Merge tag 'release-clm5.0.35' into DUSTEMIS

Update externals for cism and cime to cesm2.1.4-rc-10. cime update was needed to run on izumi.
iAdds a compset for the smyle L83 model (both 1850 and transient). BWsc1850smyle (jedwards4b)
Add SSP3-7.0 extension compset and use-case, that runs for fixed 2100 conditions with 2100 landuse
and 2100 harvest and fertilizer.

Update Nitrogen-deposition datasets with files created from WACCM simulations for SSP scenarios (SSP3-7.0,
SSP5-3.4, and SSP5-8.5).

Fix several issues.

.gitattributes

@@ -0,0 +1,6 @@
+*.svg filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -5,6 +5,7 @@ manage_externals.log
 /tools/PTCLM/
 /cime/
 /components/
+/doc/doc-builder/
 
 # ignore svn directories
 **/.svn/**
@@ -17,6 +18,23 @@ manage_externals.log
 *.swp
 *~
 
+# vim files (from https://github.com/github/gitignore/blob/master/Global/Vim.gitignore)
+# Swap
+[._]*.s[a-v][a-z]
+[._]*.sw[a-p]
+[._]s[a-rt-v][a-z]
+[._]ss[a-gi-z]
+[._]sw[a-p]
+# Session
+Session.vim
+# Temporary
+.netrwhist
+# (removed *~ because it is listed above)
+# Auto-generated tag files
+tags
+# Persistent undo
+[._]*.un~
+
 # mac files
 .DS_Store
 
@@ -72,6 +90,9 @@ clm.input_data_list
 clm.input_data_list.previous
 *.stdout.txt.o*
 
+# mksurfdata unit tests
+unit_test_build
+
 # Tools executables
 /tools/mksurfdata_map/mksurfdata_map
 /tools/mkprocdata_map/mkprocdata_map

.lfsconfig

@@ -0,0 +1,2 @@
+[lfs]
+        fetchexclude = *

.zenodo.json

@@ -0,0 +1,7 @@
+{
+    "creators": [
+        {
+            "name": "CTSM Development Team"
+        }
+    ]
+}

Externals.cfg

@@ -7,32 +7,39 @@ required = True
 [cism]
 local_path = components/cism
 protocol = git
-repo_url = https://github.com/ESCOMP/cism-wrapper
-tag = release-cesm2.0.04
+repo_url = https://github.com/ESCOMP/CISM-wrapper
+tag = cism-release-cesm2.1.2_02
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
-repo_url = https://github.com/ESCOMP/rtm
-tag = release-cesm2.0.02
+repo_url = https://github.com/ESCOMP/RTM
+tag = release-cesm2.0.04
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
-repo_url = https://github.com/ESCOMP/mosart
-tag = release-cesm2.0.03
+repo_url = https://github.com/ESCOMP/MOSART
+tag = release-cesm2.0.04
 required = True
 
 [cime]
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime_cesm2_1_rel_05
+tag = cime5.6.39
 required = True
 
+[doc-builder]
+local_path = doc/doc-builder
+protocol = git
+repo_url = https://github.com/ESMCI/doc-builder
+tag = v1.0.4
+required = False
+
 [externals_description]
 schema_version = 1.0.0
 

Externals_CLM.cfg

@@ -1,15 +1,15 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/NCAR/fates-release
-tag = fates_s1.8.1_a3.0.0
+repo_url = https://github.com/NGEET/fates
+tag = sci.1.30.0_api.8.0.0
 required = True
 
 [PTCLM]
 local_path = tools/PTCLM
 protocol = git
-repo_url = https://github.com/ESCOMP/ptclm
-tag = PTCLM2_180611
+repo_url = https://github.com/ESCOMP/PTCLM
+tag = PTCLM2_20200902
 required = True
 
 [externals_description]

README

@@ -121,6 +121,10 @@ 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/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.
 
 
 =============================================================================================

README.md

@@ -0,0 +1,59 @@
+# CTSM
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3739617.svg)](https://doi.org/10.5281/zenodo.3739617)
+
+## Overview and resources
+
+The Community Terrestrial Systems 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
+
+http://www.cesm.ucar.edu/models/cesm2.0/land/
+
+and
+
+https://escomp.github.io/ctsm-docs/
+
+For help with how to work with CTSM in git, see
+
+https://github.com/ESCOMP/CTSM/wiki/Quick-start-to-CTSM-development-with-git
+
+and
+
+https://github.com/ESCOMP/ctsm/wiki/Recommended-git-setup
+
+For support with model use, troubleshooting, etc., please use the CTSM forum (or other
+appropriate forum) here:
+
+https://xenforo.cgd.ucar.edu/cesm/
+
+To get updates on CTSM tags and important notes on CTSM developments
+join our low traffic email list:
+
+https://groups.google.com/a/ucar.edu/forum/#!forum/ctsm-dev
+
+(Send email to [email protected] if you have problems with any of this)
+
+## CTSM code management team
+
+CTSM code management is provided primarily by:
+
+Software engineering team:
+- [Erik Kluzek](https://github.com/ekluzek)
+- [Bill Sacks](https://github.com/billsacks)
+- [Mariana Vertenstein](https://github.com/mvertens)
+- [Negin Sobhani](https://github.com/negin513)
+- [Sam Levis](https://github.com/slevisconsulting)
+
+Science team:
+- [Dave Lawrence](https://github.com/dlawrenncar)
+- [Will Wieder](https://github.com/wwieder)
+- [Danica Lombardozzi](https://github.com/danicalombardozzi)
+- [Keith Oleson](https://github.com/olyson)
+- [Sean Swenson](https://github.com/swensosc)
+- [Mike Barlage](https://github.com/barlage)
+- [Rosie Fisher](https://github.com/rosiealice)
+- [Peter Lawrence](https://github.com/lawrencepj1)