Merge branch 'neon_updates'

Fixes for NEON cases

Two sets of fixes for NEON cases:

(1) Fixes for leap year handling when there are discrepancies between
the model and the DATM forcing data in terms of whether the current year
is a leap year. This involved updates to the share and cdeps externals
from Jim Edwards.

(2) Other fixes for NEON cases from Will Wieder, as documented in
#1860

Resolves #1858 (calendar error in ESMF)

Resolves #1860 (run_neon not working as expected)

Externals.cfg

@@ -55,7 +55,7 @@ local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps0.12.63
+tag = cdeps0.12.65
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
@@ -70,7 +70,7 @@ local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.12
+tag = share1.0.13
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share

cime_config/usermods_dirs/NEON/BARR/shell_commands

@@ -1,3 +1,7 @@
 ./xmlchange NEONSITE=BARR
 ./xmlchange PTS_LON=203.349781
 ./xmlchange PTS_LAT=71.281711
+./xmlchange RUN_STARTDATE=2019-01-01
+./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019,DATM_YR_END=2022
+./xmlchange STOP_N=39
+

cime_config/usermods_dirs/NEON/GUAN/shell_commands

@@ -1,4 +1,6 @@
 ./xmlchange NEONSITE=GUAN
 ./xmlchange PTS_LON=293.13112
 ./xmlchange PTS_LAT=17.96882
-./xmlchange RUN_STARTDATE=2018-06-01
+./xmlchange RUN_STARTDATE=2019-01-01
+./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 
+./xmlchange STOP_N=39

cime_config/usermods_dirs/NEON/LAJA/shell_commands

@@ -1,4 +1,8 @@
 ./xmlchange NEONSITE=LAJA
 ./xmlchange PTS_LON=292.92392
 ./xmlchange PTS_LAT=18.02184
-./xmlchange RUN_STARTDATE=2018-05-01
+./xmlchange RUN_STARTDATE=2019-01-01
+./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019                 
+./xmlchange STOP_N=39
+
+

cime_config/usermods_dirs/NEON/LENO/shell_commands

@@ -1,3 +1,7 @@
 ./xmlchange NEONSITE=LENO
 ./xmlchange PTS_LON=271.83897
 ./xmlchange PTS_LAT=31.8531
+./xmlchange RUN_STARTDATE=2021-01-01
+./xmlchange DATM_YR_ALIGN=2021,DATM_YR_START=2021
+./xmlchange STOP_N=15
+

cime_config/usermods_dirs/NEON/MLBS/shell_commands

@@ -1,3 +1,6 @@
 ./xmlchange NEONSITE=MLBS
 ./xmlchange PTS_LON=279.47575
 ./xmlchange PTS_LAT=37.37783
+./xmlchange STOP_N=24
+./xmlchange DATM_YR_END=2019
+

cime_config/usermods_dirs/NEON/MOAB/shell_commands

@@ -1,3 +1,8 @@
 ./xmlchange NEONSITE=MOAB
 ./xmlchange PTS_LON=250.61118
 ./xmlchange PTS_LAT=38.25136
+./xmlchange RUN_STARTDATE=2018-01-01
+./xmlchange DATM_YR_ALIGN=2018,DATM_YR_START=2018,DATM_YR_END=2020
+./xmlchange STOP_N=36
+
+

cime_config/usermods_dirs/NEON/ONAQ/shell_commands

@@ -1,3 +1,8 @@
 ./xmlchange NEONSITE=ONAQ
 ./xmlchange PTS_LON=276.49815
 ./xmlchange PTS_LAT=35.68839
+./xmlchange RUN_STARTDATE=2018-01-01
+./xmlchange DATM_YR_ALIGN=2018,DATM_YR_START=2018,DATM_YR_END=2019
+./xmlchange STOP_N=24
+
+

cime_config/usermods_dirs/NEON/SJER/shell_commands

@@ -1,4 +1,8 @@
 ./xmlchange NEONSITE=SJER
 ./xmlchange PTS_LON=240.267
 ./xmlchange PTS_LAT=37.107117
-./xmlchange RUN_STARTDATE=2018-09-01
+./xmlchange RUN_STARTDATE=2019-01-01
+./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019
+./xmlchange STOP_N=39
+
+#./xmlchange RUN_STARTDATE=2018-09-01

cime_config/usermods_dirs/NEON/TEAK/shell_commands

@@ -1,5 +1,7 @@
 ./xmlchange NEONSITE=TEAK
 ./xmlchange PTS_LON=240.99424199999999
 ./xmlchange PTS_LAT=37.006472
-# This site is missing data for first half of 2018
-./xmlchange RUN_STARTDATE=2018-06-01
+./xmlchange RUN_STARTDATE=2019-01-01
+./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019
+./xmlchange STOP_N=39
+

cime_config/usermods_dirs/NEON/TOOL/shell_commands

@@ -1,3 +1,8 @@
 ./xmlchange NEONSITE=TOOL
 ./xmlchange PTS_LON=210.629872
 ./xmlchange PTS_LAT=68.66045
+./xmlchange RUN_STARTDATE=2020-01-01
+./xmlchange DATM_YR_ALIGN=2020,DATM_YR_START=2020
+./xmlchange STOP_N=27
+
+

cime_config/usermods_dirs/NEON/YELL/shell_commands

@@ -1,4 +1,7 @@
 ./xmlchange NEONSITE=YELL
 ./xmlchange PTS_LON=249.45803999999998
 ./xmlchange PTS_LAT=44.95597
-./xmlchange RUN_STARTDATE=2018-08-01
+./xmlchange RUN_STARTDATE=2019-01-01
+./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019
+./xmlchange STOP_N=39
+# ./xmlchange RUN_STARTDATE=2018-08-01

cime_config/usermods_dirs/NEON/defaults/shell_commands

@@ -3,10 +3,14 @@
 ./xmlchange CLM_NML_USE_CASE=1850-2100_SSP3-7.0_transient
 ./xmlchange CCSM_CO2_PPMV=408.83
 ./xmlchange DATM_PRESAERO=SSP3-7.0
-./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2020,DATM_YR_START=2018
+./xmlchange DATM_PRESNDEP=SSP3-7.0
+./xmlchange DATM_PRESO3=SSP3-7.0
+./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018
+
 # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way)
 ./xmlchange PIO_TYPENAME=netcdf
 # BD:05/06/2022 - The PIO_REARRANGER_LND value - for global runs, PIO_REARRANGER_LND = 1 is ideal
 #                 and a value of 2 results in slow I/O.  For point runs like these, a value of 1 results in a crash (PIO bug, probably),
 #                 so we explicitly set a value of 2.
 ./xmlchange PIO_REARRANGER_LND=2
+

cime_config/usermods_dirs/NEON/defaults/user_nl_clm

@@ -22,15 +22,17 @@ flanduse_timeseries = ' '   ! This isn't needed for a non transient case, but wi
 fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_hist_78pfts_CMIP6_simyr2000_${NEONSITE}_c211102.nc"
 model_year_align_urbantv = 2018
 stream_year_first_urbantv = 2018
-stream_year_last_urbantv = 2020
+stream_year_last_urbantv = 2021
 stream_year_first_ndep = 2018
 model_year_align_ndep = 2018
-stream_year_last_ndep = 2020
+stream_year_last_ndep = 2021
 model_year_align_popdens = 2018
 stream_year_first_popdens = 2018
-stream_year_last_popdens = 2020
+stream_year_last_popdens = 2021
+
 stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc'
-stream_fldfilename_ndep = '$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc'
+!stream_fldfilename_ndep = '$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc'
+
 ! h1 output stream 
 hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI',
              'HR','SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FV','NET_NMIN_vr'

cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams

@@ -4,3 +4,13 @@ presaero.SSP3-7.0:year_last=2030
 presaero.SSP3-7.0:year_align=2018
 presaero.SSP3-7.0:dtlimit=30
 
+presndep.SSP3-7.0:datafiles = $DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc
+presndep.SSP3-7.0:year_first=2018
+presndep.SSP3-7.0:year_last=2030
+presndep.SSP3-7.0:year_align=2018
+presndep.SSP3-7.0:dtlimit=30
+
+preso3.SSP3-7.0:year_first=2018
+preso3.SSP3-7.0:year_last=2030
+preso3.SSP3-7.0:year_align=2018
+preso3.SSP3-7.0:dtlimit=30

doc/ChangeLog

@@ -1,4 +1,76 @@
 ===============================================================
+Tag name: ctsm5.1.dev111
+Originator(s): jedwards (Jim Edwards), wwieder (Will Wieder), sacks (Bill Sacks)
+Date: Wed Oct  5 13:05:52 MDT 2022
+One-line Summary: Fixes for NEON cases
+
+Purpose and description of changes
+----------------------------------
+
+Two sets of fixes for NEON cases:
+
+(1) Fixes for leap year handling when there are discrepancies between
+the model and the DATM forcing data in terms of whether the current year
+is a leap year. This involved updates to the share and cdeps externals
+from Jim Edwards.
+
+(2) Other fixes for NEON cases from Will Wieder, as documented in
+https://github.com/ESCOMP/CTSM/issues/1860
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+CTSM issues fixed (include CTSM Issue #):
+- Resolves ESCOMP/CTSM#1858 (calendar error in ESMF)
+- Resolves ESCOMP/CTSM#1860 (run_neon not working as expected)
+
+Testing summary:
+----------------
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- PASS
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: YES, but just for NEON cases
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: NEON cases
+    - what platforms/compilers: all
+    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+      larger than roundoff
+
+   In testing, answer changes only show up in SMS_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-default--clm-NEON-NIWO
+
+Other details
+-------------
+List any externals directories updated (cime, rtm, mosart, cism, fates, etc.):
+- cdeps: cdeps0.12.63 -> cdeps0.12.65
+- share: share1.0.12 -> share1.0.13
+
+Pull Requests that document the changes (include PR ids):
+https://github.com/ESCOMP/CTSM/pull/1862
+
+===============================================================
+===============================================================
 Tag name: ctsm5.1.dev110
 Originator(s): slevis (Samuel Levis, 303-665-1310)
 Date: Mon Sep 26 17:31:22 MDT 2022

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+    ctsm5.1.dev111 multiple 10/05/2022 Fixes for NEON cases
     ctsm5.1.dev110   slevis 09/26/2022 Introduction of modify_meshes tool for use in I-cases and F-cases
     ctsm5.1.dev109   slevis 09/26/2022 If not MIMICS, do not output certain MIMICS history fields
     ctsm5.1.dev108  afoster 09/08/2022 Connect ozone from atmosphere

tools/site_and_regional/neon_sites_dompft.csv

@@ -1,48 +1,48 @@
-Site,Domain,Lat,Lon,pft
-BART,1,44.06516,-71.28834,7
-HARV,1,42.53562,-72.17562,7
-BLAN,2,39.06044,-78.07115,7
-SCBI,2,38.89209,-78.13764,7
-SERC,2,38.89124,-76.55884,7
-DSNY,3,28.12919,-81.43394,14
-JERC,3,31.19608,-84.46647,1
-OSBS,3,29.68819,-81.99345,1
-GUAN,4,17.96882,-66.86888,6
-LAJA,4,18.02184,-67.07608,14
-STEI,5,45.5076,-89.5888,7
-TREE,5,45.49266,-89.58748,7
-UNDE,5,46.14103,-89.3221,7
-KONA,6,39.10828,-96.61044,18
-KONZ,6,39.1007,-96.56227,14
-UKFS,6,39.04168,-95.20495,7
-GRSM,7,35.68839,-83.50185,7
-MLBS,7,37.37783,-80.52425,7
-ORNL,7,35.57525,-84.16581,7
-DELA,8,32.54092,-87.80341,7
-LENO,8,31.8531,-88.16103,7
-TALL,8,32.95106,-87.3941,1
-DCFS,9,47.15919,-99.11251,13
-NOGP,9,46.76846,-100.91832,13
-WOOD,9,47.12833,-99.23907,13
-CPER,10,40.81297,-104.74455,14
-RMNP,10,40.27707,-105.54524,1
-STER,10,40.45984,-103.03008,18
-CLBJ,11,33.40143,-97.56725,7
-OAES,11,35.41062,-99.06044,14
-YELL,12,44.95597,-110.54196,1
-MOAB,13,38.25136,-109.38882,14
-NIWO,13,40.05236,-105.58324,12
-JORN,14,32.59052,-106.84377,14
-SRER,14,31.91068,-110.83549,9
-ONAQ,15,35.68839,-83.50185,9
-ABBY,16,45.762378,-122.329672,1
-WREF,16,45.81637,-121.95838,1
-SJER,17,37.107117,-119.733,13
-SOAP,17,37.03269,-119.2621,1
-TEAK,17,37.006472,-119.005758,1
-TOOL,17,68.66045,-149.370128,1
-BARR,18,71.281711,-156.650219,12
-BONA,19,65.15333,-147.50194,2
-DEJU,19,63.87983,-145.74765,2
-HEAL,19,63.8798,-149.21539,12
-PUUM,20,19.55309,-155.31731,4
+,Site,Domain,Lat,Lon,pft,start_year,end_year
+1,BART,1,44.06516,-71.28834,7,2018,2021
+2,HARV,1,42.53562,-72.17562,7,2018,2021
+3,BLAN,2,39.06044,-78.07115,7,2018,2021
+4,SCBI,2,38.89209,-78.13764,7,2018,2021
+5,SERC,2,38.89124,-76.55884,7,2018,2021
+6,DSNY,3,28.12919,-81.43394,14,2018,2021
+7,JERC,3,31.19608,-84.46647,1,2018,2021
+8,OSBS,3,29.68819,-81.99345,1,2018,2021
+9,GUAN,4,17.96882,-66.86888,6,2019,2021
+10,LAJA,4,18.02184,-67.07608,14,2019,2021
+11,STEI,5,45.5076,-89.5888,7,2018,2021
+12,TREE,5,45.49266,-89.58748,7,2018,2021
+13,UNDE,5,46.14103,-89.3221,7,2018,2021
+14,KONA,6,39.10828,-96.61044,18,2018,2021
+15,KONZ,6,39.1007,-96.56227,14,2018,2021
+16,UKFS,6,39.04168,-95.20495,7,2018,2021
+17,GRSM,7,35.68839,-83.50185,7,2018,2021
+18,MLBS,7,37.37783,-80.52425,7,2018,2019
+19,ORNL,7,35.57525,-84.16581,7,2018,2021
+20,DELA,8,32.54092,-87.80341,7,2018,2021
+21,LENO,8,31.8531,-88.16103,7,2021,2021
+22,TALL,8,32.95106,-87.3941,1,2018,2021
+23,DCFS,9,47.15919,-99.11251,13,2018,2021
+24,NOGP,9,46.76846,-100.91832,13,2018,2021
+25,WOOD,9,47.12833,-99.23907,13,2018,2021
+26,CPER,10,40.81297,-104.74455,14,2018,2021
+27,RMNP,10,40.27707,-105.54524,1,2018,2021
+28,STER,10,40.45984,-103.03008,18,2018,2021
+29,CLBJ,11,33.40143,-97.56725,7,2018,2021
+30,OAES,11,35.41062,-99.06044,14,2018,2021
+31,YELL,12,44.95597,-110.54196,1,2019,2021
+32,MOAB,13,38.25136,-109.38882,14,2018,2020
+33,NIWO,13,40.05236,-105.58324,12,2018,2021
+34,JORN,14,32.59052,-106.84377,14,2018,2021
+35,SRER,14,31.91068,-110.83549,9,2018,2021
+36,ONAQ,15,35.68839,-83.50185,9,2018,2019
+37,ABBY,16,45.762378,-122.329672,1,2018,2021
+38,WREF,16,45.81637,-121.95838,1,2019,2021
+39,SJER,17,37.107117,-119.733,13,2019,2021
+40,SOAP,17,37.03269,-119.2621,1,2018,2021
+41,TEAK,17,37.006472,-119.005758,1,2019,2021
+42,TOOL,17,68.66045,-149.370128,1,2020,2021
+43,BARR,18,71.281711,-156.650219,12,2019,2021
+44,BONA,19,65.15333,-147.50194,2,2018,2021
+45,DEJU,19,63.87983,-145.74765,2,2018,2021
+46,HEAL,19,63.8798,-149.21539,12,2018,2021
+47,PUUM,20,19.55309,-155.31731,4,2020,2020

tools/site_and_regional/run_neon.py

@@ -273,9 +273,9 @@ def get_parser(args, description, valid_neon_sites):
 
     if args.run_length == "0Y":
         if args.run_type == "ad":
-            run_length = "200Y"
+            run_length = "100Y"
         elif args.run_type == "postad":
-            run_length = "50Y"
+            run_length = "100Y"
         else:
             # The transient run length is set by cdeps atm buildnml to the last date of the available tower data
             # this value is not used
@@ -523,6 +523,7 @@ def run_case(
                 case.set_value("CLM_ACCELERATED_SPINUP", "on")
                 case.set_value("RUN_REFDATE", "0018-01-01")
                 case.set_value("RUN_STARTDATE", "0018-01-01")
+                case.set_value("RESUBMIT", 1)
             else:
                 case.set_value("CLM_FORCE_COLDSTART", "off")
                 case.set_value("CLM_ACCELERATED_SPINUP", "off")
@@ -543,6 +544,7 @@ def run_case(
                 case.set_value("DATM_YR_START", self.start_year)
                 case.set_value("DATM_YR_END", self.end_year)
                 case.set_value("CALENDAR", "GREGORIAN")
+                case.set_value("RESUBMIT", 0)
             else:
                 # for the spinup we want the start and end on year boundaries
                 if self.start_month == 1:
@@ -555,6 +557,11 @@ def run_case(
                     case.set_value("DATM_YR_END", self.end_year)
                 else:
                     case.set_value("DATM_YR_END", self.end_year - 1)
+
+            # Let's no be so clevar with start / end dates
+            #case.set_value("DATM_YR_ALIGN", int(args.start_date[0:4]))
+            #case.set_value("DATM_YR_START", int(args.start_date[0:4]))
+            #case.set_value("DATM_YR_END", int(args.end_date[0:4]))
 
             if not rundir:
                 rundir = case.get_value("RUNDIR")