Merge tag 'ctsm5.2.002' into dustcontrolincmeps

FATES default allometry parameter file update

This updates the default FATES parameter file which includes a number
of changes:

   - Default global tree pft allometry update
   - New allometric mode options
   - New scaling coefficients for alternative leaf maintenance respiration
   - New switch to control the use of host land model day length scaling factor

This also incorporates some testing additions and clean up, including:

   - Removes cheyenne expected failure tests that have been converted to derecho
   - Adds a 5x5_amazon test to aux_clm and the expected failures list
   - Temporarilry converts a fates 5x5_amazon test to f10 test
   - Adds namelist check and corresponding unit test to make sure fates hydro
     and fates satellite phenology mode can not be used together

The FATES externals tag is also updated which includes a number of bug fixes
and the addition of new history output.

.git-blame-ignore-revs

@@ -1,4 +1,5 @@
 # Ran python directory through black python formatter
+b429b63824e09f82e95d2982f14311cbbd8e4a37
 d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
 4cd83cb3ee6d85eb909403487abf5eeaf4d98911
 0aa2957c1f8603c63fa30b11295c06cfddff44a5
@@ -22,6 +23,7 @@ e4d38681df23ccca0ae29581a45f8362574e0630
 a9d96219902cf609636886c7073a84407f450d9a
 d866510188d26d51bcd6d37239283db690af7e82
 0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
+e096358c832ab292ddfd22dd5878826c7c788968
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
@@ -32,3 +34,13 @@ d866510188d26d51bcd6d37239283db690af7e82
 6fccf682eaf718615407d9bacdd3903b8786a03d
 2500534eb0a83cc3aff94b30fb62e915054030bf
 78d05967c2b027dc9776a884716597db6ef7f57c
+a0d014fae9550dd9ffbc934abd29ef16176f8208
+c7b7ca1d94ac19abb9ecea9fb5b712ddbdd6645d
+b565b55ce7a9f8d812a573d716a5fd3d78cfea81
+fdf72cd011e2ba318987a1e100efc5a1847c9d04
+de9a30bfbbec36f9dcacc4380005ab596da47af4
+cda0cf1412212e6f4363e6e8eb39f74c944b454d
+aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
+6c6f57e948bfa31e60b383536cc21663fedb8b70
+9660667b1267dcd4150889f5f39db540158be74a
+665cf86102e09b4c4c5a140700676dca23bc55a9

.gitignore

@@ -79,32 +79,31 @@ test_driver_*.sh
 
 # mksurfdata output
 surfdata_*.log
-surfdata_*.namelist
-landuse.timeseries_*.namelist
+*.namelist
+mksurfdata.o*
 landuse.timeseries_*.log
 landuse_timeseries_*.txt
 ctsm.input_data_list
 ctsm.input_data_list.previous
 *.stdout.txt.o*
+/tools/mksurfdata_esmf/PET*
+/tools/mksurfdata_esmf/job_name.o*
+/tools/mksurfdata_esmf/mksurfdata_in
+/tools/mksurfdata_esmf/surfdata_*.nc
+/tools/mksurfdata_esmf/landuse.timeseries_*.nc
+/tools/mksurfdata_esmf/mksurfdata_jobscript_multi.sh
+/tools/mksurfdata_esmf/mksurfdata_jobscript_single.sh
+/tools/mksurfdata_esmf/pio_iotype.txt
+/tools/mksurfdata_esmf/*.sh
+/tools/mksurfdata_esmf/tool_bld
+/tools/mksurfdata_esmf/pio_iotype.txt
 
 # mksurfdata unit tests
 unit_test_build
 
 # Tools executables
-/tools/mksurfdata_map/mksurfdata_map
 /tools/mkprocdata_map/mkprocdata_map
 
-# mksurfdata output files
-/tools/mksurfdata_map/surfdata_*.nc
-/tools/mksurfdata_map/landuse.timeseries_*.nc
-
-# mkmapdata output files
-/tools/mkmapdata/PET*.RegridWeightGen.Log
-/tools/mkmapdata/regrid.*.out
-/tools/mkmapdata/regrid.*.err
-/tools/mkmapdata/regrid.o*
-/tools/mkmapdata/map*.nc
-
 # run_neon output directories
 /tools/site_and_regional/listing.csv
 /tools/site_and_regional/????/

Externals.cfg

@@ -8,7 +8,7 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_97
+tag = cismwrap_2_1_99
 externals = Externals_CISM.cfg
 required = True
 

Externals_CLM.cfg

@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/rgknox/fates
-tag = sci.1.72.2_api.34.0.0
+repo_url = https://github.com/NGEET/fates
+tag = sci.1.73.0_api.35.0.0
 required = True
 
 [externals_description]

README

@@ -1,6 +1,6 @@
-$CTSMROOT/README                                          06/08/2018
+$CTSMROOT/README                                          04/19/2023
 
-Community Terrestrial Systems Model (CTSM) science version 5.1  series -- source code, tools, 
+Community Terrestrial Systems Model (CTSM) science version 5.2  series -- source code, tools, 
 offline-build and test scripts. This gives you everything you need
 to run CTSM with CESM with the CMEPS driver and CDEPS data models to provide CRU NCEP or GSWP3 forcing data in 
 place of a modeled atmosphere.
@@ -35,40 +35,47 @@ this checkout. For a CESM checkout $CIMEROOT will be the "cime" directory
 beneath the top level directory. For a CTSM checkout $CIMEROOT will
 be $CTSMROOT/cime.
 
+IMPORTANT NOTE ABOUT (deprecated)
+
+Anything marked with (deprecated) is something is going to be removed in a future update.
+Often this means it will be replaced with something else.
+
+
 General directory structure ($CTSMROOT):
 
 doc --------------- Documentation of CTSM.
-bld --------------- Template, configure and build-namelist scripts for clm.
+bld --------------- build-namelist scripts for CTSM.
 src --------------- CTSM Source code.
 lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model)
-test -------------- CTSM Testing scripts for CTSM offline tools.
+test -------------- CTSM Testing scripts for CTSM offline tools (deprecated)
 tools ------------- CTSM Offline tools to prepare input datasets and process output.
 cime_config ------- Configuration files of cime for compsets and CTSM settings
-manage_externals -- Script to manage the external source directories
+manage_externals -- Script to manage the external source directories (deprecated)
 py_env_create ----- Script to setup the python environment for CTSM python tools using conda
-python ------------ Some python modules mostly for use by run_sys_tests (but could be used elsewhere l
+python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts
 
 Directory structure only for a CTSM checkout:
 
 components -------- Other active sub-components needed for CTSM to run (river routing and land-ice models)
-libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO
+libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO (deprecated)
 share ------------- CESM shared code
+ccs_config -------- CIME configure files (for grids, compsets, and machines) for CESM
 
 cime/scripts --------------- cesm/cime driver scripts
 
 components/cmeps -------------------- CESM top level driver (for NUOPC driver [which is the default]) source code.
 components/cdeps -------------------- CESM top level data model shared code (for NUOPC driver).
-cime/src/externals ------------------ CESM external utility codes  (genf90)
 components/cism --------------------- CESM Community land Ice Sheet Model.
 components/mosart ------------------- Model for Scale Adaptive River Transport
 components/rtm ---------------------- CESM River Transport Model.
-components/cpl7 --------------------- CESM top level driver for MCT driver (being deprecated)
+components/cpl7 --------------------- CESM top level driver for MCT driver (deprecated will be removed)
 
 Top level documentation ($CTSMROOT):
 
 README ------------------- This file
+README.md ---------------- File that displays on github under https::/github.com/ESCOMP/CTSM.git
 README.rst --------------- File that displays under the project in github
-README_EXTERNALS.rst ----- Information on how to work with subversion externals for clm
+README_EXTERNALS.rst ----- Information on how to work with manage_externals for CTSM (deprecated)
 CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project
 Copyright ---------------- CESM Copyright file
 doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the
@@ -92,7 +99,7 @@ bld/namelist_files/namelist_defaults_ctsm.xml ----- Default values
 Important files in main directories (under $CTSMROOT):
 =============================================================================================
 
-Externals.cfg --------------- File for management of the main high level externals
+Externals.cfg --------------- File for management of the main high level external (deprecated)
 Externals_CLM.cfg ----------- File for management of the CTSM specific externals (i.e. FATES)
 
 run_sys_tests --------------- Python script to send the standard CTSM testing off (submits
@@ -103,18 +110,15 @@ parse_cime.cs.status -------- Script to parse test status files cs.status.* crea
                               (can be used along with run_sys_tests)
 doc/Quickstart.GUIDE -------- Quick guide to using NUOPC scripts.
 doc/IMPORTANT_NOTES --------- Some important notes about this version of 
-                                                 clm, configuration modes and namelist items 
+                                                 CTSM, configuration modes and namelist items 
                                                  that are not validated or functional.
 doc/ChangeLog --------------- Detailed list of changes for each model version.
 doc/ChangeSum --------------- Summary one-line list of changes for each 
                               model version.
-doc/README ------------------ Documentation similar to this file
 doc/UsersGuide -------------- CTSM Users Guide
 doc/IMPORTANT_NOTES --------- Some important notes on caveats for some configurations/namelist items
 
-bld/README ------------------ Description of how to use the configure and
-                              build-namelist scripts.
-bld/configure --------------- Script to prepare CTSM to be built.
+bld/README ------------------ Description of how to use the build-namelist scripts.
 bld/build-namelist ---------- Script to build CTSM namelists.
 
 cime_config/buildnml ------------- Build the CTSM namelist for CIME
@@ -127,23 +131,15 @@ cime_config/testdefs ------------- Directory for specification of CTSM testing
 cime_config/testdefs/ExpectedTestFails.xml -- List of tests that are expected to fail
 cime_config/usermods_dirs -------- Directories of sets of user-modification subdirs
                                    (These are directories that add specific user modifications to
-                                    simulations created using "cime/scripts/create_newcase --user-mods-dir".
-                                    Current sub directories are for various CMIP6 configurations)
-
-test/tools/test_driver.sh -- Script for general software testing of 
-                             CTSM's offline tools.
+                                    simulations created using "cime/scripts/create_newcase --user-mods-dir".)
 
-tools/mksurfdata_map ---------- Directory to build program to create surface dataset 
+tools/mksurfdata_esmf --------- Directory to build program to create surface dataset 
                                 at any resolution.
-tools/mkdatadomain ------------ Directory to build program to create datm7 or docn7 
-                                domain files from clm files.
 tools/mkprocdata_map ---------- Process history data from unstructed grids to a gridded 
                                 format.
-tools/mkmapgrids -------------- NCL script to create a SCRIP grid file for a regular lat/lon grid
-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/mkmapgrids -------------- NCL script to create a SCRIP grid file for a regular lat/lon grid (deprecated)
+tools/crop_calendars ---------- Tools to process and process and create crop calendar datasets for CTSM
+tools/modify_input_files ------ Script to modify existing CTSM input datasets in standard ways
 tools/site_and_regional ------- Scripts to create input datasets for single site and regional
                                 cases, primarily by modifying existing global datasets
 tools/contrib ----------------- Miscellansous useful scripts for pre and post processing
@@ -166,6 +162,7 @@ scr/fates --------- FATES model and sub-directories
                     Functionally Assembled Terrestrial Ecosystem Simulator (FATES)
                     Experimental Ecosystem Demography model
 src/utils --------- Utility codes
+src/self_tests ---- Internal testing (unit tests run as a part of a CTSM simulation)
 src/unit_test_shr - Unit test shared modules for unit testing
 src/unit_test_stubs Unit test stubs that replicate CTSM code simpler
 
@@ -175,11 +172,10 @@ src/unit_test_stubs Unit test stubs that replicate CTSM code simpler
 
          cd $CIMEROOT/scripts
          ./create_newcase            # get help on how to run create_newcase
-         ./create_newcase --case testI --res f19_g17_gl4 --compset I2000Clm50BgcCrop
+         ./create_newcase --case testI --res f19_g17_gl4 --compset I2000Clm60BgcCrop
                                      # create new "I" case for default machine at 1.9x2.5_gx1v7 
-                                     # with 4km greenland ice sheetres resolution
-                                     # "I2000Clm50BgcCrop" case is clm5_0 active, datm8, and inactive ice/ocn
-                                     # With no-evolve ice-sheet, and MOSART for river-routing
+                                     # "I2000Clm60BgcCrop" case is clm6_0 physics, CDEPS, and inactive ice/ocn/glc
+                                     # and MOSART for river-routing
          cd testI
          ./case.setup                # create the $CASE.run file
          ./case.build                # build model and create namelists

README.CHECKLIST.new_case

@@ -22,6 +22,8 @@ General Checklist to always do:
    (./xmlquery LND_TUNING_MODE)
  - For an "I compset" make sure you are running over the right forcing years 
    (usually ./xmlquery -p DATM_YR)
+ - Again for an "I compset" make sure the DATM streams are operating over the right years
+   (look at the CaseDocs/datm.streams.xml file)
  - First and align year for streams should be the start year of a historical simulation 
    (./xmlquery RUN_STARTDATE)
    (grep stream_year_first CaseDocs/lnd_in; grep model_year_align CaseDocs/lnd_in)

README.NUOPC_driver.md

@@ -41,15 +41,10 @@ nuopc.runseq is a text file that determines how the driver operates. You can cha
 by having an updated copy in your case directory.
 
 
-## What if I want to use the previous MCT driver?
-
-The MCT driver will be available for sometime going forward, but
-new development won't go into it, and it will eventually be removed.
-But, if you have to...
-Use the "--driver mct" command line option to create_newcase
-You can set COMP_INTERFACE in a case as well, but it won't create it with everything needed
-so we recommend setting up a case from scratch.
+## What if I want to use the MCT driver?
 
+The MCT driver is now deprecated, and will be removed. So at this point we don't
+suggest using it anymore.
 
 For more notes see:
 

README.md

@@ -50,12 +50,18 @@ Software engineering team:
 - [Ryan Knox](https://github.com/rgknox)
 
 Science team:
-- [Dave Lawrence](https://github.com/dlawrenncar)
 - [Will Wieder](https://github.com/wwieder)
+- [Dave Lawrence](https://github.com/dlawrenncar)
 - [Danica Lombardozzi](https://github.com/danicalombardozzi)
 - [Keith Oleson](https://github.com/olyson)
 - [Sean Swenson](https://github.com/swensosc)
-- [Jackie Shuman](https://github.com/jkshuman)
 - [Peter Lawrence](https://github.com/lawrencepj1)
-- [Rosie Fisher](https://github.com/rosiealice)
 - Gordon Bonan
+
+FATES Project:
+- https://github.com/NGEET/fates?tab=readme-ov-file
+
+Perturbed Parameter Experiment (PPE) Science team:
+- [Katie Dagon] (https://github.com/katiedagon)
+- [Daniel Kennedy] (https://github.com/djk2120)
+- [Linnea Hawkins] (https://github.com/linniahawkins)

README_EXTERNALS.rst

@@ -1,6 +1,11 @@
 Obtaining the full model code and associated scripting infrastructure
 =====================================================================
 
+[!CAUTION]
+This is deprecated and will be replaced with git submodules. See
+https://github.com/ESCOMP/CTSM/pull/2443
+
+
 CTSM is released via GitHub. You will need some familiarity with git in order
 to modify the code and commit these changes. However, to simply checkout and run the
 code, no git knowledge is required other than what is documented in the following steps.