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Merge pull request #1932 from adrifoster/NEON_fates
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NEON FATES capabilities
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@ekluzek
ekluzek authored Feb 2, 2023
2 parents f10353e + 0e83df3 commit 2291307
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Showing 114 changed files with 674 additions and 43 deletions.
4 changes: 4 additions & 0 deletions bld/CLMBuildNamelist.pm
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Expand Up @@ -3683,6 +3683,10 @@ sub setup_logic_fire_emis {
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

if ($opts->{'fire_emis'} ) {
if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
$log->warning("Fire emission can NOT be on when FATES is also on.\n" .
" DON'T use the '-fire_emis' option when '-bgc fates' is activated");
}
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_factors_file');
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_specifier');
} else {
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7 changes: 6 additions & 1 deletion bld/unit_testers/build-namelist_test.pl
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Expand Up @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
#
# Figure out number of tests that will run
#
my $ntests = 1846;
my $ntests = 1847;
if ( defined($opts{'compare'}) ) {
$ntests += 1254;
}
Expand Down Expand Up @@ -1006,6 +1006,11 @@ sub cat_and_create_namelistinfile {
GLC_TWO_WAY_COUPLING=>"FALSE",
phys=>"clm4_5",
},
"useFIREEMISwithFATES" =>{ options=>"-bgc fates -envxml_dir . -fire_emis --no-megan",
namelst=>"",
GLC_TWO_WAY_COUPLING=>"FALSE",
phys=>"clm4_5",
},
"useDRYDEPwithFATES" =>{ options=>"--bgc fates --envxml_dir . --no-megan --drydep",
namelst=>"",
GLC_TWO_WAY_COUPLING=>"FALSE",
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10 changes: 10 additions & 0 deletions cime_config/config_compsets.xml
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Expand Up @@ -41,11 +41,21 @@
<lname>2000_DATM%1PT_CLM51%BGC_SICE_SOCN_SROF_SGLC_SWAV</lname>
</compset>

<compset>
<alias>I1PtClm51Fates</alias>
<lname>2000_DATM%1PT_CLM51%FATES_SICE_SOCN_SROF_SGLC_SWAV</lname>
</compset>

<compset>
<alias>IHist1PtClm51Bgc</alias>
<lname>HIST_DATM%1PT_CLM51%BGC_SICE_SOCN_SROF_SGLC_SWAV</lname>
</compset>

<compset>
<alias>IHist1PtClm51Fates</alias>
<lname>HIST_DATM%1PT_CLM51%FATES_SICE_SOCN_SROF_SGLC_SWAV</lname>
</compset>

<compset>
<alias>I1PtClm51SpRs</alias>
<lname>2000_DATM%1PT_CLM51%SP_SICE_SOCN_SROF_SGLC_SWAV</lname>
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27 changes: 26 additions & 1 deletion cime_config/testdefs/ExpectedTestFails.xml
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Expand Up @@ -80,5 +80,30 @@
<issue>FATES#701</issue>
</phase>
</test>


<test name="ERS_D_Ld5.1x1_brazil.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesColdHydro">
<phase name="COMPARE_base_rest">
<status>FAIL</status>
<issue>FATES#701</issue>
</phase>
</test>

<test name="ERP_P144x2_Ld30.f45_f45_mg37.I2000Clm50FatesRs.cheyenne_intel.clm-mimicsFatesCold">
<phase name="SHAREDLIB_BUILD">
<status>PEND</status>
<issue>#1045</issue>
</phase>
</test>

<test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdPRT2">
<phase name="RUN">
<status>FAIL</status>
<issue>FATES#983</issue>
<comment>This job should time out on izumi, seems to be hanging on history output.</comment>
</phase>
</test>




</expectedFails>
11 changes: 11 additions & 0 deletions cime_config/testdefs/testlist_clm.xml
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Expand Up @@ -1552,6 +1552,17 @@
<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="I1PtClm51Fates" testmods="clm/Fates--clm/NEON/FATES/NIWO">
<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</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"/>
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4 changes: 2 additions & 2 deletions cime_config/usermods_dirs/NEON/BLAN/shell_commands
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@@ -1,3 +1,3 @@
./xmlchange NEONSITE=BLAN
./xmlchange PTS_LON=281.92885
./xmlchange PTS_LAT=39.06044
./xmlchange PTS_LON=281.958212
./xmlchange PTS_LAT=39.033698
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/ABBY/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/ABBY/shell_commands
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./xmlchange NEONSITE=ABBY
./xmlchange PTS_LON=237.67032799999998
./xmlchange PTS_LAT=45.762378
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/BARR/include_user_mods
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../defaults
11 changes: 11 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands
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#!/bin/bash

./xmlchange NEONSITE=BARR
./xmlchange PTS_LON=203.349781
./xmlchange PTS_LAT=71.281711
./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
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/BART/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/BART/shell_commands
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./xmlchange NEONSITE=BART
./xmlchange PTS_LON=288.71166
./xmlchange PTS_LAT=44.06516
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/BLAN/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands
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./xmlchange NEONSITE=BLAN
./xmlchange PTS_LON=281.958212
./xmlchange PTS_LAT=39.033698
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/BONA/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/BONA/shell_commands
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./xmlchange NEONSITE=BONA
./xmlchange PTS_LON=212.49806
./xmlchange PTS_LAT=65.15333
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/CLBJ/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/CLBJ/shell_commands
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./xmlchange NEONSITE=CLBJ
./xmlchange PTS_LON=262.43275
./xmlchange PTS_LAT=33.40143
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/CPER/include_user_mods
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../defaults
6 changes: 6 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands
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./xmlchange NEONSITE=CPER
./xmlchange PTS_LON=255.25545
./xmlchange PTS_LAT=40.81297
if [[ $compset =~ ^HIST ]]; then
./xmlchange STOP_N=50
fi
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/DCFS/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/DCFS/shell_commands
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./xmlchange NEONSITE=DCFS
./xmlchange PTS_LON=260.88749
./xmlchange PTS_LAT=47.15919
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/DEJU/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/DEJU/shell_commands
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./xmlchange NEONSITE=DEJU
./xmlchange PTS_LON=214.25235
./xmlchange PTS_LAT=63.87983
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/DELA/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/DELA/shell_commands
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./xmlchange NEONSITE=DELA
./xmlchange PTS_LON=272.19659
./xmlchange PTS_LAT=32.54092
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/DSNY/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/DSNY/shell_commands
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./xmlchange NEONSITE=DSNY
./xmlchange PTS_LON=278.56606
./xmlchange PTS_LAT=28.12919
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/GRSM/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/GRSM/shell_commands
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./xmlchange NEONSITE=GRSM
./xmlchange PTS_LON=276.49815
./xmlchange PTS_LAT=35.68839
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/GUAN/include_user_mods
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../defaults
11 changes: 11 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands
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#!/bin/bash

./xmlchange NEONSITE=GUAN
./xmlchange PTS_LON=293.13112
./xmlchange PTS_LAT=17.96882
./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
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/HARV/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/HARV/shell_commands
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./xmlchange NEONSITE=HARV
./xmlchange PTS_LON=287.82438
./xmlchange PTS_LAT=42.53562
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/HEAL/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/HEAL/shell_commands
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./xmlchange NEONSITE=HEAL
./xmlchange PTS_LON=210.78461
./xmlchange PTS_LAT=63.8798
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/JERC/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/JERC/shell_commands
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./xmlchange NEONSITE=JERC
./xmlchange PTS_LON=275.53353
./xmlchange PTS_LAT=31.19608
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/JORN/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/JORN/shell_commands
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./xmlchange NEONSITE=JORN
./xmlchange PTS_LON=253.15623
./xmlchange PTS_LAT=32.59052
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/KONZ/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/KONZ/shell_commands
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./xmlchange NEONSITE=KONZ
./xmlchange PTS_LON=263.43773
./xmlchange PTS_LAT=39.1007
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/LAJA/include_user_mods
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../defaults
12 changes: 12 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands
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#!/bin/bash
./xmlchange NEONSITE=LAJA
./xmlchange PTS_LON=292.92392
./xmlchange PTS_LAT=18.02184
./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


1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/LENO/include_user_mods
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../defaults
12 changes: 12 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands
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#!/bin/bash

./xmlchange NEONSITE=LENO
./xmlchange PTS_LON=271.83897
./xmlchange PTS_LAT=31.8531
./xmlchange DATM_YR_ALIGN=2021,DATM_YR_START=2021
# 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

1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/MLBS/include_user_mods
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../defaults
10 changes: 10 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands
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#!/bin/bash
./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
fi
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/MOAB/include_user_mods
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../defaults
10 changes: 10 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands
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#!/bin/bash
./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
fi
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/NIWO/include_user_mods
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../defaults
4 changes: 4 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands
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./xmlchange NEONSITE=NIWO
./xmlchange PTS_LON=254.41676
./xmlchange PTS_LAT=40.05236
./xmlchange DATM_YR_END=2018
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/NOGP/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/NOGP/shell_commands
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./xmlchange NEONSITE=NOGP
./xmlchange PTS_LON=259.08168
./xmlchange PTS_LAT=46.76846
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/OAES/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/OAES/shell_commands
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./xmlchange NEONSITE=OAES
./xmlchange PTS_LON=260.93956000000003
./xmlchange PTS_LAT=35.41062
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/ONAQ/include_user_mods
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../defaults
10 changes: 10 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands
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#!/bin/bash
./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
fi
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/ORNL/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands
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./xmlchange NEONSITE=ORNL
./xmlchange PTS_LON=275.717412
./xmlchange PTS_LAT=35.964128
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/OSBS/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/OSBS/shell_commands
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./xmlchange NEONSITE=OSBS
./xmlchange PTS_LON=278.00655
./xmlchange PTS_LAT=29.68819
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/PUUM/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/PUUM/shell_commands
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./xmlchange NEONSITE=PUUM
./xmlchange PTS_LON=204.68269
./xmlchange PTS_LAT=19.55309
10 changes: 10 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/README.md
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# NEON user mods directories for FATES runs

Use these user mods as you would any other user_mods, e.g.:

`./create_newcase --case FATES_ABBY_test --res CLM_USRDAT --compset I1PtClm51Fates --run-unsupported --user-mods-dir /glade/work/$user/CTSM/cime_config/usermods_dirs/NEON/FATES/ABBY`

## Note on crop sites KONA and STER

Currently you cannot run FATES at these sites because FATES does not have crops as of yet. We will add these sites back once this capability is available.

1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/RMNP/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/RMNP/shell_commands
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./xmlchange NEONSITE=RMNP
./xmlchange PTS_LON=254.45476
./xmlchange PTS_LAT=40.27707
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/SCBI/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/SCBI/shell_commands
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./xmlchange NEONSITE=SCBI
./xmlchange PTS_LON=281.86235999999997
./xmlchange PTS_LAT=38.89209
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/SERC/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/SERC/shell_commands
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./xmlchange NEONSITE=SERC
./xmlchange PTS_LON=283.44115999999997
./xmlchange PTS_LAT=38.89124
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/SJER/include_user_mods
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11 changes: 11 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands
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#!/bin/bash
./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
fi

1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/SOAP/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/SOAP/shell_commands
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./xmlchange NEONSITE=SOAP
./xmlchange PTS_LON=240.7379
./xmlchange PTS_LAT=37.03269
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/SRER/include_user_mods
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../defaults
3 changes: 3 additions & 0 deletions cime_config/usermods_dirs/NEON/FATES/SRER/shell_commands
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./xmlchange NEONSITE=SRER
./xmlchange PTS_LON=249.16451
./xmlchange PTS_LAT=31.91068
1 change: 1 addition & 0 deletions cime_config/usermods_dirs/NEON/FATES/STEI/include_user_mods
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../defaults
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