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Merge remote-tracking branch 'escomp/master' into cn-matrix_v3
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slevis resolved conflicts:
bld/unit_testers/build-namelist_test.pl
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@slevis-lmwg
slevis-lmwg committed Jul 18, 2024
2 parents c031e1c + a784f41 commit 98d0731
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Showing 34 changed files with 913 additions and 129 deletions.
2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
[submodule "fates"]
path = src/fates
url = https://github.com/NGEET/fates
fxtag = sci.1.73.0_api.35.0.0
fxtag = sci.1.77.1_api.36.0.0
fxrequired = AlwaysRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/NCAR/fates-release
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127 changes: 112 additions & 15 deletions bld/CLMBuildNamelist.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -787,9 +787,10 @@ sub setup_cmdl_fates_mode {
# dis-allow fates specific namelist items with non-fates runs
my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
"use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
"use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging",
"fates_parteh_mode","use_fates_tree_damage","fates_history_dimlevel","fates_seeddisp_cadence",
"use_fates_luh","fluh_timeseries" );
"use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
"fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries",
"flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel" );

# dis-allow fates specific namelist items with non-fates runs
foreach my $var ( @list ) {
if ( defined($nl->get_value($var)) ) {
Expand Down Expand Up @@ -3075,8 +3076,8 @@ sub setup_logic_do_harvest {
$cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)";
}

elsif (!&value_is_true($nl->get_value('use_cn')) && !&value_is_true($nl->get_value('use_fates'))) {
$cannot_be_true = "$var can only be set to true when running with either CN or FATES";
elsif (!&value_is_true($nl->get_value('use_cn'))) {
$cannot_be_true = "$var can only be set to true when running with CN. Please set use_cn to true.";
}

if ($cannot_be_true) {
Expand Down Expand Up @@ -4550,21 +4551,35 @@ sub setup_logic_fates {
if (&value_is_true( $nl_flags->{'use_fates'}) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
"use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence",
"use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage",
"use_fates_luh","fates_history_dimlevel" );
"use_fates_inventory_init","fates_seeddisp_cadence","fates_history_dimlevel",
"fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" );

foreach my $var ( @list ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
}

add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_potentialveg', 'use_fates'=>$nl_flags->{'use_fates'});
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'});
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'},
'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
'use_fates_potentialveg'=>$nl->get_value('use_fates_potentialveg'),
'fates_harvest_mode'=>remove_leading_and_trailing_quotes($nl->get_value('fates_harvest_mode')) );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'},
'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_fixed_biogeog', 'use_fates'=>$nl_flags->{'use_fates'},
'use_fates_lupft'=>$nl->get_value('use_fates_lupft'),
'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );

my $suplnitro = $nl->get_value('suplnitro');
my $parteh_mode = $nl->get_value('fates_parteh_mode');
if ( ($parteh_mode == 1) && ($suplnitro !~ /ALL/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
$log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " .
"but and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active" .
"Change suplnitro back to ALL");
}
#

# For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set
# And also check for other settings that can't be trigged on as well
#
Expand All @@ -4581,6 +4596,12 @@ sub setup_logic_fates {
if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
$log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
}

# fates landuse can't be on with FATES SP mode is active
if ( &value_is_true($nl->get_value('use_fates_luh')) ) {
$log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true');
}

# hydro isn't currently supported to work when FATES SP mode is active
if (&value_is_true( $nl->get_value('use_fates_planthydro') )) {
$log->fatal_error('fates sp mode is currently not supported to work with fates hydro');
Expand All @@ -4599,16 +4620,92 @@ sub setup_logic_fates {
}
}
}
# make sure that fates landuse x pft mode has the necessary run mode configurations
my $var = "use_fates_lupft";
if ( defined($nl->get_value($var)) ) {
if ( &value_is_true($nl->get_value($var)) ) {
my @list = ( "use_fates_luh", "use_fates_nocomp", "use_fates_fixed_biogeog" );
foreach my $var ( @list ) {
if ( ! &value_is_true($nl->get_value($var)) ) {
$log->fatal_error("$var is required when use_fates_lupft is true" );
}
}
}
}
# check that fates landuse change mode has the necessary luh2 landuse timeseries data
# and add the default if not defined. Do not add default if use_fates_potentialveg is true.
# If fixed biogeography is on, make sure that flandusepftdat is avilable.
my $var = "use_fates_luh";
if ( defined($nl->get_value($var)) ) {
if ( &value_is_true($nl->get_value($var)) ) {
$var = "fluh_timeseries";
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 );
$var = "use_fates_potentialveg";
if ( defined($nl->get_value($var)) ) {
if ( ! &value_is_true($nl->get_value($var)) ) {
$var = "fluh_timeseries";
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'});
my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
if ( ! defined($nl->get_value($var)) ) {
$log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" );
} elsif ( ! -f "$fname" ) {
$log->fatal_error("$var does NOT point to a valid filename" );
}
}
}
$var = "use_fates_fixed_biogeog";
if ( defined($nl->get_value($var)) ) {
if ( &value_is_true($nl->get_value($var)) ) {
$var = "flandusepftdat";
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 );
my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
if ( ! defined($nl->get_value($var)) ) {
$log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" );
} elsif ( ! -f "$fname" ) {
$log->fatal_error("$var does NOT point to a valid filename" );
}
}
}
}
}
# check that fates landuse is on and harvest mode is off when potential veg switch is true
my $var = "use_fates_potentialveg";
if ( defined($nl->get_value($var)) ) {
if ( &value_is_true($nl->get_value($var)) ) {
if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
$log->fatal_error("use_fates_luh must be true when $var is true" );
}
my $var = remove_leading_and_trailing_quotes($nl->get_value('fates_harvest_mode'));
if ( $var ne 'no_harvest') {
$log->fatal_error("fates_harvest_mode set to $var. It must set to no_harvest when use_potential_veg is true." );
}
my $var = "fluh_timeseries";
if ( defined($nl->get_value($var)) ) {
$log->fatal_error("fluh_timeseries can not be defined when use_fates_potentialveg is true" );
}
}
}
# Check fates_harvest_mode compatibility
my $var = "fates_harvest_mode";
if ( defined($nl->get_value($var)) ) {
# using fates_harvest mode with raw luh2 harvest data
my $mode = remove_leading_and_trailing_quotes($nl->get_value($var));
if ( $mode eq 'luhdata_area' || $mode eq 'luhdata_mass' ) {
# Make sure that use_fates_luh is true when using raw fates luh2 harvest data
if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) {
$log->fatal_error("use_fates_luh is required to be true when $var is luhdata_mass or luhdata_area" );
}
} elsif ( $mode eq 'landuse_timeseries' ) {
# Check to make sure that the user set the flanduse_timeseries file
# Since the flanduse_timeseries logic checking is upstream of the fates logic,
# don't add the default here. The onus is on the user to match the correct timeseries
# data to the correct surface dataset resolution
my $var = "flanduse_timeseries";
my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) );
if ( ! defined($nl->get_value($var)) ) {
$log->fatal_error("$var is required when use_fates_luh is set" );
$log->fatal_error("$var is required when fates_harvest_mode is landuse_timeseries" );
} elsif ( ! -f "$fname" ) {
$log->fatal_error("$fname does NOT point to a valid filename" );
$log->fatal_error("$var does NOT point to a valid filename" );
}
}
}
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30 changes: 21 additions & 9 deletions bld/namelist_files/namelist_defaults_ctsm.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -513,7 +513,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<!-- FATES default parameter file -->
<!-- ================================================================== -->

<fates_paramfile>lnd/clm2/paramdata/fates_params_api.35.0.0_12pft_c240326.nc</fates_paramfile>
<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.0.0_12pft_c240517.nc</fates_paramfile>

<!-- ================================================================== -->
<!-- Default surface roughness parameterization -->
Expand Down Expand Up @@ -2050,14 +2050,17 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
<!-- SSP5-RCP3.4 - relative to {csmdata}) -->
<!--- currently empty until needed, we can't test because of lack of ndep files for this SSP -->

<!-- Land Use Harmonization unified data sets for dynamic FATES land use change -->
<!-- Land Use Harmonization unified timeseries data sets for dynamic FATES land use change -->

<fluh_timeseries hgrid="4x5" sim_year_range="1850-2000" use_fates=".true."
>lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>

<!-- Land Use Harmonization static landuse x pft mapping data sets for FATES land use change -->
<flandusepftdat hgrid="4x5" use_fates=".true." >lnd/clm2/surfdata_map/fates-sci.1.77.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc</flandusepftdat>

<!-- This one is just for testing until Issue #2304 is resolved -->
<fluh_timeseries hgrid="4x5" sim_year_range="constant" use_fates=".true."
>lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>
>lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr0850-2015_c240216.nc</fluh_timeseries>

<!-- Fixation and Uptake of Nitrogen Model (FUN2.0) -->
<use_fun >.false.</use_fun>
Expand Down Expand Up @@ -2551,22 +2554,31 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c

<!-- ===== FATES DEFAULTS =========== -->
<fates_spitfire_mode use_fates=".true.">0</fates_spitfire_mode>
<fates_harvest_mode use_fates=".true.">no_harvest</fates_harvest_mode>
<use_fates_planthydro use_fates=".true.">.false.</use_fates_planthydro>
<use_fates_tree_damage use_fates=".true.">.false.</use_fates_tree_damage>
<use_fates_cohort_age_tracking use_fates=".true.">.false.</use_fates_cohort_age_tracking>
<use_fates_ed_st3 use_fates=".true.">.false.</use_fates_ed_st3>
<use_fates_ed_prescribed_phys use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
<use_fates_logging use_fates=".true.">.false.</use_fates_logging>
<use_fates_inventory_init use_fates=".true.">.false.</use_fates_inventory_init>
<use_fates_sp use_fates=".true.">.false.</use_fates_sp>
<use_fates_luh use_fates=".true.">.false.</use_fates_luh>
<use_fates_lupft use_fates=".true.">.false.</use_fates_lupft>
<use_fates_potentialveg use_fates=".true.">.false.</use_fates_potentialveg>
<use_fates_luh use_fates=".true." fates_harvest_mode="luhdata_area" >.true.</use_fates_luh>
<use_fates_luh use_fates=".true." fates_harvest_mode="luhdata_mass" >.true.</use_fates_luh>
<use_fates_luh use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
<use_fates_luh use_fates=".true." use_fates_potentialveg=".true.">.true.</use_fates_luh>
<use_fates_luh use_fates=".true." >.false.</use_fates_luh>
<fates_parteh_mode use_fates=".true.">1</fates_parteh_mode>
<fates_seeddisp_cadence use_fates=".true.">0</fates_seeddisp_cadence>
<use_fates_nocomp use_fates=".true." use_fates_sp=".true." >.true.</use_fates_nocomp>
<use_fates_nocomp use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_nocomp>
<use_fates_nocomp use_fates=".true." >.false.</use_fates_nocomp>
<use_fates_fixed_biogeog use_fates=".true." use_fates_sp=".true." >.true.</use_fates_fixed_biogeog>
<use_fates_fixed_biogeog use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_fixed_biogeog>
<use_fates_fixed_biogeog use_fates=".true." >.false.</use_fates_fixed_biogeog>
<fates_history_dimlevel use_fates=".true.">2,2</fates_history_dimlevel>
<use_fates_nocomp use_fates=".true." use_fates_sp=".true.">.true.</use_fates_nocomp>
<use_fates_nocomp use_fates=".true." >.false.</use_fates_nocomp>
<use_fates_fixed_biogeog use_fates=".true." use_fates_sp=".true.">.true.</use_fates_fixed_biogeog>
<use_fates_fixed_biogeog use_fates=".true." >.false.</use_fates_fixed_biogeog>


<!-- ========================================= -->
<!-- Defaults for dynamic subgrid -->
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