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README
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$CTSMROOT/README 06/08/2018
Community Land Surface Model (CLM) science version 5.0.0 series -- source code, tools,
offline-build and test scripts. This gives you everything you need
to run CLM with CESM with datm8 to provide CRU NCEP or GSWP3 forcing data in
place of a modeled atmosphere.
For lists of current bugs (issues) and current development see the CTSM GitHub page:
https://github.com/ESCOMP/ctsm
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 $CTSMROOT/cime.
General directory structure ($CTSMROOT):
doc --------------- Documentation of CLM.
bld --------------- Template, configure and build-namelist scripts for clm.
src --------------- CLM Source code.
test -------------- CLM Testing scripts for CLM offline tools.
tools ------------- CLM Offline tools to prepare input datasets and process output.
cime_config ------- Configuration files of cime for compsets and CLM settings
manage_externals -- Script to manage the external source directories
Directory structure only for a CTSM checkout:
components -------- Other active sub-components needed for CLM to run (river routing and land-ice models)
cime/scripts --------------- cesm/cime driver scripts
cime/src/drivers/mct/main ----------- CESM top level driver source code.
cime/src/drivers/mct/shr ------------ CESM top level driver shared code.
cime/src/components/data_comps/datm - CESM Data model version 8 source code.
cime/src/components/stub_comps/sice - CESM stub sea-ice model source code.
cime/src/components/stub_comps/socn - CESM stub ocean model source code.
cime/src/components/stub_comps/sglc - CESM stub glacier model source code.
cime/src/externals ------------------ CESM external utility codes
(Model Coupling Toolkit (MCT)
(Earth System Model Framework)
(timing -- code timing utility)
(pio -- Parallel Input/Output)
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.rst --------------- File that displays under the project in github
README_EXTERNALS.rst ----- Information on how to work with subversion externals for clm
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 CLM versions
doc/ChangeSum ---------------- Summary documentation of different CLM versions
Documentation of Namelist Items: (view the following in a web browser)
bld/namelist_files/namelist_definition.xml --- Definition of all namelist items
bld/namelist_files/namelist_defaults_clm4_5.xml - Default values for CLM4.5/CLM5.0
=============================================================================================
Important files in main directories (under $CTSMROOT):
=============================================================================================
Externals.cfg --------------- File for management of the main high level externals
Externals_CLM.cfg ----------- File for management of the CLM specific externals (i.e. FATES)
parse_cime.cs.status -------- Script to parse test status files cs.status.* created by create_test
doc/Quickstart.GUIDE -------- Quick guide to using cpl7 scripts.
doc/IMPORTANT_NOTES --------- Some important notes about this version of
clm, 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 -------------- CLM Users Guide
doc/CodeReference ----------- CLM Code Reference Guide
bld/README ------------------ Description of how to use the configure and
build-namelist scripts.
bld/configure --------------- Script to prepare CLM to be built.
bld/build-namelist ---------- Script to build CLM namelists.
cime_config/buildnml ------------- Build the CLM namelist for CIME
cime_config/buildlib ------------- Build the CLM library
cime_config/config_compsets.xml -- Define CLM compsets
cime_config/config_component.xml - Define CLM XML settings
cime_config/config_tests.xml ----- Define CLM specific tests
cime_config/config_pes.xml ------- Define Processor layouts for various CLM grids and compsets
cime_config/testdefs ------------- Directory for specification of CLM 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
CLM's offline tools.
tools/mksurfdata_map ---------- 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.
=============================================================================================
Source code directory structure:
=============================================================================================
src/biogeochem ---- Biogeochemisty
src/main ---------- Main control and high level code
src/cpl ----------- Land model high level MCT and ESMF drivers
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/unit_test_shr - Unit test shared modules for unit testing
src/unit_test_stubs Unit test stubs that replicate CTSM code simpler
src_clm40 --------- CLM4.0 source code directory
=============================================================================================
QUICKSTART: using the CPL7 scripts
=============================================================================================
cd $CIMEROOT/scripts
./create_newcase # get help on how to run create_newcase
./create_newcase --case testI --res f19_g17_gl4 --compset I2000Clm50BgcCrop
# 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
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)