Merge pull request #19 from ESCOMP/master

Update master branch of NorESMhub/CTSM to be in line with ESCOMP/CTSM master branch

.config_files.xml

@@ -5,22 +5,24 @@
 <entry_id>
 
   <!-- This is the same as the default entry in
-       cime/config/cesm/config_files.xml except for the value for clm:
-       In a standalone clm checkout, COMP_ROOT_DIR_LND is $SRCROOT
+       cime/config/cesm/config_files.xml except for the value for CTSM:
+       In a standalone CTSM checkout, COMP_ROOT_DIR_LND is $SRCROOT
        rather than $SRCROOT/components/clm.
 
        However, because of the way overrides are handled, we need to
        re-specify the full information here rather than just overriding
-       the value for clm.
+       the value for CTSM.
   -->
   <entry id="COMP_ROOT_DIR_LND">
     <type>char</type>
     <default_value>unset</default_value>
     <values>
-      <value component="clm"      >$SRCROOT</value>
-      <value component="dlnd"      >$CIMEROOT/src/components/data_comps/dlnd</value>
-      <value component="slnd"      >$CIMEROOT/src/components/stub_comps/slnd</value>
-      <value component="xlnd"      >$CIMEROOT/src/components/xcpl_comps/xlnd</value>
+      <value component="clm"       >$SRCROOT</value>
+      <value component="ctsm"      >$SRCROOT</value>
+      <value component="dlnd" comp_interface="mct">$CIMEROOT/src/components/data_comps_mct/dlnd</value>
+      <value component="dlnd" comp_interface="nuopc">$CIMEROOT/src/components/cdeps/dlnd</value>
+      <value component="slnd"      >$CIMEROOT/src/components/stub_comps_$COMP_INTERFACE/slnd</value>
+      <value component="xlnd"      >$CIMEROOT/src/components/xcpl_comps_$COMP_INTERFACE/xlnd</value>
     </values>
     <group>case_comps</group>
     <file>env_case.xml</file>

.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

.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).**

.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

.lfsconfig

@@ -0,0 +1,2 @@
+[lfs]
+        fetchexclude = *

.zenodo.json

@@ -0,0 +1,7 @@
+{
+    "creators": [
+        {
+            "name": "CTSM Development Team"
+        }
+    ]
+}

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
-

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]

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.
 
 
 =============================================================================================

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 [email protected] 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)