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https://github.com/escomp/ctsm

Community Terrestrial Systems Model (includes the Community Land Model of CESM)
https://github.com/escomp/ctsm

cesm climate clm ecosystem hydrology land land-surface-model ncar

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Community Terrestrial Systems Model (includes the Community Land Model of CESM)

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README 

        
$CTSMROOT/README                                          04/19/2023



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.



CMEPS is the Community Mediator for Earth Prediction Systems. And CDEPS is the

Community Data Models for Earth Prediction System. They are both NUOPC based models

used to drive the CESM (Community Earth System Model) of which CTSM is a component of.

NUOPC is the National Unified Operational Prediction Capability a standard way of building

coupled model systems. The NUOPC layer is based on the Earth System Modeling Framework (ESMF).



For lists of current bugs (issues) and current development see the CTSM GitHub page:



https://github.com/ESCOMP/CTSM



INFORMATION ON THE CMEPS DRIVER:



https://escomp.github.io/CMEPS



https://earthsystemmodeling.org/nuopc/



IMPORTANT NOTE ON CESM CHECKOUT VERSUS A CTSM CHECKOUT:



If this is the top level directory from making a clone of CTSM the 

directory structure is a little bit different than if CTSM is from 

a clone of the entire CESM. If this is part of CESM this directory

will be under components/clm alongside other CESM component models.

For a CTSM checkout this will be the top level directory.



Other documentation will refer to $CTSMROOT and it means the directory

that this file is at. CIMEROOT is the directory where "cime" is for

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 --------------- build-namelist scripts for CTSM.

src --------------- CTSM Source code.

lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model)

tools ------------- CTSM Offline tools to prepare input datasets and process output.

cime_config ------- Configuration files of cime for compsets and CTSM settings

bin/git-fleximod -- Script to manage the needed sub-component source directories (handled with git submodule)

py_env_create ----- Script to setup the python environment for CTSM python tools using conda

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: 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).

components/cism --------------------- CESM Community land Ice Sheet Model.

components/mosart ------------------- Model for Scale Adaptive River Transport

components/rtm ---------------------- CESM River Transport Model.



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_GITFLEXIMOD.rst --- Information on how to work with git-fleximod for CTSM

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

                           ChangeLog/ChangeSum files

doc/ChangeLog ------------ Documents different CTSM versions

doc/ChangeSum ------------ Summary documentation of different CTSM versions



doc/design --------------- Software Engineering and code design document files



Checklists for standard Software Engineering tasks



./doc/README.CHECKLIST.master_tags

./bld/namelist_files/README.CHECKLIST.interpolating_initial_conditions.md



Documentation of Namelist Items: (view the following in a web browser)



bld/namelist_files/namelist_definition_ctsm.xml --- Definition of all namelist items

bld/namelist_files/namelist_defaults_ctsm.xml ----- Default values



=============================================================================================

Important files in main directories (under $CTSMROOT):

=============================================================================================



run_sys_tests --------------- Python script to send the standard CTSM testing off (submits

                              the create_test test suite for several different compilers on the

                              machines we do standard CTSM testing on).



parse_cime.cs.status -------- Script to parse test status files cs.status.* created by create_test

                              (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 

                                                 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/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 build-namelist scripts.

bld/build-namelist ---------- Script to build CTSM namelists.



cime_config/buildnml ------------- Build the CTSM namelist for CIME

cime_config/buildlib ------------- Build the CTSM library

cime_config/config_compsets.xml -- Define CTSM compsets

cime_config/config_component.xml - Define CTSM XML settings

cime_config/config_tests.xml ----- Define CTSM specific tests 

cime_config/config_pes.xml ------- Define Processor layouts for various CTSM grids and compsets

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".)



tools/mksurfdata_esmf --------- Directory to build program to create surface dataset 

                                at any resolution.

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 (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

                                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.



=============================================================================================

Source code directory structure:

=============================================================================================



src/biogeochem ---- Biogeochemisty

src/main ---------- Main control and high level code

src/cpl ----------- Land model high level caps for NUOPC driver (and LILAC)

src/biogeophys ---- Biogeophysics (Hydrology)

src/dyn_subgrid --- Dynamic land unit change

src/init_interp --- Online interpolation

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



=============================================================================================

    QUICKSTART: using the NUOPC driver scripts

=============================================================================================



         cd $CIMEROOT/scripts

         ./create_newcase            # get help on how to run create_newcase

         ./create_newcase --case testI --res f19_g17_gl4 --compset I2000Clm60BgcCrop

                                     # create new "I" case for default machine at 1.9x2.5_gx1v7 

                                     # "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

         ./case.submit               # submit script

                                     # (NOTE: ./xmlchange RESUBMIT=10 to set RESUBMIT to number

                                     # #  of times to automatically resubmit -- 10 in this example)