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121 changes: 68 additions & 53 deletions Copyright
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--------------------------------------------------------------------------------
CESM1.0
--------------------------------------------------------------------------------
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.
CESM1.5: Copyright Notice and Disclaimer

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 ESMF
Institution University of Illinois/NCSA
Copyright Copyright 2002-2009, University of Illinois/NCSA Open Source License
Terms of Use http://www.gnu.org/copyleft/gpl.html
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.

Code POP, SCRIP, CICE
Institution Los Alamos National Laboratory
Copyright Copyright 2008 Los Alamos National Security, LLC
Terms of Use http://oceans11.lanl.gov/trac/CICE/wiki/CopyRight

Code Glimmer-CISM
Institution LANL/U. Bristol/U. Edinburgh/U. Montana/U. Swansea)
Copyright Copyright 2004-2010, GNU General Public License
Terms of Use GNU General Public License

Code AER RRTMG
Institution Atmospheric and Environmental Research, Inc.
Copyright Copyright 2002-2010, Atmospheric and Environmental Research, Inc.
Terms of Use http://rtweb.aer.com/rrtm_frame.html
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.

Code MCT
Institution Argonne National Laboratory
Copyright Copyright 2000, 2010, University of Chicago.
Terms of Use http://www.cesm.ucar.edu/models/cesm1.0/copyright_MCT.html
The following components are copyrighted and may only be used, modified,
or redistributed under the terms indicated below.

Code ICSSP
Institution N/A
Copyright Copyright 2003, 2010, Steve Klein and Mark Webb
Terms of Use http://gcss-dime.giss.nasa.gov/simulator.html
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

Glimmer-CISM LANL/U. Copyright GNU General Public License
Bristol/U. 2004-2010,
Edinburgh/U. GNU General
Montana/U. Public License
Swansea

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.


Code XML/Lite
Institution Wadsack-Allen Digital Group
Copyright Copyright 2001,2010 Wadsack-Allen Digital Group
Terms of Use http://aspn.activestate.com/ASPN/CodeDoc/XML-Lite/Lite.html
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.

Code Inf_NaN_Detection module
Institution Lahey Computer Systems, Inc.
Copyright Copyright(c) 2003, Lahey Computer Systems, Inc.
Terms of Use Copies of this source code, or standalone compiled files derived from
this source may not be sold without permission from Lahey Computers Systems.
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.
149 changes: 80 additions & 69 deletions README
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components/clm/README 04/07/2015
README 02/05/2018

Community Land Surface Model (CLM) science version 4.5.1 series -- source code, tools,
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 Qian or CRU NCEP forcing data in
to run CLM with CESM with datm8 to provide CRU NCEP or GSWP3 forcing data in
place of a modeled atmosphere.

General directory structure:

components/clm/doc ---- Documentation of CLM.
components/clm/bld ---- Template, configure and build-namelist scripts for clm.
components/clm/src ---- CLM Source code.
components/clm/test --- CLM Testing scripts for CLM offline tools.
components/clm/tools -- CLM Offline tools to prepare input datasets and process output.
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

cime/scripts --------------- CPL7 scripts

cime/driver_cpl/driver ---------- CESM top level driver source code.
cime/driver_cpl/shr ------------- CESM top level driver shared code.
cime/driver_cpl/shr_esmf -------- CESM top level driver shared code for ESMF.
cime/components/data_comps/datm - CESM Data model version 8 source code.
components/cism ----------------- CESM Community land Ice Sheet Model.
components/rtm ------------------ CESM River Transport Model.
cime/components/stub_comps/sice - CESM stub sea-ice model source code.
cime/components/stub_comps/socn - CESM stub ocean model source code.
cime/components/stub_comps/sglc - CESM stub glacier model source code.
cime/external ------------------- CESM external utility codes
(Model Coupling Toolkit (MCT)
(Earth System Model Framework)
(timing -- code timing utility)
(pio -- Parallel Input/Output)
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.
components/cism --------------------- CESM Community land Ice Sheet Model.
components/mosart ------------------- Model for Scale Adaptive River Transport
components/rtm ---------------------- CESM River Transport Model.
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)

Top level documentation:

README ------------------- This file
README_EXTERNALS --------- Information on how to work with subversion externals for clm
SVN_EXTERNAL_DIRECTORIES - Subversions externals to use
README_EXTERNALS.rst ----- Information on how to work with subversion externals for clm
Copyright ---------------- CESM Copyright file
UpDateChangeLog.pl ------- Script to add documentation on a tag to the
doc/UpdateChangeLog.pl ------- Script to add documentation on a tag to the
ChangeLog/ChangeSum files
ChangeLog ---------------- Documents different CLM versions
ChangeSum ---------------- Summary documentation of different CLM versions
ChangeLog/ChangeSum ------ Also copied to components/lnd/clm/doc
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)

components/clm/bld/namelist_files/namelist_definition.xml --- Definition of all namelist items
components/clm/bld/namelist_files/namelist_defaults_clm.xml - Default values
components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml - Default values for CLM4.5/CLM5.0

=============================================================================================
Important files in main directories:
=============================================================================================

components/lnd/clm/doc/Quickstart.GUIDE -------- Quick guide to using cpl7 scripts.
components/lnd/clm/doc/Quickstart.userdatasets - Quick guide to using your own datasets.
components/lnd/clm/doc/IMPORTANT_NOTES --------- Some important notes about this version of
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/Quickstart.userdatasets - Quick guide to using your own datasets.
doc/IMPORTANT_NOTES --------- Some important notes about this version of
clm, configuration modes and namelist items
that are not validated or functional.
components/clm/doc/KnownBugs --------------- List of known bugs.
components/clm/doc/KnownLimitations -------- List of known limitations and workarounds.
components/clm/doc/ChangeLog --------------- Detailed list of changes for each model version.
components/clm/doc/ChangeSum --------------- Summary one-line list of changes for each
doc/KnownBugs --------------- List of known bugs.
doc/KnownLimitations -------- List of known limitations and workarounds.
doc/ChangeLog --------------- Detailed list of changes for each model version.
doc/ChangeSum --------------- Summary one-line list of changes for each
model version.
components/clm/doc/README ------------------ Documentation similar to this file
components/clm/doc/UsersGuide -------------- CLM Users Guide
components/clm/doc/CodeReference ----------- CLM Code Reference Guide

components/clm/bld/configure --------------- Script to prepare CLM to be built.

components/clm/test/tools/test_driver.sh -- Script for general software testing of
CLM's offline tools.

components/clm/tools/clm4_5/mksurfdata_map --- Directory to build program to create surface dataset
at any resolution.
components/clm/tools/clm4_5/interpinic ------- Directory to build program to interpolate initial
conditions to any resolution.
components/clm/tools/shared/mkdatadomain ----- Directory to build program to create datm7 or docn7
domain files from clm files.
components/clm/tools/shared/mkprocdata_map --- Process history data from unstructed grids to a gridded
format.
components/clm/tools/shared/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.

components/clm/bld/README ------------- Description of how to use the configure and
doc/README ------------------ Documentation similar to this file
doc/UsersGuide -------------- CLM Users Guide
doc/CodeReference ----------- CLM Code Reference Guide

bld/configure --------------- Script to prepare CLM to be built.

test/tools/test_driver.sh -- Script for general software testing of
CLM's offline tools.

tools/clm4_5/mksurfdata_map --- Directory to build program to create surface dataset
at any resolution.
tools/clm4_5/interpinic ------- Directory to build program to interpolate initial
conditions to any resolution.
tools/shared/mkdatadomain ----- Directory to build program to create datm7 or docn7
domain files from clm files.
tools/shared/mkprocdata_map --- Process history data from unstructed grids to a gridded
format.
tools/shared/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.

bld/README ------------- Description of how to use the configure and
build-namelist scripts.

=============================================================================================
Source code directory structure:
=============================================================================================

components/clm/src/biogeochem -- Biogeochemisty
components/clm/src/main -------- Main control and high level code
components/clm/src/cpl --------- Land model high level MCT and ESMF drivers
components/clm/src/biogeophys -- Biogeophysics (Hydrology)
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

scr_clm40 ------- CLM4.0 source code directory

=============================================================================================
QUICKSTART: using the CPL7 scripts:
=============================================================================================

cd cime/scripts
./create_newcase # get help on how to run create_newcase
./create_newcase -case testI -mach bluefire -res f19_g16 -compset I
# create new "I" case for bluefire at 1.9x2.5_gx1v6 res
# "I" case is clm active, datm8, and inactive ice/ocn
./create_newcase --case testI --res f19_g16 --compset I2000Clm50BgcCrop --mach cheyenne
# create new "I" case for cheyenne_intel at 1.9x2.5_gx1v7 res
# "I2000Clm50BgcCrop" case is clm5_0 active, datm8, and inactive ice/ocn
cd testI
./cesm_setup # create the $CASE.run file
./testI.bluefire.build # build model and create namelists
./testI.bluefire.submit # submit script
./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)

62 changes: 0 additions & 62 deletions README_cime
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7 changes: 2 additions & 5 deletions doc/.ChangeLog_template
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List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):

List all files eliminated:

List all files added and what they do:

List all existing files that have been modified, and describe the changes:
Pull Requests that document the changes (include PR ids):
(https://github.com/ESCOMP/ctsm/pull)

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