Merge tag 'clm5.0.dev013' into release-clm5.0

Update cime and cism to newer versions used in release. These bring in some answer changes. The cime version updates the orbit for 2000 compsets. The cism version changes answers for two fields with NO_EVOLVE and more fields for EVOLVE. Fixes an important bug needed for use with Data Assimulation. Several changes to testing. Adding wallclock as needed, changing a few compsets so science supported compsets are used, added tput_tolerance to some tests known to be variable. Many changes to the clm tools for creating input files. Added the version by querying "git describe" and adding it as an attribute to NetCDF files. Changes to get tools working, and tested. Also changed so that tools can be run in either a CTSM checkout or a CESM checkout. Updated README files so they are accurate.
ESCOMP · Jun 12, 2018 · f0febfe · f0febfe
2 parents db6ac1c + fd7a88a
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diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -0,0 +1,21 @@
+### General Type of Issue:
+Some example types are:
+- bug
+- enhancement
+- question
+
+### Details of Issue:
+(Be sure to give enough details that the issue can be understood sufficiently 
+to replicate or to make the required changes)
+
+### For bugs fill out the following: (Otherwise remove, and remove any prompts that aren't useful)
+-----------------------------------------------------------------
+#### Important Details of your setup/configuration (compset, settings, etc.):
+
+#### Important output or errors that show the problem:
+
+#### What is the CTSM version you are using (output of git describe)?:
+
+#### What is the machine you are running on:?
+
+-----------------------------------------------------------------
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,16 @@
+### Description of changes
+
+### Specific notes
+
+CTSM Issues Fixed (include github issue #):
+
+Are answers expected to change (and if so in what way)?
+
+Any User Interface Changes (namelist or namelist defaults changes)?
+
+Testing performed:
+(List what testing you did to show your changes worked as expected)
+(This can be manual testing or running of the different test suites)
+
+**NOTE: Be sure to check your Coding style against the standard:**
+https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines
diff --git a/.gitignore b/.gitignore
@@ -65,10 +65,17 @@ clm.input_data_list.previous
 tools/mksurfdata_map/mksurfdata_map
 tools/mkprocdata_map/mkprocdata_map
 
+# mkmapdata output files
+tools/mkmapdata/PET*.RegridWeightGen.Log
+tools/mkmapdata/regrid.*.out
+tools/mkmapdata/regrid.*.err
+tools/mkmapdata/regrid.o*
+
 # build output
 *.o
 *.mod
 core.*
 *.gz
 *.log !run.log
 *.pyc
+Depends
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,44 @@
+## How to contribute:
+
+It's recommended that you first contact [email protected] to discuss the changes or additions that you propose.
+Work with them to think about the design and implemention of the changes as well as the planning
+and scheduling for the change to come into CTSM.
+
+It's also recommened that you join the [email protected] google groups in order 
+to be informed about the science that is happening in CTSM as well as the latest develepments and tags.
+The ctsm-dev group is here:
+
+https://groups.google.com/a/ucar.edu/forum/#!forum/ctsm-dev
+
+Use the help from the wiki below to setup a fork and personal branch in GitHub to put your developments
+on and keep up to date with the master branch of CTSM. Once the changes are sufficiently advanced you
+can form a Pull Request on GitHub. Either from your fork on GitHub, or from the main ESCOMP GitHub page
+for CTSM (be sure to hit the "compare across forks" link at the top of the page when you first create
+the pull request).
+
+https://github.com/ESCOMP/ctsm/pulls
+
+This allows you to show your proposed changes and start getting feedback on them (even if they aren't finished). 
+This also allows your changes to be planned for and slated for a time to come into CTSM master. In most 
+cases you won't merge the Pull Request yourself, but a software engineer responsible for CTSM will do 
+additional testing and bring the changes to CTSM master.
+
+### CTSM Developers Guide:
+
+ https://wiki.ucar.edu/display/ccsm/Community+Land+Model+Developers+Guide
+
+## Getting Started:
+
+The following resources give you information on the project and how to get started.
+
+#### CTSM Wiki:
+
+https://github.com/ESCOMP/ctsm/wiki
+
+#### Coding Practices and Style:
+
+Code conventions: https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines
+
+#### Code of Conduct:
+
+See the "CODE_OF_CONDUCT.md" file for expectations of how to work in the community.
diff --git a/Copyright b/Copyright
@@ -26,11 +26,12 @@ POP,SCRIP,CICE	Los Alamos National	Copyright 2008	Los Alamos National Security,
 					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 
+CISM            NCAR/LANL/ORNL/SNL/     Copyright       GNU Lesser General Public License v. 3
+                LBNL/NYU/U. Bristol/    2004-2018,      CISM is free software: you can redistribute it
+                U. Edinburgh/           GNU Lesser      and/or modify it under the terms of the GNU
+                U. Montana/U. Swansea   General Public  Lesser General Public License as published by the
+                                        License v. 3    Free Software Foundation, either version 3 of the
+                                                        License, or (at your option) any later version.
 
 AER RRTMG	Atmospheric		Copyright	AER RRTMG Copyright
     		and			2002-2010, 

diff --git a/Externals.cfg b/Externals.cfg
@@ -8,29 +8,29 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/cism-wrapper
-tag = release-v2.1.00
+tag = release-v2.1.01
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/rtm
-tag = rtm1_0_66
+tag = release-cesm2.0.00
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/mosart
-tag = mosart1_0_31
+tag = release-cesm2.0.00
 required = True
 
 [cime]
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-hash = a67dceae95567cc7529c4cfed153017f4b65b210
+tag = cime_cesm2_0_rel_03
 required = True
 
 [externals_description]

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -9,7 +9,7 @@ required = True
 local_path = tools/PTCLM
 protocol = git
 repo_url = https://github.com/ESCOMP/ptclm
-tag = PTCLM2_180214
+tag = PTCLM2_180611
 required = True
 
 [externals_description]

diff --git a/README b/README
@@ -1,15 +1,29 @@
-README                                          02/05/2018
+$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:
+For lists of current bugs (issues) and current development see the CTSM GitHub page:
 
 https://github.com/ESCOMP/ctsm
 
-General directory structure:
+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.
@@ -19,14 +33,15 @@ tools ------------- CLM Offline tools to prepare input datasets and process outp
 cime_config ------- Configuration files of cime for compsets and CLM settings
 manage_externals -- Script to manage the external source directories
 
-cime/scripts --------------- CPL7 scripts
+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.
-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.
@@ -35,11 +50,16 @@ cime/src/externals ------------------ CESM external utility codes
                                       (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:
+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
@@ -48,18 +68,17 @@ 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_clm4_5.xml - Default values for CLM4.5/CLM5.0
+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:
+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/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.
@@ -79,7 +98,14 @@ 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.
@@ -101,28 +127,32 @@ tools/ncl_scripts  ------------ Directory of NCL and perl scripts to do various
 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
-
-scr_clm40 ------- CLM4.0 source code directory
+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:
+    QUICKSTART: using the CPL7 scripts
 =============================================================================================
 
-         cd cime/scripts
+         cd $CIMEROOT/scripts
          ./create_newcase            # get help on how to run create_newcase
-         ./create_newcase --case testI --res f19_g17_gl4 --compset I2000Clm50BgcCrop --mach cheyenne
-                                     # create new "I" case for cheyenne_intel at 1.9x2.5_gx1v7 res
+         ./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

diff --git a/README.rst b/README.rst
@@ -4,7 +4,7 @@ CTSM
 
 The Community Terrestrial Systems Model.
 
-This includes the Community Land Model (CLM5 and CLM4.5) of the Community Earth System 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
@@ -28,4 +28,4 @@ join our low traffic email list:
 
 https://groups.google.com/a/ucar.edu/forum/#!forum/ctsm-dev
 
-(Send email to ctsm-core@ucar.edu if you have problems with any of this)
+(Send email to ctsm-software@ucar.edu if you have problems with any of this)
diff --git a/README_EXTERNALS.rst b/README_EXTERNALS.rst
@@ -1,7 +1,7 @@
 Obtaining the full model code and associated scripting infrastructure
 =====================================================================
 
-CTSM is released via github. You will need some familiarity with git in order
+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.
 
@@ -115,7 +115,7 @@ Committing your change to Externals.cfg
 After making this change, it's a good idea to commit the change in your
 local CTSM git repository. First create a branch in your local
 repository, then commit it. (Unlike with subversion, branches are stored
-locally unless you explicitly push them up to github. Feel free to
+locally unless you explicitly push them up to GitHub. Feel free to
 create whatever local branches you'd like.) For example::
 
   git checkout -b my_ctsm_branch