsm1.0.dev010 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: NO +Changes answers relative to baseline: YES + + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff; potentially new climate regionally, over Greenland + + The changes arise from changes in the meaning of + compsets. Configurations that used to use a stub GLC (compsets + with Gs in their alias) have the same meaning as before, but a + different compset alias (so in testing, this resulted in BFAILs + due to missing baselines). Configurations that previously used + CISM2%NOEVOLVE (which included most of our standard + configurations) now instead use a stub GLC. This results in + differences over Greenland (in ways described here: + ). + + If bitwise differences were observed, how did you show they were no worse + than roundoff? N/A + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- New doc-builder external (at v1.0.2) -Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/497 +Pull Requests that document the changes (include PR ids): none =============================================================== =============================================================== -Tag name: ctsm1.0.dev010 -Originator(s): sacks (Bill Sacks) -Date: Thu Aug 30 17:14:28 MDT 2018 -One-line Summary: Update cime to cime5.7.3 +Tag name: ctsm5.1.dev010 +Originator(s): sacks (Bill Sacks), jedwards (Jim Edwards) +Date: Fri Oct 23 14:36:03 MDT 2020 +One-line Summary: Fix reading netcdf variable into a different data type Purpose of changes ------------------ -Update cime from cime5.6.10 to cime5.7.3. To support this change, there -are also minor code changes related to the pause-resume implementation -(from Erik Kluzek). +Main change is to fix the reading of a variable that is one type on a +NetCDF file but a different data type in memory. Previously, this could +lead to memory corruption (not just of the variable in question, but +other variables as well). This was not causing any problems in +out-of-the-box configurations, but it sometimes tripped up some +developers when they added new fields on datasets. + +In addition, this adds new self-test code to test ncdio_pio. This module +is hard to get under unit test, but we want to have some tests of it, to +pick up problems like the one fixed in this tag. So as a compromise +solution for now, I have introduced unit test-like tests that are built +into a standard build of CTSM and run in a standard run if a given +namelist flag is set. A better long-term solution would be to integrate +these tests into the pFUnit-based unit testing framework, but that would +take some work. I have added tests of the new code, and a bit of testing +of other code in ncdio_pio, but there's still a lot in ncdio_pio that is +not tested. I figure we can gradually add tests as we make changes to +ncdio_pio. + +Finally, an unrelated change to the unit test build: files generated by +genf90 now appear in the unit test build directory rather than the +source tree. Bugs fixed or introduced ------------------------ Issues fixed (include CTSM Issue #): -- ESCOMP/ctsm#384 (VIC test is failing at f09 resolution with signal) - (I'm not sure what fixed this, but it's passing now) - -CIME Issues fixed (include issue #): many - +- Resolves ESCOMP/CTSM#1091 (Memory corruption when reading a netcdf + variable into a variable of a different type, at least with PIO1) +- Resolves ESCOMP/CTSM#1188 (In unit test build: files generated by + genf90 should go in build dir rather than source dir) Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -10103,18 +3099,21 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[ ] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): none -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- new namelist variable, for_testing_run_ncdiopio_tests Changes made to namelist defaults (e.g., changed parameter values): none @@ -10124,14 +3123,20 @@ Substantial timing or memory changes: none Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Code reviewed by: self +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Ideally the ncdio_pio self-tests would be recoded as true unit tests, + leveraging the pFUnit framework. This would get them out of the main + source code, and would give other benefits that come with a real unit + testing framework, such as that a single failure doesn't abort the + entire test suite. +- The existence of tests for ncdio_pio should NOT be taken as a sign + that all (or even most) of this module is now under unit test: in + fact, much of it is not covered yet by my new testing module. +Changes to tests or testing: +- Added a test that triggers for_testing_run_ncdiopio_tests CTSM testing: @@ -10141,62 +3146,58 @@ CTSM testing: cheyenne - not run - unit-tests (components/clm/src): + tools-tests (test/tools): - cheyenne - pass + cheyenne - not run - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): cheyenne - not run - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- pass - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass + cheyenne ---- pass + izumi ------- pass -CTSM tag used for the baseline comparisons: ctsm1.0.dev009 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: NO - bit-for-bit +Changes answers relative to baseline: NO Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -cime: cime5.6.10 -> cime5.7.3 +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none -Pull Requests that document the changes (include PR ids): none +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1189 +https://github.com/ESCOMP/CTSM/pull/1176 (old version, superseded by 1189) =============================================================== =============================================================== -Tag name: ctsm1.0.dev009 -Originator(s): sacks (Bill Sacks) -Date: Wed Aug 22 20:32:36 MDT 2018 -One-line Summary: Fix initialization of AnnET in InitAccVars +Tag name: ctsm5.1.dev009 +Originator(s): negins (Negin Sobhani,UCAR/TSS,303-497-1224) +Date: Wed Oct 21 11:14:25 MDT 2020 +One-line Summary: BFB changes for Perturbed Parameter Ensemble and Hydraulic redistribution Purpose of changes ------------------ -InitAccVars was mistakenly setting qflx_evap_tot_col rather than -AnnET. This fix allows us to remove now-redundant cold start and restart -code for AnnET. +Some BFB changes for PPE work and Hydraulic redistribution Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): -- Fixes #480 -- Partially addresses #285 +Issues fixed (include CTSM Issue #): [If none, remove this line] + - resolves ESCOMP/CTSM#881 + - resolves ESCOMP/CTSM#1020 Significant changes to scientifically-supported configurations @@ -10205,37 +3206,36 @@ Significant changes to scientifically-supported configurations Does this tag change answers significantly for any of the following physics configurations? (Details of any changes will be given in the "Answer changes" section below.) - [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): none +Caveats for users (e.g., need to interpolate initial conditions): None -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + - maxpatch_pft is removed from namelist -Changes made to namelist defaults (e.g., changed parameter values): none +Changes made to namelist defaults (e.g., changed parameter values): None -Changes to the datasets (e.g., parameter, surface or initial files): none +Changes to the datasets (e.g., parameter, surface or initial files): None -Substantial timing or memory changes: none +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): none - -Changes to tests or testing: none +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Code reviewed by: basic proposed changes reviewed by Erik Kluzek +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None +Changes to tests or testing: CTSM testing: @@ -10245,64 +3245,65 @@ CTSM testing: cheyenne - not run - unit-tests (components/clm/src): + tools-tests (test/tools): - cheyenne - pass + cheyenne - not run - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): cheyenne - not run - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + (any machine) - None regular tests (aux_clm): - cheyenne_intel ---- pass - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass + cheyenne ---- ok + izumi ------- ok -CTSM tag used for the baseline comparisons: ctsm1.0.dev008 +If the tag used for baseline comparisons was NOT the previous tag, note that here: N/A Answer changes -------------- -Changes answers relative to baseline: NO +Changes answers relative to baseline: + Four new fields regarding plant hydraulic processes has been added: + + - QHR (patch-level hydraulic redistribution) + - VEGWPLN (local noon vegetation water potential) + - VEGWPPD (predawn vegetation water potential) + - VPD_CAN: canopy vapor pressure deficit (functional input to Medlyn model) Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None -Pull Requests that document the changes (include PR ids): none +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1187 +https://github.com/ESCOMP/CTSM/pull/1126 =============================================================== =============================================================== -Tag name: ctsm1.0.dev008 -Originator(s): erik (Erik Kluzek) -Date: Tue Aug 14 10:25:12 MDT 2018 -One-line Summary: Update 1850 ndep file and last year for streams for Historical transient cases +Tag name: ctsm5.1.dev008 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Wed Oct 7 11:48:30 MDT 2020 +One-line Summary: Two answer changes: Clm45/50/51 with crop, and for 2000Clm51 Purpose of changes ------------------ -Bring in changes from release-clm5.0.05. Update to latest Nitrogen Deposition file from simulations with WACCM for 1850. -Also fix an issue with the last year for historical transient cases. - +Turn dribble_crophrv_xsmrpool_2atm when crop is on for clm4_5, clm5_0, and clm5_1 physics +Fix the finidat files being selected for 2000_control conditions for clm5_1 Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): 461 - #461 -- increase last year in streams for transient - -Known bugs found since the previous tag (include github issue ID): [If none, remove this line] - #478 -- Bare soil g1 should be missing value or zero - +Issues fixed (include CTSM Issue #): + Fixes #1158 -- Turn dribble_crophrv_xsmrpool_2atm on when crop is on for all physics versions + Another issue in #1166 -- correct finidat file for 2000Clm51 Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -10312,11 +3313,13 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 +[x] clm5_1 -[ ] clm4_5 +[x] clm5_0 -[ ] clm4_0 +[ ] ctsm5_0-nwp + +[x] clm4_5 Notes of particular relevance for users --------------------------------------- @@ -10325,22 +3328,22 @@ Caveats for users (e.g., need to interpolate initial conditions): None Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None -Changes made to namelist defaults (e.g., changed parameter values): Last year extended for transient datasets +Changes made to namelist defaults (e.g., changed parameter values): + dribble_crophrv_xsmrpool_2atm now on when crop on for all physics versions -Changes to the datasets (e.g., parameter, surface or initial files): New ndep dataset for 1850 +Changes to the datasets (e.g., parameter, surface or initial files): None -Substantial timing or memory changes: +Substantial timing or memory changes: None Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None - -Changes to tests or testing: Lengthen some tests +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Code reviewed by: self +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + The namelist dribble_crophrv_xsmrpool_2atm should now be removed as a namelist item both + in the fortran code and in build-namelist scripts. This change should be bit-for-bit. +Changes to tests or testing: None CTSM testing: regular @@ -10348,66 +3351,128 @@ CTSM testing: regular build-namelist tests: - cheyenne - PASS (11 show differences for 1850_control and 20thC_transient) + cheyenne - PASS (120 tests are different than before) - unit-tests (components/clm/src): + python testing (see instructions in python/README.md; document testing done): - cheyenne - PASS + cheyenne -- PASS regular tests (aux_clm): - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK + cheyenne ---- PASS + izumi ------- PASS -CTSM tag used for the baseline comparisons: ctsm1.0.dev007 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: Yes! +Changes answers relative to baseline: Yes Summarize any changes to answers, i.e., - - what code configurations: 1850_control or 20thC_transient for Clm50 - - what platforms/compilers: all - - nature of change: similar climate + - what code configurations: Clm45/50/51 with crop (except with prognostic CO2) and 2000Clm51 + - what platforms/compilers: All + - nature of change: same climate Detailed list of changes ------------------------ List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None -Pull Requests that document the changes (include PR ids): +Pull Requests that document the changes (include PR ids): #1177 (https://github.com/ESCOMP/ctsm/pull) - #477 -- Move changes from release-clm5.0.05 onto master + #1177 -- Two answer changes turn dribble_crophrv_xsmrpool_2atm and correct clm5_1 finidat + file for 2000 conditions =============================================================== =============================================================== -Tag name: ctsm1.0.dev007 +Tag name: ctsm5.1.dev007 Originator(s): sacks (Bill Sacks) -Date: Sun Aug 5 21:03:28 MDT 2018 -One-line Summary: Avoid glacier dynamic landunit adjustments in first time step +Date: Tue Oct 6 09:29:27 MDT 2020 +One-line Summary: CNFire: btran2 fixes and general cleanup Purpose of changes ------------------ -Always avoid generating dynamic landunit adjustments for glacier area -changes in the first timestep of a startup or hybrid run - not just for -cold start or interpolated start. See the detailed discussion in -https://github.com/ESCOMP/ctsm/issues/340 for rationale. +(1) Call routine to calculate fire's btran2 from CNFireArea; this has a + few advantages: + + - It makes the logic of CNFireArea more clear (rather than depending on + a btran2 variable that is calculated from some other part of the code) + + - This avoids having the biogeophysics depend on the biogeochemistry + + - This lets us avoid doing this btran calc if using no-fire – or other, + future, fire methods that don't need it + + Note regarding testing: In the initial step, I kept this calculation + dependent on a saved version of h2osoi_vol to avoid changing + answers; I changed this in the answer changes in step (2), as noted + below. + +(2) Answer-changing fixes to CNFire's btran2 calculation and use: + + (a) Calculate fire btran2 using updated h2osoi_vol (this is an + answer-changing cleanup step from (1)) + + (b) TEMPORARY CHANGE (reverted in the cleanup in (3)): Reinitialize + fire btran2 to spval for all patches in each time step, so that + the fire code isn't trying to use btran2 from earlier time steps + for patches that were in the exposed veg filter at one point but + no longer are. + + One implication of this is that, if there is currently no + exposed veg on a column, the new code leads to the block of code + that forces fire_m = 0 (because wtlf will be 0). Previously, in + contrast, it looks like fire_m was allowed to be non-zero even + if there is currently no exposed veg, because btran2 and wtlf + were accumulated if a patch ever was exposed in the past. + (c) Limit fire btran2 to be <= 1, rather than letting it be slightly + greater than 1. (Due to a conditional in CNFireArea, these + slightly-greater-tan-1 values were being ignored when computing + btran_col, rather than averaging in a 1 value.) + +(3) Non-answer-changing fire code cleanup: + + (a) Cleanup of the btran2 fixes, including reverting the TEMPORARY + CHANGE noted in (2b), instead relying on a better mechanism: + just doing the calculations of btran_col and wtlf over the + exposedvegp filter. Also, get rid of the checks for + shr_infnan_isnan(btran2(p)) and btran2(p) <= 1 (allowed by the + other changes in (2) and (3)). + + (b) Set btran2 to 0 over non-exposed-veg points: this changes + answers for the BTRAN2 diagnostic field, but nothing else. (This + follows what is done for the standard BTRAN.) + + (c) Move calc_fire_root_wetness for CNFireLi2021 into the base type + to avoid future bugs (assuming that the next fire module will + extend the base class but will also want to use this new version + of calc_fire_root_wetness). + + (d) Change fire looping structure to be more standard + +(4) Remove some very expensive tests from aux_clm, putting some in the + new ctsm_sci test list instead + +(5) A bit of other minor cleanup Bugs fixed or introduced ------------------------ Issues fixed (include CTSM Issue #): -- Fixes #340 (Avoid generating dynamic landunit adjustment fluxes for - glacier changes in the first timestep) - +- Resolves ESCOMP/CTSM#1139 (Decrease expense of ne0ARCTICGRISne30x8 + test and C96 tests) +- Resolves ESCOMP/CTSM#1153 (Fire btran2 is only computed for exposed + veg patches, but is used over all veg patches) +- Resolves ESCOMP/CTSM#1170 (CNFire code: btran2 should not be skipped + when it's greater than 1) +- Partially addresses ESCOMP/CTSM#1142 (Add ctsm_sci test list that + would be used for releases and making sure important resolutions run + well) Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -10417,11 +3482,13 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] -[ ] clm5_0 +[X] clm5_1 -[ ] clm4_5 +[X] clm5_0 + +[X] ctsm5_0-nwp -[ ] clm4_0 +[X] clm4_5 Notes of particular relevance for users --------------------------------------- @@ -10438,14 +3505,12 @@ Substantial timing or memory changes: none Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): none -Changes to tests or testing: none - -Code reviewed by: Erik Kluzek - +Changes to tests or testing: Remove some very expensive tests from +aux_clm, putting some in the new ctsm_sci test list instead. CTSM testing: @@ -10455,75 +3520,73 @@ CTSM testing: cheyenne - not run - unit-tests (components/clm/src): + tools-tests (test/tools): cheyenne - not run - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): cheyenne - not run - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + (any machine) - pass (on my mac) regular tests (aux_clm): - cheyenne_intel ---- ok - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass - - ok means tests pass; baseline failures as expected in these two - tests that do not use init_interp: - - FAIL ERI_N2_Ld9.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-default BASELINE ctsm1.0.dev006 - FAIL SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput BASELINE ctsm1.0.dev006 + cheyenne ---- ok + izumi ------- ok - (The glacier area on the finidat file used in these tests - - clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c180715.nc - - seems to have come from an finidat_interp_dest file, and thus does - not match the glacier area from CISM.) + ok: tests pass, many baselines fail as expected -CTSM tag used for the baseline comparisons: ctsm1.0.dev006 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): +Changes answers relative to baseline: YES, for all CN/BGC configurations Summarize any changes to answers, i.e., - - what code configurations: Startup / Hybrid runs that include CISM - (even NOEVOLVE) and do not use init_interp, due to: - - different PE layout in new case vs. the one that generated the - finidat (roundoff-level diffs) - - different glacier area on finidat file vs. what's in CISM - (greater than roundoff-level diffs) + - what code configurations: All CN/BGC configurations - what platforms/compilers: all - nature of change (roundoff; larger than roundoff/same climate; new climate): - Roundoff-level for different PE layout, larger than roundoff but - should be same climate when there is different glacier area on the - finidat file vs. what's in CISM - - The differences arise from dynamic landunit adjustments of the - below-ground C and N states in the old code, as CTSM adjusts its - areas to match CISM's. In the new code, there are no C and N - adjustments in the first time step from this adjustment. - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - + larger than roundoff; expected to be same climate, but not + investigated yet + + + To verify that the answer changes only came from expected changes, I + did a few rounds of testing. The following numbers refer to the groups + of changes listed under "Purpose of changes", above. The changes in + groups (4) and (5) were combined with those in groups (1) and (3) - + i.e., the basically non-answer-changing sets. + + First, I tested with just the changes in (1). This led to differences + in only limited configurations, as noted in + https://github.com/ESCOMP/CTSM/pull/1155#issuecomment-695035048: + - nofire tests had diffs in BTRAN2 + - dynroots tests had extensive diffs because now btran2 is calculated + after the dyn roots updates in each time step + - tests where the compared clm2 h0 file includes the 0th time step had + diffs just in BTRAN2, for reasons I couldn't determine + + Then I tested with the changes in (2), which were expected to change + answers for all CN/BGC tests. In particular, these change answers due + to: + - using updated h2osoi_vol rather than the one earlier in the time + step when calculating btran2 + - only considering points in the exposed veg filter when averaging + btran2 from patch to column, rather than using stale values from + no-longer-exposed patches (which also means having fire_m = 0 if + there are no currently-exposed veg patches in a column) (fix for + ESCOMP/CTSM#1153) + - treating btran2 values that are slightly greater than 1 as 1, rather + than ignoring them completely (fix for ESCOMP/CTSM#1170) + + Finally, I tested with all of the changes, comparing against the + baselines generated from (2). As expected, the only answer changes in + this final round were in the BTRAN2 diagnostic field (due to setting + btran2 to 0 over non-exposed-veg points). Detailed list of changes ------------------------ @@ -10531,42 +3594,28 @@ Detailed list of changes List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none Pull Requests that document the changes (include PR ids): -- #470 (Avoid glacier dynamic landunit adjustments in first time step) +https://github.com/ESCOMP/CTSM/pull/1155 =============================================================== =============================================================== -Tag name: ctsm1.0.dev006 +Tag name: ctsm5.1.dev006 Originator(s): sacks (Bill Sacks) -Date: Sat Aug 4 07:48:09 MDT 2018 -One-line Summary: Minor bug fixes, cleanup, documentation and enhancements +Date: Sat Oct 3 19:50:41 MDT 2020 +One-line Summary: Call correct routine to calculate btran2 for CNFireLi2021 Purpose of changes ------------------ -A collection of minor bug fixes, code cleanup, documentation and -enhancements, all bit-for-bit. See list of issues fixed below for -details. - +Due to a subtle code bug, CNFireLi2021 was using the btran2 calculating +routine from the base class rather than the new one that is specific to +this formulation. Bugs fixed or introduced ------------------------ Issues fixed (include CTSM Issue #): -- Fixes #24 (ncd_io_1d_log_glob is broken) -- Fixes #120 (Incorrect comments in Biogeophysics1Mod.F90 -- Fixes #217 (Change some cheyenne_gnu tests to cheyenne_intel) -- Fixes #245 (Put all .gitignore entries in top-level file) -- Fixes #272 (Code should error on missing mxsoil_color when SOIL_COLOR - is used) -- Fixes #283 (Add more helpful message about need to do init_interp with - wrong number of vertical layers) -- Fixes #367 (For cmip6 runs: Turn on cpl hist output needed to drive a - TG compset) -- Fixes #412 (Fix documentation of init_interp_method) -- Fixes #419 (Do not allow SOYFIXN diagnostic field with FUN) -- Fixes #464 (Some lines longer than 132 characters) -- Fixes #465 (Remove backwards compatibility check for snw_rds) -- Fixes #467 (Increase wallclock limit for test) +- Resolves ESCOMP/CTSM#1173 (CNFireLi2021Mod uses the wrong btran2 + routine) Significant changes to scientifically-supported configurations @@ -10577,11 +3626,13 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[X] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- @@ -10594,23 +3645,15 @@ Changes made to namelist defaults (e.g., changed parameter values): none Changes to the datasets (e.g., parameter, surface or initial files): none -Substantial timing or memory changes: none +Substantial timing or memory changes: not investigated (none expected) Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): none -Changes to tests or testing: -- Changed a single-point test from gnu to intel to get better debugging - information - (SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianGs.cheyenne_intel.clm-cropMonthOutput) -- For some single-point tests on both gnu and intel: removed one - compiler, keeping the tests on just one - -Code reviewed by: self - +Changes to tests or testing: none CTSM testing: @@ -10620,45 +3663,47 @@ CTSM testing: cheyenne - not run - unit-tests (components/clm/src): + tools-tests (test/tools): - cheyenne - pass + cheyenne - not run - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): cheyenne - not run - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- pass - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass - - NLCOMP failures as expected for tests with the cmip6 test mod + cheyenne ---- ok + izumi ------- ok - Some long single-point gnu tests failed due to running out of - wallclock time; I have removed these, just keeping them on intel - (along with removing a few other tests after I ran the testing - see - commit 5c226bdf): + ok: tests pass, Clm51Bgc baselines fail as expected - FAIL ERS_Lm54_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropGs.cheyenne_gnu.clm-cropMonthOutput RUN time=4803 - FAIL ERS_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropGs.cheyenne_gnu.clm-cropMonthOutput RUN time=6024 + Note: there were also the following BFAIL results due to missing + baselines, as documented in the previous tag: + FAIL ERS_D_Ld10.C96_C96_mg17.IHistClm50Sp.cheyenne_intel.clm-decStart BASELINE ctsm5.1.dev005: ERROR BFAIL some baseline files were missing + FAIL ERS_Ln9.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.IHistClm50SpGs.cheyenne_intel.clm-clm50cam6LndTuningMode_1979Start BASELINE ctsm5.1.dev005: ERROR BFAIL some baseline files were missing + FAIL SMS_Ln9.ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12.IHistClm50Sp.cheyenne_intel.clm-clm50cam6LndTuningMode_1979Start BASELINE ctsm5.1.dev005: ERROR BFAIL some baseline files were missing + FAIL SMS_Ln9.ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12.ISSP585Clm50BgcCrop.cheyenne_intel.clm-clm50cam6LndTuningMode BASELINE ctsm5.1.dev005: ERROR BFAIL some baseline files were missing + FAIL SMS_Ln9.ne0CONUSne30x8_ne0CONUSne30x8_mt12.IHistClm50Sp.cheyenne_intel.clm-clm50cam6LndTuningMode_2013Start BASELINE ctsm5.1.dev005: ERROR BFAIL some baseline files were missing -CTSM tag used for the baseline comparisons: ctsm1.0.dev005 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: NO - bit-for-bit - +Changes answers relative to baseline: YES + + Summarize any changes to answers, i.e., + - what code configurations: Clm51Bgc + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff; whether it is climate changing was not investigated Detailed list of changes ------------------------ @@ -10666,77 +3711,35 @@ Detailed list of changes List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none Pull Requests that document the changes (include PR ids): -- #392 (Remove old code for snw_rds restart that looks no longer needed) -- (Other changes not documented in PRs) +https://github.com/ESCOMP/CTSM/pull/1174 =============================================================== =============================================================== -Tag name: ctsm1.0.dev005 -Originator(s): sacks (Bill Sacks), mvr (Mathew Rothstein) -Date: Fri Aug 3 07:54:59 MDT 2018 -One-line Summary: Rework water data types to accommodate isotopes and other tracers - -Purpose of changes ------------------- - -This tag reworks the various water data types to allow having multiple -instances of variables that are needed for isotopes and other water -tracers. - -Specific changes include: - -(1) Separated "water state" variables into state, diagnostic and balance - check-related variables. This separation was not essential for the - work here, but was desired by Martyn Clark and others. - -(2) For each of water state, diagnostic and flux variables, separated - variables into those needed for both bulk and tracers vs. those only - needed for bulk. This way, we can have multiple instances of the - variables needed by tracers, but only a single instance of variables - that only apply to bulk water. This follows the design laid out in - https://github.com/escomp/ctsm/pull/395. The separation was based - largely on what was done in the old water isotope branch; we didn't - put a lot of thought into this, because the new design allows us to - easily migrate variables between bulk-only and bulk-and-tracer as - needed. - -(3) Moved water fluxes that were defined in science modules back into - waterflux_type or waterfluxbulk_type. This was needed for (2); there - is more discussion on this in - https://github.com/escomp/ctsm/pull/395 and the log message for - commit 711e5cd7. - -(4) Introduced a top-level water_type that holds instances of all of the - other water-related objects. This follows the design laid out in - https://github.com/escomp/ctsm/pull/395. This is particularly - valuable for the tracer instances: the logic related to number of - tracers can be encapsulated in water_type, rather than infiltrating - clm_instMod. - -(5) Added placeholders for water tracer instances - -(6) Added infrastructure to generate history / restart field names for - the tracer instances. Eventually, the isotope class can also hold - information specific to each isotope. +Tag name: ctsm5.1.dev005 +Originator(s): sacks (Bill Sacks) +Date: Fri Oct 2 09:51:08 MDT 2020 +One-line Summary: Answer changing bug fixes for clm51: fire and organic_frac_squared -This work was a joint effort between Mathew Rothstein and myself; Mat -gets much of the credit for the actual refactoring done here. +Purpose of changes +------------------ +A few bug fixes for CLM51: +- Initialize btran2 to 0 in CNFireLi2021Mod +- Remove multiplications by col%wtgcell in CNFireLi2021Mod +- Initialize nfire to 0 in CNFireLi2021Mod +- Fix organic_frac_squared default for clm5_1 Bugs fixed or introduced ------------------------ Issues fixed (include CTSM Issue #): -- Fixes #358 (Separate WaterStateType into multiple types) -- Fixes #434 (Separate WaterFluxType into a base class and a class that just applies to bulk) -- Fixes #359 (Set up infrastructure for multiple instances of WaterState and WaterFlux types) -- Fixes #458 (Implement handling of history and restart variables for water tracers) +- Resolves ESCOMP/CTSM#1171 (btran2 not initialized to zero in + CNFireLi2021Mod.F90) +- Partially addresses ESCOMP/CTSM#1169 (CNFireLi2021Mod reintroduces a + number of bugs that were fixed in earlier versions) +- Partially addresses ESCOMP/CTSM#1166 (Possible problems with namelist + defaults starting in ctsm5.0.dev001) -Known bugs introduced in this tag (include github issue ID): -- #464 (Some lines longer than 132 characters) -- #456 (Remove backwards compatibility check for snw_rds) (not a - newly-introduced issue, but it's more important to fix this with the - separation of waterstate_type) Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -10746,11 +3749,13 @@ Does this tag change answers significantly for any of the following physics conf [Put an [X] in the box for any configuration with significant answer changes.] +[X] clm5_1 + [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- @@ -10759,30 +3764,21 @@ Caveats for users (e.g., need to interpolate initial conditions): none Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none -Changes made to namelist defaults (e.g., changed parameter values): none +Changes made to namelist defaults (e.g., changed parameter values): +- Fixes default for organic_frac_squared for clm5_1 Changes to the datasets (e.g., parameter, surface or initial files): none -Substantial timing or memory changes: none +Substantial timing or memory changes: not investigated (none expected) Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Caveats for developers (e.g., code that is duplicated that requires double maintenance): -- Water tracers are not yet functional - they are just placeholders -- Whether to use water tracers and which water tracers to use are - currently hard-coded; eventually, this should be namelist-controlled +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none Changes to tests or testing: none -Code reviewed by: Mathew Rothstein and Bill Sacks worked together on -these changes and reviewed each other's changes to some extent. The -high-level design was also reviewed and co-developed by Mariana -Vertenstein. Martyn Clark contributed substantially to the breakout of -water state into state, diagnostic and balance check-related variables. - - CTSM testing: [PASS means all tests PASS and OK means tests PASS other than expected fails.] @@ -10791,34 +3787,48 @@ CTSM testing: cheyenne - not run - unit-tests (components/clm/src): + tools-tests (test/tools): - cheyenne - pass + cheyenne - not run - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): cheyenne - not run - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- pass - cheyenne_gnu ------ pass - hobart_nag -------- pass - hobart_pgi -------- pass - hobart_intel ------ pass + cheyenne ---- ok + izumi ------- ok + + ok: tests pass, baselines fail just for CLM51 cases, as expected + + NOTE: The following expensive tests did not run, due to a long queue + wait time; we are about to remove these tests from the test suite + anyway: -CTSM tag used for the baseline comparisons: ctsm1.0.dev004 + PEND ERS_D_Ld10.C96_C96_mg17.IHistClm50Sp.cheyenne_intel.clm-decStart RUN + PEND ERS_Ln9.ne0ARCTICne30x4_ne0ARCTICne30x4_mt12.IHistClm50SpGs.cheyenne_intel.clm-clm50cam6LndTuningMode_1979Start RUN + PEND SMS_Ln9.ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12.IHistClm50Sp.cheyenne_intel.clm-clm50cam6LndTuningMode_1979Start RUN + PEND SMS_Ln9.ne0ARCTICGRISne30x8_ne0ARCTICGRISne30x8_mt12.ISSP585Clm50BgcCrop.cheyenne_intel.clm-clm50cam6LndTuningMode RUN + PEND SMS_Ln9.ne0CONUSne30x8_ne0CONUSne30x8_mt12.IHistClm50Sp.cheyenne_intel.clm-clm50cam6LndTuningMode_2013Start RUN + +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: NO - bit-for-bit +Changes answers relative to baseline: YES - just for CLM51 + Summarize any changes to answers, i.e., + - what code configurations: CLM51 + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + possibly new climate Detailed list of changes ------------------------ @@ -10826,269 +3836,331 @@ Detailed list of changes List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none Pull Requests that document the changes (include PR ids): -- https://github.com/escomp/ctsm/pull/395 (documents the high-level design) +https://github.com/ESCOMP/CTSM/pull/1172 =============================================================== =============================================================== -Tag name: ctsm1.0.dev004 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Wed Jul 18 02:10:23 MDT 2018 -One-line Summary: Add some new diagnostic fields, fix a few issues, update cmip6 output +Tag name: ctsm5.1.dev004 +Originator(s): oleson (Keith Oleson), sacks (Bill Sacks) +Date: Wed Sep 30 10:45:25 MDT 2020 +One-line Summary: Improve robustness of onset and offset counters when changing dt Purpose of changes ------------------ -Add some new diagnostic fields. Some needed for CMIP6. Update the CMIP6 user-mods output. -Fix a couple issues. Get full list of history tapes working correctly. Check for valid range -of CO2. New IC file interpolated from the previous one for f19_g17_gl4 for 2000 Clm50BgcCrop. +The logic in CNPhenology for onset_counter and offset_counter was not +robust when the model time step differed from the time step used to +generate the finidat file. This showed up when running with a 20-minute +time step using a finidat file that was generated with a 30-minute time +step. See https://github.com/ESCOMP/CTSM/issues/1163 for details. + +The fix here improves the situation significantly, but I believe still +leaves some issues remaining; see +https://github.com/ESCOMP/CTSM/issues/1167 for details. Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): $210, #427, #429 - #210 -- increase number of history tapes - $427 -- Check for zero CO2 - #429 -- New IC for present day +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1163 (onset_counter variable on (all?) restart + files is not compatible with subsequent model runs using a 20 minute + time step) + +Known bugs introduced in this tag (include github issue ID): +- ESCOMP/CTSM#1167 (Rework CNPhenology onset and offset triggers to be + more robust to changes in dt) + - This issue was not exactly introduced in this tag, but it captures + some things that I think still need to be done for complete robustness Significant changes to scientifically-supported configurations -------------------------------------------------------------- -Does this tag change answers significantly for any of the following physics configurations? No +Does this tag change answers significantly for any of the following physics configurations? (Details of any changes will be given in the "Answer changes" section below.) [Put an [X] in the box for any configuration with significant answer changes.] [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): none -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): New history fields - TSKIN --- skin temperature - TSL ----- temperature of near-surface soil layer - GSSUNLN - sunlit leaf stomatal conductance at local noon - GSSHALN - shaded leaf stomatal conductance at local noon +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none -Changes made to namelist defaults (e.g., changed parameter values): None +Changes made to namelist defaults (e.g., changed parameter values): none -Changes to the datasets (e.g., parameter, surface or initial files): New finidat file f19_g17_gl4 2000 Clm50BgcCrop - New file is just interpolate from the previous file to a f19_g17_gl4 gridfor Clm50BgcCrop and 2000 simulation year +Changes to the datasets (e.g., parameter, surface or initial files): none -Substantial timing or memory changes: None +Substantial timing or memory changes: not checked (none expected) Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CLMTrunkChecklist as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): - -Changes to tests or testing: None +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Code reviewed by: self, oleson, abtawfik +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none +Changes to tests or testing: none -CTSM testing: regular +CTSM testing: [PASS means all tests PASS and OK means tests PASS other than expected fails.] build-namelist tests: - cheyenne - OK (95 are different because of finidat file change) + cheyenne - not run - unit-tests (components/clm/src): + tools-tests (test/tools): - cheyenne - PASS + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- PASS - hobart_pgi -------- FAIL - hobart_intel ------ PASS + cheyenne ---- ok + izumi ------- pass -CTSM tag used for the baseline comparisons: ctsm1.0.dev003 + ok: tests pass, one test had answer changes as noted below + +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: Yes -- only 2000 cases because of new IC +Changes answers relative to baseline: YES, but in very limited circumstances Summarize any changes to answers, i.e., - - what code configurations: Just 2000 cases - - what platforms/compilers: All - - nature of change: same climate + - what code configurations: Only when the model run uses a different + time step than the initial conditions file + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff; magnitude not investigated; in some cases, + the differences might be significant if the model actually + continues without aborting + + In the aux_clm test suite, this only appears in one test: + SMS_Ln9.ne30pg2_ne30pg2_mg17.I2000Clm50BgcCrop.cheyenne_intel.clm-clm50cam6LndTuningMode + + but it might appear more widely in cam / fully coupled testing Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) - - - #338 -- Radtemp and other new diagnostic fields +https://github.com/ESCOMP/CTSM/pull/1165 =============================================================== =============================================================== -Tag name: ctsm1.0.dev003 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Sun Jul 15 00:26:46 MDT 2018 -One-line Summary: Update cime/cism to work on upgraded hobart and with glade changes on cheyenne +Tag name: ctsm5.1.dev003 +Originator(s): ivanderkelen (Inne Vanderkelen) / sacks (Bill Sacks) +Date: Tue Sep 29 10:16:00 MDT 2020 +One-line Summary: Add capability for dynamic lakes Purpose of changes ------------------ -Update cime and cism so can work on upgraded hobart. Also fix an issue that the Nag6.2 compiler found -in CTSM. Also get working with glade changes that happened on cheyenne, DIN_LOC_ROOT_CLMFORC was -changed to a new directory. +Adds the capability for dynamic lake areas, read from the +landuse_timeseries file. This represents reservoir construction. For +now, this capability is off by default. Turning it on requires new +fields on the landuse_timeseries file which cannot yet be produced by +mksurfdata_map; these new fields will be added in +https://github.com/ESCOMP/CTSM/pull/1073. +A substantial part of this tag involved changing the accounting of water +and energy in lakes in order to conserve water and energy across +landunit transitions while not producing too large adjustment +fluxes. This change results in roundoff-level answer changes for all +transient cases. + +The core changes in this tag are from Inne Vanderkelen, in consultation +with Bill Sacks. Additional changes are from Bill Sacks, in consultation +with Inne Vanderkelen. Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): [If none, remove this line] - #441 -- Changes in glade invalidate previous softlinks and data locations - #438 -- Illegal argument aliasing caught by nag6.2 - #433 -- with hobart upgrade CTSM not working - -Known bugs introduced in this tag (include github issue ID): - #444 -- PGI fails on cheyenne and hobart - -Known bugs found since the previous tag (include github issue ID): - #443 -- Wood C:N ratios - #440 -- leafcn_max < target leafcn? +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#200 (Count energy of water in lakes in total + gridcell heat content) +- Resolves ESCOMP/CTSM#1140 (Add lake water to dynbal baselines) Significant changes to scientifically-supported configurations -------------------------------------------------------------- -Does this tag change answers significantly for any of the following physics configurations? No +Does this tag change answers significantly for any of the following physics configurations? (Details of any changes will be given in the "Answer changes" section below.) [Put an [X] in the box for any configuration with significant answer changes.] [ ] clm5_0 -[ ] clm4_5 +[ ] ctsm5_0-nwp -[ ] clm4_0 +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): None +Caveats for users (e.g., need to interpolate initial conditions): +- Using the dynamic lakes functionality will require either the + mksurfdata_map changes in https://github.com/ESCOMP/CTSM/pull/1073 or + manually adding the necessary fields to the landuse_timeseries file. -Changes to CLM's user interface (e.g., new/renamed XML or namelist variables): DIN_LOC_ROOT_CLMFORC on cheyenne - DIN_LOC_ROOT_CLMFORC was change on cheyenne +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New namelist variable for transient runs: do_transient_lakes -Changes made to namelist defaults (e.g., changed parameter values): None +Changes made to namelist defaults (e.g., changed parameter values): none -Changes to the datasets (e.g., parameter, surface or initial files): None +Changes to the datasets (e.g., parameter, surface or initial files): none -Substantial timing or memory changes: None +Substantial timing or memory changes: none Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): None +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Changes to tests or testing: path for cheyenne specific test had to be changed - Add some gnu tests on hobart - Lengthen wallclock on a test - Fix path for DA test_mod +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Using the dynamic lakes functionality will require either the + mksurfdata_map changes in https://github.com/ESCOMP/CTSM/pull/1073 or + manually adding the necessary fields to the landuse_timeseries file. +- For this reason, the new test + (ERS_Lm25.1x1_smallvilleIA.IHistClm50BgcCropQianRsGs.cheyenne_gnu.clm-smallville_dynlakes_monthly) + requires a manual step to create the necessary landuse_timeseries + file. This step is documented in the README file for the + clm-smallville_dynlakes_monthly testmod. -Code reviewed by: self +Changes to tests or testing: +- Added a single-point test covering dynamic lakes, using a + manually-created landuse_timeseries file: + ERS_Lm25.1x1_smallvilleIA.IHistClm50BgcCropQianRsGs.cheyenne_gnu.clm-smallville_dynlakes_monthly -CLM testing: regular +CTSM testing: [PASS means all tests PASS and OK means tests PASS other than expected fails.] build-namelist tests: - cheyenne - PASS + cheyenne - ok - unit-tests (components/clm/src): + Tests pass, differences from baseline as expected due to new + namelist variable - cheyenne - PASS + tools-tests (test/tools): + + cheyenne - not run - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): - cheyenne - PASS + cheyenne - not run - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - OK + (any machine) - not run regular tests (aux_clm): - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- FAIL - hobart_gnu -------- PASS - hobart_intel ------ PASS + cheyenne ---- ok + izumi ------- ok + + Tests pass, baselines differ as expected -CLM tag used for the baseline comparisons: ctsm1.0.dev002 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: No bit-for-bit +Changes answers relative to baseline: YES + + If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section): + And always remove these three lines and parts that don't apply. + + Summarize any changes to answers, i.e., + - what code configurations: Transient cases + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Mostly roundoff-level. See below for details. + + - Differences in HEAT_CONTENT1, ICE_CONTENT1, LIQUID_CONTENT1, as + expected + + - In transient tests (including Hist/SSP, Fates, CNDV and + transient glacier), roundoff-level diffs in EFLX_DYNBAL, + QFLX_ICE_DYNBAL and QFLX_LIQ_DYNBAL, along with related flux + terms, and river volume + + - In some transient tests, roundoff-level diffs in methane terms, + presumably from downstream effects of changes in VOLR due to + roundoff-level changes in fluxes. In multi-year tests, these + methane diffs grow to bigger than roundoff-level, but I think + they originate from roundoff-level diffs. (I feel like I've seen + this high sensitivity before.) + + - glcMEC_increase test + (ERP_P180x2_D_Ld5.f19_g17_gl4.I1850Clm50BgcCropG.cheyenne_intel.clm-glcMEC_increase) + shows significant differences in river-related terms, maybe due + to glacier running over lake and now lake has different states + than before; also, FILLDIFFs in h1 file because lake remains + active even when it goes to 0 area. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + - Examined cprnc RMS diffs + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: N/A + + URL for LMWG diagnostics output used to validate new climate: N/A + Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, cism - cism-wrapper to release-cesm2.0.04 - cime to cime5.6.10 +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) - #444 -- Get working on upgraded hobart and with glade changes on cheyenne +https://github.com/ESCOMP/CTSM/pull/1109 +https://github.com/billsacks/ctsm/pull/3 =============================================================== =============================================================== -Tag name: ctsm1.0.dev002 -Originator(s): erik (Erik Kluzek) -Date: Fri Jul 6 16:33:03 MDT 2018 -One-line Summary: Fix NFIX flux variables so special land-units are zeroed out, tools update, add some *_MAX fields on mksurfdata_map for transient cases +Tag name: ctsm5.1.dev002 +Originator(s): slevis (Samuel Levis,303-665-1310) +Date: Mon Sep 25 09:39:19 MDT 2020 +One-line Summary: Reduce duplication between caps Purpose of changes ------------------ -Nitrogen Fixation flux arrays were being set to missing value over non-vegetated landunits. This sets them to zero everywhere -and averages in the zero's at the gridcell level for history output. It also reads in restarts with missing values and converts -them to zero's. - -There are also some tools updates, getting the tools working on the new upgraded hobart.cgd.ucar.edu. - -And mksurfdata_map is updated to add some *_MAX files on the landuse.timeseries files that will allow us to conserve memory -for transient cases. + Eliminate duplication of the "derived quantities for required fields" + and corresponding error checking codes that repeat across the mct, + nuopc, and lilac caps. This consolidates the code and reduces + maintenance requirements. Bugs fixed or introduced ------------------------ -Issues fixed (include CTSM Issue #): #435, #436, #433 (for tools) - #435 -- intel build for tools - #426 -- Nitrogen Fixation flux variables - #433 -- hobart broken, got it working for tools - -Known bugs found since the previous tag (include github issue ID): #433, #431 +Issues fixed (include CTSM Issue #): #918 - #433 -- with hobart upgrade, hobart build isn't working - #431 -- When set_* options are used to hist_addfld be careful of ordering Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -11100,305 +4172,216 @@ Does this tag change answers significantly for any of the following physics conf [X] clm5_0 -[ ] clm4_5 +[X] ctsm5_0-nwp -[ ] clm4_0 +[X] clm4_5 Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): None -Changes to CLM's user interface (e.g., new/renamed XML or namelist variables): None +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None -Changes made to namelist defaults (e.g., changed parameter values): ndep file updated for clm5_0 for 1850 +Changes made to namelist defaults (e.g., changed parameter values): None Changes to the datasets (e.g., parameter, surface or initial files): None -Substantial timing or memory changes: None +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] None Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CLMTrunkChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -Caveats for developers (e.g., code that is duplicated that requires double maintenance): NFIX flux variables - NFIX flux variables when read from restart have special-values (missing on non veg landunits) converted to zero's - They are now initialized to zero everywhere. +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None Changes to tests or testing: None -Code reviewed by: self, wwieder, and lawrence, sacks (mksurfdata_map code) +Code reviewed by: @billsacks @slevisconsulting + -CLM testing: regular (although none on hobart!) +CTSM testing: [PASS means all tests PASS and OK means tests PASS other than expected fails.] build-namelist tests: - cheyenne - PASS (5 tests differ from previous version) + cheyenne - - unit-tests (components/clm/src): + tools-tests (test/tools): - cheyenne - PASS + cheyenne - - tools-tests (components/clm/test/tools): + PTCLM testing (tools/shared/PTCLM/test): - cheyenne - PASS - hobart --- PASS + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - regular tests (aux_clm): - cheyenne_intel ---- OK - cheyenne_gnu ------ OK + cheyenne ---- OK + izumi ------- PASS -CLM tag used for the baseline comparisons: ctsm1.0.dev001 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: clm5_0 BGC configurations with FUN and clm5_0 with BGC for new 1850 ndep file +Changes answers relative to baseline: Yes (Similar climate) Summarize any changes to answers, i.e., - - what code configurations: All clm5_0 BGC due to NFIX fields, and clm5_0 1850 BGC due to new ndep file + - what code configurations: All - what platforms/compilers: All - - nature of change: similar climate + - nature of change: Larger than roundoff/same climate + Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None - -Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull) + Changes were implemented in three steps: - #437 -- ChangeLog template - #432 -- nfix - #331 -- _MAX fields on mksurfdata_map + 1) Bit-for-bit: @billsacks simplified subroutine QSat by making three + arguments optional (es, qsdT, esdT). -=============================================================== -=============================================================== -Tag name: ctsm1.0.dev001 -Originator(s): sacks (Bill Sacks) -Date: Fri Jun 22 07:31:43 MDT 2018 -One-line Summary: Begin separating SoilHydrology flux calculations + 2) Answer-changing: @slevisconsulting replaced local calculations of + qsat in /src/cpl/mct, /src/cpl/lilac, and /src/cpl/nuopc with calls to + CTSM's subroutine QSat. Subroutine QSat uses a higher-order polynomial + approximation to estimate qsat, which explains the larger than + round-off diffs. When moving the three identical local approximations + to QSat as a temporary test instead of using the higher-order + polynomial approximation, the diffs reduce to round-off. -Note the new tag naming: Starting with this tag, we are naming tags -"ctsm..." rather than "clm...". We are starting with ctsm version 1, -which for now is nearly the same as clm version 5. We are moving to this -new tag naming now because: + 3) Bit-for-bit: @slevisconsulting consolidated repeating codes in + /src/cpl/mct, /src/cpl/lilac, and /src/cpl/nuopc by placing in the new + file /src/utils/lnd_import_export_utils.F90. -(1) The changes in this tag represent the first step towards - implementing the CTSM vision (separating the biogeophysics flux - calculations from state updates, making it easier to plug in - alternative parameterizations, etc.). +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -(2) This tag changes answers relative to the CLM5 release. (We expect - the climate to be the same, but we haven't tested this carefully - yet.) +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/CTSM/pull/1086 + https://github.com/ESCOMP/CTSM/pull/1094 +=============================================================== +=============================================================== +Tag name: ctsm5.1.dev001 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Wed Sep 23 02:29:08 MDT 2020 +One-line Summary: Start the clm5_1 physics series, with some changes to the fire model from Fang Li Purpose of changes ------------------ -First steps toward separating various flux calculations in the soil -hydrology code. The focus here is on saturated surface runoff and -infiltration excess runoff. The changes here separate flux calculations -from state updates and extract various calculations into their own -subroutines to facilitate swapping in alternative parameterizations. - -Most of the changes here are refactorings that are either bit-for-bit or -just introduce roundoff-level differences. However, there are also a few -larger answer changes, as described below. - -These are the greater-than-roundoff-level answer changes: - -(A1) Use full qflx_surf in BGC code. Previously, the subroutines ch4 and - SoilBiogeochemNLeaching had been using a flux that excluded surface - water runoff (qflx_h2osfc_surf). That was deemed to be incorrect - (by Dave Lawrence and others), so these BGC subroutines have been - changed to use the full surface runoff (saturated excess runoff + - infiltration excess runoff + h2osfc runoff). - - Configurations affected: BGC compsets - - Magnitude of change: Larger than roundoff; expected to be same - climate, but not investigated carefully - -(A2) VIC: Don't ever use the TOPModel formulation for SurfaceRunoff - - The code was using the TOPModel-based formulation for SurfaceRunoff - if frost_table > zwt_perched. Sean Swenson felt this shouldn't be - done, and refactoring will be easier if VIC always uses the - vic-looking formulation, so I'm stopping applying this formulation - when using VIC. - - Configurations affected: VIC compsets +Fang Li's latest Fire version - includes allowing clm5.1 phys version. New physics option is added +called "clm5_1", with currently the new feature to use the latest fire changes. This has some +adjustments to the fire model and includes some changes to the parameter file. Other new features +will be added into clm5_1 in future tags. - Magnitude of change: Larger than roundoff; not investigated carefully +Also bring in mksurfdata changes for the raw urban dataset change. This adds some changes to +mksurfdata for a new urban raw dataset, as well as preparation for new changes for some other +urban changes that will be a future part of clm5_1. Also use the half degree lightning dataset +by default for clm5_1. -(A3) VIC: Remove infiltration excess runoff +Start adding a new test list ctsm_sci that tests all the scientifically supported compsets. +Some of those tests fail due to existing issues, that will be fixed later. - Martyn Clark reviewed the VIC implementation, and felt that the - current implementation of infiltration excess runoff is - inconsistent with the standard VIC implementation. It appears that - what was being called VIC's infiltration excess runoff was actually - just an attempt to give a better numerical approximation to the - solution for saturated surface excess runoff. So deleting this - leaves only a first-order approximation to VIC's saturated surface - excess runoff. +Some more work done to change clm to ctsm, and allow for ctsm as a component. - Eventually we may want to put in place a more accurate solution for - VIC's saturated surface excess runoff. But Martyn's feeling is that - this can come in with other changes we want to make regarding - numerical solutions in CTSM. - - Configurations affected: VIC compsets - - Magnitude of change: Larger than roundoff; expected to be same - climate, but not investigated carefully - -(A4) Change in QOVER diagnostic field: now includes QH2OSFC. +Bugs fixed or introduced +------------------------ -These are the major refactorings (either bit-for-bit or just -roundoff-level differences): +Issues fixed (include CTSM Issue #): + Fix #1142 -- Add ctsm_sci test list + Fix #1145 -- File was corrupted on glade + Fix #1144 -- Move btran2 to just inside of fire model + Fix #889 --- Some adjustments to the Li Fire model -(R1) Extract surface runoff to its own module, and other modularization - related to what used to be subroutine SurfaceRunoff: extract a - subroutine for each fsat method, move urban surface runoff code - into different routines. +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- -(R2) Extract infiltration excess runoff to its own module, and other - modularization related to what used to be subroutine Infiltration. +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) -NOTE: For a detailed breakdown of changes, including documentation of -which changed changed answers, see the file ChangeLog_branch which was -deleted from this branch shortly before it was merged to master. + [Put an [X] in the box for any configuration with significant answer changes.] -Bugs fixed or introduced ------------------------- +[ ] clm5_0 -Issues fixed (include CTSM Issue #): -- Fixes #424 (decStart testmod is missing an `--append` in an xmlchange command) +[ ] ctsm5_0-nwp +[ ] clm4_5 Notes of particular relevance for users --------------------------------------- -Caveats for users (e.g., need to interpolate initial conditions): +Caveats for users (e.g., need to interpolate initial conditions): None -Changes to CLM's user interface (e.g., new/renamed XML or namelist variables): +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): Adds clm5_1 option to CLM_PHYSICS_VERSION + clm5_1_GSWP3v1 is the only LND_TUNING_MDOE option for clm5_1 + New compsets added for CLM51 I2000Clm51BgcCropGs, I2000Clm51BgcGs, I1850Clm51BgcGs, IHistClm51BgcGs, IHistClm51BgcCropGs + -Changes made to namelist defaults (e.g., changed parameter values): +Changes made to namelist defaults (e.g., changed parameter values): clm5_1 physics options added in + Add the ability to set the component name in filenames (default is still clm2, but can be clm4, olr clm5) + By default lightning dataset for clm5_1 is the half degree file -Changes to the datasets (e.g., parameter, surface or initial files): +Changes to the datasets (e.g., parameter, surface or initial files): All params files updated with new fields for fire -Substantial timing or memory changes: +Substantial timing or memory changes: None Notes of particular relevance for developers: (including Code reviews and testing) --------------------------------------------- -NOTE: Be sure to review the steps in .CLMTrunkChecklist as well as the coding style in the Developers Guide +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide Caveats for developers (e.g., code that is duplicated that requires double maintenance): -Changes to tests or testing: -- Shortened a 25-month f19 test to 13-months - (SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput): - This test took a long time to run, and we already have long tests of - this configuration at coarse-resolution. I suggested removing this - test entirely, but Erik Kluzek wanted to maintain a shortened version - of it. Erik's comments were: - - How about either flip it to f45 (because Rosie is using that - resolution for science) -- or leave it at f19 and have it run for 9 - months? The 25 months was to take it just past the 2-year spinup - time. From spunup initial conditions 9-months pretty much does a - full harvest cycle. f19 and f09 are the main configurations for - science and it would be good to have something longer than just - really short tests. - - I decided on Lm13, because this still completes in significantly less - than 2-hours, and if we're running for 9 months anyway, it seems - valuable to finish out the year and run a bit into the next year, - since some crop stuff triggers at the end of the year. - -Code reviewed by: Various code reviews done last Fall, when these -changes were first implemented. - -CLM testing: +Changes to tests or testing: Add ctsm_sci test list and move some clm5_0 to clm5_1 and one one clm5_1 specific test + +Code reviewed by: self + + +CTSM testing: regular, tools [PASS means all tests PASS and OK means tests PASS other than expected fails.] build-namelist tests: - cheyenne - not run + cheyenne - PASS (853 tests are different) - unit-tests (components/clm/src): + tools-tests (test/tools): cheyenne - PASS - tools-tests (components/clm/test/tools): - - cheyenne - not run - - PTCLM testing (components/clm/tools/shared/PTCLM/test): + python testing (see instructions in python/README.md; document testing done): - cheyenne - not run + cheyenne -- PASS regular tests (aux_clm): - cheyenne_intel ---- OK - cheyenne_gnu ------ OK - hobart_nag -------- OK - hobart_pgi -------- OK - hobart_intel ------ OK - - OK means tests pass, answers change as expected. + cheyenne ---- OK + izumi ------- PASS -CLM tag used for the baseline comparisons: clm5.0.dev013 +If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- -Changes answers relative to baseline: YES - - If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section): - - Summarize any changes to answers, i.e., - - what code configurations: Essentially all (except CLM4) - - what platforms/compilers: All - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - Roundoff-level changes for nearly all configurations (except CLM4). - - Greater-than-roundoff-level changes for the following - configurations: - - BGC: see (A1) note above (expected to be same climate, but not - investigated carefully) - - VIC: see (A2) and (A3) notes above (magnitude of change not - investigated carefully) - - QOVER diagnostic field: see (A4) note above - - If bitwise differences were observed, how did you show they were no worse - than roundoff? N/A - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: N/A - - URL for LMWG diagnostics output used to validate new climate: N/A - +Changes answers relative to baseline: No (although clm5_1 is a new physics option that is different) Detailed list of changes ------------------------ -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None Pull Requests that document the changes (include PR ids): -- https://github.com/ESCOMP/ctsm/pull/244 -- https://github.com/ESCOMP/ctsm/pull/190 -- Other PRs that existed on the old NCAR/clm-ctsm repository (which has - been deleted), which were not migrated to the new repository +(https://github.com/ESCOMP/ctsm/pull) + #1151 -- Move btran2 to inside CNFireBase + #1150 -- ctsm5.1 starting point + #1157 -- Urban mksurfdata_map changes + #1149 -- LILACSMOKE test change + #1146 -- Add --project to LILACS create_newcase =============================================================== +=============================================================== diff --git a/doc/ChangeSum b/doc/ChangeSum index 4d7344a666..5d0692ad68 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,98 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev038 erik 04/27/2021 Bring in minor changes from the cesm2.2.0 release tag +release-cesm2.2.01 erik 09/02/2020 Fix clm4_5 initial conditions + ctsm5.1.dev037 slevis 04/23/2021 Correct vertical interpolation in init_interp when soil thicknesses change + ctsm5.1.dev036 glemieux 04/21/2021 FATES tag update and snow occlusion of LAI fix + ctsm5.1.dev035 sacks 04/20/2021 Misc bfb enhancements and fixes + ctsm5.1.dev034 erik 04/19/2021 Bring in Arctic changes to LUNA from Leah Birch + ctsm5.1.dev033 mvertens 04/10/2021 Remove unnecessary settings of nextsw_cday + ctsm5.1.dev032 mvertens 04/10/2021 Fix bugs in co2 from atmosphere + ctsm5.1.dev031 jedwards 04/10/2021 Update externals and fixes for nuopc threading + ctsm5.1.dev030 erik 03/31/2021 New single column functionality for the NUOPC cap + ctsm5.1.dev029 mvertens 03/18/2021 Rework domain initialization for nuopc + ctsm5.1.dev028 swensosc 03/17/2021 Change limitation of top layer evaporation/sublimation + ctsm5.1.dev027 sacks 03/15/2021 Update cime and other externals; includes switch to pio2 + ctsm5.1.dev026 sacks 03/08/2021 Change f10 tests to use mg37 mask + ctsm5.1.dev025 sacks 02/23/2021 Refactor ozone code, and misc. small fixes + ctsm5.1.dev024 slevis 02/20/2021 Grid cell-level error check for H2O + ctsm5.1.dev023 erik 02/11/2021 Calculate leaf biomass for non-woody PFTS, and a few other small answer changes + ctsm5.1.dev022 glemieux 02/05/2021 Merge fates_main_api into ctsm master + ctsm5.1.dev021 erik 01/12/2021 Add option for biomass heat storage (BHS) to clm5_1 physics + ctsm5.1.dev020 erik 12/30/2020 Potential roundoff changes in preparation for bio-mass heat storage option + ctsm5.1.dev019 sacks 12/19/2020 Fix ndep from coupler + ctsm5.1.dev018 slevis 12/08/2020 Add ACTIVE (T/F) column to master hist fields table and alphabetize + ctsm5.1.dev017 slevis 11/17/2020 Write history fields master list to separate optional file + ctsm5.1.dev016 multiple 11/17/2020 Updates for nuopc + ctsm5.1.dev015 sacks 11/13/2020 A few small fixes + ctsm5.1.dev014 dll/oles 11/07/2020 Grass/crop snow burial fraction fix, and some other fixes + ctsm5.1.dev013 jedwards 11/04/2020 Allow pnetcdf for vector history files + ctsm5.1.dev012 oleson/s 11/03/2020 Allow nlevgrnd < nlevurb + ctsm5.1.dev011 sacks 11/02/2020 Change CISM2%NOEVOLVE compsets to use SGLC; documentation updates + ctsm5.1.dev010 sacks/je 10/23/2020 Fix reading netcdf variable into a different data type + ctsm5.1.dev009 negins 10/21/2020 BFB changes for Perturbed Parameter Ensemble and Hydraulic redistribution + ctsm5.1.dev008 erik 10/07/2020 Two answer changes: Clm45/50/51 with crop, and for 2000Clm51 + ctsm5.1.dev007 sacks 10/06/2020 CNFire: btran2 fixes and general cleanup + ctsm5.1.dev006 sacks 10/03/2020 Call correct routine to calculate btran2 for CNFireLi2021 + ctsm5.1.dev005 sacks 10/02/2020 Answer changing bug fixes for clm51: fire and organic_frac_squared + ctsm5.1.dev004 oleson 09/30/2020 Improve robustness of onset and offset counters when changing dt + ctsm5.1.dev003 ivanderk 09/29/2020 Add capability for dynamic lakes + ctsm5.1.dev002 slevis 09/25/2020 Reduce duplication between caps + ctsm5.1.dev001 erik 09/23/2020 Start the clm5_1 physics series, with some changes to the fire model from Fang Li + ctsm1.0.dev113 negins 09/08/2020 Some bit-for-bit changes needed for the Perturbed Parameter Ensemble work + ctsm1.0.dev112 sacks/ww 08/28/2020 Small changes to mksurfdata_map, singlept tool and run_sys_tests + ctsm1.0.dev111 erik 08/28/2020 Compsets don't use 2014 for GSWP3 forcing, LUNA prevyr changed back + ctsm1.0.dev110 jedwards 08/21/2020 Fixes needed for PIO2 + ctsm1.0.dev109 negins 08/20/2020 Allow for resorbtion in transition from live to dead wood N + ctsm1.0.dev108 erik 08/19/2020 Update default PE layouts for new SE/FV3 grids + ctsm1.0.dev107 erik 08/10/2020 Answer changes needed for CESM2.2.0 + ctsm1.0.dev106 erik 08/06/2020 Bit-for-bit updates for the CESM2.2.0 release +release-clm5.0.34 erik 04/20/2020 Update doc for release-clm5.0 (SKIPPED), and fix issues with no-anthro surface dataset creation +release-clm5.0.33 erik 04/07/2020 SKIPPED ON MASTER -- Turn irrigation on for 2300 SSP extensions +release-clm5.0.32 erik 04/02/2020 SKIPPED ON MASTER -- Extensions to 2300 for SSP5-8.5,SSP5-3.4, and SSP1-2.6 +release-clm5.0.31 erik 03/29/2020 Bring raw 2100-2300 extension (SKIPPED), some other misc. changes + ctsm1.0.dev105 erik/fis 07/23/2020 Bring in some new SE grids for CAM as well as initial condition files for them + ctsm1.0.dev104 sacks 07/06/2020 Add LILAC + ctsm1.0.dev103 slevis 06/29/2020 Gridcell-level error-check for methane (CH4) + ctsm1.0.dev102 erik/ole 06/26/2020 Some important fixes for LUNA in clm5_0, and small urban issue in clm5_0 + ctsm1.0.dev101 ole/erik 06/17/2020 Changes from Keith to bring a list of variables to the parameter file + ctsm1.0.dev100 sacks 06/09/2020 Deallocate memory after running init_interp + ctsm1.0.dev099 sacks 06/08/2020 Update cime, needed for izumi machine updates + ctsm1.0.dev098 jet/erik 05/28/2020 Bring in GFDL fv3 cubed sphere grids C24, C48, C96, C192, C384 + ctsm1.0.dev097 ycheng 05/25/2020 Add two bioenergy crops (switchgrass and miscanthus) + ctsm1.0.dev096 slevis 05/21/2020 Gridcell-level balance checks for carbon and nitrogen + ctsm1.0.dev095 sacks 05/21/2020 Update cime and cmeps externals; rework initialization of CNFire object + ctsm1.0.dev094 sacks 05/15/2020 Minor bug fixes needed for latest cime + ctsm1.0.dev093 erik 05/01/2020 Bring in changes from release-clm5.0 branch to master +release-clm5.0.30 erik 01/21/2020 Update FATES to sci.1.30.0_api.8.0.0 +release-clm5.0.29 erik 11/19/2019 Some answer changes needed for prescribed soil-moisture and clm4_5 defaults (1850-ndep, and urbantv settings) +release-clm5.0.28 erik 11/14/2019 Several bit-for-bit fixes especially around soil-moisture streams +release-clm5.0.27 erik 08/13/2019 Add presoribed soil moisture streams as an option, and a few fixes +release-clm5.0.26 sacks 07/29/2019 Add a CN precision control call to fix problems related to small negative values +release-clm5.0.25 erik 05/29/2019 Change two files from NetCDF-4 format to NetCDF-3 (because some machines have trouble with NetCDF-4 in pnetcdf) +release-clm5.0.24 erik 05/22/2019 Correct ndep end year for SSPs, 2-degree CMIP6WACCMDECK with C-isotopes off, fixes mksurfdata for high resolution +release-clm5.0.23 erik 05/15/2019 Update cime to bring in CO2 transient files for the CMIP6 SSP's as well as presaero for three of them +release-clm5.0.22 erik 05/08/2019 Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change +release-clm5.0.21 erik 05/03/2019 New ndep files, update fates, fix some issues +release-clm5.0.20 erik 03/12/2019 Update all fsurdat files and bring in files for future scenarios, remove CMIP5 rcp options, bring in some bug fixes +release-clm5.0.19 erik 03/08/2019 SKIPPED ON MASTER -- Update cime version +release-clm5.0.18 erik 02/13/2019 Add NoAnthro compset, reduce fields on fsurdat in mksurfdata_map, initial add of tools/contrib directory +release-clm5.0.17 sacks 01/23/2019 History fields for vertically-resolved sums of soil C and N, and minor fixes +release-clm5.0.16 erik 01/15/2019 PtVg and ssp_rcp future scenario options and Antarctica wetlands fix to mksurfdata, and option to dribble crop harvest XSMRPOOL flux to atmosphere +release-clm5.0.15 sacks 12/06/2018 SKIPPED ON MASTER -- Option for rain-to-snow +release-clm5.0.14 erik 11/29/2018 Update cime and fix surface dataset for f05 1850 non-crop case +release-clm5.0.13 erik 11/14/2018 Update externals with new CO2/presearo/rtm/mosart, add science_support, change testing +release-clm5.0.12 erik 11/03/2018 New IC files for clm45/clm50 coupled cases, add 2010 compset (IC FILES UPDATE SKIPPED ON MASTER) + ctsm1.0.dev092 erik 04/27/2020 Update cime to version in cesm2_2_beta04 + ctsm1.0.dev091 sacks 04/24/2020 Increase tolerance on near-zero truncation for a snow state update + ctsm1.0.dev090 negins 04/23/2020 Refactoring banded diagonal matrix code in SoilTemperature module + ctsm1.0.dev089 sacks 04/07/2020 Bring documentation source to master + ctsm1.0.dev088 sacks 04/07/2020 Fix bug in snow aerosol numerics (causes occasional HUGE aerosol values) + ctsm1.0.dev087 sacks 04/06/2020 Change hard-coded soil layers in phenology to use a target depth + ctsm1.0.dev086 mvertens 03/19/2020 Updates to NUOPC cap and minor fixes to ncdio_pio + ctsm1.0.dev085 sacks 03/16/2020 Update cime + ctsm1.0.dev084 negins 02/19/2020 Bounds assertion for C isotopes when threading is on + ctsm1.0.dev083 negins 02/06/2020 Some BFB Fixes: Resolve issues #683, # 874, #878, # 885, # 745, #838 ctsm1.0.dev082 oleson 02/01/2020 Rename variables to avoid confusion; fix QSNOEVAP diagnostic ctsm1.0.dev081 slevis 01/13/2020 Speed up restart writes ctsm1.0.dev080 sacks 12/02/2019 Update externals, minor fixes to work with latest cime, get nuopc cap working @@ -75,16 +168,16 @@ Tag Who Date Summary ctsm1.0.dev011 sacks 09/12/2018 Add water tracer consistency checks, and other water tracer work ctsm1.0.dev010 sacks 08/30/2018 Update cime to cime5.7.3 ctsm1.0.dev009 sacks 08/22/2018 Fix initialization of AnnET in InitAccVars - ctsm1.0.dev008 erik 08/14/2018 Update 1850 ndep file and last year for streams for Historical transient cases + ctsm1.0.dev008 erik 08/14/2018 Update 1850 ndep file and last year for streams for Historical transient cases (corresponds to release-clm5.0.05) ctsm1.0.dev007 sacks 08/05/2018 Avoid glacier dynamic landunit adjustments in first time step ctsm1.0.dev006 sacks 08/04/2018 Minor bug fixes, cleanup, documentation and enhancements - ctsm1.0.dev005 sacks 08/03/2018 Rework water data types to accommodate isotopes and other tracers - ctsm1.0.dev004 erik 07/18/2018 Add some new diagnostic fields, fix a few issues, update cmip6 output + ctsm1.0.dev005 sacks 08/03/2018 Rework water data types to accommodate isotopes and other tracers (skipped on release-clm5.0) + ctsm1.0.dev004 erik 07/18/2018 Add some new diagnostic fields, fix a few issues, update cmip6 output (corresponds to release-clm5.0.04) ctsm1.0.dev003 erik 07/15/2018 Update cime/cism to work on upgraded hobart and with glade changes on cheyenne ctsm1.0.dev002 erik 07/06/2018 Fix NFIX flux variables so special land-units are zeroed out, tools update, add some *_MAX fields on mksurfdata_map for transient cases - ctsm1.0.dev001 sacks 06/22/2018 Begin separating SoilHydrology flux calculations - clm5.0.dev013 erik 06/12/2018 cleanup and update cime and cism - clm5.0.dev012 sacks 05/17/2018 Fixes for variable_year orbital mode + ctsm1.0.dev001 sacks 06/22/2018 Begin separating SoilHydrology flux calculations (this was skipped on release branch) + clm5.0.dev013 erik 06/12/2018 cleanup and update cime and cism (corresponds to release-clm5.0.03) + clm5.0.dev012 sacks 05/17/2018 Fixes for variable_year orbital mode (corresponds to release-clm5.0.01 and release-clm5.0.02) clm5.0.dev011 erik 05/16/2018 1850 ndep update, cism update, PE layouts, turn BFBFLAG for testing clm5.0.dev010 erik 05/15/2018 Update cime version to version in cesm2.0.beta10, changes answers for 1850 compsets because of orbit clm5.0.dev009 sacks 05/10/2018 New init_interp method diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 0000000000..9b2c2dcd0d --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,42 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +SPHINXPROJ = clmdoc +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +# 'make fetch-images' should be run before building the +# documentation. (If building via https://github.com/ESMCI/doc-builder, +# this is run automatically for you.) This is needed because we have +# configured this repository (via an .lfsconfig file at the top level) +# to NOT automatically fetch any of the large files when cloning / +# fetching. +fetch-images: + git lfs pull --exclude="" + +.PHONY: help fetch-images Makefile + +# For the pdf, we only build the tech note, but use the conf.py file in +# the top-level source directory (the -c option says where to find +# conf.py). Note that we also override the setting of +# numfig_secnum_depth in order to have figure numbering as desired in +# the pdf, given that the pdf just contains the tech note, so doesn't +# have the top-level numbering present in the web documentation (where +# top-level section 1 is the User's Guide and section 2 is the Tech +# Note). +# +# The use of $(0) is as in the catch-all target. +latexpdf: + $(SPHINXBUILD) -M $@ "$(SOURCEDIR)/tech_note" "$(BUILDDIR)" -c "$(SOURCEDIR)" -D numfig_secnum_depth=1 $(SPHINXOPTS) $(O) + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + $(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/doc/UpdateChangelog.pl b/doc/UpdateChangelog.pl index 88f8331d03..4a5329175b 100755 --- a/doc/UpdateChangelog.pl +++ b/doc/UpdateChangelog.pl @@ -41,7 +41,7 @@ sub usage { To document a new tag - $ProgName ctsm1.0.dev012 "Description of this tag" + $ProgName ctsm5.2.dev099 "Description of this tag" EOF } @@ -177,10 +177,10 @@ sub usage { # Find header line if ( $_ =~ /=====================/ ) { print FH $_; - my $format = "%16.16s %8.8s %10.10s %s\n"; + my $format = "%18.18s %8.8s %10.10s %s\n"; if ( $update ) { $_ = ; - if ( /^(.{16}) (.{8}) (.{10}) (.+)$/ ) { + if ( /^(.{18}) (.{8}) (.{10}) (.+)$/ ) { $tag = $1; $user = $2; $sum = $4; diff --git a/doc/UsersGuide/Makefile b/doc/UsersGuide/Makefile deleted file mode 100644 index 1c76bc75bd..0000000000 --- a/doc/UsersGuide/Makefile +++ /dev/null @@ -1,193 +0,0 @@ -# -# Makefile to convert DocBook CLM Users-Guide into html and/or pdf -# (rtf, txt, ps, tex, man, dvi, and texi are also valid docbook formats) -# -VPATH := ../../tools/cprnc . .. ../../bld ../../tools/ncl_scripts \ - ../../tools/mksurfdata ../../test/system ../../bld/namelist_files \ - ../../bld/config_files ../../tools ../../../../../scripts/ccsm_utils/Tools \ - ../../../../../scripts/ccsm_utils/Tools/lnd/clm/PTCLM/ ../../src/main - -PDFUG := clm_ug.pdf -HTMLUG := book1.html -DOCBKUG := clm_ug.xml -CFGLOG := config_help -CPRLOG := cprnc_readme -BNMLOG := buildnml_help -BSTLOG := build_streams_help -RESLOG := buildnml_resolutions -USCLOG := buildnml_usecases -QCKLOG := quickstart_guide -COPLOG := filecopies -MKSLOG := mksurfdata.pl -USRLOG := quickstart_usrdat -PTCLOG := ptclm_help -PTCLST := ptclm_list -TDRLOG := test_driver.sh -GETREG := getregional_datasets -CO2DIF := addco2_datm.buildnml -DATLOG := build_date -NMLDFTBL := namelist_definition_table -NMLDLTBL := namelist_defaults_clm_table -HSFLDTBL := history_fields_table -CFGDFTBL := config_definition_table -COMPLIST := compsets_list_ofIcases.xml -SOURCES := $(DOCBKUG) $(COMPLIST) $(CFGLOG).xml $(PTCLOG).xml $(BNMLOG).xml \ - $(RESLOG).xml $(USCLOG).xml $(QCKLOG).xml $(COPLOG).xml $(PTCLST).xml \ - $(USRLOG).xml $(GETREG).xml preface.xml custom.xml special_cases.xml \ - tools.xml adding_files.xml single_point.xml addco2_datm.buildnml.xml \ - appendix.xml trouble_shooting.xml ptclm.xml $(BSTLOG).xml \ - $(MKSLOG).xml $(TDRLOG).xml $(DATLOG).xml $(CPRLOG).xml \ - $(NMLDFTBL).xml $(NMLDLTBL).xml $(CFGDFTBL).xml $(HSFLDTBL).xml - -CONVAMP := sed 's/\&/\&/g' -CONVSIGNS := sed 's/>/\>/g' | sed 's/ tmpFile.txt - addxhtmlhead.pl tmpFile.txt > $@ - $(RM) tmpFile.txt - -$(NMLDLTBL).xhtml: namelist_defaults_clm.xml namelist_defaults.xsl - xsltproc ../../bld/namelist_files/namelist_defaults.xsl $< > tmpFile.txt - addxhtmlhead.pl tmpFile.txt > $@ - $(RM) tmpFile.txt - -$(CFGDFTBL).xhtml: config_definition.xml config_definition.xsl - xsltproc ../../bld/config_files/config_definition.xsl $< > tmpFile.txt - addxhtmlhead.pl tmpFile.txt > $@ - $(RM) tmpFile.txt - -history_fields.xml: findHistFields.pl - cd ../../src/main; ./findHistFields.pl >& tmpFile.txt - $(RM) tmpFile.txt - -$(HSFLDTBL).xhtml: history_fields.xml history_fields.xsl - xsltproc ../../bld/namelist_files/history_fields.xsl $< > tmpFile.txt - addxhtmlhead.pl tmpFile.txt > $@ - $(RM) tmpFile.txt - -.xhtml.xml: - xsltproc stylesheethtml2docbook.xsl $< > $@ - -.tlog.xml: - $(CONVAMP) $< | $(CONVSIGNS) > tempFile.txt - limitLineLen.pl tempFile.txt > $@ - $(RM) tempFile.txt - -.diff.xml: - $(CONVAMP) $< | $(CONVSIGNS) > $@ - -debug: - @echo "SOURCES: $(SOURCES)" - @echo "CONVAMP: $(CONVAMP)" - @echo "CONVSIGNS: $(CONVSIGNS)" - -$(COMPLIST): - ./get_Icaselist.pl > $@ - -$(HTMLUG): $(SOURCES) - docbook2html --dsl clm_stylesheet.dsl#html $< - -$(PDFUG): $(SOURCES) - docbook2pdf --dsl clm_stylesheet.dsl#print $< - -$(BNMLOG).tlog: build-namelist - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../bld/build-namelist -help >& $@ - -$(BSTLOG).tlog: build_streams - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../../../../scripts/ccsm_utils/Tools/build_streams --help >& $@ - -$(DATLOG).tlog: - @echo "Get current build date" - date +%b-%d-%Y >& $@ - -$(RESLOG).tlog: build-namelist - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../bld/build-namelist -res list >& $@ - -$(USCLOG).tlog: build-namelist - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../bld/build-namelist -use_case list >& $@ - -$(CFGLOG).tlog: configure - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../bld/configure -help >& $@ - -$(PTCLOG).tlog: PTCLM.py - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../../../../scripts/ccsm_utils/Tools/lnd/clm/PTCLM/PTCLM.py --help >& $@ - -$(PTCLST).tlog: PTCLM.py - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - cd ../../../../../scripts/ccsm_utils/Tools/lnd/clm/PTCLM; \ - PTCLM.py --list >& $(CURDIR)/$@ - -$(MKSLOG).tlog: mksurfdata.pl - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../tools/mksurfdata/mksurfdata.pl -help >& $@ - -$(TDRLOG).tlog: test_driver.sh - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $@ is good and redo your make" - ../../test/system/test_driver.sh -help >& $@ - -$(QCKLOG).tlog: Quickstart.GUIDE - cp $< $@ - -$(COPLOG).tlog: README.filecopies - cp $< $@ - -$(CPRLOG).tlog: README - cp $< $@ - -$(USRLOG).tlog: Quickstart.userdatasets - cp $< $@ - -$(GETREG).tlog: getregional_datasets.pl - @echo "The following line will fail in the make as it calls die -- but that is expected" - @echo "Check that the output $(GETREG) is good and redo your make" - ../../tools/ncl_scripts/getregional_datasets.pl -help >& $@ - -clean: - $(RM) -f $(HTMLUG) $(PDFUG) *.tlog $(DATLOG).xml *.xhtml *.tex - -realclean: clean - $(RM) -f f*.html c*.html x*.html a*.html i*.html $(COMPLIST) $(CFGLOG).xml \ - $(BNMLOG).xml $(BSTLOG).xml $(PTCLOG).xml $(PTCLST).xml \ - $(RESLOG).xml $(USCLOG).xml $(USRLOG).xml $(GETREG).xml $(QCKLOG).xml \ - $(CO2DIF).xml *.tlog $(MKSLOG).xml $(TDRLOG).xml $(DATLOG).xml \ - $(NMLDFTBL).xml $(NMLDLTBL).xml $(CFGDFTBL).xml $(CPRLOG).xml \ - $(COPLOG).xml diff --git a/doc/UsersGuide/addco2_datm.buildnml.diff b/doc/UsersGuide/addco2_datm.buildnml.diff deleted file mode 100644 index b8fbf34e36..0000000000 --- a/doc/UsersGuide/addco2_datm.buildnml.diff +++ /dev/null @@ -1,59 +0,0 @@ -*** datm.buildnml.csh.orig 2010-06-11 10:59:29.246523532 -0600 ---- datm.buildnml.csh 2010-06-11 11:06:30.710784206 -0600 -*************** -*** 34,48 **** - streams = 'clm_qian.T62.stream.Solar.txt 1895 1948 1972 ', - 'clm_qian.T62.stream.Precip.txt 1895 1948 1972 ', - 'clm_qian.T62.stream.TPQW.txt 1895 1948 1972 ', -! 'presaero.stream.txt 1849 1849 2006' - vectors = 'null' - mapmask = 'nomask', - 'nomask', - 'nomask', - 'nomask' - tintalgo = 'coszen', - 'nearest', - 'linear', - 'linear' - / - EOF1 ---- 34,56 ---- - streams = 'clm_qian.T62.stream.Solar.txt 1895 1948 1972 ', - 'clm_qian.T62.stream.Precip.txt 1895 1948 1972 ', - 'clm_qian.T62.stream.TPQW.txt 1895 1948 1972 ', -! 'presaero.stream.txt 1849 1849 2006', -! 'datm.global1val.stream.CO2.txt 1766 1766 2005 ' - vectors = 'null' - mapmask = 'nomask', - 'nomask', - 'nomask', -+ 'nomask', - 'nomask' -+ mapalgo = 'bilinear', -+ 'bilinear', -+ 'bilinear', -+ 'bilinear', -+ 'nn' - tintalgo = 'coszen', - 'nearest', - 'linear', -+ 'linear', - 'linear' - / - EOF1 -*************** -*** 1112,1121 **** ---- 1120,1132 ---- - - EOF1 - -+ cp $CASEBUILD/co2_streams.txt datm.global1val.stream.CO2.txt -+ - - $CASETOOLS/listfilesin_streams -input_data_list -t clm_qian.T62.stream.Solar.txt >> $CASEBUILD/datm.input_data_list - $CASETOOLS/listfilesin_streams -input_data_list -t clm_qian.T62.stream.Precip.txt >> $CASEBUILD/datm.input_data_list - $CASETOOLS/listfilesin_streams -input_data_list -t clm_qian.T62.stream.TPQW.txt >> $CASEBUILD/datm.input_data_list -+ $CASETOOLS/listfilesin_streams -input_data_list -t datm.global1val.stream.CO2.txt >> $CASEBUILD/datm.input_data_list - - cat >! presaero.stream.txt << EOF1 - diff --git a/doc/UsersGuide/adding_files.xml b/doc/UsersGuide/adding_files.xml deleted file mode 100644 index 18c034cbbb..0000000000 --- a/doc/UsersGuide/adding_files.xml +++ /dev/null @@ -1,357 +0,0 @@ - - -Adding New Resolutions or New Files to the build-namelist Database - -In the last chapter we gave the details on how to create new files for input into -CLM. These files could be either global resolutions, regional-grids or even a single -grid point. If you want to easily have these files available for continued use in your -development you will then want to include them in the build-namelist database so -that build-namelist can easily find them for you. You can deal with them, just by -editing your namelist by hand (or using a &usernlclm; namelist file), or by using -&CLMUSRDAT;. Another way to deal with them is to enter them into -the database for build-namelist, so that build-namelist can find them for you. -This keeps one central database for all your files, rather than having multiple locations -to keep track of files. If you have a LOT of files to keep track of it also might -be easier than keeping track by hand, especially if you have to periodically update -your files. If you just have a few quick experiments to try, for a short time period -you might be best off using the other methods mentioned above. - - -There are two parts to adding files to the build-namelist database. The first part -is adding new resolution names which is done in the -models/lnd/clm/bld/namelist_files/namelist_definition.xml file -(and in the -models/lnd/clm/bld/config_files/config_definition.xml file -when adding supported single-point datasets). -The second part is actually adding the new filenames which is done in the -models/lnd/clm/bld/namelist_files/namelist_defaults_clm.xml file -(models/lnd/clm/bld/namelist_files/namelist_defaults_clm_tools.xml -file for CLM tools). -If you aren't adding any new resolutions, and you are just changing the files for existing -resolutions, you don't need to edit the namelist_definition file. - - - -Managing Your Own Data-files - -If you are running on a supported machine (such as bluefire or jaguar) the standard -input datasets will already be available and you won't have to check them out of the -subversion inputdata server. However, you also will NOT be able to add your own datafiles -to these standard inputdata directories -- because most likely you won't have permissions -to do so. In order to add files to the XML database or to use &CLMUSRDAT; you need -to put data in the standard locations so that they can be found. The recommended -way to do this is to use the link_dirtree tool in the &cesm; scripts. -Some information on link_dirtree is available in the -&cesmrel; Scripts User's Guide. We also have -some examples of it's use here and in other sections of this User's Guide. - - -Using link_dirtree is quite simple, you give the directory where -data exists and then the directory that you want to create where datasets will point -to the original source files. In the example below we use "$HOME/inputdata", but -MYCSMDATA could be any directory you have access to where you want to -put your data. - -> cd scripts -# First make sure you have a inputdata location that you can write to -# You only need to do this step once, so you won't need to do this in the future -# (except to bring in any updated files in the original $CSMDATA location). -> setenv MYCSMDATA $HOME/inputdata # Set env var for the directory for input data -> ./link_dirtree $CSMDATA $MYCSMDATA - -Then when you create a case you will change DIN_LOC_ROOT_CSMDATA to -point to the location you linked to rather than the default location. - -> ./xmlchange -file env_run.xml -id DIN_LOC_ROOT_CSMDATA -val $MYCSMDATA - - - -In order to list the files that you have created you merely need to use the UNIX -command find to find the files that are NOT softlinks. So for -example executing the following command: - -> find $MYCSMDATA -type f -print - -for me gives the following list of &CLMUSRDAT; files that I have created. - -/blhome/erik/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_monthly_1849-2006_1x1pt_US-Ha1.nc -/blhome/erik/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_monthly_1849-2006_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp8.5_monthly_1850-2100_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_rcp4.5_monthly_1850-2100_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/atm/datm7/domain.clm/domain.lnd.1x1pt_US-Ha1_USGS.nc -/blhome/erik/inputdata/atm/datm7/domain.clm/domain.lnd.13x12pt_f19_alaskaUSA_gx1v6.nc -/blhome/erik/inputdata/lnd/clm2/griddata/fracdata_13x12pt_f19_alaskaUSA_gx1v6.nc -/blhome/erik/inputdata/lnd/clm2/griddata/fracdata_1x1pt_US-Ha1_USGS.nc -/blhome/erik/inputdata/lnd/clm2/griddata/topodata_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/lnd/clm2/griddata/griddata_1x1pt_US-Ha1.nc -/blhome/erik/inputdata/lnd/clm2/griddata/griddata_13x12pt_f19_alaskaUSA.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata_13x12pt_f19_alaskaUSA_simyr1850.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata_1x1pt_US-Ha1_simyr2000.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_rcp4.5_13x12pt_f19_alaskaUSA_simyr1850-2100.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata_1x1pt_US-Ha1_simyr1850.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata_13x12pt_f19_alaskaUSA_simyr2000.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_1x1pt_US-Ha1_simyr1849-2006.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_13x12pt_f19_alaskaUSA_simyr1850-2100.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_rcp8.5_13x12pt_f19_alaskaUSA_simyr1850-2100.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_13x12pt_f19_alaskaUSA_simyr1849-2006.nc -/blhome/erik/inputdata/lnd/clm2/surfdata/surfdata.pftdyn_1x1pt_US-Ha1_simyr1850-2100.nc - -You can also use find to list files that have a particular pattern -in the name as well (using the -name option with wildcards). Also you can always rerun the -link_dirtree command if any new files are added that you need to be -linked into your directory tree. Since, the files are soft-links -- it doesn't take up -much space other than the files that you add there. This way all of the files are kept -in one place, they are organized by usage according to &cesm; standards, and you can -easily find your own files, and &clm; can find them as well. - - - - -Adding Resolution Names - -If you are adding files for new resolutions which aren't covered in the -namelist_definition file -- you'll need to add them in. The list of valid resolutions -is in the id="res" entry in the -models/lnd/clm/bld/namelist_files/namelist_definition.xml file. -You need to choose a name for your new resolution and simply add it to the comma -delimited -list of valid_values for the id="res" entry. The convention for global Gaussian grids -is number_of_latitudes x number_of_longitudes. The convention for global finite -volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude -is measured in degrees. For regional or single-point datasets the names have a grid size -number_of_latitudes x number_of_longitudes followed by an underscore and then a -descriptive name such as a City name followed by an abbreviation for the Country in caps. -The only hard requirement is that names be unique for different grid files. -Here's what the entry for resolutions looks like in the file: - -<entry id="res" type="char*30" category="default_settings" - group="default_settings" - valid_values= -"128x256,64x128,48x96,32x64,8x16,94x192,0.23x0.31,0.47x0.63, -0.9x1.25,1.9x2.5,2.65x3.33,4x5,10x15,5x5_amazon, -1x1_camdenNJ,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ, -1x1_brazil,1x1_urbanc_alpha,0.5x0.5"> -Horizontal resolutions -</entry> - -As you can see you just add your new resolution names to the end of the valid_values -list. - - -When using &ptclm; and adding supported single-point resolutions, you'll also want to -add these resolutions to the -models/lnd/clm/bld/config_files/config_definition.xml under -the sitespf_pt name. The entry in that file looks like: - -<entry id="sitespf_pt" -valid_values="none,1x1_brazil,5x5_amazon, -1x1_camdenNJ,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ, -1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA" -value="none" category="physics"> -Flag to turn on site specific special configuration flags for supported single -point resolutions. -Currently the only special settings are for MEXICOCITY and VANCOUVER, which make -changes to urban parameters. -</entry> - -&ptclm; assumes that any supported single-point resolutions are valid settings for -sitespf_pt. - - - - -Adding or Changing Default Filenames - -To add or change the default filenames you edit the -models/lnd/clm/bld/namelist_files/namelist_defaults_clm.xml -and either change an existing filename or add a new one. Most entries in the -default namelist files, include different attributes that describe the different -properties that describe the differences in the datasets. Attributes include -the: resolution, year to simulation, range of years to simulate for transient -datafiles, the land-mask, the representative concentration pathway (rcp) for future -scenarios, and the type of biogeochemistry (bgc) model used. For example the -fatmgrid for the 1.9x2.5 resolution is as follows: - -<fatmgrid hgrid="1.9x2.5" >lnd/clm2/griddata/griddata_1.9x2.5_060404.nc -</fatmgrid> - -Other fatmgrid files are distinguished from this one by -their resolution (hgrid) attribute. - - -To add or change the default filenames for &clm; tools edit the -models/lnd/clm/bld/namelist_files/namelist_defaults_clm_tools.xml -and either change an existing filename or add a new one. Editing this file is -similar to the namelist_defaults_clm.xml talked about above. - - -What are the required files? - -Different types of simulations and different types of configurations for &clm; require -different lists of files. The Carbon Nitrogen (cn) Biogeochemistry model for example -requires stream_fldfilename_ndep files, which are NOT required by -other bgc modes. Transient simulations also require transient datasets, and the names -of these datasets are sometimes different from the static versions (sometimes both are -required as in the dynamic PFT cases). - - -In the following table we list the different files used by CLM, they are listed -in order of importance, dependencies, and customizing. So the required files -are all near the top, and the files used only under different conditions are listed -later, and files with the fewest dependencies are near the top, as are the files -that are least likely to be customized. - - -Required Files for Different Configurations and Simulation Types - - - - - - - Filename - Config. type - Simulation type - Resol. Dependent? - Other Dependencies? - - - Notes - - - - - - fpftcon - ALL - ALL - No - No - - - Not usually customized, as describes plant function -type properties. &ptclm; copies the file for you so that you can customize it if you -like, see . - - - fsnowoptics - ALL - ALL - No - No - - - Not usually customized as describes global snow optical properties. - - - fsnowaging - ALL - ALL - No - No - - - Not usually customized as describes global snow aging properties. - - - fatmgrid - ALL - ALL - Yes - No - - - Creating, using mkgriddata -usually gives you the amount of customization -you need, as it just describes the grid and grid extents. - - - fatmlndfrc - ALL - ALL - Yes - land-mask - - - Describes the land-mask for points with active land, as well as the fraction -of each grid-cell covered by land. You might customize it to make sure the land-fraction -of your grid-cell matches the expected values for your site. But, usually you will just -use what mkgriddata gives you. - - - fsurdat - ALL - ALL - Yes - simulation-year - - - Describes percentages of different land-units, columns and -vegetation types within each grid-cell. To customize for a specific point -or region you may want to use custom input datasets to mksurfdata when -creating the file. mksurfdata also allows you to customize the PFT, -and soil types to it see . &ptclm; takes -advantage of this to create customized datasets as well, see the chapter on &ptclm; -at . - - - flanduse_timeseries - ALL - transient land-use land-cover change - Yes - Simulation year range, and representative concentration pathway (rcp) - - - See notes on fsurdat files. - - - frivinp_rtm - RTM only - ALL - No - No - - - We only provide a half-degree global river routing file. If you want -to model river flow for a smaller scale, or a basin regional scale, you would -need to create your own custom file to do that. Normally, we turn river-routing -OFF for regional or single point simulations. - - - finidat - ALL - RUN_TYPE="startup", CLM_FORCE_COLDSTART="off" - Yes - mask, maxpft, bgc, simulation-year, start-date - - - Used for starting the model from a spun-up state. -Create these files by running the model -for multiple years and saving the restart file from the end of a spin-up -simulation. - - - - stream_fldfilename_ndep - bgc=cn/cndv - Yes - No - simulation-year - - - -You may customize this file to get the Nitrogen deposition characteristics -of your site if available. This file will be interpolated while the model is -running from it's resolution to the resolution that &clm; is running at. - - - - - -
    -     - -     - -     - diff --git a/doc/UsersGuide/addxhtmlhead.pl b/doc/UsersGuide/addxhtmlhead.pl deleted file mode 100755 index d5f9615c58..0000000000 --- a/doc/UsersGuide/addxhtmlhead.pl +++ /dev/null @@ -1,78 +0,0 @@ -#!/usr/bin/env perl -# -use strict; -use Cwd; -use English; -use IO::File; -use Getopt::Long; -use IO::Handle; -#----------------------------------------------------------------------------------------------- - -# Get the directory name and filename of this script. If the command was -# issued using a relative or absolute path, that path is in $ProgDir. Otherwise assume -# the -# command was issued from the current working directory. - -(my $ProgName = $0) =~ s!(.*)/!!; # name of this script -my $ProgDir = $1; # name of directory containing this script -- may be a - # relative or absolute path, or null if the script - # is in - # the user's PATH -my $nm = "$ProgName::"; # name to use if script dies -my $scrdir; -if ($ProgDir) { - $scrdir = $ProgDir; -} else { - $scrdir = getcwd() -} - -sub usage { - my $msg = shift; - - print "ERROR:: $msg\n"; - die < -OPTIONS - NONE -EOF -} - -my %opts = ( ); - -GetOptions( -) or usage(); - -if ( $#ARGV != 0 ) { - &usage( "Wrong number of command line arguments" ); -} - -my $inputFile = $ARGV[0]; - -if ( ! -f $inputFile ) { - &usage( "Input file does NOT exist : $inputFile" ); -} - -my $fh = IO::File->new($inputFile, '<') or die "** $nm - can't open input file: -$inputFile\n"; - -# -# Add in XML XHTML headers -# -print <<"EOF"; - - - -EOF -while (my $line = <$fh>) { - if ( $line =~ /^$/ ) { - print "
    \n"; - } elsif ( $line =~ /^'."\n"; - } else { - print $line; - } -} -$fh->close(); diff --git a/doc/UsersGuide/appendix.xml b/doc/UsersGuide/appendix.xml deleted file mode 100644 index 058e67d577..0000000000 --- a/doc/UsersGuide/appendix.xml +++ /dev/null @@ -1,305 +0,0 @@ - -Editing Template Files Before Configure - -The last kind of customization that you can do for a case, before configure is run -is to edit the templates. The &clm; template is in -models/lnd/clm/bld/clm.cpl7.template, the &datm; template is -in models/atm/datm/bld/datm.cpl7.template, and the driver templates -are in the models/drv/bld directory and are named: -ccsm.template and cpl.template. When a case is -created they are also copied to the Tools/Templates directory -underneath your case. If you want to make changes that will impact all your cases, you -should edit the template files under the models directory, but -if you want to make a change ONLY for a particular case you should edit the template -under that specific case. - - - -Editing the template files is NOT for the faint of heart! We recommend this ONLY for -experts! It's difficult to do because the template is a script that actually creates -another script. So part of the script is echoing the script to be created and part of -it is a script that is run when "configure -case" is run. As a result any variables -in the part of the script that is being echoed have to be escaped like this: - -\$VARIABLE - -But, in other parts of the script that is run, you can NOT escape variables. So you -need to understand if you are in a part of the script that is echoing the script to -be created, or in the part of the script that is actually run. - - - -If you can customize your case using: compsets, env_*.xml variables, -or a user namelist, as outlined in you should do so. -The main reason to actually edit the template files, is if you are in a situation where -the template aborts when you try it run it when "configure -case" is run. The other -reason to edit the template is if you are &clm; developer and need to make adjustments -to the template because of code or script updates. An example of modifying the &datm; -template is in where sed is used to modify the path -for &CPLHIST; data. - - -Outline of the &clm; template - -The outline of the &clm; template is as follows: - -# set up options for clm configure and then run clm configure -$CODEROOT/lnd/clm*/bld/configure <options> -# set up options for clm build-namelist and then run clm build-namelist -$CODEROOT/lnd/clm*/bld/build-namelist <options> -# echo the $CASEBUILD/clm.buildnml.csh script out -cat >! $CASEBUILD/clm.buildnml.csh << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -# Remove temporary namelist files - -# echo the $CASEBUILD/clm.buildexe.csh script out -cat > $CASEBUILD/clm.buildexe.csh <<EOF2 -# NOTE: variables in this section must be escaped -EOF2 -# Remove temporary configure files - - - - - -Outline of the &datm; template - -The outline of the &datm; template is as follows: - -# Check $GRID to set the $DOMAINFILE and $DOMAINPATH - -# Check DATM_PRESAERO to set the prescribed aerosol option -# If &CLMUSRDAT; is set and $DOMAINFILE is NOT -- set it by &CLMUSRDAT; -# Ensure $DOMAINFILE is set or else abort - -#============================================================================== -# Create resolved prestage data script -#============================================================================== -cat >! $CASEBUILD/datm.buildnml.csh << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -# Major if blocks look at DATM_MODE: -# the if blocks setup streams and run Tools/build_streams to create stream files -#----- CLM_QIAN mode ---------------------------------------------------------- -else if ($DATM_MODE == "&CLMQIAN;" ) then -. - # Customize &CLMQIAN; options here - - # A.) Setup datm_atm_in namelist -cat >! $CASEBUILD/datm.buildnml.csh << EOF -cat >! datm_atm_in << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -EOF - - # B.) Setup options to build_streams -. -. -. -#----- CLM1PT mode ---------------------------------------------------------- -else if ($DATM_MODE == "CLM1PT" ) then -. - # Customize CLM1PT options here - - # A.) Setup datm_atm_in namelist -cat >! $CASEBUILD/datm.buildnml.csh << EOF -cat >! datm_atm_in << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -EOF - - # B.) Setup options to build_streams -. -. -. -. -#----- CPLHIST 3-hourly time-averaging mode ----------------------------------------------------------- -else if ($DATM_MODE == "&CPLHIST;" ) then -. - # Customize &CPLHIST; options here - - # A.) Setup datm_atm_in namelist -cat >! $CASEBUILD/datm.buildnml.csh << EOF -cat >! datm_atm_in << EOF1 -# NOTE: variables in this section must be escaped -EOF1 -EOF - - # B.) Setup options to build_streams -. -. -. -. - -#----- INVALID mode -----------------------------------------------------------else - echo "ERROR: unrecognized DATM_MODE = \$DATM_MODE " - exit -1 -endif - -#============================================================================== -# Create prescribed aero streams if appropriate -#============================================================================== -. -. -. -#============================================================================== -# Create remaining resolved namelist -#============================================================================== - -cat >! $CASEBUILD/datm.buildnml.csh << EOF -cat >! datm_in << EOF1 -# NOTE: variables in this section must be escaped -. -. -. -EOF1 - -EOF - -#============================================================================== -# Create script to build executable -#============================================================================== - -cat > $CASEBUILD/datm.buildexe.csh <<EOF -#! /bin/csh -f -# NOTE: variables in this section must be escaped -EOF - -#============================================================================== -# end of script -#============================================================================== - - - - - -Adding a new DATM_MODE to the &datm; template - - The steps to adding a new DATM_MODE - -Add a new "if" block to the &datm; template - -As you can see from above -there are major "if" blocks for the different DATM_MODE's. So adding a new -DATM_MODE means adding a new "if" block. The two major parts of each DATM_MODE -block are: - -Setup datm_atm_in namelist -Setup options to build_streams - - - - -In the "if" block create the <filename>datm_atm_in</filename> namelist - -See for some notes about the -&datm; namelist and streams files. That and the - -&datm; User's Guide should give you guidance on how to -setup the namelist for your case. - - - -In the "if" block create options to and call <command>build_streams</command> - -The next part of the "if" block in the &datm; template file to work with is the -call to build_streams. You may need to add additional options -to it. You may also need to call it multiple times for multiple streams. You will -also likely need to add a new source option to it with the "-s" option. For more -information on build_streams do the following. - -Getting help with <command>build_streams</command> for &datm; - -> scripts/ccsm_utils/Tools/build_streams -help - - -The output of the above command is: - - -&build_streams_help; - - - - - -Add new streams templates to the &datm; -<filename>datm.template.streams.xml</filename> file - -As part of modifying the behavior of build_streams you will also -have to edit the models/atm/datm7/bld/datm.template.streams.xml -file as well (or the local version in your -$CASENAME/Tools/Templates directory for a particular case). -The template is an XML file much like the output streams file, but there are attributes -to distinguish which fields will be used based on things like: RESOLUTION or datasource. -And there are filename indicators (starting with a "%") that get translated into various -things such as: - -%c = Case (from above -case command line option) -%do = Use domain file -%y = Year (through range given from begyear to endyear) -%ym = Year-Month (all 12 months through year range) -%6ym = Like %ym but 6 digit year (ie. %YYYYYY-MM). (can replace the 6 with any digit 1-9) - - - - -Add a new valid_value to the <filename>config_definition.xml</filename> file in -scripts. - -Adding a new DATM_MODE also requires adding a new valid_value to -scripts/ccsm_utils/Case.template/config_definition.xml. This -enables the scripts to recognize the new value as a valid option to DATM_MODE -in the &envconf; file. - - - - - - - -Building the Users-Guide Documentation for &clm; - -All of the documentation for &clm; can be built using GNU Makefiles that are -available in the appropriate directories. The Makefiles require the following -utilities: docbook2html, docbook2pdf, -protex, and latex2html. - - -To build the Users Guide for &clm; (requires docbook). - -> cd models/lnd/clm/doc/UsersGuide -> gmake - -Note, that when the Users-Guide is built it will get output from other &clm; -utilities that by nature abort, and hence stop the make from continuing. However, -this is expected so you should simply run gmake again until -it either completes or comes upon a legitimate issue. Here is what a sample -warning looks like when gmake is run. - -The following line will fail in the make as it calls die -- but that is expected -Check that the output config_help.tlog is good and redo your make -../../bld/configure -help >&` config_help.tlog -make: *** [config_help.tlog] Error 255 - -To build the Code Reference Guide for &clm; (requires protex and -latex2html). The make here uses a Filepath -file that points to the list of directories that you want protex -to run over. You should examine this file and make sure it is appropriate for what -you need to do, before running the make. - -> cd models/lnd/clm/doc/CodeReference -> gmake - -To build the table of tests for the &clm; test suite. The make here runs a UNIX -shell script to create a html table of the list of tests run on the different machines -from the &clm; test suite. - -> cd models/lnd/clm/test/system -> gmake - - - - - diff --git a/doc/UsersGuide/badpergro.jpg b/doc/UsersGuide/badpergro.jpg deleted file mode 100644 index 4a378cf52d..0000000000 Binary files a/doc/UsersGuide/badpergro.jpg and /dev/null differ diff --git a/doc/UsersGuide/clm_stylesheet.dsl b/doc/UsersGuide/clm_stylesheet.dsl deleted file mode 100644 index 7bc3ed0036..0000000000 --- a/doc/UsersGuide/clm_stylesheet.dsl +++ /dev/null @@ -1,154 +0,0 @@ - - -]> - - - - - - - - - -;;Default extension for filenames -(define %html-ext% ".html") -;;What font would you like for the body? -(define %body-font-family% - "Arial") - -(element emphasis -(if (equal? (normalize "bold") (attribute-string (normalize "role"))) - ($bold-seq$) - ($italic-seq$))) - -(element tgroup - (let* ((wrapper (parent (current-node))) - (frameattr (attribute-string (normalize "frame") wrapper)) - (pgwide (attribute-string (normalize "pgwide") wrapper)) - (footnotes (select-elements (descendants (current-node)) - (normalize "footnote"))) - (border (if (equal? frameattr (normalize "none")) - '(("BORDER" "0")) - '(("BORDER" "1")))) - (bgcolor '(("BGCOLOR" "#E0E0E0"))) - (width (if (equal? pgwide "1") - (list (list "WIDTH" ($table-width$))) - '())) - (head (select-elements (children (current-node)) (normalize "thead"))) - (body (select-elements (children (current-node)) (normalize "tbody"))) - (feet (select-elements (children (current-node)) (normalize "tfoot")))) - (make element gi: "TABLE" - attributes: (append - border - width - bgcolor - '(("CELLSPACING" "0")) - '(("CELLPADDING" "4")) - (if %cals-table-class% - (list (list "CLASS" %cals-table-class%)) - '())) - (process-node-list head) - (process-node-list body) - (process-node-list feet) - (make-table-endnotes)))) - - -;;Should verbatim items be 'shaded' with a table? -(define %shade-verbatim% - #t) - -;;Define shade-verbatim attributes -(define ($shade-verbatim-attr$) - (list - (list "BORDER" "0") - (list "BGCOLOR" "#E0E0E0") - (list "WIDTH" ($table-width$)))) - -;;Index -(define (generate-index) - ("1")) - -;;======================== -;;Title Pages for Books -;;======================= - -(define (book-titlepage-recto-elements) - (list (normalize "title") - (normalize "subtitle") - (normalize "authorgroup") - (normalize "author") - (normalize "date") - (normalize "releaseinfo") - (normalize "orgname") - (normalize "graphic") - (normalize "copyright") - (normalize "legalnotice"))) - - - - - - - - - -;;Index -(define ($insert.xref.page.number$) - ("yes")) - -;;Index -(define ($generate-index$) - ("1")) - -;;Tex Backend off -(define tex-backend - #f) - -;;What elements should have a LOT? -(define ($generate-book-lot-list$) - (list (normalize "example") - (normalize "table") - (normalize "figure") - (normalize "equation"))) - -;;======================== -;;Title Pages for Books -;;======================= - -(define (book-titlepage-recto-elements) - (list (normalize "title") - (normalize "subtitle") - (normalize "authorgroup") - (normalize "author") - (normalize "date") - (normalize "orgname") - (normalize "graphic") - (normalize "copyright") - (normalize "legalnotice") - (normalize "releaseinfo"))) - -(define %show-ulinks% - ;; Display URLs after ULinks? - #t) - -(define %indent-screen-lines% - ;; Indent lines in a 'Screen'? - " ") - - - - - - - - diff --git a/doc/UsersGuide/clm_ug.xml b/doc/UsersGuide/clm_ug.xml deleted file mode 100644 index 68aa69b1d6..0000000000 --- a/doc/UsersGuide/clm_ug.xml +++ /dev/null @@ -1,191 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - build-namelist"> - configure"> - NCAR"> - CCSM"> - CCSM4.0"> - CESM"> - CESM1.0"> - CESM1.0.1"> - CESM1.0.2"> - CESM1.0.3"> - - PTCLM"> - PTCLM1"> - PTCLM1.110504"> - CLM"> - CLMCN"> - CLMSP"> - CLMU"> - CLM3.0"> - CLM3.5"> - CLM4"> - CLM4.0.00"> - - - - - - - - DATM"> - models/lnd/clm/doc/KnownBugs"> - NetCDF"> - FORTRAN"> - FORTRAN-90"> - MPI"> - PIO"> - OpenMP"> - NCL"> - Perl"> - XML"> - xmlchange"> - 2"> - - - - env_run.xml"> - env_build.xml"> - env_conf.xml"> - user_nl_clm"> - - - PTS_MODE"> - CSMDATA"> - CLM_FORCE_COLDSTART"> - CLM_CONFIG_OPTS"> - CLM_BLDNML_OPTS"> - CLM_NML_USE_CASE"> - CLM_NAMELIST_OPTS"> - CLM_PT1_NAME"> - CLM_QIAN"> - CPLHIST3HrWx"> - CLM_USRDAT_NAME"> - CLM_CO2_TYPE"> - DIN_LOC_ROOT"> - - - CLM_QIAN"> - - - - %ISOamsa; - ]]> - - - - %ISOgrk1; - ]]> - -]> - - - - -&cesm; Research Tools: &clmrel; User's Guide Documentation - - - CESM - CLM - community earth system model - climate - climate model - earth system model - land surface model - hydrology - biogeochemistry - urban model - documentation - - - - - - Erik - Kluzek - - NCAR - - - - - - - -The user's guide to &clmrel; which is the active land surface model component of &cesmrel;. -The purpose of this guide is to instruct both the novice and experienced user, as well as -&clm; developers in the use of &clm4; for land-surface climate modeling. - - - -$URL$ - -&build_date; - - - - - -Dedicated to the Land Model Working Group, winners of the 2008 &ccsm; Distinguished Achievement Award. -May you continue to collaborate together well, and continue to drive -the science of land surface modeling forward with your diligent and persistent efforts. - - - - -&preface; -&custom; -&tools; -&adding_files; -&special_cases; -&single_point; -&ptclmdoc; -&trouble; -&testing; -&appendix; - - diff --git a/doc/UsersGuide/co2_streams.txt b/doc/UsersGuide/co2_streams.txt deleted file mode 100644 index 4d38c6d06e..0000000000 --- a/doc/UsersGuide/co2_streams.txt +++ /dev/null @@ -1,50 +0,0 @@ - - - This is a streams file to pass historical CO2 from datm8 to the other - surface models. It reads in a historical dataset derived from data used - by CAM. The getco2_historical.ncl script in components/clm/tools/ncl_scripts - was used to convert the CAM file to a streams compatible format (adding domain - information and making CO2 have latitude/longitude even if only for a single - point. - - - - Input stream description file for historical CO2 reconstruction data - - 04 March 2010: Converted to form that can be used by datm8 by Erik Kluzek - 18 December 2009: Prepared by B. Eaton using data provided by - Jean-Francois Lamarque. All variables except f11 are directly from - PRE2005_MIDYR_CONC.DAT. Data from 1765 to 2007 with 2006/2007 just - a repeat of 2005. - - - CLMNCEP - - - - time time - lonc lon - latc lat - area area - mask mask - - - /fis/cgd/cseg/csm/inputdata/atm/datm7/CO2 - - - fco2_datm_1765-2007_c100614.nc - - - - - CO2 co2diag - - - /fis/cgd/cseg/csm/inputdata/atm/datm7/CO2 - - - fco2_datm_1765-2007_c100614.nc - - - - diff --git a/doc/UsersGuide/custom.xml b/doc/UsersGuide/custom.xml deleted file mode 100644 index d6a60a28f7..0000000000 --- a/doc/UsersGuide/custom.xml +++ /dev/null @@ -1,1615 +0,0 @@ - - - - - - - component set - compset - "I" compsets - "B" compsets - "E" compsets - "F" compsets - &CLMCONFIG; - &CLMNAMELIST; - &CLMFORCECOLD; - &CLMUSECASE; - &CLM1PT; - &CLMUSRDAT; - &CLMCO2; - - -How to customize the configuration for a case with &clm; - - -The -&cesm; User's Guide gives you the details on how to setup, &configure;, build, and run -a case. That is the document to give you the details on using the &cesm; scripts. The purpose -of this document is to give you the details when using &cesm; with &clm; on how to customize -and use advanced features in &clm;. You should be familiar with the &cesm; User's Guide and -how to setup cases with &cesmrel; before referring to this document. - - -In this chapter we deal with three different ways of customizing a case: Choosing a compset, -Customizing Configuration options, and customizing the &clm; Namelist. There are many different -compsets that use &clm; and many are setup to enable special features of &clm; from the start. So -the first thing you want to be familiar with are the different options in the compsets. The -next section shows the different options for customizing the configuration options for -&clm;. -Here we introduce the &clm; &configure; and &buildnml; scripts and how using the options in -&envconf; you can customize the configuration and the initial -namelist. The final section tells you about the &clm; namelist and how you can customize the -namelist once you have run "&configure; -case" and have an initial namelist in -BuildConf/clm.buildnml.csh. You can also -use &envconf; options to change your namelist as well, before "&configure; -case" is -run. - - - -Choosing a compset using &clm; - - -When setting up a new case one of the first choices to make is which "component -set" (or compset) to use. The -compset refers to which component models are used as well as specific settings for them. We label the different -types of compsets with a different letter of the alphabet from "A" (for all data model) to "X" (for all dead model). -The compsets of interest when working with &clm; are the "I" compsets (which contain -&clm; with a data atmosphere model -and a stub ocean, and stub sea-ice models), "E" and "F" compsets (which contain &clm; -with the active atmosphere model (CAM), -prescribed sea-ice model, and a data ocean model), and "B" compsets which have all active components. Below we -go into details on the "I" compsets which emphasize &clm; as the only active model, and just mention the two other categories. - - -When working with &clm; you usually want to start with a relevant "I" compset before moving to the more -complex cases that involve other active model components. The "I" compsets can exercise -&clm; in a way that -is similar to the coupled modes, but with much lower computational cost and faster turnaround times. - - -Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets) -&compsets_list; - - - - Compsets coupled to active atmosphere with data ocean - - CAM compsets are compsets that start with "E" or "F" in the name. They are - described more fully in the scripts documentation or the CAM documentation. "E" compsets have -a slab ocean model while "F" compsets have a data ocean model. - - - - -Fully coupled compsets with fully active ocean, sea-ice, and atmosphere - - Fully coupled compsets are compsets that start with "B" in the name. They are - described more fully in the scripts documentation. - - - - -Conclusion to choosing a compset - -We've introduced the basic type of compsets that use &clm; and given some further details -for the "standalone &clm;" (or "I" compsets). The - -config_compsets.xml lists all of the compsets and gives a full description -of each of them. In the next section we look into customizing the &configure; time options -for compsets using &clm;. - - - - - - - -Customizing the &clm; configuration - -The "Creating a Case" section of the -&cesm1; Scripts -User's-Guide -gives instructions on creating a case. What is of interest here is how to customize your -use of &clm; -for the case that you created. In this section we discuss how to customize your case before the first -step -- the "&configure; -case" step is done. In the next section we will discuss how to customize your -&clm; namelist after "&configure; -case" has already been done. - - -For &clm; when "&configure; -case" is called there are two steps that take place: - - -The &clm; "&configure;" script is called to setup the build-time -configuration for &clm; (more information on &configure; is given in -). -The &clm; "&buildnml;" script is called to generate the initial -run-time namelist for &clm; (more information on &buildnml; is given below in -. - - -When customizing your case at the &configure; step you are able to modify the process by effecting either one -or both of these steps. The &clm; "&configure;" and "&buildnml;" scripts are both available in the "models/lnd/clm/bld" -directory in the distribution. Both of these scripts have a "-help" option that is useful to examine to see what -types of options you can give either of them. - - -There are five different types of customization for the configuration that we will -discuss: &cesm1; &clm; configuration items, Configure time User Namelist, -other noteworthy &cesm; configuration items, the &clm; &configure; script options, and -the &clm; &buildnml; script options. - - -Information on all of the script, configuration, build and run items is found under -scripts/ccsm_utils/Case.template -in the -config_definition.xml - file. - - - -&clm; Script configuration items - -Below we list each of the &cesm; configuration items that are specific to &clm;. All -of these are available in your: &envconf; file. - - - - &CLMCONFIG; - &CLMBLDNML; - &CLMNAMELIST; - &CLMFORCECOLD; - &CLMUSECASE; - &CLM1PT; - &CLMUSRDAT; - &CLMCO2; - -For the precedence of the different options to &buildnml; see the section on -precedence below. - - -The first item &CLMCONFIG; has to do with customizing the &clm; configuration options for your case, the rest -all have to do with generating the initial namelist. - - - -&CLMCONFIG; - - -The option &CLMCONFIG; is all about passing command line arguments to the &clm; &configure; script. It is important -to note that some compsets, may already put a value into the &CLMCONFIG; variable. You can still add more -options to your &CLMCONFIG; but make sure you add to what is already there rather than replacing it. Hence, -we recommend using the "-append" option to the xmlchange script. In - -below we will go into more details on options that can be customized in the &clm; "&configure;" script. It's -also important to note that the &clm; template may already invoke certain &clm; &configure; options and as such those -command line options are NOT going to be available to change at this step (nor would you want to change them). -The options to &configure; are given with the "-help" option which is given in -. - - - - - -&CLMUSECASE; - - -&CLMUSECASE; is used to set a particular set of conditions that set multiple namelist items, all centering around -a particular usage of the model. -To list the valid options do the following: - - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -use_case list - - -The output of the above command is: - - -&usecases_list; - - - -See the section for the precedence of this -option relative to the others. - - - - - - -&CLMBLDNML; - - -The option &CLMBLDNML; is for passing options to the &clm; "&buildnml;" script. As with the "&configure;" -script the &clm; template may already invoke certain options and as such those options will NOT be available to be -set here. The best way to see what options can be sent to the "&buildnml;" script is to do - - -> cd models/lnd/clm/bld -> ./&buildnml; -help - - -Here is the output from the above. - - -./&buildnml_help; - - -The &clm; template already sets the resolution and mask as well as the &configure; file, -the start-type, the co2_ppmv, rtm_tstep, and rtm_res, and defines an input -namelist and namelist input file, and it normally sets either "-ignore_ic_year" or -"-ignore_ic_date". Also many -of the options are designed solely for &clm; stand-alone testing and hence should NOT -be used (any of the options starting -with a "datm_" or "drv_" prefix. Hence there are then only five different options that could be set: - - - --lnd_res --sim_year --rcp --clm_demand --verbose - - - -"-lnd_res" is used to run &clm; in fine-mesh mode at a higher resolution than the atmospheric model. This can -be useful to get higher resolution from the land model, but saving computer time -by running the more expensive atmospheric model at a lower resolution. -To get a list of valid resolutions to run at do the following: - - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -lnd_res list - - - -The fine-mesh mode is considered experimental, and you may run into problems when you use -it. Another option is to use the CESM level "tri-grid" capability to run the land model -on a different grid than the atmospheric model. Read the CESM User's-Guide to learn how -to do this. - - - - - -See the section for the precedence of this -option relative to the others. - - - - -"-clm_demand" asks the &buildnml; step to require that the list of variables -entered be set. Typically, this is used to require that optional filenames be used and ensure -they are set before continuing. For example, you may want to require that -flanduse_timeseries be set to get dynamically changing vegetation types. To do this -you would do the following. - -> ./xmlchange -file env_conf.xml -id &CLMBLDNML; -val "-clm_demand flanduse_timeseries" - -To see a list of valid variables that you could set do this: - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -clm_demand list - - - - -Using a 20th-Century transient compset or the 20thC_transient use-case -using &CLMUSECASE; would set this as well, but would also use -dynamic nitrogen and aerosol deposition files, so using -clm_demand would be a way -to get just dynamic vegetation types and NOT the other files as well. - - - -"-sim_year" is used to set the simulation year you want the data-sets to simulate conditions for in the input -datasets. The simulation "year" can also be a range of years in order to do simulations -with changes in the dataset values as the simulation progresses. To list the valid -options do the following: - - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -sim_year list - - -"-rcp" is used to set the representative concentration pathway for the future scenarios -you want the data-sets to simulate conditions for, in the input -datasets. To list the valid options do the following: - - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -rcp list - - - - - -&CLMNAMELIST; - - -The option &CLMNAMELIST; is for passing namelist items into the "clm_inparm" namelist. -Any items that are set in &CLMNAMELIST; will be set in your namelist after "&configure; --case" is done. - - - -For character namelist items you need to use "&apos;" as quotes for strings so that the -scripts don't get confused with other quotes they use. - - - -Example, you want to set hist_dov2xy to .false. -so that you get vector output to your history files. To do so edit -&envconf; and add a setting for hist_dov2xy. -So do the following: - -> ./xmlchange -file env_conf.xml -id &CLMNAMELIST; -val hist_dov2xy=.false. - - - -Example, you want to set hist_fincl1 to add the variable 'HK' -to your history files. To do so edit -&envconf; and add a setting for hist_fincl1. -So do the following: - -> ./xmlchange -file env_conf.xml -id &CLMNAMELIST; -val "hist_fincl1=&apos;HK&apos;" - -For a list of the history fields available see -&clm; History Fields. - - - -See the section for the precedence of this -option relative to the others. - - - - - - -&CLMCO2; - - -&CLMCO2; sets the type of input &CO2; for either "constant", "diagnostic" or prognostic". -If "constant" the value from CCSM_CO2_PPMV will be used. If "diagnostic" -or "prognostic" the values MUST be sent from the atmosphere model. For more information on how -to send &CO2; from the data atmosphere model see . - - - - - -&CLMFORCECOLD; - - -&CLMFORCECOLD; when set to on, requires that -your simulation do a cold start from arbitrary initial conditions. If this is NOT set, it -will use an initial condition file if it can find an appropriate one, and otherwise do a cold -start. &CLMFORCECOLD; is a good way to ensure that you are doing a cold -start if that is what you want to do. - - - - - -&CLM1PT; - - -&CLM1PT; is used ONLY for a pt1_pt1 -resolution simulation to set the name of the single-point files to use. -To see a list of the valid resolutions do this: - -> cd models/lnd/clm/doc -> ../bld/&buildnml; -res list - - - -The output of the above command is: - - -&res_list; - - -the valid resolutions that can be used with &CLM1PT; are the ones that -have city or nation names such as: 5x5_amazon, 1x1_vancouverCAN 1x1_mexicocityMEX, or -1x1_brazil. The "1x1_" prefix means the file is for a single-point, while "5x5_" prefix means -it's for a region of five points in latitude by five points in longitude. Both regional -and single point datasets can be used for &CLM1PT;. If you create your own datasets -you can also use &CLM1PT; along with &CLMUSRDAT; (documented below), setting &CLM1PT; to -the value in &CLMUSRDAT; so that your datasets are used rather than the standard ones.o - - - - - -&CLMUSRDAT; - - -&CLMUSRDAT; provides a way to enter your own datasets into the initial -namelist setup at "&configure; -case". The files you create must be named with -specific naming conventions outlined in: . -To see what the expected names of the files are, use the -queryDefaultNamelist.pl to see -what the names will need to be. For example if your &CLMUSRDAT; will -be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, -the following will list what your filenames should be: - -> cd models/lnd/clm/bld -> queryDefaultNamelist.pl -usrname "1x1_boulderCO" -options \ -mask=navy,sim_year=1850,sim_year_range="constant" -csmdata $CSMDATA - -An example of using &CLMUSRDAT; for a simulation is given in -. - - - -See the section for the precedence of this -option relative to the others. - - - - - - - - - -Configure time User Namelist - -&CLMNAMELIST; as described above allows you to set any -extra namelist items you would like to appear in your namelist after first &configure;d. -However, it only allows you a single line to enter namelist items, and strings must -be quoted with &apos; which is a bit awkward. If you have a long list of namelist -items you want to set (such as a long list of history fields) a convenient way to do it -is to create a &usernlclm; that contains just the list of namelist -variables you want to add to your initial namelist. The &usernlclm; -will only be used when &configure; is run, so if you change it after &configure; -- it won't -change anything. The file needs to be in valid FORTRAN namelist format, and the &configure; -step will abort if there are syntax errors. It merely needs to be named correctly -&usernlclm; and placed in your case directory (where your other -env_*.xml files are). The namelist name actually doesn't have to be -valid, but all the variable names must be. Here's an example &usernlclm; -namelist that sets a bunch of history file related items, to create output history files -monthly, daily, every six and 1 hours. - -Example &usernlclm; namelist file - -&clmexp - hist_fincl2 = 'TG','TBOT','FIRE','FIRA','FLDS','FSDS', - 'FSR','FSA','FGEV','FSH','FGR','TSOI', - 'ERRSOI','BUILDHEAT','SABV','SABG', - 'FSDSVD','FSDSND','FSDSVI','FSDSNI', - 'FSRVD','FSRND','FSRVI','FSRNI', - 'TSA','FCTR','FCEV','QBOT','RH2M','H2OSOI', - 'H2OSNO','SOILLIQ','SOILICE', - 'TSA_U', 'TSA_R', - 'TREFMNAV_U', 'TREFMNAV_R', - 'TREFMXAV_U', 'TREFMXAV_R', - 'TG_U', 'TG_R', - 'RH2M_U', 'RH2M_R', - 'QRUNOFF_U', 'QRUNOFF_R', - 'SoilAlpha_U', - 'Qanth', 'SWup', 'LWup', 'URBAN_AC', 'URBAN_HEAT' - hist_fincl3 = 'TG:I', 'FSA:I', 'SWup:I', 'URBAN_AC:I', 'URBAN_HEAT:I', - 'TG_U:I', 'TG_R:I', - hist_fincl4 = 'TG', 'FSA', 'SWup', 'URBAN_AC', 'URBAN_HEAT' - hist_mfilt = 1, 30, 28, 24 - hist_nhtfrq = 0, -24, -6, -1 -/ - - - - -See the section for the precedence of this -option relative to the others. - - - - -In the above example we use an invalid namelist name &clmexp -- but it works anyway -because the &clm; &buildnml; knows the namelist that specific variable names belong to, and -it puts them there. - - -Obviously, all of this would be difficult to put in the &CLMNAMELIST; -variable, especially having to put &apos; around all the character strings. For -more information on the namelist variables being set here and what they mean, see -the section on &clm; namelists below, as well as the namelist definition that gives -details on each variable. - - - - -Precedence of Options - -Note: The precedence for setting the values of namelist variables with the -different env_conf options is (highest to lowest): - -Namelist values set by specific command-line options, like, -d, -sim_year -(i.e. &CLMBLDNML; env_conf variable) -Values set on the command-line using the -namelist option, -(i.e. &CLMNAMELIST; env_conf variable) -Values read from the file specified by -infile, -(i.e. &usernlclm; file) -Datasets from the -clm_usr_name option, -(i.e. &CLMUSRDAT; env_conf variable) -Values set from a use-case scenario, e.g., -use_case -(i.e. &CLMUSECASE;env_conf variable) -Values from the namelist defaults file. - -Thus a setting in &CLMBLDNML; will override a setting for the same thing given in -a use case with &CLMUSECASE;. Likewise, a setting in &CLMNAMELIST; will override a -setting in &usernlclm;. - - - - -Setting Your Initial Conditions File - -Especially with &clmcn; starting from initial conditions is very important. Even -with &clmsp; it takes many simulation years to get the model fully spunup. There -are a couple different ways to provide an initial condition file. - - - - - - - - -Your initial condition file MUST agree with the surface dataset you are using -to run the simulation. If the two files do NOT agree you will get a -run-time about a mis-match in PFT weights, or in the number of PFT's or -columns. To get around this you'll need to use -to interpolate your initial condition dataset. - - - - - -Doing a hybrid simulation to provide initial conditions - -The first option is to setup a hybrid simulation and give a -RUN_REFCASE and RUN_REFDATE to specify the -reference case simulation name to use. -When you setup most cases, at the standard resolutions of "f09" or "f19" it -will already do this for you. For example, if you run an "I2000CN" compset -at "f09_g16" resolution the following settings will already be done for you. - -./xmlchange -file env_conf.xml -id RUN_TYPE -val hybrid -./xmlchange -file env_conf.xml -id RUN_REFCASE -val I2000CN_f09_g16_c100503 -./xmlchange -file env_conf.xml -id RUN_REFDATE -val 0001-01-01 -./xmlchange -file env_conf.xml -id GET_REFCASE -val TRUE - -Setting the GET_REFCASE option to TRUE means it -will copy the files from the: -$DIN_LOC_ROOT/ccsm4_init/I2000CN_f09_g16_c100503/0001-01-01 -directory. Note, that the RUN_REFCASE and -RUN_REFDATE variables are expanded to get the directory name -above. If you do NOT set GET_REFCASE to TRUE then -you will need to have placed the file in your run directory yourself. In either -case, the file is expected to be named: -$RUN_REFCASE.clm2.r.$RUN_REFDATE-00000.nc with the variables -expanded of course. - - - - -Doing a branch simulation to provide initial conditions - -The setup for running a branch simulation is essentially the same as for a hybrid. -With the exception of setting RUN_TYPE to branch -rather than hybrid. A branch simulation runs the case essentially -as restarting from it's place before to exactly reproduce it. While a hybrid simulation -allows you to change namelist items, and use a different code base that may have -fewer fields on it than a full restart file. The GET_REFCASE works -similarily for a branch case as for a hybrid. - - - - -Providing a finidat file in your &usernlclm; file - -Setting up a branch or hybrid simulation requires the initial condition file -to follow a standard naming convention, and a standard input directory if you -use the GET_REFCASE option. If you want to name your file willy -nilly and place it anywhere, you can set it in your &usernlclm; file as in this -example. - -&clm_inparm - finidat = '/glade/home/$USER/myinitdata/clmi_I1850CN_f09_g16_0182-01-01.c120329.nc' -/ - -Note, if you provide an initial condition file -- you can NOT set &CLMFORCECOLD; to -TRUE. - - - - -Adding a finidat file to the XML database - -Like other datasets, if you want to use a given initial condition file to -be used for all (or most of) your cases you'll want to put it in the XML -database so it will be used by default. The initial condition files, are -resolution dependent, and dependent on the number of PFT's and other variables -such as GLC_NEC or if irrigation is on or off. -See for more information on this. - - - - - -Other noteworthy configuration items - -For running "I" cases there are several other noteworthy configuration items that -you may want to work with. Most of these involve settings for the &datm;, but one -CCSM_CO2_PPMV applies to all models. If you are running an B, E, -or F case that doesn't use the &datm; obviously the DATM_* settings will not be used. -All of the settings below are in your &envconf; file - - CCSM_CO2_PPMV - CCSM_VOC - DATM_MODE - DATM_PRESAERO - DATM_CLMNCEP_YR_ALIGN - DATM_CLMNCEP_YR_START - DATM_CLMNCEP_YR_END - DATM_CPL_CASE - DATM_CPL_YR_ALIGN - DATM_CPL_YR_START - DATM_CPL_YR_END - - - - - -CCSM_CO2_PPMV - -CCSM_CO2_PPMV sets the mixing ratio of &CO2; in -parts per million by volume for ALL &cesm; components to use. Note that most compsets -already set this value to something reasonable. Also note that some compsets may -tell the atmosphere model to override this value with either historic or ramped -values. If the CCSM_BGC variable is set to something other than "none" -the atmosphere model will determine &CO2;, and &clm; will listen -and use what the atmosphere sends it. On the &clm; side the namelist item -co2_type tells &clm; to use the value sent from the atmosphere rather than -a value set on it's own namelist. - - - - -CCSM_VOC - -CCSM_VOC enables passing of the Volatile Organic Compounds (VOC) from -&clm; to the atmospheric model. This of course is only important if the atmosphere -model is a fully active model that can use these fields in it's chemistry calculations. - - - - -DATM_MODE - -DATM_MODE sets the mode that the &datm; model should run in this determines -how data is handled as well as what the source of the data will be. Many of the modes -are setup specifically to be used for ocean and/or sea-ice modeling. The modes -that are designed for use by &clm; are: - -&CLMQIAN; -CLM1PT -&CPLHIST; - - - -&CLMQIAN; is for the standard mode of using global atmospheric data -that was developed by Qian et. al. for &clm; using NCEP data from 1948 to 2004. -See for more information on -the &datm; settings for &CLMQIAN; mode. -CLM1PT is for the special cases where we have single-point tower -data for particular sites. Right now we only have data for three urban locations: -MexicoCity Mexico, Vancouver Canada, and the urban-c alpha site. -See for more information on -the &datm; settings for CLM1PT mode. -&CPLHIST; is for running with atmospheric forcing from a previous &cesm; simulation. -See for more information on -the &datm; settings for &CPLHIST; mode. - - -There is a problem with running simulations for the CLM1PT mode -that are greater than one data cycle, where the atm forcing will be held constant. -This will result in useless -results as all atmosphere forcing fields will be held constant at the last value. -See bug 1377 in the &KnownBugs; file on how to fix this problem. - - - - - - - -DATM_PRESAERO - -DATM_PRESAERO sets the prescribed aerosol mode for the data atmosphere -model. The list of valid options include: - -clim_1850 = constant year 1850 conditions -clim_2000 = constant year 2000 conditions -trans_1850-2000 = transient 1850 to year 2000 conditions -rcp2.6 = transient conditions for the rcp=2.6 -W/m2 future -scenario -rcp4.5 = transient conditions for the rcp=4.5 -W/m2 future -scenario -rcp6.0 = transient conditions for the rcp=6.0 -W/m2 future -scenario -rcp8.5 = transient conditions for the rcp=8.5 -W/m2 future -scenario -pt1_pt1 = read in single-point or regional datasets - - - - - -DATM_CLMNCEP_YR_START - -DATM_CLMNCEP_YR_START sets the beginning year to cycle the atmospheric -data over for the &CLMQIAN; mode. - - - - -DATM_CLMNCEP_YR_END - -DATM_CLMNCEP_YR_END sets the ending year to cycle the atmospheric -data over for the &CLMQIAN; mode. - - - - -DATM_CLMNCEP_YR_ALIGN - -DATM_CLMNCEP_YR_START and DATM_CLMNCEP_YR_END determine -the range of years to cycle the atmospheric data over, and DATM_CLMNCEP_YR_ALIGN -determines which year in that range of years the simulation will start with. - - - - -DATM_CPL_CASE - -DATM_CPL_CASE sets the casename to use for the &CPLHIST; mode. - - - - -DATM_CPL_YR_START - -DATM_CPL_YR_START sets the beginning year to cycle the atmospheric -data over for the &CPLHIST; mode. - - - - -DATM_CPL_YR_END - -DATM_CPL_YR_END sets the ending year to cycle the atmospheric -data over for the &CPLHIST; mode. - - - - -DATM_CPL_YR_ALIGN - -DATM_CPL_YR_START and DATM_CPL_YR_END determine -the range of years to cycle the atmospheric data over, and DATM_CPL_YR_ALIGN -determines which year in that range of years the simulation will start with. - - - - - - - - -Downloading DATM Forcing Data - -In Chapter One of the -&cesm; User's Guide -there is a section on "Downloading input data". The normal process of setting up -cases will use the "scripts/ccsm_utils/Tools/check_input_data" script to retrieve -data from the &cesm; subversion inputdata repository. However, the DATM forcing data -is unique -- because it is large compared to the rest of the input data (56 Gbytes). Most of the -data is stored in the directory set by the &envrun; variable -DIN_LOC_ROOT_CSMDATA. The &CLMQIAN; forcing data is in a (possibly) -separate directory using the &envrun; variable DIN_LOC_ROOT_CLMQIAN. -In most cases this directory will be in the directory: -atm/datm7/atm_forcing.datm7.Qian.T62.c080727 under -DIN_LOC_ROOT_CSMDATA. On bluefire there is a separate path for -the &CLMQIAN; forcing data. We have the full set of data available on a few of -the machines we use: bluefire, jaguarpf, and edinburgh. As of October, 18th, 2011 -we've uploaded the entire set of forcing data into the input data repository so -now it can be treated like other input datasets and the check_input_data script -can retreive it for you. Previously only two years of data was available. -You can also download the data from the -Earth System Grid for other machines. See the -Model Forcing Data -link under the -&clm; Documentation Page - - - - -Customizing via the template files - -The final thing that the user may wish to do before &configure; is run is to edit -the template files which determine the configuration and initial namelist. The -variables in &envconf; typically mean you will NOT have -to edit the template. But, there are rare instances where it is useful to do so. - gives the details on how to do this. -The template files are copied to your case directory and are available under -Tools/Templates. -The list of template files you might wish to edit are: - - clm.cpl7.template - datm.cpl7.template - cpl.template - - - - - - -More information on the &clm; &configure; script - -The &configure; script defines the details of a clm configuration and summarizes it into a -config_cache.xml file. The config_cache.xml -will be placed in your case directory under Buildconf/clmconf. -The config_definition.xml -in models/lnd/clm/bld/config_files -gives a definition of each &clm; configuration item, it is viewable in a web-browser. -Many of these items are things that you would NOT change, but looking through the -list gives you the valid options, and a good description of each. Below we repeat -the config_definition.xml files contents: - - - - - -Help on &clm; &configure; - -Coupling this with looking at the options to &configure; with -"-help" as below will enable you to understand how to set the different options. - -> cd models/lnd/clm/bld -> &configure; -help - - - -The output to the above command is as follows: - - -&config_help; - - -We've given details on how to use the options in &envconf; to -interact with the &clm; "&configure;" and "&buildnml;" scripts, as well as giving a good -understanding of how these scripts work and the options to them. In the next section we -give further details on the &clm; namelist. You could customize the namelist for these -options after "&configure; -case" is run. - - - - - - - - - - Customizing the &clm; namelist - -Once a case is &configure;d, we can then customize the case further, by editing the -run-time namelist for &clm;. First let's list the definition of each namelist -item and their valid values, and then we'll list the default values for them. -Next for some of the most used or tricky namelist items we'll give examples of their -use, and give you example namelists that highlight these features. - - - - -Definition of Namelist items and their default values - -Here we point to you where you can find the definition of each namelist item and -separately the default values for them. The default values may change depending on -the resolution, land-mask, simulation-year and other attributes. Both of these -files are viewable in your web browser. Below we provide the link for them, and -then expand each in turn. - - - -Definition of each Namelist Item - - -Default values of each -&clm; Namelist Item - - - -One set of the namelist items allows you to add fields to the output history files: -hist_fincl1, hist_fincl2, -hist_fincl3, hist_fincl4, -hist_fincl5, and hist_fincl6. The link -&clm; History Fields -documents all of the history fields available and gives the long-name and units -for each. - - - - - -&hisfldtbl; - - - - - - - -Examples of using different namelist features - -Below we will give examples of user namelists that activate different commonly used -namelist features. We will discuss the namelist features in different examples and then -show a user namelist that includes an example of the use of these features. First we -will show the default namelist that doesn't activate any user options. - - - -The default namelist - -Here we give the default namelist as it would be created for a I1850CN compset at 0.9x1.25 -resolution with a gx1v6 land-mask. To edit the namelist you would edit the -BuildConf/clm.buildnml.csh under your case (or before &configure; -include a user namelist with just the items you want to change). For simplicity we will -just show the namelist and NOT the entire file. In the sections below, for simplicity - we will just show the user namelist (&usernlclm;) that will add (or modify existing) -namelist items to the namelist. Again, just adding the &usernlclm; file to your case -directory, before "&configure; -case" is invoked will cause the given namelist items to -appear in your &clm; namelist. - -Default &clm; Namelist - -&clm_inparm - co2_ppmv = 284.7 - co2_type = 'constant' - create_crop_landunit = .false. - dtime = 1800 - fatmgrid = '$DIN_LOC_ROOT/lnd/clm2/griddata/griddata_0.9x1.25_070212.nc' - fatmlndfrc = -'$DIN_LOC_ROOT/lnd/clm2/griddata/fracdata_0.9x1.25_gx1v6_c090317.nc' - finidat = 'I1850CN_f09_g16_c100503.clm2.r.0001-01-01-00000.nc' - fpftcon = '$DIN_LOC_ROOT/lnd/clm2/pftdata/pft-physiology.c110425.nc' - frivinp_rtm = '$DIN_LOC_ROOT/lnd/clm2/rtmdata/rdirc_0.5x0.5_simyr2000_slpmxvl_c120717.nc' - fsnowaging = -'$DIN_LOC_ROOT/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc' - fsnowoptics = -'$DIN_LOC_ROOT/lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc' - fsurdat = -'$DIN_LOC_ROOT/lnd/clm2/surfdata/surfdata_0.9x1.25_simyr1850_c091006.nc' - ice_runoff = .true. - outnc_large_files = .true. - rtm_nsteps = 6 - urban_hac = 'ON_WASTEHEAT' - urban_traffic = .false. -/ -&ndepdyn_nml - stream_fldfilename_ndep = -'$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_hist_simyr1849-2006_1.9x2.5_c100428.nc' - stream_year_first_ndep = 1850 - stream_year_last_ndep = 1850 -/ - - -Note that the namelist introduces some of the history namelist options that will be -talked about in further detail below (hist_mfilt and -hist_nhtfrq). - - - - -Adding/removing fields on your primary history file - -The primary history files are output monthly, and contain an extensive list of -fieldnames, but the list of fieldnames can be added to using hist_fincl1 -or removed from by adding fieldnames to hist_fexcl1. -A sample user namelist &usernlclm; adding few new fields -(cosine of solar zenith angle, and solar declination) and excluding a few -standard fields is (ground temperature, vegetation temperature, soil temperature and soil water).: - -Example &usernlclm; namelist adding and removing fields on primary history file - -&clm_inparm - hist_fincl1 = 'COSZEN', 'DECL' - hist_fexcl1 = 'TG', 'TV', 'TSOI', 'H2OSOI' -/ - - - - - - -Adding auxiliary history files and changing output -frequency - -The hist_fincl2 through hist_fincl6 set of -namelist variables add given history fieldnames to auxiliary history file "streams", and -hist_fexcl2 through hist_fexcl6 set of -namelist variables remove given history fieldnames from history file auxiliary "streams". -A history "stream" is a set of history files that are produced at a given frequency. -By default there is only one stream of monthly data files. To add more streams you -add history fieldnames to hist_fincl2 through -hist_fincl6. The output frequency and the way averaging is done -can be different for each history file stream. By default the primary history files -are monthly and any others are daily. You can have up to six active history streams, but you need -to activate them in order. So if you activate stream "6" by setting -hist_fincl6, but if any of hist_fincl2 through -hist_fincl5 are unset, only the history streams up to the first blank one -will be activated. - - -The frequency of the history file streams is given by the namelist variable -hist_nhtfrq which is an array of rank six for each history stream. -The values of the array hist_nhtfrq must be integers, where the -following values have the given meaning: - -Positive value means the output frequency is the number of -model steps between output. - -Negative value means the output frequency is the absolute -value in hours given (i.e -1 would mean an hour and -24 would mean a full day). Daily -(-24) is the default value for all auxiliary files. - -Zero means the output frequency is monthly. This is the -default for the primary history files. - - - - -The number of samples on each history file stream is given by the namelist variable -hist_mfilt which is an array of rank six for each history stream. -The values of the array hist_mfilt must be positive integers. By -default the primary history file stream has one time sample on it (i.e. output is -to separate monthly files), and all other streams have thirty time samples on them. - - -A sample user namelist &usernlclm; turning on four extra file -streams for output: daily, six-hourly, hourly, and every time-step, -leaving the primary history files as monthly, and changing the number -of samples on the streams to: yearly (12), thirty, weekly (28), daily (24), and daily -(48) is: - -Example &usernlclm; namelist adding auxiliary history files and changing output frequency - -&clm_inparm - hist_fincl2 = 'TG', 'TV' - hist_fincl3 = 'TG', 'TV' - hist_fincl4 = 'TG', 'TV' - hist_fincl5 = 'TG', 'TV' - hist_nhtfrq = 0, -24, -6, -1, 1 - hist_mfilt = 12, 30, 28, 24, 48 -/ - - - - - - -Removing all history fields - -Sometimes for various reasons you want to remove all the history fields either -because you want to do testing without any output, or you only want a very small -custom list of output fields rather than the default extensive list of fields. -By default only the primary history files are active, so technically using -hist_fexcl1 explained in the first example, you could list -ALL of the history fields that are output in -hist_fexcl1 and then you wouldn't get any output. However, as -the list is very extensive this would be a cumbersome thing to do. So to facilitate -this hist_empty_htapes allows you to turn off all default output. -You can still use hist_fincl1 to turn your own list of fields -on, but you then start from a clean slate. -A sample user namelist &usernlclm; turning off all history -fields and then activating just a few selected fields (ground and vegetation temperatures -and absorbed solar radiation) is: - -Example &usernlclm; namelist removing all history fields - -&clm_inparm - hist_empty_htapes = .true. - hist_fincl1 = 'TG', 'TV', 'FSA' -/ - - -Note, you could also build adding the "-noio" option to &CLMCONFIG;. But, this would -build the model without history output and you wouldn't be able to add that in later. - - - - -Various ways to change history output averaging flags - -There are two ways to change the averaging of output history fields. The first is using -hist_avgflag_pertape which gives a default value for each history -stream, the second is when you add fields using hist_fincl*, you add -an averaging flag to the end of the field name after a colon (for example 'TSOI:X', would -output the maximum of TSOI). -The types of averaging that can be done are: - -A Average, over the output interval. -I Instantaneous, output the value at the output interval. -X Maximum, over the output interval. -M Minimum, over the output interval. - - -The default averaging depends on the specific fields, but for most fields is an average. -A sample user namelist &usernlclm; making the monthly output -fields all averages (except TSOI for the first two streams and FIRE for the 5th stream), -and adding auxiliary file streams for instantaneous (6-hourly), -maximum (daily), minimum (daily), and average (daily). For some of the fields we -diverge from the per-tape value given and customize to some different type of -optimization. - -Example &usernlclm; namelist with various ways to average history fields - -&clm_inparm - hist_empty_htapes = .true. - hist_fincl1 = 'TSOI:X', 'TG', 'TV', 'FIRE', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_fincl2 = 'TSOI:X', 'TG', 'TV', 'FIRE', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_fincl3 = 'TSOI', 'TG:I', 'TV', 'FIRE', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_fincl4 = 'TSOI', 'TG', 'TV:I', 'FIRE', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_fincl5 = 'TSOI', 'TG', 'TV', 'FIRE:I', 'FSR', 'FSH', - 'EFLX_LH_TOT', 'WT' - hist_avgflag_pertape = 'A', 'I', 'X', 'M', 'A' - hist_nhtfrq = 0, -6, -24, -24, -24 -/ - - - - - -In the example we put the same list of fields on each of the tapes: soil-temperature, -ground temperature, vegetation temperature, emitted longwave radiation, reflected -solar radiation, sensible heat, total latent-heat, and total water storage. We also -modify the soil-temperature for the primary and secondary auxiliary tapes by outputting -them for a maximum instead of the prescribed per-tape of average and instantaneous -respectively. For the tertiary auxiliary tape we output ground temperature instantaneous -instead of as a maximum, and for the fourth auxiliary tape we output vegetation -temperature instantaneous instead of as a minimum. Finally, for the fifth auxiliary -tapes we output FIRE instantaneously instead of as an average. - - - - -We also use hist_empty_htapes as in the previous example, -so we can list ONLY the fields that we want on the primary history tapes. - - - - - -Outputting history files as a vector in order to analyze -the plant function types within gridcells - -By default the output to history files are the grid-cell average of all land-units, and -vegetation types within that grid-cell, and output is on the -full 2D latitude/longitude grid with ocean masked out. Sometimes it's important to -understand how different land-units or vegetation types are acting within a grid-cell. -The way to do this is to output history files as a 1D-vector of all land-units and vegetation -types. In order to display this, you'll need to do extensive post-processing to make sense -of the output. Often you may only be interested in a few points, so once you figure out the -1D indices for the grid-cells of interest, you can easily view that data. 1D vector output -can also be useful for single point datasets, since it's then obvious that all data is for the -same grid cell. - - -To do this you use hist_dov2xy which is an array of rank six for -each history stream. Set it to -.false. if you want one of the history streams to be a 1D vector. -You can also use hist_type1d_pertape if you want to average over all the: -Plant-Function-Types, columns, land-units, or grid-cells. -A sample user namelist &usernlclm; leaving the primary monthly -files as 2D, and then doing grid-cell (GRID), column (COLS), -and no averaging over auxiliary tapes output daily for a single field -(ground temperature) is: - -Example &usernlclm; namelist outputting some files in 1D Vector format - -&clm_inparm - hist_fincl2 = 'TG' - hist_fincl3 = 'TG' - hist_fincl4 = 'TG' - hist_fincl5 = 'TG' - hist_fincl6 = 'TG' - hist_dov2xy = .true., .false., .false., .false. - hist_type2d_pertape = ' ', 'GRID', 'COLS', ' ' - hist_nhtfrq = 0, -24, -24, -24 -/ - - - - -LAND and COLS are also options to the pertape averaging, but currently there is a bug -with them and they fail to work. - - - - - -Technically the default for hist_nhtfrq is for primary files -output monthly and the other auxiliary tapes for daily, so we don't actually have -to include hist_nhtfrq, we could use the default for it. Here -we specify it for clarity. - - - - -Visualizing global 1D vector files will take effort. You'll probably want -to do some post-processing and possibly just extract out single points of interest -to see what is going on. Since, the output is a 1D vector, of only land-points -traditional plots won't be helpful. The number of points per grid-cell will also -vary for anything, but grid-cell averaging. You'll need to use the output fields -pfts1d_ixy, and pfts1d_jxy, to get the mapping -of the fields to the global 2D array. pfts1d_itype_veg gives you -the PFT number for each PFT. Most likely you'll want to do this analysis in a -data processing tool (such as NCL, Matlab, Mathmatica, IDL, etcetera that is able -to read and process &netcdf; data files). - - - - - -Outputting multi-layer snow history fields - -A number of history fields provide information about individual snow layers: -SNO_ABS, SNO_T, SNO_GS, -SNO_Z, SNO_LIQH2O, -SNO_ICE, SNO_TK, and -SNO_BW; there is also an auxiliary field to aid -interpretation: SNO_EXISTENCE (described below). These fields -are inactive by default, but can be enabled like other history fields. If the -maximum number of snow layers is 5 (for example), then the layers of these -fields are arranged on the history file so that layer 1 is at the top of the -snow pack, and layer 5 only exists if the snow is deep enough to support all -layers. - - -Because snow layers can come into and out of existence, these fields can be -challenging to interpret. It is easiest to analyze these fields if you do output -every time step, and do not average to the grid cell (i.e., dov2xy = -.false.). Otherwise, a few principles should be kept in mind when -working with these fields: - -Temporal averages are taken only over times when a given snow layer exists -Grid cell averages are taken only over columns in which a given snow layer exists -SNO_EXISTENCE gives the fraction of the averaging -period in which a given snow layer existed. For grid cell averages, this gives -the weighted spatial fraction of the columns in which a snow layer existed for -this averaging period. This is most useful for subsetting grid cells for -analysis. For example, grid cells that have SNO_EXISTENCE = 1 -for all snow layers can be analyzed most easily. - - - -Here is a simple example illustrating this averaging; this considers a given -snow layer, L: - - -Assume a grid cell with 2 columns, with averaging done over 4 time steps. Column -#1 has subgrid weight 0.2, and no snow in layer L in any time -step. Column #2 has subgrid weight 0.8, and has snow in layer -L in time steps 3 and 4; the snow field of interest has -values 1.0 and 2.0 in these two time steps, for this layer. - - -SNO_EXISTENCE is then 0.8*(2/4) = 0.4. The snow field's value -would be 1.5 (note that times and columns with no snow in this layer are simply -ignored). - - -Finally, note that the SNOABS field is not computed for urban -columns, so it will have a missing value if snow only exists over urban columns -for a given snow layer. - - - - -Conclusion to namelist examples - -We've given various examples of namelists that feature the use of different namelist options -to customize a case for particular uses. Most the examples revolve around how to customize the -output history fields. This should give you a good basis for setting up your own &clm; namelist. - - - - - - - - - -Customizing the &datm; Namelist and Streams files - -When running "I" compsets with &clm; you use the &datm; model to give atmospheric -forcing data to &clm;. There are four ways to customize &datm;: - - -&datm; Main Namelist (datm_in) - - -&datm; Stream Namelist (datm_atm_in) - - -&datm; stream files - - -&datm; template file -(Tools/Templates.datm.cpl7.template) - - -The -Data Model Documentation gives the details of all the options for the data -models and for &datm; specifically. It goes into detail on all namelist items both for -&datm; -and for &datm; streams. It shows examples of stream files and talks about their use. In - we talk about editing the CLM and &datm; -template files. So here we won't talk about the &datm; template file, and we won't list -ALL of the &datm; namelist options, nor go into great details about stream files. But, -we will talk about a few of the different options that are relevant for running with -&clm;. All of the options for changing the namelists or stream files is done by editing -the Buildconf/datm.buildnml.csh file. - - -Because, they aren't useful for work with &clm; we will NOT discuss any of the options -for the main &datm; namelist. Use the &datm; Users Guide at the link above to find -details of that. For the streams namelist we will discuss three items: - - -mapalgo - - -taxmode - - -tintalgo - - -And for the streams file itself we will discuss: - - offset - -Again everything else (and including the above items) are discussed in the Data Model -User's Guide. Of the above the last three: offset, taxmode and tintalgo are all closely -related and have to do with the time interpolation of the &datm; data. - - - - -mapalgo - -mapalgo sets the spatial interpolation method to go from the -&datm; input data to the output &datm; model grid. The default is -bilinear. For CLM1PT we set it to nn to just -select the nearest neighbor. This saves time and we also had problems running the -interpolation for single-point mode. - - - - -taxmode - -taxmode is the time axis mode. For &clm; we usually have it -set to cycle which means that once the end of the data is reached -it will start over at the beginning. The extend modes is used -have it use the last time-step of the forcing data once it reaches the end of forcing -data (or use the first time-step before it reaches where the forcing data starts). -See the warning below about the extend mode. - - -THE extend OPTION NEEDS TO BE USED WITH CAUTION! -It is only invoked by default for the CLM1PT mode and is only intended for the -supported urban datasets to extend the data for a single time-step. If you have the -model run extensively through periods in this mode you will effectively -be repeating that last time-step over that entire period. This means the -output of your simulation will be worthless. See bug 1377 in the &KnownBugs; file for -more information on this issue. - - - - - - -offset (in the stream file) - -offset is the time offset in seconds to give to each stream -of data. Normally it is NOT used because the time-stamps for data is set correctly -for each stream of data. Note, the offset may NEED to be -adjusted depending on the taxmode described above, or it may -need to be adjusted to account for data that is time-stamped at the END of an -interval rather than the middle or beginning of interval. The -offset can is set in the stream file rather than on the -stream namelist. For data with a taxmode method of -coszen the time-stamp needs to be for the beginning of the interval, -while for other data it should be the midpoint. The offset can be -used to adjust the time-stamps to get the data to line up correctly. - - - - -tintalgo - -tintalgo is the time interpolation algorithm. For &clm; we usually -use one of three modes: coszen, nearest, or -linear. We use coszen for solar data, -nearest for precipitation data, and linear -for everything else. If your data is half-hourly or hourly, nearest -will work fine for everything. The coszen scaling is useful for -longer periods (three hours or more) to try to get the solar to match the cosine of -the solar zenith angle over that longer period of time. If you use -linear for longer intervals, the solar will cut out at night-time -anyway, and the straight line will be a poor approximation of the cosine of the -solar zenith angle of actual solar data. nearest likewise would -be bad for longer periods where it would be much higher than the actual values. - - -For coszen the time-stamps of the data should correspond to the -beginning of the interval the data is measured for. Either make sure the time-stamps -on the datafiles is set this way, or use the offset described above -to set it. - - - - -For nearest and linear the time-stamps of the -data should correspond to the middle of the interval the data is measured for. Either -make sure the time-stamps on the datafiles is set this way, or use the -offset described above to set it. - - - - - - -In the sections below we go over each of the relevant DATM_MODE -options and what the above &datm; settings are for each. This gives you examples -of actual usage for the settings. We also describe in what ways you might want -to customize them for your own case. - - - -&CLMQIAN; mode and it's &datm; settings - -In &CLMQIAN; mode the Qian dataset is used which has 6-hourly -solar and precipitation data, and 3-hourly for everything else. -The dataset is divided into those three data streams: solar, precipitation, -and everything else (temperature, pressure, humidity and wind). The time-stamps -of the data were also adjusted so that they are the beginning of the interval -for solar, and the middle for the other two. Because, of this the -offset is set to zero, and the tintalgo -is: coszen, nearest, and -linear for the solar, precipitation and other data -respectively. taxmode is set to cycle -and mapalgo is set to bilinear so that -the data is spatially interpolated from the input T62 grid to the grid the atmosphere -model is being run at. - - -Normally you wouldn't customize the &CLMQIAN; settings, but you might replicate -it's use for your own global data that had similar temporal characteristics. - - - - -CLM1PT mode and it's &datm; settings - -In CLM1PT mode the model is assumed to have half-hourly or hourly data -for a single-point. For the supported datasets that is exactly what it has. -But, if you add your own data you may need to make adjustments accordingly. -Using the &CLMUSRDAT; option you can easily extend this mode for your own -datasets that may be regional or even global and could be at different temporal -frequencies. If you do so you'll need to make adjustments to your &datm; settings. -The dataset has all data in a single stream file. The time-stamps -of the data were also adjusted so that they are at the middle of the interval. -Because, of this the offset is set to zero, and the -tintalgo is set to nearest. -taxmode is set to extend -and mapalgo is set to nn so that -simply the nearest point is used. - - -If you are using your own data for this mode and it's not at least hourly -you'll want to adjust the &datm; settings for it. If the data is three or -six hourly, you'll need to divide it up into separate streams like in -&CLMQIAN; mode which will require fairly extensive changes to the &datm; -namelist and streams files. For an example of doing this see -. - - - - -&CPLHIST; mode and it's &datm; settings - -In &CPLHIST; mode the model is assumed to have 3-hourly for a global grid from -a previous &cesm; simulation. Like &CLMQIAN; mode the data is divided into -three streams: one for precipitation, one for solar, and one for everything else. -The time-stamps for Coupler history files for &cesm; is at the end of the interval, -so the offset needs to be set in order to adjust the time-stamps to what it needs -to be for the tintalgo settings. For precipitation -taxmode is set to nearest so the -offset is set to -5400 seconds so that -the ending time-step is adjusted by an hour and half to the middle of the interval. -For solar taxmode is set to coszen so the -offset is set to -10800 seconds so that -the ending time-step is adjust by three hours to the beginning of the interval. -For everything else taxmode is set to -linear so the offset is set to --5400 seconds so that the ending time-step is adjusted by an -hour and half to the middle of the interval. - - -Normally you wouldn't modify the &datm; settings for this mode. However, if you -had data at a different frequency than 3-hours you would need to modify the -offset and possibly the taxmode. The other -two things that you might modify would be the path to the data (which you can -change in the &datm; template see ) or -the domain file for the resolution (which is currently hardwired to f09). For -data at a different input resolution you would need to change the domain file -in the streams file to use a domain file to the resolution that the data comes in -on. - - - - - - - -Conclusion to customizing chapter - -We've given extensive details on customizing cases with &clm;, by choosing compsets, by changing -&configure; options and interacting with the &clm; "&configure;" and "&buildnml;" scripts, -we've given details on all of the &clm; namelist items, and finally given some -instruction in customizing the &datm; namelist and streams files. In the next chapter we talk -about further ways to customize cases with &clm; by creating your own datasets using the tools -provided in &clm;. - - - - diff --git a/doc/UsersGuide/get_Icaselist.pl b/doc/UsersGuide/get_Icaselist.pl deleted file mode 100755 index 6aefc26159..0000000000 --- a/doc/UsersGuide/get_Icaselist.pl +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env perl -#----------------------------------------------------------------------------------------------- -# -# get_Icaselist.pl -# -# This utility gets a list of the I cases from the CCSM compset database. -# -#----------------------------------------------------------------------------------------------- - -use strict; -use Cwd; -use English; -use Getopt::Long; -use IO::File; -use IO::Handle; -#----------------------------------------------------------------------------------------------- - -sub usage { - die <autoflush(); - -#----------------------------------------------------------------------------------------------- -my $cwd = getcwd(); # current working directory -my $cfgdir; # absolute pathname of directory that contains this script -$cfgdir = $cwd; - -#----------------------------------------------------------------------------------------------- -# Parse command-line options. -my %opts = ( - ); -GetOptions( - "h|help" => \$opts{'help'}, -) or usage(); - -# Give usage message. -usage() if $opts{'help'}; - -# Check for unparsed argumentss -if (@ARGV) { - print "ERROR: unrecognized arguments: @ARGV\n"; - usage(); -} - -# Check for manditory case input if not just listing valid values - -my %cfg = (); # build configuration - -#----------------------------------------------------------------------------------------------- - -# Check for the configuration definition file. -my $config_def_file = "config_definition.xml"; -my $case_def_dir = "$cfgdir/../../../../../scripts/ccsm_utils/Case.template"; -(-f "$case_def_dir/$config_def_file") or die <<"EOF"; -** Cannot find configuration definition file \"$config_def_file\" in directory - \"$case_def_dir\" ** -EOF - -# Compset definition file. -my $compset_file = 'config_compsets.xml'; -(-f "$case_def_dir/$compset_file") or die <<"EOF"; -** Cannot find compset parameters file \"$compset_file\" in directory - \"$case_def_dir\" ** -EOF - -my $xml_dir = "$cfgdir/../../../../../scripts/ccsm_utils/Tools/perl5lib"; -# The XML::Lite module is required to parse the XML configuration files. -(-f "$xml_dir/XML/Lite.pm") or die <<"EOF"; -** Cannot find perl module \"XML/Lite.pm\" in directory - \"$xml_dir\" ** -EOF - - -#----------------------------------------------------------------------------------------------- -my @dirs = ( $cfgdir, $xml_dir, $case_def_dir ); -unshift @INC, @dirs; -require XML::Lite; -require ConfigCase; - -#----------------------------------------------------------------------------------------------- -my $cfg_ref = ConfigCase->new("$case_def_dir/$config_def_file"); -print_compsets( "$case_def_dir/$compset_file" ); - -#----------------------------------------------------------------------------------------------- -# FINNISHED #################################################################################### -#----------------------------------------------------------------------------------------------- - -#------------------------------------------------------------------------------- - -sub print_compsets -{ - # Print all currently supported valid compsets - - my ($compset_file) = @_; - my $xml = XML::Lite->new( $compset_file ); - my $root = $xml->root_element(); - - # Check for valid root node - my $name = $root->get_name(); - $name eq "config_compset" or die - "file $compset_file is not a compset parameters file\n"; - - # Read the compset parameters from $compset_file. - my @e = $xml->elements_by_name( "compset" ); - my %a = (); - my %data; - while ( my $e = shift @e ) { - %a = $e->get_attributes(); - my $sname = $a{'SHORTNAME'}; - if ($a{GRID_MATCH} && exists($data{$sname}) && defined($data{$sname}{'DESC'} && defined($a{'DESC'}) ) ) { - if ( $data{$sname}{'DESC'} =~ /^INVALID:/ ) { - $data{$sname}{'DESC'} = $a{'DESC'}; - } - } elsif ( $a{'SHORTNAME'} =~ /^I/ ) { - $data{$sname}{'NAME'} = $a{'NAME'}; - $data{$sname}{'DESC'} = $a{'DESC'}; - } - } - print "\n"; - foreach my $sname ( sort(keys(%data)) ) { - print "$data{$sname}{'NAME'}" . - "($sname)\n"; - print "$data{$sname}{'DESC'}\n"; - } - print "\n"; -} - diff --git a/doc/UsersGuide/limitLineLen.pl b/doc/UsersGuide/limitLineLen.pl deleted file mode 100755 index 25f1216d06..0000000000 --- a/doc/UsersGuide/limitLineLen.pl +++ /dev/null @@ -1,104 +0,0 @@ -#!/usr/bin/env perl -# -# Limit the line length for output designed to go into the document. -# -use strict; -use Cwd; -use English; -use IO::File; -use Getopt::Long; -use IO::Handle; -#----------------------------------------------------------------------------------------------- - -# Get the directory name and filename of this script. If the command was -# issued using a relative or absolute path, that path is in $ProgDir. Otherwise assume the -# command was issued from the current working directory. - -(my $ProgName = $0) =~ s!(.*)/!!; # name of this script -my $ProgDir = $1; # name of directory containing this script -- may be a - # relative or absolute path, or null if the script - # is in - # the user's PATH -my $nm = "$ProgName::"; # name to use if script dies -my $scrdir; -if ($ProgDir) { - $scrdir = $ProgDir; -} else { - $scrdir = getcwd() -} -my $limitLen = 99; - -sub usage { - my $msg = shift; - - print "ERROR:: $msg\n"; - die < -OPTIONS - -l = Limit line length to this value (default $limitLen) -EOF -} - -sub LengthofwhiteSpaceNearLength { - my $line = shift; - my $leng = shift; - - my $l = $leng; - while( substr( $line, $l, 1 ) !~ /\s|:|,|\// ) { - # First search for white-space before desired length -- and then after - if ( $l <= $leng ) { - $l--; - } else { - $l++; - } - # Once reach beginning of line, go to the desired length+1 and increment - if ( $l < 0 ) { $l = $leng+1; } - # Once reach the very end of the line die as couldn't break it - if ( $l >= length($line) ) { - die "ERROR : went through entire line and did NOT find a place to break it\n"; - } - } - return( $l ); -} - -my %opts = ( limitLen => $limitLen ); - -GetOptions( - "l=s" => \$opts{'limitLen'}, -) or usage(); - -if ( $#ARGV != 0 ) { - &usage( "Wrong number of command line arguments" ); -} - -$limitLen = $opts{'limitLen'}; - -my $inputFile = $ARGV[0]; - -if ( ! -f $inputFile ) { - &usage( "Input file does NOT exist : $inputFile" ); -} - -my $fh = IO::File->new($inputFile, '<') or die "** $nm - can't open input file: $inputFile\n"; - -while (my $line = <$fh>) { - - while( length($line) > $limitLen ) { - print STDERR "Line length over $limitLen\n"; - my $lenlim = &LengthofwhiteSpaceNearLength( $line, $limitLen ); - if ( ($lenlim == length($line)) || $lenlim < 0 ) { - print "Can NOT truncate long line: $line\n"; - die "ERROR : Having trouble breaking a long line\n"; - } - my $substring = substr( $line, 0, $lenlim+1 ); - print "$substring \\ \n"; - my $newline = " " . substr( $line, $lenlim+1, length($line) ); - $line = $newline; - } - print $line; - -} -$fh->close; - - diff --git a/doc/UsersGuide/modelnl/Makefile b/doc/UsersGuide/modelnl/Makefile deleted file mode 100644 index 595a1b3a3e..0000000000 --- a/doc/UsersGuide/modelnl/Makefile +++ /dev/null @@ -1,85 +0,0 @@ -# -# Makefile to create HTML documentation of namelists -# -SCRNLDIR := ../../../../../../scripts/doc/modelnl -VPATH := . $(SCRNLDIR) ../../../../../drv/bld/namelist_files ../../../../../glc/cism/bld/namelist_files \ - ../../../../../atm/datm/bld/namelist_files ../../../../../../scripts/ccsm_utils/Case.template \ - ../../../../../../scripts/ccsm_utils/Machines ../../../../../rof/rtm/bld/namelist_files \ - ../../../bld/namelist_files ../.. -SOURCES := namelist_definition_drv.xml namelist_definition_cism.xml namelist_definition.xml \ - namelist_definition_rtm.xm namelist_definition_datm.xml config_definition.xml \ - config_grid.xml config_machines.xml config_compsets.xml ChangeSum -TAGFILE := clmtag.txt - -CWD := $(shell pwd ) -ALLOUT := $(CWD)/clm_nl_drv.html $(CWD)/clm_nl_cism.html $(CWD)/clm_nl_clm.html $(CWD)/clm_nl_rtm.html \ - $(CWD)/clm_nl_datm.html $(CWD)/clm_env_case.html $(CWD)/clm_env_build.html $(CWD)/clm_env_pesetup.html \ - $(CWD)/clm_env_run.html $(CWD)/clm_grid.html $(CWD)/clm_machines.html $(CWD)/clm_compsets.html \ - $(TAGFILE) $(CWD)/index.html - -all: $(ALLOUT) - -debug: - @echo "SOURCES = $(SOURCES)" - @echo "VPATH = $(VPATH)" - @echo "ALLOUT = $(ALLOUT)" - @echo "SCRNLDIR = $(SCRNLDIR)" - @echo "CWD = $(CWD)" - @echo "TAGFILE = $(TAGFILE)" - -.SUFFIXES: -.SUFFIXES: .xml .html .txt - -RM := /bin/rm - -CTAGNAME = $(shell cat $(TAGFILE) ) - - -$(TAGFILE): ChangeSum - head -3 $< | tail -1 | awk '{print $$1}' > $@ - -$(CWD)/index.html: $(TAGFILE) index.cpp - sed 's/CLMTAGNAME/$(CTAGNAME)/' index.cpp > $@ - -$(CWD)/clm_nl_drv.html: namelist_definition_drv.xml - cd $(SCRNLDIR) ; ./nldef2html_drv > $@ - -$(CWD)/clm_nl_cism.html: namelist_definition_cism.xml - cd $(SCRNLDIR) ; ./nldef2html_cism > $@ - -$(CWD)/clm_nl_clm.html: namelist_definition.xml - cd $(SCRNLDIR) ; ./nldef2html_clm > $@ - -$(CWD)/clm_nl_rtm.html: namelist_definition_rtm.xml - cd $(SCRNLDIR) ; ./nldef2html_rtm > $@ - -$(CWD)/clm_nl_datm.html: namelist_definition_datm.xml - cd $(SCRNLDIR) ; ./nldef2html_datm > $@ - -$(CWD)/clm_env_case.html: config_definition.xml - cd $(SCRNLDIR) ; ./xmldef2html_env_case > $@ - -$(CWD)/clm_env_build.html: config_definition.xml - cd $(SCRNLDIR) ; ./xmldef2html_env_build > $@ - -$(CWD)/clm_env_pesetup.html: config_definition.xml - cd $(SCRNLDIR) ; ./xmldef2html_env_pesetup > $@ - -$(CWD)/clm_env_run.html: config_definition.xml - cd $(SCRNLDIR) ; ./xmldef2html_env_run > $@ - -$(CWD)/clm_grid.html: config_grid.xml - cd $(SCRNLDIR) ; ./xmldef2html_grid > $@ - -$(CWD)/clm_machines.html: config_machines.xml - cd $(SCRNLDIR) ; ./xmldef2html_machines > $@ - -$(CWD)/clm_compsets.html: config_compsets.xml - cd $(SCRNLDIR) ; ./xmldef2html_compsets > $@ - -clean: - $(RM) -f $(ALLOUT) - -realclean: clean - $(RM) -f $(TAGFILE) - diff --git a/doc/UsersGuide/modelnl/index.cpp b/doc/UsersGuide/modelnl/index.cpp deleted file mode 100644 index c55aa64159..0000000000 --- a/doc/UsersGuide/modelnl/index.cpp +++ /dev/null @@ -1,45 +0,0 @@ - - - - - -CLM Namelist Definitions (CLMTAGNAME) - - - - - - -
    - - -

    CLM Tag: CLMTAGNAME

    - -

    Component Namelist Definitions

    - - -

    create_newcase files (supported machines, grids, compsets)

    - - -

    $CASEROOT xml files

    - - - - - - diff --git a/doc/UsersGuide/modelnl/showinfo.js b/doc/UsersGuide/modelnl/showinfo.js deleted file mode 100644 index fd8a608472..0000000000 --- a/doc/UsersGuide/modelnl/showinfo.js +++ /dev/null @@ -1,193 +0,0 @@ - function applyFilter(filter_text) { - - // applying a filter hides all standard names not matching filter_text - // if filter_text contains no spaces, it is treated as a regexp - // otherwise, all substrings must occur somewhere - - var is_match = false; - var search_type = 'regexp'; - var search_help_text = false; - var num_matches = 0; - var is_boolean_and = true; - - search_help_text = (document.getElementById('search_help_text').checked); - is_boolean_and = (document.getElementById('logical_operator_and').checked); - - if (filter_text.indexOf(' ') == -1) { - search_type = 'regexp'; - var re = new RegExp(filter_text, 'i') - } - else { - search_type = 'string'; - var string_parts = filter_text.split(' '); - } - - allTRs = document.getElementsByTagName('tr'); 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- filter_matches_num.innerHTML = num_matches; - filter_matches_query.innerHTML = filter_text; - } - else { - filter_matches.style.visibility = 'hidden'; - } - - } // end function applyFilter() - - function clearFilter() { - - allTRs = document.getElementsByTagName('tr'); - - for (var i = 0; i < allTRs.length; i++) { - curTR = allTRs[i]; - if (curTR.id != '') { - curTR.style.display = ''; - hideHelp(curTR.id.substring(0,curTR.id.length - 3)); - - } - } - - var filter_matches = document.getElementById('filter_matches'); - filter_matches.style.visibility = 'hidden'; - - document.getElementById('filter_text').value = ''; - } - - function toggleHelp(standard_name) { - - // check for the existence of the help "tr" object for this standard_name - - var helpDiv = document.getElementById(standard_name + '_help'); - - if (helpDiv) { - - if (helpDiv.style.display != 'none') { - - helpDiv.style.display = 'none'; - - curArrow = document.getElementById(standard_name + '_arrow'); - curArrow.src = "./images/arrow_right.gif"; - } - else { - helpDiv.style.display = ''; - - curArrow = document.getElementById(standard_name + '_arrow'); - curArrow.src = "./images/arrow_down.gif"; - } - } - } - - - function showHelp(standard_name) { - - var helpDiv = document.getElementById(standard_name + '_help'); - - if (helpDiv) { - - helpDiv.style.display = ''; - curArrow = document.getElementById(standard_name + '_arrow'); - curArrow.src = "./images/arrow_down.gif"; - } - } - - function hideHelp(standard_name) { - - var helpDiv = document.getElementById(standard_name + '_help'); - - if (helpDiv) { - helpDiv.style.display = 'none'; - curArrow = document.getElementById(standard_name + '_arrow'); - curArrow.src = "./images/arrow_right.gif"; - } - } - diff --git a/doc/UsersGuide/modelnl/xmldef2html_compsets b/doc/UsersGuide/modelnl/xmldef2html_compsets deleted file mode 100755 index 2659beed17..0000000000 --- a/doc/UsersGuide/modelnl/xmldef2html_compsets +++ /dev/null @@ -1,162 +0,0 @@ -#!/usr/bin/env perl - -use strict; - -if ( $#ARGV != 0 ) { - die "Wrong number of input arguments -- should just enter one filename\n"; -} -my $infilename = $ARGV[0]; -if ( ! -f $infilename ) { - die "Input file: $infilename does NOT exist\n"; -} - -my @dirs = ('../../../../../../scripts/ccsm_utils/Tools/per5lib', '../../../../../../scripts//ccsm_utils/Tools/perl5lib/Build'); -unshift @INC, @dirs; -require XML::Lite; -use lib "../../../../../../scripts/ccsm_utils/Tools/perl5lib"; - -my $image_dir = "./images"; - -print <<"END_of_Start"; - - - - - - - CESM Component Models Namelist Definitions - - - - - - -

    Search or Browse supported component sets

    -

    -This page contains the complete list of config_grid.xml variables available. They are grouped -by categories designed to aid browsing. Clicking on the name of a variable will display descriptive -information. If search terms are entered in the text box below, the list will be condensed to contain -only matched variables. -

    - -
    - - - - - - -
    - - - -
    - - - (separate search terms with spaces) -
    - -
    -
    - - - -END_of_Start - -my $xml = XML::Lite->new( $infilename ); -my $root = $xml->root_element(); - -# Check for valid root node -my $name = $root->get_name(); -$name eq "config_compset" or die - "file $infilename is not a compset definition file\n"; - -# Print table -print_start_table("config_compsets.xml variables"); -my @e = $xml->elements_by_name( "compset" ); -my %a = (); -while ( my $e = shift @e ) { - %a = $e->get_attributes(); - - if ($a{'NAME'} =~ /I_/ ) { - my $var = $a{'NAME'}; - my $doc = "Description: $a{DESC} \n"; - my $grp = "$a{SHORTNAME}"; - print_row($var, $doc, $grp); - } -} -print_end_table(); - -# Finish -print <<"END_of_html"; - - -END_of_html - -#-------------------------------------------------------------------------------------------- - -sub print_start_table { - my $hdr = shift; - -print <<"START_table"; -

    $hdr

    - - - -START_table -} - -#-------------------------------------------------------------------------------------------- - -sub print_row { - - my $name = shift; - my $doc = shift; - my $grp = shift; - -print <<"END_of_row"; - - - - -END_of_row -} - -#-------------------------------------------------------------------------------------------- - -sub print_end_table { - -print <<"END_table"; -
    Compset NameShort Name
    - - - $name - - - $grp
    -END_table -} - -#-------------------------------------------------------------------------------------------- - diff --git a/doc/UsersGuide/pergro.jpg b/doc/UsersGuide/pergro.jpg deleted file mode 100644 index a0cb81e046..0000000000 Binary files a/doc/UsersGuide/pergro.jpg and /dev/null differ diff --git a/doc/UsersGuide/preface.xml b/doc/UsersGuide/preface.xml deleted file mode 100644 index ed063ce774..0000000000 --- a/doc/UsersGuide/preface.xml +++ /dev/null @@ -1,1419 +0,0 @@ - - - -$Id$ - -Acknowledgments - -I want to acknowledge all of the people that helped review or edit the model -documentation: David Lawrence, Samuel Levis, Keith Oleson, and Sean Swenson. -Thank you for your help in catching errors, and making the document more -understandable and readable. Our readers thank you as well, as now it is much -easier for them to digest. Any mistakes, or errors are all mine. If you run -across one of those errors, please let us know, by following -. -I also want to thank Sheri -Mickelson, for her work in doing perturbation analysis on bluefire and intrepid, -which was used in our initial versions of this User's Guide. We also want to -thank the original authors of &ptclm;: Daniel M. Ricciuto, Dali Wang, Peter E. Thornton, -Wilfred M. Post, and R. Quinn Thomas for providing a nice addition to the &cesm; -effort. We also want to thank the folks at University of Michigan Biological Stations -(US-UMB) who allowed us to use their Fluxnet station data and import it into our -inputdata repository, especially Gil Bohrer the PI on record for this site -(see for permission information on using this -data). - - - - -Introduction - - -The Community Land Model (&clmrel;) is the latest in a series of -global land models developed by the &cesm; Land Model Working Group -(LMWG) and maintained at the National Center for -Atmospheric Research (&ncar;). This guide is intended to instruct both -the novice and experienced user on running &clm;. This guide pertains to the -latest version &clmrel; available for download from the public release -subversion repository as a part of &cesmrel;. Documentation may be different if you are using an -older version, you should either update to the latest version, or use the -documentation inside your own source tree. There is information in the -ChangeLog file and in the -regarding the changes from previous versions of &cesm;. - - - -The novice user should read - in detail before beginning work, while the -expert user should read and - chapters, and then use the more detailed -chapters as reference. Before novice users go onto more technical problems covered -in , , , or they -should know the material covered in and be able -to replicate some of the examples given there. - - -All users should read the - -and sections to understand the document conventions -and the various ways of getting help on using &clm4;. Users should also read -the section to see if their planned use of the -model is something that has been scientifically validated and well tested. Users -that are NOT using &ncar; machines or our list of well tested machines should also -read the section to make sure they have -all the required UNIX utilities on the system they want to do their work. - - - - - -Introduction to the &clm4; User's Guide -What is in here anyway? - - -Here in the introduction we first give a simple guide to understand the document -conventions in . The next section -describes the differences between &clmrel; and &clm40; (for each &cesm; release version -up to &cesmrel;) as well as between -&clm40; and &clm35;, both from a scientific -as well as a software engineering point of view. It also talks about differences in the -configuration, namelist, and history fields. The next section -is for users that are already experts in using &clm; and gives a quickstart guide to the -bare details on how to use &clm4;. The next tells -you about what has been extensively tested and scientifically validated (and maybe more -importantly) what has NOT. lists the UNIX utilities -required to use &clm4; and is important if you are running on non-&ncar; machines, generic -local machines, or machines NOT as well tested by us at &ncar;. Next we -have to detail some of the best practices for using -&clm4; for science. The last introductory section is which lists -different resources for getting help with &cesm1; and &clm4;. - - - - goes into detail on how to setup and run simulations with -&clm4; and especially how to customize cases. Details of &configure; -modes and &buildnml; options as well as namelist options are given in this chapter. - - - - gives instructions on the &clm4; tools for creating input datasets -for use by &clm;, for the expert user. There's an overview of what each tool does, and some general notes on how to build -the FORTRAN tools. Then each tool is described in detail along with different ways in -which the tool might be used. -A final section -on how to customize datasets for observational sites for very savvy expert users is given as the last section of this chapter. - - - -As a followup to the tools chapter, tells how to add files to the -XML database for &buildnml; to use. This is important if you want to use the XML database to automatically select -user-created input files that you have created when you setup new cases with &clm;. - - - -In , again for the expert user, we give details on how to do some particularly -difficult special cases. For example, we give the protocol for spinning up both the &clmcn; model and &clm; with dynamic -vegetation active (CNDV). We give instructions to do a spinup case -from a previous case with Coupler history output for atmospheric forcing. We also give -instructions on running the prognostic crop model and its irrigation option. We also review -how to validate a port to a new machine using the Perturbation error -growth technique. Lastly we tell the user how to use the DATM model to send historical &CO2; data to &clm;. - - - - outlines how to do single-point or -regional simulations using &clm4;. -This is useful to either compare &clm; simulations with point observational stations, -such as tower sites (which might include your own atmospheric forcing), or -to do quick simulations with &clm; for example to test a new parameterization. There are -several different ways given on how to perform -single-point simulations which range from simple &PTSMODE; to more complex where you create all your own datasets, tying into - and also to add the -files into the &buildnml; XML database. After this chapter - chapter outlines how to use the &ptclm; python script to -help you run single-point simulations. - - - -Finally, gives some guidance on trouble-shooting -problems when using &clm4;. It doesn't cover all possible problems with &clm;, but gives -you some guidelines for things that can be done for some common problems. - - - -In the appendices we talk about some issues that are useful for advanced users and -developers of &clm;. -In we give some basic background to the &clm; -developer on how to edit the models/lnd/clm/bld/clm.cpl7.template. -This is a very difficult exercise and we don't recommend it for any, but the most -advanced users of &clm; who are also experts in UNIX and UNIX scripting. - - -In we go over how to run the script -runinit_ibm.csh" that will interpolate standard resolution -initial condition dataset to several other resolutions at once. It also runs &clm; -to create template files as well as doing the interpolation using -interpinic. In general this is only something that a developer -would want to do. Most users will only want to interpolate for a few specific -resolutions. - - -In we go over the automated testing scripts for -validating that the &clm; is working correctly. The test scripts run many different -configurations and options with &clm; making sure that they work, as well as doing -automated testing to verify restarts are working correctly, and testing at many -different resolutions. In general this is an activity important only for a developer -of &clm;, but could also be used by users who are doing extensive code modifications -and want to ensure that the model continues to work correctly. - - -Finally in we give instructions on how to build -the documentation associated with &clm; (i.e. how to build this document). This -document is included in every &clm; distribution and can be built so that you can -view a local copy rather than having to go to the &cesm; website. This also could -be useful for developers who need to update the documentation due to changes they -have made. - - - - - - - - - -Important Notes and Best Practices for Usage of &clm4; - - - -When running with CN, it is critical to begin with initial conditions -hat are provided with the release or to spin the model up following the CN spinup -procedure before conducting scientific runs (see . -Simulations without a proper spinup will effectively be starting from an unvegetated -world. See for information on how to -provide initial conditions for your simulation. - - -Initial condition files are provided for fully coupled BCN and offline -ICN cases for 1850 and 2000 at 1deg, 2deg, and T31 resolutions. There's also an -initial condition file for ICN with the prognostic crop model for 2000 at 2deg -resolution, and one with &clmsp; for 2000 at 2deg resolution. We also have initial -conditions for offline CNDV for 1850. And there are interpolated datasets for 4x5 and -10x15 resolution for 1850. The 1850 initial condition -files are in 'reasonable' equilibrium. The 2000 initial condition files represent -the model state for the year 2000, and have been taken from transient simulations. -Therefore, by design the year 2000 initial condition files do not represent an -equilibrium state. Note also that spinning the 2000 initial conditions out to -equilibrium will not reflect the best estimate of the real carbon/nitrogen state -for the year 2000. - - -Users can generate initial condition files at different resolutions by -using the &clm; tool interpinic to interpolate from one of the -provided resolutions to the resolution of interest. Interpolated initial condition -files may no longer be in 'reasonable' equilibrium. - - -Aerosol deposition is a required field to &clm4; sent from the -atmosphere model. Simulations without aerosol deposition will exhibit unreasonably -high snow albedos. The model sends aerosol deposition from the atmospheric model (either -CAM or &datm;). When running with prescribed aerosol the atmosphere -model will interpolate the aerosols from 2-degree resolution to the resolution the -atmosphere model is running at. - - - - - - - - - - - - - $EDITOR - - - -How to Use This Document -Conventions used in the document for code and commands - - -This section provides the details in using &clm; with the &cesm; modeling -system. Links to descriptions and definitions have been provided in the code below. -We use the same conventions used in the &cesm; documentation as outlined below. - - - -Throughout the document this style is used to indicate shell -commands and options, fragments of code, namelist variables, etc. -Where examples from an interactive shell session are presented, lines -starting with > indicate the shell prompt. A backslash "\" at the end -of a line means the line continues onto the next one (as it does in -standard UNIX shell). Note that $EDITOR" is used to refer to the -text editor of your choice. $EDITOR is a standard UNIX environment -variable and should be set on most UNIX systems. Comment lines are -signaled with a "#" sign, which is the standard UNIX comment sign as well. -$CSMDATA is used to denote the path to the inputdata directory for -your &cesm; data. - -> This is a shell prompt with commands \ -that continues to the following line. -> $EDITOR filename # means you are using a text editor to edit "filename" -# This is a comment line - - - - - - - - - - - &clmcn; - &clmsp; - - -What is new with &clmrel; since previous public releases? - -In this section we list the updates that have occurred to &clm4; since previous -public releases. In the first sections we describe changes in &clmrel; since the &ccsm4; release, -and in the last one we describe changes from &clm35; to &clm40; release. Note, that -the changes in the last section do NOT include the more recent changes given in the -first section, but only list the changes from &clm35; to the &clm40; release that -was part of the &ccsm4; public release. We will describe both the -changes in the science in the model as the software engineering changes. Software -engineering changes includes the configure and namelist changes, as well as the new -history fields. - - -What is new with &clmrel; since the December 8th, 2010 &cesm102; release? - - - -What is new with &clmrel; Science since &clmcesm102;? - -A prognostic crop model option was added in (based on Agro-IBIS) from work by -Samuel Levis. The crop model adds in four new vegetation types for: soybean, -winter and spring temperate cereals, and corn on their own separate columns. Winter -cereal was added as a PFT type, but doesn't exist in the input datasets, only -spring cereal is used. Winter cereal also has NOT been scientifically validated -or tested. The model manages these by modeling both planting and harvesting. See for an example of running with it. - - -An irrigation model was added from work by Samuel Levis and Bill Sacks. This -model takes water from runoff and adds it to the crop pfts for areas equipped -for irrigation. See for an example of running with it. -Please note that the irrigation model only works with the crop model active. - - - - -What is new with &clmrel; Software since &clmcesm102;? - -Since &clmcesm102; all Input/Output uses &pio; (Parallel Input/Output package). -Restart history files are now &netcdf;. Input and output files can be read/written -in parallel using PIO. We removed a list of old CPP defines and removed the -old misc/preproc.h files. Also a new tool for working with single-point sites was -added into the &cesm; scripts the Python tool &ptclm;. We have a complete chapter on it's use. - - -New configuration options: - --crop --noio - - - -Configuration options removed: - --dust --progsslt - - - -New build-namelist options: - --co2_ppmv --rtm_res --rtm_tstep - - - -New precedence for build-namelist options is... - -Values set on the command-line using the -namelist option -(&CLMNAMELIST;). -Values read from the file specified by -infile (&usernlclm; file). -Datasets from the -clm_usr_name option (&CLMUSRDAT;). -Values set from a use-case scenario, e.g., -use_case (&CLMUSECASE;). -Values from the namelist defaults file. - - - -Namelist options renamed: - -carbon_only => suplnitro (can be set to NONE or ALL) - - - -namelist options removed: - -carbon_only => suplnitro -scaled_harvest -hist_crtinic -hist_pioflag -ncd_lowmem2d -ncd_pio_def -ncd_pio_UseRearranger -ncd_pio_UseBoxRearr -ncd_pio_SerialCDF -ncd_pio_IODOF_rootonly -ncd_pio_DebugLevel -ncd_pio_num_iotasks - - - -New history fields: - -A5TMIN 5-day running mean of min 2-m temperature -(K) -A10TMIN 10-day running mean of min 2-m temperature -(K) -GDD0 Growing degree days base 0C from planting -(ddays) -GDD8 Growing degree days base 8C from planting -(ddays) -GDD10 Growing degree days base 10C from planting -(ddays) -GDD020 Twenty year average of growing degree days base 0C from planting -(ddays) -GDD820 Twenty year average of growing degree days base 8C from planting -(ddays) -GDD1020 Twenty year average of growing degree days base 10C from planting -(ddays) -GDDPLANT Accumulated growing degree days past planting date for crop -(ddays) -GDDHARV Growing degree days (gdd) needed to harvest -(ddays) -GDDTSOI Growing degree-days from planting (top two soil layers) -(ddays) -QIRRIG water added through irrigation -(mm/s) - - - -SNOWLIQ and SNOWICE changed from average to instantaneous output. - - - - -What was new with &clm4014; (in &cesm102;) since the September 17th, 2010 &cesm101; release? - -Since, &clm4010; in the &cesm101; release there were several developments made -to &clmrel;. Several new namelist items were added -a few new history fields. There were also some updates for -running the model with single-point mode. - - -Configuration options that were renamed: - -prog_seasalt => progsslt - - - -Namelist items removed: - -prog_seasalt => progsslt - - - -What was new with &clm4014; Science since &clm4010;? - -A long simulation at the course resolution of T31 (typically used for Paleo-climate -studies) was done and an spun-up initial condition file was provided for this -resolution (also by default the namelist variable ice_runoff was -turned off for T31). Also a new surface dataset and transient land-cover dataset was -provided for half-degree resolution. - - - -What was new with &clm4014; Software since &clm4010;? - -New configuration options - -sitespf_pt - - - -sitespf_pt is used for single-point/regional mode and is set to the site-name -that will be used (see the config_definition.xml for the -list of valid options). - - -Configuration options that were renamed: - -prog_seasalt => progsslt - - - -Namelist items removed: - -faerdep -fndepdat -fndepdyn -use_ndepstream - - - -Nitrogen deposition datasets are now only entered through the -ndepdyn_nml namelist (removing fndepdat, fndepdyn, and -use_ndepstream). Aerosol deposition is now a required input from -the atmosphere model, hence faerdep is removed. - - -New history fields: - -U10 10-m wind (m/s) -U10_DUST 10-m wind for dust model (m/s) -VA atmospheric wind speed plus convective velocity (m/s) -VOLR RTM storage: LIQ (m3) -VOLR_ICE RTM storage: ICE (m3) - - - - - - -What was new with &clm4010; (in &cesm101;) since the April 1st, 2010 &ccsm4; release? - -From, &clm40; in the &ccsm4; release to &clm4010; there were several developments made -to &clm;. A glacier multiple elevation class option was added that allows the -use of &clm4; with a glacier land ice model the Community Ice Sheet Model (CISM). -A bug-fix for the snow hydrology was added. Several new namelist items were added -a few new history fields. Also the capability of reading aerosol and nitrogen -deposition from stream files at one resolution and regridded on the fly rather than -with datasets at the model resolution was added in. This was important for higher -resolutions so that large datasets do not have to be created before running the model, -nor are datasets for every resolution required. - - -What was new with &clm4010; Science since &ccsm4;? - -In general, snow layers should not be thinner than - -dzmin = wice/rhoice + wliq/rholiq - -If dz < dzmin, then the value of "void" computed in subroutine -SnowCompaction is negative, which is unphysical. This doesn't cause -problems with the compaction itself, but results in unrealistic values -of vol_ice, vol_liq, and eff_porosity in subroutine SnowWater. We can -have vol_ice = 1 and vol_liq = 0 even when liquid is present, which cuts -off the runoff (qout) from the lowest snow layer. Liquid water then -accumulates in the snow column without draining, which leads to further -problems and eventually a code crash. - - -The solution to this problem was to adjust layer thickness dz for any water+ice content -changes in excess of previous layer thickness, e.g., - -dz(c,j) = max(dz(c,j),h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice) - -at appropriate steps in the snow hydrology subroutines. - - - -Snow hydrology bug fix. -Add multiple elevation class option for glaciers so can interact with -the land ice sheet model. - - - - -What was new with &clm4010; Software since &ccsm4;? - -New configuration options - -glc_nec - - - -glc_nec can be 1,3,5, or 10 and MUST match the number on the input surface dataset -the elevation classes themselves are read from the surface dataset - - -New namelist items: - -carbon_only -create_glacier_mec_landunit -glc_dyntopo -ice_runoff -ndepmapalgo -scaled_harvest - - - -carbon_only = If true, and CLMCN carbon-nitrogen model is on, Nitrogen is unlimited - rather than prognosed and vegetation will be over-productive (replaces the supplemental Nitrogen #ifdef) - - - create_glacier_mec_landunit (= T when these landunits are created; F by default) - - - glc_dyntopo (= T if &clm; topography changes dynamically; currently F) - (NOT fully implemented yet) - - -ice_runoff = If true, river runoff will be split up into liquid and ice streams, - otherwise ice runoff will be zero and all runoff directed to liquid stream - - - ndepmapalgo = Mapping method from Nitrogen deposition input file to the model - resolution (can be bilinear,nn,nnoni,nnonj,spval,copy, bilinear by default) - - -scaled_harvest = If true, harvesting will be scaled according to coefficients - determined by Johann Feddema, 2009 - - -New history fields: - -aais_area Antarctic ice area (km^2) -aais_mask Antarctic mask (unitless) -gris_area Greenland ice area (km^2) -gris_mask Greenland mask (unitless) -QICE ice growth/melt (mm/s) -QICEYR ice growth/melt (mm/s) -QTOPSOIL water input to surface (mm/s) -VOLR RTM storage: LIQ (m3) -VOLR_ICE RTM storage: ICE (m3) - - - - - - - -What was new with &clm40; since &clm35;? - - -From &clm35; to &clm40; there were advances in both the science and the software infrastructure. -There were also new configure and namelist options as well as new history fields. In this -section we will describe each of these changes in turn. - - - -What was new with &clm40; Science? - -The following aspects are changes to the science in &clm40; since &clm35;. - - -Biogeophysics and Hydrology - -Changes to &clm40; beyond &clm35; (Oleson et al., 2008a; Stockli et al., 2008) include -updates throughout the model. The hydrology scheme has been modified with a revised -numerical solution of the Richards equation (Zeng and Decker, 2009; Decker and Zeng, -2009); a revised soil evaporation parameterization that removes the soil resistance term -introduced in &clm35; and replaces it with a so-called &Bgr; formulation, as well as accounts for the role of litter and within- -canopy stability (Sakaguchi and Zeng, 2009). -&clm4; also includes a representation of the thermal and hydraulic properties of organic -soil that operates in conjunction with the mineral soil properties (Lawrence and Slater, -2008). The ground column has been extended to ~50-m depth by adding five additional -hydrologically inactive ground layers (making a total of 15 ground layers, 10 soil -layers and 5 bedrock layers; Lawrence et al., 2008). An urban landunit and associated -urban canyon model (&clmu;) has been added which permits the study of urban climate -and urban heat island effects (Oleson et al., 2008b). - - - - -Snow Model - -The snow model is significantly modified via incorporation of SNICAR (SNow and Ice Aerosol Radiation) which represents the effect of aerosol deposition (e.g. black and organic carbon and dust) on albedo, introduces a grain-size dependent snow aging parameterization, and permits vertically resolved snowpack heating (Flanner and Zender, 2005; Flanner and Zender, 2006; Flanner et al., 2007). The new snow model also includes a new density-dependent snow cover fraction parameterization (Niu and Yang, 2007), a revised snow burial fraction over short vegetation (Wang and Zeng, 2009) and corrections to snow compaction (Lawrence and Slater, 2009). - - - - -Surface Datasets - -The PFT distribution is as in Lawrence and -Chase (2007) except that a new cropping dataset is used (Ramankutty et al., 2008) and -a grass PFT restriction has been put in place to reduce a high grass PFT bias in -forested regions by replacing the herbaceous fraction with low trees rather than grass. -Grass and crop PFT optical properties have been adjusted according to values presented -in Asner et al. (1998), resulting in significantly reduced albedo biases. Soil colors -have been re-derived according to the new PFT distribution. - - - - -Biogeochemistry - -The model is extended with a carbon-nitrogen biogeochemical model (Thornton et al., 2007; -Thornton et al., 2009; Randerson et al., 2009) which is referred to as &clmcn;. CN is -based on the terrestrial biogeochemistry Biome-BGC model with prognostic carbon and -nitrogen cycle (Thornton et al., 2002; Thornton and Rosenbloom, 2005). &clmcn; is -prognostic with respect to carbon and nitrogen state variables in the vegetation, litter, -and soil organic matter. Vegetation phenology and canopy heights are also prognostic. A -detailed description of the biogeochemical component can be found in Thornton et al. -(2007). Note that &clm40; can be run with either prescribed satellite phenology -(&clmsp;) or with prognostic phenology provided by the carbon- nitrogen cycle model -(&clmcn;). Additionally, a transient land cover and land use change, including wood harvest, -capability has been introduced that enables the evaluation of the impact of historic and -future land cover and land use change on energy, water, and momentum fluxes as well as -carbon and nitrogen fluxes. The dynamic global vegetation model in &clm3; has been -revised such that the carbon dynamics (e.g. productivity, decomposition, phenology, -allocation, etc.) are controlled by CN and only the dynamic vegetation biogeography -(competition) aspect of the &clm3; DGVM is retained. -The biogenic volatile organic compounds model (BVOC) that was available in &clm3; has -been replaced with the MEGAN BVOC model (Heald et al. 2008). - - - - -Miscellaneous Changes - -Several other minor changes have been incorporated including a change to the atmospheric reference height so that it is the height above zo+d for all surface types. The convergence of -canopy roughness length zo and displacement height d to bare soil values as the -above-ground biomass, or the sum of leaf and stem area indices, goes to zero is ensured -(Zeng and Wang, 2007). Several corrections have been made to the way the offline forcing -data is interpreted. The main change is a vastly improved and smooth diurnal cycle of -incoming solar radiation that conserves the total incoming solar radiation from the -forcing dataset. Additionally, in offline mode rather than partitioning incoming solar -radiation into a constant 70%/30% direct vs diffuse split, it is partitioned according to -empirical equations that are a function of total solar radiation. Finally, to improve -global energy conservation in fully coupled simulations, runoff is split into separate -liquid and ice water streams that are passed separately to the ocean. Input to the ice -water comes from excess snowfall in snow-capped regions. - - - - -Summary of Science Changes - -Taken together, these augmentations to &clm35; in &clm40; result in improved soil moisture dynamics -that lead to higher soil moisture variability and drier soils. Excessively wet and -unvarying soil moisture was recognized as a deficiency in &clm35; (Oleson et al. 2008a, -Decker and Zeng, 2009). The revised model also simulates, on average, higher snow cover, -cooler soil temperatures in organic-rich soils, greater global river discharge, lower -albedos over forests and grasslands, and higher transition-season albedos in snow covered -regions, all of which are improvements compared to &clm35;. - - - - - -What is new with &clm40; Software Infrastructure? - -The following aspects are changes to the software infrastructure in &clm40; since &clm35;. - - - - Update to cpl7 and scripts. - Remove offline and cpl6 modes. - Remove support for CASA model. - Update to datm8 atmospheric data model. - Add gx3v7 land mask for T31 and fv-4x5 horizontal resolutions. - Add gx1v6 land mask for f05, f09, and f19 horizontal resolutions. - Add tx1v1 land mask and 1.9x2.5_tx1v1 horizontal resolution. - Add in 2.5x3.33 horizontal resolution. - Add in T62 horizontal resolution so can run at same resolution as input &datm; -data. - Allow first history tape to be 1D. - Add ability to use own version of input datasets with &CLMUSRDAT; -variable. - Add a script to extract out regional datasets. - New &buildnml; system with XML file describing all namelist -items. - Add glacier_mec use-case and stub glacier model. - Make default of maxpatch_pft=numpft+1 instead of 4. - Only output static 3D fields on first h0 history file to save space. - Add new fields for VOC (Volatile Organic Compounds) on surface datasets, - needed for the new MEGAN VOC model. - Add multiple elevation class option for glaciers in mksurfdata tool (NOT used -in &clm; yet). - Add ascale field to land model in support of model running on it's own -grid. - - - - - -What are The New Configuration Options in &clm40;? - -Describe any changes made to build system: - - - -Change directory structure to match &ccsm;. -Add BGP target. -Add choice between ESMF and MCT frameworks. -Start removing #ifdef and directives that supported Cray-X1 Phoenix as now -decommissioned. -Make default of maxpatch_pft=numpft+1 instead of 4 for all -configurations. -By default turn on CLAMP when either CN or CASA is enabled -New SNICAR_FRC, CARBON_AERO, and C13 CPP ifdef tokens. - - - - -New options added to &configure;: -More information on options to &clm; &configure; are given in . - - - - -OptionDescription --comp_intf <name>Component interface to use (ESMF or MCT) (default -MCT) --nofireTurn off wildfires for bgc setting of CN (default includes -fire for CN) --pio <name>Switch enables building with Parallel I/O library. [on -| off] (default is on) --snicar_frc <name>Turn on SNICAR radiative forcing calculation. [on | -off] (default is off) - -More information on options to &clm; &configure; are given in . - - - - -What are The New Namelist Options in &clm40;? - -&buildnml; now checks the validity of your namelist you generate by looking at data in -the namelist_definition.xml file. In order to add new namelist items you need to -change the code and also edit this file (e.g. a namelist option required for your -research project that is not currently an option in &clm40;). To view information -on the namelist view the -file: models/lnd/clm/bld/namelist_files/namelist_definition.xml -in a browser and you'll see the names, type, description and valid_values for all -namelist variables. - - -Changes to &buildnml;: - -Allow simulation year entered to include ranges of years (i.e. 1850-2000) -Remove cam_hist_case option. -Make sure options ONLY used for stand-alone testing have a "drv_" or "datm_" - prefix in them and list these options all together and last when asking for - help from &buildnml;. - - - - New option to &buildnml;: - - -clm_usr_name "name" Dataset resolution/descriptor for personal datasets. - Default: not used - Example: 1x1pt_boulderCO_c090722 to describe location, - number of pts, and date files created - - - - New list options to &buildnml; - - cd models/lnd/clm/bld - ./&buildnml; -res list # List valid resolutions - ./&buildnml; -mask list # List valid land-masks - ./&buildnml; -sim_year list # List valid simulation years and simulation year ranges - ./&buildnml; -clm_demand list # List namelist variables including those you could - # demand to be set. - ./&buildnml; -use_case list # List valid use-cases - - - - -New use-cases for &buildnml;: - - 1850_control = Conditions to simulate 1850 land-use - 2000_control = Conditions to simulate 2000 land-use -20thC_transient = Simulate transient land-use, aerosol and Nitrogen deposition - from 1850 to 2005 - - - - - New namelist items: - - urban_hac = OFF, ON or ON_WASTEHEAT (default OFF) Flag for urban Heating - and Air-Conditioning - OFF = Building internal temperature is un-regulated. - ON = Building internal temperature is bounded to reasonable range. - ON_WASTEHEAT = Building internal temperature is bounded and resultant waste - heat is given off. - urban_traffic = .true. or .false. Flag to include additional multiplicative - factor of urban traffic to sensible heat flux. - (default .false.) - fsnowoptics = filename file for snow/aerosol optical properties (required) - fsnowaging = filename file for snow aging parameters (required) - -More information on the &buildnml; options are given in -. -and in -&CLMBLDNML;. - - -More information on the &buildnml; options are given in in . - - - - -What are The New History Fields? - -New history variables: (note watt vs. W in units, 26 vs. 76) - - - - -NameLong-nameUnitsActive/Inactive -BCDEPtotal BC deposition (dry+wet) from -atmospherekg/m^2/s -BIOGENCObiogenic CO -fluxuGC/M2/H -C13_PRODUCT_CLOSSC13 total carbon loss from wood product -poolsgC13/m^2/s -DSTDEPtotal dust deposition (dry+wet) from -atmospherekg/m^2/s -EFLX_DYNBALdynamic land cover change conversion energy -fluxW/m^2 -FGR12heat flux between soil layers 1 and -2watt/m^2 -FSATfractional area with water table at -surfaceunitless -FSH_NODYNLNDUSEsensible heat flux not including correction for land use change - watt/m^2 -GC_HEAT1initial gridcell total heat -contentJ/m^2 -GC_HEAT2post land cover change total heat -contentJ/m^2inactive -GC_ICE1initial gridcell total ice -contentmm/s -GC_ICE2post land cover change total ice -contentmm/sinactive -GC_LIQ1initial gridcell total liq -contentmm -GC_LIQ2initial gridcell total liq content -mminactive -H2OSNO_TOPmass of snow in top snow -layerkg - HEAT_FROM_ACsensible heat flux put into canyon due to heat -removed from air conditioningwatt/m^2 -HKhydraulic -conductivitymm/sinactive -ISOPRENEisoprene fluxuGC/M2/H -LAND_USE_FLUXtotal C emitted from land cover conversion and -wood product poolsgC/m^2/s -LAND_UPTAKENEE minus LAND_USE_FLUX, negative for -updategC/m^2/s -LWupupwelling longwave -radiationwatt/m^2inactive -MONOTERPmonoterpene -fluxuGC/M2/H -NBPnet biome production, includes fire, landuse, and harvest -flux, positive for sinkgC/m^2/s -OCDEPtotal OC deposition (dry+wet) from -atmospherekg/m^2/s -OVOCother VOC fluxuGC/M2/H -ORVOCother reactive VOC -fluxuGC/M2/H -PBOTatmospheric pressurePa -PCO2atmospheric partial pressure of -&CO2;Pa -PRODUCT_CLOSStotal carbon loss from wood product -poolsgC/m^2/s -PRODUCT_NLOSStotal N loss from wood product -poolsgN/m^2/s -Qairatmospheric specific -humiditykg/kginactive -Qanthanthropogenic heat -fluxwatt/m^2inactive -Qtaumomentum fluxkg/m/s^2 -QFLX_LIQ_DYNBALliq dynamic land cover change conversion -runoff fluxmm/s -QFLX_ICE_DYNBALice dynamic land cover change conversion -runoff fluxmm/s -QRUNOFF_NODYNLNDUSEtotal liquid runoff not including correction for land use change (does not include QSNWCPICE) -mm/s -QSNWCPICEexcess snowfall due to snow -cappingmm/s -QSNWCPICE_NODYNLNDUSEexcess snowfall due to snow capping not including correction for land use change -mm/s -QSNWCPLIQexcess rainfall due to snow -cappingmm/sinactive -SMPsoil matric -potentialmminactive -SNOAERFRC2Lsurface forcing of all aerosols in snow, averaged only when snow is present (land) -watt/m^2 -SNOAERFRCLsurface forcing of all aerosols in snow -(land)watt/m^2 -SNOBCFRCLsurface forcing of BC in snow -(land)watt/m^2 -SNOBCMCLmass of BC in snow -columnkg/m2 -SNOBCMSLmass of BC in top snow -layerkg/m2 -SNOdTdzLtop snow layer temperature gradient -(land)K/m -SNODSTFRC2Lsurface forcing of dust in snow, averaged only when snow is present (land) -watt/m^2 -SNODSTFRCLsurface forcing of dust in snow -(land)watt/m^2 -SNODSTMCLmass of dust in snow -columnkg/m2 -SNODSTMSLmass of dust in top snow -layerkg/m2 -SNOFSRNDdirect nir reflected solar radiation from -snowwatt/m^2inactive -SNOFSRNIdiffuse nir reflected solar radiation from -snowwatt/m^2inactive -SNOFSRVDdirect vis reflected solar radiation from -snowwatt/m^2inactive -SNOFSRVIdiffuse vis reflected solar radiation from -snowwatt/m^2inactive -SNOFSDSNDdirect nir incident solar radiation on -snowwatt/m^2inactive -SNOFSDSNIdiffuse nir incident solar radiation on -snowwatt/m^2inactive -SNOFSDSVDdirect vis incident solar radiation on -snowwatt/m^2inactive -SNOFSDSVIdiffuse vis incident solar radiation on -snowwatt/m^2inactive -SNOLIQFLtop snow layer liquid water fraction -(land)fractioninactive -SNOOCMCLmass of OC in snow -columnkg/m2 -SNOOCMSLmass of OC in top snow -layerKg/m2 -SNOOCFRC2Lsurface forcing of OC in snow, averaged only when snow is present (land) -watt/m^2 -SNOOCFRCLsurface forcing of OC in snow -(land)watt/m^2 -SNORDSLtop snow layer effective grain -radiusm^-6inactive -SNOTTOPLsnow temperature (top -layer)K/minactive -SWupupwelling shortwave -radiationwatt/m^2inactive -TSOI_10CMsoil temperature in top 10cm of -soilK -URBAN_ACurban air conditioning -fluxwatt/m^2 -URBAN_HEATurban heating -fluxwatt/m^2 -VOCFLXTtotal VOC flux into -atmosphereuGC/M2/H -Windatmospheric wind velocity -magnitudem/sinactive -WOOD_HARVESTCwood harvest (to product -pools)gC/m^2/s -WOOD_HARVESTwood harvest (to product -pools)gN/m^2/s - - - - - History field name changes: - - -OldNew -ANNSUM_PLANT_NDEMAND= -ANNSUM_POTENTIAL_GPP -ANNSUM_RETRANSN= ANNMAX_RETRANSN -C13_DWT_PROD10C_LOSS= C13_PROD10C_LOSS -C13_DWT_PROD100C_LOSS= C13_PROD100C_LOSS -C13_DWT_PROD10N_LOSS= C13_PROD10N_LOSS -C13_DWT_PROD100C_LOSS= C13_PROD100C_LOSS -DWT_PROD100N_LOSS= PROD10N_LOSS -DWT_PROD100N_LOSS= PROD100N_LOSS -DWT_PROD100C_LOSS= PROD10C_LOSS -DWT_PROD100C_LOSS= PROD100C_LOSS -HCSOISNO= HC -TEMPSUM_PLANT_NDEMAND= -TEMPSUM_POTENTIAL_GPP -TEMPSUM_RETRANSN= TEMPMAX_RETRANSN - - - -History field names deleted include: SNOWAGE, TSNOW, FMICR, FCO2, DMI, QFLX_SNOWCAP - - - -Add new urban oriented _U, and _R (Urban and Rural) for the following history variables: -EFLX_LH_TOT, FGR, FIRA, FSH, FSM, Q2M, QRUNOFF, RH2M, SoilAlpha, TG, TREFMNAV, -TREFMXAV, and TSA (missing _R for SoilAlpha as the regular SoilAlpha is only defined -for rural areas anyway) - - - -We are missing the Rural soil-alpha variable: SoilAlpha_R on purpose. -SoilAlpha_U is only defined over pervious road, and missing everywhere else. -SoilAlpha is defined only for rural areas. - - - - - - - - - - - -Quickstart to using &clm4; - -Before working with &clm4; read the QuickStart Guide in the -&cesmrel; -Scripts User's Guide. Once you are familiar with how to setup cases for -any type of simulation with &cesm; you will want to direct your attention to the specifics -of using &clm;. - - -For some of the details of setting up cases for &clm4; read the README and text files available -from the "models/lnd/clm/doc" directory (see the "&clm; Web pages" section for a link to the list -of these files). Here are the important ones that you should be familiar with. - -README file describing the directory structure. -Quickstart.userdatasets file describing how to -use your own datasets in the model (also see ). -&KnownBugs; file describing known -problems in &clm4; (that we expect to eventually fix). -KnownLimitations file -describing known limitations in &clm4; and workarounds that we do NOT expect to -fix. - - -The IMPORTANT_NOTES file is given in the next chapter on what -is functional/validated in &clm4;? - -The ChangeLog/ChangeSum files are largely explained in the previous chapter on "What is new with -&clm4;?" - -Note other directories have README files that explain different components and tools used -when running &clm; and are useful in -understanding how those parts of the model work and should be consulted when using tools in those directories. -For more details on configuring and customizing a case with &clm; see . - -The Quickstart.GUIDE (which can be found in -models/lnd/clm/doc) is repeated here. - -&quickstart_guide; - - - - -What is scientifically validated and functional in &clm4;? - -In this section we go over what has been extensively tested and scientifically validated -with &clm4;, and maybe more importantly what has NOT been tested and may NOT be -scientifically validated. You can use all features of &clm;, but need to realize that -some things haven't been tested extensively or validated scientifically. When you use -these features you may run into trouble doing so, and will need to do your own work to -make sure the science is reasonable. - - - -Standard Configuration and Namelist Options that are Validated - -The standard version of the model is &clmcn; at 1-degree horizontal resolution (0.9x1.25). This version has been scientifically -validated with long simulations for: fully coupled simulations ("B" cases), coupled to -atmosphere model CAM ("F" cases), and stand-alone &clm; -cases ("I" cases). We've also done both long simulations for 1850 conditions, and transient 20th century simulations from 1850 to 2005 (with -transient land-use, Nitrogen and Aerosol deposition). There have also been transient -future scenario simulations done for fully coupled cases for different "representative -concentration pathway" (RCP) scenarios (RCP2.6, RCP4.5, RCP6.0, and RCP8.5). -To a lesser extent there have also -been simulations done at T31 and 2-degree horizontal -resolution (1.9x2.5), and with &clmsp; for these resolutions. As such we have provided -appropriate 1-degree, 2-degree, and T31 initial condition -datasets for these configurations. The irrigation and prognostic crop models were both -validated at 2-degree resolution. The irrigation model for &clmsp; for present day -conditions for an "I" compset, and the prognostic crop model for present day conditions -for a case coupled to the active land model, but using a data ocean model (an "F" -compset). Other resolutions, configurations, and namelist options are less well tested or scientifically validated. -The further you get away from the standard configurations and resolutions, the more likely you are to run into trouble, and/or need to -scientifically validate your work. - - -In the sections below we go through configuration and/or namelist options or modes that the user should be especially wary of using. You -are of course free to use these options, and you may find that they work functionally. Although in some cases you will find issues even -with functionality of using them. If so you will need to test, debug and find solutions for these issues on your own. But in every case -you will need to go through more extensive work to validate these options from a scientific standpoint. - - - - -Configure Modes NOT scientifically validated, documented, supported or, in some -cases, even advised to be used: - - - - - C13(-c13) -The C13 mode for bgc=cn is NOT scientifically validated or documented and is NOT -recommended for use. - - - - - - CASA(-bgc casa) -The bgc=casa mode is NOT scientifically validated or documented and is NOT -recommended for use. - - - - - - SNICAR_FRC(-snicar_frc) - This mode is tested and functional, but is NOT constantly scientifically validated, and should be - considered experimental. - - - - - - - -Namelist options that should NOT be exercised: - -Build-Namelist options that should NOT be exercised: - - --irrig with -bgc cn -We have only run the irrigation model with &clmsp; (i.e. without the CN model). We -recommend that if you want to run the irrigation model with CN, that you do a spinup. -But, more than that you may need to make adjustments to -irrig_factor in -models/lnd/clm/src/biogeophys/CanopyFluxesMod.F90. See the -notes on this in the description of the irrigation model in the - -Technical Descriptions of the Interactive Crop Management and Interactive -Irrigation Models. - - --irrig with -crop on -Irrigation doesn't work with the prognostic crop model. Irrigation is only applied to -generic crop currently, which negates it's practical usage. We also have a known -problem when both are on (see bug 1326 in the &KnownBugs; file). -If you try to run in this mode, the &clm; &buildnml; will return with an error. - - --lnd_res: Fine-mesh mode, functional, but experimental - --rcp: Representative Concentration Pathway (RCP) -for future scenarios, functional for limited resolutions, but experimental - --datm_*: All options that start with "datm_" they are -only used for &clm; stand-alone testing. - --drv_*: All options that start with "drv_" they are -only used for &clm; stand-alone testing. - - - - - - -Namelist items that should NOT be exercised: - - -casa namelist options: lnpp, lalloc, q10, spunup, and fcpool - - CASA has NOT been scientifically validated in &clm4;. - - - - suplnitro='ALL' - The suplnitro namelist option to the CN Biogeochemistry model supplies -unlimited nitrogen and therefore vegetation is over-productive in this mode. - - - -urban_traffic: Not currently functional - - - - - - - - - -What are the UNIX utilities required to use &clm;? - -Running the &clm; requires a suite of UNIX utilities and programs and you should -make sure you have all of these available before trying to go forward with using -it. If you are missing one of these you should contact the systems administrator -for the machine you wish to run on and make sure they are installed. - -&FORTRAN90; compiler -"C" compiler -GNU make -UNIX csh and tcsh shells -UNIX sh shell -UNIX bash shell -UNIX awk -UNIX sed -&netcdf; library -MPI Library -"C" pre-processor -&perl; -Autoconf -m4 macro processor -Parallel &netcdf; (optional) -&ncl; (for some of the offline tools for creating/modifying &clm; input -datasets see for more information on &ncl;) -Python (optional, needed for &ptclm;) -xsltproc, docbook and docbook utilities (optional, needed to build the Users-Guide) -protex and latex2html (optional, needed to build the Code-Reference Guide) - - - - - - - - - &cesm; Online Bulletin Board - &cesmrel; Scripts User's Guide - - -Other resources to get help from - - -In addition to this users-guide there are several other resources that are available -to help you use &clm4;. The first one is the &cesm; User's-Guide, which documents the entire -process of creating cases with &cesm;. The next is the &cesm; bulletin board which is -a web-site for exchanging information between users of &cesm;. There are also &clm; -web-pages specific for &clm;, and finally there is an email address to report bugs that -you find in &cesm1;. - - - -The &cesm; User's-Guide - -&clmrel; is always run from within the standard &cesmrel; build and run scripts. Therefore, the -user of &clm4; -should familiarize themselves with the &cesmrel; scripts and understand how to work with them. -User's-Guide documentation on the &cesmrel; scripts are available from the following web-page. The purpose -of this &clmrel; User's Guide is to give the &clm4; user more complete details on how to work -with &clm; and the set of tools that support &clm;, as well as to give examples that are unique to the use -of &clm;. However, the &cesmrel; Scripts User's-Guide remains the primary source to get detailed -information on how to build and run the &cesm; system. - -&cesm1; Scripts -User's-Guide - - - - - -The &cesm; Bulletin Board - -There is a rich and diverse set of people that use the &cesm;, and often it is useful to be in contact with -others to get help in solving problems or trying something new. To facilitate this we have an online -Bulletin Board for questions on the &cesm;. There are also different sections in the Bulletin Board for -the different component models or for different topics. - -&cesm; Online Bulletin Board - - - - - -The &clm; web pages - -The main &clm; web page contains information on the &clm;, it's history, developers, as well as -downloads for previous model versions. There are also documentation text files in the -models/lnd/clm/doc directory that give some quick information on using &clm;. - -&clm; web page -&clm; Documentation Text Files - -Also note that several of the XML database files can be viewed in a web browser to get -a nice table of namelist options, namelist defaults, or compsets. Simply view them -as a local file and bring up one of the following files: - -models/lnd/clm/bld/namelist_files/namelist_definition.xml --- definition of &clm; namelist items. -models/lnd/clm/bld/namelist_files/namelist_defaults_clm.xml --- default values for &clm; namelist items. -scripts/ccsm_utils/Case.template/config_definition.xml --- definition of all env_*.xml items. -scripts/ccsm_utils/Case.template/config_compsets.xml --- definition of all the compsets. -models/lnd/clm/bld/namelist_files/history_fields.xml --- definition of &clm; history fields. - - - - - -Reporting bugs in &clm4; - -If you have any problems, additional questions, bug reports, or any other feedback, please send an email to -cesmhelp@cgd.ucar.edu. If you find bad, wrong, or misleading information - in this users guide send an email to erik@ucar.edu. The current list of -known issues for &clmrel; is in the &KnownBugs; file, and the list of issues for -&cesmrel; is at... - -&cesmwebmodelrel;/tags/cesm1_0_3/#PROBLEMS -. - - - - - - - - diff --git a/doc/UsersGuide/ptclm.xml b/doc/UsersGuide/ptclm.xml deleted file mode 100644 index 6c0ef2aec8..0000000000 --- a/doc/UsersGuide/ptclm.xml +++ /dev/null @@ -1,992 +0,0 @@ - - -How to run &ptclm; - -&ptclm; (pronounced point clime) is a Python script to help you set up PoinT CLM -simulations. It runs the &clm; tools for you to get datasets set up, and copies them -to a location you can use them according to the &CLMUSRDAT; naming convention. Then -it runs create_newcase for you and modifies the env settings and -namelist appropriately. &ptclm; has a simple ASCII text file for storing basic -information for your sites. We also have complete lists for AmeriFlux and Fluxnet-Canada -sites, although we only have the meteorology data for one site. For other sites you -will need to obtain the meteorology data and translate it to a format that the &cesm; -datm model can use. But, even without meteorology data &ptclm; is useful to setup -datasets to run with standard &CLMQIAN; data. - - - -The original authors of &ptclm; are: Daniel M. Ricciuto, Dali Wang, Peter E. Thornton, -Wilfred M. Post all at Environmental Sciences Division, Oak Ridge National Laboratory -(ORNL) and R. Quinn Thomas at Cornell University. It was then modified -fairly extensively by Erik Kluzek at &ncar;. We want to thank all of these individuals -for this contribution to the &cesm; effort. We also want to thank the folks at -University of Michigan Biological Stations (US-UMB) who allowed us to use their Fluxnet -station data and import it into our inputdata repository, especially Gil Bohrer the -PI on record for this site. - - - -Introduction to PTCLM - -To get help on &ptclm; use the "--help" option as follows. - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -> ./PTCLM.py --help - - - -The output to the above command is as follows: - - - -&ptclm_help; - - - - -Here we give a simple example of using &ptclm; for a straightforward case of running -at the US-UMB Fluxnet site on bluefire where we already have the meteorology data on -the machine. Note, see for permission information -to use this data. - -Example of running &ptclm; for US-UMB on bluefire - -setenv CSMDATA /fis/cgd/cseg/csm/inputdata -setenv MYCSMDATA $HOME/inputdata -setenv SITE US-UMB -setenv MYMACH bluefire -setenv MYCASE testPTCLM - -# First link the standard input files to a location you have write access -cd scripts -./link_dirtree $CSMDATA $MYCSMDATA - -# Next build all of the clm tools you will need -cd ../models/lnd/clm/tools/mksurfdata -gmake -gmake clean -cd ../mkdatadomain -gmake -gmake clean -cd ../mkgriddata -gmake -gmake clean -# next run PTCLM (NOTE -- MAKE SURE python IS IN YOUR PATH) -cd ../../../../../scripts/ccsm_utils/Tools/lnd/clm/PTCLM -./PTCLM.py -m $MYMACH --case=$MYCASE --site=$SITE --csmdata=$MYCSMDATA \ - --aerdepgrid --ndepgrid -# NOTE: we use --aerdepgrid --ndepgrid so that you use the global -# aerosol and Nitrogen deposition files rather than site-specific ones. -cd ../../../../../$MYCASE -# Finally configure, build, and run the case as normal - - - - - - -Guide to the options of &ptclm; - -There are three types of options to &ptclm;: required, configure/run-time, and -dataset generation options. The three required options are the three settings that -MUST be specified for &ptclm; to work at all. The other settings have default -values that will default to something useful. The configure/run-time options control -how the simulation will be setup and run. The dataset generation options control -the generation of datasets needed when &ptclm; is run. Most options use a double -dash "--" "longname" such as "--list", but the most common options also have a short-name -with a single dash (such as -m instead of --machine). - - -The required options to &ptclm; are: inputdata directory (-d), machine (-m) and -site-name (-s). Inputdata directory is the directory where you have the &cesm; -inputdata files, you need to have write access to this directory, so if you are -running on a machine that you do NOT have write access to the standard inputdata -location (such as &ncar; bluefire or ORNL jaguar) you need -to link the standard files to a location you do have control over. We recommend -using the scripts/link_dirtree tool to do that. "machine" is -the scripts name for the machine/compiler you will be using for your case. And -finally site-name is the name of the site that you want to run for. Site-name -can either be a valid &CLM1PT; supported dataset name or a Fluxnet site name -from the list of sites you are running on (see the --sitegroupname for more information -about the site lists). - - -After &ptclm; is run a case directory where you can then configure, build and run -your &cesm; case as normal. It also creates a README.PTCLM -in that directory that documents the commandline options to &ptclm; that were used -to create it. - - -After "help" the "list" option is one of the most useful options for getting -help on using &ptclm;. This option gives you information about some of the other -options to &ptclm;. To get a list of the machine, sites, and compsets that can be -used for &ptclm; use the "--list" option as follows. - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -> ./PTCLM.py --list - - - -The output to the above command is as follows: - - - -&ptclm_list; - - - - -Overview on using &ptclm; - -Steps in running &ptclm; - -Setup Inputdata directory with write access (use -<command>link_dirtree</command> script) - -You need to setup an inputdata directory where you have write access to it. -Normally, for &ncar; machines the data is on an inputdata where the user -does NOT have write access to it. A way that you can get around this is -to use the link_dirtree script to create softlinks from -the normal location to a location you have write access to. So for example -on bluefire: - -> setenv CSMDATA /fs/cgd/csm/inputdata -> setenv MYCSMDATA $HOME/inputdata -> mkdir $MYCSMDATA -> cd scripts -> ./link_dirtree $CSMDATA $MYCSMDATA - -See for more information on this. - - - -Build the &clm; tools - -Next you need to make sure all the &clm; &FORTRAN; tools are built. - -> cd models/lnd/clm/tools/mkgriddata -> gmake -> gmake clean -> cd ../mkdatadomain -> gmake -> gmake clean -> cd ../mksurfdata -> gmake -> gmake clean - - - - -Run &ptclm; - -Next you actually run &ptclm; which does the different things listed below: - - - -&ptclm; names your case based on your input - -&ptclm; names you case based on the input you give to it. - -[Prefix_]SiteCode_Compset[_QIAN][_spinuptype] -Where: - Prefix is from the caseidprefix option (or blank if not used). - SiteCode is the site name you entered with the -s option. - Compset is the compset name you entered with the -c option. - _QIAN is part of the name only if the useQIAN is used. - _spinuptype is part of the name if one of: ad_spinup, exit_spinup, or - final_spinup is used, and the exact spinup name chosen is used. - -For example, the casename for the following will be: - -> cd scripts -> ./PTCLM.py -m bluefire -s US-UMB -d $MYCSMDATA -c I_2000_CN --ad_spinup --useQIAN - -"US-UMB_I_2000_CN_QIAN_ad_spinup". - - - -&ptclm; creates datasets for you - -It will populate $MYCSMDATA with new datasets it creates using the -&clm; tools. - - - -If a transient compset and &ptclm; finds a <filename>_dynpftdata.txt</filename> -file - -If you are running a transient compset (such as the "I_1850-2000_CN" compset) -AND you there is a file in the PTCLM_sitedata directory under -the &ptclm; directory called $SITE_dynpftdata.txt it will use -this file for the land-use changes. Otherwise it will leave land-use constant, unless -you use the pftgrid option so it uses the global dataset for landuse changes. -See for more information on this. There -is a sample transient dataset called US-Ha1_dynpftdata.txt. -Transient compsets, are compsets that create transient land-use change and -forcing conditions such as: -'I_1850-2000', 'I_1850-2000_CN', 'I_RCP8.5_CN', 'I_RCP6.0_CN', 'I_RCP4.5_CN', -or 'I_RCP2.6_CN'. - - - -&ptclm; creates a <filename>pft-physiology</filename> for you - -&ptclm; will create a local copy of the pft-physiology -specific for your site that you could then customize with changes specific -for that site. - - - -&ptclm; creates a <filename>README.PTCLM</filename> for you - -&ptclm; will create a simple text file with the command line for it in a file -called README.PTCLM in the case directory it creates for you. - - - - - - -Customize, configure, build and run case as normal - -You then customize your case as you would normally. See the chapter for more information on doing this. - - - - - - - -Details on the options of &ptclm; - -Next we discuss the configure and run-time options, dividing them up into -configure, spinup, and run-time options. - - -Configure options include: - --c MYCOMPSET, --compset=MYCOMPSET ---caseidprefix=MYCASEID ---cesm_root=BASE_CESM ---namelist=NAMELIST ---rmold ---scratchroot=SCRATCHROOT ---sitegroupname=SITEGROUP ---QIAN_tower_yrs ---useQIAN - - - - - ---compset - -The "-c" option is the most commonly used option after the required options, as it -specifies the &cesm; scripts component set to use with &ptclm;. The default compset -is the "ICN" compset with CN on for present day conditions. - - - - - ---caseidprefix - -This option gives a prefix to include in the casename when the case is created, in -case you want to customize your casenames a bit. By default, casenames are figured -out based on the other options. The argument to this option can either be a name to -prefix casenames with and/or a pathname to include. Hence, if you want cases to -appear in a specific directory you can give the pathname to that directory with this -option. - - - - - ---cesm_root - -This option is for running &ptclm; with a different root directory to &cesm; than the -version &ptclm; exists in. Normally you do NOT need to use this option. - - - - - ---namelist - -This option adds any items given into the &clm; &usernlclm; namelist. This allows you to -add customizations to the namelist before the clm.buildnml.csh file -is created for the case. - - - - - ---rmold - -This option will remove an old case directory of the same name if one exists. Otherwise, -if an old case directory already exists and you try to run &ptclm; it will return with -an error. - - - - - ---scratchroot - -This option is ONLY valid when using one of the generic machines (the -m option). -This passed onto create_newcase and gives the location where cases -will be built and run. - - - - - ---sitegroupname - -In the &ptclm; directory there is a subdirectory "PTCLM_sitedata" that contains -files with the site, PFT and soil data information for groups of sites. These site groups -are all separate ASCII files with the same prefix followed by a "_*data.txt" name. -See for more information on these files. -By default we have provided three different valid group names: - -EXAMPLE -AmeriFlux -Fluxnet-Canada - -The EXAMPLE is the group used by default and ONLY includes the US-UMB site as that -is the only site we have data provided for. The other two site groups include the -site information for all of both the AmeriFlux and Fluxnet-Canada sites. You can use -the "sitegroupname" option to use one of the other lists, or you can create your own -lists using the EXAMPLE file as an example. Your list of sites could be real world -locations or could be theoretical "virtual" sites given to exercise &clm; on -differing biomes for example. Note, see with -permission information to use the US-UMB data. - - - - - ---useQIAN - -This option says to use the standard &clm; global Qian T62 atmospheric forcing rather -than any tower site forcing data available. Otherwise, &ptclm; will try to find tower -forcing data for the specific site entered. - - - - - ---QIAN_tower_yrs - -This option is used with the "useQIAN" option to set the years to cycle over for -the Qian data. In this case Qian atmospheric forcing will be used, but the -simulation will run over the same years that tower site is available for this site. - - - - - - -Spinup options include: - ---coldstart ---ad_spinup ---exit_spinup ---final_spinup ---finidat=FINIDAT - - - - -The spinup options enable the different CN spinup modes, but also set the run -length. The coldstart option says to startup with OUT an initial condition file, while -the finidat option explicitly gives the initial condition file to use. Obviously, -the different spinup options can NOT be used together, nor can the coldstart and -finidat options be either. - - ---coldstart - -This option ensures that a cold-start will be done with arbitrary initial conditions. - - - - - ---ad_spinup - -This option enables the accelerated decomposition mode when a CN compset is used. It -also sets the run-length as given in the example for running exit spinup in -. - - - - - ---exit_spinup - -This option enables the exit spinup mode when a CN compset is used. It also sets the -run-length to a year just as given in the example for running exit spinup in -. - - - - - ---final_spinup - -This option sets the run length as given in the example for a final spinup in -. This option can be used for any compset. - - -There is a bug in the final_spinup mode for setting the run length. Because of the -bug, final_spinup mode only runs for a very short time, you'll need to edit -the run length by hand to be 50 years. See bug 1367 in the &KnownBugs; file. - - - - - - - ---finidat - -This option sets the initial condition file to startup the simulation from. - - - - - - - - - -Run-time options include: - ---debug ---run_n=MYRUN_N ---run_units=MYRUN_UNITS ---stdurbpt - - - - - - - ---debug - -This option tells &ptclm; to echo what it would do if it were run, but NOT actually -run anything. So it will show you the dataset creation commands it would use. -It does however, run create_newcase, but then it only displays -the xmlchange commands and changes that it would do. Also note -that if you give the "--rmold" option it won't delete the case directory beforehand. -Primarily this is intended for debugging the operation of &ptclm;. - - - - - ---run_n - -This option along with run_units is used to set the length for the simulation. "run_n" -is the number of units to use. -The default run length depends on the site, compset, -and configuration and for example if a "spinup" option is selected. - - - - - ---run_units - -This option is the units of time to use for the length of the simulation. It is used -along with "run_n" to set the length of the simulation. -The default run length depends on the site, compset, -and configuration and for example if a "spinup" option is selected. - - - - - ---stdurbpt - -This option turns on the "stdurbpt_pd" use-case for &CLMUSECASE;. This option -can NOT be used for compsets that set the use-case to something besides present-day. - - - - - - - - -Lastly we discuss the dataset generation options. The dataset generation options are: - ---aerdepgrid ---ndepgrid ---pftgrid ---soilgrid ---nopointdata ---owritesrfaer - - - - -The options that with a "grid" suffix all mean to create datasets using the global -gridded information rather than using the site specific point data. By default the -site specific point data is used. The "nopointdata" and "owritesrfaer" options have to -do with file creation. - - -Because supported single-point datasets already have the data created for them, you -MUST use the "nopointdata" and "ndepgrid" options when you are using a supported -single-point site. You must use "ndepgrid" even for a compset without CN. You also -can NOT use the options: "soilgrid", "pftgrid", "aerdepgrid", or "owritesrfaer". - - - - - ---aerdepgrid - -This option says to use the aerosol deposition files from the global dataset rather -than creating an interpolated version. - - -This option must NOT be used when you you are using a site that -is a supported single point dataset. - - - - - ---ndepgrid - -This option says to use the Nitrogen deposition files from the global dataset rather -than creating an interpolated version. This is only needed for compsets with CN. - - - -This option is required when you you are using a site that -is a supported single point dataset. This is true even when you are NOT using a -compset with CN. - - - - - - ---pftgrid - -This option says to use the PFT values provided on the global dataset rather than -using the specific site based values from the -PTCLM_sitedata/*_pftdata.txt file when creating the surface dataset. - - -This option must NOT be used when you you are using a site that -is a supported single point dataset. - - - - - ---soilgrid - -This option says to use the soil values provided on the global dataset rather than -using the specific site based values from the -PTCLM_sitedata/*_soildata.txt file when creating the surface dataset. - - -This option must NOT be used when you you are using a site that -is a supported single point dataset. - - - - - ---nopointdata - -This option says to NOT create any input datasets -- assume this step has already been -done. If datasets weren't already created, your case will fail when you try to run it. -In general the first time you run &ptclm; for a new site you want it to generate new -datasets, but the next time and future times you want to use this option so that it -doesn't waste a lot of time rebuilding datasets over again. - - - -This option is required when you you are using a site that -is a supported single point dataset. - - - - - - ---owritesrfaer - -This option says to overwrite any surface and/or aerosol deposition datasets that -were already created. Otherwise, the creation of these files will be skipped if a file -is already found (but it WILL create files if they don't exist). - - -This option must NOT be used when you you are using a site that -is a supported single point dataset. - - - - - - - - -Note on the aerosol and Nitrogen deposition files. When the "aerdepgrid" and "ndepgrid" -options are NOT used -- aerosol and Nitrogen deposition files will be created by -interpolating from the global datasets. However, after these interpolated files -are created you could customize them for your site with data that you provide. You -could then write protect the files and use the "nopointdata" option so that &ptclm; -doesn't try to overwrite them in the future. - - - - - - -Examples using &ptclm; - -Now let's give a few more complex examples using some of the options we have -discussed above. - - -In this first example, we'll demonstrate using a supported single point dataset, -which then requires using the "nopointdata" and "ndepgrid" options. We'll also -demonstrate the compset option, "stdurbpt" and "caseidprefix" options. - -Example of running &ptclm; for the Mexicocity supported single point -dataset - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -> ./PTCLM.py -m bluefire -s 1x1_mexicocityMEX -d $CSMDATA --nopointdata --ndepgrid \ ---stdurbpt -c I --caseidprefix `pwd`/myPTCLMcases/site -> cd myPTCLMcases/site_1x1_mexicocityMEX_I -> ./configure -case -# Now build and run normally -> ./site_1x1_mexicocityMEX_I.bluefire.build -# Here we show running interactively -> ./site_1x1_mexicocityMEX_I.bluefire.run - - - - - -Now, let's demonstrate using a different group list, doing a spinup, running with Qian -global forcing data, but using tower years to set the years to run over. This uses -the options: sitegroupname, ad_spinup, useQIAN, and QIANtower_years. - -Example of running &ptclm; for a spinup simulation with Qian data for tower years. - - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -> ./PTCLM.py -m bluefire -s US-Ha1 -d $CSMDATA --sitegroupname AmeriFlux \ ---ad_spinup --useQIAN --QIAN_tower_yrs -> cd ../../../../../US-Ha1_ICN_QIAN_ad_spinup -> ./configure -case -# Now build and run normally -> ./US-Ha1_ICN_QIAN_ad_spinup.bluefire.build -# Here we show running interactively -> ./US-Ha1_ICN_QIAN_ad_spinup.bluefire.run - - - - - -Finally, let's demonstrate using a generic machine (which then requires the scratchroot -option), using the global grid for PFT and soil types, and setting the run length -to two months. - -Example of running &ptclm; on a generic machine with global PFT and soil types -dataset - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -# Note, see the with permission information -# to use the US-UMB data. -> ./PTCLM.py -m generic_darwin_intel -s US-UMB -d $CSMDATA --pftgrid --soilgrid \ ---scratchroot $HOME --run_n 2 --run_units nmonths -> cd ../../../../../US-UMB_ICN -> ./configure -case -# Now build -> ./US-UMB_ICN.generic_darwin_intel.build -# To get the files from the svn server... -# First list the files from the streams text file -> ../ccsm_utils/Tools/listfilesin_streams \ --t $HOME/US-UMB_ICN/run/clm1PT.1x1pt_US-UMB.stream.txt -l \ -> Buildconf/datm.input_data_list -# And now run the script to export data to your machine -> ../ccsm_utils/Tools/check_input_data -export -# Here we show running interactively -> ./US-UMB_ICN.generic_darwin_intel.run - - - - -Because of Bug 1364, when running this case as above we get a floating point -error after reaching time-step 124 for the example exactly as above. Other -machines or compilers probably won't have this problem. See the &KnownBugs; file -for more information on this problem. - - - - -As documented in Bug 1368, spinning up the US-UMB site for a I2000CN compset gives -zero Gross Primary Production (GPP). If the user wishes to use this site for &clmcn;, -they'll need to address this issue. -See the &KnownBugs; file for more information on this problem. - - - - - - -Adding data for use by &ptclm; - -&ptclm; Group Site Lists - -The "sitegroupname" option to &ptclm; looks for groups of sites in the -files in the PTCLM_sitedata directory under the &ptclm; directory. -You can add new names available for this option including your own lists of sites, by -adding more files in this directory. There are three files for each "sitegroupname": -$SITEGROUP_sitedata.txt, -$SITEGROUP_soildata.txt -and $SITEGROUP_pftdata.txt (where $SITEGROUP is the name that would -be entered as "sitegroupname" to &ptclm;). Each file needs to have the same list of sites, -but gives different information: site data, PFT data, and soil data respectively. -Although the site codes need to be the same between the three files, the files do NOT -have to be in the same order. Each file has a one-line header that lists the contents -of each column which are separated by commas. The first column for each of the files -is the "site_code" which must be consistent between the three files. The site code -can be any unique character string, but in general we use the AmeriFlux site code. - - -Site data file: $SITEGROUP_sitedata.txt): The header for -this file is: - -site_code,name,state,lon,lat,elev,startyear,endyear,alignyear - -The columns: name, state, and elevation are informational only. Name is a longer -descriptive name of the site, and state is the state for U.S. sites or country -for non U.S. sites. The columns: lon and lat are the longitude and latitude of -the location in decimal degrees. The last three columns are the start and ending -year for the data and the align year for an 1850 case for the data. The align year -is currently unused. - - -Soil data file: $SITEGROUP_soildata.txt): The header for this -file is: - -site_code,soil_depth,n_layers,layer_depth,layer_sand%,layer_clay% - -The first three fields after "site_code" are currently unused. The only two that -are used are the percent sand and clay columns to set the soil texture. - - -PFT data file: $SITEGROUP_pftdata.txt): The header for this -file is: - -site_code,pft_f1,pft_c1,pft_f2,pft_c2,pft_f3,pft_c3,pft_f4,pft_c4,pft_f5,pft_c5 - -This file gives the vegetation coverage for the different vegetation types for the site. -The file only supports up to five PFT's at the same time. The columns with "pft_f" are -the fractions for each PFT, and the columns with "pft_c" is the integer index of the -given PFT. Look at the pft-physiology file to see what the PFT index for each PFT type -is. - - - - -Dynamic Land-Use Change Files for use by &ptclm; - -There is a mechanism for giving site-specific land-use change in &ptclm;. Adding -site specific files to the PTCLM_sitedata directory under -&ptclm; allows you to specify the change in vegetation and change in harvesting -(for the CN model) for that site. Files are named: -$SITE_dynpftdata.txt. There is a sample file for the US-Ha1 -site called: US-Ha1_dynpftdata.txt. The file has a one-line -header with the information that the file has, and then one-line for each year -with a transition. The header line is as follows: - -trans_year,pft_f1,pft_c1,pft_f2,pft_c2,pft_f3,pft_c3,pft_f4,pft_c4,pft_f5,pft_c5,har_vh1,har_vh2,har_sh1,har_sh2,har_sh3,graze,hold_harv,hold_graze - -This file only requires a line for each year where a transition or harvest happens. As -in the "pftdata" file above "pft_f" refers to the fraction and "pft_c" refers to the -PFT index, and only up to five vegetation types are allowed to co-exist. The last -eight columns have to do with harvesting and grazing. The last two columns are whether -to hold harvesting and/or grazing constant until the next transition year and will -just be either 1 or 0. This file will be converted by the -PTCLM_sitedata/cnvrt_trnsyrs2_landuse_timeseries_txtfile.pl script in the &ptclm; -directory to a format that mksurfdata can read that has an entry -for each year for the range of years valid for the compset in question. - - - - -Converting AmeriFlux Data for use by &ptclm; - -AmeriFlux data comes in comma separated format and is available from: - -http://public.ornl.gov/ameriflux/dataproducts.shtml. Before you -download the data you need to agree to the usage terms. - - -Here is a copy of the usage terms from the web-site on June/13/2011. - - -"The AmeriFlux data provided on this site are freely available and were furnished by -individual AmeriFlux scientists who encourage their use. Please kindly inform the -appropriate AmeriFlux scientist(s) of how you are using the data and of any publication -plans. Please acknowledge the data source as a citation or in the acknowledgments if the -data are not yet published. If the AmeriFlux Principal Investigators (PIs) feel that they -should be acknowledged or offered participation as authors, they will let you know and we -assume that an agreement on such matters will be reached before publishing and/or use of -the data for publication. If your work directly competes with the PI's analysis they may -ask that they have the opportunity to submit a manuscript before you submit one that uses -unpublished data. In addition, when publishing, please acknowledge the agency that -supported the research. Lastly, we kindly request that those publishing papers using -AmeriFlux data provide preprints to the PIs providing the data and to the data archive at -the Carbon Dioxide Information Analysis Center (CDIAC)." - - -The above agreement applies to the "US-UMB" dataset imported into our repository as -well, and Gil Bohrer is the PI on record for that dataset. - - -The &cesm; can NOT handle missing data, so we recommend using the "Level 4" Gap filled -datasets. -The fields will also need to be renamed. The "WS" column becomes "WIND", "PREC" becomes -"PRECmms", "RH" stays as "RH", "TA" becomes "TBOT", "Rg" becomes "FSDS", "Rgl" becomes -"FLDS", "PRESS" becomes "PSRF". "ZBOT" can just be set to the constant of "30" (m). -The units of Temperature need to be converted from "Celsius" to "Kelvin" (use the -value in SHR_CONST_TKFRZ in the file -models/csm_share/shr/shr_const.F90 of 273.15. -The units of Pressure also need to be converted from "kPa" to "Pa". LATIXY, and -LONGXY should also be set to the latitude and longitude of the site. - - - -&ptclm; transient example over a shorter time period - - -Example of running &ptclm; for transient land-use 1991-2006 for US-Ha1 on bluefire - -This is an example of using &ptclm; for Harvard Forest (AmeriFlux site code US-Ha1). In -order to do this we would've needed to have converted the AmeriFlux data into &netcdf; -format as show in the section above. Also note -that this site has a site-specific dynamic land-use change file for it -PTCLM_sitedata/US-Ha1_dynpftdata.txt in the &ptclm; directory -and this file will be used for land-use change and harvesting rather than the -global dataset. - - -> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM -# We are going to use forcing data over 1991 to 2006, but we need to start with -# a transient compset to do so, so we use the 20th Century transient: 1850-2000 -# Note: When creating the flanduse_timeseries dataset for this site it will use the -# PTCLM_sitedata/US-Ha1_dynpftdata.txt -# file for land-use change and harvesting -> ./PTCLM.py -m bluefire -s US-Ha1 -d $MYCSMDATA --sitegroupname AmeriFlux \ --c I_1850-2000_CN -> mkdir $MYCSMDATA/atm/datm7/CLM1PT_data/1x1pt_US-Ha1 -> cd $MYCSMDATA/atm/datm7/CLM1PT_data/1x1pt_US-Ha1 -# Copy data in &netcdf; format to this directory, filenames should be YYYY-MM.nc -# The fieldnames on the file should be: -# FLDS,FSDS,LATIXY, LONGXY, PRECTmms,PSRF,RH,TBOT,WIND,ZBOT -# With units -# W/m2,W/m2,degrees_N,degrees_E,mm/s, Pa, %, K, m/s, m -# The time coordinate units should be: days since YYYY-MM-DD 00:00:00 -> cd ../../../../../US-Ha1_I_1850-2000_CN -# We need to turn cold-start on, so it doesn't expect an initial condition file -# preferably, you would generate your own initial condition file and then use -# the --finidat option to &ptclm; to enter it -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -# Now we need to set the start date to 1991, and have it cycle forcing data -# over 1991 to 2006 -> ./xmlchange -file env_conf.xml -id RUN_STARTDATE -val 1991-01-01 -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_ALIGN -val 1991 -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_END -val 2006 -> ./xmlchange -file env_conf.xml -id CLM_NAMELIST_OPTS -val \ -# Similarly for Nitrogen deposition data we cycle over: 1991 to 2006 -"model_year_align_ndep=1991,stream_year_first_ndep=1991,stream_year_last_ndep=2006" -# Now configure the case, and we'll edit the datm namelist for prescribed aerosols -> ./configure -case -# We also need to change the datm to run with aerosols over the 1991-2006 period -cat << EOF > patch.diff -*** datm.buildnml.csh.orig 2011-06-14 09:28:20.000000000 -0600 ---- datm.buildnml.csh 2011-06-14 09:28:57.000000000 -0600 -*************** -*** 32,38 **** - dataMode = 'CLMNCEP' - domainFile = '$DOMAINFILE' - streams = 'clm1PT.1x1pt_US-Ha1.stream.txt 1991 1991 2006 ', -! 'presaero.stream.txt 1849 1849 2006' - vectors = 'null','null' - mapmask = 'nomask','nomask' - mapalgo = 'nn','nn' ---- 32,38 ---- - dataMode = 'CLMNCEP' - domainFile = '$DOMAINFILE' - streams = 'clm1PT.1x1pt_US-Ha1.stream.txt 1991 1991 2006 ', -! 'presaero.stream.txt 1991 1991 2006' - vectors = 'null','null' - mapmask = 'nomask','nomask' - mapalgo = 'nn','nn' -EOF -# Apply the above patch to the datm build namelist file -> patch Buildconf/datm.buildnml.csh patch.diff - - - - - - -Because of bug 1361, this won't work out of the box. You'll need to add the change -to PTCLM.py given in the KnownBugs file on this issue. - - - - - - - - -A bit about the structure of &ptclm;, what it does, and how it works - -A large part of &ptclm; just sets up the different options and does error checking -on the options given. &ptclm; then uses the options provided to use -create_newcase to create a new case. It then queries both the -case directory and/or the XML database (using -queryDefaultNamelist.pl in models/lnd/clm/bld -and does other settings for the case. It then runs the different &clm; tools in turn to -create the necessary datasets and points to them in the case with the &CLMUSRDAT; option. -It runs mkgriddata, mksurfdata.pl, and -mkdatadomain as well as the aerdepregrid.ncl and -ndepregrid.ncl &ncl; scripts. mkgriddata and -mkdatadomain have template namelist files in the -scripts/ccsm_utils/Tools/lnd/clm/PTCLM/usr_files directory. -When running mksurfdata.pl if it finds a -$SITE_dynpftdata.txt in the -scripts/ccsm_utils/Tools/lnd/clm/PTCLM/PTCLM_sitedata directory -it will use that file for transient landuse changes (there's a sample file for -"US-Ha1" called US-Ha1_dynpftdata.txt). -It modifies the different env*.xml using -xmlchange and creates an initial &usernlclm; filename. After -&ptclm; is run you can then make changes to the case by hand, and configure, build -and run as normal. - - -There is a simple test script to test &ptclm;. See -for more information on using it. - - - - - diff --git a/doc/UsersGuide/single_point.xml b/doc/UsersGuide/single_point.xml deleted file mode 100644 index b07f76ecb6..0000000000 --- a/doc/UsersGuide/single_point.xml +++ /dev/null @@ -1,930 +0,0 @@ - - - -How to run Single-Point/Regional cases - -The &clm; also allows you to set up and run cases with a single-point or a local region as well -as global resolutions. This is often useful for running quick cases for testing, evaluating -specific vegetation types, or land-units, or running with observed data for a specific site. -There are four different ways to do this: &PTSMODE;, -&CLM1PT;, &CLMUSRDAT;, and with &ptclm;. - -&PTSMODE; -- to run for a single point -using global datasets. -&CLM1PT; -- to run for a supported single-point -or regional dataset. -&CLMUSRDAT; -- to run using your own datasets (single-point -or regional). -&ptclm; -- to easily setup simulations to run for -tower sites.. - - - - -&PTSMODE; and &ptclm; only work for a single point, while the other two options can -also work for regional datasets as well. - - - -Which Single Point Option Should I choose? - -In general is the quick and dirty method -that gets you started without having to create datasets -- but has limitations. It's -good for an initial attempt at seeing results for a point of interest, but since you -can NOT restart with it, it's usage is limited. It is the quickest method as you can -create a case for it directly from create_newcase. Although you -can't restart, running a single point is very fast, and you can run for long -simulation times even without restarts. If you need restarts a good solution is to use -getregional_datasets.pl and &CLMUSRDAT; -which can get you running almost as quickly as well as -&PTSMODE;. Like -&PTSMODE; - only runs for points that exist within -a global dataset. - - -Running &CLM1PT; is a great solution, if one of the supported -single-point/regional datasets, is your region of interest (see -). All the datasets are -created for you, and you can easily select one and run, pretty much, out of the box -with it. The problem is that there is a very limited set of supported datasets. You -can also use this method for your own datasets, but you have to create the datasets, -and add them to the XML database and to the &datm;. This is worthwhile if you want to -repeat many multiple cases for a given point or region. - - -Next, &CLMUSRDAT; is the best way to setup cases quickly -where you have to create your own datasets (see -). With this method you don't have to -change &datm; or add files to the XML database -- but you have to follow a strict -naming convention for files. However, once the files are named and in the proper -location, you can easily setup new cases that use these datasets. This is good -for treating all the required datasets as a "group" and for a particular -model version. For advanced &clm; developers who need to track dataset changes with -different model versions you would be best off adding these datasets as supported -datasets with the &CLM1PT; method. - - -Lastly &ptclm; is a great way to easily create datasets, -setup simulations and run simulations for tower sites. It takes advantage of both -&CLM1PT; and &CLMUSRDAT; internally. A big advantage to it, is that it's one-stop -shopping, it runs tools to create datasets, and runs create_newcase -and sets the appropriate env variables for you. So you only have to learn how to run -one tool, rather than work with many different ones. &ptclm; is described in the next -chapter . - - -Finally, if you also have meteorology data that you want to force your &clm; simulations -with you'll need to setup cases as described in . -You'll need to create &clm; datasets either according to &CLM1PT; -or &CLMUSRDAT;, but you'll also need to modify &datm; to use -your forcing data. And you'll need to change your forcing data to be in a format that -&datm; can use. In the &ptclm; chapter the -section tells you how to use AmeriFlux data for atmospheric forcing. - - - - -Running &PTSMODE; configurations - -&PTSMODE; enables you to run the model using global datasets, but just picking a -single point from those datasets and operating on it. It can be a very quick way to do fast -simulations and get a quick turnaround. - - -To setup a &PTSMODE; simulation you use the "-pts_lat" and "-pts_lon" -arguments to create_newcase to give the latitude and longitude of the point you want to -simulate for (the code will pick the point on the global grid nearest to the point you -give. Here's an example to setup a simulation for the nearest point at 2-degree resolution -to Boulder Colorado. - -> cd scripts -> ./create_newcase -case testPTS_MODE -res f19_g16 -compset I -mach bluefire \ --pts_lat 40.0 -pts_lon -105 -> cd testPTS_MODE -# We make sure the model will start up cold rather than using initial conditions -> ./xmlchange -file env_conf.xml -id &CLMFORCECOLD; -val on -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup - -Then configure, build and run as normal. We make sure initial conditions are NOT used -since &PTSMODE; currently CAN NOT run with initial conditions. - - - -By default it sets up to run with -USE_MPISERIAL (in the env_build.xml file) turned on, -which allows you to run the model interactively. On some machines this mode is NOT -supported and you may need to change it to FALSE before you are able to build. - - - - -&PTSMODE; currently does NOT restart nor -is it able to startup from global initial condition files. See bugs "1017 and 1025" -in the KnownLimitations file. - - - - -You can change the point you are simulating for at run-time by changing the values of -PTS_LAT and PTS_LON in the env_run.xml file. - - - - -Note, that when running with &PTSMODE; the number of processors -is automatically set to one. When running a single grid point you can only use a single -processor. You might also want to set the "env_conf" variable: USE_MPISERIAL to -TRUE so that you can also run interactively without having to use -&mpi; to start up your job. - - - - -Warning about Running with a Single-Processor on a Batch Machine - -This problem always comes up when running for a single point, because you can only use -a single-processor, but may come up in other instances when you are running with -one processor. This applies to all the different ways of running in single-point mode. - - - -A warning for submitting single-point simulations to the batch que when only using -one processor. On many machines this will mean using up at least an entire node, and -being charged for all the CPU's on that node even if you aren't using them. For example, -on the &ncar; machine bluefire, there are 32 processors for each node -and the batch scripts are setup to have exclusive use of that node (and hence be charged -for all 32 processors). There are similar issues on other machines, below we show you -what to do when running on bluefire. - - -To change this on bluefire -- change the following: - -#BSUB -q regular -#BSUB -N -#BSUB -x - -to... - -#BSUB -q share -#BSUB -N - -so remove the "#BSUB -x" which gives you the entire node exclusively, and change to the -share que. One other machines you may have to do something similar, but the particulars -depend on the given machine, hence you will need to consult with the system -administrators for the given machine you are running on. - - - - -Another similar problem on many machines is that some batch ques have a minimum number -of nodes or processors that can be used. On these machine you may have to change the -queue (in some way similar to the above for bluefire) and possibly the time-limits of -the job, to get it to run in the batch que. - - - -Another way to get around this problem is to run the job interactively using -USE_MPISERIAL so that you don't submit the job to the batch que. -For single point mode you also may want to consider using a smaller workstation or -cluster, rather than a super-computer, because you can't take advantage of the -multi-processing power of the super-computer anyway. - - - - -Running Supported Single-point/Regional Datasets - -In addition to &PTSMODE; the &clm; supports running using single-point or -regional datasets that are customized to a particular region. In the section below we -tell the user how to create their own dataset, but we also support a small number of -single-point and regional datasets that are ready to setup and run in the CESM modeling -system. - - -To get the list of supported dataset resolutions see the method given in the -section on use of &CLM1PT;, which results in the following: - -&res_list; - -The resolution names that have an underscore in them ("_") are all single-point or -regional resolutions. -To run with the supported single-point and regional datasets, you setup a simulation for the -"pt1_pt1" resolution and give the short-name for the file to use in the -env_conf.xml file. - - -To run for the Brazil test site -do the following: - -Example of running &clm; over a single-point test site in Brazil -with the default Qian atmosphere data forcing. - - -> cd scripts -> ./create_newcase -case testSPDATASET -res pt1_pt1 -compset I \ --mach bluefire -> cd testSPDATASET -# Configure to run for the test site -> set SITE=1x1_brazil -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-sitespf_pt $SITE" -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val $SITE - - - - -Then configure, build and run normally. - - -Then to run for the urban Mexico City Mexico test site that also has atmosphere -forcing data, but to run it with the Qian forcing data, but over the period for -which it's own forcing data is provided do the following: - -Example of running &clm; over the single-point of Mexicocity Mexico -with the default Qian atmosphere data forcing. - - -> cd scripts -> ./create_newcase -case testSPDATASET -res pt1_pt1 -compset I \ --mach bluefire -> cd testSPDATASET -# Set a variable to the site you want to use (as it's used several times below) -> set SITE=1x1_mexicocityMEX -# Configure to run for the urban test site -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-sitespf_pt $SITE" -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val $SITE -# Set &datm; prescribed aerosols to single-point dataset -# Will then use the dataset with just the point for this $SITE -> ./xmlchange -file env_conf.xml -id DATM_PRESAERO -val pt1_pt1 -# -# Set some of the settings that are particular to this site, by values contained -# in the XML database. For some sites, or for new sites this information won't be -# stored. And the queryDefaultNamelist.pl command will abort. -# -# Set &datm; start and end range (optional just to run over the same years that -# atmospheric forcing data is available for this site) -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_START -val \ -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var datm_cycle_beg_year -justvalue` -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_END -val \ -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var datm_cycle_end_year -justvalue` - - - - -Then configure, build and run normally. - - - -Just like &PTSMODE; above, By default it sets up to run with -USE_MPISERIAL (in the env_build.xml file) turned on, -which allows you to run the model interactively. On some machines this mode is NOT -supported and you may need to change it to FALSE before you are able to build. - - - - -See for a warning about running single-point jobs -on batch machines. - - - - -Note, that when running a pt1_pt1 resolution the number of processors -is automatically set to one. When running a single grid point you can only use a single -processor. You might also want to set the "env_conf" variable: USE_MPISERIAL to -TRUE so that you can also run interactively without having to use -mpi to start up your job. - - - -Running Supported Single-point Datasets that have their own Atmospheric Forcing - -Of the supported single-point datasets we have three that also have atmospheric forcing data -that go with them: Mexico City (Mexico), Vancouver, (Canada, British Columbia), and -urbanc_alpha (test data for an Urban inter-comparison project). Mexico city and Vancouver -also have "#ifdef" in the source code for them to work with modified urban data -parameters that are particular to these locations. They can be turned on by using -the &CLMCONFIG; &envconf; variable to set the "-sitespf_pt" option in the &clm; -&configure;. To turn on the atmospheric forcing for these datasets, you set the -&envconf; DATM_MODE variable to "CLM1PT", and then the atmospheric -forcing datasets will be used for the point picked. - - -When running with datasets that have their own atmospheric forcing you need to be careful -to run over the period that data is available. If you have at least one year of forcing -it will cycle over the available data over and over again no matter how long of a simulation -you run. However, if you have less than a years worth of data (or if the start date doesn't -start at the beginning of the year, or the end date doesn't end at the end of the year) then -you won't be able to run over anything but the data extent. In this case you will need to -carefully set the RUN_STARTDATE, START_TOD and -STOP_N/STOP_OPTION variables for your case to run over the entire time extent -of your data. For the supported data points, these values are in the XML database -and you can use the queryDefaultNamelist.pl script to query the values -and set them for your case (they are set for the three urban test cases: Mexicocity, Vancouver, and -urbanc_alpha). - - -In the example below we will show how to do this for the Vancouver, Canada point. - - -Example of running &clm; over the single-point of Vancouver Canada with -supplied atmospheric forcing data for Vancouver. - - -> cd scripts -# Create a case at the single-point resolutions -> ./create_newcase -case testSPDATASETnAtmForcing -res pt1_pt1 -compset I \ --mach bluefire -> cd testSPDATASETnAtmForcing -# Set a variable to the site you want to use (as it's used several times below) -> set SITE=1x1_vancouverCAN -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-sitespf_pt $SITE" -# Now set the CLM single-point variable to the site name -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val $SITE -# Set the aerosols to use the single-point dataset for 2000 conditions -# You could also use the default global dataset, but running would be a bit slower -> ./xmlchange -file env_conf.xml -id DATM_MODE -val CLM1PT -# Set the coupling frequency to once an hour -> ./xmlchange -file env_conf.xml -id ATM_NCPL -val 24 -# Set the standard namelist options for an urban test site -> ./xmlchange -file env_conf.xml -id CLM_NML_USE_CASE -val stdurbpt -# Set many of the settings that are particular to this site, by values contained -# in the XML database. For some sites, or for new sites this information won't be -# stored. And the queryDefaultNamelist.pl command will abort. -# -# Set the start date -> setenv RUN_STARTDATE \ -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var run_startdate -justvalue` -> setenv STARTDATE `echo $RUN_STARTDATE | sed s/-//g` -> @ START_YEAR = $STARTDATE / 10000 -> ./xmlchange -file env_conf.xml -id RUN_STARTDATE -val $RUN_STARTDATE -# Set the run length and start time of day -> ./xmlchange -file env_run.xml -id STOP_OPTION \ --val `../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist seq_timemgr_inparm -silent -var stop_option -justvalue` -> setenv STOP_N \ -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist seq_timemgr_inparm -silent -var stop_n -justvalue` -> ./xmlchange -file env_run.xml -id STOP_N -val $STOP_N -> ./xmlchange -file env_run.xml -id START_TOD \ --val `../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist seq_timemgr_inparm -silent -var start_tod -justvalue` -# Set &datm; start and end range... -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_START -val -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var datm_cycle_beg_year -justvalue` -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_END -val -`../../models/lnd/clm/bld/queryDefaultNamelist.pl -res $SITE \ --namelist default_settings -silent -var datm_cycle_end_year -justvalue` -# Set the User namelist to set the output frequencies of the history files -# Setting the stdurbpt use-case option create three history file streams -# The frequencies and number of time-samples needs to be set -> cat << EOF > &usernlclm; -&clm_inparm - hist_mfilt = $STOP_N,$STOP_N,$STOP_N - hist_nhtfrq = -1,-1,-1 -/ -EOF -# Set align year to start year as defined above -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_ALIGN -val $START_YEAR -# Set &datm; prescribed aerosols to single-point dataset -# Will then use the dataset with just the point for this site -> ./xmlchange -file env_conf.xml -id DATM_PRESAERO -val pt1_pt1 -> ./configure -case - - - - -If you don't set the start-year and run-length carefully as shown above the -model will abort with a "dtlimit error" in the atmosphere model (see bug 1110 in -the KnownLimitations file for documentation on this). Since, the forcing data for -this site (and the MexicoCity site) is less than a year, the model won't be able to -run for a full year. The 1x1_urbanc_alpha site has data for more -than a full year, but neither year is complete hence, it has the same problem (see the -problem for this site above). - - - - -Just like &PTSMODE; above, By default it sets up to run with -USE_MPISERIAL (in the env_build.xml file) turned on, -which allows you to run the model interactively. On some machines this mode is NOT -supported and you may need to change it to FALSE before you are able to build. - - - - -See for a warning about running single-point jobs -on batch machines. - - - - -Note, that when running a pt1_pt1 resolution the number of processors -is automatically set to one. When running a single grid point you can only use a single -processor. You might also want to set the "env_conf" variable: USE_MPISERIAL to -TRUE so that you can also run interactively without having to use -mpi to start up your job. - - - - - - -Creating your own single-point/regional surface datasets - -The file: -Quickstart.userdatasets in the -models/lnd/clm/doc directory gives guidelines on how to create and run -with your own single-point or regional datasets. Below we reprint the above guide. - -&quickstart_userdata; - - - - -Using getregional_datasets.pl to get a complete suite of single-point/regional -surface datasets from global ones - -Use the regional extraction script to get regional datasets from the global ones -The getregional_datasets.pl script to extract out regional datasets of interest. -Note, the script works on all files other than the "finidat" file as it's a 1D vector file. -The script will extract out a block of gridpoints from all the input global datasets, -and create the full suite of input datasets to run over that block. The input datasets -will be named according to the input "id" you give them and the id can then be used -as input to &CLMUSRDAT; to create a case that uses it. See -the section on &clm; Script Configuration Items for -more information on setting &CLMUSRDAT; (in ). The list of files extracted by -their name used in the namelists are: -fatmgrid, fatmlndfrc, -fsurdat, flanduse_timeseries, -stream_fldfilename_ndep, and the &datm; files -domainfile, and faerdep. -For more information on these files see the Table on required files. - - -The alternatives to using this script are to use &PTSMODE;, -discussed earlier, to use &ptclm; discussed in the next chapter, or creating the files -individually using the different file creation tools (given in the -Tools Chapter). Creating -all the files individually takes quite a bit of effort and time. &PTSMODE; -has some limitations as discussed earlier, but also as it uses global files, is -a bit slower when running simulations than using files that just have the set -of points you want to run over. Another advantage is that once you've created the -files using this script you can customize them if you have data on this specific -location that you can replace with what's already in these files. - - -The script requires the use of both "Perl" and "NCL". See the NCL Script section in the Tools Chapter -on getting and using NCL and NCL scripts. The main script to use is a &perl; script -which will then in turn call the NCL script that actually creates the output files. -The ncl script gets it's settings from environment variables set by the perl script. -To get help with the script use "-help" as follows: - -> cd models/lnd/clm/tools/ncl_scripts -> ./getregional_datasets.pl -help - -The output of the above is: - -&getreg_datasets; - - - -The required options are: -id, --ne, and -se, for the output identifier -name to use in the filenames, latitude and longitude of the Northeast corner, and -latitude and longitude of the SouthEast corner (in degrees). Options that specify -which files will be used are: -mask, -res, --rcp, -sim_year, and -sim_yr_rng -for the land-mask to use, global resolution name, representative concentration pathway -for future scenarios, simulation year, and simulation year range. The location of the -input and output files will be determined by the option -mycsmdata -(can also be set by using the environment variable $CSMDATA). If -you are running on a machine like at &ncar; where you do NOT have write permission -to the CESM inputdata files, you should use the scripts/link_dirtree -script to create soft-links of the original files to a location that you can write -to. This way you can use both your new files you created as well as the original -files and use them from the same location. - - -The remaining options to the script are -debug, -and -verbose. -debug is used to show what -would happen if the script was run, without creating the actual files. --verbose adds extra log output while creating the files so you -can more easily see what the script is doing. - - -For example, Run the extraction for data from 52-73 North latitude, 190-220 longitude -that creates 13x12 gridcell region from the f19 (1.9x2.5) global resolution over Alaska. - -Example of running <command>getregional_datasets.pl</command> to get -datasets for a specific region over Alaska - -> cd scripts -# First make sure you have a inputdata location that you can write to -# You only need to do this step once, so you won't need to do this in the future -> setenv MYCSMDATA $HOME/inputdata # Set env var for the directory for input data -> ./link_dirtree $CSMDATA $MYCSMDATA -> cd ../models/lnd/clm/tools/ncl_scripts -> ./getregional_datasets.pl -sw 52,190 -ne 73,220 -id 13x12pt_f19_alaskaUSA -mycsmdata $MYCSMDATA - - -Repeat this process if you need files for multiple sim_year, resolutions, land-masks, -and sim_year_range values. - - - -See for a warning about running single-point jobs -on batch machines. - - - - -See for notes about managing your data -when using link_dirtree. - - - -Now to run a simulation with the datasets created above, you create a single-point -case, and set &CLMUSRDAT; to the identifier used above. Note that in the example below -we set the number of processors to use to one (-pecount 1). For a single point, you -should only use a single processor, but for a regional grid, such as the example below -you could use up to the number of grid points (12x13=156 processors. - - -Example of using &CLMUSRDAT; to run a simulation using user datasets for a -specific region over Alaska - -> cd scripts -# Create the case and set it to only use one processor -> ./create_newcase -case my_userdataset_test -res pt1_pt1 -compset I1850 \ --mach bluefire -> cd my_userdataset_test/ -> ./xmlchange -file env_run.xml -id DIN_LOC_ROOT_CSMDATA -val $MYCSMDATA -> ./xmlchange -file env_conf.xml -id &CLMUSRDAT; -val 13x12pt_f19_alaskaUSA -> ./xmlchange -file env_conf.xml -id &CLMBLDNML; -val '-mask gx1v6' -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val 13x12pt_f19_alaskaUSA -> ./configure -case - - - - - - - -Running with your own atmosphere forcing - -Here we want to run with our own customized datasets for &clm; as well as -running with our own supplied atmosphere forcing datasets. Thus we effectively -combine the information from with -. First we need to follow -the procedures in to come up with &clm; -datasets that are customized for our point or region in question. This includes -running link_dirtree to create a directory location where you -can add your own files to it. Next, set -DATM_MODE to "CLM1PT" and &CLM1PT; and &CLMUSRDAT; to the -id of the data you created. To see a list of what the filenames need to be -see the section on setting &CLMUSRDAT;. - - -Next we need to setup the atmosphere forcing data in &netcdf; format that can be -read by &datm;. There is a list of eight variables that are expected to be on the input -files with the names and units on the following table (in the table TDEW and SHUM -are optional fields that can be used in place of RH). In the table we also list -which of the fields are required and if not required what the code will do to -replace them. If the names of the fields are different or the list is changed -from the standard list of eight fields: FLDS, FSDS, PRECTmms, -PSRF, RH, TBOT, WIND, and ZBOT, the resulting streams file will need to be modified -to take this into account (see an example streams file for this in below). - -Atmosphere Forcing Fields - - - - Short-name - Description - Units - Required? - If NOT required how replaced - - - - - FLDSincident longwave -(FLDS)W/m2No -calculates based on Temperature, Pressure and Humidity - - - FSDSincident solar -(FSDS)W/m2Yes- - - - FSDSdifincident solar (FSDS) -diffuseW/m2Nobased on FSDS - - - FSDSdirincident solar (FSDS) -directW/m2Nobased on FSDS - - - PRECTmmsprecipitation -(PRECTmms)mm/sYes- - - - PSRFpressure at the lowest atm level -(PSRF)PaNoassumes standard-pressure - - - RHrelative humidity at the lowest atm level -(RH)%Nocan be replaced with SHUM or TDEW - - - SHUMspecific humidity at the lowest atm level -kg/kgOptional in place of RHcan be replaced with RH or TDEW - - - TBOTtemperature at the lowest atm level -(TBOT)K (or can be C)Yes- - - - TDEWdew point temperature -K (or can be C)Optional in place of RHcan be replaced with RH or SHUM - - - WINDwind at the lowest atm level -(WIND)m/sYes- - - - ZBOTobservational heightmNo -assumes 30 meters - - - -
    -All of the variables should be dimensioned: time, lat, lon, with time being the unlimited -dimension. The coordinate variable "time" is also required with CF-compliant units in -days, hours, minutes, or seconds. It can also have a calendar attribute that can -be "noleap" or "gregorian". Normally the files will be placed in the: -$MYCSMDATA/atm/datm7/CLM1PT_data/$MYUSRDAT directory with separate files per -month called YYYY-MM.nc where YYYY-MM corresponds to the four -digit year and two digit month with a dash in-between. You also need a domain file that -gives the coordinate information for the data that should be placed in: -$MYCSMDATA/atm/datm7/domain.lnd.$MYUSRDAT_USGS.nc. - -Example of setting up a case with your own atmosphere forcing - -> cd scripts -# First make sure you have a inputdata location that you can write to -# You only need to do this step once, so you won't need to do this in the future -> setenv MYCSMDATA $HOME/inputdata # Set env var for the directory for input data -> ./link_dirtree $CSMDATA $MYCSMDATA -# Next create and move all your datasets into $MYCSMDATA with id $MYUSRDAT -# See above for naming conventions - -# Now create a single-point case -> ./create_newcase -case my_atmforc_test -res pt1_pt1 -compset I1850 \ --mach bluefire -> cd my_atmforc_test -# Set the data root to your inputdata directory, and set &CLM1PT; and &CLMUSRDAT; -# to the user id you created for your datasets above -> ./xmlchange -file env_run.xml -id DIN_LOC_ROOT_CSMDATA -val $MYCSMDATA -> ./xmlchange -file env_conf.xml -id &CLM1PT; -val $MYUSRDAT -> ./xmlchange -file env_conf.xml -id &CLMUSRDAT; -val $MYUSRDAT -# Set the land-mask to USGS, so both clm and &datm; can find files -> ./xmlchange -file env_conf.xml -id &CLMBLDNML; -val '-mask USGS' -# Then set DATM_MODE to single-point mode so &datm; will use your forcing datasets -# Put your forcing datasets into $MYCSMDATA/atm/datm7/CLM1PT_data/$MYUSRDAT -> ./xmlchange -file env_conf.xml -id DATM_MODE -val CLM1PT -> ./configure -case -# If the list of fields, or filenames, filepaths, or fieldnames are different -# you'll need to edit the &datm; namelist streams file to make it consistent -> $EDITOR Buildconf/datm.buildnml.csh - - -     - - -See for a warning about running single-point jobs -on batch machines. - - - - -See for notes about managing your data -when using link_dirtree. - - - - -Now, we'll show an example of what the &datm; streams file might look like for a case -with your own forcing data with 3-hourly forcing. In this example, we'll leave off the -fields: ZBOT, and FLDS so they'll be calculated as given in the - table above. We'll also include: -FSDSdif and FSDSdir which aren't required, and we'll use TDEW in place of RH. In this -example the datafiles are in &netcdf; format and contain the fields: TA, Tdew, WS, -PREC, Rg, Rgdir, Rgdif, and PRESS which are translated into the &datm; internal names -in this streams file. There is also a domain file that has the position information -for this location. The normal assumption for CLM1PT mode in the &datm; is that data is -hourly or half-hourly and as such is often enough that using the data on the nearest -time-stamp is reasonable and as such the data is in a single streams file (see - for more information on -the default settings for &datm; and how to change them. If the data is less often three to six hours -- see -below, where you will need to modify the time-interpolation method as well as the -time stamp offsets. In the example below we also have to divide the single -stream file into three files to manage the time-stamps and time interpolation -algorithm for the different types of data differently. - -Example of &datm; streams files with your own forcing for 3-hourly data - -Precipitation streams file -(clm1PT.1x1pt_lapazMEX.precip.stream.txt file) . - - -<streamstemplate> -<stream> - <dataSource> - CLMNCEP - </dataSource> - <domainInfo> - <variableNames> - time time - xc lon - yc lat - area area - mask mask - </variableNames> - <filePath> - $DIN_LOC_ROOT/atm/datm7/domain.clm - </filePath> - <fileNames> - domain.lnd.1x1pt_lapazMEX_navy.nc - </fileNames> - </domainInfo> - <fieldInfo> - <variableNames> - PRECTmms PREC - </variableNames> - <offset> - -5400 - </offset> - <filePath> - $DIN_LOC_ROOT/atm/datm7/CLM1PT_data/1x1pt_lapazMEX - </filePath> - <fileNames> - 2004-01.nc - 2004-02.nc - 2004-03.nc -. -. -. - 2009-12.nc - </fileNames> - </fieldInfo> -</stream> -</streamstemplate> - - -Solar streams file (clm1PT.1x1pt_lapazMEX.solar.stream.txt file). - - -<streamstemplate> -<stream> - <dataSource> - CLMNCEP - </dataSource> - <domainInfo> - <variableNames> - time time - xc lon - yc lat - area area - mask mask - </variableNames> - <filePath> - $DIN_LOC_ROOT/atm/datm7/domain.clm - </filePath> - <fileNames> - domain.lnd.1x1pt_lapazMEX_navy.nc - </fileNames> - </domainInfo> - <fieldInfo> - <variableNames> - FSDS Rg - FSDSdir Rgdir - FSDSdif Rgdif - </variableNames> - <offset> - -10800 - </offset> - <filePath> - $DIN_LOC_ROOT/atm/datm7/CLM1PT_data/1x1pt_lapazMEX - </filePath> - <fileNames> - 2004-01.nc - 2004-02.nc - 2004-03.nc -. -. -. - 2009-12.nc - </fileNames> - </fieldInfo> -</stream> -</streamstemplate> - - -Other fields streams file. -(clm1PT.1x1pt_lapazMEX.other.stream.txt file) . - - -<streamstemplate> -<stream> - <dataSource> - CLMNCEP - </dataSource> - <domainInfo> - <variableNames> - time time - xc lon - yc lat - area area - mask mask - </variableNames> - <filePath> - $DIN_LOC_ROOT/atm/datm7/domain.clm - </filePath> - <fileNames> - domain.lnd.1x1pt_lapazMEX_navy.nc - </fileNames> - </domainInfo> - <fieldInfo> - <variableNames> - TBOT TA - TDEW Tdew - WIND WS - PSRF PRESS - </variableNames> - <offset> - -5400 - </offset> - <filePath> - $DIN_LOC_ROOT/atm/datm7/CLM1PT_data/1x1pt_lapazMEX - </filePath> - <fileNames> - 2004-01.nc - 2004-02.nc - 2004-03.nc -. -. -. - 2009-12.nc - </fileNames> - </fieldInfo> -</stream> -</streamstemplate> - - -Example streams namelist for the above streams files: - - - &shr_strdata_nml - dataMode = 'CLMNCEP' - domainFile = '$DOMAINFILE' - streams = 'clm1PT.1x1pt_lapazMEX.solar.stream.txt 1 2004 2009 ', - 'clm1PT.1x1pt_lapazMEX.precip.stream.txt 1 2004 2009 ', - 'clm1PT.1x1pt_lapazMEX.other.stream.txt 1 2004 2009 ', - 'presaero.stream.txt 1 2000 2000' - vectors = 'null','null','null','null' - mapmask = 'nomask','nomask','nomask','nomask' - mapalgo = 'nn','nn','nn','nn' - tintalgo = 'coszen','nearest','linear','linear' - taxmode = 'cycle','cycle','cycle','cycle' - / - - - - - -The example above shows the resolved namelist and streams file after &configure; -has been run. In order to save this configuration for future use, you would need -to edit the &datm; template adding new DATM_MODE see - for more information on how to do this. - - - - -We've outlined and given a few examples of using your own atmosphere -forcing. In the next chapter we go into the details of using &ptclm;. - - -     - -     - diff --git a/doc/UsersGuide/special_cases.xml b/doc/UsersGuide/special_cases.xml deleted file mode 100644 index ac5c7fef3b..0000000000 --- a/doc/UsersGuide/special_cases.xml +++ /dev/null @@ -1,916 +0,0 @@ - - -How to run some special cases - -In this chapter we describe how to run some special cases that take more than one step -to do. The straightforward cases have compsets and/or build-namelist use-cases setup for -them or require simple editing of a single-case. All of the cases here require you -to do at least two simulations with different configurations, or require more complex -editing of the case (changing the streams files). - - -The nine cases we will describe are: - - - -Running with the prognostic crop model on - - - - -Running with the irrigation model on - - - - -Spinning up the Satellite Phenology Model (&clmsp; spinup) - - - - -Spinning up the biogeochemistry Carbon-Nitrogen Model (CN spinup) - - - - -Spinning up the Carbon-Nitrogen Dynamic Global Vegetation Model (CNDV spinup) - - - - -Running with MOAR data as atmospheric forcing to spinup the model - - - - -Running with your own previous simulation as atmospheric forcing to spinup the model - - - - -Doing perturbation error growth tests - - - - -Running stand-alone &clm; with transient historical &CO2; -concentration - - - - - - -The cases in this chapter are more sophisticated and require more technical knowledge -and skill than cases in previous chapters. The user should be very familiar with doing -simple cases before moving onto the cases described here. - - - -Running with the prognostic crop model on - - -In &clmcesm103; a prognostic crop model was added to &clm4;. The prognostic crop -model is setup to work with CN for present day conditions and we have surface -and initial condition datasets at f19 resolution. In order to use the initial condition -file, we need to set the RUN_TYPE to startup rather -than hybrid since the compset for f19 sets up to use an initial -condition file without crop active. To activate the crop model we simply add "-crop on" -to &CLMCONFIG;. - -Example Crop Simulation - -> cd scripts -> ./create_newcase -case CROP -res f19_g16 -compset ICN -mach bluefire -> cd CROP -# Append "-crop on" to &CLMCONFIG; in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-crop on" -append -# Change to startup type so uses spunup initial conditions file for crop if it exists -# By default the model will do a hybrid startup with an initial condition file -# incompatible with the crop surface dataset. -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -> ./configure -case -# Now build and run normally -> ./CROP.bluefire.build -> ./CROP.bluefire.submit - - - - - - -Running with the irrigation model on - - -In &clmcesm103; an irrigation model for generic crop was added to &clm4;. Currently, -irrigation and crop can NOT be used together see bug number 1326 in the -&KnownBugs; file. -The irrigation model is tuned to work only with &clmsp; see the caution below for -for more information on this. To turn on -irrigation we simply add "-irrig on" to &CLMBLDNML;. Just as in the crop example we -also change RUN_TYPE to startup so that we don't use -an initial condition file that is incompatible with irrigation. - -Example Irrigation Simulation - -> cd scripts -# Note here we do a &clmsp; simulation as that is what has been validated -> ./create_newcase -case IRRIG -res f19_g16 -compset I -mach bluefire -> cd IRRIG -# Append "-irrig on" to &CLMBLDNML; in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id &CLMBLDNML; -val "-irrig" -append -# Change to startup type so uses spunup initial conditions file for irrigation if it exists -# By default the model will do a hybrid startup with an initial condition file -# incompatible with the irrigation surface dataset. -> xmlchange -file env_conf.xml -id RUN_TYPE -val startup -> ./configure -case -# Now build and run normally -> ./IRRIG.bluefire.build -> ./IRRIG.bluefire.submit - - - - -We have only run the irrigation model with &clmsp; (i.e. without the CN model). We -recommend that if you want to run the irrigation model with CN, that you do a spinup -as outlined in the examples below. But, more than that you may need to make -the adjustments we discuss in . - - - - - - -Spinning up the Satellite Phenology Model (&clmsp; spinup) - - -To spin-up the &clmsp; model you merely need to run &clmsp; for 50 simulation -years starting from arbitrary initial conditions. You then use the final -restart file for initial conditions in other simulations. -Because, this is a straight forward operation we will NOT give -the details on how to do that here, but leave it as an exercise for the reader. -See the as an example of doing this -as the last step for &clmcn;. - - - - -Spinning up the biogeochemistry Carbon-Nitrogen Model (CN spinup) - -To get the &clmcn; model to a steady state, you first run it from arbitrary initial conditions -using the "accelerated decomposition spinup" (-ad_spinup in configure) mode for 600 simulation years. After -this you branch from this mode in the "exit spinup" (-exit_spinup in configure), run -for a simulation year, and then save a restart from that and use it as initial conditions -for further spinup of CN (at least 50 simulation years). - - -Spinup of &clmcn; - -AD_SPINUP - -For the first step of running 600 years in "-ad_spinup" mode, you will setup -a case, and then edit the values in env_conf.xml and -env_run.xml so that the right configuration is turned on and -the simulation is setup to run for the required length of simulation time. -So do the following: - -Example AD_SPINUP Simulation - -> cd scripts -> ./create_newcase -case CN_spinup -res f19_g16 -compset ICN -mach bluefire -> cd CN_spinup -# Append "-ad_spinup on" to &CLMCONFIG; in env_conf.xml -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-ad_spinup on" -append -# The following sets &CLMFORCECOLD; to "on" in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id &CLMFORCECOLD; -val on -# Make the output history files only annual, by adding the following to the &usernlclm; namelist -> echo '&clm_inparm hist_nhtfrq = -8760 /' > &usernlclm; -# Now configure -> ./configure -case -> ./xmlchange -file env_run.xml -id STOP_DATE -val 6010101 -# Now build -> ./CN_spinup.bluefire.build -# The following sets RESUBMIT to 30 times in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id RESUBMIT -val 30 -# The following sets STOP_OPTION to "nyears" in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -# The following sets STOP_N to 20 years in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_N -val 20 -# The following sets STOP_DATE to Jan/1 of year 601 in env_run.xml (you could also use an editor) -# Now run normally -> ./CN_spinup.bluefire.submit - - -Afterwards save the last restart file from this simulation to use in the next step. - - - - -EXIT_SPINIP - - -Example EXIT_SPINUP Simulation - -> cd scripts -> ./create_newcase -case CN_exitspinup -res f19_g16 -compset ICN -mach bluefire -> cd CN_exitspinup -# Append "-exit_spinup on" to &CLMCONFIG; in env_conf.xml -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-exit_spinup on" -append -# Change run type to branch and branch from the last year of the last simulation -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val branch -> ./xmlchange -file env_conf.xml -id RUN_REFCASE -val CN_spinup -> ./xmlchange -file env_conf.xml -id RUN_REFDATE -val 0601-01-01 -> ./xmlchange -file env_conf.xml -id GET_REFCASE -val FALSE -> ./configure -case -# Go ahead and build, so that the run directory is created -> ./CN_exitspinup.bluefire.build -# Now, Copy the last restart files from the earlier case into your run directory -> cp /ptmp/$LOGIN/archive/CN_spinup/rest/CN_spinup.*.r*.0601-01-01-00000* /ptmp/$LOGIN/CN_exitspinup -# And copy the rpointer files for datm and drv from the earlier case -> cp /ptmp/$LOGIN/archive/CN_spinup/rest/rpointer.atm /ptmp/$LOGIN/CN_exitspinup -> cp /ptmp/$LOGIN/archive/CN_spinup/rest/rpointer.drv /ptmp/$LOGIN/CN_exitspinup -# The following sets STOP_OPTION to "nyears" in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -> ./xmlchange -file env_run.xml -id STOP_N -val 1 -# Now run normally -> ./CN_exitspinup.bluefire.submit - - - - - - -Final spinup - -Next save the last restart file from this step and use it as the "finidat" file to -use for one more spinup for at least 50 years in normal mode. -So do the following: - -Example Final CN Spinup Simulation - -> cd scripts -> ./create_newcase -case CN_finalspinup -res f19_g16 -compset ICN -mach bluefire -> cd CN_finalspinup -# The following sets &CLMFORCECOLD; to "on" in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id &CLMFORCECOLD; -val on -# Now, Copy the last &clm; restart file from the earlier case into your run directory -> cp /ptmp/$LOGIN/archive/CN_exitspinup/rest/CN_exitspinup.clm*.r*.0602-01-01-00000.nc \ -/ptmp/$LOGIN/CN_finalspinup -# And copy the rpointer files for datm and drv from the earlier case -> cp /ptmp/$LOGIN/archive/CN_exitspinup/rest/rpointer.atm /ptmp/$LOGIN/CN_finalspinup -> cp /ptmp/$LOGIN/archive/CN_exitspinup/rest/rpointer.drv /ptmp/$LOGIN/CN_finalspinup -# Set the finidat file to the last restart file saved in previous step -> echo '&clm_inparm finidat = "CN_exitspinup.clm2.r.0602-01-01-00000.nc" /' > &usernlclm; -# Now configure -> ./configure -case -> $EDITOR Buildconf/clm.buildnml.csh -> Now build -> .CN_finalspinup.bluefire.build -# The following sets RESUBMIT to 5 times in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id RESUBMIT -val 5 -# The following sets STOP_OPTION to "nyears" in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -# The following sets STOP_N to 10 years in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_N -val 10 -> Now run as normal -> .CN_finalspinup.bluefire.submit - - - - -To assess if the model is spunup plot trends of CN variables of interest. If you see -a trend, you may need to run the simulation longer. -Finally save the restart file from the end of this simulation to use as an "finidat" file for future -simulations. - - - - - - -Spinning up the Carbon-Nitrogen Dynamic Global Vegetation Model (CNDV spinup) - -To spinup the &clm; CNDV model -- you first follow the procedures above to spinup the CN model. -Then you take the CN initial state file you created for the spinup with just CN, and -run CNDV for 200 more years. -We've provided such spunup files for two resolutions (f09 and f19) and two time-periods -(1850 and 2000), so in this example we will use the files provided to start from. -We've also provided a spinup file at f19 resolution for CNDV, hence the following is -NOT required when running at f19. -If you were to start from your own &clmcn; spunup files -- the procedure would require -some modification. -There are no compsets using CNDV, so in -env_conf.xml change CLM_CONFIG_OPTS to --bgc cndv. - -Example CNDV Spinup Simulation - -> cd scripts -> ./create_newcase -case CNDV_spinup -res f09_g16 -compset ICN -mach bluefire -> cd CNDV_spinup -# Set run type to startup and do a cold start -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -# The following sets CLM_CONFIG_OPTS to "-bgc cndv" in env_conf.xml (you could also use an editor) -> ./xmlchange -file env_conf.xml -id CLM_CONFIG_OPTS -val "-bgc cndv" -# Make the default primary history file annual and add an annual 1D vector auxiliary file -# By putting the following in a &usernlclm; file. -> cat << EOF > &usernlclm; -&clm_inparm - hist_nhtfrq = -8760, -8760 - hist_mfilt = 1, 1 - hist_fincl2 = 'TLAI', 'TSAI', 'HTOP', 'HBOT', 'NPP' - hist_dov2xy = .true., .false. -/ -> ./configure -case -# NOTE: If you were using your own CN spinup files you would edit the namelist to use it -# $EDITOR Buildconf/clm.buildnml.csh -# -# Now build and run as normal -> ./CNDV_spinup.bluefire.build -# The following sets RESUBMIT to 10 times in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id RESUBMIT -val 10 -# The following sets STOP_OPTION to "nyears" in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -# The following sets STOP_N to 20 years in env_run.xml (you could also use an editor) -> ./xmlchange -file env_run.xml -id STOP_N -val 20 -# Make sure you turn archiving on, so you save your files to long term archival -> ./xmlchange -file env_run.xml -id DOUT_L_MS -val TRUE -> ./CNDV_spinup.bluefire.submit - - - - - -There is a build bug with &clmcesm103; see bug 1370 in the &KnownBugs; on -how to address this. - - - - - -In a data analysis tool you should examine the auxiliary file and examine the -pfts1d_wtgcell to see where and what types of vegetation have -been established. See the caution in for more -information on visualizing and analyzing 1D vector fields. - - - -CNDV also writes out two vector fields to "hv" auxiliary files, on an annual basis by -default. - - - - -We've provided a spinup file for CNDV at f19 resolution, you could also use -interpinic to interpolate this file to other resolutions. - - - - - -Running with MOAR data as atmospheric forcing to spinup the model - -Because it takes so long to spinup the CN model (as we just saw previously), if you -are doing fully coupled simulations with active atmosphere and ocean, you will want -to do the spinup portion of this "offline". So instead of doing expensive fully -coupled simulations for the spinup duration, you run &clm; in a very cheap "I" -compset using atmospheric forcing from a shorter fully coupled simulation -(or a simulation run previously by someone else). - - -In this example we will use the I1850SPINUPCN compset to setup -&clm; to run with atmospheric forcing from a previous fully coupled simulation with -data that is already stored on disk on bluefire. There are several simulations that -have high frequency data for which we can do this. You can also do this on a machine -other than bluefire, but would need to download the data from the Earth System Grid and -change the datapath similar to . -This compset is designed for constant -1850 conditions, but unfortunately (because of bug 1354 see the &KnownBugs; file) by -default it points to a transient simulation instead of an 1850 simulation. Here we -point to an 1850 simulation and setup the forcing years to run over. - -Example Simulation with MOAR Data on bluefire - -> cd scripts -> ./create_newcase -case MOARforce1850 -res f19_g16 -compset I1850SPINUPCN -mach bluefire -> cd MOARforce1850 -# The following sets the casename to point to for atm forcing (you could also use an editor) -> ./xmlchange -file env_conf.xml -id DATM_CPL_CASE -val b40.1850.track1.1deg.006a -# The following sets the align year and years to run over for atm forcing -# (you could also use an editor) -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_ALIGN -val 1 -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_START -val 960 -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_END -val 1030 -> ./configure -case -# Now build and run as normal -> ./MOARforce1850.bluefire.build -> ./MOARforce1850.bluefire.submit - - - - -Because of bug 1339 (see the &KnownBugs; file on this) -you can't run with 83 or more years of forcing. If you do need to run with more years of -forcing, you'll need to address the issue as outlined in the &KnownBugs; file. - - - - - - -Running with your own previous simulation as atmospheric forcing to spinup the model - -Another way that you might want to spinup the model is to run your own simulation -for a relatively short period (either a B, E, or F compset) and then use it as forcing -for your "I" case later. By only running 20 to 50 years for the fully coupled case, -you'll save a substantial amount of computer time rather than running the entire spinup -period with a fully coupled model. - - -The first thing we need to do is to run a fully coupled case and save the atmospheric -coupling fields on a three hourly basis. In this example, we will run on bluefire -and archive the data to a local disk that we can then use in the next simulation. - -Example Fully Coupled Simulation to Create Data to Force Next Example Simulation - -> cd scripts -> ./create_newcase -case myBCN1850 -res f09_g16 -compset B1850CN -mach bluefire -> cd myBCN1850 -> ./configure -case -# Set histaux_a2x3hr to .true. in cpl.buildnml.csh so output from the atmosphere model -# will be saved 3 hourly -$EDITOR BuildConf/cpl.buildnml.csh -# Now build -> ./myBCN1850.bluefire.build -# The following sets the archival disk space (you could also use an editor) -> ./xmlchange -file env_run.xml -id DOUT_S_ROOT -val '/glade/home/$USER/$CASE' -# Make sure files are archived to disk, but NOT to long term storage -# (you could also use an editor) -> ./xmlchange -file env_run.xml -id DOUT_S -val TRUE -> ./xmlchange -file env_run.xml -id DOUT_L_MS -val FALSE -# Set the run length to run a total of 20 years (you could also use an editor) -> ./xmlchange -file env_run.xml -id RESUBMIT -val 9 -> ./xmlchange -file env_run.xml -id STOP_OPTION -val nyears -> ./xmlchange -file env_run.xml -id STOP_N -val 2 -# Now run as normal -> ./myBCN1850.bluefire.submit - - - - -Now we run an I compset forced with the data from the previous simulation using -the &CPLHIST; option to DATM_MODE. See - for more information on the -&datm; settings for &CPLHIST; mode. - -Example Simulation Forced with Data from the Previous Simulation - -> cd scripts -> ./create_newcase -case frcwmyBCN1850 -res f09_g16 -compset I1850SPINUPCN -mach bluefire -> cd frcWmyBCN1850 -# The following sets the casename to point to for atm forcing (you could also use an editor) -> ./xmlchange -file env_conf.xml -id DATM_CPL_CASE -val "myBCN1850" -# The following sets the align year and years to run over for atm forcing -# (you could also use an editor) -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_ALIGN -val "1" -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_START -val "1" -> ./xmlchange -file env_conf.xml -id DATM_CPL_YR_END -val "20" -# Set the datapath in the template to the archival path from the case above -> sed -E 's#set datapath = ".+"#set datapath = "/glade/home/$USER/%c/cpl/hist"#' \ - Tools/Templates/datm.cpl7.template > new.datm.cpl7.template -> mv -f new.datm.cpl7.template Tools/Templates/datm.cpl7.template -> chmod +x Tools/Templates/datm.cpl7.template -> ./configure -case -# Now build and run as normal -> ./frcwmyBCN1850.bluefire.build -> ./frcwmyBCN1850.bluefire.submit - - - - -In order to accomplish this we needed to edit the &datm; template file. See - for more information on doing this. -If your input case was at a resolution besides f09 you would have to edit -the &datm; template file even further to use a domain file at the input resolution. - - - - - - -Doing perturbation error growth tests - -Doing perturbation error growth tests is a way to validate a port of -the model to a new machine or to verify that changes are only roundoff. -The steps are the same in either case, but in the discussion below I will -assume you are doing a port validation to a new machine (but in parentheses -I will put a reminder that it could also be for code-mods). -The basic idea is to run a case on the trusted machine (trusted code) and -another with initial conditions perturbed by roundoff and compare the results of -the two. The difference between these two simulations (the error) will grow over time -and describe a curve that we compare with the error growth on the new machine (code -changes). The error growth on the new machine is the difference between the non-perturbed -state on the trusted machine and the non-perturbed state on the new machine (code -changes). If the new machine (code changes) are well-behaved -the plot of this error growth compared to the error growth curve on the trusted machine -should be similar. If the -changes are NOT well-behaved the changes from the new machine (code changes) will be -larger than the perturbation changes. In summary the simulations and steps that need to be performed are: - - -Run a simulation with the trusted code on the trusted machine. -(optionally you can use a dataset from inputdata repository). - - - -Run a simulation with the trusted code on the trusted machine with initial conditions -perturbed by roundoff (using a namelist item to do so). -(this is optional is you are using inputdata repository datasets) - - - -Run a simulation with the new code on the non-trusted machine (code changes). - - -Do a plot of the RMS difference of history variables between simulation 1 and simulation 2. - - -Do a plot of the RMS difference of history variables between simulation 1 and simulation 3. - - -Compare the two plots in steps 4 and 5. - - -If the plots compare well the new machine (code changes) is running as well as the trusted machine. - - -If the plots do NOTcompare well the new machine is -NOTrunning as well as the trusted machine. Typically the -recommendation here is to lower the optimization level on the new machine and try -again (or in the case of code changes, modify or simplify the code changes to get -something that should be closer). - -The history variables we have used to do this is either 'TSOI', and/or 'TSA'. 'TSOI' are -the 3D snow and soil temperatures for vegetated land-units. If there is a change in -soil physics it should show up in this field (and it should show up even for something -that is at a pretty deep soil depth). However, as 'TSOI' is only for vegetated -land-units, changes in lake or urban land-units -- will NOT show up. 'TSA' by contrast is -the 2m surface temperature across all land-units, so changes in urban or lake land-units -will show up. However, changes in deep soil physics will only show up as it propagates -to the surface. So one field may show something that the other doesn't. In the examples, -we use 'TSOI', but 'TSA' can be used as well. And in most cases you should check both. - - - -Now we will give a detailed description of the procedure with examples and the -exact steps to perform. - - -Using Perturbation Error Growth Analysis to Verify a Port to a New Machine - -Running non-perturbed on trusted machine - -The first step is to run a non-perturbed case on the trusted machine. You need to run -all of the steps with the same compset and same resolution. For these examples we will -use 2-degree resolution with the ICN compset for 2000 conditions. You need to run for -three days with a cold-start. - - - -As we describe below, This is optional if you will be using datasets from the -inputdata repository to take place of this step. - - - - -Example non-perturbed error growth simulation - -> cd scripts -> ./create_newcase -case trustedMachinePergro0 -compset ICN -res f19_g16 \ --mach bluefire -> cd trustedMachinePergro0 -# Set the non-perturbed PERGRO use-case -> ./xmlchange -file env_conf.xml -id CLM_NML_USE_CASE -val pergro0_pd -# Set coldstart on so arbitrary initial conditions will be used -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -# Set PERGRO on in the configure -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-pergro on" -append -# Now configure and build -> ./configure -case -> ./trustedMachinePergro0.bluefire.build -# Set it to run for three days and turn archiving off -> ./xmlchange -file env_run.xml -id STOP_N -val 3 -> ./xmlchange -file env_run.xml -id DOUT_S -val FALSE -# Run the case and then you will save the history file output for later use -> ./trustedMachinePergro0.bluefire.submit - - - - - -If you aren't able to do this step, as you don't have access to a trusted machine, you -can use datasets that are available from the svn inputdata repository to take place of -running it yourself. The disadvantage is that this is only done for certain model -versions and for exactly the configuration/namelist given here. You won't be able to -test it for your own custom code or configurations. - - - - -Running perturbed on the trusted machine - -The next step is to run a perturbed case on the trusted machine. - -Example perturbed error growth simulation - -> cd scripts -> ./create_newcase -case trustedMachinePergroRnd -compset ICN -res f19_g16 \ --mach bluefire -> cd trustedMachinePergroRnd -# Set the perturbed PERGRO use-case -> ./xmlchange -file env_conf.xml -id CLM_NML_USE_CASE -val pergro_pd -# Set coldstart on so arbitrary initial conditions will be used -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -# Set PERGRO on in the configure -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-pergro on" -append -# Now configure and build -> ./configure -case -> ./trustedMachinePergroRnd.bluefire.build -# Set it to run for three days and turn archiving off -> ./xmlchange -file env_run.xml -id STOP_N -val 3 -> ./xmlchange -file env_run.xml -id DOUT_S -val FALSE -# Run the case and then you will save the history file output for later use -> ./trustedMachinePergroRnd.bluefire.submit - - - - - -If you aren't able to do this step, as you don't have access to a trusted machine, you -can use datasets that are available from the svn inputdata repository to take place of -running it yourself. The disadvantage is that this is only done for certain model -versions and for exactly the configuration/namelist given here. You won't be able to -test it for your own custom code or configurations. - - - - -Running non-perturbed on the new machine - -The next step is to run a non-perturbed case on the new machine. Here -we will demonstrate using the machine intrepid. For the previous two steps -you have the option of using datasets provided in the subversion inputdata -repository to take their place -- however this step is required. - -> cd scripts -> ./create_newcase -case newMachinePergro0 -compset ICN -res f19_g16 \ --mach intrepid -> cd newMachinePergro0 -# Set the non-perturbed PERGRO use-case -> ./xmlchange -file env_conf.xml -id CLM_NML_USE_CASE -val pergro0_pd -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -> ./xmlchange -file env_conf.xml -id RUN_TYPE -val startup -# Set PERGRO on in the configure -> ./xmlchange -file env_conf.xml -id &CLMCONFIG; -val "-pergro on" -append -# Now configure and build -> ./configure -case -> ./newMachinePergro0.intrepid.build -# Set it to run for three days and turn archiving off -> ./xmlchange -file env_run.xml -id STOP_N -val 3 -> ./xmlchange -file env_run.xml -id DOUT_S -val FALSE -# Run the case and then you will save the history file output for later use -> ./newMachinePergro0.intrepid.submit - - - - - -Plotting the differences - -You can use the cprnc program to compute root mean square differences -between the relevant history files. See for more information -on it and how to build it. On many platforms you will need to set some environment -variables in order to complete the build (see for -more information on building the tools). - -# Build the cprnc program -> cd models/lnd/clm/tools/cprnc -> gmake -# Now go to your case directory and run cprnc on the trusted-machine with and without -# perturbation -> cd ../../../../../scripts/trustedMachinePergro0 -> ../../models/lnd/clm/tools/cprnc/cprnc trustedMachinePergro0.clm2.h0.001-01-01.00000.nc \ -../trustedMachinePergroRnd/trustedMachinePergroRnd.clm2.h0.001-01-01.00000.nc > trustedPergro.log -# Copy the history file from the new machine to here -# -# And now run cprnc on the trusted-machine and the new machine both without perturbation -> ../../models/lnd/clm/tools/cprnc/cprnc trustedMachinePergro0.clm2.h0.001-01-01.00000.nc \ -../newMachinePergro0/newMachinePergro0.clm2.h0.001-01-01.00000.nc > newPergro.log -# Now extract out the RMS differences of TSOI for both -# You may want to extract out the RMS differences for TSA as well -# Changes in urban or lake land-units won't be detected with TSOI -> grep "RMS TSOI" trustedPergro.log | awk '{print $3}' > RMStrusted.dat -> grep "RMS TSOI" newPergro.log | awk '{print $3}' > RMSnewmachine.dat -# And plot the two curves up to your screen -> env TYPE=x11 RMSDAT=RMSnewmachine.dat RMSDAT2=RMStrusted.dat ncl \ -../../models/lnd/clm/tools/ncl_scripts/pergroPlot.ncl - -Here is a sample plot for several trusted machines: bluefire, intrepid, jaguar, -and edinburgh (with both the lahey and intel compilers). -The green line is the error growth for bluefire, the red is the error growth -for intrepid, the dashed navy is for jaguar, the dashed maroon is for the intel -compiler on edinburgh, and the thick dashed goldenrod line is for edinburgh with the -lahey compiler. Note, the data for this plot is in -models/lnd/clm/tools/ncl_scripts the files are named: -according to the legend. Note, that the lines tend to cluster together and follow -quite closely to the bluefire line which is our main trusted machine. -
    -Sample Good Perturbation Error Growth Curves (within roundoff) - - - -
    -     - - -When you do NOT have access to a trusted machine you can use the trusted file from -bluefire that is available on the inputdata repository. - -# Build the cprnc program -> cd models/lnd/clm/tools/cprnc -> gmake -# Get the unperturbed file from the subversion repository -> cd ../../../../../scripts/newMachinePergro0 -> set dir = "lnd/clm2/pergrodata" -> set file = bluefirePergro0.ICN.0001-01-01_1.9x2.5_gx1v6_simyr2000_clm4-cesm1_0_3.c110617.nc -> echo "trustedfile = DIN_LOC_ROOT/$dir/$file" > clm.input_data_list -> ../ccsm_utils/Tools/check_input_data -datalistdir . -export -inputdata $DIN_LOC_ROOT -# And now run cprnc on the bluefire file and the new machine both without perturbation -> ../../models/lnd/clm/tools/cprnc/cprnc $file \ -../newMachinePergro0/newMachinePergro0.clm2.h0.001-01-01.00000.nc > newPergro.log -# Now extract out the RMS difference -# You may want to extract out the RMS differences for TSA as well -# Changes in urban or lake land-units won't be detected with TSOI -> grep "RMS TSOI" newPergro.log | awk '{print $3}' > RMSnewmachine.dat -# And plot the new curve versus the trusted curve up to your screen -> env TYPE=x11 RMSDAT=RMSnewmachine.dat \ -RMSDAT2=../../models/lnd/clm/tools/ncl_scripts/RMSbluefire.dat \ -../../models/lnd/clm/tools/ncl_scripts/pergroPlot.ncl - - - -In the figure below we now show example of curves for changes that are larger than -roundoff. Once again the green curve is the trusted error growth from bluefire. The -other curves are for changes that may be fairly small, but are larger than roundoff. The -goldenrod curve is for using the 1850, and the navy is for using the 1999 Nitrogen -deposition files rather than for year 2000. The red is for using the 1850 aerosol -dataset rather than 2000, and the maroon is for adding the snow combination bug in. The -differences in changes that are greater than roundoff is that the curves climb very -steeply to the 10-6 value and then level off, while the -curve for bluefire climbs much more slowly and gradually. The curves also don't mimic -each other in any way, like the trusted machine plots do. -
    -Sample Bad Perturbation Error Growth Curves (changes greater than roundoff) - - - -
    - -     -     -     -     - - -Running stand-alone &clm; with transient historical &CO2; -concentration - -In this case you want to run a simulation with stand-alone &clm; responding -to changes in &CO2; for a historical period. -For this example, we will start with the "I_1850-2000_CN" compset that -has transient: land-use, Nitrogen and Aerosol deposition already. You could -also use another compset if you didn't want these other features to be transient. -In order to get &CO2; to be transient we need to edit the -&datm; template so that we add an extra streams file to describe how -&CO2; varies over the historical period. You also need -a &netcdf; datafile that datm can read that gives the variation. You could -supply your own file, but we have a standard file that is used by CAM for this -and our example will make use of this file. - - - -Most everything here has to do with changing datm rather than &clm; -to allow this to happen. As such the user that wishes to do this should -first become more familiar with datm and read the -&cesm; Data -Model User's Guide especially as it pertains to the datm. Note, also -that in this example we show how to edit the datm "buildnml" file for your -case, but you could do something similar by editing the datm template. - - - - -This section documents the process for doing something that is non-standard. -There may be errors with the documentation and process, and you may have to do -some work before all of this works for you. If that is the case, we recommend -that you do further research into understanding the process and the files, as -well as understanding the datm and how it works. You may have to read documentation -found in the code for datm as well as "csm_share". - - - -The datm has "streams" files that have rough XML-like syntax and specify the -location and file to get data from, as well as information on the variable names -and the data locations of the grid points. The datm expects specific variable names -and the datm "maps" the expected variable names from the file to the names expected -by datm. The file we are working with here is a file with a single-point, that covers -the entire globe (so the vertices go from -90 to 90 degrees in latitude and 0 to 360 -degrees in longitude). Since it's a single point it's a little easier to work with -than datasets that may be at a given horizontal resolution. The datm also expects -that variables will be in certain units, and only expects a limited number of -variables so arbitrary fields can NOT be exchanged this way. However, the process -would be similar for datasets that do contain more than one point. - - -The three things that are needed: a domain file, a data file, and a streams text file. -The domain file is a CF-compliant &netcdf; file that has information -on the grid points (latitudes and longitudes for cell-centers and vertices, mask -, fraction, and areas). The datafile is a CF-compliant &netcdf; file with the data that -will be mapped. The streams text file is the XML-like file that tells datm how to find -the files and how to map the variables datm knows about to the variable names on the -&netcdf; files. Note, that in our case the domain file and the data file are the same -file. In other cases, the domain file may be separate from the data file. - - -First we are going to create a case, and we will edit -the Buildconf/datm.buildnml.csh so that we add a -&CO2; data stream in. There is a streams text file -available in models/lnd/clm/doc/UsersGuide/co2_streams.txt, -that includes file with a &CO2; time-series from 1765 to 2007. - -Example Transient Simulation with Historical &CO2; - -> cd scripts -> ./create_newcase -case DATM_CO2_TSERIES -res f19_g16 -compset I_1850-2000_CN \ --mach bluefire -> cd DATM_CO2_TSERIES -# Set CCSM_BGC to CO2A so that CO2 will be passed from atmosphere to land -> ./xmlchange -file env_conf.xml -id CCSM_BGC -val CO2A -# Set CLM_CO2_TYPE to diagnostic so that the land will use the value sent from the atmosphere -> ./xmlchange -file env_conf.xml -id CLM_CO2_TYPE -val diagnostic -> ./configure -case -> cd Buildconf -# Copy the sample streams file over -> cp ../../../models/lnd/clm/doc/UsersGuide/co2_streams.txt . - - -The first thing we will do is to edit the datm buildnml script to add -a CO2 file stream in. To do this we will apply a patch with the differences -needed. The patch file addco2_datm.buildnml.diff is -in models/lnd/clm/doc/UsersGuide and looks like this... - -&co2streams_diff; - -So to apply the patch you do this... - -> cd scripts/DATM_CO2_TSERIES/Buildconf -> patch < ../../../models/lnd/clm/doc/UsersGuide/addco2_datm.buildnml.diff - -Once, you've done that you can build and run your case normally. - - - -The patch assumes you are using a I_1850-2000_CN compset out of the box, with -DATM_PRESAERO equal to trans_1850-2000. So it assumes standard -Qian atmosphere forcing, and transient prescribed aerosols from streams files. If your case changes -anything here the patch will fail, and you will need to put the changes in by hand. - - - - - -If the patch fails, you will have to add the changes to the -datm.buildnml.csh found in the above -patch file by hand. Basically, it adds an extra streams file for &CO2; to the end of the streams variable, -and other arrays associated with streams (adding mapalgo as a new array with bilinear for everything, but -the &CO2; file which should be "nn" for nearest neighbor). - - - - - -The streams file above is hard-coded for the path of the file on &ncar; computers. To use it on an outside -machine you'll need to edit the filepath in the streams file to point to the location where you have the file. - - - - -After going through these steps, you will have a case where you have datm reading -in an extra streams text file that points to a data file with &CO2; -data on it that will send that data to the &clm;. - - -     - diff --git a/doc/UsersGuide/stylesheethtml2docbook.xsl b/doc/UsersGuide/stylesheethtml2docbook.xsl deleted file mode 100644 index 13c30ff71d..0000000000 --- a/doc/UsersGuide/stylesheethtml2docbook.xsl +++ /dev/null @@ -1,579 +0,0 @@ - - - - - -wb -file:///epicuser/AISolutions/graphics/AIWorkbench/ - - - - - - - - - - <xsl:value-of select=".//html:h1[1] - |.//html:h2[1] - |.//html:h3[1]"/> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - _ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inlinemediaobject - - mediaobject - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Matched -
    - -
    -     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - No template for - - - - - - No template for - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    -     - - - - - - - _ - - - - - - - - - - - - - - _ - - - - - - - - - - - - - - - - - - - - - - - - - <xsl:value-of select=".//html:caption"/> - - - - - - - - - - - - - - - -
    -     - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Attempting to count columns on a non-table element - - - Row parameter is not a valid row - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -     - diff --git a/doc/UsersGuide/tools.xml b/doc/UsersGuide/tools.xml deleted file mode 100644 index f5fd8beac4..0000000000 --- a/doc/UsersGuide/tools.xml +++ /dev/null @@ -1,1396 +0,0 @@ - - -Using the &clm; tools to create your own input datasets - -There are several tools provided with &clm; that allow you to create your own input -datasets at resolutions you choose, or to interpolate initial conditions to a different -resolution, or used to compare &clm; history files between different cases. The tools are -all available in the models/lnd/clm/tools directory. Most of the tools -are &FORTRAN; stand-alone programs in their own directory, but there is also a suite of -&ncl; -scripts in the ncl_scripts directory. Some of the &ncl; scripts are -very specialized and not meant for general use, and we won't document them here. They -still contain documentation in the script itself and the README file in the tools -directory. But, the list of generally important scripts and programs are: - - - cprnc to compare &netcdf; files with a time axis. - - - interpinic to interpolate initial condition files. - - - mkgriddata to create grid datasets. - - - mkdatadomain to create domain files from grid datasets -used by &datm; or docn. - - - mksurfdata to create surface datasets from grid datasets. - - - ncl_scripts/getregional_datasets.pl script to extract a -region or a single-point from global input datasets. See the single-point chapter -for more information on this. - - - ncl_scripts/npdepregrid.ncl interpolate the Nitrogen -deposition datasets to a new resolution. - - - ncl_scripts/aerdepregrid.ncl interpolate the Aerosol -deposition datasets to a new resolution. - - - - - -In the sections to come we will go into detailed description of how to use each of -these tools in turn. First, however we will discuss the common environment variables -and options that are used by all of the &FORTRAN; tools. Second, we go over the outline -of the entire file creation process for all input files needed by &clm; for a new -resolution, then we turn to each tool. In the last section we will -discuss how to customize files for particular observational sites. - - - -Common environment variables and options used in building the &FORTRAN; -tools - -The &FORTRAN; tools all have similar makefiles, and similar options for building. -All of the Makefiles use GNU Make extensions and thus require that you use GNU make -to use them. They also auto detect the type of platform you are on, using "uname -s" -and set the compiler, compiler flags and such accordingly. There are also environment -variables that can be set to set things that must be customized. All the tools use -&netcdf; and hence require the path to the &netcdf; libraries and include files. -On some platforms (such as Linux) multiple compilers can be used, and hence there -are env variables that can be set to change the &FORTRAN; and/or "C" compilers used. -The tools other than cprnc also allow finer control, by also -allowing the user to add compiler flags they choose, for both &FORTRAN; and "C", as -well as picking the compiler, linker and and add linker options. Finally the tools -other than cprnc allow you to turn -optimization on (which is off by default but on for the mksurfdata and -interpinic -programs) with the OPT flag so that the -tool will run faster. To get even faster performance, the interpinic, -mksurfdata, and -mkgriddata programs allow you to also use the SMP to -turn on multiple shared memory processors. -When SMP=TRUE you set the number of threads used by the program with -the OMP_NUM_THREADS environment variable. - - -Options used by all: cprnc, interpinic, -mkdatadomain, mkgriddata, and -mksurfdata - -LIB_NETCDF -- sets the location of the &netcdf; library. -INC_NETCDF -- sets the location of the &netcdf; include files. -USER_FC -- sets the name of the &FORTRAN; compiler. - -Options used by: interpinic, mkdatadomain, -mkgriddata, and mksurfdata - -MOD_NETCDF -- sets the location of the &netcdf; &FORTRAN; module. -USER_LINKER -- sets the name of the linker to use. -USER_CPPDEFS -- adds any CPP defines to use. -USER_CFLAGS -- add any "C" compiler flags to use. -USER_FFLAGS -- add any &FORTRAN; compiler flags to use. -USER_LDFLAGS -- add any linker flags to use. -USER_CC -- sets the name of the "C" compiler to use. -OPT -- set to TRUE to compile the code optimized (TRUE or FALSE) - -Options used by: interpinic, mkgriddata, and mksurfdata: - -SMP -- set to TRUE to turn on shared memory parallelism (i.e. -&omp;) (TRUE or FALSE) -Filepath -- list of directories to build source code from. -Srcfiles -- list of source code filenames to build executable from. - -Options used only by cprnc: - -EXEDIR -- sets the location where the executable will be built. -VPATH -- colon delimited path list to find the source files. - -More details on each environment variable. - - -LIB_NETCDF - -This variable sets the path to the &netcdf; library file -(libnetcdf.a). If not -set it defaults to /usr/local/lib. In order to use the tools -you need to build the &netcdf; library and be able to link to it. In order to build -the model with a particular compiler you may have to compile the &netcdf; library with -the same compiler (or at least a compatible one). - - - - - -INC_NETCDF - -This variable sets the path to the &netcdf; include directory (in order to find -the include file netcdf.inc). -if not set it defaults to /usr/local/include. - - - - - -MOD_NETCDF - -This variable sets the path to the &netcdf; module directory (in order to find -the &netcdf; &FORTRAN90; module file when &netcdf; is used with a &FORTRAN90; -use statement. When not set it defaults to the -LIB_NETCDF value. - - - - - -USER_FC - -This variable sets the command name to the &FORTRAN90; compiler to use when -compiling the tool. The default compiler to use depends on the platform. And -for example, on the AIX platform this variable is NOT used - - - - - -USER_LINKER - -This variable sets the command name to the linker to use when linking the object -files from the compiler together to build the executable. By default this is set to -the value of the &FORTRAN90; compiler used to compile the source code. - - - - - -USER_CPPDEFS - -This variable adds additional optional values to define for the C preprocessor. -Normally, there is no reason to do this as there are very few CPP tokens in the CLM -tools. However, if you modify the tools there may be a reason to define new CPP -tokens. - - - - - -USER_CC - -This variable sets the command name to the "C" compiler to use when -compiling the tool. The default compiler to use depends on the platform. And -for example, on the AIX platform this variable is NOT used - - - - - -USER_CFLAGS - -This variable adds additional compiler options for the "C" compiler to use -when compiling the tool. By default the compiler options are picked according -to the platform and compiler that will be used. - - - - - -USER_FFLAGS - -This variable adds additional compiler options for the &FORTRAN90; compiler to use -when compiling the tool. By default the compiler options are picked according -to the platform and compiler that will be used. - - - - - -USER_LDFLAGS - -This variable adds additional options to the linker that will be used when linking -the object files into the executable. By default the linker options are picked according -to the platform and compiler that is used. - - - - - -SMP - -This variable flags if shared memory parallelism (using i&omp;) should be used when -compiling the tool. It can be set to either TRUE or -FALSE, by default it is set to FALSE, so -shared memory parallelism is NOT used. When set to TRUE you can -set the number of threads by using the OMP_NUM_THREADS environment -variable. Normally, the most you would set this to would be to the number of on-node -CPU processors. Turning this on should make the tool run much faster. - - - -Note, that depending on the compiler answers may be different when SMP -is activated. - - - - - - -OPT - -This variable flags if compiler optimization should be used when -compiling the tool. It can be set to either TRUE or -FALSE, by default it is set to FALSE for -mkdatadomain and TRUE for -mksurfdata and interpinic. -Turning this on should make the tool run much faster. - - - -Note, you should expect that answers will be different when OPT -is activated. - - - - - - -Filepath - -All of the tools are stand-alone and don't need any outside code to operate. The -Filepath is the list of directories needed to compile -and hence is always simply "." the current directory. Several tools use -copies of code outside their directory that is in the &cesm; -distribution (either csm_share code or &clm; source code). - - - - - -Srcfiles - -The Srcfiles lists the filenames of the source code to use -when building the tool. - - - - - -EXEDIR - -The cprnc tool uses this variable to set the location of where the executable -will be built. The default is the current directory. - - - - - -VPATH - -The cprnc tool uses this variable to set the colon delimited pathnames of where -the source code exists. The default is the current directory. - - - - - - - - - -There are several files that are copies of the original files from either -models/lnd/clm/src/main, -models/csm_share/shr, or copies from other tool -directories. By having copies the tools can all be made stand-alone, but -any changes to the originals will have to be put into the tool directories -as well. - - - -The README.filecopies (which can be found in -models/lnd/clm/tools) is repeated here. - -&filecopies; - - - - - -General information on running the &FORTRAN; tools - -The tools run either one of two ways, with a namelist to provide options, or -with command line arguments (and NOT both). interpinic and -cprnc run with command line arguments, and the other tools -run with namelists. - - -Running &FORTRAN; tools with namelists - -mkgridata, mksurfdata and -mkdatadomain run with namelists that are read from -standard input. Hence, you create a namelist and then run them by -redirecting the namelist file into standard input as follows: - -./program < namelist - -For programs with namelists there is at least one sample namelist with the -name "program".namelist (i.e. mksurfdata.namelist -for the mksurfdata program). There may also be other sample -namelists that end in a different name besides "namelist". Namelists that you create -should be similar to the example namelist. The namelist values are also documented -along with the other namelists in the: - -models/lnd/clm/bld/namelist_files/namelist_definition.xml -file and default values in the: - -models/lnd/clm/bld/namelist_files/namelist_defaults_clm_tools.xml -file. - - - -Running &FORTRAN; tools with command line options - -interpinic and cprnc run with command line -arguments. The detailed sections below will give you more information on the command -line arguments specific to each tool. Also running the tool without any arguments -will give you a general synopsis on how to run the tool. For example to get help -on running interpinic do the following. - -cd models/lnd/clm/tools/interpinic -gmake -./interpinic - - - - -Running &FORTRAN; tools built with SMP=TRUE - -When you enable SMP=TRUE on your build of one of the tools that -make use of it, you are using &omp; for shared memory parallelism (SMP). In -SMP loops are run in parallel with different threads run on different processors -all of which access the same memory (called on-node). Thus you can only usefully -run up to the number of processors that are available on a single-node of the machine -you are running on. For example, on the &ncar; machine bluefire there are 32 processors -per node, but the SMT hardware on the machine allows you to submit twice as many -threads or 64 threads. So to run the mksurfdata on bluefire -optimized, with 64 threads you would do the following: - -cd models/lnd/clm/tools/mksurfdata -gmake OPT=TRUE SMP=TRUE -setenv OMP_NUM_THREADS 64 -./mksurfdata < mksurfdata.namelist - - - - - - -The File Creation Process - - -When just creating a replacement file for an existing one, the relevant tool should -be used directly to create the file. When you are creating a set of files for a new -resolution there are some dependencies between the tools that you need to keep in mind -when creating them. The main dependency is that the mkgriddata MUST -be done first as the grid dataset is then input into the other tools. Also look at -. - - - -Creating a complete set of files for input to &clm; - -Create grid and fraction datasets - -First use mkgriddata to create grid and fraction datasets. -See for more information on this. - - - - -Create domain dataset (if NOT already done) - -Next use mkdatadomain to create a domain file for use by -&datm; from the grid and fraction datasets just created. This is required, unless -a domain file already created was input into mkgriddata on -the previous step. -See for more information on this. - - - - -Create surface datasets - -Next use mksurfdata to create a surface dataset, using the grid -dataset as input. -See for more information on this. - - - - -Interpolate aerosol deposition datasets (optional) - -By default the atmosphere model will interpolate -these datasets on the fly, so you don't normally need to do this step. -A reason you might want to do this is to make the read and interpolation faster, -by reducing the amount of data read in and removing the need for the interpolation. -So, if you do, you can use aerdepregrid.ncl to regrid aerosol -deposition datasets to your new resolution using the grid dataset as input. -See for more information on this. - - - - -Interpolate Nitrogen deposition datasets (optional, but only needed if running &clmcn;) - -By default Nitrogen deposition is read in from stream -files at 2-degree resolution and interpolated to the resolution you are running at, -so you don't need to do this step. As with aerosol deposition datasets a reason -you might want to do this is to make the read and interpolation faster, -by reducing the amount of data read in and removing the need for the interpolation. -So, if you do you can use ndepregrid.ncl -to regrid Nitrogen deposition datasets to your new resolution using the grid dataset -as input. -See for more information on this. - - - - -Create some sort of initial condition dataset - - -You then need to do one of the following three options to have an initial dataset -to start from. - - - - - -Use spinup-procedures to create initial condition datasets - -The first option is to do the spinup procedures from arbitrary initial conditions -to get good initial datasets. This is the most robust method to use. -See , , or - for more information on this. - - - - -Use <command>interpinic</command> to interpolate existing initial -condition datasets - -The next option is to interpolate from spunup datasets at a different resolution, using -interpinic. -See for more information on this. - - - - -Start up from arbitrary initial conditions - -The last alternative is to run from arbitrary initial conditions without using any -spun-up datasets. This is inappropriate when using &clmcn; (bgc=cn or cndv) as it -takes a long time to spinup Carbon pools. - - -This is NOT recommended as many fields in &clm; take a long time to equilibrate. - - - - - - - - - - -Enter the new datasets into the &buildnml; XML database - -The last optional thing to do is to enter the new datasets into the &buildnml; -XML database. See for more information on -doing this. This is optional because the user may enter these files into their -namelists manually. The advantage of entering them into the database is so that -they automatically come up when you create new cases. - - - - - - - - -Using the <command>cprnc</command> tool to compare two history files - -cprnc is a tool shared by both CAM and &clm; to compare two -&netcdf; history files. -It differences every field that has a time-axis that is also shared on both files, -and reports a summary of the difference. The summary includes the three largest -differences, as well as the root mean square (RMS) difference. It also gives some -summary information on the field as well. You have to enter at least one file, and up to -two files. With one file it gives you summary information on the file, and with two it -gives you information on the differences between the two. At the end it will give you a -summary of the fields compared and how many fields were different and how many were -identical. - - -Options: - --m = do NOT align time-stamps before comparing --v = verbose output --ipr --jpr --kpr - -See the cprnc -README file for more details which is -repeated here: - -&cprnc_readme; - - - -To compare files with OUT a time axis you can use the cprnc.ncl -&ncl; script in models/lnd/clm/tools/ncl_scripts. It won't give -you the details on the differences but will report if the files are identical or -different. - - - - - - -Using <command>interpinic</command> to interpolate initial conditions to different -resolutions - -"interpinic" is used to interpolate initial conditions from one resolution to another. -In order to do the interpolation you must first run &clm; to create a restart file to -use as the "template" to interpolate into. Running from arbitrary initial conditions -(i.e. finidat = ' ') for a single time-step is sufficient to do this. Make sure the -model produces a restart file. You also need to make sure that you setup the same -configuration that you want to run the model with, when you create the template file. - - -Command line options to interpinic: - --i = Input filename to interpolate from --o = Output interpolated file, and starting template file - - - -There is a sample template file in the models/lnd/clm/tools/interpinic -directory and can be used to run interpolate to. -However, this file was created with an older version of &clm; and hence -we actually recommend that you would do a short run with &clm; to create a template file -to use. - - - - -Example of running &clm; to create a template file for -<command>interpinic</command> to interpolate to - -> cd scripts -> ./create_newcase -case cr_f10_TmpltI1850CN -res f10_f10 -compset I1850CN \ --mach bluefire -> cd cr_f10_TmpltI1850CN -# Set starting date to end of year -> ./xmlchange -file env_conf.xml -id RUN_STARTDATE -val 1948-12-31 -# Set year align to starting year -> ./xmlchange -file env_conf.xml -id DATM_CLMNCEP_YR_ALIGN -val 1948 -# Set to run a cold start -> ./xmlchange -file env_conf.xml -id CLM_FORCE_COLDSTART -val on -# Set to run only a single day, so a restart file will be created on Jan/1/1949 -> ./xmlchange -file env_run.xml -id STOP_N -val 1 -# Then configure, build and run as normal -> ./configure -case -> ./cr_f10_TmpltI1850CN.bluefire.build -> ./cr_f10_TmpltI1850CN.bluefire.submit -# And copy the resulting restart file to your interpinic directory -> cd ../models/lnd/clm/tools/interpinic -> cp /ptmp/$LOGIN/cr_f10_TmpltI1850CN/run/cr_f10_TmpltI1850CN.clm2.r.1949-01-01-00000.nc . - - - - -In the next example we build interpinic optimized with shared -memory on for 64 threads so that it runs as fast as possible, to interpolate one of -the standard 1-degree datasets to the above 10x15 template file that we created. - - -Example of building and running <command>interpinic</command> to -interpolate a 1-degree <filename>finidat</filename> dataset to 10x15 - -> cd models/lnd/clm/tools/interpinic -> gmake OPT=TRUE SMP=TRUE -> env OMP_NUM_THREADS=64 ./interpinic -o cr_f10_TmpltI1850CN.clm2.r.1949-01-01-00000.nc / --i /fs/cgd/csm/inputdata/ccsm4_init/b40.1850.track1.1deg.006/0863-01-01/b40.1850.track1.1deg.006.clm2.r.0863-01-01-00000.nc - - - - -Running interpinic at high resolution can take a long time, so we -recommend that you always build it optimized and with shared memory processing on, to -cut down the run time as much as possible. - - - - -interpinic does NOT work for CNDV (bgc=cndv). - - - - - - -In we give a simpler way to run -interpinic for several standard resolutions at once, with a script -to loop over several resolutions. This is useful for &clm; developers who need to -create many finidat files at once. - - - - - -Using <command>mkgriddata</command> to create grid datasets - -mkgriddata is used to create grid, fraction, and topography -datasets to run &clm; at a new resolution. It is typically the first step in creating -datasets needed to run &clm; at a new resolution (followed by -mksurfdata, and -then the interpolation programs, aerdepregrid.ncl, and -ndepregrid.ncl when running with CN). - - - -mkgriddata namelist - -mkgriddata is controlled by a namelist. There are ten different -namelist items, and you need to use enough of them so that files will be output. -The different types of input datasets contain different input data types, that -correspond to the three different types of output files: grid, fraction, and topography. -Output files for each of these will only be output if there is input data that -correspond to these. If you only have input data for grid locations -- you will only -get an output grid file. If you have both grid and fraction data you will get grid and -fraction data files. If you also have topography data you will also get topo files. - - -Namelist options to mkgriddata include: - -mksrf_fnavyoro -- Navy orography file to use for land fraction -and surface heights. -mksrf_frawtopo -- Raw topography file with just surface -heights. -mksrf_fcamfile -- CAM initial conditions file with -land-fractions and topography -mksrf_fclmgrid -- &clm; grid file -mksrf_fccsmdom -- &cesm; domain file -mksrf_fcamtopo -- CAM topography file -mksrf_lsmlon -- number of longitude for regional grid -mksrf_lsmlatnumber of latitudes for regional grid -mksrf_edgen -- Northern edge for regional grid -mksrf_edgee -- Southern edge for regional grid -mksrf_edges -- Eastern edge for regional grid -mksrf_edgew -- Western edge for regional grid - - - -You need to enter one of the following four options: - - mksrf_fnavyoro - high resolution topo dataset (topo data) - mksrf_lsmlon - number of longitudes - mksrf_lsmlat - number of latitudes - mksrf_edgen - northern edge of grid (degrees) - mksrf_edgee - eastern edge of grid (degrees) - mksrf_edges - southern edge of grid (degrees) - mksrf_edgew - western edge of grid (degrees) - -or - - mksrf_fcamfile - CAM topo file (grid and possibly fraction data) - -or - - mksrf_fccsmdom - &cesm; domain file (both grid, and fraction data) - -or - - mksrf_fclmgrid - &clm; grid or surface dataset file (grid data) - -Note, you can provide more than one of the needed datasets, and the output -data will be determined by the datasets according to an order of precedence. -The order of precedence for data is as follows: - -mksrf_fcamfile -mksrf_fclmgrid -mksrf_fnavyoro -mksrf_fccsmdom - -Grid data then will be established by the file with the highest precedence. -&cesm; domain files sometimes have latitudes and longitudes that are "off" from -the standard by a small amount. By establishing an order of precedence you can ensure -that grid locations exactly match a given standard file, even if the values in the domain -file are off from that. - - - -There are three different major modes for using "mkgriddata" to create grid files -for &clm;: - -mksrf_fnavyoro -- Navy orography file to use for land fraction -and surface heights. -mksrf_frawtopo -- Raw topography file with just surface -heights. -mksrf_fcamfile -- CAM initial conditions file with -land-fractions and topography -mksrf_fclmgrid -- &clm; grid file -mksrf_fccsmdom -- &cesm; domain file -mksrf_fcamtopo -- CAM topography file -mksrf_lsmlon -- number of longitude for regional grid -mksrf_lsmlat -- number of latitudes for regional grid -mksrf_edgen -- Northern edge for regional grid -mksrf_edgee -- Southern edge for regional grid -mksrf_edges -- Eastern edge for regional grid -mksrf_edgew -- Western edge for regional grid - - - -You need to enter one of the following four options: - - mksrf_fnavyoro - high resolution topo dataset (topo data) - mksrf_lsmlon - number of longitudes - mksrf_lsmlat - number of latitudes - mksrf_edgen - northern edge of grid (degrees) - mksrf_edgee - eastern edge of grid (degrees) - mksrf_edges - southern edge of grid (degrees) - mksrf_edgew - western edge of grid (degrees) - -or - - mksrf_fcamfile - CAM topo file (grid and possibly fraction data) - -or - - mksrf_fccsmdom - &cesm; domain file (both grid, and fraction data) - -or - - mksrf_fclmgrid - &clm; grid or surface dataset file (grid data) - -Note, you can provide more than one of the needed datasets, and the output -data will be determined by the datasets according to an order of precedence. -The order of precedence for data is as follows: - -mksrf_fcamfile -mksrf_fclmgrid -mksrf_fnavyoro -mksrf_fccsmdom - -Grid data then will be established by the file with the highest precedence. -&cesm; domain files sometimes have latitudes and longitudes that are "off" from -the standard by a small amount. By establishing an order of precedence you can ensure -that grid locations exactly match a given standard file, even if the values in the domain -file are off from that. - - - -There are three different major modes for using mkgriddata to -create grid files for &clm;: - -Convert &cesm; domain files to &clm; grid files -Create single point or regional area grid files -Convert CAM files to &clm; grid files - - - - - -Convert &cesm; domain files to &clm; grid files - -&cesm; domain files such as used for &datm;, include all the information -needed to create &clm; grid and fraction files. - -Example <command>mkgriddata</command> namelist to convert &cesm; 4x5 domain files to &clm; grid files - -&clmexp - mksrf_fccsmdom= -'/fs/cgd/csm/inputdata/lnd/dlnd7/domain.lnd.4x5_gx3v5.060404.nc' - mksrf_fclmgrid= -'/fs/cgd/csm/inputdata/lnd/clm2/griddata/griddata_4x5_060404.nc' -/ - - - - -Notice that in the above example, a &clm; grid file is included as well, even though -it's not required. The reason for this is to ensure that the latitude and longitudes -on the output files exactly match a standard grid file. - - - - - - -Create single point or regional area grid files - -The process to create single-point or regional area &clm; grid files is the same. -You enter the number of latitudes and longitudes you want on your output file and -the extent of the grid: North, East, South and West. You also tell -mkgriddata that -you are entering a "regional" grid and you also enter the standard Navy orography -dataset (or your own orography file if desired). For a single point you simply -enter "1" for the number of latitudes and longitudes, but you still enter the -grid extent (of the single grid cell). Here is a sample regional namelist to create -a 5x5 regional grid over the Amazon: - -Example <command>mkgriddata</command> namelist to create regional grid over Amazon - -&clmexp - mksrf_fnavyoro= -"/fs/cgd/csm/inputdata/lnd/clm2/rawdata/mksrf_navyoro_20min.c010129.nc" - mksrf_lsmlon = 5 - mksrf_lsmlat = 5 - mksrf_edgee = 303.75 - mksrf_edgew = 286.25 - mksrf_edges = -15. - mksrf_edgen = -4. -/ - - - - - -Currently you can NOT have regional grids that straddle both -sides of the Greenwich (longitude = zero) line. - - - - -You should enter longitudes with values from 0 to 360 East. - - - - - -Convert <acronym>CAM</acronym> files to &clm; grid files (deprecated) - -Older CAM initial files included all the information needed to create &clm; -grid files. Newer CAM files no longer include land fraction data. Hence you -can use CAM files to give you the grid coordinates, but you need other data -to give you the land-mask and topography. Since, CAM files no longer -contain the needed information, this option is now deprecated. In most cases you should -use one of the other two options. - - - - - - - -Using <command>mkdatadomain</command> to create domain datasets for &datm; or docn from &clm; grid datasets - -"mkdatadomain" is used to convert &clm; grid and fraction datasets into domain datasets -that can be used by either the "datm" or "docn" models. Most often &clm; users will want -to convert the grid datasets they just created using mkgriddata into -domain datasets to be used by &datm; for an "I" case. mkdatadomain is -controlled by a namelist, and has a very straight forward operation with only four -namelist items all of which are required. You specify which output mode you want "datm" -or "docn", and then set the input &clm; grid and frac datasets, and the output domain file. - - -Example <command>mkdatadomain</command> namelist to create a domain file from -&clm; frac and grid data files - -&domain_nl - dtype = "datm" - f_fracdata = -'/fs/cgd/csm/inputdata/lnd/clm2/griddata/fracdata_4x5_USGS_070110.nc' - f_griddata = -'/fs/cgd/csm/inputdata/lnd/clm2/griddata/griddata_4x5_060404.nc' - f_domain = -'domain.lnd.fv4x5_USGS.090117.nc' -/ - - - - - -Using mksurfdata to create surface datasets from grid datasets - -mksurfdata is used to create surface-datasets from grid datasets and raw datafiles -at half-degree resolution to produce files that describe the surface characteristics -needed by &clm; (fraction of grid cell covered by different land-unit types, and fraction -for different vegetation types, as well as things like soil color, and soil texture, -etc.). To run mksurfdata you can either use the -mksurfdata.pl script which will create namelists for you using the &buildnml; -XML database, or you can run it by hand using a namelist that you provide (possibly -modeled after an example provided in the -models/lnd/clm/tools/mksurfdata directory). The namelist for -mksurfdata is sufficiently complex that we recommend using the -mksurfdata.pl tool to build them. In the next section -we describe how to use the mksurfdata.pl script and the following -section gives more details on running mksurfdata by hand and the -various namelist input variables to it. - - -Running <command>mksurfdata.pl</command> - -The script mksurfdata.pl can be used to run the -mksurfdata program for several configurations, resolutions, -simulation-years and simulation year ranges. It will create the needed namelists for -you and move the files -over to your inputdata directory location (and create a list of the files created, and -for developers this file is also a script to import the files into the svn inputdata -repository). It will also use the &buildnml; XML database -to determine the correct input files to use, and for transient cases it will create -the appropriate mksrf_fdynuse file with the list of files for each -year needed for this case. And in the case of urban single-point -datasets (where surface datasets are actually input into mksurfdata) -it will do the additional processing required so that the output dataset -can be used once again by mksurfdata. Because, it figures out -namelist and input files for you, it is recommended that you use this script for creation -of standard surface datasets. If you need to create surface datasets for customized -cases, you might need to run mksurfdata on it's own. But you -could use mksurfdata.pl with the "-debug" option to give you -a namelist to start from. -For help on mksurfdata.pl you can use the "-help" option as below: - -> cd models/lnd/clm/tools/mksurfdata -> mksurdata.pl -help - -The output of the above command is: - -&mksurfdatapl; - - - -To run the script with optimized mksurfdata for a 4x5 degree grid -for 1850 conditions, on bluefire you would do the following: - -Example of running <command>mksurfdata.pl</command> to create a 4x5 resolution -<filename>fsurdat</filename> for a 1850 simulation year - -> cd models/lnd/clm/tools/mksurfdata -> gmake -> mksurfdata.pl -y 1850 -r 4x5 - - - - - - -Running <command>mksurfdata</command> by Hand - -In the above section we show how to run mksurfdata through -the mksurfdata.pl using input datasets that are in the &buildnml; -XML database. When you are running with input datasets that are NOT available in -the XML database you either need to add them as outlined in -, or you need to run mksurfdata -by hand, as we will outline here. - - - -Preparing your <command>mksurfdata</command> namelist - -When running mksurfdata by hand you will need to prepare your -own input namelist. There are sample namelists that are setup for running on the -&ncar; machine bluefire. You will need to change the filepaths to -run on a different machine. The list of sample namelists include - -mksurfdata.namelist -- standard sample namelist. -mksurfdata.regional -- sample namelist to -build for a regional grid dataset (5x5_amazon) -mksurfdata.singlept -- sample namelist to -build for a single point grid dataset (1x1_brazil) - -Note, that one of the inputs mksrf_fdynuse is a filename that -includes the filepaths to other files. The filepaths in this file will have to -be changed as well. You also need to make sure that the line lengths remain the same -as the read is a formatted read, so the placement of the year in the file, must remain -the same, even with the new filenames. One advantage of the mksurfdata.pl -script is that it will create the mksrf_fdynuse file for you. - - -We list the namelist items below. Most of the namelist items are filepaths to give to -the input half degree resolution datasets that you will use to scale from to the -resolution of your grid dataset. -You must first specify the input grid dataset for the resolution to output for: - -mksrf_fgrid Grid dataset - -Then you must specify settings for input high resolution datafiles - -mksrf_ffrac land fraction and land mask dataset -mksrf_fglacier Glacier dataset -mksrf_fglacierregion Glacier region ID dataset -mksrf_flai Leaf Area Index dataset -mksrf_flanwat Land water dataset -mksrf_forganic Organic soil carbon dataset -mksrf_fmax Max fractional saturated area dataset -mksrf_fsoicol Soil color dataset -mksrf_fsoitex Soil texture dataset -mksrf_ftopo Topography dataset (this is used to limit -the extent of urban regions and is used for glacier multiple elevation classes) - -mksrf_furban Urban dataset -mksrf_fvegtyp PFT vegetation type dataset -mksrf_fvocef Volatile Organic Compound Emission Factor -dataset -mksrf_fgdp GDP dataset -mksrf_fpeat Peatland dataset -mksrf_fabm Agricultural fire peak month dataset -mksrf_ftopostats Topography statistics dataset -mksrf_fvic VIC parameters dataset -mksrf_fch4 Inversion-derived CH4 parameters dataset - -You specify the ASCII text file with the land-use files. - -mksrf_fdynuse "dynamic land use" for transient -land-use/land-cover changes. This is an ASCII text file that lists the filepaths -to files for each year and then the year it represents (note: you MUST change the -filepaths inside the file when running on a machine NOT at &ncar;). -We always use this file, even for creating datasets of a fixed year. Also note -that when using the "pft_" settings this file will be an XML-like file with settings -for PFT's rather than filepaths (see below). - - - -And optionally you can specify settings for: - -all_urban If entire area is urban (typically used for -single-point urban datasets, that you want to be exclusively urban) -no_inlandwet If TRUE, set wetland to 0% over land -(renormalizing other landcover types as needed); wetland will only be used for ocean -points. (Only applies to CLM4.5 version of mksurfdata_map, for which the default is -TRUE.) -mksrf_firrig Irrigation dataset, if you want -activate the irrigation model over generic cropland -(experimental mode, normally NOT used) -mksrf_gridnm Name of output grid resolution (if not -set the files will be named according to the number of longitudes by latitudes) -mksrf_gridtype Type of grid (default is 'global') -nglcec number of glacier multiple elevation classes. -Can be 0, 1, 3, 5, or 10. When using the resulting dataset with &clm; you can then run -with glc_nec of either 0 or this value. - (experimental normally use the default of 0, when running with the land-ice -model in practice only 10 has been used) -numpft number of Plant Function Types (PFT) -in the input vegetation mksrf_fvegtyp dataset. You change -this to 20, if you want to create a dataset with prognostic crop activated. The -vegetation dataset also needs to have prognostic crop types on it as well. - (experimental normally not changed from the default of 16) -outnc_large_files If output should be in &netcdf; large file -format -outnc_double If output should be in double -precision (normally we turn this on) -pft_frc array of fractions to override PFT -data with for all gridpoints (experimental mode, normally NOT used). -pft_idx array of PFT indices to override PFT -data with for all gridpoints (experimental mode, normally NOT used). -soil_clay percent clay soil to override -all gridpoints with (experimental mode, normally NOT used). -soil_color Soil color to override -all gridpoints with (experimental mode, normally NOT used). -soil_fmax Soil maximum fraction to override -all gridpoints with (experimental mode, normally NOT used). -soil_sand percent sandy soil to -override all gridpoints with (experimental mode, normally NOT used). - - - -After creating your namelist, -when running on a non &ncar; machine you will need to get the files -from the inputdata repository. -In order to retrieve the files needed for mksurfdata you can do the following on your -namelist to get the files from the inputdata repository, using the -check_input_data script which also allows you to export data to -your local disk. - -Getting the raw datasets for <command>mksurfdata</command> to your local -machine using the <command>check_input_data</command> script - -> cd models/lnd/clm/tools/mksurfdata -# First remove any quotes and copy into a filename that can be read by the -# check_input_data script -> sed "s/'//g" namelist > clm.input_data_list -# Run the script with -export and give the location of your inputdata with $CSMDATA -> ../../../../../scripts/ccsm_utils/Tools/check_input_data -datalistdir . \ --inputdata $CSMDATA -check -export -# You must then do the same with the flanduse_timeseries file referred to in the namelist -# in this case we add a file = to the beginning of each line -> awk '{print "file = "$1}' landuse_timeseries_hist_simyr2000-2000.txt > clm.input_data_list -# Run the script with -export and give the location of your inputdata with $CSMDATA -> ../../../../../scripts/ccsm_utils/Tools/check_input_data -datalistdir . \ --inputdata $CSMDATA -check -export - - - - -Experimental options to <command>mksurfdata</command> - -The options: pft_frc, pft_idx, soil_clay, soil_color, soil_fmax, and soil_sand are also -new and considered experimental. They provide a way to override the PFT and soil -values for all grid points to the given values that you set. This is useful for -running with single-point tower sites where the soil type and vegetation is known. -Note that when you use pft_frc, all other landunits will be zeroed out, and the -sum of your pft_frc array MUST equal 100.0. Also note that when using the "pft_" -options the mksrf_fdynuse file instead of having filepath's -will be an XML-like file with PFT settings. Unlike the file of file-paths, you will -have to create this file by hand, mksurfdata.pl will NOT be able -to create it for you (other than the first year which will be set to the values -entered on the command line). Note, that when &ptclm; is run, it CAN create these -files for you from a simpler format (see ). -Instead of a filepath you have a list of XML elements that give information on the PFT's -and harvesting for example: - -<pft_f>100</pft_f><pft_i>1</pft_i><harv>0,0,0,0,0</harv><graz>0</graz> - -So the <pft_f> tags give the PFT fractions and the <pft_i> tags give the -index for that fraction. Harvest is an array of five elements, and grazing is a single -value. Like the usual file each list of XML elements goes with a year, and there is -limit on the number of characters that can be used. - - - - - -Standard Practices when using <command>mksurfdata</command> - -In this section we give the recommendations for how to use mksurfdata -to give similar results to the files that we created when using it. - - -If you look at the standard surface datasets that we have created and provided for use, -there are three practices that we have consistently done in each (you also see these in -the sample namelists and in the mksurfdata.pl script). The first is -that we always output data in double precision (hence outnc_double -is set to .true.). The next is that we always use the procedure -for creating transient datasets (using mksrf_fdynuse) even when -creating datasets for a fixed simulation year. This is to ensure that the fixed year -datasets will be consistent with the transient datasets. When this is done a -"landuse_timeseries" dataset will be created -- but will NOT be used in &clm;. If you look -at the sample namelist mksurfdata.namelist you note that it -sets mksrf_fdynuse to the file -landuse_timeseries_hist_simyr2000.txt, where the single file entered is -the same PFT file used in the rest of the namelist (as mksrf_fvegtyp). -The last practice that we always do is to always set mksrf_ftopo, -even if glacier elevation classes are NOT active. This is -important in limiting urban areas based on topographic height, and hence is important -to use all the time. The glacier multiple elevation classes will be used as well if -you are running a compset with the active glacier model. - - -There are two other important practices for creating urban single point datasets. The -first is that you often will want to set all_urban to -.true. so that the dataset will have 100% of the gridcell output -as urban rather than some mix of: urban, vegetation types, and other landunits. The -next practice is that most of our specialized urban datasets have custom values for -the urban parameters, hence we do NOT want to use the global urban dataset to get -urban parameters -- we use a previous version of the surface dataset for the urban -parameters. However, in order to do this, we need to append onto the previous surface -dataset the grid and land mask/land fraction information from the grid and fraction -datasets. This is done in mksurfdata.pl using the NCO -program ncks. An example of doing this for the Mexico City, Mexico -urban surface dataset is as follows: - -> ncks -A $CSMDATA/lnd/clm2/griddata/griddata_1x1pt_mexicocityMEX_c090715.nc \ -$CSMDATA/lnd/clm2/surfdata/surfdata_1x1_mexicocityMEX_simyr2000_c100407.nc -> ncks -A $CSMDATA/lnd/clm2/griddata/fracdata_1x1pt_mexicocityMEX_navy_c090715.nc \ -$CSMDATA/lnd/clm2/surfdata/surfdata_1x1_mexicocityMEX_simyr2000_c100407.nc - -Note, if you look at the current single point urban surface datasets you will note -that the above has already been done. - - -The final issue is how to build mksurfdata. When NOT optimized -mksurfdata is very slow, and can take many hours to days to -even run for medium resolutions such as one or two degree. So usually you will want -to run it optimized. Possibly you also want to use shared memory parallelism using -&omp; with the SMP option. The problem with running optimized is that -answers will be different when running optimized versus non-optimized for most -compilers. So if you want answers to be the same as a previous surface dataset, you -will need to run it on the same platform and optimization level. Likewise, running -with or without &omp; may also change answers (for most compilers it will NOT, however -it does for the IBM compiler). However, answers should be the same regardless of the -number of threads used when &omp; is enabled. Note, that the output surface datasets -will have attributes that describe whether the file was written out optimized or not, -with threading or not and the number of threads used, to enable the user to more -easily try to match datasets created previously. For more information on the different -compiler options for the &clm4; tools see . - - - - - - - -Using &ncl; scripts <command>ndepregrid.ncl</command> and -<command>aerdepregrid.ncl</command> to interpolate aerosol deposition datasets - -Unlike the other tools, these are &ncar; Command Language (&ncl;) scripts -and you will need to get a copy of &ncl; in order to use them. You also won't have to -build an executable in order to use them, hence no Makefile is provided. &ncl; is provided -for free download as either binaries or source code from: -http://www.ncl.ucar.edu/. The &ncl; -web-site also contains documentation on &ncl; and it's use. - - -By default at this point neither of these scripts HAS to be used, -as the model is now constructed to read aerosol and Nitrogen deposition from 2-degree -datasets and interpolate to the model resolution on the fly. The main reason you might -want to do this now, is for better performance for single-point simulations. - - -Both the ndepregrid.ncl and aerdepregrid.ncl -scripts have similar interfaces and you customize the output resolution and -characteristics based on the settings of environment variables that you set (if you -don't set any of the variables, the script has defaults that it will use). -The list of environment variables that can be set are: - -RES -- output resolution name -RCP -- representative concentration pathway for future scenarios -(example 2.6, 4.5, 6, or 8.5) -SIM_YR -- simulation year (example 1850 or 2000) -SIM_YR_RNG -- simulation year range (example 1850-2000 or -1850-2100) -GRDFIL -- full pathname of grid file to use -(in place of getting the default grid file based on the RES value) -CSMDATA -- &cesm; inputdata directory -CLM_ROOT -- root directory for &clm; (models/lnd/clm directory) - - - - -You MUST provide either RES or both -GRDFIL AND RES. If you -just give RES the default namelist database in -models/lnd/clm/bld will be used to find the default grid -file based on the resolution name RES. If you provide -GRDFIL the input pathname of the gridfile provided will be used, -and the output filename will include RES as part of it's name -to designate it as an output file at that resolution. - - - -Both scripts assume that you will be interpolating from a native resolution of 1.9x2.5 -and using the default files found in the namelist database to interpolate from. If you -want to interpolate from another resolution or use other files, you would need to edit -the scripts to do so. Both scripts also use a bilinear interpolation to do the -regridding. The environment variables: RCP, SIM_YR, -and SIM_YR_RNG will be used to query the namelist database to -determine which native dataset to interpolate from. If you don't provide valid -values for these variables, it won't be able to find a dataset to interpolate from. -You can use the build-namelist script to query what the valid values for these can -be. Likewise, when you use RES to determine the grid file to interpolate -to, it needs to be a valid value from the namelist database. - - -The scripts can be used to interpolate from (and create output) constant or -transient datasets. -Constant datasets specify the SIM_YR and set SIM_YR_RNG -to constant (which is also the default). Transient datasets need -to specify both SIM_YR and SIM_YR_RNG, where -SIM_YR is set to the first year in the interval (typically 1850). - - -The default for CSMDATA works for &ncar; computers, but will need to -be set to the top level directory location of your &cesm; input data on other computers. -If you set this as a default for your shell when you login (for example with your -$HOME/.cshrc if you use csh) you won't have to set it each time -you run the script. CLM_ROOT will default to the proper location -when you run it in the models/lnd/clm/tools/ncl_script -directory. It is only useful if you want to run the script out of a different -directory. - - -Using <command>ndepregrid.ncl</command> to interpolate Nitrogen deposition datasets - -ndepregrid.ncl interpolates the Nitrogen deposition datasets from one resolution -to another. - - - -Interpolating Nitrogen deposition files is no longer needed, because the model can -read Nitrogen deposition files at one resolution and interpolate to the resolution the -model is running at on the fly. Interpolating to another -resolution is only useful for very course resolutions, if you want to save some computing -resources in reading larger datasets. For example, this may be useful in obtaining -single-point datasets. - - - -For example, to interpolate to an output resolution of 0.9x1.25, for a constant -simulation-year of 1850, you would do the following: - -> env RES=0.9x1.25 SIM_YR=1850 ncl ndepregrid.ncl - - - - - -Using <command>aerdepregrid.ncl</command> to interpolate Aerosol deposition datasets - -aerdepregrid.ncl interpolates the Aerosol deposition datasets from one resolution. -It can be used to interpolate either constant datasets (for example: -aerosoldep_monthly_2000_0.9x1.25_c090828.nc) or transient datasets (for example: -aerosoldep_monthly_1849-2006_0.9x1.25_c090830.nc). - - - -Interpolating aerosol deposition files is no longer needed, because the &datm; model can -read aerosol deposition files at one resolution and interpolate to the resolution the -model is running at on the fly. Interpolating to another -resolution is only useful for very course resolutions, if you want to save some computing -resources in reading larger datasets. For example, this may be useful in obtaining -single-point datasets. - - - -For example, to interpolate to an output resolution of 4x5, for a transient -simulation-year range of 1850 to 2100 and the rcp of 8.5, you would do the following: - -> env RES=4x5 SIM_YR=1850 SIM_YR_RNG=1850-2100 RCP=8.5 ncl ndepregrid.ncl - - - - - - -How to Customize Datasets for particular Observational Sites - -There are two ways to customize datasets for a particular observational site. The first -is to customize the input to the tools that create the dataset, and the second is to -over-write the default data after you've created a given dataset. Depending on the tool -it might be easier to do it one way or the other. In we list the files that are most likely to be -customized and the way they might be customized. Of those files, the ones you are most -likely to customize are: fatmlndfrc, fsurdat, faerdep (for &datm;), and -stream_fldfilename_ndep. Note mksurfdata as documented previously -has options to overwrite the vegetation and soil types. For more information on this also see - and &ptclm; uses these methods to -customize datasets see . - - -Another aspect of customizing your input datasets is customizing the input atmospheric -forcing datasets. See the for more -information on this. Also the chapter on &ptclm; in -has information on using the AmeriFlux tower site data as atmospheric forcing. - - - - -Conclusion of tools description - -We've given a description of how to use the different tools with &clm; to create -customized datasets. In the next chapter we will talk about how to make these -files available for build-namelist so that you can easily create simulations -that include them. In the chapter on single-point and regional datasets we also -give an alternative way to enter new datasets without having to edit files. - - - - - diff --git a/doc/UsersGuide/trouble_shooting.xml b/doc/UsersGuide/trouble_shooting.xml deleted file mode 100644 index 418cfabaae..0000000000 --- a/doc/UsersGuide/trouble_shooting.xml +++ /dev/null @@ -1,545 +0,0 @@ - - -Trouble Shooting Problems - -In this chapter we give some guidance on what to do when you encounter some of the -most common problems. We can't cover all the problems that a user could potentially -have, but we will try to help you recognize some of the most common situations. -And we'll give you some suggestions on how to approach the problem to come up with -a solution. - - -In general you will run into one of three type of problems: - -configure-time -build-time -run-time - -You may also run into problems with create_newcase itself, or -with the archiving scripts -- for those problems you should consult the -&cesmrel; Scripts User's Guide. - - - -Trouble with Configuration - -The first type of problem happens when you invoke the configure -case -command. This indicates there is something wrong with your template files, or input -datasets, or the details of what you are trying to configure the model to do. -There's also a trouble-shooting chapter in the &cesmrel; -Scripts User's Guide. Many of the problems with configuration can be resolved -with the guidelines given there. Here we will restrict ourselves to problems from the -&clm; or &datm; templates or input files. - -Example of configure problem with missing datasets - -> ./create_newcase -case T31rcp6 -res T31_g37 -compset IRCP60CN \ --mach bluefire -> ./configure -case - -The following is what is displayed to the screen. - -Generating resolved namelist, prestage, and build scripts -configure done. -adding use_case 1850-2100_rcp6_transient defaults for var clm_demand with val flanduse_timeseries -adding use_case 1850-2100_rcp6_transient defaults for var clm_start_type with val startup -adding use_case 1850-2100_rcp6_transient defaults for var model_year_align_ndep with val -1850 -adding use_case 1850-2100_rcp6_transient defaults for var rcp with val 6 -adding use_case 1850-2100_rcp6_transient defaults for var sim_year with val 1850 -adding use_case 1850-2100_rcp6_transient defaults for var sim_year_range with val -1850-2100 -adding use_case 1850-2100_rcp6_transient defaults for var stream_year_first_ndep with val -1850 -adding use_case 1850-2100_rcp6_transient defaults for var stream_year_last_ndep with val -2100 -adding use_case 1850-2100_rcp6_transient defaults for var use_case_desc with val Simulate -transient land-use, aerosol and Nitrogen deposition changes with historical data from -1850 to 2005 and then with the RCP6 scenario from AIM - -build-namelist - No default value found for flanduse_timeseries. - Are defaults provided for this resolution and land mask? -ERROR: generate_resolved.csh error for lnd template -configure error: configure generated error in attempting to created resolved scripts - - -The important thing to note here is the line: - -ERROR: generate_resolved.csh error for lnd template - -which tells us that the problem is in the land template. It may also indicate problems -in one of the other templates (atm, ccsm, cpl, glc, ice, or ocn), in which case you -should consult the appropriate model user's guide, and examine the given template file -in Tools/Templates. For more information on working with template -files see . - - -In the example above, it's obvious that the problem is coming from the &clm; &buildnml;, -in other situations it might not be so obvious where the problem is occurring. In such -cases it might be useful to add a "set echo" command to the top of the template file so -that each command in the template will be echoed to the screen and you can see what -is happening and where the error is occurring. - -set echo - - - -In the example, the error is that the &clm; XML database does NOT have a -flanduse_timeseries for the given resolution, rcp scenario and ocean mask. -That means you will need to create the file and then supply the file into your case. See - for more information on creating files, and see - for more information on adding files to the -XML database. Alternatively, you can provide the file to your case by creating -a user namelist as shown in . - - - -The two most common problems from your &clm; template will be errors from the &clm; -&configure; or &buildnml;. For more information on these scripts see: - and -the section on &CLMBLDNML;. - - - - - -Trouble with Building - -Here's an example of running the build for a case and having it fail in the land model -build. As you can see it lists which model component is being built and the build log -for that component. - - CCSM BUILDEXE SCRIPT STARTING - - Build Libraries: mct pio csm_share -Sat Jun 19 21:21:19 MDT 2010 /ptmp/erik/test_build/mct/mct.bldlog.100619-212107 -Sat Jun 19 21:22:18 MDT 2010 /ptmp/erik/test_build/pio/pio.bldlog.100619-212107 -Sat Jun 19 21:23:18 MDT 2010 -/ptmp/erik/test_build/csm_share/csm_share.bldlog.100619-212107 -Sat Jun 19 21:24:00 MDT 2010 /ptmp/erik/test_build/run/cpl.bldlog.100619-212107 -Sat Jun 19 21:24:00 MDT 2010 /ptmp/erik/test_build/run/atm.bldlog.100619-212107 -Sat Jun 19 21:24:06 MDT 2010 /ptmp/erik/test_build/run/lnd.bldlog.100619-212107 -ERROR: clm.buildexe.csh failed, see /ptmp/erik/test_build/run/lnd.bldlog.100619-212107 -ERROR: cat /ptmp/erik/test_build/run/lnd.bldlog.100619-212107 - -You can then examine the build log that failed and see what went wrong. Most compilers -will give the full filepath and line number for the file that filed to compile. - - - - -Trouble with Running - -Tracking down problems while the model is running is much more difficult to do -than configure or build problems. In this section we will give some suggestions -on how to find run time problems. Below we show the log file results of a job -that aborted while running. - - CCSM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY -Sun Jun 20 18:24:06 MDT 2010 -- CSM EXECUTION BEGINS HERE -Sun Jun 20 18:24:35 MDT 2010 -- CSM EXECUTION HAS FINISHED -Model did not complete - see /ptmp/erik/test_run/run/cpl.log.100620-182358 - -In the next section we will talk about using the different log files to track -down problems, and find out where the problem is coming from. In the section -after that we give some general advice on debugging problems and some suggestions -on ideas that may be helpful to track the problem down. Some of the examples -below are from the &KnownBugs; file. - - -Tracking Problems by Querying Log Files - -The first thing to do when tracking down problems is to query the different log -files to see if you can discover where the problem occurs, and any error messages about -it. It's important to figure out if the problem comes in at initialization or in the -run phase of the model, and in which model component the problem happens. There -are different log files for the different major components, and they all end -with the date and time in YYMMDD-HHMMSS format (2-digit: year, month, day, hour -minute and second). When the model runs to completion the log files will be copied -to the logs directory in the script directory, but when the -model fails they will remain in the run directory. Here's an example list of -log files from an "I" case where the model dies in the land model initialization. -For "I" cases the sea-ice and ocean components are just stubs and don't create -log files (and unless running with the active land-ice model "glc" log files won't -be created either). - -atm.log.100620-182358 -ccsm.log.100620-182358 -cpl.log.100620-182358 -lnd.log.100620-182358 - - - - -The coupler log file - -The first log file to check is the coupler log file so that you can see where -the model dies and which model component it fails in. When the model dies at -initialization the last model component listed is the component that failed. - - -Example of a case that fails in the &clm; land model initialization. - -(seq_timemgr_clockPrint) Prev Time = 00001201 00000 -(seq_timemgr_clockPrint) Next Time = 99991201 00000 -(seq_timemgr_clockPrint) Intervl yms = 9999 0 0 - -(seq_mct_drv) : Initialize each component: atm, lnd, ocn, and ice -(seq_mct_drv) : Initialize atm component -(seq_mct_drv) : Initialize lnd component - - - - - -The ccsm log file - -The ccsm log files are to some extent the "garbage collection" of log output. The -&clm; sends it's output from it's master processor, but sends other output and possibly -errors to the ccsm log file. Because, of this, often error messages are somewhere in the -ccsm log file. However, since there is so much other output it may be difficult to find. -For example, here is some output from an older version of &cesm; (&cesm102;) where the -RTM river routing file (before it was converted to &netcdf;) was not provided and -the error on the open statement for the file was embedded near the end of the ccsm log -file. - -NODE# NAME -( 0) be1105en.ucar.edu -"/gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/lnd/clm/src/riverroute/RtmMod.F90", line -239: 1525-155 The file name provided in the OPEN statement for unit 1 has zero length or -contains all blanks. The program will recover by ignoring the OPEN statement. -"/gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/lnd/clm/src/riverroute/RtmMod.F90", line -241: 1525-001 The READ statement on the file fort.1 cannot be completed because the end -of the file was reached. The program will stop. - -Running: ./ccsm.exe -Please wait... - -Memory usage for ./ccsm.exe (task # 0) is: 51696 KB. Exit status: 1. Signal: 0 - -Although the example is from an earlier version of the model it still serves to -illustrate finding problems from the ccsm log file. - - -When working with the ccsm log file, for a run-time problem, you will need to be able -to separate it's output into three categories: pre-crash, crash, and post-crash. The -pre-crash section is everything that is normal output for good operation of the model. -The crash section is the section where the model dies and reports on the actual problem. -the post-crash section is the cleanup and finalization after the model dies. The most -important part of this of course is the crash section. The tricky part is distinguishing -it from the other sections. Also because the ccsm log file most likely has duplicated -output from multiple processors it is even more difficult to distinguish the different -sections and to some extent the sections may be intertwined, as different processors -reach the different sections at different times. Because, of this reducing the number of -processors for your simulation may help you sort out the output in the file (see -). Also much of the output from the ccsm log file are -system level information having to do with &mpi; multiprocessing. Usually you can ignore -this information, but it makes it more difficult to trudge through. - - -Sometimes the ccsm log file is the ONLY file available, because the model terminates -early in initialization. In this case understanding the output in the ccsm log file -becomes even more important. This also indicates the model did NOT advance far enough -to reach the initialization of the individual model components. This may mean that the -initialization of the multiprocessing for &mpi; and/or &omp; failed, or that the -reading of the driver namelist file "drv_in" failed. - - -Here we show those three sections for a ccsm log file where a two task job failed on -reading the namelist file. For a typical job with many tasks similar sections of this -will be repeated not just twice but for each task and hence make it harder to read. - - -Pre-crash section of the ccsm log file - -ATTENTION: 0031-386 MP_INSTANCES setting ignored when LoadLeveler is not being used. -ATTENTION: 0031-386 MP_INSTANCES setting ignored when LoadLeveler is not being used. -ATTENTION: 0031-378 MP_EUIDEVICE setting ignored when LoadLeveler is not being used. -ATTENTION: 0031-386 MP_INSTANCES setting ignored when LoadLeveler is not being used. - 0:INFO: 0031-724 Executing program: </usr/local/lsf/7.0/aix5-64/bin/lsnrt_run> - 1:INFO: 0031-724 Executing program: </usr/local/lsf/7.0/aix5-64/bin/lsnrt_run> - 0:/contrib/bin/ccsm_launch: process 401894 bound to logical CPU 0 on host be0310en.ucar.edu ... - 1:/contrib/bin/ccsm_launch: process 439264 bound to logical CPU 1 on host be0310en.ucar.edu ... - 0:INFO: 0031-619 64bit(us, Packet striping on) ppe_rmas MPCI_MSG: MPI/MPCI library was compiled on Wed Aug 5 13:36:06 2009 - 0: - 1:LAPI version #14.26 2008/11/23 11:02:30 1.296 src/rsct/lapi/lapi.c, lapi, rsct_rpt53, rpt53s004a 09/04/29 64bit(us) library compiled on Wed Apr 29 15:30:42 2009 - 1:. - 1:LAPI is using lightweight lock. - 0:LAPI version #14.26 2008/11/23 11:02:30 1.296 src/rsct/lapi/lapi.c, lapi, rsct_rpt53, rpt53s004a 09/04/29 64bit(us) library compiled on Wed Apr 29 15:30:42 2009 - 0:. - 0:LAPI is using lightweight lock. - 0:Use health ping for failover/recovery - 1:Use health ping for failover/recovery - 0:Initial communication over instance 2. - 1:Initial communication over instance 0. - 1:IB RDMA initialization completed successfully - 1:The MPI shared memory protocol is used for the job - 0:IB RDMA initialization completed successfully - 0:LAPI job ID for this job is: 1684890719 - 0:The MPI shared memory protocol is used for the job - 0:(seq_comm_setcomm) initialize ID ( 7 GLOBAL ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 2 ATM ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 1 LND ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 4 ICE ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 5 GLC ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 3 OCN ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_setcomm) initialize ID ( 6 CPL ) pelist = 0 1 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 8 CPLATM ) join IDs = 6 2 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 9 CPLLND ) join IDs = 6 1 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 10 CPLICE ) join IDs = 6 4 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 11 CPLOCN ) join IDs = 6 3 ( npes = 2) ( nthreads = 1) - 0:(seq_comm_joincomm) initialize ID ( 12 CPLGLC ) join IDs = 6 5 ( npes = 2) ( nthreads = 1) - 0: - 0: (seq_comm_printcomms) ID layout : global pes vs local pe for each ID - 0: gpe LND ATM OCN ICE GLC CPL GLOBAL CPLATM CPLLND CPLICE CPLOCN CPLGLC nthrds - 0: --- ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ ------ - 0: 0 : 0 0 0 0 0 0 0 0 0 0 0 0 1 - 1: 1 : 1 1 1 1 1 1 1 1 1 1 1 1 1 - 1: - 0: (t_initf) Read in prof_inparm namelist from: drv_in - 1: (seq_io_init) cpl_io_stride, iotasks or root out of bounds - resetting to defaults 4 0 1 - 0: piolib_mod.f90 1353 1 2 1 2 - 1: piolib_mod.f90 1353 1 2 1 2 - 0: pio_support::pio_die:: myrank= 0 : ERROR: piolib_mod.f90: 1354 : not enough procs for the stride - 1: pio_support::pio_die:: myrank= 1 : ERROR: piolib_mod.f90: 1354 : not enough procs for the stride - - - -Crash section of the ccsm log file - - 0: - 0: Traceback: - 1: - 1: Traceback: - 0: Offset 0x00000c4c in procedure __pio_support_NMOD_piodie, near line 88 in file pio_support.F90.in - 1: Offset 0x00000c4c in procedure __pio_support_NMOD_piodie, near line 88 in file pio_support.F90.in - 0: Offset 0x00000fd0 in procedure __piolib_mod_NMOD_init, near line 1354 in file piolib_mod.F90 - 1: Offset 0x00000fd0 in procedure __piolib_mod_NMOD_init, near line 1354 in file piolib_mod.F90 - 1: Offset 0x00000398 in procedure __seq_io_mod_NMOD_seq_io_init, near line 247 in file /gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/drv/shr/seq_io_mod.F90 - 0: Offset 0x00000398 in procedure __seq_io_mod_NMOD_seq_io_init, near line 247 in file /gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/drv/shr/seq_io_mod.F90 - 0: Offset 0x0001aa88 in procedure ccsm_driver, near line 465 in file /gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/drv/driver/ccsm_driver.F90 - 0: --- End of call chain --- - 1: Offset 0x0001aa88 in procedure ccsm_driver, near line 465 in file /gpfs/proj2/fis/cgd/home/erik/clm_trunk/models/drv/driver/ccsm_driver.F90 - 1: --- End of call chain --- - - - -Post-crash section of the ccsm log file - - 1:Communication statistics of task 1 is associated with task key: 1684890719_1 - 0:Communication statistics of task 0 is associated with task key: 1684890719_0 - 0: - 0:Running: ./ccsm.exe - 0:Please wait... - 0: - 0:Memory usage for ./ccsm.exe (task # 0) is: 198892 KB. Exit status: 134. Signal: 0 - 1: - 1:Running: ./ccsm.exe - 1:Please wait... - 1: - 1:Memory usage for ./ccsm.exe (task # 0) is: 198572 KB. Exit status: 134. Signal: 0 -INFO: 0031-656 I/O file STDOUT closed by task 0 -INFO: 0031-656 I/O file STDERR closed by task 0 -ERROR: 0031-250 task 0: IOT/Abort trap -INFO: 0031-656 I/O file STDOUT closed by task 1 -INFO: 0031-656 I/O file STDERR closed by task 1 -ERROR: 0031-250 task 1: IOT/Abort trap -INFO: 0031-639 Exit status from pm_respond = 0 -ATTENTION: 0031-386 MP_INSTANCES setting ignored when LoadLeveler is not being used. -Job /usr/local/lsf/7.0/aix5-64/bin/poejob /contrib/bin/ccsm_launch /contrib/bin/job_memusage.exe ./ccsm.exe - -TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME -===== ========== ================ ======================= =================== -00000 be0310en /contrib/bin/ccs Exit (134) 08/31/2010 12:32:57 -00001 be0310en /contrib/bin/ccs Exit (134) 08/31/2010 12:32:57 - - - - - -The &clm; log file - -Of course when you are working with and making changes to &clm;, most of your focus -will be on the &clm; log file and the errors it shows. As already pointed out -if you don't see errors in the lnd.log.* file you should look -in the ccsm.log.* to see if any errors showed up there. - - -Here's an example of the lnd.log.* file when running -&PTSMODE; with initial conditions (this is bug 1025 in the &KnownBugs; file). - - Successfully initialized variables for accumulation - - reading restart file I2000CN_f09_g16_c100503.clm2.r.0001-01-01-00000.nc - Reading restart dataset - ERROR - setlatlon.F:Cant get variable dim for lat or lsmlat - ENDRUN: called without a message string - - - - - -The &datm; log file - -When working with "I cases" the second most common problems after &clm; problems are -problems with the data atmosphere model. So examining the atm.log.* -is important. - - -Here's an example of a problem that occurs when the wrong prescribed aerosol file -is given to a pt1_pt1 simulation. - -(datm_comp_init) atm mode = CLMNCEP -(shr_strdata_init) calling shr_dmodel_mapSet for fill -(shr_strdata_init) calling shr_dmodel_mapSet for remap - ('shr_map_getWts') ERROR: yd outside bounds 19.5000000000000000 -(shr_sys_abort) ERROR: ('shr_map_getWts') ERROR yd outside 90 degree bounds -(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping - - - - - -The batch log files - -The names of the batch log files will depend on the batch system of the machine -that is being used. They will normally be in the script directory. Usually, they -don't contain important information, but they are a last resort place to look for -error messages. On the &ncar; IBM system "bluefire" the batch files are called -with names that start with "poe" and then either "stderr" or "stdout", with the -job number at the end. - - - - - - -General Advice on Debugging Run time Problems - -Here are some suggestions on how to track down a problem while running. In general -if the problem still occurs for a simpler case, it will be easier to track down. - -Run in DEBUG mode -Run with a smaller set of processors -Run in serial mode with a single processor -Run at a lower resolution -Run a simpler case -Run with a debugger - - - - -Run in DEBUG mode - -The first thing to try is to run in DEBUG mode so that float point trapping will be -triggered as well as array bounds checking and other things the compiler can turn -on to help you find problems. To do this edit the &envbuild; file and set DEBUG - to TRUE as follows: - -> ./xmlchange -file env_build.xml -id DEBUG -val TRUE - - - - - -Run with a smaller set of processors - -Another way to simplify the system is to run with a smaller set of processors. You -will need to clean the configure and edit the env_mach_pes.xml. -For example, to run with four processors: - -> ./configure -cleanall -> ./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_OCN -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_CPL -val 4 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_GLC -val 4 -> ./configure -case - -Another recommended simplification is to run without threading, so set the -NTHRDS for each component to "1" if it isn't already. Sometimes, -multiprocessing problems require a certain number of processors before they occur -so you may not be able to debug the problem without enough processors. But, it's always -good to reduce it to as low a number as possible to make it simpler. For threading -problems you may have to have threading enabled to find the problem, but you can run -with 1, 2, or 3 threads to see what happens. - - - - -Run in serial mode with a single processor - -Simplifying to one processor removes all multi-processing problems and makes -the case as simple as possible. If you can enable USE_MPI_SERIAL -you will also be able to run interactively rather than having to submit to a job -queue, which sometimes makes it easier to run and debug. If you can use -USE_MPI_SERIAL you can also use threading, but still run interactively -in order to use more processors to make it faster if needed. - -> ./configure -cleanall -# Set tasks and threads for each component to 1 -# You could also set threads to something > 1 for speed, but still -# run interactively if threading isn't an issue. -> ./xmlchange -file env_mach_pes.xml -id NTASKS_ATM -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_ATM -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_LND -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_LND -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_ICE -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_ICE -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_OCN -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_OCN -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_CPL -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_CPL -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTASKS_GLC -val 1 -> ./xmlchange -file env_mach_pes.xml -id NTHRDS_GLC -val 1 -# If mpi-serial capability is available on the machine you are using -# set USE_MPI_SERIAL to true so that you can run interactively -> ./xmlchange -file env_conf.xml -id USE_MPI_SERIAL -val TRUE -> ./configure -case -# Then build your case -# And finally run, by running the *.run script interactively -# (If you were able to set USE_MPI_SERIAL to true) - - - - - -Run at a lower resolution - -If you can create a new case running at a lower resolution and replicate the problem -it may be easier to solve. This of course requires creating a whole new case, and trying -out different lower resolutions. - - - - -Run a simpler case - -Along the same lines, you might try running a simpler case, trying another compset -with a simpler setup and see if you can replicate the problem and then debug from that -simpler case. Again, of course you will need to create new cases to do this. - - - - -Run with a debugger - -Another suggestion is to run the model with a debugger such as: dbx, -gdb, or totalview. Often to run with a debugger -you will need to reduce the number of processors as outlined above. Some debuggers such -as dbx will only work with one processor, while more advanced -debuggers such as totalview can work with both &mpi; tasks and OMP -threads. Even simple debuggers though can be used to query core files, to see where -the code was at when it died (for example using the where in -dbx for a core file can be very helpful. For help in running -with a debugger you will need to contact your system administrators for the machine -you are running on. - - - - - - - - diff --git a/doc/build_docs b/doc/build_docs new file mode 100755 index 0000000000..97fb7aa9b2 --- /dev/null +++ b/doc/build_docs @@ -0,0 +1,8 @@ +#!/usr/bin/env bash + +if [ -f doc-builder/build_docs ]; then + echo "Running: doc-builder/build_docs --fetch-images $@" + doc-builder/build_docs --fetch-images "$@" +else + echo "Obtain doc-builder by running ./manage_externals/checkout_externals -o from the top-level" +fi diff --git a/doc/ctsm1_0_ChangeLog b/doc/ctsm1_0_ChangeLog new file mode 100644 index 0000000000..e02561d30a --- /dev/null +++ b/doc/ctsm1_0_ChangeLog @@ -0,0 +1,14843 @@ +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev113 +Originator(s): negins (Negin Sobhani,UCAR/TSS,303-497-1224) +Date: Tue Sep 8 15:57:49 MDT 2020 +One-line Summary: Some bit-for-bit changes needed for the Perturbed Parameter Ensemble work + +Purpose of changes +------------------ + +Some BFB fixes including bug fixes needed for PPE simulations. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1060 (Some code cleanup of luna bug fixes) +- Resolves ESCOMP/CTSM#1062 (PPE namelist parameter defaults) +- Resolves ESCOMP/CTSM#1053 (Non-standard namelist parameter) +- Resolves ESCOMP/CTSM#1055 (Expand potential vcmax:jmax ratio) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +cmb_cmplt_fact was a parameter under namelist control pertaining to the fire +model (combusion completion factor [unitless]), which previously included an array. +This parameter is now splitted into two real values i.e. cmb_cmplt_fact_litter and +cmb_cmplt_fact_cwd. +If the users have cmb_cmplt_fact in a user_nl_clm file that worked before, it +won't work anymore since it is now splitted into cmb_cmplt_fact_litter +and cmb_cmplt_fact_cwd. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +Previously, denitrif_nitrateconc_exponent and denitrif_nitrateconc_coefficient +were on the params file but ALSO on the namelist. They are now removed from the namelist. + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: [For timing changes, can check PFS +test(s) in the test suite] None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double +maintenance): None + +Changes to tests or testing: None + + +CTSM testing: + + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- PASS (except for NLCOMP) + izumi ------- PASS (except for NLCOMP) + +If the tag used for baseline comparisons was NOT the previous tag, note that here: +ctsm1.0.dev111 + + +Answer changes +-------------- + +Changes answers relative to baseline: None + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +None + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1102 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev112 +Originator(s): sacks (Bill Sacks), wwieder (Will Wieder) +Date: Fri Aug 28 17:10:57 MDT 2020 +One-line Summary: Small changes to mksurfdata_map, singlept tool and run_sys_tests + +Purpose of changes +------------------ + +(1) Move mksurfdata_map rounding of special landunits to before wetland + fill: I think this may be important to avoid errors and/or wrong + behavior in some edge cases where we have < 0.5% cover of glacier + and/or lake, and other cases. See + https://github.com/ESCOMP/CTSM/issues/1118 for detailed + thoughts. May change answers in rare cases, but no answer changes + observed for present-day surface datasets at standard resolutions + (f09, f19, f10, f45). + +(2) run_sys_tests: record command-line arguments in SRCROOT_GIT_STATUS + file + +(3) (From Will Wieder) Updates to current surfdata & landuse files in + tools/contrib/singlept + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1118 (mksurfdata_map rounding/truncation of + special landunits should happen before wetland filling) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - PASS + + Note: ran tools testing on code based off of ctsm1.0.dev110 (before + merging with ctsm1.0.dev111) + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - PASS on mac (bishorn) + + regular tests (aux_clm): + + cheyenne ---- not run + izumi ------- not run + +If the tag used for baseline comparisons was NOT the previous tag, note that here: ctsm1.0.dev110 + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +In principle, the changes to mksurfdata_map could change answers for +rare cases. No answer changes were observed for present-day surface +datasets at resolutions f09, f19, f10 or f45. Also note that no surface +datasets were actually updated in this tag, so if any answer changes +appear from these changes, they would appear the next time we update +surface datasets. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1119 +https://github.com/ESCOMP/CTSM/pull/1120 +https://github.com/ESCOMP/CTSM/pull/1122 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev111 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Fri Aug 28 14:08:25 MDT 2020 +One-line Summary: Compsets don't use 2014 for GSWP3 forcing, LUNA prevyr changed back + +Purpose of changes +------------------ + +Update cime so that default end year for GSWP3 forcing is 2013 because 2014 data is bad. Also update +the prevyr default for vcmax/jmax to what it was before ctsm1.0.dev102. + +Fix some issues for finding initial condition files for Clm45 compsets. Also bring in updated CDEPS/CMEPS +as they were required with the cime update. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): + Fixes #1107 -- Change initial values of LUNA back to previous global values + Fixes #1067 -- Stop using PIO2 in the LILAC build + Fixes #1121 -- FMOZ test fails + +CIME Issues fixed (include issue #): + Fixes ESMCI/cime#3683 -- Avoid artificial limit on string lengths in shr_string_listMerge + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + Last time-step in Dec/2013 for GSWP3 data still has zero humidity + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + cime is pointing to a branch_tag we should update it to a trunk tag as soon as possible + +Changes to tests or testing: build-namelist unit testing improved to find problems like #1121 a #1125 + +Code reviewed by: self + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (all identical to previous tag) + + tools-tests (test/tools): + + cheyenne - PASS + + python testing (see instructions in python/README.md; document testing done): + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes (similar climate) + + Summarize any changes to answers, i.e., + - what code configurations: (2010 and SSP compsets) and Clm50 with LUNA on (Bgc or Sp) + - what platforms/compilers: All + - nature of change: similar climate + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, cmeps, cdeps + (fox removed as a separate checkout) + cime to branch_tags/cime5.8.31_a01 + +Pull Requests that document the changes (include PR ids): #1114 +(https://github.com/ESCOMP/ctsm/pull) + #1114 -- Update cime so default end year for GSWP3 forcing is 2013 and change prevyr default for vcmax/jmax + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev110 +Originator(s): jedwards (Jim Edwards) +Date: Fri Aug 21 10:49:08 MDT 2020 +One-line Summary: Fixes needed for PIO2 + +Purpose of changes +------------------ + +Fixes needed for CTSM to work with PIO2. There is an additional fix +needed in PIO2 itself; this is available in a later version of cime that +we will bring in soon. + +Note that this PR also includes a change in config_files.xml that is +needed for a newer version of cime when running compsets with dlnd, slnd +or xlnd; this may be incompatible with the current version of the cime +external, but this does not impact compsets with CTSM. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +The changes in this tag, together with a cime update that will be coming +in soon, resolve the following issues (I'm not sure off-hand which +issues are resolved by the changes here alone and which ones require the +cime update): +- Resolves ESCOMP/CTSM#1029 (FATES tests fail with PIO2) +- Resolves ESCOMP/CTSM#1030 (mpi-serial nag case fails with pio2 when + defining h1 history restart file) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- May not be able to run configurations with dlnd, slnd or xlnd from this tag + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: Not investigated, but almost definitely not + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- PASS + izumi ------- PASS + + Note: Standard testing was done using PIO1 (as this is still the + default), but separate testing was also done using PIO2 (using an + updated cime) and tests were found to pass. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1095 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev109 +Originator(s): negins (Negin Sobhani,UCAR/TSS,303-497-1224) +Date: Thu Aug 20 11:40:07 MDT 2020 +One-line Summary: Allow for resorbtion in transition from live to dead wood N + +Purpose of changes +------------------ + +This PR allows for resorbtion in transition from live to dead wood N, which also move +to NPOOL for free. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): Issue #443 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[x] clm5_0 + +[x] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist +variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] + +Notes of particular relevance for developers: None +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: None + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- PASS + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (similar climate) + + Summarize any changes to answers, i.e., + - what code configurations: Clm50 with Bgc or Cn + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new + climate): larger than roundoff/same climate + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + + Will Wieder thought the changes were small enough that we didn't need to do + a long simulation. Erik Kluzek thinks the changes were verified with single + point simulations. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev108 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Wed Aug 19 17:23:47 MDT 2020 +One-line Summary: Update default PE layouts for new SE/FV3 grids + +Purpose of changes +------------------ + +Change PE layouts for new high resolution SE/FV3 grids. Have a version for cheyenne and a default one +as well. + +Update externals: cime, cism, CMEPS, CDEPS +Change single point tests to use stub ROF +Change tests to use gx1v7 rather than gx1v6 +Update waccmx_offline to use START=1979 + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): + Fixes #1108 Change single point tests to use stub ROF + Fixes #1098 ARCTICGRIS PE layout is very slow + Fixes #1105 Default new FV3/SE grid PE layouts are problematic + Fixes #1103 Some changes to prevent missing file for WACCMX testing + Fixes #1113 ARCTIC test is failing + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Some tests were chagned to use stub ROF and one to stub GLC. @billsacks suggest we should also change + other tests in this same way. + +Changes to tests or testing: Yes + +Code reviewed by: self + + +CTSM testing: regular, tools + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + tools-tests (test/tools): + + cheyenne - PASS + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - OK + + python testing (see instructions in python/README.md; document testing done): + + cheyenne -- PASS + + regular tests (aux_clm): + + cheyenne ---- PASS + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No (except for waccmx_offline test) + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, cism, CDEPS, CMEPS + cism to cism2_1_69 + cime to cime5.8.30 + Update hash for CDEPS and CMEPS (so that nuopc test will run) + +Pull Requests that document the changes (include PR ids): #1111 +(https://github.com/ESCOMP/ctsm/pull) + + #1111 -- Adjust FV3/SE PE layouts + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev107 +Originator(s): erik (Erik Kluzek) +Date: Mon Aug 10 02:21:12 MDT 2020 +One-line Summary: Answer changes needed for CESM2.2.0 + +Purpose of changes +------------------ + +A list of small answer changes needed for CESM2.2.0. Nitrogen deposition file now properly +ends in 2015 rather than 2005. Have 2010_control compset match the 2000 IOC file rather than 2010. +Modify the waccmx_offline tests to more closely match the CAM tests. + +Interpolate IC files for an exact match. Answers are identical for an exact match, but different +when used for other resolutions. + +Two small bit-for-bit changes remove levurb and string_len dimensions on restart files. +Remove xsmrpool_loss when use_crop is NOT true. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): [If none, remove this line] + Answer changing fixes: + Fixes #1004 -- stream_year_last_ndep is set to 2005 instead of 2015 for historical with ctsm1.0.dev093 + Fixes #1012 -- Help prevent problems with WACCM-X testing by modifying our waccmx_offline test + Fixes #1090 -- Have 2010_control compset match 2000 simulation-year rather than 2010 + Fixes #1089 -- Failure in FXHIST test when running with CAM + Fixes #1037 -- Interpolate out-of-the-box initial conditions files for CESM2.2 release + (only changes answers for resolutions other than IC file resolution) + + Bit-for-bit changes: + Fixes #1101 -- levurb and string_len dimensions no longer needed on the restart files + Fixes #1097 -- xsmrpool_loss should only be written to the restart file if use_crop is true + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + 2010_control doesn't match 2010 finidat file + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): Interpolated IC files + Add f19 2003 IC file, f09 and 19 1979 IC file + Remove 2010 IC file + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: waccm_offline test changed to more closely match the FXHIST CAM test + +Code reviewed by: self + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (115 tests are different than before) + + python testing (see instructions in python/README.md; document testing done): + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- PASS + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! (very small) + + Hist and SSP BGC compsets change answers because of the correction of the end year for ndep. + You wouldn't think this would matter until you get to the end of the time-sequence -- but it + does for the first time-step. + + The 2010 compset changes answers because of using the 2000 finidat file rather than 2010 + + Some finidat files interpolated to the resolution they are designed for. This causes an apparent + change of answers when these datasets are used for other resolutions (even though it does NOT for + the resolution it's interpolated to) + + waccm_offline tests are also changed in order to more closely match the FXHIST tests in CAM. + + Summarize any changes to answers, i.e., + - what code configurations: Hist, SSP, 2010 compsets, Clm45 and some f10, 1x1 because of IC files + - what platforms/compilers: All + - nature of change: same climate + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #1100 +(https://github.com/ESCOMP/ctsm/pull) + #1100 -- Answer changes needed for CESM2.2.0 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev106 +Originator(s): erik (Erik Kluzek) +Date: Thu Aug 6 15:35:47 MDT 2020 +One-line Summary: Bit-for-bit updates for the CESM2.2.0 release + +Purpose of changes +------------------ + +Fix some bit-for-bit things needed for the CESM2.2.0 release +Bring changes needed from release-clm5.0.31-34 to trunk. ndep change. +Brings in some changes for PtVg datasets for no-anthro compset. +Do some refactoring of Fire class so that it makes sense for FATES to use the base class. +Update RTM and MOSART with NUOPC changes and an update of a NetCDF-4 file to NetCDF-5 +needed for the cesm2.2.0 release. + +The 2010 finidat file is now set in the 2010_control use-case rather than relying on the +finidat dataset matching. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): + Fixes #1087 -- wrong finidat file + Fixes #1096 -- failing tests + Fixes #1036 -- ne30 case fails + Fixes #946 --- better error message + Fixes #983 --- Fire method renames + Fixes #938 --- mscripgrid issue + +Known bugs found since the previous tag (include github issue ID): + #1098 -- ARCTICGRIS PE-layout is very slow... + #1097 -- xsmrpool_loss should only be written to the restart file if use_crop is true + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + if ndep file isn't found die with a warning rather than fatal error. + The warning allows you to override with CLM_BLDNML_OPTS="-ignore_warnings" + + finidat file matching will now use the sim_year rather than start-year + for a control case (transient cases used the start-year) + Add 2010 f09 finidat file for clm5_0_cam6.0 + +Changes made to namelist defaults (e.g., changed parameter values): + +Changes to the datasets (e.g., parameter, surface or initial files): + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: + Add clm45cam6LndTuningMode testmod + Some tests needed more wallclock + +Code reviewed by: self + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (one test is different than ctsm1.0.dev105) + + python testing (see instructions in python/README.md; document testing done): + + cheyenne -= PASS + + regular tests (aux_clm): + + cheyenne ---- PASS + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No (bit-for-bit) + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): rtm, mosart + RTM to rtm1_0_72 + MOSART to mosart1_0_37 + +Pull Requests that document the changes (include PR ids): #1079 +(https://github.com/ESCOMP/ctsm/pull) + #1079 -- Bit-for-bit updates for the CESM2.2.0 release + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev105 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) / Chris Fischer +Date: Thu Jul 23 08:59:37 MDT 2020 +One-line Summary: Bring in some new SE grids for CAM as well as initial condition files for them + +Purpose of changes +------------------ + Add new SE (Spectral Element) grids: ne30np4.pg2, ne30np4.pg3, ne30np4, ne60np4, ne120np4, ne120np4.pg2, ne120np4.pg3, + ne0np4CONUS.ne30x8, ne0np4.ARCTIC.ne30x4, ne0np4.ARCTICGRIS.ne30x8 + Add new datasets for them, some new tests, and add support for their creation. + + Also add some new initial condition (IC) files for 1979, 2000, and 2013 for use when coupled to CAM + + The process for picking initial condition files was improved so that there can be more than one year that matches + and it will do the best to pick the best match. Also added the possibility for 1982 and 2013 simulation years for + specific grid matches. + + Also update cime to a newer version that supports these new grids. And update CMEPS (and hence add in fox, CDEPS) + to latest used on the nuopc_dev branch. Testing with nuopc wouldn't work without this update. The cime version updates + the tables for dry-deposition and changes answers for dry-deposition when it's turned on. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #992 #994 + Fixes #992 -- New initial conditions for 1979, 2000 + Fixes #994 -- New CAM SE grids + Fixes #888 -- Add support for various "physics grids" needed by CAM +CIME Issues fixed (include issue #): #3593, #3569, #3564, PR#3557 + cime/#3593 -- Fix mapping files for new grids + cime/#3569 -- Fix cime regression testing + cime/#3564 -- Change alias for arctic grids + cime/#3557 -- updates to dry deposition data (PR) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + Initial conditions (IC) for 1979 start date is technically 1982 + New initial condition files are ONLY for when coupled to CAM (B and F compsets) + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): Allow for new grids + User updates to cime: + - Allow a user supplied config_grids.xml file. + - Improved error message for incorrect setting of cime model. + +Changes made to namelist defaults (e.g., changed parameter values): Add IC files for 1982 and 2013 years + +Changes to the datasets (e.g., parameter, surface or initial files): New SE grid datasets + Remove conus_30_x8 grid (previous name for new ne0np4CONUS.ne30x8 grid + Add new grids: ne30np4.pg2, ne30np4.pg3, ne30np4, ne60np4, ne120np4, ne120np4.pg2, ne120np4.pg3, + ne0np4CONUS.ne30x8, ne0np4.ARCTIC.ne30x4, ne0np4.ARCTICGRIS.ne30x8 + Add new mask: tx0.1v3 + New IC files: 1982 for ARCTIC and ARCTICGRIS, ne120np4 for 2000 and 2013 for CONUS all when coupled to CAM + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Initial condition picking will pick the file it finds with the closet simulation year to the request + for the lnd_tuning_mode desired. It will pick based on year over an exact match in resolution. + You can get around this by setting use_init_interp to be specific for a resolution + + Also realized that there is a dependence between the namelist_defaults_ctsm.xml file and namelist_defaults_overall.xml + for the clm_start_type item. It must be coordinated with use_init_interp, init_interp_attributes and finidat + to work properly. I added a comment about this. We should probably just move them into the same file. + +Changes to tests or testing: Added tests for new grids + +Code reviewed by: self, fischer-ncar, adamrher + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - OK (130 tests fail comparison to previous verison due to new IC files) + + tools-tests (test/tools): + + izumi - OK + + PTCLM testing (tools/shared/PTCLM/test): + + izumi - OK + + python testing (see instructions in python/README.md; document testing done): + + izumi -- PASS + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No bit-for-bit (unless running with CAM because of new finidat files) + Running with nuopc changes answers because of updates to nuopc drivers + Dry-deposition changes answers when turned on (but doesn't effect anything else) + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, cmeps, cdeps, fox + cime updated to cime5.8.28 (from branch_tags/cime5.8.24_a01) + fox, and cdeps added in + cmeps, cdeps and fox updated to hashes used in the nuopc_dev branch of CESM + +Pull Requests that document the changes (include PR ids): #1038 +(https://github.com/ESCOMP/ctsm/pull) + #1038 -- New fsufdat and landuse time series files for ne grids + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev104 +Originator(s): sacks (Bill Sacks) +Date: Mon Jul 6 09:58:15 MDT 2020 +One-line Summary: Add LILAC + +Purpose of changes +------------------ + +Add LILAC: The Lightweight Infrastructure for Land-Atmosphere +Coupling. This infrastructure consists of two major pieces: + +(1) A lightweight coupling infrastructure built on top of ESMF that + makes it easier for atmosphere models to call CTSM directly, rather + than using the hub-and-spoke architecture that is used by CESM. + +(2) A set of python-based tools for building CTSM and creating its + runtime inputs when running in an atmosphere model via + LILAC. Although these tools are built on top of cime, details of the + create_newcase / case.setup / case.build process are hidden from the + user, because many of the aspects of this workflow don't make sense + in the LILAC context. + +So far we have used LILAC to couple CTSM to WRF. There are plans to use +the same infrastructure to couple CTSM to other regional atmosphere +models. + +Documentation of LILAC is provided in +https://escomp.github.io/ctsm-docs/versions/master/html/lilac/index.html +(though there are still some missing sections), as well as in various +presentations on the wiki +(https://github.com/ESCOMP/CTSM/wiki/Presentations). + +There have been many contributors besides myself to the development, +testing and documentation of LILAC; chief among them being Mariana +Vertenstein, Negin Sobhani, Joe Hamman, Sam Levis, Mike Barlage and Dave +Lawrence. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- See issues in the Done column of https://github.com/ESCOMP/CTSM/projects/23 + +Known bugs introduced in this tag (include github issue ID): +- Although LILAC is working to first order, there is still some work to +do. See outstanding issues in https://github.com/ESCOMP/CTSM/projects/23 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- dtime no longer specified on the namelist: just obtained from driver + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Added LILACSMOKE test + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - ok + + Baseline comparisons fail as expected. One test failed, but it also + failed for me on master (https://github.com/ESCOMP/CTSM/issues/1074) + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - pass on my mac + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1068 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev103 +Originator(s): slevis (Samuel Levis, SLevis Consulting LLC,303-665-1310) +Date: Mon Jun 29 17:16:29 MDT 2020 +One-line Summary: Gridcell-level balance-check for methane (CH4) + +Purpose of changes +------------------ + + Bracket the model time-step loop to calculate balance checks at the + gridcell level, as detailed in issue #315. The column-level check + remains unchanged. + + Subroutine ch4_init_balance_check is replaced with + ch4_init_column_balance_check. Subroutine + ch4_init_gridcell_balance_check is added. + + The implementation is similar to the one for carbon and nitrogen (see + tag ctsm1.0.dev096). + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #315 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + None + +Changes made to namelist defaults (e.g., changed parameter values): + None + +Changes to the datasets (e.g., parameter, surface or initial files): + None + +Substantial timing or memory changes: + No + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + None + +Changes to tests or testing: + None + +Code reviewed by: + @billsacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- PASS + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + None + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/CTSM/pull/1022 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev102 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Fri Jun 26 01:32:04 MDT 2020 +One-line Summary: Some important fixes for LUNA in clm5_0, and small urban issue in clm5_0 + +Purpose of changes +------------------ + +Fix some important issues that were found in LUNA for the arctic. These changes were large enough +that we had to re-tune the clm5_0 parameters to give a similar simulation. Leah Birch noticed +that the formulations in the code disagreed with the paper. Correcting this caused arctic plants +to be less productive. In order to compensate parameters for leafcn, and slatop were adjusted for +broadleaf_deciduous_boreal_shrub and c3_arctic_grass for clm5_0. + +The total vegetation carbon threshold on exit_spinup (from accelerated decomposition (AD) mode) was +increased from 0.1 to 1.0. Without this change some PFT's can die out in exit spinup even when +they have significant carbon stores from the AD spinup mode. + +There is an implicit assumption in the urban building energy model that building width equals +street width. However, this assumption can/should be relaxed and building width can be derived +from the morphology dataset. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #738 #803 #953 #958 #1056 + Fixes #1056 -- Remove allpfts dimension + Fixes #953 -- Incorrect formula in LUNA uses day time rather than average of day/night + Fixes #958 -- LUNA day length factor missing + Fixes #738 -- Totvegc threshold increased from 0.1 to 1. + Fixes #803 -- No longer assume building width + +Known bugs introduced in this tag (include github issue ID): #1060 + #1060 -- Some code cleanup of luna bug fixes + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[x] clm5_0 + +[x] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): clm5_0 climate adjusted for arctic plants + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): + +Changes to the datasets (e.g., parameter, surface or initial files): New parameter files + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): We + chose some bad names for variables, so we'll clean this up in a seperate step (see #1060) + +Changes to tests or testing: None + +Code reviewed by: self, olyson, bill-sacks, wweider + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (266 compare differently because of update in paramsfile and jmaxb1) + + python testing (see instructions in python/README.md; document testing done): + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- PASS + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes for clm5_0 (important change required retuning) + + Summarize any changes to answers, i.e., + - what code configurations: clm5_0 when Luna on as well as smaller changes for urban + - what platforms/compilers: all + - nature of change: climate changing, but tuned to respond similar to clm5.0 + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + luna changes: oleson case clm50_ctsm10d089_2deg_GSWP3V1_luna3_jmaxb1-0.17_slatopA_leafcnA_hist + + URL for LMWG diagnostics output used to validate new climate: + + urban changes: + + +http://webext.cgd.ucar.edu/I2000/clm50_ctsm10d098_1deg_GSWP3V1_CON_FIXBUILDENERGY_2000/lnd/clm50_ctsm10d098_1deg_GSWP3V1_CON_FIXBUILDENERGY_2000.1991_2010-clm50_ctsm10d098_1deg_GSWP3V1_CON_2000.1991_2010/setsIndex.html + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #1034 and #962 +(https://github.com/ESCOMP/ctsm/pull) + #1034 -- Building energy fix + #962 --- Fixes for the LUNA dayl bugs + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev101 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326), oleson (Keith Oleson) +Date: Wed Jun 17 23:51:22 MDT 2020 +One-line Summary: Changes from Keith to bring a list of variables to the parameter file + +Purpose of changes +------------------ + +Change some hardcoded parameters to go on the parameter files. This is needed in preparation +of running the Perturbed Parameter Ensemble. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #995 #138, #206 + +Fixes #995 -- Soil turnover times are on paramfile and hardcoded +Fixes #138 -- use tau_ values on paramfile +Fixes #206 -- add prh30 to paramfile +Some work on #290 -- LUNA refactoring + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): paramfile for both clm4_5 and clm5_0 + Add 51 new parameters to the paramsfile: + bsw_adjustfactor,cpha,csol_clay,csol_om,csol_sand,denitrif_nitrateconc_coefficient,denitrif_nitrateconc_exponent, + denitrif_respiration_coefficient,denitrif_respiration_exponent,drift_gs,e_ice,enzyme_turnover_daily,eta0_anderson, + eta0_vionnet,fnps,hksat_adjustfactor,ignition_efficiency,jmaxb0,jmaxha,jmaxhd,kcha,koha,kp25ratio,lmrha,lmrhd, + lmrse,luna_theta_cj,minrelh,n_baseflow,pd,perched_baseflow_scalar,prh30,relhExp,ssi,sucsat_adjustfactor,theta_cj, + theta_ip,theta_psii,tpuha,tpuhd,tkd_clay,tkd_om,tkd_sand,tkm_om,tpu25ratio,vcmaxha,vcmaxhd,watsat_adjustfactor, + wc2wjb0,wimp,wind_min + k_nitr_max removed and replaced with k_nitr_max_perday + meta-data for the tau_* variables changed, and a roundoff difference in the clm4_5 paramfile + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): prh30 not used for clm4_5 + prh30 was added in but won't be used for the CNFireLi2014 formulation. + It's only used for the clm5_0 and following formulations + +Changes to tests or testing: None + +Code reviewed by: self, oleson + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (170 tests differ from baseline because of new paramfiles) + + python testing (see instructions in python/README.md; document testing done): + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No bit-for-bit + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #1039 +(https://github.com/ESCOMP/ctsm/pull) + #1039 -- move hardcoded parameters to paramfile + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev100 +Originator(s): sacks (Bill Sacks) +Date: Tue Jun 9 06:15:15 MDT 2020 +One-line Summary: Deallocate memory after running init_interp + +Purpose of changes +------------------ + +Many of the pointer arrays in init_interp were not being deallocated +when init_interp finished. This was a particular problem because some of +these arrays were allocated for the full global source grid on each +processor, so the memory use was significant. This tag fixes this issue. + +This issue is documented in https://github.com/ESCOMP/CTSM/issues/1010 +and https://github.com/ESCOMP/CTSM/issues/1032. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1032 (Memory isn't deallocated in some of the + init_interp code) + +Known bugs found since the previous tag (include github issue ID): +- This does NOT resolve ESCOMP/CTSM#1010 (WACCMX test fails with + ctsm1.0.dev093 in cesm2_2_alpha05c), even though that was the original + hope. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +- The initial run of the PFS test showed a very long time taken in + initialization. However, it appears that this was a system issue: + rerunning twice showed times back to normal. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - pass (on my mac) + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + + Most testing was done on f332fafc. After that, I made a minor change + that was needed for the unit tests to pass. I then reran (1) + clm_short on cheyenne, and (2) this subset of the test list on + izumi: + + SMS.f10_f10_musgs.I2000Clm50BgcCrop.izumi_gnu.clm-crop + SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.izumi_gnu.clm-crop + PEM_Ld1.f10_f10_musgs.I2000Clm50BgcCropGs.izumi_intel.clm-crop + SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.izumi_intel.clm-crop + SMS.f10_f10_musgs.I2000Clm50BgcCrop.izumi_pgi.clm-crop + SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.izumi_pgi.clm-crop + SMS_Ld5_D_P48x1.f10_f10_musgs.IHistClm50Bgc.izumi_nag.clm-monthly + ERP_Ld5_P48x1.f10_f10_musgs.I1850Clm50Bgc.izumi_nag.clm-default + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev099 +Originator(s): sacks (Bill Sacks) +Date: Mon Jun 8 09:29:38 MDT 2020 +One-line Summary: Update cime, needed for izumi machine updates + +Purpose of changes +------------------ + +Update cime. The most important change here is an update for izumi, +which is needed for the recent izumi machine updates. + +Also: Change izumi PEM test to use SGLC (after the machine updates, the +PEM test was failing; see also +https://github.com/ESCOMP/CTSM/issues/840). + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: not investigated; none expected + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Changed izumi PEM test to use SGLC (after the machine updates, the PEM +test was failing; see also https://github.com/ESCOMP/CTSM/issues/840). + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- ok + + izumi: tests pass, some baselines fail as expected + + ERP_D_Ld3.f09_g17.I2000Clm50SpGs.cheyenne_intel.clm-prescribed + showed differences from the stored baselines, but it appears that + the stored baselines were incorrect: when I reran this test from + master, the master version differed from the stored baselines and + was identical to this branch. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, just on izumi due to machine updates + + Summarize any changes to answers, i.e., + - what code configurations: some izumi tests + - what platforms/compilers: izumi gnu & pgi + - nature of change (roundoff; larger than roundoff/same climate; new climate): + not investigated; expected to be roundoff + + Answer changes were observed in these tests: + - SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.izumi_gnu.clm-crop + - SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.izumi_pgi.clm-crop + - SMS.f10_f10_musgs.I2000Clm50BgcCrop.izumi_pgi.clm-crop + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: branch_tags/cime5.8.23_a01 -> branch_tags/cime5.8.24_a01 + Point to a cime branch tag that is equivalent to cime5.8.24 but uses + pio1 rather than pio2, even for mpi-serial cases (the changes in + branch_tags/cime5.8.24_a01 relative to cime5.8.24 are equivalent to the + changes in branch_tags/cime5.8.23_a01 relative to cime5.8.23). + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev098 +Originator(s): John Truesdale,UCAR/AMP,303-497-1386 +Date: Thu May 28 14:39:27 MDT 2020 +One-line Summary: Bring in GFDL fv3 cubed sphere grids C24, C48, C96, C192, C384 + +Purpose of changes +------------------ + +Add support for new GFDL fv3 curbed sphere grids. Low resolution C24, and C48 +Moderate resolution C96, and high resolution C192 and C384. Add in mapping files +so all can be created. Make C96 a default resolution created with new surface +datasets. For all of these only the crop versions of surface and landuse.timeseries +are in place, as non-crop can run in CLM without needing different datasets. Also for +historical landuse.timeseries we use the SSP5-8.5 timeseries files, so that it can be +used for future, historical and beyond 2015 present day. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #1025 + Fixes #1025 -- By default only create crop version of surface/landuse.timeseries datasets + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): New surface and landuse.timeseries files + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: Add C96 tests + +Code reviewed by: @ekluzek + +CTSM testing: regular, tools + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (15 new tests for new resolutions) + + tools-tests (test/tools): + + cheyenne - OK + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - PASS (cheyenne) + + regular tests (aux_clm): + + cheyenne ---- PASS + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + + +Answer changes +-------------- + +Changes answers relative to baseline: No bit-for-bit + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #891 +(https://github.com/ESCOMP/ctsm/pull) + + #891 -- add definitions/defaults for GFDL fv3 cubed sphere grids C24, C48, C96, C192, C384 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev097 +Originator(s): ycheng (Yanyan Cheng); final changes & testing by Bill Sacks +Date: Mon May 25 15:14:56 MDT 2020 +One-line Summary: Add two bioenergy crops (switchgrass and miscanthus) + +Purpose of changes +------------------ + +Main change is from Yanyan Cheng: adding parameters and code for two +bioenergy crops, switchgrass and miscanthus. Along with this, there is a +new potential flux from crop leaves and stems to the crop product pool +at harvest, representing biofuel products; a new pft-specific parameter +controls this flux (biofuel_harvfrac). Currently, the out-of-the-box +surface datasets do not specify any area for these crops, but the new +parameter file will allow them to be present if specified on the surface +dataset or landuse_timeseries file. Note that this is only an option for +CLM5.0, NOT for CLM4.5. (See https://github.com/ESCOMP/CTSM/pull/884 for +details.) + +Also, some minor fixes from Bill Sacks: See notes under "bugs fixed" +below. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#203 - Fixes creation of harvest-related variables + on surface datasets created with the all_veg option - smallville, + PTCLM, etc. (documented in https://github.com/ESCOMP/CTSM/pull/1019) +- Resolves ESCOMP/CTSM#930 - Makes gindex_ocn intent(inout) rather than + intent(out) +- Resolves ESCOMP/CTSM#1021 - Changes SSP test to only do symlink if + needed + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- For transient crop cases, now more crops in memory. This creates a + need for interpolation of initial conditions for initial conditions + generated from a transient case. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): +- Changed parameter values for switchgrass and miscanthus (only for clm5.0) +- New pft-specific parameter, biofuel_harvfrac (for both clm4.5 and clm5.0) + +Changes to the datasets (e.g., parameter, surface or initial files): +- New parameter files with the above changes + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Changed smallville ERS_Lm20 test to be cold start (see comment in + commit 8368f222 for details) +- Added a multi-year smallville test that includes these new crops + +Code reviewed by: Bill Sacks, Danica Lombardozzi + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - ok + + Pass except for expected baseline failures + + Ran on 633be0eb, with comparison against ctsm1.0.dev095; tests pass + except these expected baseline failures: + + 030 blf84 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_clm4_5^buildtools ....................\c + rc=7 FAIL + + 032 blfc4 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Cycle_clm4_5^buildtools ..............\c + rc=7 FAIL + + Diffs for these are just in the harvest-related fields on the surface dataset, as expected. + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- pass + + For cheyenne testing: a few tests had baseline failures. The + differences just arise in the h1 (vector) files, due to differences + in dimension sizes. These differences are expected. See below for + details. + + Ran most testing on 8309c213. Reran two SSP tests on 4665c9ce + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, but diagnostic only due to +change in dimension sizes - does not change answers in any meaningful +way + + Summarize any changes to answers, i.e., + - what code configurations: Transient CLM50 cases with crops; just + changes dimensions on vector (h1) history files + - what platforms/compilers: All + - nature of change (roundoff; larger than roundoff/same climate; new climate): + diagnostic change only + + Differences were observed in the following tests: + + ERS_Ly3_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianGs.cheyenne_gnu.clm-cropMonthOutput + SMS_Ld5.f10_f10_musgs.ISSP245Clm50BgcCrop.cheyenne_gnu.clm-ciso_dec2050Start + SMS_Ld5.f10_f10_musgs.ISSP370Clm50BgcCrop.cheyenne_gnu.clm-ciso_dec2050Start + ERP_D_Ld10_P36x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_decStart + ERP_D_Ld5.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-allActive + ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput + ERS_D_Ld7_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropGs.cheyenne_intel.clm-decStart1851_noinitial + ERS_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCropG.cheyenne_intel.clm-cropMonthOutput + ERS_Ly5_P144x1.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput + ERS_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropQianGs.cheyenne_intel.clm-cropMonthOutput + LCISO_Lm13.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_monthly + SMS_Ld5.f10_f10_musgs.ISSP585Clm50BgcCrop.cheyenne_intel.clm-ciso_dec2050Start + + The differences just arise in the h1 files, due to differences in + dimension sizes. I reran these tests with a paramfile where I + reverted the mergeToPft variable; then they were all bfb with + master. + + Other than this, there were FIELDLIST differences, as expected. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/CTSM/pull/884 +- https://github.com/ESCOMP/CTSM/pull/1019 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev096 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Thu May 21 19:18:24 MDT 2020 +One-line Summary: Gridcell-level balance checks for carbon and nitrogen + +Purpose of changes +------------------ + + Bracket the model's time-step loop to calculate balance checks at the + gridcell level because there are terms in the carbon and nitrogen + cycles not accounted for at the column level. Balance checks at the + column level remain unchanged for now. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #314 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: + @billsacks + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/CTSM/pull/984 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev095 +Originator(s): sacks (Bill Sacks) +Date: Thu May 21 10:25:16 MDT 2020 +One-line Summary: Update cime and cmeps externals; rework initialization of CNFire object + +Purpose of changes +------------------ + +Main change is to update cime and cmeps externals. cime is now +essentially at the version used in cesm2_2_beta05 (but with one change +backed out); cmeps is at latest master. + +Also, reworks initialization of CNFire object to avoid occasional +segmentation faults. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1018 (Occasional seg faults when initializing + CNFire object) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +- Note: Because of a change in cime, datm now uses netcdf rather than + pnetcdf, but it doesn't seem that that impacts performance + significantly + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- pass + + cheyenne tests pass; some answer changes as expected (as noted below) + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (small) + + Summarize any changes to answers, i.e., + - what code configurations: + - cheyenne_gnu - due to compiler version update + - nuopc - presumably due to the major cmeps update + - what platforms/compilers: see above + - nature of change (roundoff; larger than roundoff/same climate; new climate): + - Not investigated + + I have verified that gnu tests in 59d1dd4a are identical to those + in dcaad375 - i.e., the rework of the initialization logic for fire + didn't change answers + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.8.19 -> branch_tags/cime5.8.23_a01 + (same as cime5.8.23, but reverts to using pio1 for mpi-serial cases, + since some mpi-serial cases failed with pio2) +- cmeps + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev094 +Originator(s): sacks (Bill Sacks) +Date: Fri May 15 13:41:01 MDT 2020 +One-line Summary: Minor bug fixes needed for latest cime + +Purpose of changes +------------------ + +(1) Refactor a conditional to avoid divide by 0 (ESCOMP/CTSM#1013) + +(2) Remove some FATES coordinate variables that were writing garbage + (temporary workaround for ESCOMP/CTSM#1014) + +(3) Minor update to manage_externals + +(4) Document authorship in README.md and .zenodo.json + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1013 +- Workaround for ESCOMP/CTSM#1014, but doesn't properly resolve that issue + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: not checked; none expected + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/1006 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev093 +Originator(s): erik (Erik Kluzek) +Date: Fri May 1 22:27:16 MDT 2020 +One-line Summary: Bring in changes from release-clm5.0 branch to master + +Purpose of changes +------------------ + +Move changes from release-clm5.0.12.13/14/16/17/18/20/21/22/23/24/25/26/27/28/29/30 to master +(note excludes release-clm5.0.15, release-clm5.0.19) + +Answer changing! +Updates FATES with PARTEH option. + +Remove CRUNCEP half degree, ne120np4, f05 surface datasets +Landuse-timeseries files for just: f09, f19, f10, ne30np4, 1x1_numaIA, 1x1_smallvilleIA, 1x1_brazil +Add datasets needed for SSP scenarios (only Tier I for ndep). Add ZWT_inversion dataset for methane. + +Add new ability to use prescribed soil moisture data (from streams files based on an earlier CTSM simulation). + +Add new MODISv2 mapping files for mksurfdata_map. Remove T5 and T21 mapping files. Add conus_30_x8 mapping files, +and T62 mapping files + +Add contrib directory to tools with contributed tools and scripts. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): 31 issues.... + #873 -- Release clm5.0.12 changes + #871 -- don't check for valid resolution for CESM cases by default + #836 -- add izumi as a place that can run tools tests + #831 -- add namelist tint_algo settings for input streams + #817 -- Have clm4_5 use the same ndep file as clm5_0 for 1850 + #809 -- mkmapdata using an old version of intel + #804 -- mksurfdata option + #791 -- fix threading for prescribed LAI and soil-moisture + #786 -- allow use_init_interp for a branch + #746 -- Some CLM45 configurations use CLM50 initial conditions files + #741 -- C13_HR, C13_NBP, FPI values result in numeric conversion not representable error (changes answers) + #734 -- Isotope historical files off of NetCDF-4 + #716 -- 2 degree CMIP6WACCMDECK needs Carbon isotopes off + #707 -- Missing mapping files for hirespft + #673 -- Ice shelf wetland fix in mksurfdata_map can lead to glacier+lake > 100% on surface datasets (changes surface dataset creation) + #653 -- To save disk on fsurdat files use zwt0 on finindated file + #629 -- Remove unused fields from surface datasets + #624 -- QSNOEVAP history output incorrect + #621 -- Fully remove rcp in place of only ssp_rcp + #608 -- Odd (blocky) spatial patterns in generic crop leafc for BGC simulation when initialized from BGC-Crop (changes answers) + #589 -- Existence of content in the lai_streams namelist makes it confusing to users + #557 -- no-anthro compset and options + #553 -- More robust mksurfdata_map logic for determining where to put wetlands + #547 -- Add conus_30_x8 grid as valid option for CTSM and mksurfdata_map + #545 -- Antarctica ice shelves are being treated as wetlands rather than glaciers + #544 -- Transient cases are matching wrong IC file + #533 -- Add -no-anthro option to mksurfdata + #276 -- Tests for pre_alpha/pre_beta + #262 -- hirespft option to mksurfdata.pl + #175 -- Set stream_year_first_urbantv/last for CLM4.5 + #150 -- mksurfdata code cleanup + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): New surface datasets do mean initial conditions + will need to be interpolated + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): Add 2010 compset option + New namelist items: ndep_tintalgo, lai_tintalgo, lightng_tintalgo, urbantv_tintalgo, dribble_crophrv_xsmrpool_2atm + New soil moisture namelist items: use_soil_moisture_streams, stream_year_first_soilm, stream_year_last_soilm, model_year_align_soilm, + model_year_align_soilm, soilm_tintalgo, soilm_offset, soilm_ignore_data_if_missing + New namelist items for FATES: fates_parteh_mode + New 2010, no-anthro, SSP use cases + New compsets: I2010Clm50Sp, I2000Clm50BgcCropQianGs, I1850Clm50BgcNoAnthro, I1850Clm50SpNoAnthro, IHistClm50SpCru, IHistClm50SpCru, + IHistClm45SpGs, IHistClm45SpGs + New SSP compsets: ISSP585Clm50BgcCrop, ISSP126Clm50BgcCrop, ISSP126Clm50BgcCrop, ISSP245Clm50BgcCrop, ISSP370Clm50BgcCrop, + ISSP434Clm50BgcCrop, ISSP460Clm50BgcCrop, ISSP460Clm50BgcCrop + LAI streams options don't show up in the namelist unless you ask for them + finundation comes from streams files, no longer from the surface dataset + FATES adds a list of new history variables and dimension types + +Changes made to namelist defaults (e.g., changed parameter values): New fsurdat files, SSP C13/C14 files + Add PtVg surface dataset + most finidat files now need to be interpolated, a few added in to get testing to work + New ndep datasets + +Changes to the datasets (e.g., parameter, surface or initial files): + New fsurdat files, finidat files need to be interpolated from now + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Threshold to reseed dead vegetation increased from zero to 1.0 as a hard coded parameter. + Reseeding also happens for generic crop types and not just natural vegetation now. + The ability to read in 3D streams was added (input files have to be at the same resolution as the model) + +Changes to tests or testing: + Add no-anthro, 2010, f19 waccm and SSP tests + Make sure prealpha/prebeta tests are also run by aux_clm + Add prescribed soil moisture test + Lengthen waccm_offline test + Remove hcru_hcru and edison tests + Add some aux_cime_baseline tests + +Code reviewed by: self + + +CTSM testing: regular, tools + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (345 are different than baseline) + + tools-tests (test/tools): + + cheyenne - OK + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - OK + + python testing (see instructions in python/README.md; document testing done): + + cheyennne -- PASS (when ncar_pylib run) + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes (small) + + Updates in all fsurdat files leads to changes in answers + Also there are updated finidat files as they had to be interpolated + to work with the new fsurdat files + Reseeding change can effect answers on startup if activated + Extra call to SoilBiogeochemPrecisionControl can cause a small answer change + + Summarize any changes to answers, i.e., + - what code configurations: all global + - what platforms/compilers: all + - nature of change: Main change is around Antarctica + + CMIP6 simulations and release branch simulations were run with these surface datasets + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates, PTCLM + + fates to sci.1.30.0_api.8.0.0 + PTCLM to PTCLM2_20200121 + + FATES now points to the NGEET repository rather than the NCAR fates-release + +Pull Requests that document the changes (include PR ids): #998, #883, #849, #567, #564, #561 +(https://github.com/ESCOMP/ctsm/pull) + #998 -- Remove Copyright file + #883 -- Bring changes on release-clm5.0 branch to master PR status: ready priority: high type: enhancement + #849 -- Fix link to new forums + #567 -- Ignore patterns for vim + #564 -- Update mksurfdata_map to include glaciers outside of pft landmask + #561 -- Add list of checks that should be done when making new surface datasets + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev092 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Mon Apr 27 14:51:21 MDT 2020 +One-line Summary: Update cime to version in cesm2_2_beta04 + +Purpose of changes +------------------ + +Update cime to latest in cesm2.2 beta tag (cesm2_2_beta04) +Fix two small issues that had gone on the release-clm5.0 branch. +Update manage_externals (to manic-v1.1.8) + +NOTE: Part of the reason for updating cime, was because of some problems +Mike Mills was having on cheyenne with inputdata files being deleted out +from under him before setting up his cases. We think system issues were +interacting with issues with cime putting in place zero length +missing files for the version of cime he was using. Those issues went +away with a cime update, so we hope updating to a newer cime version here +will help prevent those issues for CTSM users. + +cime updates: + +some cleanup from the last maint-5.6 update +Add ne5np4.pg4 grid. +case.setup: Add --keep option +Add omip as option to DATM_CO2_TSERIES + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #974 #966 + Fixes #974 -- python 3 problem in ssp test + Fixes #966 -- a few history fields need to be made CF compliant +CIME Issues fixed (include issue #): 3459 3466 + 3459 -- case.setup refuses to fix corrupted env_mach_specfic.xml + 3466 -- fix for aquap + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + ./case.setup now has a --keep option + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + tools-tests (test/tools): + + cheyenne - OK + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - OK + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + + +Answer changes +-------------- + +Changes answers relative to baseline: None bit-for-bit + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime + cime to cime5.8.19 + (NOTE: CMEPS is pointing to a newer hash than used in the beta tag) + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + #996 -- Update cime to latest cesm2.2 beta tag + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev091 +Originator(s): sacks (Bill Sacks) +Date: Fri Apr 24 07:43:46 MDT 2020 +One-line Summary: Increase tolerance on near-zero truncation for a snow state update + +Purpose of changes +------------------ + +In UpdateState_TopLayerFluxes, the tolerance of 1.e-13 was occasionally +exceeded. Although I haven't done a careful analysis, it seems okay to +me to increase this tolerance slightly. Here I increase it to 1.e-12. + +Previously, if top-layer h2osoi_ice or h2osoi_liq were reduced to less +than 1e-13 times the original value (in an absolute value sense), these +masses were set to 0; now we set these masses to 0 if they are reduced +to less than 1e-12 times the original. So we can now occasionally set a +value to exactly 0 when before it was left at slightly different from +zero. If the previous code led to a small positive value, between 1e-13 +and 1e-12 times the original, this tag will change answers slightly. If +the previous code led to a small negative number, it would cause the +model to abort, leading to the issue reported in ESCOMP/CTSM#988; this +change should fix those occasional aborts. + +This tag also introduces the general ability to set tolerances to a +custom value in calls to truncate_small_values. + +See ESCOMP/CTSM#988 for details. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#988 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none expected (not checked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, in theory (but none in test suite) + + Summarize any changes to answers, i.e., + - what code configurations: potentially all, but very rarely + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Roundoff + + Potentially changes answers by roundoff (see notes above), but no + changes were observed in any test in the test suite + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/989 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev090 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Thu Apr 23 09:21:18 MDT 2020 +One-line Summary: Refactoring banded diagonal matrix and solve system in SoilTemperature module + +Purpose of changes +------------------ + +Previously, the SoilTemperature module has a high level of nested subroutine +calls, which hurt its performance and readability. There were many +redundancies, logical issues, and nested conditionals in the modular code +as discussed in issue #323. In this PR, SoilTemperature module is optimized +and rewritten for better readability and performance while maintaining bfb +compatibility. + + +This PR addresses issue ESCOMP/ctsm#323 + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): + -ESCOMP/ctsm#323 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: The revised code improved the +performance of the previous code by ~1.5-2x. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +Externals used for the testing: + [cism] + tag = cism2_1_68 + [rtm] + tag = rtm1_0_70 + [mosart] + tag = mosart1_0_35 + [cime] + tag = branch_tags/cime5.8.15_a01 + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/CTSM/pull/979) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev089 +Originator(s): sacks (Bill Sacks) +Date: Tue Apr 7 12:01:59 MDT 2020 +One-line Summary: Bring documentation source to master + +Purpose of changes +------------------ + +1. Bring documentation source to master: Pulls in the source from + https://github.com/escomp/ctsm-docs. This is important so that + documentation can remain in sync with changes in the model + code. Images are stored here using git-lfs (Git Large File + Storage). I also made some minor fixes to get the pdf build of the + tech note working. + +2. Use a different documentation theme that supports a version dropdown + menu, and add the code needed to support this versioning on the + documentation web pages. At a high level, the way the versioned + documentation works is to have separate subdirectories in the + gh-pages branch of the ctsm-docs repository for each version of the + documentation we want to support. There is then a bit of JavaScript + code which uses a json file in the gh-pages branch to determine which + versions exist and how these should be named in the dropdown + menu. Most of these changes were borrowed from ESMCI/cime#3439, which + in turn borrowed from ESCOMP/CISM-wrapper#23, which in turn was a + slight modification of an implementation provided by @mnlevy1981 for + the MARBL documentation, which in turn borrowed from an + implementation put together by Unidata (credit where credit is due). + + I am not aware of out-of-the-box support for a version pull-down in + out-of-the-box sphinx themes (though the last time I looked was in + Fall, 2018, so there may be something available now). However, + support for a version dropdown exists in an open PR in the sphinx + readthedocs theme repository: readthedocs/sphinx_rtd_theme#438. I + have pushed this branch to a new repository in ESMCI + (https://github.com/ESMCI/sphinx_rtd_theme) to facilitate long-term + maintenance of this branch in case it disappears from the official + sphinx_rtd_theme repository. I have also cherry-picked a commit onto + that branch, which is needed to fix search functionality in sphinx1.8 + (from readthedocs/sphinx_rtd_theme#672) (which is another reason for + maintaining our own copy of this branch). The branch in this + repository is now named version-dropdown-with-fixes (branching off of + the version-dropdown branch in the sphinx_rtd_theme repository). In + the long-term, I am a little concerned about using this theme that + isn't showing any signs of being merged to the main branch of the + readthedocs theme, but this has been working for us in other projects + for the last 2 years, so I feel this is a reasonable approach in the + short-medium term. + +The new process for building the documentation is given here: +https://github.com/ESCOMP/CTSM/wiki/Directions-for-editing-CLM-documentation-on-github-and-sphinx + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#239 (Move documentation source to master) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- not run! + izumi ------- not run! + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/954 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev088 +Originator(s): sacks (Bill Sacks) +Date: Tue Apr 7 10:43:03 MDT 2020 +One-line Summary: Fix bug in snow aerosol numerics (causes occasional HUGE aerosol values) + +Purpose of changes +------------------ + +Multiplications / divisions by dtime were missing in a few places, in +some code that ensures that aerosol mass fluxes between the snow layers +don't exceed the total mass. This bug was introduced in ctsm1.0.dev065, +when a term was changed from a mass to a flux (per unit time), but some +of the code wasn't changed correspondingly. + +In one case this bug caused a crash, but in other cases it just causes +incorrect answers. The issue can be seen by examining the history +variables SNOBCMCL, SNOOCMCL and SNODSTMCL. In the case that led to the +crash, SNOBCMCL and SNOOCMCL became huge in one grid cell (~ 10^12) for +a long period before the crash. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#965 (Bug in snow aerosol numerics can cause + aerosol masses to blow up, starting with ctsm1.0.dev065) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none (not checked, but none expected) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek, Keith Oleson + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- pass + + ok means tests pass, some answer changes as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (Small) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff/same climate + + Answer changes arise due to a bug fix for a condition that only + appears infrequently. When it does appear, answer changes can + potentially be enormous (e.g., snow aerosol concentrations 20 + orders of magnitude too large), though answer changes observed in + the test suite all appear relatively small. + + Answer changes just appeared for the following tests: + + FAIL ERP_D_P36x2_Ld3.f10_f10_musgs.I2000Clm45BgcCrop.cheyenne_gnu.clm-no_subgrid_fluxes BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_Ld1.nldas2_rnldas2_mnldas2.I2000Ctsm50NwpSpNldasGs.cheyenne_gnu.clm-default BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_Ld1.nldas2_rnldas2_mnldas2.I2000Ctsm50NwpSpNldasRsGs.cheyenne_gnu.clm-default BASELINE ctsm1.0.dev087: DIFF + FAIL ERI_D_Ld9.ne30_g16.I2000Clm50BgcCruGs.cheyenne_intel.clm-vrtlay BASELINE ctsm1.0.dev087: DIFF + FAIL ERI_D_Ld9.T31_g37.I2000Clm50Sp.cheyenne_intel.clm-SNICARFRC BASELINE ctsm1.0.dev087: DIFF + FAIL ERI_Ld9.f45_g37.I2000Clm50BgcCruGs.cheyenne_intel.clm-nofire BASELINE ctsm1.0.dev087: DIFF + FAIL ERI_N2_Ld9.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-default BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_D_Lm6.f45_f45_mg37.I2000Clm50Fates.cheyenne_intel.clm-FatesColdDef BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_D_Lm6_P144x1.f45_f45_mg37.I2000Clm50Fates.cheyenne_intel.clm-FatesColdDef BASELINE ctsm1.0.dev087: DIFF + FAIL SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput BASELINE ctsm1.0.dev087: DIFF + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/971 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev087 +Originator(s): sacks (Bill Sacks) +Date: Mon Apr 6 11:23:51 MDT 2020 +One-line Summary: Change hard-coded soil layers in phenology to use a target depth + +Purpose of changes +------------------ + +Adds infrastructure for finding the soil layer containing a given depth +(covered by unit tests). + +In phenology code, replaces hard-coded level 3 with a target soil +depth. This value is read from the parameter file. The default value is +set in a way that is bit-for-bit for standard CLM45 and CLM50 +configurations, but this will change answers for non-SP configurations +using the NWP soil layer structure or non-standard soil layer +structures. + +This is important for the sake of supporting flexible soil layers, as in +the NWP configuration. + +Also, some cleanup of the CNPhenology parameter reading code. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#952 (Change hard coded soil layers in phenology + to use a target depth) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[X] ctsm5_0-nwp -- only for non-SP cases + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +- New parameter added to NetCDF parameter file: phenology_soil_depth + +Substantial timing or memory changes: none expected (not checked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- pass + + ok means tests pass, a few answer changes as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes (only Non-SP cases with NWP) + + Summarize any changes to answers, i.e., + - what code configurations: Non-SP cases with NWP or non-standard + soil layer structures + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff; same vs. new climate not investigated + + Differences in non-SP cases with soil layer structure different + from that of standard clm45 or clm50. Differences observed in + tests + ERS_D_Ld3.f10_f10_musgs.I2000Clm50BgcCruGs.cheyenne_intel.clm-deepsoil_bedrock + and + SOILSTRUCTUD_Ld5.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-default. + + ERP_P36x2_D_Ld5.f10_f10_musgs.I2000Ctsm50NwpBgcCropGswpGs.cheyenne_intel.clm-default + had no differences; I'm guessing this is just because there didn't + happen to be the appropriate PFTs present to show differences in + this short, coarse-resolution test. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/963 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev086 +Originator(s): mvertens (Mariana Vertenstein) +Date: Thu Mar 19 16:03:26 MDT 2020 +One-line Summary: Updates to NUOPC cap and minor fixes to ncdio_pio + +Purpose of changes +------------------ + +This tag has updates to the NUOPC cap that are needed for the latest +version of CMEPS. + +Now each component NUOPC cap needs to compute possibly time varying +orbital parameters. Before, in cpl7, this was done in the driver and +passed to the components via seq_infodata. However, now the driver is +really just a simple ascii file - so those calculations needed to +migrate to the component caps. + +In addition, this tag contains changes to ncdio_pio.F90 that improve +performance in some situations. + +This also updates MOSART and RTM tags to include fixes for the NUOPC cap +for MOSART and implementation of an initial NUOPC cap for RTM. + +Also, I1Pt compsets now use SROF rather than using an active runoff +model in 'null' mode. This leads to differences in namelists, but not in +results. + +Mariana Vertenstein implemented most of the changes in this tag; Jim +Edwards implemented the ncdio_pio changes; Bill Sacks did final testing +and integration. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#943 (NUOPC tests will fail in ctsm1.0.dev085) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- I1Pt tests and cases now use SROF rather than an active runoff model + with a null grid (only impacts namelists, not results) +- Changed nuopc test to use MOSART rather than SROF +- Changed finidat file used by LII test to solve a problem that was + uncovered with the ncdio_pio changes in this tag + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (just for NUOPC configurations) + + Summarize any changes to answers, i.e., + - what code configurations: Just some NUOPC configurations + - what platforms/compilers: + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Not investigated carefully, but likely to be larger than roundoff + / same climate (due to introduction of time-varying orbital parameters) + + Differences are expected in NUOPC configurations using time-varying + orbital parameters. Note that no differences showed up in the test + suite, however, because the only nuopc test in the test suite is + new in this tag (so did not have baselines). + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- mosart: mosart1_0_35 -> mosart1_0_36 +- rtm: rtm1_0_70 -> rtm1_0_71 +- cmeps + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/issues/943 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev085 +Originator(s): sacks (Bill Sacks) +Date: Mon Mar 16 09:19:57 MDT 2020 +One-line Summary: Update cime + +Purpose of changes +------------------ + +Update to latest version of cime master + +Bugs fixed or introduced +------------------------ + +Known bugs introduced in this tag (include github issue ID): +- https://github.com/ESCOMP/CTSM/issues/943 - NUOPC tests will fail in ctsm1.0.dev085 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- NUOPC cases will fail from a standalone checkout + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- pass + + Two test failures: + + PEND SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default SHAREDLIB_BUILD + I have added this to the expected fails list for now + FAIL SMS_P720x1_Ln6.hcru_hcru.I2000Clm50BgcCruGs.cheyenne_intel.clm-coldStart BASELINE ctsm1.0.dev084: ERROR BFAIL baseline directory '/glade/p/cgd/tss/ctsm_baselines/ctsm1.0.dev084/SMS_P720x1_Ln6.hcru_hcru.I2000Clm50BgcCruGs.cheyenne_intel.clm-coldStart' does not exist + This test was added in the previous tag, but apparently wasn't run from there + + Note: I did testing using cime hash + 4f1880756a66ff12d304937d3c166d451ea50cf9, then updated to the tag + (cime5.8.17). The two are identical except for the cime ChangeLog. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +cime: branch_tags/cime5.8.15_a01 -> cime5.8.17 + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev084 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Wed Feb 19 15:05:03 MST 2020 +One-line Summary: Bounds assertion for C isotopes when threading is on + +Purpose of changes +------------------ + +Previously, the bounds of c13 and c14 in subroutines TruncateCStates and +TruncateCandNStates were not checked when threading was on. This PR allows us +to handle c13 and c14 arrays like everything else in CTSM including (bounds +checking). + +This PR resolves issue ESCOMP/ctsm#811 + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): + -ESCOMP/ctsm#811 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: + - There was an issue (wrong wallclock time ) for one of the tests in the test + definitions which got fixed: (SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs..) + - Also, I tried making the wallclocktime for all tests in + cime_config/testdefs/testlist_clm.xml consistent in the format of hh:mm:ss. + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/CTSM/pull/923) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev083 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Thu Feb 6 12:12:26 MST 2020 +One-line Summary: Some BFB Fixes: Resolve issues #683, # 874, #878, # 885, # 745, #838 + +Purpose of changes +------------------ + +Resolved issues: + +ESCOMP/ctsm#683 : Writing out FATES parameters only on masterproc. +ESCOMP/ctsm#874 : Changing the number of timesteps to run for + SMS_P720x1_Ln3.hcru_hcru.I2000Clm50BgcCruGs.cheyenne_intel.clm-coldStar + to prevent failing with CMEPS. +ESCOMP/ctsm#878 : Removing the unused atm2lnd field. +ESCOMP/ctsm#885 : Changing the defaults for br_root in namelist_defaults to + enable FUN with CLM4.5. +ESCOMP/ctsm#745 : Removing ReadNL private subroutine from initVerticalMod.F90. +ESCOMP/ctsm#838 : Clarifying ZISNO in the variable long name. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +Resolves : + - ESCOMP/ctsm#683 + - ESCOMP/ctsm#874 + - ESCOMP/ctsm#878 + - ESCOMP/ctsm#885 + - ESCOMP/ctsm#745 + - ESCOMP/ctsm#838 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): + Not any changes in parameter values. + changing the default for br_root in namelist_defaults to enable FUN with + CLM4.5. + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: + Changed the number of timesteps from Ln3 to Ln6 for + SMS_P720x1_Ln3.hcru_hcru.I2000Clm50BgcCruGs.cheyenne_intel.clm-coldStar + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/897 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev082 +Originator(s): oleson (Keith Oleson) +Date: Sat Feb 1 09:28:41 MST 2020 +One-line Summary: Rename variables to avoid confusion; fix QSNOEVAP diagnostic + +Purpose of changes +------------------ + +Renamed variables as discussed in ESCOMP/ctsm#118 throughout the code. + +Also made a couple of minor changes to fix a couple of potential +problems with these variables as described in the branch commit logs. + +Tested for bfb before changing the history field variables +themselves. These changes are all bfb (with the exception of QSNOEVAP) +for a 1 month global 2deg simulation, but may not be bfb under all +conditions. QSNOEVAP is not bfb because I've added in qflx_ev_snow for +lakes. + +Also, update cime slightly with a fix for izumi machine updates + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#118 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none expected (not checked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok: tests pass, answer changes in QSNOEVAP but nothing else (as expected) + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (only one diagnostic field) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + Larger than roundoff, but only in the diagnostic field QSNOEVAP + + Possibility of other answer changes in rare circumstances, not + observed in testing. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.8.15 -> branch_tags/cime5.8.15_a01 + Minor update for izumi machine changes + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/893 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev081 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Mon Jan 13 15:37:07 MST 2020 +One-line Summary: Speed up restart writes + +Purpose of changes +------------------ + + E3SM#3163 made some changes to speed up restart writes. I use E3SM#3163 + function GetGlobalIndexArray in place of GetGlobalIndex so as to get + global indices by array rather than looping over every element. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #801 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: Limited testing did not show substantial timing changes + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: + @billsacks + @bishtgautam + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No + + @billsacks recommended running a global test in the branch vs. in master (i.e. + with vs. without the code mods) to compare restart files because the test suite + does not compare restart files and an error in the subgrid indices on the + restart file might go undetected. I ran this test: + ERS_D_Ld6.f10_f10_musgs.I1850Clm45BgcCrop.cheyenne_intel.clm-clm50CMIP6frc + and got identical values for all variables in the two restart files. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/880 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev080 +Originator(s): sacks (Bill Sacks) +Date: Mon Dec 2 12:23:22 MST 2019 +One-line Summary: Update externals, minor fixes to work with latest cime, get nuopc cap working + +Purpose of changes +------------------ + +(1) Update to latest version of externals. This includes a significant + cime update. + +(2) Minor fixes to get things working with the latest version of cime. + +(3) Fix from Mariana Vertenstein to get NUOPC cap working, fixes to + externals cfg files to allow running NUOPC cases out of the box, and + add a NUOPC test. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +CIME update brings in some changes, e.g., in mapping files; otherwise, none. + +Substantial timing or memory changes: not investigated + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Added NUOPC test: + SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests passed, some baseline comparisons failed as expected + + Note: Most testing was done on ad1ad752; then, from the latest + version, I ran a 2-test test list of: + - SMS_D_Vnuopc.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default + - SMS_D.f10_f10_musgs.I2000Clm50SpRsGs.cheyenne_intel.clm-default + + In addition to verifying that the above tests passed, I also + inspected the sharedlib build area to verify that separate builds of + the clm library were done for mct and nuopc. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: +- cheyenne tests compared against ctsm1.0.dev078, since cheyenne testing +was not run on ctsm1.0.dev079. + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (only f10, same climate) + + Summarize any changes to answers, i.e., + - what code configurations: Cases at f10 resolution + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff, but probably same climate + + Answer changes are due to https://github.com/esmci/cime/pull/3186 + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: branch_tags/cime5.8.3_chint17-05 -> cime5.8.15 +- rtm: rtm1_0_68 -> rtm1_0_70 +- mosart: mosart1_0_34 -> mosart1_0_35 +- cmeps: 471ac52 -> 181ff1ed9dfb279e619e8a2173f43baf7bf1dce3 + Also, note that cmeps is now checked out automatically + + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/845 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev079 +Originator(s): sacks (Bill Sacks) +Date: Mon Nov 4 14:41:41 MST 2019 +One-line Summary: Change a few uses of shr_kind + +Purpose of changes +------------------ + +Change a few uses of shr_kind to work with latest cime. These changes +are from Mariana Vertenstein. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- NOT RUN! + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev078 +Originator(s): oleson (Keith Oleson) +Date: Thu Oct 31 12:30:00 MDT 2019 +One-line Summary: Fix rootr calculation with use_hydrstress true + +Purpose of changes +------------------ + +In cases with use_hydrstress=.true., both rootr_patch and rootr_col had +problems. This affected the diagnostic fields ROOTR and ROOTR_COLUMN, +and (in BGC cases) fed back on other parts of the system via affecting +the methane code. See https://github.com/ESCOMP/CTSM/issues/812 for more +details. + +This tag fixes this issue via these specific changes: + +1. Calculate btran in SoilMoistStressMod.F90 regardless of + use_hydrstress + +2. Comment on the applicability of this calculation and that of rootr in + SoilMoistStressMod.F90 + +3. Add the following comment to uses of rootr and rootr_col throughout + the code: "SMS method only" + +4. Allow ROOTR_COL history field only if use_hydrstress = .false. + +5. Remove the calculation of rootr_col in subroutine + Compute_EffecRootFrac_And_VertTranSink_HydStress within module + SoilWaterPlantSinkMod.F90 since that calculation is invalid for PHS. + +6. Normalize root resistances for pervious road over nlevgrnd, not + nlevsoi + +Note that the rootr calculation is done using the non-PHS (i.e., SMS) +method. So rootr is not really consistent with PHS; this is something +that should probably be revisited later. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes ESCOMP/ctsm#812 (Problems with rootr when use_hydrstress=.true.) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: not checked; none expected + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (PHS and methane) (same climate) + + Summarize any changes to answers, i.e., + - what code configurations: Clm50Bgc (cases with both use_hydrstress=.true. and methane active) + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff / same climate + + For details on differences, see + https://github.com/ESCOMP/CTSM/issues/812#issuecomment-547924289 + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: clm50_ctsm10d074_2deg_GSWP3V1_rootr_hist + + URL for LMWG diagnostics output used to validate new climate: + http://webext.cgd.ucar.edu/I20TR/clm50_ctsm10d074_2deg_GSWP3V1_rootr_hist/lnd/clm50_ctsm10d074_2deg_GSWP3V1_rootr_hist.1995_2014-clm50_ctsm10d074_2deg_GSWP3V1_hist.1995_2014/setsIndex.html + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev077 +Originator(s): sacks (Bill Sacks) +Date: Sun Oct 27 16:23:39 MDT 2019 +One-line Summary: Consistently use frac_sno_eff rather than frac_sno in qg calculations + +Purpose of changes +------------------ + +Consistently use frac_sno_eff rather than frac_sno in qg calculations + +The change here only changes answers for (1) urban pervious road, and +(2) more broadly with use_subgrid_fluxes = .false. + +Previously, code in CalculateSurfaceHumidity was inconsistent regarding +the use of frac_sno vs. frac_sno_eff. I wanted to make this consistent +to facilitate upcoming cleanup of CalculateSurfaceHumidity. I went back +and forth as to which one we should use here. (See also +https://github.com/ESCOMP/CTSM/issues/822). + +Argument for frac_sno_eff: This is consistent with the use of +frac_sno_eff elsewhere in the calculation of surface fluxes. + +Argument for frac_sno: Even in CLM4.0 (prior to the introduction of +frac_sno_eff and frac_h2osfc), frac_sno was used to calculate surface +relative humidity. That makes me think that the parameterizations were +improved by using frac_sno here, even though frac_sno at that point was +mainly just used for albedo / radiation calculations. So sticking with +frac_sno would be more consistent with what has been done for a long +time, and would presumably be a bit better scientifically. + +However, when I tried changing this to use frac_sno rather than +frac_sno_eff: + + qg(c) = frac_sno_eff(c)*qg_snow(c) + (1._r8 - frac_sno_eff(c) - frac_h2osfc(c))*qg_soil(c) & + + frac_h2osfc(c) * qg_h2osfc(c) + +I got a crash with use_subgrid_fluxes false (test +SMS_D_Ld1_P4x1.f10_f10_musgs.I2000Clm45BgcCropQianRsGs.bishorn_gnu.clm-no_subgrid_fluxes), +due to a check I put in relatively recently to ensure that the top-layer +soil liquid never goes significantly negative: + +WJS 218: frac_sno, frac_sno_eff, frac_h2osfc, snl = 6.6447358408778726E-005 1.0000000000000000 0.0000000000000000 -1 + qg_snow, qg_soil, qg_h2osfc, qg = 3.8414454029812475E-003 3.6634834595404343E-003 3.6635176705822736E-003 3.6634952846414733E-003 + ERROR: In UpdateState_TopLayerFluxes, h2osoi_liq has gone significantly negative + Bulk/tracer name = bulk + c, lev_top(c) = 218 0 + h2osoi_liq_top_orig = 6.6448689668604415E-004 + h2osoi_liq = -2.6754040213948407E-004 + frac_sno_eff = 1.0000000000000000 + qflx_liq_grnd*dtime = 0.0000000000000000 + qflx_dew_grnd*dtime = 0.0000000000000000 + qflx_evap_grnd*dtime = 9.3202729882552822E-004 + ENDRUN: + ERROR: In UpdateState_TopLayerFluxes, h2osoi_liq has gone significantly negative + +What seems to be going on is: With a little bit of snow present, when I +use frac_sno rather than frac_sno_eff, we end up with a qg value very +close to that of soil. But I think the later evaporation happens from +the snow, at which point I guess the dryer air above leads to there +being too large evaporation from the snow. + +So in the end, I decided to consistently use frac_sno_eff, even though +this might be a small step backwards in terms of the accuracy of surface +humidity for urban pervious road and with use_subgrid_fluxes = .false. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self (but approved conceptually by Sean Swenson and +Keith Oleson) + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (Small) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Expected to be larger than roundoff/same climate, but not + investigated carefully + + For the default configuration with use_subgrid_fluxes = .true., + differences are restricted to urban pervious road. I spot-checked + a few tests to ensure that we only saw differences in FSH for + urban landunits; this was generally true, with the exception of + ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput, + which also had differences over crop and natural veg + landunits. This spillover effect seems to be related to the + non-local interactions that arise from methane's dependence on + TWS, though I don't understand why I only saw this in a transient + case, and not in similar non-transient cases. See + https://github.com/ESCOMP/CTSM/issues/658#issuecomment-546740771 + for more details. + + For the non-default use_subgrid_fluxes = .false., there + differences in the natural vegetation and crop landunits, too. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev076 +Originator(s): sacks (Bill Sacks) +Date: Fri Oct 25 16:04:20 MDT 2019 +One-line Summary: Set frac_sno_eff=0 if frac_sno is 0; avoid unnecessary calls to QSat + +Purpose of changes +------------------ + +Two changes that are bit-for-bit except for changes in the FSNO_EFF +diagnostic field, both with an eye towards cleaning up +SurfaceHumidityMod in preparation for adding water tracers to that +module: + +(1) Set frac_sno_eff to 0 if frac_sno is 0. Previously, for cases where + frac_sno_eff was a binary 0/1 rather than being set equal to + frac_sno, frac_sno_eff was always being set to 1, even if there was + no snow. Sean Swenson thinks that didn't matter, but I found it + confusing, and it could be more problematic with some upcoming + changes I plan to make (where I'm going to use frac_sno_eff as a + weighting factor in calculating qg terms, including for landunits + that use a binary 0/1 frac_sno_eff.) + +(2) Avoid unnecessary calls to QSat, since this function is relatively + expensive. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: No substantial changes; from a +single run of PFS_Ld20.f09_g17.I2000Clm50BgcCrop.cheyenne_intel, max +timing of the main changed section (bgp1) decreased by about 10%; this +may be within machine variability, though. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answer changes as expected just for FSNO_EFF + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, but just for the diagnostic field FSNO_EFF + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + diagnostic only: just changes FSNO_EFF + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev075 +Originator(s): sacks (Bill Sacks) +Date: Fri Oct 25 15:44:52 MDT 2019 +One-line Summary: Lakes: Adjust frac_sno after updating 0-layer snow pack for dew & sublimation + +Purpose of changes +------------------ + +Main change is: for lakes, possibly adjust frac_sno after updating +0-layer snow pack for dew & sub, ensuring that zero vs. non-zero values +of frac_sno agree with whether the snow pack has zero or non-zero +amounts of snow. The main motivation for this is to ensure that, if we +have any snow, then frac_sno should be non-zero. Along with this, I'm +also ensuring that, if we go down to 0 snow, then we also go down to 0 +frac_sno. + +A related change was to move the code ensuring that h2osno_no_layers +doesn't go negative: I have moved this to before h2osno_no_layers is +referenced, to assure we don't get a slightly negative snow depth. (I +haven't noticed any problems due to the old placement, but it seems +safer to put the limiting before the reference to h2osno_no_layers.) + +Also, an unrelated change in run_sys_tests: Add option for rerunning +existing failed tests. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#827 (Lake frac_sno can remain 0 even when there + is some snow addition from frost) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: None expected + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - pass (on my mac: 'make test' with python2 & python3 and 'make lint') + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (Small) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Expected to be larger than roundoff/same climate + + Changes are introduced only over lake columns, and these changes + should be small, since they only relate to the setting of frac_sno + when there is dew or sublimation on a very thin snow + pack. + + Although the direct changes should only affect lakes, I did + observe changes in crop columns in a transient test that I + spot-checked + (ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput) + - maybe due to some of the non-local interactions in + https://github.com/ESCOMP/CTSM/wiki/Parameterizations-that-can-cause-nonlocal-interactions, + or maybe due to some other non-local interaction, either known or + buggy. (In non-transient tests that I spot checked + (ERP_P72x2_Lm36.f10_f10_musgs.I2000Clm50BgcCrop.cheyenne_intel.clm-clm50cropIrrigMonth_interp + and + SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput): + diffs in FSH in h1 file are just over lake landunits, as + expected.) + + Update: it seems that these changes in crop columns arise from + the nonlocal interactions caused by the dependence of methane + on TWS, though I don't understand why I only saw this in a + transient case, and not in similar non-transient cases. See + https://github.com/ESCOMP/CTSM/issues/658#issuecomment-546740771 + for more details. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev074 +Originator(s): sacks (Bill Sacks) +Date: Wed Oct 23 19:25:21 MDT 2019 +One-line Summary: For lakes: when reading finidat, set frac_sno=1 if h2osno_total > 0 + +Purpose of changes +------------------ + +Due to ESCOMP/ctsm#783, frac_sno used to be 0 for all lake points. That +was mostly fixed, but the issue is still present on initial conditions +files that were generated prior to that fix (which includes most or all +of our out-of-the-box restart files). This causes frac_sno to be 0 for +lake points at the start of the simulation, even if there is a snow pack +present. Currently this doesn't cause significant problems, but I'd like +to change the calculation of frac_sno_eff so that it is 0 if frac_sno is +0 - and then this frac_sno problem becomes an issue (causing divide by 0 +in at least one place). + +However, further problems were introduced if I tried to always apply +this correction: It appears that sometimes the restart file legitimately +has frac_sno == 0 for lake columns with non-zero snow cover. To avoid +changing answers for newer restart files, I am writing metadata to the +restart file documenting whether the fix has already been applied on +that restart file, and if so, we avoid reapplying the fix. + +Getting this restart metadata correct was tricky, especially when +running init_interp. I have introduced a new module to encapsulate this +complexity. This can be used in general for writing / reading metadata +on which issues have been fixed on a given restart file. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): [If none, remove this line] +- Resolves ESCOMP/ctsm#783 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- The setting of initial lake frac_sno to 1 isn't exactly correct, but + it's better than the old value of 0. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +- I didn't check the PFS test, but the only change that could have + likely led to performance changes was the addition of a metadata copy + in init_interp. I checked the timing of this piece, and found it to be + a negligible portion of the total init_interp time + (https://github.com/ESCOMP/CTSM/pull/825#issuecomment-545219601). + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek gave this an initial look and gave general +approval for the restart file metadata mechanism I have added. He may +give it a more careful look, possibly accompanied by a further cleanup +tag addressing any issues he finds. + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests passed, baselines fail as expected. + + Note that the FUNIT test failed initially; I got it passing on my + Mac, but didn't rerun it on cheyenne. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (same climate, only at startup) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff/same climate + + The only change is in initial lake frac_sno. This should only + affect the start of the simulation, and only over lake points. I + verified that changes are only over lake points via: For both + SMS_D_Ld1.f09_g17.I1850Clm50Sp.cheyenne_intel.clm-default (which + doesn't use init_interp) and + SMS_D_Ld3.f10_f10_musgs.I2000Clm50BgcCruGs.cheyenne_gnu.clm-default + (which uses init_interp): I checked which points have differences + in FSH in the h1 (vector) history file. Diffs were only over lake + points. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/825 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev073 +Originator(s): sacks (Bill Sacks) +Date: Tue Oct 22 06:14:24 MDT 2019 +One-line Summary: Fix bug in calculation of dqgdT + +Purpose of changes +------------------ + +The calculation of dqgdT, which gives the derivative, d(qg)/dT, was +incorrect for soil/crop landunits when there is no snow. This tag fixes +that bug. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#824 (dqgdT incorrect when there is no snow) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: not checked, but none expected + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson reviewed and approved my plan, though not the final code + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (small) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff/same climate + + I checked the impact from one-day averages in test + SMS_D_Ld1_P4x1.f10_f10_musgs.I2000Clm50BgcCropQianRsGs.bishorn_gnu.clm-default, + by looking at differences in EFLX_LH_TOT. The impact is small: + daily-average differences in that variable are typically 0.01 W + m-2 or less; most grid cells have significantly less difference + than that; only one or a few f10 grid cells have significantly + greater differences, with the biggest difference being about 0.1 W + m-2. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev072 +Originator(s): mvertens (Mariana Vertenstein) +Date: Tue Oct 15 09:41:50 MDT 2019 +One-line Summary: Add NUOPC cap + +Purpose of changes +------------------ + +Add NUOPC cap in order to run with the new NUOPC driver/mediator. There +was some code movement / refactoring of existing code to support this, +with the biggest change being the introduction of a new subdirectory +under src/cpl. + +Most changes are from Mariana Vertenstein and Jim Edwards. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none expected (not checked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- NUOPC cap currently does not have any tests in the aux_clm test suite +- There are currently no tests ensuring that the nuopc and mct caps give + bit-for-bit answers, though the nuopc_cap_bfb testmod could be used to + support such a test + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- mosart: mosart1_0_33 -> mosart1_0_34 (supports nuopc cap) + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev071 +Originator(s): sacks (Bill Sacks) +Date: Fri Oct 11 07:03:40 MDT 2019 +One-line Summary: Split CanopyTemperature into separate pieces + +Purpose of changes +------------------ + +CanopyTemperature was doing a few unrelated things, none of which +actually had anything to do with calculating canopy temperature. At the +driver level, I have split CanopyTemperature into BiogeophysPreFluxCalcs +and CalculateSurfaceHumidity. BiogeophysPreFluxCalcs calls out to a +number of separate routines, some in that same module and some +elsewhere, including a new routine in FrictionVelocityMod. + +Also some minor related cleanup, including + +- Made FrictionVelocityMod object-oriented + +- A bit of rework of how qflx_evap_veg and qflx_tran_veg are set. This + changes answers for the (default inactive) QFLX_EVAP_VEG history field + (see also ESCOMP/ctsm#816). + +- Removed qsat conditionals that should never be invoked + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes ESCOMP/ctsm#816 (QFLX_EVAP_VEG should be 0 over lakes) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, but only for the (default-inactive) field QFLX_EVAP_VEG + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff, but only for the default-inactive field QFLX_EVAP_VEG + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev070 +Originator(s): sacks (Bill Sacks) +Date: Wed Oct 9 06:16:39 MDT 2019 +One-line Summary: Fix for writing 0-d variables with PIO2 + +Purpose of changes +------------------ + +Previously, there were problems when writing 0-d (scalar) variables with +PIO2 in DEBUG mode. This change fixes that issue. + +Jim Edwards put in place an initial fix; I put in place the final fix +based on changes Mariana Vertenstein made in MOSART. I have not tested +this with PIO2, but am hopeful that it fixes the PIO2 problem since the +similar MOSART changes fixed that problem. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self; earlier version reviewed by Erik Kluzek and Mariana Vertenstein + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/810 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev069 +Originator(s): sacks (Bill Sacks) +Date: Mon Oct 7 10:22:22 MDT 2019 +One-line Summary: Misc. code cleanup and minor bug fixes + +Purpose of changes +------------------ + +Resolve a variety of "simple bfb" issues. Note that some of these result +in answer changes for select diagnostic fields. See specific notes below +for details, under "Issues fixed" and answer changes. + +The fix for ESCOMP/ctsm#27 changes answers for some diagnostic fields, +as noted below. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#27 (BTRAN should be spval over all special + landunits) + - Also fixed some related fields, as noted below, under answer changes + +- Resolves ESCOMP/ctsm#31 (some CLM history fields don't restart + properly) + - This was mostly resolved previously; here I just did some final + cleanup and fixing of NFIRE + +- Resolves ESCOMP/ctsm#48 (code for initializing some isotope carbon + state variables looks wrong) + - Removed the incorrect code, which was never being exercised + +- Resolves ESCOMP/ctsm#58 (Change SHR_ASSERT calls to avoid using + errMsg) + - Purpose was to speed up DEBUG runs on some machines/compilers + +- Resolves ESCOMP/ctsm#111 (Precision of constants in + SoilTemperature.F90 is not double) + - No answer changes, because 1 (single prec) = 1 (double prec) + +- Resolves ESCOMP/ctsm#334 (Introduce a new activelayer_type) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: potentially speeds up debug runs on some machines/compilers + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, some baseline comparisons fail as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES, but just for select diagnostic fields + + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Greater than roundoff, but only in select diagnostic field - no impact on climate + + There were changes in the following diagnostic fields, which are + now averaged over only vegetated landunits (see ESCOMP/ctsm#27): + - BTRAN + - BTRANMN + - RSSHA + - RSSUN + - ROOTR (inactive by default) + - ROOTR_COLUMN (inactive by default) + - RRESIS (inactive by default) + + Changes are also possible in rare circumstances for the NFIRE + diagnostic field, in transient cases, although no differences were + observed for this field in the test suite (see ESCOMP/ctsm#31). + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev068 +Originator(s): sacks (Bill Sacks) +Date: Mon Sep 30 09:57:04 MDT 2019 +One-line Summary: Add water tracers to CombineSnowLayers, DivideSnowLayers, ZeroEmptySnowLayers + +Purpose of changes +------------------ + +Add water tracers to CombineSnowLayers, DivideSnowLayers and +ZeroEmptySnowLayers. This completes the tracerization of the core snow +code: most or all of the code in SnowHydrologyMod is now tracerized. + +In contrast to most routines that I have tracerized, the tracerization +of these routines is done by embedding loops over tracers inside +existing code structures, rather than splitting out separate routines +that operate on bulk or tracer quantities. This is because (1) it didn't +make sense to introduce explicit fluxes for the state updates done here, +so we didn't have the extra need of having separate routines for flux +calculations vs. state updates; (2) the state updates were embedded in +loops over levels and conditionals in a way that would have been awkward +and messy to try to separately update bulk-and-tracer quantities +(h2osoi_liq, h2osoi_ice, etc.) from bulk-only quantities (dz, etc.). + +Also, a bit of reordering of LakeHydrologyMod in order to keep the snow +code more together. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#778 (Implement water tracers for combining and + dividing snow layers) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: I don't think so + Based on the changes introduced, I expect *very* small increases in + runtime of the modified routines (which would show up in the + hydro_without_drainage timer), even for cases without water tracers, + but I wouldn't expect this to have a significant impact. From PFS + test, and specifically looking at the timing of + hydro_without_drainage in that test, I see a possible small increase + (a few percent) in the timing of that section, though the differences + are within typical machine variability, so don't seem necessarily + significant. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev067 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Thu Sep 26 15:02:39 MDT 2019 +One-line Summary: Add config_archive.xml to CTSM cime_config -- no testing + +Purpose of changes +------------------ + +Add config_archive.xml to cime_config for CTSM. Update the CODE_OF_CONDUCT +to the August/2019 UCAR version. + +No testing done. + +Bugs fixed or introduced +------------------------ + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self + + +CTSM testing: doc (no standard testing done) + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + src unit-tests: + + cheyenne - PASS + + regular tests (aux_clm): None + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + + +Answer changes +-------------- + +Changes answers relative to baseline: No! + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): None +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev066 +Originator(s): sacks (Bill Sacks) +Date: Fri Sep 20 09:07:23 MDT 2019 +One-line Summary: Add water tracers to SnowCapping + +Purpose of changes +------------------ + +Update water tracer terms in SnowCapping. As I have done elsewhere, this +has involved splitting each piece of SnowCapping into its own subroutine, +which operates either on bulk, tracers, or bulk + tracers. + +This is supported by calls to ResetCheckedTracers prior to the call to +SnowCapping, since some intervening code is not yet tracerized. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#777 (Implement water tracers for SnowCapping) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + Small increase in total runtime of PFS test, but the relevant timing + section, hydro_without_drainage, took slightly *less* time compared + with the last tag. + + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + izumi ------- pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev065 +Originator(s): sacks (Bill Sacks) +Date: Sat Sep 14 12:52:42 MDT 2019 +One-line Summary: Add water tracers to SnowWater + +Purpose of changes +------------------ + +Update water tracer terms in SnowWater. As I have done elsewhere, this +has involved splitting each piece of SnowWater into its own subroutine, +which operates either on bulk, tracers, or bulk + tracers. + +This is supported by calls to ResetCheckedTracers prior to the call to +SnowWater, since some intervening code is not yet tracerized. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#776 (Implement water tracers for SnowWater) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + izumi ------- ok + + ok means tests pass, baselines fail as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (roundoff) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + Roundoff level: answer changes just arise because I have made + qflx_snow_percolation_col a true flux, with units of + per-unit-time; this involved dividing by dtime, and later + multiplying by dtime when it is applied to states. Previously, the + corresponding variable (qout / qin) was not per-unit-time. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + I ran comparisons against a version off of master that had the + minimal changes to exhibit these roundoff-level changes. Diffs for + this are below. My branch is bit-for-bit with this version. + + diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 + index cad47e28..0abcc49f 100644 + --- a/src/biogeophys/SnowHydrologyMod.F90 + +++ b/src/biogeophys/SnowHydrologyMod.F90 + @@ -1140,17 +1140,17 @@ subroutine SnowWater(bounds, & + c = filter_snowc(fc) + if (j >= snl(c)+1) then + + - h2osoi_liq(c,j) = h2osoi_liq(c,j) + qin(c) + + h2osoi_liq(c,j) = h2osoi_liq(c,j) + qin(c)*dtime + + - mss_bcphi(c,j) = mss_bcphi(c,j) + qin_bc_phi(c) + - mss_bcpho(c,j) = mss_bcpho(c,j) + qin_bc_pho(c) + - mss_ocphi(c,j) = mss_ocphi(c,j) + qin_oc_phi(c) + - mss_ocpho(c,j) = mss_ocpho(c,j) + qin_oc_pho(c) + + mss_bcphi(c,j) = mss_bcphi(c,j) + qin_bc_phi(c)*dtime + + mss_bcpho(c,j) = mss_bcpho(c,j) + qin_bc_pho(c)*dtime + + mss_ocphi(c,j) = mss_ocphi(c,j) + qin_oc_phi(c)*dtime + + mss_ocpho(c,j) = mss_ocpho(c,j) + qin_oc_pho(c)*dtime + + - mss_dst1(c,j) = mss_dst1(c,j) + qin_dst1(c) + - mss_dst2(c,j) = mss_dst2(c,j) + qin_dst2(c) + - mss_dst3(c,j) = mss_dst3(c,j) + qin_dst3(c) + - mss_dst4(c,j) = mss_dst4(c,j) + qin_dst4(c) + + mss_dst1(c,j) = mss_dst1(c,j) + qin_dst1(c)*dtime + + mss_dst2(c,j) = mss_dst2(c,j) + qin_dst2(c)*dtime + + mss_dst3(c,j) = mss_dst3(c,j) + qin_dst3(c)*dtime + + mss_dst4(c,j) = mss_dst4(c,j) + qin_dst4(c)*dtime + + if (j <= -1) then + ! No runoff over snow surface, just ponding on surface + @@ -1167,8 +1167,8 @@ subroutine SnowWater(bounds, & + qout(c) = max(0._r8,(vol_liq(c,j) & + - ssi*eff_porosity(c,j))*dz(c,j)*frac_sno_eff(c)) + end if + - qout(c) = qout(c)*1000._r8 + - h2osoi_liq(c,j) = h2osoi_liq(c,j) - qout(c) + + qout(c) = (qout(c)*1000._r8)/dtime + + h2osoi_liq(c,j) = h2osoi_liq(c,j) - qout(c)*dtime + qin(c) = qout(c) + + ! mass of ice+water: in extremely rare circumstances, this can + @@ -1187,7 +1187,7 @@ subroutine SnowWater(bounds, & + if (qout_bc_phi(c) > mss_bcphi(c,j)) then + qout_bc_phi(c) = mss_bcphi(c,j) + endif + - mss_bcphi(c,j) = mss_bcphi(c,j) - qout_bc_phi(c) + + mss_bcphi(c,j) = mss_bcphi(c,j) - qout_bc_phi(c)*dtime + qin_bc_phi(c) = qout_bc_phi(c) + + ! BCPHO: + @@ -1196,7 +1196,7 @@ subroutine SnowWater(bounds, & + if (qout_bc_pho(c) > mss_bcpho(c,j)) then + qout_bc_pho(c) = mss_bcpho(c,j) + endif + - mss_bcpho(c,j) = mss_bcpho(c,j) - qout_bc_pho(c) + + mss_bcpho(c,j) = mss_bcpho(c,j) - qout_bc_pho(c)*dtime + qin_bc_pho(c) = qout_bc_pho(c) + + ! OCPHI: + @@ -1205,7 +1205,7 @@ subroutine SnowWater(bounds, & + if (qout_oc_phi(c) > mss_ocphi(c,j)) then + qout_oc_phi(c) = mss_ocphi(c,j) + endif + - mss_ocphi(c,j) = mss_ocphi(c,j) - qout_oc_phi(c) + + mss_ocphi(c,j) = mss_ocphi(c,j) - qout_oc_phi(c)*dtime + qin_oc_phi(c) = qout_oc_phi(c) + + ! OCPHO: + @@ -1214,7 +1214,7 @@ subroutine SnowWater(bounds, & + if (qout_oc_pho(c) > mss_ocpho(c,j)) then + qout_oc_pho(c) = mss_ocpho(c,j) + endif + - mss_ocpho(c,j) = mss_ocpho(c,j) - qout_oc_pho(c) + + mss_ocpho(c,j) = mss_ocpho(c,j) - qout_oc_pho(c)*dtime + qin_oc_pho(c) = qout_oc_pho(c) + + ! DUST 1: + @@ -1223,7 +1223,7 @@ subroutine SnowWater(bounds, & + if (qout_dst1(c) > mss_dst1(c,j)) then + qout_dst1(c) = mss_dst1(c,j) + endif + - mss_dst1(c,j) = mss_dst1(c,j) - qout_dst1(c) + + mss_dst1(c,j) = mss_dst1(c,j) - qout_dst1(c)*dtime + qin_dst1(c) = qout_dst1(c) + + ! DUST 2: + @@ -1232,7 +1232,7 @@ subroutine SnowWater(bounds, & + if (qout_dst2(c) > mss_dst2(c,j)) then + qout_dst2(c) = mss_dst2(c,j) + endif + - mss_dst2(c,j) = mss_dst2(c,j) - qout_dst2(c) + + mss_dst2(c,j) = mss_dst2(c,j) - qout_dst2(c)*dtime + qin_dst2(c) = qout_dst2(c) + + ! DUST 3: + @@ -1241,7 +1241,7 @@ subroutine SnowWater(bounds, & + if (qout_dst3(c) > mss_dst3(c,j)) then + qout_dst3(c) = mss_dst3(c,j) + endif + - mss_dst3(c,j) = mss_dst3(c,j) - qout_dst3(c) + + mss_dst3(c,j) = mss_dst3(c,j) - qout_dst3(c)*dtime + qin_dst3(c) = qout_dst3(c) + + ! DUST 4: + @@ -1250,7 +1250,7 @@ subroutine SnowWater(bounds, & + if (qout_dst4(c) > mss_dst4(c,j)) then + qout_dst4(c) = mss_dst4(c,j) + endif + - mss_dst4(c,j) = mss_dst4(c,j) - qout_dst4(c) + + mss_dst4(c,j) = mss_dst4(c,j) - qout_dst4(c)*dtime + qin_dst4(c) = qout_dst4(c) + + end if + @@ -1280,9 +1280,9 @@ subroutine SnowWater(bounds, & + do fc = 1, num_snowc + c = filter_snowc(fc) + ! Qout from snow bottom + - qflx_snow_drain(c) = qflx_snow_drain(c) + (qout(c) / dtime) + + qflx_snow_drain(c) = qflx_snow_drain(c) + qout(c) + + - qflx_rain_plus_snomelt(c) = (qout(c) / dtime) & + + qflx_rain_plus_snomelt(c) = qout(c) & + + (1.0_r8 - frac_sno_eff(c)) * qflx_liq_grnd(c) + int_snow(c) = int_snow(c) + frac_sno_eff(c) & + * (qflx_dew_snow(c) + qflx_dew_grnd(c) + qflx_liq_grnd(c)) * dtime + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev064 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Mon Sep 9 13:14:51 MDT 2019 +One-line Summary: User defined top-two snow layers + +Purpose of changes +------------------ + + Instead of hardcoding, we now set: + + dzmin(1) = snow_dzmin_1 + dzmax_l(1) = snow_dzmax_l_1 + dzmax_u(1) = snow_dzmax_u_1 + dzmin(2) = snow_dzmin_2 + dzmax_l(2) = snow_dzmax_l_2 + dzmax_u(2) = snow_dzmax_u_2 + + where the right-hand-side variables get namelist-defined values and the + model calculates dzmin and dzmax_* for the remaining snow layers using + recursive formulas. The calculation is intended to match the previously + hardcoded values, except for the bottom snow layer when nlevsno < 12. + The bottom layer now always gets dzmax_* = huge(1._r8). The formulas + appear in a document titled "A firn model for CLM" that is linked to + #729. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #729 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New namelist parameters for specifying the top-two snow layers: + snow_dzmin_1, snow_dzmax_l_1, snow_dzmax_u_1 + snow_dzmin_2, snow_dzmax_l_2, snow_dzmax_u_2 + +Changes made to namelist defaults (e.g., changed parameter values): + Introduced default values for the new parameters so as to maintain + same answers to within roundoff + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: @billsacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (roundoff) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change: roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + Introduced temporary code to overwrite dzmin(j), dzmax_l(j), and + dzmax_u(j) with their original values when different by less than + 1e-13 from their original values for all but the bottom snow layer. + The bottom layer was left as dzmax_l = dzmax_u(j) = huge(1._8), i.e. + the new value. The test resulted in bit-for-bit same answers. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/792 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev063 +Originator(s): erik (Erik Kluzek) +Date: Thu Sep 5 21:28:02 MDT 2019 +One-line Summary: Two answer changing fixes (fire, DWT_SLASH) and fix for urban streams for Clm45 + +Purpose of changes +------------------ + +Fire bug fix and DWT_SLASH change and fix urban stream years for clm4_5. +The latitude used in an expression for Bgc-Fire model Li2016 (used in Clm50) +had latitude in degrees rather than in radians as it should have been. The +term is used for ignition and the cosine was being taken in degrees rather +than radians, hence the spatial pattern for ignition with latitude was incorrect. + +The history field DWT_SLASH_CFLUX was being calculated on the column, but +really should have been a patch level variable. In the same way other fields +were handled we made DWT_SLASH_CFLUX a grid-cell variable, and added +DWT_SLASH_CFLUX_PATCH on the patch level that could be added to output. The same +is true of the C13_ and C14_ versions of it. + +Clm45 was setting urbantv to year 2000, rather than 1850 or historical as it should +have. The urbantv file for Clm45 doesn't actually change, so this doesn't actually +make a difference. But, it does make the namelist look wrong. + +Note, that SP cases, Vic cases and Fates cases do NOT change answers. Or if fire is +off, or certain single-point cases. Some cold-start cases don't seem to be sensitive +to it either. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #175, #787, #780 + fixes #175 urban stream years for clm4_5 + fixes #787 DWT_SLASH field + fixes #780 Bug in CN Fire Li 2016 which used latitude in degrees rather than radians + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): Defaults for urbantv for clm4_5 + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self, @olywon + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (62 compare fail due to namelist changes) + + regular tests (aux_clm): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! (important clm5_0-BGC) + + Summarize any changes to answers, i.e., + - what code configurations: Clm50Bgc and some Clm45Bgc cases + - what platforms/compilers: All + - nature of change: similar climate (but fire ignition pattern changes by latitude) + DWT_SLASH_* history fields change because moved to gridcell quantity (so change is relatively minor) + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: oleson/clm50_cesm20R_2deg_GSWP3V1_issue780_hist (for the fire change) + + URL for LMWG diagnostics output used to validate new climate: +http://webext.cgd.ucar.edu/I20TR/clm50_cesm20R_2deg_GSWP3V1_issue780_hist/lnd/clm50_cesm20R_2deg_GSWP3V1_issue780_hist.1995_2014-clm50_cesm20R_2deg_GSWP3V1_hist.1995_2014/setsIndex.html + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #802 +(https://github.com/ESCOMP/ctsm/pull) + #802 -- Three answer changing fixes (fire, DWT_SLASH, urban streams for clm4_5) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev062 +Originator(s): sacks (Bill Sacks) +Date: Tue Sep 3 16:04:28 MDT 2019 +One-line Summary: Move hobart tests to izumi + +Purpose of changes +------------------ + +Move all hobart testing to izumi. + + +Bugs fixed or introduced +------------------------ + +Known bugs introduced in this tag (include github issue ID): +- Recurrence of ESCOMP/ctsm#174 (ne30 case fails on hobart_nag due to floating overflow) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Testing should now be run on izumi, not hobart + +Changes to tests or testing: +- All hobart tests moved to izumi + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- not run + izumi ------- pass + + Also ran prealpha and prebeta tests that I moved from hobart to izumi. These passed except: + - ERP_D_Ld5.ne30_g16.I1850Clm50BgcCrop.izumi_nag.clm-default (#174) + - ERP_Ld5.f19_g17.I2000Clm50SpRtmFl.izumi_pgi.clm-default + - SMS_D_Ld1.f19_g17.I1850Clm45Cn.izumi_pgi.clm-default + + The last two failed with errors like: + + i011.unified.ucar.edu.44619hfi_userinit: mmap of status page (dabbad0008040000) failed: Operation not permitted + + I wonder if the issue is that multi-node pgi cases don't work on izumi? + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.8.3_chint17-04 -> cime5.8.3_chint17-05 + Minor change on izumi to allow using run_sys_tests + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev061 +Originator(s): erik (Erik Kluzek) +Date: Sun Sep 1 22:37:07 MDT 2019 +One-line Summary: Simple b4b fixes: new params file, remove override_nsrest/anoxia_wtsat, DV deprecated + +Purpose of changes +------------------ + +New clm5 paramsfile that has the bad date of 631 changed to 701. Along with some simple bit for +bit changes. Removing some problematic options. Making Dynamic Vegetation a deprecated option +that requires you to use -ignore_warnings with it. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #463 #79 #97 #98 #104 #122 #173 #794 #795 #796 + + Fixes #463 bad date on params file that didn't allow using ESMF library with Crop + Fixes #79 correct documentation of qflx_evap_tot + Fixes #97 remove override_nsrest + Fixes #98 add warning when using single instance of a startup file for multi-instance cases + Fixes #104 use get_step_size_real when putting into a real variable + Fixes #122 decomp pool arrays should not start at 0 but 1 + Fixes #173 remove psi_soil_ref as not used + Fixes #794 remove anoxia_wtsat + Fixes #795 Correct documentation of -light_res + Fixes #796 Deprecate Dynamic Vegetation + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): Remove namelist items + Remove namelist items: anoxia_wtsat, override_nsrest + Turning dynamic Vegetation on, now displays a warning, and requires using -ignore_warnings in CLM_BLDNML_OPTS + +Changes made to namelist defaults (e.g., changed parameter values): New paramdata files + +Changes to the datasets (e.g., parameter, surface or initial files): + clm5 paramdata file has correct date for crop of 701 (rather than incorrect 631) + clm5 and clm4_5 paramdata file removed an unused variable + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: DV tests removed or changed + +Code reviewed by: self + +CTSM testing: regular + + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (compare shows changes becausse of paramdata files) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +An additional fail is ERP_P36x2_D_Ld5.f10_f10_musgs.I2000Clm50Cn.cheyenne_gnu.clm-default, because +of #798. Because it's an issue with cime, I'm not marking it as an expected error. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: previous + + +Answer changes +-------------- + +Changes answers relative to baseline: No bit-for-bit + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #797 +(https://github.com/ESCOMP/ctsm/pull) + + #797 -- Simple b4b fixes: new params file, remove override_nsrest/anoxia_wtsat, DV deprecated + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev060 +Originator(s): sacks (Bill Sacks) +Date: Thu Aug 29 11:18:20 MDT 2019 +One-line Summary: In SnowWater, truncate small h2osoi residuals + +Purpose of changes +------------------ + +Previously, in the handling of sublimation and evaporation from the snow +pack, if these fluxes led to negative h2osoi_ice or h2osoi_liq, these +negative values would be passed down the snow pack until they found a +layer with a large enough positive state to absorb them. This logic was +going to be a challenge for adding water tracers. + +I have done some tests to verify that these negative values never exceed +roundoff-level in either an absolute or relative sense (with tolerance +of 1.e-13). Specifically, I ran the full aux_clm test suite with the +diffs below and verified that the endrun calls were never triggered. + +So here, I simplify this logic: After truncating any near-zero states to +exactly zero, I check to confirm that the states are never negative. I +then removed the code that passed these negative values down the snow +pack: if they are only roundoff-level negative, then it seems safe to +just throw them away rather than trying to handle them. + +Here were the diffs used to verify that the negative values are never +greater than roundoff-level; these endrun calls were never triggered in +a run of the full aux_clm test suite: + + diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 + index 3dd555cc..07776123 100644 + --- a/src/biogeophys/SnowHydrologyMod.F90 + +++ b/src/biogeophys/SnowHydrologyMod.F90 + @@ -970,6 +970,8 @@ subroutine SnowWater(bounds, & + real(r8) :: vol_ice(bounds%begc:bounds%endc,-nlevsno+1:0) ! partial volume of ice lens in layer + real(r8) :: eff_porosity(bounds%begc:bounds%endc,-nlevsno+1:0) ! effective porosity = porosity - vol_ice + real(r8) :: mss_liqice(bounds%begc:bounds%endc,-nlevsno+1:0) ! mass of liquid+ice in a layer + + real(r8) :: h2osoi_ice_orig + + real(r8) :: h2osoi_liq_orig + !----------------------------------------------------------------------- + + associate( & + @@ -1017,10 +1019,23 @@ subroutine SnowWater(bounds, & + c = filter_snowc(fc) + l=col%landunit(c) + + + h2osoi_ice_orig = h2osoi_ice(c,snl(c)+1) + + h2osoi_liq_orig = h2osoi_liq(c,snl(c)+1) + + + wgdif = h2osoi_ice(c,snl(c)+1) & + + frac_sno_eff(c) * (qflx_dew_snow(c) - qflx_sub_snow(c)) * dtime + h2osoi_ice(c,snl(c)+1) = wgdif + if (wgdif < 0._r8) then + + if (wgdif < -1.e-13_r8) then + + write(iulog,*) 'WJS: big abs wgdif ice: ', c, wgdif, h2osoi_ice_orig + + call endrun('WJS: big abs wgdif ice') + + end if + + if (h2osoi_ice_orig > 0._r8) then + + if (abs(wgdif / h2osoi_ice_orig) > 1.e-13_r8) then + + write(iulog,*) 'WJS: big rel wgdif ice: ', c, wgdif, h2osoi_ice_orig + + call endrun('WJS: big rel wgdif ice') + + end if + + end if + h2osoi_ice(c,snl(c)+1) = 0._r8 + h2osoi_liq(c,snl(c)+1) = h2osoi_liq(c,snl(c)+1) + wgdif + end if + @@ -1030,6 +1045,16 @@ subroutine SnowWater(bounds, & + + ! if negative, reduce deeper layer's liquid water content sequentially + if(h2osoi_liq(c,snl(c)+1) < 0._r8) then + + if (h2osoi_liq(c,snl(c)+1) < -1.e-13_r8) then + + write(iulog,*) 'WJS: big abs wgdif liq: ', c, h2osoi_liq(c,snl(c)+1), h2osoi_liq_orig + + call endrun('WJS: big abs wgdif liq') + + end if + + if (h2osoi_liq_orig > 0._r8) then + + if (abs(h2osoi_liq(c,snl(c)+1) / h2osoi_liq_orig) > 1.e-13_r8) then + + write(iulog,*) 'WJS: big rel wgdif liq: ', c, h2osoi_liq(c,snl(c)+1), h2osoi_liq_orig + + call endrun('WJS: big rel wgdif liq') + + end if + + end if + do j = snl(c)+1, 1 + wgdif=h2osoi_liq(c,j) + if (wgdif >= 0._r8) exit + +Bugs fixed or introduced +------------------------ + +None + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- It's possible that the extra error checks I have added (to ensure we + don't have greater-than-roundoff-level negative residuals) will be + triggered in rare circumstances in a production run, even though they + were never triggered in the test suite. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +Although there was a very small increase in total lnd run time, the +timing of hydro_without_drainage actually decreased slightly in the PFS +test relative to the last tag. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- It's possible that the extra error checks I have added (to ensure we + don't have greater-than-roundoff-level negative residuals) will be + triggered in rare circumstances in a production run, even though they + were never triggered in the test suite. + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests passed, some answer changes as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (roundoff) + + Summarize any changes to answers, i.e., + - what code configurations: potentially all, though only show up in + a few tests + - what platforms/compilers: potentially all, though only show up in + a few tests + - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + First, I did some preliminary analyses as documented above, to + ensure that any negative residuals were no greater than roundoff. + + Second, note that the use of truncate_small_values can only + introduce roundoff-level changes (by truncating values that are + roundoff-level different from zero to exactly zero). + + Third, only a few tests showed answer changes, and these were only + in limited fields, and were fairly small RMS differences: + + ERP_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput + ERS_Ly3.f10_f10_musgs.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic + ERS_Ly3_P72x2.f10_f10_musgs.IHistClm50BgcCropG.cheyenne_intel.clm-cropMonthOutput + ERS_Ly5_P144x1.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-cropMonthOutput + + I actually expected more tests to show differences, but most tests + were bit-for-bit. I'm guessing this is because the code added a + roundoff-level term to a larger term, and this ended up not + changing the larger term. + + Finally, as an extra precaution, I ran the test suite twice, on + two different implementations of the truncation: the final one + (which uses truncate_small_values), and one in which I did the + truncation using custom, inline code (commit 0d21ccb5). These two + were bit-for-bit with each other, giving me more confidence that I + didn't make a mistake with either implementation. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev059 +Originator(s): sacks (Bill Sacks) +Date: Sat Aug 24 15:14:06 MDT 2019 +One-line Summary: Continue adding water tracers to LakeHydrology + +Purpose of changes +------------------ + +Finish implementing water tracers for initial snow-related code in +LakeHydrology. This involved refactoring code in order to reuse existing +code in SnowHydrology rather than having near-duplicates of that code in +LakeHydrology. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#775 (Implement water tracers for initial + snow-related code in LakeHydrology) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +Many tests took longer, including the PFS test. However, by looking at +more detailed timing numbers in the PFS test, the main increases in time +were in initialization and atm run: lnd run only showed a very small +increase. This suggests that glade slowness was probably primarily +responsible for the increased time. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: Increased allowed wallclock time for a few tests +These tests took longer, likely due to machine variability. Increasing +their wallclock time to prevent them from timing out. + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev058 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Thu Aug 22 10:02:49 MDT 2019 +One-line Summary: Soil texture interpolation bug-fix + +Purpose of changes +------------------ + + When assigning soil texture values from dataset soil levels to model + soil levels, we should be comparing zsoi (NOT zisoi) in the model with + zisoi on the file, i.e. we should be asking whether the node + center (NOT interface) of a given model level falls between two + interface depths on the file. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #772 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: + Unexpected failure of test + SMS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.hobart_nag.clm-tracer_consistency + Bill Sacks did some follow-up testing and concluded that this may be a + compiler-specific issue, so he changed the test from "nag" to "intel" + and generated the new test's corresponding baseline + +Code reviewed by: @billsacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes (clm5) small + + Summarize any changes to answers, i.e., + - what code configurations: not clm45 (clm5_0 and ctsm5_0-nwp) + - what platforms/compilers: all + - nature of change: larger than roundoff/same climate + based on the assumption that shifting soil texture assignments by + one level in model soil levels below the top-most level should not + generate climate-changing differences. + +Detailed list of changes +------------------------ + 1. Changed zisoi to zsoi as described in the Purpose section above. + This caused the larger than roundoff changes. Before the fix some + model soil levels were getting assigned soil textures from a deeper + soil level in the dataset than they should. + 2. In the same section of code I completed the if-block to address all + zsoi vs. zisoifl comparisons. This ensures explicit assignment of + soil textures for all model soil levels and avoids leaving some + model soil levels with the texture assignment of the previous model + soil level. + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull/788) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev057 +Originator(s): sacks (Bill Sacks) +Date: Tue Aug 20 13:17:39 MDT 2019 +One-line Summary: Fix frac_sno bugs + +Purpose of changes +------------------ + +Two bug fixes related to frac_sno, and a third change involving +replacing a frac_sno calculation with a simpler equation that is +algebraically equivalent: + +(1) Fix lake frac_sno always being 0 + (https://github.com/ESCOMP/ctsm/issues/783). This fixes the albedo + calculation (and possibly others) over snow-covered lake surfaces. + +(2) Fix threshold for explicit snow pack initiation to use frac_sno_eff, + not frac_sno (https://github.com/ESCOMP/ctsm/issues/785). For + standard runs (which have use_subgrid_fluxes = .true.), this just + changes answers for urban columns. This also changes answers more + widely for runs with use_subgrid_fluxes = .false. + +(3) Rewrite Swenson & Lawrence 2012 frac_sno equation to be more + straightforward and less sensitive to roundoff errors + (https://github.com/ESCOMP/ctsm/issues/784) + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#783 (frac_sno is always 0 for lake points) +- Resolves ESCOMP/ctsm#785 (Threshold for explicit snow pack initiation + should use frac_sno_eff, not frac_sno) +- Resolves ESCOMP/ctsm#784 (Suggested algebraic rework of frac_sno + calculation) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + + Ran most testing on 95dad328 (before 8f1263a7, which removes a + temporary endrun error check). Just reran + SMS_Ld5_D_P48x1.f10_f10_musgs.IHistClm50Bgc.hobart_nag.clm-decStart + on the final version. + + There was a memleak for this test: + + FAIL SMS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.hobart_nag.clm-tracer_consistency MEMLEAK memleak detected, memory went from 1250.830000 to 1518.500000 in 8 days + + I have had memleak issues for this test before + (https://github.com/ESCOMP/ctsm/issues/763), which I have chalked up + to a compiler-specific issue. I have simply increased the tolerance + for memleaks for this test moving forward. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (small) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff; expected to be same climate in general, + because the only impacts are on urban and lake points, which + represent a small fraction of most grid cells. However, this needs + further investigation. + + See above (under "Purpose of changes") for a description of the + different answer changes in this tag. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + I verified that change (3) is no greater than roundoff by + temporarily putting in an endrun if the new frac_sno differs from + the old by more than 1e-13; this was not triggered for any test in + the aux_clm test suite. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev056 +Originator(s): sacks (Bill Sacks) +Date: Fri Aug 16 11:44:43 MDT 2019 +One-line Summary: Start adding water tracers to LakeHydrology, and related refactoring + +Purpose of changes +------------------ + +Start adding water tracers to LakeHydrology, beginning with some initial +things done for snow. + +This also includes some significant refactoring to allow LakeHydrology +to reuse some of the same snow code used for non-lake columns. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Partially addresses ESCOMP/ctsm#775 (Implement water tracers for + initial snow-related code in LakeHydrology) + +Known bugs found since the previous tag (include github issue ID): +The following will be fixed in an upcoming tag: +- ESCOMP/ctsm#783 (frac_sno is always 0 for lake points) +- ESCOMP/ctsm#784 (Suggested algebraic rework of frac_sno calculation) +- ESCOMP/ctsm#785 (Threshold for explicit snow pack initiation should + use frac_sno_eff, not frac_sno) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + + Note: Did most testing on 054dc95b (before the small change in + 7e4e52a9); just ran + LWISO_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_gnu.clm-coldStart + on the final commit + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (small) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff + + There are two answer-changes here: + + (1) Roundoff-level changes due to changing some order of operations + for the updating of snow_depth and dz for lakes: The previous + code effectively used (qflx_snow_grnd(c)/bifall(c))*dtime, + whereas the new code uses (qflx_snow_grnd(c)*dtime)/bifall(c); + similarly, the dz update differs. + + (2) A change in FSNO_EFF for lakes: previously, this was set to 0 + when there was no snow. Now this is set consistently with other + landunits, for which it is 1 even if there is no snow. Note that + this only affects the FSNO_EFF diagnostic field, and nothing + else. + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + I confirmed that the order-of-operations change is the only + answer-changing part of this tag by comparing against a one-off + from master with the following diffs; this comparison was + bit-for-bit except for changes in the FSNO_EFF diagnostic field: + + diff --git a/src/biogeophys/LakeHydrologyMod.F90 b/src/biogeophys/LakeHydrologyMod.F90 + index 91ddfc79..9711dad7 100644 + --- a/src/biogeophys/LakeHydrologyMod.F90 + +++ b/src/biogeophys/LakeHydrologyMod.F90 + @@ -126,6 +126,8 @@ subroutine LakeHydrology(bounds, & + real(r8) :: heatsum(bounds%begc:bounds%endc) ! used in case above [J/m^2] + real(r8) :: snowmass ! liquid+ice snow mass in a layer [kg/m2] + real(r8) :: snowcap_scl_fct ! temporary factor used to correct for snow capping + + real(r8) :: temp_snow_depth + + real(r8) :: newsnow + real(r8), parameter :: snow_bd = 250._r8 ! assumed snow bulk density (for lakes w/out resolved snow layers) [kg/m^3] + ! Should only be used for frost below. + !----------------------------------------------------------------------- + @@ -246,8 +248,10 @@ subroutine LakeHydrology(bounds, & + ! U.S.Department of Agriculture Forest Service, Project F, + ! Progress Rep. 1, Alta Avalanche Study Center:Snow Layer Densification. + + - dz_snowf = qflx_snow_grnd(c)/bifall(c) + - snow_depth(c) = snow_depth(c) + dz_snowf*dtime + + temp_snow_depth = snow_depth(c) + + newsnow = qflx_snow_grnd(c)*dtime + + snow_depth(c) = snow_depth(c) + newsnow/bifall(c) + + dz_snowf = (snow_depth(c) - temp_snow_depth)/dtime + if (snl(c) == 0) then + h2osno_no_layers(c) = h2osno_no_layers(c) + qflx_snow_grnd(c)*dtime ! snow water equivalent (mm) + else + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev055 +Originator(s): sacks (Bill Sacks) +Date: Tue Aug 6 14:06:50 MDT 2019 +One-line Summary: Modularize snow cover fraction method + +Purpose of changes +------------------ + +This tag moves the calculation of frac_sno - and the related updates of +snow_depth - into a new set of classes, with one class for each +parameterization (Niu & Yang 2007 and Swenson & Lawrence 2012). + +Previously, the code always calculated frac_sno the new way, but then +possibly overwrote it if using the older Niu & Yang method. The new code +cleans this up, only doing the calculations that are needed for each +method. + +In addition, other code that is specific to one of the two methods is +now moved to a home that makes this dependence on method explicit. This +includes the addition of newsnow to int_snow: previously, int_snow was +always updated using an equation specific to the newer CLM5 +parameterization of frac_sno, which was not appropriate if using the Niu +& Yang parameterization; this doesn't make a difference currently, since +int_snow is only referenced if using the Swenson & Lawrence +parameterization, but this clears up some confusion. Also, time-constant +parameters read from namelist or the netCDF parameter file now reside in +the appropriate class rather than being more global. + +This tag also renames two namelist options to increase clarity: +- subgridflag is renamed to use_subgrid_fluxes, and is now a logical +- oldfflag is renamed to snow_cover_fraction_method, and is now a string + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#502 (oldfflag can NOT be used with + subgridflag==1, and rename subgridflag) +- Resolves ESCOMP/ctsm#503 (Clean up CanopyHydrology) + - This tag does the last piece of cleanup called for in that issue +- Resolves ESCOMP/ctsm#571 (Add a system test: turning on water isotopes + shouldn't change answers) + - This is unrelated to the other changes in this tag + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +This tag renames two namelist options to increase clarity: +- subgridflag is renamed to use_subgrid_fluxes, and is now a logical +- oldfflag is renamed to snow_cover_fraction_method, and is now a string + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Added a LWISO test, which confirms that turning on water isotopes + doesn't change answers for bulk +- Added a test with the newer snow cover fraction method but + use_subgrid_fluxes false (testmod no_subgrid_fluxes) + +Code reviewed by: Sean Swenson, Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - ok + + Tests pass; baseline comparisons not done (baseline comparisons + expected to differ) + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + + Additional tests: Compared both of these against ctsm1.0.dev052 (which + should be bit-for-bit with ctsm1.0.dev054): Both were bit-for-bit: + + ERP_D_P36x2_Ld3.f10_f10_musgs.I2000Clm45BgcCrop.cheyenne_gnu.clm-no_subgrid_fluxes + This is a new test, so did not have baselines; I created baselines + from ctsm1.0.dev052 and compared against those + SMS_Ly3.f10_f10_musgs.I2000Clm45BgcCrop.cheyenne_intel.clm-oldhyd_monthly + This was a temporary test for the sake of running a longer test with + the oldhyd testmod. This testmod was created as a one-off by + changing the current oldhyd testmod to inherit from monthly rather + than default. I ran baselines like this from ctsm1.0.dev052 then ran + this test from this branch and compared against those baselines. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/769 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev054 +Originator(s): sacks (Bill Sacks) +Date: Fri Aug 2 07:57:51 MDT 2019 +One-line Summary: Fix interpolation of surfdat soil layers so we can use interpolation for 10SL case + +Purpose of changes +------------------ + +Previously, on master, there was special-purpose code for the 10SL case +that avoided doing interpolation from the surface dataset to the soil +variables in the model. It would be cleaner - especially now that we +allow user-defined soil layer structures - if we could use the general +interpolation code always, rather than sometimes having special-purpose +code that avoids doing the interpolation. + +This tag accomplishes that generality. In order to preserve answers for +clm45 cases, I needed to make three changes: + +1. The constant 0.025 needed an _r8 appended to it; otherwise, zisoifl + could differ by roundoff from zisoi. + +2. I changed which level is used when zisoi(lev) is exactly equal to + zisoifl(j) for some j: I changed the conditional in the following: + + if (zisoi(lev) >= zisoifl(j) .AND. zisoi(lev) < zisoifl(j+1)) then + clay = clay3d(g,j+1) + sand = sand3d(g,j+1) + om_frac = organic3d(g,j+1)/organic_max + endif + + to: + + if (zisoi(lev) > zisoifl(j) .AND. zisoi(lev) <= zisoifl(j+1)) then + + Previously, when the zisoi values in the model exactly lined up with + the zisoi values in the file, we would set clay in model level j + equal to the value from level j+1 from the surface dataset (and + similarly for sand and om_frac); in the new code, we use level j from + the surface dataset for model level j in this case. + +3. I changed the way zisoifl is calculated for the lowest layer, so that + it matches zisoi(nlevsoi) when running with 10SL_3.5m. Previously, we + had: + + zisoi(10) = 0.38018819123227207690E+01 + zisoifl(10) = 0.34330930154359391437E+01 + + This tag changes zisoifl(10) to match zisoi(10). + +Bugs fixed or introduced +------------------------ + +Known bugs found since the previous tag (include github issue ID): +- #772: Interpolation of clay, sand and om_frac can use the wrong layer + (points out more fundamental issues with this interpolation of layers + from the surface dataset) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sam Levis + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO (but see note below) + + In principle, the changes in this tag could change answers for some + soil layer structures, but there were no answer changes for any of + the cases covered by the test suite. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/771 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev053 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Thu Aug 1 16:56:09 MDT 2019 +One-line Summary: Soil layer definition clean-up and user-defined option + +Purpose of changes +------------------ + + Code clean-up clarifes that there are two types of soil layer + definition: the node-based and the thickness-based. + + User-defined option allows user to specify a soil layer profile in the + form of a dzsoi vector (values in meters) in the thickness-based + approach. + + Default nlevsoi for NWP configurations had to change from 5 to 4 for + consistency with the new error check described in known bugs below. + + Other code clean-up removes a couple of sections of repeating code. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #279 #728 + +Known bugs found since the previous tag (include github issue ID): + #759 (this PR) bug causes model to abort when nlevsoi = nlevgrnd; + bug has been corrected with an error check + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[X] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + if neither soil_layerstruct_predefined nor soil_layerstruct_userdefined + get specified in the namelist, then the model sets + soil_layerstruct_predefined to the old default setting for + soil_layerstruct (clm5: 20SL_8.5m, clm4.5: 10SL_3.5m) + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + renamed soil_layerstruct to soil_layerstruct_predefined and added + soil_layerstruct_userdefined + +Changes made to namelist defaults (e.g., changed parameter values): + Default nlevsoi for NWP configurations had to change from 5 to 4 for + consistency with the new error check described in known bugs below + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers +-------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: + 1) New test... + ERP_P36x2_D_Ld5.f10_f10_musgs.I2000Ctsm50NwpBgcCropGswpGs.cheyenne_intel.clm-default + replaces existing test + ERS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-rm_indiv_lunits_and_collapse_to_dom + to check the correction described in known bugs above; the new test + together with existing unit tests cover what the old test was testing + + 2) New test and new test type... + SOILSTRUCTUD_Ld5.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-default + ensures that soil_layerstruct_userdefined gives bfb same answers as + soil_layerstruct_predefined = '4SL_2m' when set with the same dzsoi + values. The new test type was put together by: + - listing the test in (1) testlist_clm.xml (as all tests) and (2) config_tests.xml + - creating the file .../cime_config/SystemTests/soilstructud.py named after the test in lower case + +Code reviewed by: @billsacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (just for NWP configurations) + + Summarize any changes to answers, i.e., + - what code configurations: nwp + - what platforms/compilers: all + - nature of change: larger than roundoff/same climate + This is due to the change of nlevsoi from 5 to 4 (more info above). + I confirmed that nwp does return bfb same answers when I revert this + change. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/759 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev052 +Originator(s): sacks (Bill Sacks) +Date: Mon Jul 22 14:02:43 MDT 2019 +One-line Summary: Fix rare soil color bug in mksurfdata_map + +Purpose of changes +------------------ + +Under rare conditions, mksurfdata_map could put the default soil color +in an output cell where there is actually more information. This tag +fixes that issue. None of the out-of-the-box surface datasets are +impacted by this bug, so I have not recreated any surface datasets. (I +checked all out-of-the-box surface datasets except for +surfdata_0.125x0.125_mp24_simyr2000_c150114.nc, because it doesn't get +remade cleanly out of the box.) + +Also: + +- Add some unit tests for the creation of soil color in mksurfdata_map + +- Point to correct (existing) surface dataset for year-1850 at f05 + resolution + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#4 (Minor bug in creation of soil color in + mksurfdata_map: points can be given the default soil color, when they + should have a real color) +- Resolves ESCOMP/ctsm#765 (Year-1850 f05 surface dataset missing from + inputdata repository) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +- Year-1850 f05 surface dataset now points to a file that actually exists + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - ok + + Most tests pass, including baseline comparisons. The following tests fail, but also failed for me on master: + + 019 smiS4 TSMscript_tools.sh ncl_scripts getregional_datasets.pl getregional ....................\c + rc=6 FAIL + 020 bliS4 TBLscript_tools.sh ncl_scripts getregional_datasets.pl getregional ....................\c + rc=4 FAIL + 027 smf84 TSMscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_clm4_5^buildtools ....................\c + rc=6 FAIL + 028 blf84 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_clm4_5^buildtools ....................\c + rc=4 FAIL + 029 smfc4 TSMscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Cycle_clm4_5^buildtools ..............\c + rc=6 FAIL + 030 blfc4 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Cycle_clm4_5^buildtools ..............\c + rc=4 FAIL + 031 smfg4 TSMscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Global_clm4_5^buildtools .............\c + rc=6 FAIL + 032 blfg4 TBLscript_tools.sh PTCLM PTCLMmkdata PTCLM_USUMB_Global_clm4_5^buildtools .............\c + rc=4 FAIL + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- not run + hobart ------ not run + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev051 +Originator(s): sacks (Bill Sacks) +Date: Fri Jul 19 13:26:25 MDT 2019 +One-line Summary: Update water tracers for remainder of first stage of hydrology + +Purpose of changes +------------------ + +Main change is to do tracer updates for final pieces of first stage of +hydrology: HandleNewSnow and UpdateFracH2oSfc. Along with this, I have +introduced greater modularity into these routines (breaking the +operations down into more granular steps). + +Other changes included here (somewhat related to the main changes) are: + +- Added a routine that resets checked tracers to bulk*ratio to allow + running the tracer consistency check for more than one time step; we + now run it for 10 days + +- Change logic for rain-snow conversion terms: Use rain diff in rain to + snow, snow diff in snow to rain. This is less sensitive to roundoff + errors, and was needed in order to get the 10-day tracer consistency + test to pass. + +- Setting of qflx_snow_h2osfc moved to CanopyInterceptionAndThroughfall + +- Add col%lun_itype. col%lun_itype(ci) is the same as + lun%itype(col%landunit(ci)), but is often a more convenient way to + access this type. I got tired of having to get the landunit index just + for the sake of getting the landunit's type of a given column. I have + NOT gone through the code and replaced lun%itype(l) with + col%lun_itype(c) where applicable, but this will be useful for the + future. + +- Removed unnecessary code for backwards compatibility of FH2OSFC from + restart files + +- Point to slightly modified initial conditions files for two CLm45 + initial conditions files. These two had FH2OSFC > 0 for some glc_mec + points. I'm not sure how that came to be, but Sean Swenson and I think + that shouldn't be the case. This caused soil balance errors in these + tests: + + ERS_Ly5_P72x1.f10_f10_musgs.IHistClm45BgcCrop.cheyenne_intel.clm-cropMonthOutput + SMS_D_Ld1.f09_g17.I1850Clm45BgcCruGs.cheyenne_intel.clm-default + + I'm fixing the problem by pointing to updated files with FH2OSFC set + to 0 for special landunits, using the following python: + + ctypel = dat.variables['cols1d_ityplun'][:] + dat.variables['FH2OSFC'][ctypel > 2] = 0 + +- Small cime update to fix the SHAREDLIBBUILD phase of + ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#718 (Implement water tracers for HandleNewSnow + and FracH2oSfc) +- Resolves ESCOMP/ctsm#498 (Do tracer consistency checks every time + step, not just first) + +CIME Issues fixed (include issue #): +- ESCMI/cime#3717 (Cheyenne ESMF missing for WACCM X) + +Known bugs introduced in this tag (include github issue ID): +- ESCOMP/ctsm#762 (Water tracers: Make sure calls to ResetCheckedTracers + are removed) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- If you have an initial conditions file with non-zero FH2OSFC for + glacier (this was the case for some out-of-the-box clm45 files, which + are now fixed), may run into soil balance errors. To fix this, set + FH2OSFC to 0 in your restart file for all special landunits. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +- Point to slightly modified initial conditions files for two CLm45 + initial conditions files: see above for details. + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Changed tracer consistency test to 10 days rather than a single time step + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, some roundoff-level diffs in baseline + comparisons, as noted below + + Also, in order to have a more powerful test of the changes in + SurfaceWaterMod (since the relevant code isn't triggered very often), + I introduced the following diffs: + + diff --git a/src/biogeophys/SurfaceWaterMod.F90 b/src/biogeophys/SurfaceWaterMod.F90 + index 1bc03cae..be656a15 100644 + --- a/src/biogeophys/SurfaceWaterMod.F90 + +++ b/src/biogeophys/SurfaceWaterMod.F90 + @@ -12,6 +12,7 @@ module SurfaceWaterMod + use shr_spfn_mod , only : erf => shr_spfn_erf + use clm_varcon , only : denh2o, denice, roverg, wimp, tfrz, pc, mu, rpi + use clm_varpar , only : nlevsno, nlevgrnd + + use clm_varctl , only : iulog + use clm_time_manager , only : get_step_size + use column_varcon , only : icol_roof, icol_road_imperv, icol_sunwall, icol_shadewall, icol_road_perv + use decompMod , only : bounds_type + @@ -201,7 +202,7 @@ subroutine BulkDiag_FracH2oSfc(bounds, num_soilc, filter_soilc, & + SHR_ASSERT_FL((ubound(qflx_too_small_h2osfc_to_soil, 1) == bounds%endc), sourcefile, __LINE__) + + ! arbitrary lower limit on h2osfc for safer numerics... + - min_h2osfc=1.e-8_r8 + + min_h2osfc=1.e0_r8 + + do f = 1, num_soilc + c = filter_soilc(f) + @@ -230,6 +231,9 @@ subroutine BulkDiag_FracH2oSfc(bounds, num_soilc, filter_soilc, & + + else + frac_h2osfc(c) = 0._r8 + + if (h2osfc(c) > 0._r8) then + + write(iulog,*) 'WJS: in else' + + end if + qflx_too_small_h2osfc_to_soil(c) = h2osfc(c) / dtime + ! The update of h2osfc is deferred to later, keeping with our standard + ! separation of flux calculations from state updates, and because the state + + With those diffs, I ran the tracer consistency test; it passed. In + addition, I ran + SMS_D_Ld1_P4x1.f10_f10_musgs.I2000Clm50BgcCropQianRsGs.bishorn_gnu.clm-default + with comparison against master, with the following diffs on master + (the first change changes behavior to force the relevant code to be + triggered, and is the same on master and on the branch; the second + change on master divides then multiplies by dtime to avoid + roundoff-level diffs): + + diff --git a/src/biogeophys/SurfaceWaterMod.F90 b/src/biogeophys/SurfaceWaterMod.F90 + index 959d539b..4a4a4824 100644 + --- a/src/biogeophys/SurfaceWaterMod.F90 + +++ b/src/biogeophys/SurfaceWaterMod.F90 + @@ -77,7 +77,7 @@ subroutine FracH2oSfc(bounds, num_nolakec, filter_nolakec, & + ) + + ! arbitrary lower limit on h2osfc for safer numerics... + - min_h2osfc=1.e-8_r8 + + min_h2osfc=1.e0_r8 + + call waterstatebulk_inst%CalculateTotalH2osno(bounds, num_nolakec, filter_nolakec, & + caller = 'FracH2oSfc', & + @@ -112,7 +112,7 @@ subroutine FracH2oSfc(bounds, num_nolakec, filter_nolakec, & + + else + frac_h2osfc(c) = 0._r8 + - h2osoi_liq(c,1) = h2osoi_liq(c,1) + h2osfc(c) + + h2osoi_liq(c,1) = h2osoi_liq(c,1) + (h2osfc(c) / get_step_size()) * get_step_size() + h2osfc(c)=0._r8 + endif + + This test passed and was bit-for-bit with master with the above changes. + + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes (roundoff level) + + Summarize any changes to answers, i.e., + - what code configurations: Many/all + - what platforms/compilers: All + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Roundoff: just roundoff-level changes in FSH_PRECIP_CONVERSION, + FSH_TO_COUPLER, l2x_Fall_sen due to refactored calculation of + FSH_PRECIP_CONVERSION + + If bitwise differences were observed, how did you show they were no worse + than roundoff? via summarize_cprnc_diffs + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: branch_tags/cime5.8.3_chint17-03 -> branch_tags/cime5.8.3_chint17-04 + Fixes ESMCI/cime#3171 + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev050 +Originator(s): slevis (Samuel Levis,SLevisConsulting LLC,303-665-1310) +Date: Mon Jul 15 11:40:09 MDT 2019 +One-line Summary: dz --> dz_lake bug-fix in LakeTemperatureMod.F90 line 960 + +Purpose of changes +------------------ + + Bug-fix to prevent the model from aborting when running with fewer soil + layers than lake layers; not to imply that this was not a bug when the + model wasn't aborting. It was. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #760 + +Known bugs found since the previous tag (include github issue ID): #759 bug causing model to abort when nlevsoi = nlevgrnd + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers +-------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: @dlawrenncar @billsacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes (when methane on) (diagnostic only) + + Summarize any changes to answers, i.e., + - what code configurations: use_lch4 = .true. + - what platforms/compilers: all + - nature of change: diagnostic variable WTGQ only + Confirmed this on cheynne and hobart by running + ./summarize_cprnc_diffs -baseline .../tests_0712... -testid '*' + and inspecting the file cprnc.summary.*.by_varname + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/761 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev049 +Originator(s): erik (Erik Kluzek) +Date: Sun Jun 23 20:56:55 MDT 2019 +One-line Summary: Update mosart and intel to intel-19 on cheyenne + +Purpose of changes +------------------ + +Update mosart to trunk tag (that has a roundoff change to history file +output). And update intel compiler on cheyenne to intel-19. + +Bugs fixed or introduced None +------------------------ + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes (roundoff level change when MOSART on) + + Summarize any changes to answers, i.e., + - what code configurations: some compsets with mosart + - what platforms/compilers: cheyenne/intel + - nature of change: roundoff + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, and mosart + mosart to mosart1_0_33 + cime to branch_tags/cime5.8.3_chint17-03 + +Pull Requests that document the changes (include PR ids): #753 +(https://github.com/ESCOMP/ctsm/pull) + #753 -- Update cheyenne to intel/19 and update mosart + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev048 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Sun Jun 23 15:16:01 MDT 2019 +One-line Summary: Updates for buildlib changes and cime and externals updates + +Purpose of changes +------------------ + +Update of most externals: cime, mosart, rtm, cism. The cime update also includes a required CESM-wide +change in buildlib. Uses a function to get the Macros filename "get_standard_makefile_args". +The cime update brought in some answer chagnes, with an update of the intel compiler (but we backed those +out by using a cime branch). There is also a roundoff change by going to the trunk version of RTM. + +Bugs fixed or introduced None +------------------------ + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: @jedwards, self + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + tools-tests (test/tools): + + cheyenne - PASS + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - PASS + + python testing (see instructions in python/README.md; document testing done): + + cheyenne - PASS (for python3) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes, but only for a few cases (compsets with RTM) + + Summarize any changes to answers, i.e., + - what code configurations: With RTM + - what platforms/compilers: All + - nature of change: roundoff + fieldlist is different for CISM in some cases + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, mosart, rtm, cism + cime to branch_tags/cime5.8.3_chint17-02 + cism to cism2_0_68 + rtm to rtm1_0_68 + mosart to nldas-grid.n02_mosart1_0_31 + +Pull Requests that document the changes (include PR ids): #752 +(https://github.com/ESCOMP/ctsm/pull) + + #752 -- buildlib, cime and externals update + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev047 +Originator(s): sacks (Bill Sacks) +Date: Sun Jun 16 13:04:38 MDT 2019 +One-line Summary: Fix negative snow compaction during snow melt + +Purpose of changes +------------------ + +Fix an issue reported by @kjetilaas: In the presence of surface water, +the old and new snow cover fractions are inconsistently calculated in +subroutine "SnowCompaction". This can result in significant negative +compaction (snow depth increase) during snow melt. + +More details from @kjetilaas (copied from +https://github.com/escomp/ctsm/issues/573): + +There is an inconsistency in the calculation of snow cover fraction +(FSNO) in the SnowCompaction subroutine when there is surface water +present. The actual snow cover is limited to 0.99 when surface water is +present (and the surface water fraction is set to 0.01). However, +SnowCompaction recalculates the old FSNO without accounting for this +limitation. This results in an apparent decrease in FSNO, and +corresponding negative snow compaction from snow melt (ddz3). + +This can result in substantial, artificial increase in snow depth during +summer (can be more than 0.5 m during a single season). + +The problem might be masked in monthly output, but could be significant +whenever snow cover is close to 1 and surface water present. Snow mass +is indirectly affected by this as radiation and temperature fluxes in +the snow pack will be affected by artificially thick snow layers. + +This tag fixes this issue. The fix was implemented and tested by +@swensosc (Sean Swenson). + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#573 (Snow depth increase due to inconsistent snow + cover fraction calculation) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson, @kjetilaas, Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (similar climate) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff/same climate + + Sean Swenson ran the LMWG diagnostics package and looked at the + results with Keith Oleson. Their main findings were: + + - Snow depth is a bit smaller over Greenland and polar regions on + average, as expected (up to 5-10% decrease in average snow depth + averaged over the Canadian Arctic) + + - There is a small increase in h2osno over Greenland: about 30 mm + averaged over Greenland; it looks like the main changes are + around the coasts (which makes sense given that this bug only + affects vegetated landunits) + + - There are small changes in runoff over Greenland + + - Changes in snow cover fraction are tiny + + - Overall, this doesn't look climate changing, but could + potentially have a significant impact on select grid cells, and + on some variables in polar regions + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev046 +Originator(s): sacks (Bill Sacks) +Date: Sat Jun 15 15:54:44 MDT 2019 +One-line Summary: Separate the two uses of h2osno + +Purpose of changes +------------------ + +Until now, h2osno has been used in two ways: + +1. When there are explicit snow layers, h2osno is the sum of snow + (liquid + ice) in all layers + +2. When there is a little bit of snow, but not enough to create a snow + layer, h2osno gives the amount of this very thin snow pack (assumed + to be all ice) + +This is confusing and complicates the addition of water tracers to the +code. This tag separates h2osno into two different variables: + +1. h2osno_no_layers is a fundamental state variable that gives the + amount of snow in the case where we don't have explicit snow layers + +2. h2osno_total is purely a diagnostic variable that is the sum of snow + in all explicit layers, plus h2osno_unresolved. This exists in + waterdiagnosticbulk_type, but the version there is just set once at + the end of the time step, so that version is only meant for + diagnostic (history) output. Code that needs the current sum of + h2osno at a given point now computes it locally, via a new method on + waterstate_type: CalculateTotalH2osno. If running in debug mode, that + routine also performs some consistency checks. + +Also, an unrelated change to prevent user from trying to interpolate a +file onto itself. + +Also, add a compset for testing, which is good for use on my mac. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#733 (Make h2osno purely a diagnostic variable) +- Resolves ESCOMP/ctsm#749 (h2osno inconsistent when interpolating from + initial conditions with different snow layers) +- Resolves ESCOMP/ctsm#750 (Prevent user from trying to use the same + filename for init_interp source and destination files) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none (possibly a small improvement +in timing based on PFS run time) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass; baseline comparisons fail as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes (mostly roundoff) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Mostly roundoff; greater than roundoff/same climate for cases for + which number of snow layers is less in the case than in its + initial conditions file, due to fixing #749 + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + There was one point where h2osno_total differed from the old h2osno + by roundoff, as verified by a run of the test suite (where I verified + that (a) it only differed by 1e-11 or less, and (b) if I reset it, + there were just roundoff-level changes in a few diagnostic + fields). That one place with roundoff-level diffs can lead to + propagation of diffs, causing differences in many fields in the final + run of the test suite. In particular: I ran the test suite on + 69823de4 (which had this temporary check and reset of h2osno_total + vs. old h2osno). For nearly all tests, there were only roundoff-level + changes in a few diagnostic fields. I then removed the temporary + check and reset and ran the test suite on the result + (4353cc90). Finally, I ran the test suite on the final, cleaned-up + code, with comparison against 4353cc90 and verified bfb. + + In my testing on 69823de4: There were a few tests with greater than + roundoff-level changes due just to differences in the initial value + of h2osno_total (which was incorrect in the old due to #749). I + verified that these only had roundoff-level changes in a few + diagnostic fields if I used the following diffs in both the baseline + and my branch, indicating that the diffs just arose due to the fix of + #749: + + diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 + index 793b36ac..f10ee5e1 100644 + --- a/src/main/clm_initializeMod.F90 + +++ b/src/main/clm_initializeMod.F90 + @@ -762,6 +762,18 @@ subroutine initialize2( ) + !$OMP END PARALLEL DO + end if + + do c = bounds_proc%begc, bounds_proc%endc + + if (col%snl(c) < 0) then + + water_inst%waterstatebulk_inst%h2osno_col(c) = 0._r8 + + do j = col%snl(c)+1, 0 + + water_inst%waterstatebulk_inst%h2osno_col(c) = & + + water_inst%waterstatebulk_inst%h2osno_col(c) + & + + water_inst%waterstatebulk_inst%h2osoi_ice_col(c,j) + & + + water_inst%waterstatebulk_inst%h2osoi_liq_col(c,j) + + end do + + end if + + end do + + + end subroutine initialize2 + end module clm_initializeMod + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev045 +Originator(s): sacks (Bill Sacks) +Date: Thu Jun 6 12:26:57 MDT 2019 +One-line Summary: Recalculate h2osno for the sake of SnowCapping + +Purpose of changes +------------------ + +SnowCapping decides whether to remove excess snow based on +h2osno. However, at the point where this is called,h2osno is out of sync +with (h2osoi_liq + h2osoi_ice): Those variables can be changed slightly +in SnowWater (which is called before SnowCapping), yet h2osno isn't +recalculated based on those changes. + +I don't think this causes a big problem in practice, but it seems like +it would improve code understandability if we had the general rule that +any code that references h2osno is using a version of h2osno that is in +sync with (h2osoi_liq + h2osoi_ice). This is also needed to prevent +answer changes in an upcoming major refactor. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#736 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson signed off on the change, but didn't +review the final code + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (should be small) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff/same climate + + Answer changes are expected to be small, since this should just + change the timing of snow capping a bit, but I haven't looked + closely at the magnitude of the answer changes. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev044 +Originator(s): sacks (Bill Sacks) +Date: Thu Jun 6 12:14:39 MDT 2019 +One-line Summary: Make wetland snow resetting behavior more explicit + +Purpose of changes +------------------ + +There is some code that zeroes out h2osno over thawed wetlands. It seems +like the intended behavior here is to zero out the entire snow +pack. Currently, however, this only zeros out a very thin (zero-layer) +snow pack. For now, I'm adding an snl==0 conditional to make this +behavior explicit; long-term, we'd like to change this to actually zero +out the whole snow pack. (At that time, this code block should probably +be moved to a more appropriate home, as noted in comments in issue +ESCOMP/ctsm#735.) + +Also, unrelated change in run_sys_tests: support machine-specific +baseline directory, in order to support new default location for CTSM +baselines on cheyenne. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Partially addresses, but does NOT fix, ESCOMP/ctsm#735 + +Known bugs introduced in this tag (include github issue ID): +- Partially addresses, but does NOT fix, ESCOMP/ctsm#735 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson and Keith Oleson approved this change, +though didn't actually review the final code. + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + python testing (see instructions in python/README.md; document testing done): + + (any machine) - pass on cgdm-bishorn + make python=python2 test + make pyhton=python3 test + make lint + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + + Also ran SMS_Ly1.f09_g17.I2000Clm50SpGs.cheyenne_intel.clm-monthly + with comparison against baselines: passed and bit-for-bit. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO (but see notes below) + + It seems theoretically possible for this to change answers, but no + answer changes were observed in the aux_clm test suite or + SMS_Ly1.f09_g17.I2000Clm50SpGs.cheyenne_intel.clm-monthly. + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev043 +Originator(s): erik (Erik Kluzek) +Date: Wed Jun 5 10:17:06 MDT 2019 +One-line Summary: Fix FUN bug (frac_ideal_C_use was backwards in regard to delta_CN), and replace Ball-Berry mbbopt with the CLM4.5 version + +Purpose of changes +------------------ + +Carbon allocation to uptake responds to CN(uptake-cost) and CN(actual). The intended implementation is: For C:N +less than the target C:N, C allocation is reduced with cost. For C:N greater than the target C:N, C allocation +is increased with high C:N. However, the actual implementation is reversed. This change fixes that problem. + +Also the Ball-Berry mbbopt values had been changed in the creation of CLM5.0, as part of the tuning, but the new +values don't work well (as our final tuning uses Medlyn photosynshesis rather than Ball-Berry). This brings the values +for Ball-Berry for CLM5.0 back to the CLM4.5 values. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #704 #705 + + Fixes #705 -- Ball-Berry parameters in CLM5.0 should go back to the previous values in CLM4.5 + Fixes #704 -- FUN code logic to reduce or increase carbon allocation used for uptake is reversed + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): New clm5.0 paramdata file + +Changes to the datasets (e.g., parameter, surface or initial files): mbbopt now use the clm4_5 values + rather than the pretuned clm5_0 values (before Medlyn was being used) + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: self, olyson + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (134 tests are different from baseline as expected) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! (Important when FUN model on) + + Summarize any changes to answers, i.e., + - what code configurations: Anything with use_FUN=T (so Clm50Bgc compsets) + Also with Clm5.0 and Ball-Berry (stomatalcond_method='Ball-Berry1987') (so Clm50Nwp compsets) + - what platforms/compilers: All + - nature of change: climate is similar + + "Our assessment is that the impact is relatively small, but would affect climate; + however it doesn’t appear to strongly affect transient C response." + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + Experiments were done on the release branch + - casename: oleson/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_1850 + oleson/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_hist + + URL for LMWG diagnostics output used to validate new climate: + +http://webext.cgd.ucar.edu/I1850/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_1850/lnd/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_1850.21_40-clm50_release-clm5.0.15_2deg_GSWP3V1_1850.21_40/setsIndex.html + +We've also completed a historical run. Diagnostics are here: + +http://webext.cgd.ucar.edu/I20TR/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_hist/lnd/clm50_release-clm5.0.15_delta_CN_FUNbug_2deg_GSWP3V1_hist.1995_2014-clm50_release-clm5.0.15_2deg_GSWP3V1_hist.1995_2014/setsIndex.html + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #727 +(https://github.com/ESCOMP/ctsm/pull) + + #727 -- Fix the FUN bug, where an if statement was backwards + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev042 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Tue May 21 23:29:31 MDT 2019 +One-line Summary: Rename, correct, and simplify parameters dewmx and sno_stor_max + +Purpose of changes +------------------ + + To rename + dewmx to liq_canopy_storage_scalar + sno_stor_max to sno_canopy_storage_scalar + in the code and in the clm45 and clm50 param files. + + To change snocanmx, liqcanmx, and fcansno to... + snocanmx = params_inst%snow_canopy_storage_scalar(p) * (elai(p) + esai(p)) + liqcanmx = params_inst%liq_canopy_storage_scalar(p) * (elai(p) + esai(p)) + fcansno(p) = (snocan(p) / (vegt * params_inst%sno_stor_max))**0.15_r8 + + Rewrote fwet(p) to follow the same format as fcansno(p). + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #710 + Fixes #710 -- rename dewmx + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): New default parameter file + +Changes to the datasets (e.g., parameter, surface or initial files): + Pointing to new clm45 and clm50 param files containing the two renamed + parameters listed above. + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: None + +Code reviewed by: + @billsacks + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (196 different because of new param file) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + Roundoff changes were expected. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! (roundoff) + + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change: roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + The code modifications causing the change were of the order-of-calculations + type in two lines of code. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/719 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev041 +Originator(s): sacks (Bill Sacks) +Date: Fri May 17 06:02:38 MDT 2019 +One-line Summary: Add water tracers to CanopyHydrologyMod + +Purpose of changes +------------------ + +Major overhaul of CanopyHydrologyMod in order to support water tracers. + +The part of CanopyHydrology that was actually dealing with canopy +hydrology has now been broken out into a number of small routines in +order to separate flux calculations from state updates. This is needed +in order to calculate tracer versions of the relevant variables, which +is now done here. + +The parts of CanopyHydrology that were NOT dealing with canopy hydrology +have been moved to more appropriate homes. They have not yet been +tracerized, but will be soon. + +This also makes some minor changes to diagnostic fields related to +canopy hydrology. Of particular note: QDRIP now has a different meaning: +it now corresponds to the excess liquid water that runs off from the +canopy (and is inactive by default). + +The design of this broken-out code was developed in consultation with +Mike Barlage, Erik Kluzek, Negin Sobhani, Sean Swenson and Mariana +Vertenstein. We plan to apply this design moving forward to other parts +of the code that need tracerization. See also +. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#360 - Implement water isotopes for + CanopyHydrology +- Resolves ESCOMP/ctsm#709 - QDRIP diagnostic field misleadingly named +- Partially addresses ESCOMP/ctsm#503 - Clean up CanopyHydrology + (We still need to clean up / tracerize the parts that have now been + moved elsewhere.) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Changed meaning of QDRIP diagnostic field: it now corresponds to + qflx_liqcanfall rather than qflx_prec_grnd_patch, and is default + inactive. (There is no longer a diagnostic field corresponding to + qflx_prec_grnd_patch, but there are separate diagnostic fields for the + rain and snow portions of this, both default inactive.) + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none +- checked timing of hydro1 timer vs. previous canhydro timer from my + dev039 testing: differences are negligible + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: +- Design reviewed by Mike Barlage, Erik Kluzek, Negin Sobhani, Sean + Swenson and Mariana Vertenstein +- Final code reviewed only by self + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, baseline comparisons fail as expected + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (roundoff) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + Ensured no-greater-than-roundoff-level by: + + First, generated baselines using code with these diffs (note extra + parentheses in multiplication): + + diff --git a/src/biogeophys/CanopyHydrologyMod.F90 b/src/biogeophys/CanopyHydrologyMod.F90 + index f848f520..31c8c550 100644 + --- a/src/biogeophys/CanopyHydrologyMod.F90 + +++ b/src/biogeophys/CanopyHydrologyMod.F90 + @@ -338,8 +338,8 @@ subroutine CanopyHydrology(bounds, & + ! Intercepted precipitation [mm/s] + qflx_prec_intr(p) = forc_snow(c)*fpisnow + qflx_liq_above_canopy(p)*fpi + ! storage of intercepted snowfall, rain, and dew + - snocan(p) = max(0._r8, snocan(p) + dtime*forc_snow(c)*fpisnow) + - liqcan(p) = max(0._r8, liqcan(p) + dtime*qflx_liq_above_canopy(p)*fpi) + + snocan(p) = max(0._r8, snocan(p) + dtime*(forc_snow(c)*fpisnow)) + + liqcan(p) = max(0._r8, liqcan(p) + dtime*(qflx_liq_above_canopy(p)*fpi)) + + ! Initialize rate of canopy runoff and snow falling off canopy + qflx_snocanfall(p) = 0._r8 + + + Then ran test suite on 1cc9d38a. This is very close to the final + branch, but had a few small tweaks in place to get bit-for-bit: + + 1. Under some conditions, the final branch code resets slightly + negative snocan and liqcan to 0, where master did not. This + commit puts in place temporary code to maintain the slightly + negative values under these conditions, along with a check to + ensure that the values are really always only slightly negative + in this situation. + + 2. When snocan > snocanmx, master reset snocan to exactly snocanmx, + whereas the final branch code can result in snocan being + roundoff-level different from snocanmx, and similar for + liqcan. This commit puts in place temporary code to set snocan + to snocanmx under appropriate circumstances, and liqcan to + liqcanmx, along with a check to ensure that this is only leading + to roundoff-level changes in these state variables. + + 3. Multiplies then divides a flux by dtime in one place + + 4. Has parentheses around a partial sum to ensure same order of + operations as before + + This was bfb with the baselines generated with the diff noted + above, except for roundoff-level changes in SNOCAN in one grid cell + in just one test + (SMS_D_Ld1.f19_g17.I1850Clm45Cn.hobart_gnu.clm-default; old: + -8.15e-322, new: -2e-323). + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +None. But see +https://github.com/billsacks/prototypes-ctsm-canopyhydrology_tracers, +which was the source of our design discussions and contains notes from +these discussions. + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev040 +Originator(s): slevis (Samuel Levis,SLevis Consulting LLC,303-665-1310) +Date: Fri May 03 10:34:46 MDT 2019 +One-line Summary: Move some hard-coded parameters from code to params.nc file + +Purpose of changes +------------------ + + Reduce the number of parameters that get hardwired directly in the code + by placing in the params.nc file where they become visible and easier + to modify. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #680 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users: + None + +Changes to CTSM's user interface: + Parameters that were hardwired in the code can now be seen and changed + in the params.nc file. + +Changes made to namelist defaults (e.g., changed parameter values): + None + +Changes to the datasets (e.g., parameter, surface or initial files): + Various parameters have moved out of the code and into the params.nc file. + +Substantial timing or memory changes: [For timing changes, can check PFS test(s) in the test suite] + +Notes of particular relevance for developers: + None +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + None + +Changes to tests or testing: + None + +Code reviewed by: + @ekluzek + @billsacks + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - + + tools-tests (test/tools): + + cheyenne - + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + Answers change as expected. + +CTSM tag used for the baseline comparisons: + ctsm1.0.dev039 + +Answer changes +-------------- + +Changes answers relative to baseline: YES (single precision roundoff) + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change: single-precision roundoff + Changes are due to four parameters: + accum_factor + ko25_coef + kc25_coef + frac_sat_soil_dsl_init + that were not declared "_r8" when hardwired in the code, + while now they are declared "double" in the params.nc files. I + showed that the change was no greater than single-precision roundoff + by writing the new and old values to the lnd and cesm log files and + confirming differences smaller than 1.e-6. + +Detailed list of changes +------------------------ + + - Updated the clm5 and clm4.5 params.nc files to contain the previously + hard-coded parameters that Katie Dagon recommended moving out of the + code (listed here: https://docs.google.com/spreadsheets/d/1cRmcB0xz7CjVP6ljUoCehJx49Usxsore5ma4mWcvQwM/edit#gid=0) + - Now read the parameters in the modules that use them + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/684 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev039 +Originator(s): sacks (Bill Sacks) +Date: Wed May 1 11:12:34 MDT 2019 +One-line Summary: Remove excess canopy liquid/snow regardless of temperature + +Purpose of changes +------------------ + +Previously: if it was above freezing, snow was allowed to accumulate on +the canopy beyond the specified capacity, and if it was below freezing, +liquid was allowed to accumulate beyond the specified capacity. Sean +Swenson, Keith Oleson and Dave Lawrence agreed that this seems wrong. + +This tag changes the behavior so that both liquid and snow canopy +capacities are enforced regardless of temperature. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#699 (Canopy liquid and snow capacities not + enforced consistently?) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Keith Oleson + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev038 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (small) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff; likely same climate, but this still requires + investigation + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/703 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev038 +Originator(s): sacks (Bill Sacks) +Date: Wed May 1 10:53:02 MDT 2019 +One-line Summary: Support for NWP configuration, NLDAS grid and NLDAS datm forcing + +Purpose of changes +------------------ + +This tag includes a set of changes that, together, provide support for +running an initial Numerical Weather Prediction version of CTSM over the +Continental U.S. + +(1) NWP configuration: The changes in this configuration relative to the + climate (CLM5) configuration mainly target decreasing runtime by + removing features that are expensive and not as important for NWP + time scales (days to months rather than many years) and space scales + (high resolution): + + - Single dominant landunit; if vegetated, single dominant PFT + + - Only 5 soil layers, down to 3 m + + - Only 5 snow layers + + - Plant hydraulic stress off + + - Ball-Berry rather than Medlyn stomatal conductance method (this is + a side-effect of turning plant hydraulic stress off, and is not + itself a critical aspect of the NWP configuration) + + - Maximum of 3 iterations to compute canopy fluxes + + - MEGAN is off + + Note that the NWP compset triggers changes in two new xml variables: + CLM_CONFIGURATION ('clm' vs. 'nwp'; this controls things of a more + scientific nature, like whether plant hydraulic stress is on or + off), and CLM_STRUCTURE ('standard' vs. 'fast'; this controls + structural things like the maximum number of landunits per grid cell + and the soil layer structure). Thus, you can create a case that is a + hybrid between the CLM and NWP configurations by changing these two + xml variables independently. + +(2) NLDAS2 regional grid: 0.125 deg grid over the Continental U.S. + +(3) Updated version of MOSART with support for the same NLDAS2 regional + grid + +(4) NLDAS2 data atmosphere forcing: over the same regional grid; forcing + data are available from 1980 - 2018. (We have excluded 1979 because + a small amount of data were missing for that year, and we didn't + have a good way to handle those missing data.) + +These changes can be used independently or all together. However, note +that you will get garbage if you try to use the new NLDAS2 datm forcing +for a run that extends beyond the boundaries of the NLDAS2 domain. + +There are three new NWP compsets: +- I2000Ctsm50NwpSpGswpGs: GSWP3 datm forcing; meant for global runs or + regional runs outside the NLDAS domain +- I2000Ctsm50NwpSpNldasGs: NLDAS2 datm forcing; meant for regional runs + over the NLDAS domain or some portion of it +- I2000Ctsm50NwpSpNldasRsGs: Same as above, but with a stub runoff model + in place of MOSART, for runs that aren't interested in having a runoff + model and for which you want improved throughput + +The alias for the new grid is: nldas2_rnldas2_mnldas2 (indicating that +we're using the nldas2 grid for land/atmosphere, runoff ('r') and the +ocean mask ('m'). + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#451 (Add NWP physics option) +- Resolves ESCOMP/ctsm#452 (Add an NWP compset) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- The NWP configuration is still a work in progress +- The NLDAS surface data set is still a work in progress (will soon + update this to use high-res PFTs) + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New xml variables: + - CLM_CONFIGURATION (will eventually be renamed to CTSM_CONFIGURATION) + - CLM_STRUCTURE (will eventually be renamed to CTSM_STRUCTURE) +- New namelist variable: + - itmax_canopy_fluxes + +Changes made to namelist defaults (e.g., changed parameter values): +No changes for existing CLM compsets; new defaults for NWP compsets + +Changes to the datasets (e.g., parameter, surface or initial files): +No changes for existing grids; new surface dataset for nldas2 grid + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- New tests covering NWP compsets, nldas grid and nldas datm forcing + +Code reviewed by: Mike Barlage, Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - ok + + tests pass; namelists change as expected + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev037 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- MOSART: release-cesm2.0.00 -> nldas-grid.n01_mosart1_0_31 +- CIME: ctsm/ctsm1.0/cime5.7.9/n04 -> ctsm/ctsm1.0/cime5.7.9/n05 + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/682 +- https://github.com/ESCOMP/ctsm/pull/685 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev037 +Originator(s): sacks (Bill Sacks) +Date: Mon Apr 29 16:11:47 MDT 2019 +One-line Summary: Change year alignment for present-day I compsets + +Purpose of changes +------------------ + +Change year alignment for present-day I compsets (typically, these +compsets have aliases beginning with "I2000"), in order to work better +for cases that are meant to replicate particular years. + +(1) Start the model in year 2000 rather than year 1 + +(2) Change datm's year alignment so that model year 2000 uses +observations from year 2000, model year 2001 uses observations from year +2001, etc. + +(This change was requested by Sean Swenson and supported by Dave +Lawrence.) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Year-2000 compsets now start in model year 2000 rather than 1 + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: cime changes reviewed by Erik Kluzek and others + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, year-2000 cases change answers as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev036 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (small) + + Summarize any changes to answers, i.e., + - what code configurations: Present-day compsets (I2000, I1Pt; also I2010 once those compsets are added) + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + larger than roundoff/same climate + + This changes the year alignment of datm. Climatological averages + should be the same as before, but the alignment of model year to + datm year changes. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: ctsm/ctsm1.0/cime5.7.9/n03 -> ctsm/ctsm1.0/cime5.7.9/n04 + +Pull Requests that document the changes (include PR ids): +- cime changes documented in https://github.com/ESMCI/cime/pull/3093 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev036 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Fri Apr 26 01:20:57 MDT 2019 +One-line Summary: Fix carbon isotope bug that caused wrong answers for isotopes under transient land-use change + +Purpose of changes +------------------ + +We currently have a bug so that for transient land-use change cases answers are different starting in soil +carbon when Carbon isotopes (use_c13, or use_c14) are on versus off. Answers are identical if there is no +land-use change. The bug does cause bulk Carbon (C12) to be slightly different, but qualitatively the same. +There is a significant impact to the Carbon isotope simulation however. The bug was causing changes in isotopic +pools to be directed to the bulk Carbon. Because, isotopes are so much smaller than bulk Carbon, this doesn't +cause a marked difference in the bulk Carbon simulation. But, the lack of the change in the isotopic pool +does have a meaningful impact on the simulation of the Carbon isotopic fields. + +Also added a general test for this and specific one to catch this case. And did some updates on documentation +files, and a small bug fix for run_sys_tests. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #692 #675 #686 + #675 -- Answers differ when carbon isotopes are on under transient cases + #686 -- Add a system test to make sure turning on carbon isotopes doesn't change answers + #692 -- run_sys_test issue + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: Added LCISO test type and a 13 month Hist test to make sure carbon isotopes + don't cause a change to answers + +Code reviewed by: dlawren, billsacks, klindsey, bishtgautum + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + tools-tests (test/tools): + + cheyenne - PASS + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - PASS (compare tests fail, because of namelist updates) + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +CTSM tag used for the baseline comparisons: ctsm1.0.dev035 + + +Answer changes +-------------- + +Changes answers relative to baseline: Only for Carbon isotopes on under transient land-use change! + + Summarize any changes to answers, i.e., + - what code configurations: Bgc with use_c13 or use_c14 T and with a transient land-use change after each year boundary + - what platforms/compilers: All + - nature of change: same climate for bulk Carbon, isotopic Carbon is quite different for regions with land-use change + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime + cime from -- ctsm/ctsm1.0/cime5.7.9/n01 to ctsm/ctsm1.0/cime5.7.9/n03 + cime update allows the new test to work and starts adding NLDAS grid in + +Pull Requests that document the changes (include PR ids): #696 #694 +(https://github.com/ESCOMP/ctsm/pull) + #696 -- run_sys_test small fix + #694 -- Carbon isotope fix + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev035 +Originator(s): sacks (Bill Sacks) +Date: Mon Apr 22 20:17:40 MDT 2019 +One-line Summary: Change h2ocan to a purely diagnostic variable + +Purpose of changes +------------------ + +Previously, h2ocan_patch was maintained through the driver loop as the +sum of liqcan_patch and snocan_patch. However, there were places where +it was updated separately (though consistently) - i.e., it was not +simply a matter of 'h2ocan = liqcan + snocan'. This made the code +more complex, especially for the upcoming addition of water tracers. + +This tag changes h2ocan_patch to be a purely diagnostic variable, set +once at the end of the driver loop. Prognostic equations that used to +use h2ocan now use liqcan and snocan, either directly or indirectly via +a temporary variable set equal to the current value of liqcan+snocan. + +This tag also completely removes support for snowveg_flag = 'OFF' in +order to clean up the code. + +In addition, this tag renames the namelist variable snowveg_flag to +snowveg_affects_radiation (now a logical). + +Finally, this tag includes a minor change to always compute fcansno, +even if snowveg_affects_radiation is false, in order to simplify the +code. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#199 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- snowveg_flag renamed to snowveg_affects_radiation, and changed to a + logical flag + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: +- Answer-changing portion of these changes reviewed by Keith Oleson and + (at least to some extent) Sean Swenson + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev034 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (roundoff) + + Summarize any changes to answers, i.e., + - what code configurations: all + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + roundoff + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + I split these changes into two pieces: (1) an answer-changing piece + where I made minimal changes to replace uses of h2ocan_patch with + liqcan+snocan (via temporary h2ocan variables holding this sum), + and (2) non-answer-changing code cleanup. (1) consisted of the + first two commits on this branch (461cafea and f195c105). With the + changes in (1), I added checks near each change to ensure that the + new expression differed by no more than roundoff from the old + (using an absolute cutoff of 1e-13). I ran the full test suite with + these checks in place, and generated new baselines. I then compared + the changes in (2) with the baselines from (1); this cleanup step + was bit-for-bit except for roundoff-level changes in the + now-diagnostic-only field H2OCAN. + + As noted in ESCOMP/ctsm#689, the changes in (1) were larger than I + expected, presumably because initially roundoff-level differences + can lead to divergent code behavior. The most obvious example of + this is in the check of h2ocan > 0 in subroutine FracWet. I have + found that, due to roundoff errors, it is possible for h2ocan_patch + > 0 by roundoff, while (liqcan_patch + snocan_patch) <= 0 by + roundoff. (Presumably the reverse could also be true, though I + haven't seen that – but I haven't spent much time looking for it.) + + Soon, we plan to do a more rigorous test to double check that this + change is not climate-changing. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- First part of changes in https://github.com/ESCOMP/ctsm/pull/689 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev034 +Originator(s): sacks (Bill Sacks) +Date: Sat Apr 20 06:11:23 MDT 2019 +One-line Summary: Change clm4_5: Use Justin Perket snow on vegetation + +Purpose of changes +------------------ + +This tag changes the behavior of clm4_5, making it now use Justin +Perket's snow on vegetation parameterization. This parameterization was +originally introduced in clm4_5_1_r112. At the time it was only used for +clm5_0 cases. This tag uses that parameterization for clm4_5 cases, too, +so that (like clm5_0) they use snowveg_flag = 'ON_RAD' (i.e., vegetation +snow canopy on with albedo influence). + +This changes climate for clm4_5, mainly through albedo changes, +particularly in the shoulder seasons. + +The reason for this change is to allow an upcoming cleanup of the +relationship between h2ocan, snocan and liqcan. (See +https://github.com/escomp/ctsm/issues/199 for details.) + +This tag also no longer allows snowveg_flag = 'OFF'. However, code +cleanup is deferred to a follow-on tag, in order to separate the answer +changes in this tag from the no-greater-than-roundoff-level changes in +the follow-on tag. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- First step towards addressing ESCOMP/ctsm#199 (Clean up relationship + between h2ocan, snocan and liqcan) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[X] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Changes the scientific configuration of clm4_5 cases, as noted above + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): +- For clm4_5: snowveg_flag = 'ON_RAD' rather than 'OFF' + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Need to clean up code involving snowveg_flag, liqcan, snocan and + h2ocan. I will do this in a follow-on tag. + +Changes to tests or testing: +- Added a test with snowveg_flag = 'ON'. (At least some of the code + paths triggered by this setting were previously covered by clm45 + cases. Now that both clm45 and clm50 use snowveg_flag = 'ON_RAD', + there was some uncovered code. This new test covers this code.) +- Changed long single-point tests to use Qian forcing: With the default + GSWP3 forcing, the vast majority of the runtime was being spent in + datm. In addition, I was getting repeated failures of + ERS_Lm54_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropGs.cheyenne_intel.clm-cropMonthOutput, + I think due to memory issues; I'm hopeful that changing the datm + forcing will help with that. + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass; NLCOMP and BASELINE failures for Clm45 cases, + as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev033 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (clm4_5) Important + + Summarize any changes to answers, i.e., + - what code configurations: Clm45 compsets + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + New climate (as in clm4_5_1_r112 for clm5_0); the main impact is + through albedo changes, particularly in the shoulder seasons. + + Changes in clm4_5 cases are due to: + + (1) Using snowveg_flag = 'ON_RAD' rather than 'OFF' + + (2) Changed initial conditions for canopy water: Rather than using + H2OCAN, which is the meaningful state variable on previous + clm4_5 initial conditions files, now we use LIQCAN and + SNOCAN. These may be 0, although at least some clm4_5 initial + conditions files (including the two non-Fates out-of-the-box + clm4_5 initial conditions files) have non-zero (though still + reasonable) LIQCAN for reasons I can't understand. + + (Also changes answers for + ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline, + which uses a clm45 initial file.) + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev033 +Originator(s): slevis (Samuel Levis, SLevis Consulting LLC, 303-665-1310) +Date: Thu Apr 11 10:51:29 MDT 2019 +One-line Summary: Limit landunit presence with thresholds set in the namelist + +Purpose of changes +------------------ + + Faster simulations. Motivated by NWP applications: + - Introduce user-defined namelist parameters to use as thresholds + above which landunit areas are kept and + below which landunit areas are removed. + - Introduce user-defined logical namelist parameter to collapse the up to + three urban landunits to the dominant urban landunit. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #581 + Fixes #581 -- Allow zeroing out special landunits if their area is below some threshold + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No + +Notes of particular relevance for users +--------------------------------------- + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + - New namelist variables with valid real values from 0._r8 to 100._r8, where + 0 means "do nothing" and other values determine the threshold above + which to keep the landunit in a gridcell. The new variables are: + toosmall_soil + toosmall_crop + toosmall_glacier + toosmall_lake + toosmall_wetland + toosmall_urban + - New logical namelist variable collapse_urban. If .true. then the up to + three urban landunits collapse to the dominant urban landunit. + +--------------------------------------------- +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + There's a typo in the name for n_dom_landunits (missing the s) in bld/CLMBuildNamelist.pm + build-namelist doesn't check for toosmall_* below 0 or above 100, but the code does + +Changes to tests or testing: Yes + New unit tests subroutine test_collapse_individual_lunits and + test_collapse_all_lunit_opts_active in test_surfrdUtils.pf + Modified standard suite test + ERS_D_Ld10.f10_f10_musgs.IHistClm50BgcCropGs.cheyenne_intel.clm-collapse_to_dominant_decStart + to + ERS_D_Ld10.f10_f10_musgs.I2000Clm50BgcCropGs.cheyenne_intel.clm-rm_indiv_lunits_and_collapse_to_dom + and introduced fatal error message when namelist parameters toosmall_* > 0 or + n_dom_* > 0 in transient simulations + +Code reviewed by: Erik Kluzek, Bill Sacks + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (384 differences because of new namelist items) + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + +CTSM tag used for the baseline comparisons: + cheyenne ctsm1.0.dev031 + hobart ctsm1.0.dev032 + + +Answer changes +-------------- + +Changes answers relative to baseline: No + Note: Comparison to baseline gives NLCOMP failures because the new namelist + parameters always appear in the namelist now, even when they have not been + changed from their default value by the user. + +Detailed list of changes +------------------------ + - Introduced call to new subroutine collapse_individual_lunits that uses + the user-defined namelist variables listed above to determine whether + a landunit gets kept or removed from a gridcell. + - Introduced new call to collapse_to_dominant for when collapse_urban = .true. + - Introduced error checks that do not allow coexistence of transient + simulations and the toosmall_* variables OR the n_dom_pfts/n_dom_landunits + variables OR the collapse_urban parameter. + +Pull Requests that document the changes (include PR ids): #641 + https://github.com/ESCOMP/ctsm/pull/641 + #641 -- Ability to remove individual landunits for faster runs + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev032 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Mon Apr 8 08:26:57 MDT 2019 +One-line Summary: Fixing the balance check to check for possible errors over all columns/patches + +Purpose of changes +------------------ +Up until now, the BalanceCheckMod code in biogeophysics did not check all +the possible errors over all columns or patches with the error threshold for +aborting clm and it merely compared the last column/patch found (where +warning threshold is met) with the error threshold. +Therefore, there was always a possibility that the abort is not triggered +when it should have been. This issue was first mentioned in ctsm issue #55 +for soil energy balance check, but a similar issue is also present for +other balance checks in BalanceCheckMod.F90 . + +Below is the list of the balance checks with a similar issue: +1. Water balance check +2. Snow balance check +3. Solar radiation energy balance check +4. Longwave radiation energy balance check +5. Surface energy balance check +6. Soil energy balance check (Issue #55) + +For remediating this issue, we used MAXVAL and MAXLOC Fortran intrinsic functions +to compare the largest error with the warning and error thresholds instead +of checking the last column or looping over all columns. + + +In addition, this PR also makes slight changes to ./run_sys_tests outputi/case +directory structure. Previously for each case in a test suite, there were +two set of directories created by run_sys_tests as follows: + * one directory which included run/ and bld/ and named as $SCRATCH/[case-name].... + * The case directory which included logs , timings, CaseDocs/, and misc. scripts + for ./case.build, ./case.submit... under $SCRATCH/tests-[testID]/[case-name].... + +This made debugging confusing and populated many folders in user's scratch. +Now, for every case in a test, all directories related to that case +including bld/ and run/ directories are nested under the case directory under $SCRATCH/tests-[testID]/[case-name].... +This is now similar to ./create_test output folder structure. + + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm issue#55 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: + - ./run_sys_test is changed so that it nests bld/ and run/ directories under the case directory as $SCRATCH/tests-[testID]/[case-name]... + The output folder structure now is similar to ./create_test for each case in a test. + +Code reviewed by: Bill Sacks + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + +CTSM tag used for the baseline comparisons: ctsm1.0.dev031 + + +Answer changes +-------------- + +Changes answers relative to baseline: No + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/670 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev031 +Originator(s): sacks (Bill Sacks) +Date: Wed Mar 13 15:03:42 MDT 2019 +One-line Summary: Subtract virtual states to reduce dynbal fluxes for transient glaciers + +Purpose of changes +------------------ + +Up until now, when computing the dynbal correction (conservation) fluxes +for transient glacier columns, we have been (1) counting the mass and +energy in the ice column as if that is a real state, but on the other +hand (2) NOT accounting for the fact that glacier columns don't +represent the soil under glacier. These two issues work in opposite +directions, but (1) dominates, because there is much more ice (and +energy, I think) in the roughly 50 m of glacial ice than there is in a +typical 50 m soil column. + +In discussing this issue with Bill Lipscomb, we came up with the idea of +subtracting some baseline value from each glacier column. I think that, +as long as we subtract the same baseline value throughout an entire +simulation for a given column, we will still conserve mass and energy +through dynamic landunit transitions. + +So, here we subtract baseline values from glacier columns, accounting +for the two issues mentioned above: (1) we subtract the water and energy +in the glacier ice, because this is a virtual state in CTSM, and (2) we +add the water and energy from the vegetated column(s), to account for +the fact that we don't have an explicit representation of +soil-under-glacier (this carries the assumption that the +soil-under-glacier has the same state as the initial vegetated state in +that grid cell). We set these baselines in initialization, so they begin +equal to the cold start state. Water and ice in the glacial ice stay +fixed over the course of a simulation, so the cold start values should +be the same as the current values at any point in time. The heat content +of the glacial ice does change over time, but by subtracting this +baseline value, we can potentially reduce the dynbal sensible heat +fluxes (however, note that it's also possible that these sensible heat +fluxes could increase when subtracting the cold start value, if ice +temperatures are closer to 0 deg C than to the cold start value, +currently 250 K). + +In addition, this introduces a new namelist flag, +reset_dynbal_baselines, which allows the user to reset these baselines +at some desired point in the simulation. I think that, in general, this +resetting would break conservation. But as long as it is done before the +onset of transient glaciers, I think this should be okay. In this way, +the user can minimize dynbal fluxes even further, by resetting the +baselines after the system has spun up. If the states haven't changed +much from this point to the point when glacier dynamics occur, then the +dynbal fluxes should now be very small. (See the documentation of this +flag in namelist_definition_ctsm.xml for more details.) + +Without this change, dynbal fluxes for a grid cell that undergoes 100% +glaciation / deglaciation in a single year are around 50 m ice, 1 m +liquid water, and a few tens of W m-2 (where those quantities of ice and +water are dribbled throughout the year, so we end up with an ice flux of +about 1.5e-6 mm/s throughout the year; and the energy flux is applied +evenly throughout the year - i.e., tens of W m-2 every time step for a +year). With this change, and with reset_dynbal_baselines set at an +appropriate time, these fluxes can be reduced to close to zero. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Partially addresses ESCOMP/ctsm#274 (Dynamic landunits: improve water + and energy conservation) + +CIME Issues fixed (include issue #): +- Fixes three issues related to inputdata checksum: + - ESCMI/cime#3033 + - ESCMI/cime#3034 + - ESCMI/cime#3036 + +Known bugs introduced in this tag (include github issue ID): +- ESCOMP/ctsm#659 (Subtract dynbal baselines from begwb and endwb) + - This can't be fixed until we're okay having this answer change on + master + +Known bugs found since the previous tag (include github issue ID): +- ESCOMP/ctsm#658 (Methane should not depend on gridcell-level TWS) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] clm4_5 + +Significant answer changes for runs with transient glaciers. + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- For runs with transient glaciers, careful thought should be given to + when to set reset_dynbal_baselines +- Inconsistency between begwb/endwb and liq1/liq2/ice1/ice2 (see ESCOMP/ctsm#659) + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New namelist variable: reset_dynbal_baselines + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Inconsistency between begwb/endwb and liq1/liq2/ice1/ice2 (see ESCOMP/ctsm#659) + +Changes to tests or testing: +- Tweaked a test with transient glacier areas, including adding this new + flag to the test + +Code reviewed by: Bill Lipscomb reviewed the conceptual ideas, but +nobody has reviewed the actual code + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev030 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (Important) + + Summarize any changes to answers, i.e., + - what code configurations: ALL, but different configurations show + different levels of changes, as noted below + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + - new climate (at least regionally) for some configurations; + roundoff for others: see below + + There are three levels of changes here: + + (1) For runs with transient glaciers, there are large answer changes + in regions with changing glacier area. These answer changes are + in the various dynbal fluxes - for liquid water and ice runoff, + and for the dynbal sensible heat flux. + + (2) For runs with transient vegetation (Hist, Dv and Fates), there + are roundoff-level changes in the dynbal fluxes. For liquid + water and ice, these changes appear to only occur in grid cells + where there is some glacier area (because now both the before + and after gridcell water contents have changed by the same fixed + amount, which changes the difference at the roundoff level). For + heat, there are roundoff-level changes everywhere (because of + changes in the order of operations). + + (3) All runs have large changes in the diagnostic variables, + ICE_CONTENT1, LIQUID_CONTENT1 and HEAT_CONTENT1, over grid cells + containing some glacier area. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.7.9 -> ctsm/ctsm1.0/cime5.7.9/n01 + - Fixes issues related to inputdata checksum + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/650 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev030 +Originator(s): sacks (Bill Sacks) +Date: Fri Mar 8 15:08:34 MST 2019 +One-line Summary: Update CIME; hookup expected test fails + +Purpose of changes +------------------ + +Two main changes: + +(1) Update to latest cime (from ctsm/ctsm1.0/cime5.7.5/n01 to + cime5.7.9). Some of the important changes are: + - Fix for recent cheyenne system changes + - New domain file for f19_g17 (changes answers at the roundoff + level) + - New domain file for T31_g37 (changes answers by greater than + roundoff) + +(2) In system tests: Annotate cs.status output with expected failures + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes ESCOMP/ctsm#654 + +CIME Issues fixed (include issue #): (Many) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none? + The PFS test showed a significant speedup (170s in the previous tag, + 124s in this tag). However, some other tests showed either a slowdown + or not much change. So I'm not sure there is a consistent pattern of + speedup in this tag. + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, some baselines failed as noted below + + Most testing done with cime at eb2eb704f - excluded PR #3030, which + updated support for CAM-SE grids (but the changes in this PR were + very limited). Ran SSP tests with the final version of cime (so I'd + have a few tests covering the latest cime). + +CTSM tag used for the baseline comparisons: ctsm1.0.dev029 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (f19_g17, T31_g37 small) + + Summarize any changes to answers, i.e., + - what code configurations: f19_g17, T31_g37 + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + - f19_g17: roundoff-level, presumably due to new domain file (some + diffs grew to greater than roundoff-level: some methane + variables in a long test - + SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput; + and many variables in test with flooding - + ERP_P180x2_D.f19_g17.I2000Clm50SpRtmFl.cheyenne_intel.clm-default) + + - T31_g37: greater than roundoff-level, presumably due to new + domain file from cime commit 4fcf592ee + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: ctsm/ctsm1.0/cime5.7.5/n01 -> cime5.7.9 + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/602 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev029 +Originator(s): slevis (Samuel Levis, SLevis Consulting LLC, 303-665-1310) +Date: Tue Feb 26 23:42:39 MST 2019 +One-line Summary: Collapse landunits to the N most dominant + +Purpose of changes +------------------ + + Allows the collapse to fewer landunits using the concept of + N most dominant for the purpose of faster runs, eg in the context + of NWP (Numerical Weather Prediction). + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #581 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New namelist variable n_dom_landunits with valid integer values from 0 to + max_lunit currently equal to 9, where 0 means “do nothing†and other + values determine the number of active landunits when running the model. + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + There is a question left in on whether the collapse call needs to also + be moved to inside dynamic landunits reading. + +Changes to tests or testing: Yes + ERS_D_Ld10.f10_f10_musgs.IHistClm50BgcCropGs.cheyenne_intel.clm-collapse_to_dominant_decStart + now replaces (by combining with) this test introduced in ctsm1.0.dev026 + ERS_D_Ld10.f10_f10_musgs.IHistClm50BgcCropGs.cheyenne_intel.clm-collapse_nat_pfts_decStart + I added subroutine test_collapse_to_dom_landunits to test_surfrdUtils.pf + to include new Unit Tests. In same file I renamed + subroutine test_collapse_nat_pfts to test_collapse_to_dom_pfts + to accurately describe the contents of the subroutine. + +Code reviewed by: Erik Kluzek + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +CTSM tag used for the baseline comparisons: + ctsm1.0.dev028 + + +Answer changes +-------------- + +Changes answers relative to baseline: No + +Detailed list of changes +------------------------ + + Replaced existing subroutine collapse_nat_pfts with + subroutine collapse_to_dominant which can collapse to the + N dominant landunits or N dominant pfts by performing the + same actions on the data. + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #639 + https://github.com/ESCOMP/ctsm/pull/639 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev028 +Originator(s): sacks (Bill Sacks) +Date: Tue Feb 26 14:35:01 MST 2019 +One-line Summary: Interpolate out-of-the-box initial conditions and remove expensive tests + +Purpose of changes +------------------ + +Two main changes (plus some small additional changes): + +1. Removed / reworked some expensive tests + +2. Interpolated all out-of-the-box initial conditions, so that the + out-of-the-box version is now compatible with our current + configuration. The changes from before were (a) our standard + configuration now uses the gx1v7 rather than gx1v6 land mask; (b) + many inactive points are now absent in memory. + +See https://github.com/ESCOMP/ctsm/pull/622 for details. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#312 +- Partially addresses ESCOMP/ctsm#275 (just a bit) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): +- New finidat files + +Substantial timing or memory changes: +- Faster initialization times for cases that no longer need to interpolate initial conditions + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Removed or reworked expensive tests: see details in https://github.com/ESCOMP/ctsm/pull/622 + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok: tests pass, baselines fail as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev027 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (just for initial conditions) + + Summarize any changes to answers, i.e., + - what code configurations: all configurations that still need use_init_interp = .true. + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Not investigated carefully, but expected to be larger than roundoff/same climate + + Answers change for cases that still need to do interpolation from + these out-of-the-box finidat files. + + I first confirmed that the new finidat files are good via: + + - Compared `ncdump -h` of old vs. new initial conditions files + + - Ran the following tests, with comparison against master; verified that + these all pass and are bit-for-bit, that they use the new initial + conditions files, and that they now have `use_init_interp` unset + (whereas they used to have `use_init_interp` set to `.true.`); note + that these cover 6 of the 7 new initial conditions files: + + ``` + SMS_Ld1.f09_g17.I1850Clm45BgcGs.cheyenne_intel.clm-default + SMS_Ld1.f09_g17.I1850Clm45BgcCruGs.cheyenne_intel.clm-default + SMS_Ld1.f09_g17.I1850Clm50Sp.cheyenne_intel.clm-default + SMS_Ld1.f09_g17.I1850Clm50BgcCrop.cheyenne_intel.clm-ciso + SMS_Ld1.f09_g17.I1850Clm50BgcCropCru.cheyenne_intel.clm-ciso + SMS_Ld1.f09_g17.I1850Clm50SpCru.cheyenne_intel.clm-default + ``` + + - To cover the last new initial conditions file, ran the following test + (with the same checks as above: passes and bit-for-bit, checked + finidat, and checked `use_init_interp`), with `./xmlchange + LND_TUNING_MODE=clm5_0_cam6.0` (for the baseline for this test, I set + `init_interp_method = 'use_finidat_areas'`, which I also used in + interpolating this initial conditions file): + + ``` + SMS_Ld1.f09_g17.I1850Clm50BgcCrop.cheyenne_intel + ``` + + Details on answer changes: + + As noted above, these changes are bit-for-bit for configurations + that can now use the out-of-the-box initial conditions without + interpolation. However, answers change for configurations that still + require interpolation of the out-of-the-box initial conditions + (e.g., because they are at a different resolution than the finidat + file). + + I expected these answer changes around the Caspian Sea, due to the + fact that we are now effectively interpolating twice from the + original file: once to produce the new out-of-the-box file (which + includes an interpolation from `gx1v6` to `gx1v7`, and so + interpolates onto the Caspian Sea region) and once to go from + `f09_g17` to the target resolution (rather than interpolating + directly from `f09_g16` to the target resolution). + + However, when I ran a test with comparison to baselines - + `ERP_Ld5.f19_g17.I1850Clm50Bgc.cheyenne_intel.clm-default` - I saw + changes in regions further afield than simply around the Caspian + Sea. See images in https://github.com/ESCOMP/ctsm/pull/622 for + details. It's possible that the other differences are also due to + the Caspian Sea change, but it's also possible that there is some + other cause here that I don't understand. But Erik Kluzek and I + agreed that it isn't worth trying to understand these other + (isolated) differences. + + Also note: While most f09_g17 tests are bit-for-bit with the earlier + tag (because now use_init_interp is .false. for those tests), + `SMS_Ld2_D.f09_g17.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic_interp` + differs in some glc forcing fields for a few grid cells in + Antarctica. This is perhaps not surprising, since this test needs to + use interpolation to get fields for the Antarctica virtual columns; + so, while I don't completely understand the cause of these answer + changes, I suspect the root cause is similar to the isolated answer + changes I saw sprinkled around the world for + `ERP_Ld5.f19_g17.I1850Clm50Bgc.cheyenne_intel.clm-default`. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/622 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev027 +Originator(s): negins (Negin Sobhani,UCAR/CSEG,303-497-1224) +Date: Tue Feb 19 12:57:12 MST 2019 +One-line Summary: Non-constant time initialization for soil hydrology types are moved to SoilHydrologyType.F90. + +Purpose of changes +------------------ + +Initalization of time-varying `zwt`, `zwt_perched`, and `frost_table` are moved to `InitCold` in `SoilHydrologyType.F90`. + +Previously, `zwt`, `zwt_perched`, and `frost_table` were initialized in `SoilHydrologyInitTimeConstMod.F90`, which caused confusions. + +Bugs fixed or introduced +------------------------ +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#575 ("Some variables initialized in SoilHydrologyInitTimeConstMod are not time-constant") + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: Updated a test. The test added in previous tag included decStart with transient glaciers, which would not work. Hence, this test is modified so the compset does not include G. +Test IHistClm50SpG is updated to IHistClm50Sp. + +Code reviewed by: +Bill Sacks +Erik Kluzek + +CTSM testing: + + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, except for the expected failures. + +CTSM tag used for the baseline comparisons: +ctsm1.0.dev026 + +Answer changes +------------- + +Changes answers relative to baseline: no + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): +PR #631 Soil hydrology initialization of time-constant variables moved to SoilHydrologyType +https://github.com/ESCOMP/ctsm/pull/631 + + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev026 +Originator(s): slevis (Samuel Levis, SLevis Consulting LLC, 303-665-1310) +Date: Tue Feb 5 17:08:48 MST 2019 +One-line Summary: Collapse unmanaged PFTs to the N most dominant + +Purpose of changes +------------------ + +To run simulations fast for applications such as NWP (Numerical Weather +Prediction), allow collapsing natural PFT's to the number the user wants. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): 457 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +New namelist parameter n_dom_pfts with valid integer values from 0 to +14, where 0 means “do nothing†and other values determine the number +of active pfts when running the model + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None (unless new option invoked) + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: updated tests, added new test +Updated standard testing test to include decStart +(December start). Confirmed that answers were bit-for-bit same with +baseline before introducing the change. +Added standard testing test to test n_dom_pfts = 2 in a +transient vegetation case with December start. +Added subroutine test_collapse_nat_pfts to test_surfrdUtils.pf to +include new Unit Tests. + +Code reviewed by: +Erik Kluzek +Bill Sacks + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne ---- OK + hobart ------ OK + +CTSM tag used for the baseline comparisons: +ctsm1.0.dev025 + +Answer changes +-------------- + +Changes answers relative to baseline: No (bit-for-bit) + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/588 -- NWP collapse pfts to the N most dominant +https://github.com/ESCOMP/ctsm/pull/583 -- Add routine to find indices of max k values in data + +Added new subroutines collapse_nat_pfts and collapse_crop_var and called +them from surfrdMod.F90. The second of these subroutines is not needed +when collapsing unmanaged PFTs; however, I created it early in the PR +and decided to keep it for use soon with crop-related variables like +irrigation water and fertilizer. + +Bill Sacks made changes to include subroutine find_k_max_indices for the +benefit of this PR (#583) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev025 +Originator(s): Keith Oleson, Bill Sacks +Date: Wed Jan 23 10:48:01 MST 2019 +One-line Summary: History fields for vertically-resolved sums of soil C and N, and minor fixes + +Purpose of changes +------------------ + +Main change is from Keith Oleson: Add history fields for +vertically-resolved sums of SOIL1C, SOIL2C, and SOIL3C for C12, C13, +C14, and similarly for N. New fields are SOILC_vr, C13_SOILC_vr, and +C14_SOILC_vr, and SOILN_vr. For runs that use the output_bgc usermods, +including cmip6 runs, we no longer output 'SOIL1C_vr', 'SOIL1N_vr', +'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr'; instead we output +'SOILC_vr', 'SOILN_vr', and similarly for C isotopes. + +Also minor fixes: +- Output cpl hist files in SSP test (resolves ESCOMP/ctsm#61) +- Remove FATES-related commented-out code in OzoneMod (this has been + moved to https://github.com/ESCOMP/ctsm/issues/618) +- Minor tweak to run_sys_tests + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#61 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): +- For runs that use the output_bgc usermods, including cmip6 runs, we no + longer output 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', + 'SOIL3C_vr', 'SOIL3N_vr'; instead we output 'SOILC_vr', 'SOILN_vr', + and similarly for C isotopes. + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Bill Sacks; Erik Kluzek reviewed the changes to the SSP test + + +CTSM testing: + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev024 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/551 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev024 +Originator(s): slevis (Samuel Levis,SLevis Consulting, LLC, 303-665-1310) +Date: Mon Jan 14 11:07:04 MST 2019 +One-line Summary: Remove unnecessary restart variables + +Purpose of changes +------------------ + +Remove unnecessary restart variables to conserve on computing resources +and disk space + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): 285 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + +Changes made to namelist defaults (e.g., changed parameter values): + +Changes to the datasets (e.g., parameter, surface or initial files): + +Substantial timing or memory changes: + +Notes of particular relevance for developers: +Code reviewed by Bill Sacks. +Standard testing (cheyenne and hobart) OK +Unit testing PASS +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: + +Code reviewed by: Bill Sacks + +CTSM testing: +Regular testing (cheyenne and hobart) OK +Unit testing PASS + +CTSM tag used for the baseline comparisons: +ctsm1.0.dev023 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO (bfb) + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/598 + +Variables removed from restart: +plant_nalloc +pot_f_nit_vr* +f_nit_vr* +root_depth +qflx_floodg +snounload +qflx_snofrz_lyr +sminn_to_plant_fun_patch + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev023 +Originator(s): sacks (Bill Sacks) +Date: Thu Jan 10 13:00:42 MST 2019 +One-line Summary: Remove CLM4.0 + +Purpose of changes +------------------ + +Remove CLM4.0. This consists of removing code and other files that are +specific to CLM4.0, and doing some resulting cleanup of code that was +shared between CLM4.0 and later versions (primarily in build-namelist). + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves #455 (Remove CLM4.0) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Can no longer run CLM4.0 cases + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- CLM4.0 compsets no longer supported + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: Removed CLM4.0 tests + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + build-namelist tests: + + cheyenne - pass + + tools-tests (test/tools): + + cheyenne - pass + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - ok + + Total number of tests = 52 + Number of tests that PASS = 51 + Number of tests that Fail = 1 + Number of compare tests that PASS = 37 + Number of compare tests that Fail = 4 + Number of tests without compare = 11 + + The one failing test is: + FAIL fail-no_towerdata.-d+/glade/p/cesmdata/cseg/inputdata++-s+RF-Bra+--debug+--pftgrid+--soilgrid. + + These same failures occurred in ctsm1.0.dev022 (including the + compare tests that Fail). Erik Kluzek says these failures are + okay. + + regular tests (aux_clm): + + cheyenne ---- pass + hobart ------ pass + + Notes on testing: + + - Most testing done on b5380c7e8. Since then, updated to a version of + cime that fixes cime's configure tool (but this isn't invoked in + system tests, so I didn't rerun the system tests) and pointed cime + to a tag rather than a hash. + + - For tools tests: In baseline, cherry-picked commit 148bc2158 into + cime + +CTSM tag used for the baseline comparisons: ctsm1.0.dev022 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: points to branch tag off of cime5.7.5 + (ctsm/ctsm1.0/cime5.7.5/n01), with changes for: + (1) Removal of support for CLM4.0 (equivalent to the changes in + https://github.com/ESMCI/cime/pull/2968) + + (2) Fix for cime configure (cherry-picked 148bc2158) + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/609 (Remove CLM4.0) +- https://github.com/ESCOMP/ctsm/pull/601 (Print git status and related + info when running run_sys_tests) + + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev022 +Originator(s): sacks (Bill Sacks) +Date: Tue Jan 8 11:01:38 MST 2019 +One-line Summary: Set tracer version of irrigation fluxes + +Purpose of changes +------------------ + +Set tracer version of irrigation fluxes. + +This required a substantial rewrite of ApplyIrrigation (now renamed to +CalcIrrigationFluxes). The problem was that the code was written to +compute the total irrigation withdrawal from groundwater, then use this +to compute the application fluxes (drip/sprinkler), then later divide +this total withdrawal by layer. But for tracer fluxes to be computed +correctly, we needed to reorder this, so that the per-layer withdrawals +are determined before determining the application fluxes. This is +because the application flux needs to know the tracer concentrations of +the source, which requires knowing which layers the source is drawing +from. This was made more challenging because of the mix of patch-level +and column-level variables at play: irrigation demand is patch-level, +groundwater availability and extraction is column-level, but application +is back to patch-level. + +In a somewhat-related change, I also reworked the passing of information +between soil hydrology (groundwater availability) and irrigation: +Previously, there was some near-duplicate code in +CalcAvailableUnconfinedAquifer (which was called prior to +ApplyIrrigation) and WithdrawGroundwaterIrrigation (which was called +after ApplyIrrigation). I have reworked the code to remove this +duplication, calling the new CalcIrrigWithdrawals in the midst of +CalcIrrigationFluxes. In doing so, I reconciled an accidental +discrepancy between the two original routines (see +https://github.com/escomp/ctsm/issues/595). + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#521 (Set tracer versions of fluxes set by + ApplyIrrigation) +- Resolves ESCOMP/ctsm#593 (Generalize groundwater irrigation availability to + handle multiple patches per column) +- Resolves ESCOMP/ctsm#595 (Inconsistency between CalcAvailableUnconfinedAquifer + and WithdrawGroundwaterIrrigation) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: + +- Sean Swenson reviewed the initial parts of the rework of + ApplyIrrigation and the passing of information between soil hydrology + and irrigation + +CTSM testing: + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, expected baseline failures as noted below + + Additional manual testing: + + - Out of the box, the one-timestep tracer consistency test + (SMS_D_Ln1.f10_f10_musgs.I2000Clm50BgcCropGs.hobart_nag.clm-tracer_consistency) + passed when the new check was inserted after the irrigation call, + even without the changes in this tag. Presumably this is because no + irrigation was being done in the first time step of this test. To + confirm that the changes here were both necessary and effective, I + hacked the code to force irrigation of all types (surface and + groundwater) on the first time step (see + https://github.com/billsacks/ctsm/commit/d28a03145). I confirmed + that this test, with those code hacks, failed before the changes in + this tag, and passed with these changes in place. + + - I used a multi-step process to confirm that these changes are only + roundoff-level different for groundwater irrigation (because + feedbacks in the system result in + SMS_D_Ld5.f10_f10_musgs.I2000Clm50BgcCrop.hobart_nag.clm-irrig_alternate + looking greater-than-roundoff-level different from the baseline): + + (1) Confirmed that e507fe603 is only roundoff-level different from + baseline using cprnc output from this test. + + (2) Confirmed that a4a1a626c is only roundoff-level different from + e507fe603. This was the tricky part. I did this by introducing + some temporary code that (a) computed some fluxes in both the + old and new ways, (b) compared the old and new methods for each + point and time step, confirming that they were no more than + roundoff-level different, then (c) set the fluxes to the old + method. I confirmed that this was bit-for-bit with e507fe603, + and the checks for greater-than-roundoff-level differences + between the old and new methods were never triggered. (See + https://github.com/billsacks/ctsm/commit/7d23e9e and the earlier + commits on that branch.) + + (3) Confirmed that remaining changes an the branch are bit-for-bit + with a4a1a626c. + +CTSM tag used for the baseline comparisons: ctsm1.0.dev021 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (small) + + Summarize any changes to answers, i.e., + - what code configurations: + + - Small answer changes when groundwater irrigation is enabled. In + principle, could change answers by greater than roundoff due to + fix of #595, but I didn't see any answer changes in my 7-month + test due to that change. Other than that, just roundoff-level + changes. + + - Answer changes when tracers are enabled. + + - Roundoff-level changes in the diagnostic field, + QIRRIG_FROM_SURFACE, for many tests + + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + See notes under "what code configurations" for details. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/600 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev021 +Originator(s): mvr (Mathew Rothstein,UCAR/CSEG,303-497-1304) +Date: Wed Dec 26 16:29:06 MST 2018 +One-line Summary: Added tracer ratio capability and included it in consistency checks + +Purpose of changes +------------------ + +These changes are needed to support the implementation of water isotopes by ensuring +that isotope-related variables are being updated consistently throughout the model. +The consistency checks include the testing of a bulk tracer that should always be +equal to the bulk, and also test tracers that maintain a fixed ratio (other than +one) to the bulk. This commit includes fixes to the cold start initialization for +the water tracers with ratios other than one. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): [If none, remove this line] +#541 Only do water tracer consistency checks on tracers that are + supposed to maintain a fixed ratio +#459 Fix cold start initialization of water tracers +#508 Remove unused variables in new Water types +#357 Put in place Water isotope consistency checks + + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: added unit tests + +Code reviewed by: bill sacks + + +CTSM testing: + + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- PASS + hobart ------ PASS + +CTSM tag used for the baseline comparisons: ctsm1.0.dev020 + + +Answer changes +-------------- + +Changes answers relative to baseline: no, b4b + + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): #599 Adding isotope + tracer ratios +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev020 +Originator(s): Sean Swenson, Bill Sacks +Date: Mon Dec 3 11:51:24 MST 2018 +One-line Summary: New options for irrigation and crop fsat + +Purpose of changes +------------------ + +Introduce three new options: + +(1) Ability to withdraw irrigation water from groundwater if not enough + water is available from rivers. This is controlled via new namelist + flag, use_groundwater_irrigation. Water can be withdrawn from both + the unconfined (from the soil column) and confined (from wa) + aquifers. + +(2) Irrigation method: sprinkler (above canopy) vs. drip (below + canopy). This can be set on a per-crop and per-gridcell basis on the + surface dataset, but out-of-the-box support for creating the + necessary surface dataset field is not yet in place (see + ESCOMP/ctsm#565). For now, it can be controlled globally via a new + namelist flag, irrig_method_default. The default is drip, which was + what we were previously using implicitly. + +(3) Set crop fsat to zero. This is controlled by a new namelist option, + crop_fsat_equals_zero. + +Default behavior is the same as before for all three options. + +Also: + +- If use_aquifer_layer is false (which is the default for CLM50), no + longer reset wa_col every time step + +- Adds indices to vector history files giving column, landunit and + gridcell indices for each patch, etc. (Resolves ESCOMP/ctsm#81: + "Restart files are different for CLM when run over different number of + tasks" (issue name is a misnomer of the remaining to-dos in that + issue.) + +- Writes 3d time-constant fields on first history file for all tapes, + not just the first + +- Small performance improvements to irrigation + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Resolves ESCOMP/ctsm#81 ("Restart files are different for CLM when run + over different number of tasks", but that name was a misnomer for the + remaining work needed on the issue) + +Known bugs introduced in this tag (include github issue ID): +- ESCOMP/ctsm#565: Surface dataset enhancements needed for irrigation method + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New namelist variables: + - use_groundwater_irrigation + - irrig_method_default + - crop_fsat_equals_zero +- Partial support for new surface dataset field: irrigation_method + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: +- Added two tests of the new irrigation options +- Added an _includes directory to hold things that should be included by + testmods (not used directly) + + +Code reviewed by: Bill Sacks and Sean Swenson reviewed each other's code + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - ok + + Tests pass, namelists differ as expected + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ pass + + ok: tests pass, some answers change as noted below + +CTSM tag used for the baseline comparisons: ctsm1.0.dev019 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (same climate) + + Summarize any changes to answers, i.e., + - what code configurations: Some CLM50 cases that are either cold start + or (unusually) use a CLM45 initial conditions file; it's possible + that non-cold-start configurations would see differences rarely. + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff, same climate + + Differences arise due to no longer resetting wa_col to + aquifer_water_baseline every time step in BeginWaterBalanceSingle + if use_aquifer_layer is false (which is the default for + CLM50). (This change is needed to conserve water properly with the + new groundwater-based irrigation.) For the most part, wa_col + wasn't being changed when use_aquifer_layer is false (so no longer + resetting it has no effect if groundwater irrigation isn't being + used), but the one exception is the "work around of the negative + liquid water" added by Jinyun Tang in subroutine SoilWater (dated + Jan 14, 2015), which can be exercised when use_flexibleCN is + true. Sean Swenson did some experimentation, and found that the + code that updates wa_col is only exercised in the first time step + of a cold start run, and that finding is borne out in the test + suite results. However, it's possible that there are rare cases + when this is exercised later in a run. + + I have confirmed that this branch is bit-for-bit with the baseline + if I revert the addition of the use_aquifer_layer conditional + around the wa_col resetting in + BeginWaterBalanceSingle. Alternatively, nearly all tests are + bit-for-bit with the baseline if I remove the one line updating + wa_col in subroutine SoilWater (and also remove the endrun for + water balance errors from BalanceCheck); the one exception is the + waccmx_offline test, which uses a CLM45 initial conditions file in + a CLM50 configuration. + + The following tests had baseline failures: + + Cold start tests: + + ERP_D_Ld5.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-allActive + ERP_D_P36x2_Ld3.f10_f10_musgs.I2000Clm50BgcCrop.cheyenne_intel.clm-cropColdStart + ERP_P180x2_D_Ld5.f19_g17.I2000Clm50BgcDvCrop.cheyenne_intel.clm-crop + ERP_P36x2_Lm25.f10_f10_musgs.I2000Clm50BgcDvCrop.cheyenne_intel.clm-monthly + ERP_P72x2_Lm25.f10_f10_musgs.I2000Clm50BgcDvCrop.cheyenne_intel.clm-monthly + + Test that uses a CLM45 initial conditions file in a CLM50 + configuration: + + ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/523 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev019 +Originator(s): sacks (Bill Sacks) +Date: Fri Nov 30 13:36:57 MST 2018 +One-line Summary: Rework cold start initialization of wa and zwt + +Purpose of changes +------------------ + +Rework cold start initialization of wa and zwt when use_aquifer_layer is +false to reduce answer changes in upcoming groundwater_irrigation +branch. + +In the groundwater_irrigation branch +(https://github.com/ESCOMP/ctsm/pull/523), Sean Swenson has stopped +resetting wa_col each time step if use_aquifer_layer is false. However, +this leads to having a substantially different value of wa_col when +use_aquifer_layer is false: previously, it was reset to +aquifer_water_baseline each time step, but with Sean's changes, it stays +close to its initial values, which have been 4000 in most places. This +tag changes the initial values to match the value it was being reset to, +so it simply starts at aquifer_water_baseline - so the +every-time-step-resetting to aquifer_water_baseline can be removed +without massively changing the value of wa_col. + +In addition to changing the cold start initialization of wa_col, we are +also changing the cold start initialization of zwt in this case where +use_aquifer_layer is false: The old initialization of zwt wouldn't work +as intended now that we have changed the initial value of wa_col; Sean +Swenson suggested this new initialization method instead. This +initialization to zi(c,nbedrock(c)) is correct if there are no saturated +layers, and close enough for a decent cold start even if there are. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Sean Swenson + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, answers change as expected for some cases + +CTSM tag used for the baseline comparisons: ctsm1.0.dev018 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (small) + + Summarize any changes to answers, i.e., + - what code configurations: CLM50 cold start or transient (Hist) cases + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + Larger than roundoff, same climate (not investigated completely + rigorously through long simulations, but Sean Swenson and Bill + Sacks are both pretty confident that the resulting changes will be + small, partly based on difference statistics from the test suite, + and partly based on the fact that the only change in this tag is + in cold start initialization of some values). + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/577 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev018 +Originator(s): sacks (Bill Sacks) +Date: Thu Nov 29 16:03:50 MST 2018 +One-line Summary: Water tracer updates for initial things in driver loop + +Purpose of changes +------------------ + +Update water tracers for initial stuff done in driver loop. This includes +atm2lnd forcings (non-downscaled and downscaled), balance check initialization, +and dyn subgrid updates. + +Broadly speaking, the changes here are: + +(1) Reworked WaterType to make it easier / more robust for other code to loop + over tracers or bulk+tracers + +(2) The most interesting changes are probably the code to update the atm2lnd + water tracers (in Wateratm2lndType.F90 and WaterTracerUtils.F90) + +(3) In various other places, do some infrastructurey stuff (initializing water + balance, doing dyn subgrid stuff) for tracers as well as bulk + +(4) Supporting unit tests and unit test infrastructure + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +Resolves ESCOMP/ctsm#487 +Resolves ESCOMP/ctsm#488 +Resolves ESCOMP/ctsm#489 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- We have chosen not to set all water tracers as soon as possible, but instead + to do these tracer settings later in the driver loop. This keeps the driver + loop cleaner, but means that you cannot arbitrarily sprinkle calls to + TracerConsistencyCheck throughout the driver. Specifically for this tag: the + non-downscaled, gridcell-level atm2lnd water tracers are not updated until + after the call to downscale_forcings, so tracer consistency checks before that + point would fail. + +Changes to tests or testing: +- Added a PFS test + +Code reviewed by: Portions of the design (and possibly code) have been reviewed +by Mat Rothstein, David Noone and Mariana Vertenstein + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, some answers change as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev017 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (roundoff) + + Summarize any changes to answers, i.e., + - what code configurations: many + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + roundoff-level changes in sensible heat flux from precip conversion due to + refactoring this calculation; everything else bit-for-bit + + If bitwise differences were observed, how did you show they were no worse + than roundoff? via summarize_cprnc_diffs to see differences in the test suite + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/ctsm/pull/572 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev017 +Originator(s): slevis (Samuel Levis, Slevis Consulting LLC,303-665-1310) +Date: Wed Nov 28 14:27:50 MST 2018 +One-line Summary: Merge the collapse2gencrop branch + +Purpose of changes +------------------ + +These changes allow the model to not need to read 16-pft +datasets and rather read 78-pft datasets. The 78-pft datasets were +developed for use with prognostic crops originally. The current changes +allow the model to use the 78-pft datasets in 16-pft runs by +collapsing the crop pfts (cfts) from specific types to the model's +generic crop types. The changes are generic so that the model may still +read 16-pft datasets for 16-pft runs. Ultimately these changes will +permit users to run with any number of pfts, while the ctsm group +maintains a single set of input pft data. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): Fixes #509 (partial) + #509 -- irrigate in 1850 is off for runs with use_crop but on for those without + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Changes made to namelist defaults (e.g., changed parameter values): +- maxpatch_pft made obsolete +- nnegcrit was increased because of failure in the TRENDY simulations. +This was done in the source, rather than the namelist but does have an +effect on user behavior. + +Substantial timing or memory changes: No + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + + The "irrigate" attribute should now be removed from all fsurdat files for namelist generation. + Thus irrigate on or off is now an option for non-crop cases. + + +Renamed parameters: +maxpatch_pft is obsolete; remove from namelist-related scripts in future PR +numpft + 1 ---> maxsoil_patches +maxpatch_pft ---> maxsoil_patches in CNDV +numpft ---> maxveg +numpft_ed ---> maxveg_fates + +Several modules were made default private. The list of variables in them +that are public are explicitly listed now: +LakeCon.F90 +clm_initializeMod.F90 +clm_instMod.F90 +clm_varpar.F90 +pftconMod.F90 +subgridAveMod.F90 + +Changes to tests or testing: +New test +New unit tests in test_surfrdUtils.pf, all containing the prefix +test_collapse_crop_types_* + +Code reviewed by: +Erik Kluzek and Bill Sacks + +CTSM testing: +Regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- PASS + hobart_pgi -------- OK + hobart_intel ------ PASS + +CTSM tag used for the baseline comparisons: ctsm1.0.dev016 + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #483 + +Sam Levis cloned Erik Kluzek's collapse2gencrop branch and then +tested, corrected errors, resolved conflicts, added unit tests, while +updating to newer tags as needed. + + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev016 +Originator(s): sacks (Bill Sacks) +Date: Thu Nov 1 07:27:48 MDT 2018 +One-line Summary: Update cime, fix FATES DEBUG token, add script to easily run system tests + +Purpose of changes +------------------ + +(1) Update to latest version of cime master + +(2) Update FATES with a minor change: change DEBUG to debug, to allow + working with a preprocessor-defined DEBUG token + +(3) Add a script (run_sys_tests) that allows easily running all system + tests (see + https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide#running-test-suites-with-the-run-sys-tests-wrapper + for details) + +(4) As part of (3), start work on a CTSM python library and associated + test infrastructure. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes ESCOMP/ctsm#535 (Run Fortran unit tests as part of create_test) + +CIME Issues fixed (include issue #): +- Various - see CIME ChangeLog for details + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] clm4_5 + +[X] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- New run_sys_tests wrapper +- Fortran unit tests now run as part of aux_clm + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + tools-tests (test/tools): + + cheyenne - not run + + PTCLM testing (tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne ---- ok + hobart ------ ok + + ok means tests pass, baselines fail as expected + +CTSM tag used for the baseline comparisons: ctsm1.0.dev015 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (new presaesro and CO2 datasets) + + Summarize any changes to answers, i.e., + - what code configurations: All I compsets (except spinup test that uses cplhist datm forcing) + - what platforms/compilers: All + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Potentially new climate + + Changes answers for I compsets due to datm update as part of the cime + update: new presaero and CO2 datasets + (https://github.com/esmci/cime/pull/2828) + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cime: cime5.7.3 -> cime5.7.5 +- fates: fates_s1.8.1_a3.0.0 -> fates_s1.8.1_a3.0.0_rev2 + +Pull Requests that document the changes (include PR ids): +- https://github.com/escomp/ctsm/pull/493 (Wrapper to system tests, and + start of a ctsm python library) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev015 +Originator(s): sacks (Bill Sacks) +Date: Sun Oct 28 14:29:30 MDT 2018 +One-line Summary: CMIP6 compset modifiers, usermods for typical output, and other output enhancements + +Purpose of changes +------------------ + +(1) Support %BGC-CROP-CMIP6DECK and %BGC-CROP-CMIP6WACCMDECK compset + modifiers, so that we can turn on the necessary options + (output-related and others) via new CMIP6-specific compsets. + +(2) Turn on carbon isotopes in CMIP6 runs (from Erik Kluzek) + +(3) Remove setting of CCSM_BGC=CO2A in the cmip6 usermods + +(4) Add usermods directories for getting typical extra output that's + wanted in many cases: output_crop, output_crop_highfreq, output_bgc, + output_bgc_highfreq, output_sp, and output_sp_highfreq. These can be + enabled by adding something like '--user-mods-dir output_crop' on + the create_newcase line (that short-hand works for an I compset; for + F or B compsets, you need to provide the full path to the usermod + directory). + +(4) Allow holes in the number of history tapes. Holes are cases where, + for example, we have h0, h1 and h3 tapes, but no h2 tape (because + there are no fields on the h2 tape). (This is needed for (3).) + +(5) Fix reading and writing of 1-d logical global arrays. This fixes + ESCOMP/ctsm#24 for real (rather than just preventing an attempt to + read/write 1-d logical arrays, as was done in the previous 'fix'). + +(6) Add C13_NBP and C14_NBP diagnostic fields (from Keith Oleson) + +(7) Make a bunch of carbon isotope diagnostic fields inactive by default + +(8) Don't allow interpolation (use_init_interp) from a case without + carbon isotopes to a case with carbon isotopes: Due to + https://github.com/ESCOMP/ctsm/issues/67, interpolation from a case + without carbon isotopes to a case with carbon isotopes yields + incorrect initialization values for the carbon isotopes. Now that + we're turning carbon isotopes on via some semi-out-of-the-box + usermods (for cmip6), it is becoming more important to check to make + sure someone doesn't shoot themselves in the foot this way. + +(9) Add tests of the new output usermods as well as of the CMIP6 compset + modifiers + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes #24 for real (ncd_io_1d_log_glob is broken) +- Fixes #529 (Organize usermods_dirs to facilitate running cases with + the right output) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New namelist variable, just for testing purposes: + for_testing_allow_interp_non_ciso_to_ciso. This bypasses an error + check, and should only be used in tests. + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Reworked tests of cmip6_deck usermods to use the new + %BGC-CROP-CMIP6DECK compset modifier, and changed f09_g16 to f09_g17 +- Added a test of the %BGC-CROP-CMIP6WACCMDECK compset modifier +- Added tests of output_crop_highfreq, output_bgc_highfreq and + output_sp_highfreq usermods directories +- Note that there are NO tests covering the cmip6_evolving_icesheet + usermods: this usermod directory adds very little beyond cmip6_deck, + so it didn't seem worth its own test + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - pass + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- pass + cheyenne_gnu ------ pass + hobart_nag -------- pass + hobart_pgi -------- pass + hobart_intel ------ pass + + ERI_D_Ld9.T31_g37.I2000Clm50Sp.cheyenne_intel.clm-SNICARFRC + initially failed COMPARE_base_hybrid, COMPARE_base_rest and BASELINE + comparisons. I reran it and it passed. + + Manually compared all history files from + ERS_Ly3.f10_f10_musgs.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic + with baseline + ERS_Ly3.f10_f10_musgs.I1850Clm50BgcCrop.cheyenne_intel.clm-cmip6. They + were all identical. Also compared all history files from + SMS_Ld5_D.f09_g17.I1850Clm50BgcCropCmip6.cheyenne_intel.clm-basic + with baseline + SMS_Ld5_D.f09_g17.I1850Clm50BgcCrop.cheyenne_intel.clm-cmip6. They + were all identical (but note that this basically just compared the + cpl.hi file: the test was too short to produce monthly files.) + +CTSM tag used for the baseline comparisons: ctsm1.0.dev014 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/536 - Allow holes in the number of + history tapes and reorganize cmip6 usermods (main PR containing all of + these changes) +- https://github.com/ESCOMP/ctsm/pull/527 - Add carbon_isotope user-mod + directory to turn on c13 and c14 +- https://github.com/ESCOMP/ctsm/pull/539 - Support a %CMIP6DECK compset + modifier + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev014 +Originator(s): sacks (Bill Sacks) +Date: Fri Oct 26 06:20:34 MDT 2018 +One-line Summary: Miscellaneous minor, bit-for-bit bug fixes + +Purpose of changes +------------------ + +Four miscellaneous minor, bit-for-bit bug fixes: + +(1) Py3 pylint check and address cime issue ESMCI/cime#2822 (from Jim + Edwards: ESCOMP/ctsm#526) + +(2) Change uppercase DEBUG variables to lowercase debug (requested by + Jim Edwards to avoid conflicting with the DEBUG CPP token) + (Fixes ESCOMP/ctsm#534) + +(3) Remove unnecessary line of code in LunaMod.F90 that was causing + problems with some compilers due to an uninitialized variable + (Fixes ESCOMP/ctsm#322) + +(4) Add r8 to 0 constant to fix build issue with XLF compiler (from Jim + Edwards: ESCOMP/ctsm#531) + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes ESCOMP/ctsm#322 (ERS_D_Ld5.f19_g16.I2000Clm50BgcCruGs run FAIL (intel)) +- Fixes ESCOMP/ctsm#534 (Rename DEBUG to debug in a few places) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: none + +Code reviewed by: different pieces reviewed by different people + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - pass + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- ok + cheyenne_gnu ------ ok + hobart_nag -------- ok + hobart_pgi -------- ok + hobart_intel ------ ok + + ok means tests and baseline comparisons pass. There were unexpected + NLCOMP diffs. From spot-checking a few tests, I see the following: + + + (1) On both cheyenne and hobart: Diffs in logfile. This looks like a + problem in cime: it says: + + BASE: logfile = 'rof.log.136342.hobart.cgd.ucar.edu + COMP: logfile = 'rof.log + + (2) On hobart: Diffs in pio_typename: netcdf vs. pnetcdf (says that + new uses pnetcdf): but when I compare files by hand, they look + the same in this respect (both baseline and new use netcdf), so + maybe this is due to a problem in the timing of when nlcomp is + run? + + Since these both look like problems in the comparison script rather + than in the tag, I'm letting these go, but will open a cime issue if + we see this again. + + +CTSM tag used for the baseline comparisons: ctsm1.0.dev013 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/531 (fix build issue with xlf compiler) +- https://github.com/ESCOMP/ctsm/pull/526 (fix cime issue 2822 and pylint chk) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev013 +Originator(s): erik (Erik Kluzek)/slevisconsulting +Date: Thu Oct 25 18:09:47 MDT 2018 +One-line Summary: Fix the fact that transient Bgc and SP cases had constant crop area in time + +Purpose of changes +------------------ + +Fix transient non-crop cases that had constant crop area so that crop area will change in time +(and hence natural veg area will also change corresponding to it). + +Also bring in changes to update mksurfdata_map to handle SSP-RCP future scenarios. Right now +it can handle SSP5-8.5 out of the box. Also add a new test for that. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #538 + #538 -- In transient pft simulations with use_crop=.false., %crop does not advance from 1850 values + +Known bugs found since the previous tag (include github issue ID): #545 + #545 -- Antarctica ice shelves are being treated as wetlands rather than glaciers + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[X] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): A few more namelist checks + Added a check to make sure do_transient_pfts was the same as do_transient_crops + Don't allow use_fertilizer for non-crop case + namelist checks that create_crop_landunit=T except for FATES + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New -ssp_rcp option to mksurfdata.pl + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): New mksrfpft datasets in XML for SSP5-8.5 + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in ../CTSMMasterChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Now, do_transient_pfts and do_transient_crops only work in unison, and hence + should be simplified to one logical called do_transient_veg + +Changes to tests or testing: Add new SSP5-8.5 mksurf test + +Code reviewed by: self, slevisconsulting, billsacks + +CTSM testing: regular, tools + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (18 of the transient test namelists are different to baseline as expected) + + unit-tests (components/clm/src): + + cheyenne - PASS + + tools-tests (components/clm/test/tools): + + cheyenne - OK (PTCLM tests fail) + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- OK + hobart_pgi -------- OK + hobart_intel ------ OK + +CTSM tag used for the baseline comparisons: ctsm1.0.dev012 + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! (Important) + + Summarize any changes to answers, i.e., + - what code configurations: clm4_5/clm5_0 transient simulations without Crop (either Bgc or SP) + - what platforms/compilers: All + - nature of change: crop areas increase in time and impact simulations + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: dll/clm50_r267_1deg_GSWP3V1_iso_hist_nocrop_transientfix + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): #546, #540 +(https://github.com/ESCOMP/ctsm/pull) + + #546 -- Add in ability for mksurfdata_map to handle ssp_rcp scenarios and specifically SSP5-8.5 + $540 -- Transient PFT issue + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev012 +Originator(s): erik (Erik Kluzek) +Date: Sat Sep 29 11:49:35 MDT 2018 +One-line Summary: Add snow-free fields for snowmip, fix several issues + +Purpose of changes +------------------ + +Bring in new diagnostic fields added by Justin Perket, Sean Swenson and Mark Flanner +for Snow-MIP. Most of those are fields that represent "Snow Free" data. + +Also bring in fixes for a list of issues. Add handling of the new CO2 which includes +both latitude-band and global average versions. Add some changes to make it easier +for input data processing including NOT doing the slow 1km map file creation. Have +the number of steps that are skipped at startup dependent on the time-step size. Add +a test for some requirements of WACCMX (time-step and use of ESMF). Calculations of +local time are now done in a global subroutine, that can handle negative longitudes. +Fix how FFIX_TO_SMINN is handled for history output. The namelist logical "calc_human_stress_indices" +changed from logical to a character string of three values: FAST, NONE, ALL. FAST +is the default so the less expensive ones are output, NONE turns them all off, and ] +ALL does all of them including the expensive ones. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #428, #474, #475, #476, #450, #482, #481, #491 + Fix #428 -- Update getco2_historical.ncl to handle latitude varying CO2 + Fix #474 -- Add ability to send GRIDFILE to regridbatch.sh script + Fix #475 -- Have number of steps to skip balance-check based on time + Fix #476 -- Add a test for WACCMX standalone + Fix #450 -- Add option to use global average of terrain standard deviation on surfdata files + (partial fix with simplest option) + Fix #482 -- Add extra field on CO2 streams file for global/time-averaged data + Fix #481 -- FFIX_TO_SMINN needs to be output when FUN is on + Fix #491 -- Calculations of local noon assume that longitude is 0 to 360 rather than -180 to 180 + +Known bugs introduced in this tag (include github issue ID): cime#2801 + cime#2801 -- Problem building with ESMF_LIB + +Known bugs found since the previous tag (include github issue ID): #507, #505 + #507 -- Albedo's are bad at night with negative longitudes + #505 -- CTSM input data-set tools can only work on 0-360 grids, and require monotone increasing longitude + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + + New namelist: + use_ssre -- Turn on show free fields needed for SnowMIP + + Changed namelist: + calc_human_stress_indices changed from logical to character with options: ALL, FAST, NONE + + New history fields: + Mostly added Snow Free (SF) fields + ALBDSF + ALBISF + FSRSF + FSRSFND + FSRSFNDLN + FSRSFNI + FSRSFVD + FSRSFVDLN + FSRSFVI + SSRE_FSR + SSRE_FSRND + SSRE_FSRNDLN + SSRE_FSRNI + SSRE_FSRVD + SSRE_FSRVDLN + SSRE_FSRVI + +Changes made to namelist defaults (e.g., changed parameter values): + calc_human_stress_indices = 'FAST' is now the default + +Changes to the datasets (e.g., parameter, surface or initial files): + mkghg_bndtvghg -- Update with new CO2 files, both monthly, lat-bands and yearly, global + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + I was able to reduce the duplication in SurfaceAlbedoMod where the original implementation added a cut + and paste copy of code. But, there is still a lot of duplication in this file that could be improved, by + making smaller functions/subroutines to do sections of code that are essentially repeated many times. + There's a bit of an increase in complexity to reduce the duplication, but reducing the duplication was worth it. + +Changes to tests or testing: + Add a new waccmx_offline test mods and test with it + New test expected fail because of cime issue: ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline + Turn use_ssre on for most tests, off for reducedOutput + And set calc_human_stress_indices=NONE for reducedOutput, FAST for most, and ALL for KitchenSink and KSMOut tests + +Code reviewed by: self, @olyson, @billsacks + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + unit-tests (components/clm/src): + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- OK + hobart_pgi -------- OK + hobart_intel ------ OK + +CTSM tag used for the baseline comparisons: ctsm1.0.dev011 + + +Answer changes +-------------- + +Changes answers relative to baseline: no bit-for-bit + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): No + +Pull Requests that document the changes (include PR ids): #462 #449 +(https://github.com/ESCOMP/ctsm/pull) + + #462 -- Add namelist item to calculate all heat stress indices only if requested; to speed up model + #449 -- Bring in snowmip diagnostic fields + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev011 +Originator(s): sacks (Bill Sacks), mvr (Mathew Rothstein) +Date: Wed Sep 12 10:50:31 MDT 2018 +One-line Summary: Add water tracer consistency checks, and other water tracer work + +Purpose of changes +------------------ + +1. Add water tracer consistency checks + +2. Add infrastructure for looping over all water tracers - currently + just used for the tracer consistency checks + +3. Breakout of atm2lnd and lnd2atm water variables, needed for water tracers + +4. Add some namelist control over the addition of water tracers + +5. Add a system test that exercises the water tracer consistency checks + +6. Add a 'ratio' variable for each water tracer + +7. Add some unit tests of the new water tracer infrastructure + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Partially addresses #357 +- Resolves #479 +- Resolves #492 + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): +- Don't be fooled by the new namelist variable, enable_water_isotopes: + This is just a place-holder for now, not implying that water isotopes + are actually working. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New namelist variables: enable_water_tracer_consistency_checks and + enable_water_isotopes. The latter is just a place-holder for now. + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: New test that runs the water tracer consistency check + I ran this test on cheyenne_gnu and cheyenne_intel along with the + out-of-the-box hobart_nag version + +Code reviewed by: Mat Rothstein and I have worked together on many of +these changes, but not all code has been reviewed by the other. + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - ok (tests pass, clm4_5 and clm5_0 namelists differ from + baseline as expected) + + unit-tests (components/clm/src): + + cheyenne - pass + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- pass + cheyenne_gnu ------ pass + hobart_nag -------- pass + hobart_pgi -------- pass + hobart_intel ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev010 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/497 + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev010 +Originator(s): sacks (Bill Sacks) +Date: Thu Aug 30 17:14:28 MDT 2018 +One-line Summary: Update cime to cime5.7.3 + +Purpose of changes +------------------ + +Update cime from cime5.6.10 to cime5.7.3. To support this change, there +are also minor code changes related to the pause-resume implementation +(from Erik Kluzek). + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- ESCOMP/ctsm#384 (VIC test is failing at f09 resolution with signal) + (I'm not sure what fixed this, but it's passing now) + +CIME Issues fixed (include issue #): many + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - pass + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- pass + cheyenne_gnu ------ pass + hobart_nag -------- pass + hobart_pgi -------- pass + hobart_intel ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev009 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO - bit-for-bit + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +cime: cime5.6.10 -> cime5.7.3 + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev009 +Originator(s): sacks (Bill Sacks) +Date: Wed Aug 22 20:32:36 MDT 2018 +One-line Summary: Fix initialization of AnnET in InitAccVars + +Purpose of changes +------------------ + +InitAccVars was mistakenly setting qflx_evap_tot_col rather than +AnnET. This fix allows us to remove now-redundant cold start and restart +code for AnnET. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes #480 +- Partially addresses #285 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: basic proposed changes reviewed by Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - pass + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- pass + cheyenne_gnu ------ pass + hobart_nag -------- pass + hobart_pgi -------- pass + hobart_intel ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev008 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): none + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev008 +Originator(s): erik (Erik Kluzek) +Date: Tue Aug 14 10:25:12 MDT 2018 +One-line Summary: Update 1850 ndep file and last year for streams for Historical transient cases + +Purpose of changes +------------------ + +Bring in changes from release-clm5.0.05. Update to latest Nitrogen Deposition file from simulations with WACCM for 1850. +Also fix an issue with the last year for historical transient cases. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): 461 + #461 -- increase last year in streams for transient + +Known bugs found since the previous tag (include github issue ID): [If none, remove this line] + #478 -- Bare soil g1 should be missing value or zero + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): Last year extended for transient datasets + +Changes to the datasets (e.g., parameter, surface or initial files): New ndep dataset for 1850 + +Substantial timing or memory changes: + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: Lengthen some tests + +Code reviewed by: self + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (11 show differences for 1850_control and 20thC_transient) + + unit-tests (components/clm/src): + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- OK + hobart_pgi -------- OK + hobart_intel ------ OK + +CTSM tag used for the baseline comparisons: ctsm1.0.dev007 + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes! (ndep files, and steams years) + + Summarize any changes to answers, i.e., + - what code configurations: 1850_control or 20thC_transient for Clm50 + - what platforms/compilers: all + - nature of change: similar climate + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + + #477 -- Move changes from release-clm5.0.05 onto master + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev007 +Originator(s): sacks (Bill Sacks) +Date: Sun Aug 5 21:03:28 MDT 2018 +One-line Summary: Avoid glacier dynamic landunit adjustments in first time step + +Purpose of changes +------------------ + +Always avoid generating dynamic landunit adjustments for glacier area +changes in the first timestep of a startup or hybrid run - not just for +cold start or interpolated start. See the detailed discussion in +https://github.com/ESCOMP/ctsm/issues/340 for rationale. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes #340 (Avoid generating dynamic landunit adjustment fluxes for + glacier changes in the first timestep) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: none + +Code reviewed by: Erik Kluzek + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - not run + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- ok + cheyenne_gnu ------ pass + hobart_nag -------- pass + hobart_pgi -------- pass + hobart_intel ------ pass + + ok means tests pass; baseline failures as expected in these two + tests that do not use init_interp: + + FAIL ERI_N2_Ld9.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-default BASELINE ctsm1.0.dev006 + FAIL SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput BASELINE ctsm1.0.dev006 + + (The glacier area on the finidat file used in these tests - + clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c180715.nc + - seems to have come from an finidat_interp_dest file, and thus does + not match the glacier area from CISM.) + +CTSM tag used for the baseline comparisons: ctsm1.0.dev006 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (small) + + Summarize any changes to answers, i.e., + - what code configurations: Startup / Hybrid runs that include CISM + (even NOEVOLVE) and do not use init_interp, due to: + - different PE layout in new case vs. the one that generated the + finidat (roundoff-level diffs) + - different glacier area on finidat file vs. what's in CISM + (greater than roundoff-level diffs) + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Roundoff-level for different PE layout, larger than roundoff but + should be same climate when there is different glacier area on the + finidat file vs. what's in CISM + + The differences arise from dynamic landunit adjustments of the + below-ground C and N states in the old code, as CTSM adjusts its + areas to match CISM's. In the new code, there are no C and N + adjustments in the first time step from this adjustment. + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- #470 (Avoid glacier dynamic landunit adjustments in first time step) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev006 +Originator(s): sacks (Bill Sacks) +Date: Sat Aug 4 07:48:09 MDT 2018 +One-line Summary: Minor bug fixes, cleanup, documentation and enhancements + +Purpose of changes +------------------ + +A collection of minor bug fixes, code cleanup, documentation and +enhancements, all bit-for-bit. See list of issues fixed below for +details. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes #24 (ncd_io_1d_log_glob is broken) +- Fixes #120 (Incorrect comments in Biogeophysics1Mod.F90 +- Fixes #217 (Change some cheyenne_gnu tests to cheyenne_intel) +- Fixes #245 (Put all .gitignore entries in top-level file) +- Fixes #272 (Code should error on missing mxsoil_color when SOIL_COLOR + is used) +- Fixes #283 (Add more helpful message about need to do init_interp with + wrong number of vertical layers) +- Fixes #367 (For cmip6 runs: Turn on cpl hist output needed to drive a + TG compset) +- Fixes #412 (Fix documentation of init_interp_method) +- Fixes #419 (Do not allow SOYFIXN diagnostic field with FUN) +- Fixes #464 (Some lines longer than 132 characters) +- Fixes #465 (Remove backwards compatibility check for snw_rds) +- Fixes #467 (Increase wallclock limit for test) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): none + +Changes to tests or testing: +- Changed a single-point test from gnu to intel to get better debugging + information + (SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianGs.cheyenne_intel.clm-cropMonthOutput) +- For some single-point tests on both gnu and intel: removed one + compiler, keeping the tests on just one + +Code reviewed by: self + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - pass + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- pass + cheyenne_gnu ------ pass + hobart_nag -------- pass + hobart_pgi -------- pass + hobart_intel ------ pass + + NLCOMP failures as expected for tests with the cmip6 test mod + + Some long single-point gnu tests failed due to running out of + wallclock time; I have removed these, just keeping them on intel + (along with removing a few other tests after I ran the testing - see + commit 5c226bdf): + + FAIL ERS_Lm54_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropGs.cheyenne_gnu.clm-cropMonthOutput RUN time=4803 + FAIL ERS_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm50BgcCropGs.cheyenne_gnu.clm-cropMonthOutput RUN time=6024 + + +CTSM tag used for the baseline comparisons: ctsm1.0.dev005 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO - bit-for-bit + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- #392 (Remove old code for snw_rds restart that looks no longer needed) +- (Other changes not documented in PRs) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev005 +Originator(s): sacks (Bill Sacks), mvr (Mathew Rothstein) +Date: Fri Aug 3 07:54:59 MDT 2018 +One-line Summary: Rework water data types to accommodate isotopes and other tracers + +Purpose of changes +------------------ + +This tag reworks the various water data types to allow having multiple +instances of variables that are needed for isotopes and other water +tracers. + +Specific changes include: + +(1) Separated "water state" variables into state, diagnostic and balance + check-related variables. This separation was not essential for the + work here, but was desired by Martyn Clark and others. + +(2) For each of water state, diagnostic and flux variables, separated + variables into those needed for both bulk and tracers vs. those only + needed for bulk. This way, we can have multiple instances of the + variables needed by tracers, but only a single instance of variables + that only apply to bulk water. This follows the design laid out in + https://github.com/escomp/ctsm/pull/395. The separation was based + largely on what was done in the old water isotope branch; we didn't + put a lot of thought into this, because the new design allows us to + easily migrate variables between bulk-only and bulk-and-tracer as + needed. + +(3) Moved water fluxes that were defined in science modules back into + waterflux_type or waterfluxbulk_type. This was needed for (2); there + is more discussion on this in + https://github.com/escomp/ctsm/pull/395 and the log message for + commit 711e5cd7. + +(4) Introduced a top-level water_type that holds instances of all of the + other water-related objects. This follows the design laid out in + https://github.com/escomp/ctsm/pull/395. This is particularly + valuable for the tracer instances: the logic related to number of + tracers can be encapsulated in water_type, rather than infiltrating + clm_instMod. + +(5) Added placeholders for water tracer instances + +(6) Added infrastructure to generate history / restart field names for + the tracer instances. Eventually, the isotope class can also hold + information specific to each isotope. + +This work was a joint effort between Mathew Rothstein and myself; Mat +gets much of the credit for the actual refactoring done here. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes #358 (Separate WaterStateType into multiple types) +- Fixes #434 (Separate WaterFluxType into a base class and a class that just applies to bulk) +- Fixes #359 (Set up infrastructure for multiple instances of WaterState and WaterFlux types) +- Fixes #458 (Implement handling of history and restart variables for water tracers) + +Known bugs introduced in this tag (include github issue ID): +- #464 (Some lines longer than 132 characters) +- #456 (Remove backwards compatibility check for snw_rds) (not a + newly-introduced issue, but it's more important to fix this with the + separation of waterstate_type) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: none + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- Water tracers are not yet functional - they are just placeholders +- Whether to use water tracers and which water tracers to use are + currently hard-coded; eventually, this should be namelist-controlled + +Changes to tests or testing: none + +Code reviewed by: Mathew Rothstein and Bill Sacks worked together on +these changes and reviewed each other's changes to some extent. The +high-level design was also reviewed and co-developed by Mariana +Vertenstein. Martyn Clark contributed substantially to the breakout of +water state into state, diagnostic and balance check-related variables. + + +CTSM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - pass + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- pass + cheyenne_gnu ------ pass + hobart_nag -------- pass + hobart_pgi -------- pass + hobart_intel ------ pass + +CTSM tag used for the baseline comparisons: ctsm1.0.dev004 + + +Answer changes +-------------- + +Changes answers relative to baseline: NO - bit-for-bit + + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/escomp/ctsm/pull/395 (documents the high-level design) + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev004 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Wed Jul 18 02:10:23 MDT 2018 +One-line Summary: Add some new diagnostic fields, fix a few issues, update cmip6 output + +Purpose of changes +------------------ + +Add some new diagnostic fields. Some needed for CMIP6. Update the CMIP6 user-mods output. +Fix a couple issues. Get full list of history tapes working correctly. Check for valid range +of CO2. New IC file interpolated from the previous one for f19_g17_gl4 for 2000 Clm50BgcCrop. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): $210, #427, #429 + #210 -- increase number of history tapes + $427 -- Check for zero CO2 + #429 -- New IC for present day + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): New history fields + TSKIN --- skin temperature + TSL ----- temperature of near-surface soil layer + GSSUNLN - sunlit leaf stomatal conductance at local noon + GSSHALN - shaded leaf stomatal conductance at local noon + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): New finidat file f19_g17_gl4 2000 Clm50BgcCrop + New file is just interpolate from the previous file to a f19_g17_gl4 gridfor Clm50BgcCrop and 2000 simulation year + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CLMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: None + +Code reviewed by: self, oleson, abtawfik + + +CTSM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - OK (95 are different because of finidat file change) + + unit-tests (components/clm/src): + + cheyenne - PASS + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- PASS + hobart_pgi -------- FAIL + hobart_intel ------ PASS + +CTSM tag used for the baseline comparisons: ctsm1.0.dev003 + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes -- only 2000 cases because of new IC + + Summarize any changes to answers, i.e., + - what code configurations: Just 2000 cases + - what platforms/compilers: All + - nature of change: same climate + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + + + #338 -- Radtemp and other new diagnostic fields + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev003 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Sun Jul 15 00:26:46 MDT 2018 +One-line Summary: Update cime/cism to work on upgraded hobart and with glade changes on cheyenne + +Purpose of changes +------------------ + +Update cime and cism so can work on upgraded hobart. Also fix an issue that the Nag6.2 compiler found +in CTSM. Also get working with glade changes that happened on cheyenne, DIN_LOC_ROOT_CLMFORC was +changed to a new directory. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): [If none, remove this line] + #441 -- Changes in glade invalidate previous softlinks and data locations + #438 -- Illegal argument aliasing caught by nag6.2 + #433 -- with hobart upgrade CTSM not working + +Known bugs introduced in this tag (include github issue ID): + #444 -- PGI fails on cheyenne and hobart + +Known bugs found since the previous tag (include github issue ID): + #443 -- Wood C:N ratios + #440 -- leafcn_max < target leafcn? + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? No +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CLM's user interface (e.g., new/renamed XML or namelist variables): DIN_LOC_ROOT_CLMFORC on cheyenne + DIN_LOC_ROOT_CLMFORC was change on cheyenne + +Changes made to namelist defaults (e.g., changed parameter values): None + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CTSMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): None + +Changes to tests or testing: path for cheyenne specific test had to be changed + Add some gnu tests on hobart + Lengthen wallclock on a test + Fix path for DA test_mod + +Code reviewed by: self + +CLM testing: regular + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + unit-tests (components/clm/src): + + cheyenne - PASS + + tools-tests (components/clm/test/tools): + + cheyenne - PASS + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - OK + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- OK + hobart_pgi -------- FAIL + hobart_gnu -------- PASS + hobart_intel ------ PASS + +CLM tag used for the baseline comparisons: ctsm1.0.dev002 + + +Answer changes +-------------- + +Changes answers relative to baseline: No bit-for-bit + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime, cism + cism-wrapper to release-cesm2.0.04 + cime to cime5.6.10 + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + #444 -- Get working on upgraded hobart and with glade changes on cheyenne + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev002 +Originator(s): erik (Erik Kluzek) +Date: Fri Jul 6 16:33:03 MDT 2018 +One-line Summary: Fix NFIX flux variables so special land-units are zeroed out, tools update, add some *_MAX fields on mksurfdata_map for transient cases + +Purpose of changes +------------------ + +Nitrogen Fixation flux arrays were being set to missing value over non-vegetated landunits. This sets them to zero everywhere +and averages in the zero's at the gridcell level for history output. It also reads in restarts with missing values and converts +them to zero's. + +There are also some tools updates, getting the tools working on the new upgraded hobart.cgd.ucar.edu. + +And mksurfdata_map is updated to add some *_MAX files on the landuse.timeseries files that will allow us to conserve memory +for transient cases. + + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): #435, #436, #433 (for tools) + #435 -- intel build for tools + #426 -- Nitrogen Fixation flux variables + #433 -- hobart broken, got it working for tools + +Known bugs found since the previous tag (include github issue ID): #433, #431 + + #433 -- with hobart upgrade, hobart build isn't working + #431 -- When set_* options are used to hist_addfld be careful of ordering + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_0 + +[ ] clm4_5 + +[ ] clm4_0 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): None + +Changes to CLM's user interface (e.g., new/renamed XML or namelist variables): None + +Changes made to namelist defaults (e.g., changed parameter values): ndep file updated for clm5_0 for 1850 + +Changes to the datasets (e.g., parameter, surface or initial files): None + +Substantial timing or memory changes: None + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CLMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): NFIX flux variables + NFIX flux variables when read from restart have special-values (missing on non veg landunits) converted to zero's + They are now initialized to zero everywhere. + +Changes to tests or testing: None + +Code reviewed by: self, wwieder, and lawrence, sacks (mksurfdata_map code) + +CLM testing: regular (although none on hobart!) + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS (5 tests differ from previous version) + + unit-tests (components/clm/src): + + cheyenne - PASS + + tools-tests (components/clm/test/tools): + + cheyenne - PASS + hobart --- PASS + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + +CLM tag used for the baseline comparisons: ctsm1.0.dev001 + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes, clm5_0 BGC configurations with FUN and clm5_0 with BGC for new 1850 ndep file + + Summarize any changes to answers, i.e., + - what code configurations: All clm5_0 BGC due to NFIX fields, and clm5_0 1850 BGC due to new ndep file + - what platforms/compilers: All + - nature of change: similar climate + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): None + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + + #437 -- ChangeLog template + #432 -- nfix + #331 -- _MAX fields on mksurfdata_map + +=============================================================== +=============================================================== +Tag name: ctsm1.0.dev001 +Originator(s): sacks (Bill Sacks) +Date: Fri Jun 22 07:31:43 MDT 2018 +One-line Summary: Begin separating SoilHydrology flux calculations + +Note the new tag naming: Starting with this tag, we are naming tags +"ctsm..." rather than "clm...". We are starting with ctsm version 1, +which for now is nearly the same as clm version 5. We are moving to this +new tag naming now because: + +(1) The changes in this tag represent the first step towards + implementing the CTSM vision (separating the biogeophysics flux + calculations from state updates, making it easier to plug in + alternative parameterizations, etc.). + +(2) This tag changes answers relative to the CLM5 release. (We expect + the climate to be the same, but we haven't tested this carefully + yet.) + +Purpose of changes +------------------ + +First steps toward separating various flux calculations in the soil +hydrology code. The focus here is on saturated surface runoff and +infiltration excess runoff. The changes here separate flux calculations +from state updates and extract various calculations into their own +subroutines to facilitate swapping in alternative parameterizations. + +Most of the changes here are refactorings that are either bit-for-bit or +just introduce roundoff-level differences. However, there are also a few +larger answer changes, as described below. + +These are the greater-than-roundoff-level answer changes: + +(A1) Use full qflx_surf in BGC code. Previously, the subroutines ch4 and + SoilBiogeochemNLeaching had been using a flux that excluded surface + water runoff (qflx_h2osfc_surf). That was deemed to be incorrect + (by Dave Lawrence and others), so these BGC subroutines have been + changed to use the full surface runoff (saturated excess runoff + + infiltration excess runoff + h2osfc runoff). + + Configurations affected: BGC compsets + + Magnitude of change: Larger than roundoff; expected to be same + climate, but not investigated carefully + +(A2) VIC: Don't ever use the TOPModel formulation for SurfaceRunoff + + The code was using the TOPModel-based formulation for SurfaceRunoff + if frost_table > zwt_perched. Sean Swenson felt this shouldn't be + done, and refactoring will be easier if VIC always uses the + vic-looking formulation, so I'm stopping applying this formulation + when using VIC. + + Configurations affected: VIC compsets + + Magnitude of change: Larger than roundoff; not investigated carefully + +(A3) VIC: Remove infiltration excess runoff + + Martyn Clark reviewed the VIC implementation, and felt that the + current implementation of infiltration excess runoff is + inconsistent with the standard VIC implementation. It appears that + what was being called VIC's infiltration excess runoff was actually + just an attempt to give a better numerical approximation to the + solution for saturated surface excess runoff. So deleting this + leaves only a first-order approximation to VIC's saturated surface + excess runoff. + + Eventually we may want to put in place a more accurate solution for + VIC's saturated surface excess runoff. But Martyn's feeling is that + this can come in with other changes we want to make regarding + numerical solutions in CTSM. + + Configurations affected: VIC compsets + + Magnitude of change: Larger than roundoff; expected to be same + climate, but not investigated carefully + +(A4) Change in QOVER diagnostic field: now includes QH2OSFC. + +These are the major refactorings (either bit-for-bit or just +roundoff-level differences): + +(R1) Extract surface runoff to its own module, and other modularization + related to what used to be subroutine SurfaceRunoff: extract a + subroutine for each fsat method, move urban surface runoff code + into different routines. + +(R2) Extract infiltration excess runoff to its own module, and other + modularization related to what used to be subroutine Infiltration. + +NOTE: For a detailed breakdown of changes, including documentation of +which changed changed answers, see the file ChangeLog_branch which was +deleted from this branch shortly before it was merged to master. + +Bugs fixed or introduced +------------------------ + +Issues fixed (include CTSM Issue #): +- Fixes #424 (decStart testmod is missing an `--append` in an xmlchange command) + + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CLM's user interface (e.g., new/renamed XML or namelist variables): + +Changes made to namelist defaults (e.g., changed parameter values): + +Changes to the datasets (e.g., parameter, surface or initial files): + +Substantial timing or memory changes: + +Notes of particular relevance for developers: (including Code reviews and testing) +--------------------------------------------- +NOTE: Be sure to review the steps in .CLMTrunkChecklist as well as the coding style in the Developers Guide + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: +- Shortened a 25-month f19 test to 13-months + (SMS_Lm13.f19_g17.I2000Clm50BgcCrop.cheyenne_intel.clm-cropMonthOutput): + This test took a long time to run, and we already have long tests of + this configuration at coarse-resolution. I suggested removing this + test entirely, but Erik Kluzek wanted to maintain a shortened version + of it. Erik's comments were: + + How about either flip it to f45 (because Rosie is using that + resolution for science) -- or leave it at f19 and have it run for 9 + months? The 25 months was to take it just past the 2-year spinup + time. From spunup initial conditions 9-months pretty much does a + full harvest cycle. f19 and f09 are the main configurations for + science and it would be good to have something longer than just + really short tests. + + I decided on Lm13, because this still completes in significantly less + than 2-hours, and if we're running for 9 months anyway, it seems + valuable to finish out the year and run a bit into the next year, + since some crop stuff triggers at the end of the year. + +Code reviewed by: Various code reviews done last Fall, when these +changes were first implemented. + +CLM testing: + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - not run + + unit-tests (components/clm/src): + + cheyenne - PASS + + tools-tests (components/clm/test/tools): + + cheyenne - not run + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - not run + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + hobart_nag -------- OK + hobart_pgi -------- OK + hobart_intel ------ OK + + OK means tests pass, answers change as expected. + +CLM tag used for the baseline comparisons: clm5.0.dev013 + + +Answer changes +-------------- + +Changes answers relative to baseline: YES (roundoff) + + Summarize any changes to answers, i.e., + - what code configurations: Essentially all (except CLM4) + - what platforms/compilers: All + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + Roundoff-level changes for nearly all configurations (except CLM4). + + Greater-than-roundoff-level changes for the following + configurations: + - BGC: see (A1) note above (expected to be same climate, but not + investigated carefully) + - VIC: see (A2) and (A3) notes above (magnitude of change not + investigated carefully) + - QOVER diagnostic field: see (A4) note above + +Detailed list of changes +------------------------ + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): none + +Pull Requests that document the changes (include PR ids): +- https://github.com/ESCOMP/ctsm/pull/244 +- https://github.com/ESCOMP/ctsm/pull/190 +- Other PRs that existed on the old NCAR/clm-ctsm repository (which has + been deleted), which were not migrated to the new repository + +=============================================================== diff --git a/doc/release-cesm2.2.ChangeLog b/doc/release-cesm2.2.ChangeLog new file mode 100644 index 0000000000..1f61e49095 --- /dev/null +++ b/doc/release-cesm2.2.ChangeLog @@ -0,0 +1,96 @@ +=============================================================== +Tag name: release-cesm2.2.01 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Wed Sep 2 02:44:01 MDT 2020 +One-line Summary: Fix clm4_5 initial conditions + +Purpose of this version: +------------------------ + +Update cime so that default end year for GSWP3 forcing is 2013 because 2014 data is bad. + +Fix some issues for finding initial condition files for Clm45 compsets. Also bring in updated CDEPS/CMEPS +as they were required with the cime update. Also get the CLM offline tools working as well as the tools +testing. + + +CTSM Master Tag This Corresponds To: ctsm1.0.dev108 (with most changes from ctsm1.0.dev111) + +Summary of changes: +------------------- + +Issues fixed (include CTSM Issue #): + Fixes #1134 mkmapdata.sh is not working + Fixes #1129 two FATES tests that fail + Fixes #1128 missing compset + Fixes #1067 -- Stop using PIO2 in the LILAC build + Fixes #1121 -- FMOZ test fails +CIME Issues fixed (include issue #): + Fixes ESMCI/cime#3683 -- Avoid artificial limit on string lengths in shr_string_listMerge +PTCLM Issues fixed: + Fixes PTCLM#11 -- not running on cheyenne + +Science changes since: ctsm1.0.dev108 + 2010 and SSP compsets have forcing end in 2013 rather than 2014 + +Software changes since: ctsm1.0.dev108 + Fix issues for finding IC files for clm45 + +Changes to User Interface since: ctsm1.0.dev108 + +Testing: +-------- + + [PASS means all tests PASS and OK means tests PASS other than expected fails.] + + build-namelist tests: + + cheyenne - PASS + + tools-tests (components/clm/test/tools): + + cheyenne - PASS + izumi ---- PASS + + PTCLM testing (components/clm/tools/shared/PTCLM/test): + + cheyenne - OK + + regular tests (aux_clm): + + cheyenne_intel ---- OK + cheyenne_gnu ------ OK + izumi_nag --------- OK + izumi_pgi --------- OK + izumi_intel ------- OK + +Summary of Answer changes: +------------------------- + +If the tag used for baseline comparisons was NOT the previous tag, note that here: ctsm1.0.dev108 + +Changes answers relative to baseline: yes + + Summarize any changes to answers, i.e., + - what code configurations: 2010 and SSP compsets (because of cime update) + - what platforms/compilers: all + - nature of change: same climate + +Detailed list of changes: +------------------------ + +Externals being used: cesm2_2_alpha06e versions + CISM at cism2_1_69 + RTM at rtm1_0_72 + MOSART at mosart1_0_37 + cime at cime5.8.32 + FATES at sci.1.30.0_api.8.0.0 + PTCLM at PTCLM2_20200902 + +CTSM Tag versions pulled over from master development branch: ctsm1.0.dev111 + +Pull Requests that document the changes (include PR ids): N/A +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== diff --git a/doc/source/_static/css/custom.css b/doc/source/_static/css/custom.css new file mode 100644 index 0000000000..10abb45722 --- /dev/null +++ b/doc/source/_static/css/custom.css @@ -0,0 +1,17 @@ +/* Make equation numbers float to the right */ +.eqno { + margin-left: 5px; + float: right; +} +/* Hide the link... */ +.math .headerlink { + display: none; + visibility: hidden; +} +/* ...unless the equation is hovered */ +.math:hover .headerlink { + display: inline-block; + visibility: visible; + /* Place link in margin and keep equation number aligned with boundary */ + margin-right: -0.7em; +} diff --git a/doc/source/_static/pop_ver.js b/doc/source/_static/pop_ver.js new file mode 100644 index 0000000000..b8c58658a8 --- /dev/null +++ b/doc/source/_static/pop_ver.js @@ -0,0 +1,37 @@ +$(document).ready(function() { + /* For a URL that looks like + https://blah.github.io/versions/VERSIONFOO/html/bar/index.html, set cur_version_dir to + 'VERSIONFOO' (i.e., the portion of the path following 'versions'). + */ + var proj_end = document.baseURI.indexOf("versions") + 9; + var end = document.baseURI.indexOf("/", proj_end); + var cur_version_dir = document.baseURI.substring(proj_end, end); + var mylist = $("#version-list"); + mylist.empty(); + $.getJSON(version_json_loc, function(data) { + if (data.hasOwnProperty(cur_version_dir)) { + /* First add the current version so that it appears first in the drop-down + menu and starts as the selected element of the menu. If you click on the + current version, you should stay at the current page. + + The conditional around this block should generally be true, but we check it + just in case the current version is missing from the versions.json file for + some reason. + */ + cur_version_name = data[cur_version_dir]; + mylist.append($("