ESCOMP · ekluzek · May 9, 2023 · Feb 21, 2023 · Feb 21, 2023 · Mar 7, 2023
diff --git a/Externals.cfg b/Externals.cfg
@@ -55,7 +55,7 @@ local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.9
+tag = cdeps1.0.11
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps

diff --git a/cime_config/buildnml b/cime_config/buildnml
@@ -3,7 +3,7 @@
 """
 CTSM namelist creator
 """
-import sys, os, shutil
+import sys, os, shutil, re
 
 _CIMEROOT = os.environ.get("CIMEROOT")
 if _CIMEROOT is None:
@@ -41,6 +41,7 @@ def buildnml(case, caseroot, compname):
     configuration = case.get_value("CLM_CONFIGURATION")
     structure = case.get_value("CLM_STRUCTURE")
     ccsm_co2_ppmv = case.get_value("CCSM_CO2_PPMV")
+    casename = case.get_value("CASE")
     clm_co2_type = case.get_value("CLM_CO2_TYPE")
     clm_namelist_opts = case.get_value("CLM_NAMELIST_OPTS")
     clm_bldnml_opts = case.get_value("CLM_BLDNML_OPTS")
@@ -133,6 +134,13 @@ def buildnml(case, caseroot, compname):
         clm_usrdat_name = case.get_value("CLM_USRDAT_NAME")
         lnd_grid = clm_usrdat_name
         clmusr = " -clm_usr_name %s "%clm_usrdat_name
+        # Write warning about initial condition data
+        if "NEON" in clm_usrdat_name and clm_force_coldstart == "off":
+            if ("_transient" in clm_nml_use_case) \
+            and (re.fullmatch(r"\w\w\w\w\.transient",  casename) is None \
+            or clm_usrdat_name is "NEON.PRISM"):
+                logger.warning( "WARNING: Do you have approriprate initial conditions for this simulation?" \
+                + " Check that the finidat file used in the lnd_in namelist is apprporiately spunup for your case" )
 
     if comp_atm != "datm":
         nomeg = "-no-megan"

diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
@@ -241,10 +241,13 @@
     <default_value>UNSET</default_value>
     <group>run_component_ctsm</group>
     <file>env_run.xml</file>
-    <desc>Dataset name for user-created datasets. This is used as the argument
-      in Buildconf/clm.buildnml to build-namelist -clm_usr_name. An example of
-      such a dataset would be 1x1pt_boulderCO_c090722. The default value is UNSET.
-      This is an advanced flag and should only be used by expert users.</desc>
+    <desc>Resolution name for user-created resolutions. This is especially used
+      for single point and regional resolutions created via subset_data from
+      the global datasets. This should be set when you use CLM_USRDAT as the grid
+      to create_newcase.  The default value is UNSET.
+      For NEON cases, this can be set to either NEON or NEON.PRISM, the latter of which would
+      use PRISM precipitation instead of the default NEON precipitation. NEON cases then also
+      use the variable NEONSITE to specify the exact site.</desc>
   </entry>
 
   <entry id="CLM_USRDAT_DIR">
@@ -295,6 +298,26 @@
       ABBY,BLAN,CPER,DEJU,GRSM,HEAL,KONA,LENO,NIWO,ONAQ,PUUM,SERC,SRER,TALL,TREE,WOOD,
       BARR,BONA,DCFS,DELA,GUAN,JERC,KONZ,MLBS,NOGP,ORNL,RMNP,SJER,STEI,TEAK,UKFS,WREF,
       BART,CLBJ,DSNY,HARV,JORN,LAJA,MOAB,OAES,OSBS,SCBI,SOAP,STER,TOOL,UNDE,YELL,
+      NEON_PRECIP.ABBY,NEON_PRECIP.BLAN,NEON_PRECIP.CPER,NEON_PRECIP.DEJU,NEON_PRECIP.GRSM,
+      NEON_PRECIP.HEAL,NEON_PRECIP.KONA,NEON_PRECIP.LENO,NEON_PRECIP.NIWO,NEON_PRECIP.ONAQ,
+      NEON_PRECIP.PUUM,NEON_PRECIP.SERC,NEON_PRECIP.SRER,NEON_PRECIP.TALL,NEON_PRECIP.TREE,
+      NEON_PRECIP.WOOD,NEON_PRECIP.BARR,NEON_PRECIP.BONA,NEON_PRECIP.DCFS,NEON_PRECIP.DELA,
+      NEON_PRECIP.GUAN,NEON_PRECIP.JERC,NEON_PRECIP.KONZ,NEON_PRECIP.MLBS,NEON_PRECIP.NOGP,
+      NEON_PRECIP.ORNL,NEON_PRECIP.RMNP,NEON_PRECIP.SJER,NEON_PRECIP.STEI,NEON_PRECIP.TEAK,
+      NEON_PRECIP.UKFS,NEON_PRECIP.WREF,NEON_PRECIP.BART,NEON_PRECIP.CLBJ,NEON_PRECIP.DSNY,
+      NEON_PRECIP.HARV,NEON_PRECIP.JORN,NEON_PRECIP.LAJA,NEON_PRECIP.MOAB,NEON_PRECIP.OAES,
+      NEON_PRECIP.OSBS,NEON_PRECIP.SCBI,NEON_PRECIP.SOAP,NEON_PRECIP.STER,NEON_PRECIP.TOOL,
+      NEON_PRECIP.UNDE,NEON_PRECIP.YELL,
+      PRISM_PRECIP.ABBY,PRISM_PRECIP.BLAN,PRISM_PRECIP.CPER,PRISM_PRECIP.GRSM,
+      PRISM_PRECIP.KONA,PRISM_PRECIP.LENO,PRISM_PRECIP.NIWO,PRISM_PRECIP.ONAQ,
+      PRISM_PRECIP.SERC,PRISM_PRECIP.SRER,PRISM_PRECIP.TALL,PRISM_PRECIP.TREE,
+      PRISM_PRECIP.WOOD,PRISM_PRECIP.DCFS,PRISM_PRECIP.DELA,PRISM_PRECIP.JERC,
+      PRISM_PRECIP.KONZ,PRISM_PRECIP.MLBS,PRISM_PRECIP.NOGP,PRISM_PRECIP.ORNL,
+      PRISM_PRECIP.RMNP,PRISM_PRECIP.SJER,PRISM_PRECIP.STEI,PRISM_PRECIP.TEAK,
+      PRISM_PRECIP.UKFS,PRISM_PRECIP.WREF,PRISM_PRECIP.BART,PRISM_PRECIP.CLBJ,
+      PRISM_PRECIP.DSNY,PRISM_PRECIP.HARV,PRISM_PRECIP.JORN,PRISM_PRECIP.MOAB,
+      PRISM_PRECIP.OAES,PRISM_PRECIP.OSBS,PRISM_PRECIP.SCBI,PRISM_PRECIP.SOAP,
+      PRISM_PRECIP.STER,PRISM_PRECIP.UNDE,PRISM_PRECIP.YELL,
     </valid_values>
     <default_value/>
     <group>run_component_ctsm</group>
@@ -304,7 +327,7 @@
 
   <entry id="NEONVERSION">
     <type>char</type>
-    <valid_values>v1,v2,latest</valid_values>
+    <valid_values>v1,v2,v3,latest</valid_values>
     <default_value>latest</default_value>
     <group>run_component_ctsm</group>
     <file>env_run.xml</file>

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -1561,6 +1561,16 @@
       <option name="comment"  >Add at least one test of a NEON site</option>
     </options>
   </test>
+  <test name="SMS_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/NEON/MOAB--clm/PRISM">
+    <machines>
+      <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="tput_tolerance">0.5</option>
+      <option name="comment"  >Add at least one test of a NEON site with PRISM precipitation</option>
+    </options>
+  </test>
   <test name="SMS_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/Fates--clm/NEON/FATES/NIWO">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
@@ -1572,6 +1582,17 @@
       <option name="comment"  >Add at least one test of a FATES NEON site</option>
     </options>
   </test>
+  <test name="SMS_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesPRISM--clm/NEON/FATES/YELL">
+    <machines>
+      <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+      <machine name="izumi"    compiler="nag"   category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="tput_tolerance">0.5</option>
+      <option name="comment"  >Add at least one test of a FATES NEON site with PRISM precipitation</option>
+    </options>
+  </test>
   <test name="SMS_D_Vmct_Lm1_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm50SpRs" testmods="clm/USUMB_mct">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesPRISM/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesPRISM/include_user_mods
@@ -0,0 +1 @@
+../Fates
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesPRISM/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesPRISM/shell_commands
@@ -0,0 +1,2 @@
+#!/bin/bash
+./xmlchange CLM_USRDAT_NAME=NEON.PRISM
diff --git a/cime_config/testdefs/testmods_dirs/clm/PRISM/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/PRISM/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/cime_config/testdefs/testmods_dirs/clm/PRISM/shell_commands b/cime_config/testdefs/testmods_dirs/clm/PRISM/shell_commands
@@ -0,0 +1,2 @@
+#!/bin/bash
+./xmlchange CLM_USRDAT_NAME=NEON.PRISM
diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands
@@ -1,5 +1,6 @@
 #!/bin/bash
 ./xmlchange CLM_USRDAT_NAME=NEON
+# CLM_USRDAT_NAME can also be set to NEON.PRISM
 ./xmlchange CCSM_CO2_PPMV=408.83
 # Set data forcing data to future scenario so will have data from 2018 to present-day
 ./xmlchange DATM_PRESAERO=SSP3-7.0

diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands
@@ -2,9 +2,15 @@
 ./xmlchange NEONSITE=MLBS
 ./xmlchange PTS_LON=279.47575
 ./xmlchange PTS_LAT=37.37783
-./xmlchange DATM_YR_END=2019
-# Different default number of months to run for transient case
-if  [[ $compset =~ ^HIST ]]; then
-  ./xmlchange DATM_YR_END=2020
-  ./xmlchange STOP_N=24
+# NEON precipitation data for this site is bad so end early
+# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data
+if [ $CLM_USRDAT_NAME=='NEON']
+then
+  ./xmlchange DATM_YR_END=2019  
+  # Different default number of months to run for transient case
+  if  [[ $compset =~ ^HIST ]]
+  then
+    ./xmlchange DATM_YR_END=2020
+    ./xmlchange STOP_N=24
+  fi
 fi
diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands
@@ -2,9 +2,13 @@
 ./xmlchange NEONSITE=MOAB
 ./xmlchange PTS_LON=250.61118
 ./xmlchange PTS_LAT=38.25136
-./xmlchange DATM_YR_END=2020
-# Different default number of months to run for transient case
-if  [[ $compset =~ ^HIST ]]; then
-  ./xmlchange DATM_YR_END=2021
-  ./xmlchange STOP_N=36
+# NEON precipitation data for this site is bad so end early
+# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data
+if [$CLM_USRDAT_NAME=='NEON']; then
+  ./xmlchange DATM_YR_END=2020
+  # Different default number of months to run for transient case
+  if  [[ $compset =~ ^HIST ]]; then
+    ./xmlchange DATM_YR_END=2021
+    ./xmlchange STOP_N=36
+  fi
 fi
diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/NIWO/shell_commands
@@ -1,4 +1,10 @@
+#!/bin/bash
 ./xmlchange NEONSITE=NIWO
 ./xmlchange PTS_LON=254.41676
 ./xmlchange PTS_LAT=40.05236
-./xmlchange DATM_YR_END=2018
+# NEON precipitation data for this site is bad so end early
+# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data
+if [ $CLM_USRDAT_NAME=="NEON" ]
+then
+  ./xmlchange DATM_YR_END=2018
+fi
diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands
@@ -2,9 +2,15 @@
 ./xmlchange NEONSITE=ONAQ
 ./xmlchange PTS_LON=247.54755
 ./xmlchange PTS_LAT=40.17760
-./xmlchange DATM_YR_END=2019
-# Different default number of months to run for transient case
-if  [[ $compset =~ ^HIST ]]; then
-  ./xmlchange DATM_YR_END=2020
-  ./xmlchange STOP_N=24
+# NEON precipitation data for this site is bad so end early
+# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data
+if [ $CLM_USRDAT_NAME=='NEON' ]
+then
+  ./xmlchange DATM_YR_END=2019
+  # Different default number of months to run for transient case
+  if  [[ $compset =~ ^HIST ]]
+  then
+    ./xmlchange DATM_YR_END=2020
+    ./xmlchange STOP_N=24
+  fi
 fi
diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands
@@ -2,10 +2,17 @@
 ./xmlchange NEONSITE=SJER
 ./xmlchange PTS_LON=240.267
 ./xmlchange PTS_LAT=37.107117
-./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019
-# Different default start date and number of months to run for transient case
-if  [[ $compset =~ ^HIST ]]; then
-  ./xmlchange RUN_STARTDATE=2019-01-01
-  ./xmlchange STOP_N=39
+./xmlchange DATM_YR_ALIGN=2019
+# NEON precipitation data for this site is bad so end early
+# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data
+if [ $CLM_USRDAT_NAME=='NEON' ]
+then
+  ./xmlchange DATM_YR_START=2019
+  # Different default start date and number of months to run for transient case
+  if  [[ $compset =~ ^HIST ]]
+  then
+    ./xmlchange RUN_STARTDATE=2019-01-01
+    ./xmlchange STOP_N=39
+  fi
 fi
 
diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands
@@ -2,9 +2,16 @@
 ./xmlchange NEONSITE=TEAK
 ./xmlchange PTS_LON=240.99424199999999
 ./xmlchange PTS_LAT=37.006472
-./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 
-# Different default start date and number of months to run for transient case
-if  [[ $compset =~ ^HIST ]]; then
-  ./xmlchange RUN_STARTDATE=2019-01-01
-  ./xmlchange STOP_N=39
+./xmlchange DATM_YR_ALIGN=2019
+# NEON precipitation data for this site is bad so end early
+# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data
+if [ $CLM_USRDAT_NAME=='NEON']
+then
+  ./xmlchange DATM_YR_START=2019
+  # Different default start date and number of months to run for transient case
+  if  [[ $compset =~ ^HIST ]]
+  then
+    ./xmlchange RUN_STARTDATE=2019-01-01
+    ./xmlchange STOP_N=39
+  fi
 fi
diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands
@@ -2,9 +2,16 @@
 ./xmlchange NEONSITE=WREF
 ./xmlchange PTS_LON=238.04162
 ./xmlchange PTS_LAT=45.81637
-./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 
-# Different default start date and number of months to run for transient case
-if  [[ $compset =~ ^HIST ]]; then
-  ./xmlchange RUN_STARTDATE=2019-01-01
-  ./xmlchange STOP_N=39
+./xmlchange DATM_YR_ALIGN=2019 
+# NEON precipitation data for this site is bad so end early
+# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data
+if [ $CLM_USRDAT_NAME=='NEON' ]
+then
+  # Different default start date and number of months to run for transient case
+  ./xmlchange DATM_YR_START=2019
+  if  [[ $compset =~ ^HIST ]]
+  then
+    ./xmlchange RUN_STARTDATE=2019-01-01
+    ./xmlchange STOP_N=39
+  fi
 fi
diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands
@@ -2,9 +2,16 @@
 ./xmlchange NEONSITE=YELL
 ./xmlchange PTS_LON=249.45803999999998
 ./xmlchange PTS_LAT=44.95597
-./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 
-# Different default start date and number of months to run for transient case
-if  [[ $compset =~ ^HIST ]]; then
-  ./xmlchange RUN_STARTDATE=2019-01-01
-  ./xmlchange STOP_N=39
+./xmlchange DATM_YR_ALIGN=2019
+# NEON precipitation data for this site is bad so end early
+# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data
+if [ $CLM_USRDAT_NAME=='NEON' ]
+then
+  # Different default start date and number of months to run for transient case
+  ./xmlchange DATM_YR_START=2019
+  if  [[ $compset =~ ^HIST ]]
+  then
+    ./xmlchange RUN_STARTDATE=2019-01-01
+    ./xmlchange STOP_N=39
+  fi
 fi
diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands
@@ -1,5 +1,6 @@
 #!/bin/bash
 ./xmlchange CLM_USRDAT_NAME=NEON
+# CLM_USRDAT_NAME can be set to either NEON or NEON.PRISM
 ./xmlchange CCSM_CO2_PPMV=408.83
 # Set data forcing data to future scenario so will have data from 2018 to present-day
 ./xmlchange DATM_PRESAERO=SSP3-7.0

diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams
@@ -37,3 +37,4 @@ preso3.SSP3-7.0:year_first=2018
 preso3.SSP3-7.0:year_last=2022
 preso3.SSP3-7.0:year_align=2018
 preso3.SSP3-7.0:dtlimit=30
+
diff --git a/test/tools/README.testnames b/test/tools/README.testnames
@@ -43,6 +43,7 @@ m is the resolution
 9 -- 4x5
 a -- NEON YELL
 b -- NEON KONA
+c -- NEON OSBS
 d -- region1
 c -- single point from the 0.9x1.25 grid
 g -- unused

diff --git a/test/tools/input_tests_master b/test/tools/input_tests_master
@@ -24,8 +24,10 @@ bli58 TBLscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_10x15_crp_1850-200
 smi64 TSMscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_5x5_amazon_hirespft_2005^tools__ds
 bli64 TBLscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_5x5_amazon_hirespft_2005^tools__ds
 
-sm0a1 TSMscript_tools.sh site_and_regional run_neon.py run_neon_OSBS
-bl0a1 TBLscript_tools.sh site_and_regional run_neon.py run_neon_OSBS
+sm0c1 TSMscript_tools.sh site_and_regional run_neon.py run_neon_OSBS
+bl0c1 TBLscript_tools.sh site_and_regional run_neon.py run_neon_OSBS
+sm0a1 TSMscript_tools.sh site_and_regional run_neon.py run_neon_YELL_PRISM
+bl0a1 TBLscript_tools.sh site_and_regional run_neon.py run_neon_YELL_PRISM
 
 smba1 TSMscript_tools.sh site_and_regional subset_data subset_data_YELL
 blba1 TBLscript_tools.sh site_and_regional subset_data subset_data_YELL

diff --git a/test/tools/nl_files/run_neon_YELL_PRISM b/test/tools/nl_files/run_neon_YELL_PRISM
@@ -0,0 +1 @@
+--verbose --run-type transient --setup-only --neon-site YELL --prism --neon-version v2 --experiment toolstest
diff --git a/test/tools/tests_pretag_nompi_neon b/test/tools/tests_pretag_nompi_neon
@@ -1,4 +1,5 @@
 sm0a1             bl0a1
+sm0c1             bl0c1
 smaa2             blaa2
 smba1             blba1
 smbb1             blbb1
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#!/bin/bash
		./xmlchange CLM_USRDAT_NAME=NEON.PRISM
Original file line number	Diff line number	Diff line change
Expand Up		@@ -37,3 +37,4 @@ preso3.SSP3-7.0:year_first=2018
		preso3.SSP3-7.0:year_last=2022
		preso3.SSP3-7.0:year_align=2018
		preso3.SSP3-7.0:dtlimit=30
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		--verbose --run-type transient --setup-only --neon-site YELL --prism --neon-version v2 --experiment toolstest