Neon updates

.gitignore

@@ -105,6 +105,13 @@ unit_test_build
 /tools/mkmapdata/regrid.o*
 /tools/mkmapdata/map*.nc
 
+# run_neon output directories
+/tools/site_and_regional/listing.csv
+/tools/site_and_regional/????/
+/tools/site_and_regional/????.ad/
+/tools/site_and_regional/????.postad/
+/tools/site_and_regional/????.transient/
+
 # build output
 *.o
 *.mod

bld/CLMBuildNamelist.pm

@@ -4560,6 +4560,8 @@ sub check_use_case_name {
     } else {
       $log->fatal_error($diestring);
     }
+  } elsif ( $use_case =~ /^([0-9]+|PI)-PD_*($desc)_transient$/   ) {
+     # valid name
   } elsif ( $use_case =~ /^([0-9]+)_*($desc)_control$/   ) {
      # valid name
   } elsif ( $use_case =~ /^($desc)_pd$/   ) {

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -25,6 +25,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <co2_ppmv sim_year="2000"      >379.0</co2_ppmv>
 <co2_ppmv sim_year="2010"      >388.8</co2_ppmv>
 <co2_ppmv sim_year="2015"      >397.5</co2_ppmv>
+<co2_ppmv sim_year="2018"      >408.83</co2_ppmv>
 <co2_ppmv sim_year="1850"      >284.7</co2_ppmv>
 <co2_ppmv sim_year="PtVg"      >284.7</co2_ppmv>
 
@@ -1449,6 +1450,9 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <stream_year_last_ndep  phys="clm5_1"  use_cn=".true." sim_year_range="1850-2100"  >2101</stream_year_last_ndep>
 <model_year_align_ndep  phys="clm5_1"  use_cn=".true." sim_year_range="1850-2100"  >2015</model_year_align_ndep>
 
+<stream_year_first_ndep use_cn=".true."   sim_year="2018" >2018</stream_year_first_ndep>
+<stream_year_last_ndep  use_cn=".true."   sim_year="2018" >2018</stream_year_last_ndep>
+
 <stream_year_first_ndep use_cn=".true."   sim_year="2010" >2010</stream_year_first_ndep>
 <stream_year_last_ndep  use_cn=".true."   sim_year="2010" >2010</stream_year_last_ndep>
 
@@ -1601,6 +1605,9 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <stream_year_last_popdens  phys="clm5_1"  cnfireson=".true." sim_year_range="1850-2100"  >2100</stream_year_last_popdens>
 <model_year_align_popdens  phys="clm5_1"  cnfireson=".true." sim_year_range="1850-2100"  >2015</model_year_align_popdens>
 
+<stream_year_first_popdens use_cn=".true."   sim_year="2018" >2018</stream_year_first_popdens>
+<stream_year_last_popdens  use_cn=".true."   sim_year="2018" >2018</stream_year_last_popdens>
+
 <stream_year_first_popdens use_cn=".true."   sim_year="2010" >2010</stream_year_first_popdens>
 <stream_year_last_popdens  use_cn=".true."   sim_year="2010" >2010</stream_year_last_popdens>
 
@@ -1619,6 +1626,9 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <stream_year_first_popdens use_cn=".true."   sim_year="constant" sim_year_range="1000-1004" >2000</stream_year_first_popdens>
 <stream_year_last_popdens  use_cn=".true."   sim_year="constant" sim_year_range="1000-1004" >2000</stream_year_last_popdens>
 
+<stream_year_first_popdens use_fates=".true." sim_year="2018" >2018</stream_year_first_popdens>
+<stream_year_last_popdens  use_fates=".true." sim_year="2018" >2018</stream_year_last_popdens>
+
 <stream_year_first_popdens use_fates=".true." sim_year="2010" >2010</stream_year_first_popdens>
 <stream_year_last_popdens  use_fates=".true." sim_year="2010" >2010</stream_year_last_popdens>
 
@@ -1706,6 +1716,12 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts
 <stream_year_last_urbantv  phys="clm4_5"  sim_year_range="1850-2100" >2106</stream_year_last_urbantv>
 <model_year_align_urbantv  phys="clm4_5"  sim_year_range="1850-2100" >2015</model_year_align_urbantv>
 
+<stream_year_first_urbantv sim_year="2018" >2018</stream_year_first_urbantv>
+<stream_year_last_urbantv  sim_year="2018" >2018</stream_year_last_urbantv>
+
+<stream_year_first_urbantv sim_year="2010" >2010</stream_year_first_urbantv>
+<stream_year_last_urbantv  sim_year="2010" >2010</stream_year_last_urbantv>
+
 <stream_year_first_urbantv sim_year="2000" >2000</stream_year_first_urbantv>
 <stream_year_last_urbantv  sim_year="2000" >2000</stream_year_last_urbantv>
 

bld/namelist_files/namelist_definition_ctsm.xml

@@ -2057,7 +2057,7 @@ If 1, turn on the MEGAN model for BVOC's (Biogenic Volitile Organic Compounds)
 
 <entry id="sim_year" type="char*4" category="default_settings"
        group="default_settings" valid_values=
-"PtVg,1000,850,1100,1350,1600,1850,1855,1865,1875,1885,1895,1905,1915,1925,1935,1945,1955,1965,1975,1979,1980,1982,1985,1995,2000,2005,2010,2013,2015,2025,2035,2045,2055,2065,2075,2085,2095,2105">
+"PtVg,1000,850,1100,1350,1600,1850,1855,1865,1875,1885,1895,1905,1915,1925,1935,1945,1955,1965,1975,1979,1980,1982,1985,1995,2000,2005,2010,2013,2015,2018,2025,2035,2045,2055,2065,2075,2085,2095,2105">
 Year to simulate and to provide datasets for (such as surface datasets, initial conditions, aerosol-deposition, Nitrogen deposition rates etc.)
 A sim_year of 1000 corresponds to data used for testing only, NOT corresponding to any real datasets.
 A sim_year greater than 2015 corresponds to ssp_rcp scenario data

bld/namelist_files/use_cases/2018-PD_transient.xml

@@ -0,0 +1,29 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc>Simulate transient land-use, and aerosol deposition changes from 2018 to current day with a mix of historical data, and future scenario data</use_case_desc>
+
+<!-- Have a minimal list of things set here, sim_year, sim_year_range, and ssp_rcp, other things should be dependent on these and
+     set in a namelist_defaults xml file -->
+
+<sim_year>2018</sim_year>
+
+<sim_year_range>1850-2100</sim_year_range>
+
+<!-- Use future data as needed from the SSP3-7.0 scenario-->
+<ssp_rcp>SSP3-7.0</ssp_rcp>
+
+<stream_year_first_ndep use_cn=".true."   >2018</stream_year_first_ndep>
+<stream_year_last_ndep  use_cn=".true."   >2022</stream_year_last_ndep>
+<model_year_align_ndep  use_cn=".true."   >2018</model_year_align_ndep>
+
+<stream_year_first_popdens cnfireson=".true."   >2018</stream_year_first_popdens>
+<stream_year_last_popdens  cnfireson=".true."   >2022</stream_year_last_popdens>
+<model_year_align_popdens  cnfireson=".true."   >2018</model_year_align_popdens>
+
+<stream_year_first_urbantv >2018</stream_year_first_urbantv>
+<stream_year_last_urbantv  >2022</stream_year_last_urbantv>
+<model_year_align_urbantv  >2018</model_year_align_urbantv>
+
+</namelist_defaults>

bld/namelist_files/use_cases/2018_control.xml

@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+
+<namelist_defaults>
+
+<use_case_desc>Conditions to simulate 2018 land-use</use_case_desc>
+
+<sim_year>2018</sim_year>
+
+<sim_year_range>constant</sim_year_range>
+
+<!-- Use future data as needed from the SSP3-7.0 scenario-->
+<ssp_rcp>SSP3-7.0</ssp_rcp>
+
+</namelist_defaults>

bld/namelist_files/use_cases/README

@@ -17,6 +17,10 @@ Transient cases:
 
    20thC$desc_transient  (means nominal 1850-2000 although some datasets are 1850-2005)
 
+   or
+
+   yyyy-PD_$desc_transient (means nominal year yyyy through present day (PD) (with the year for PD advancing)
+
 Control cases:
 
    yyyy$desc_control
@@ -30,6 +34,7 @@ Where
 
 yyyy      = Simulation year (such as 1850 or 2000).
 yyyy-yyyy = Range of simulation years to run over (i.e.. 1850-2000).
+yyyy-PD   = Range of simulation years to run over until present day (i.e.. 2018-2024).
 $ssp_rcp  = Shared Socieconomic Pathway (SSP) Representative concentration pathway (RCP) description string
             for future scenarios:
             SSP#-#.# (for example: SSP5-8.5, SSP1-2.6, SSP4-6.0

bld/unit_testers/build-namelist_test.pl

@@ -393,7 +393,7 @@ sub cat_and_create_namelistinfile {
    #
    # Now run  the site
    #
-   my $options = "-res CLM_USRDAT -clm_usr_name NEON -no-megan -bgc bgc -sim_year 2000 -infile $namelistfile";
+   my $options = "-res CLM_USRDAT -clm_usr_name NEON -no-megan -bgc bgc -sim_year 2018 -infile $namelistfile";
    eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); };
    is( $@, '', "options: $options" );
    $cfiles->checkfilesexist( "$options", $mode );

cime_config/usermods_dirs/NEON/BARR/shell_commands

@@ -1,7 +1,11 @@
+#!/bin/bash
+
 ./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
-
+./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
+fi

cime_config/usermods_dirs/NEON/CPER/shell_commands

@@ -1,3 +1,6 @@
 ./xmlchange NEONSITE=CPER
 ./xmlchange PTS_LON=255.25545
 ./xmlchange PTS_LAT=40.81297
+if  [[ $compset =~ ^HIST ]]; then
+  ./xmlchange STOP_N=50
+fi

cime_config/usermods_dirs/NEON/GUAN/shell_commands

@@ -1,6 +1,11 @@
+#!/bin/bash
+
 ./xmlchange NEONSITE=GUAN
 ./xmlchange PTS_LON=293.13112
 ./xmlchange PTS_LAT=17.96882
-./xmlchange RUN_STARTDATE=2019-01-01
 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 
-./xmlchange STOP_N=39
+# 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

cime_config/usermods_dirs/NEON/KONA/shell_commands

@@ -1,3 +1,7 @@
 ./xmlchange NEONSITE=KONA
 ./xmlchange PTS_LON=263.38956
 ./xmlchange PTS_LAT=39.10828
+# Setup to run with prognostic crops for this site
+# If you want to explicitly run in SP mode or add other
+# options you'll need to add that after this...
+./xmlchange CLM_BLDNML_OPTS="--bgc bgc --crop"

cime_config/usermods_dirs/NEON/LAJA/shell_commands

@@ -1,8 +1,12 @@
+#!/bin/bash
 ./xmlchange NEONSITE=LAJA
 ./xmlchange PTS_LON=292.92392
 ./xmlchange PTS_LAT=18.02184
-./xmlchange RUN_STARTDATE=2019-01-01
 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019                 
-./xmlchange STOP_N=39
+# 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
 
 

cime_config/usermods_dirs/NEON/LENO/shell_commands

@@ -1,7 +1,12 @@
+#!/bin/bash
+
 ./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
+# Different default start date and number of months to run for transient case
+if  [[ $compset =~ ^HIST ]]; then
+  ./xmlchange RUN_STARTDATE=2021-01-01
+  ./xmlchange STOP_N=15
+fi
 

cime_config/usermods_dirs/NEON/MLBS/shell_commands

@@ -1,6 +1,10 @@
+#!/bin/bash
 ./xmlchange NEONSITE=MLBS
 ./xmlchange PTS_LON=279.47575
 ./xmlchange PTS_LAT=37.37783
-./xmlchange STOP_N=24
 ./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

cime_config/usermods_dirs/NEON/MOAB/shell_commands

@@ -1,8 +1,10 @@
+#!/bin/bash
 ./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
-
-
+./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

cime_config/usermods_dirs/NEON/ONAQ/shell_commands

@@ -1,8 +1,10 @@
+#!/bin/bash
 ./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
-
-
+./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

cime_config/usermods_dirs/NEON/SJER/shell_commands

@@ -1,8 +1,11 @@
+#!/bin/bash
 ./xmlchange NEONSITE=SJER
 ./xmlchange PTS_LON=240.267
 ./xmlchange PTS_LAT=37.107117
-./xmlchange RUN_STARTDATE=2019-01-01
 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019
-./xmlchange STOP_N=39
+# 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
 
-#./xmlchange RUN_STARTDATE=2018-09-01

cime_config/usermods_dirs/NEON/STER/shell_commands

@@ -1,3 +1,7 @@
 ./xmlchange NEONSITE=STER
 ./xmlchange PTS_LON=256.96992
 ./xmlchange PTS_LAT=40.45984
+# Setup to run with prognostic crops for this site
+# If you want to explicitly run in SP mode or add other
+# # options you'll need to add that after this...
+./xmlchange CLM_BLDNML_OPTS="--bgc bgc --crop"

cime_config/usermods_dirs/NEON/TEAK/shell_commands

@@ -1,7 +1,10 @@
+#!/bin/bash
 ./xmlchange NEONSITE=TEAK
 ./xmlchange PTS_LON=240.99424199999999
 ./xmlchange PTS_LAT=37.006472
-./xmlchange RUN_STARTDATE=2019-01-01
-./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019
-./xmlchange STOP_N=39
-
+./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
+fi

cime_config/usermods_dirs/NEON/TOOL/shell_commands

@@ -1,8 +1,10 @@
+#!/bin/bash
 ./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
-
-
+# Different default start date and number of months to run for transient case
+if  [[ $compset =~ ^HIST ]]; then
+  ./xmlchange RUN_STARTDATE=2020-01-01
+  ./xmlchange STOP_N=27
+fi

cime_config/usermods_dirs/NEON/WREF/shell_commands

@@ -1,3 +1,10 @@
+#!/bin/bash
 ./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
+fi

cime_config/usermods_dirs/NEON/YELL/shell_commands

@@ -1,7 +1,10 @@
+#!/bin/bash
 ./xmlchange NEONSITE=YELL
 ./xmlchange PTS_LON=249.45803999999998
 ./xmlchange PTS_LAT=44.95597
-./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
+./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
+fi

cime_config/usermods_dirs/NEON/defaults/shell_commands

@@ -1,16 +1,26 @@
+#!/bin/bash
 ./xmlchange CLM_USRDAT_NAME=NEON
-./xmlchange RUN_STARTDATE=2018-01-01
-./xmlchange CLM_NML_USE_CASE=1850-2100_SSP3-7.0_transient
 ./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
 ./xmlchange DATM_PRESNDEP=SSP3-7.0
 ./xmlchange DATM_PRESO3=SSP3-7.0
+# Explicitly set the MPI library to mpi-serial so won't have the build/run complexity of a full MPI library
+./xmlchange MPILIB=mpi-serial
+# Set years to run forcing data over
 ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018
+compset=`./xmlquery COMPSET --value`
+# For a transient case run the whole length and don't cycle
+if  [[ $compset =~ ^HIST ]]; then
+  ./xmlchange DATM_YR_END=2022
+  ./xmlchange RUN_STARTDATE=2018-01-01
+  # Number of months that can be run for the full transient case
+  ./xmlchange STOP_OPTION="nmonths"
+  ./xmlchange STOP_N=51
+  ./xmlchange CLM_NML_USE_CASE="2018-PD_transient"
+else
+  ./xmlchange CLM_NML_USE_CASE="2018_control"
+fi
 
 # 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
-