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Merge tag 'ctsm5.1.dev142' into soil-gas-diffusivity-bugfix
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b4b changes to Python scripts, history lists, tech note, and clm_time_manager.

* Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081)
* Rework master_list* files etc. (ESCOMP#2087)
* Fixes to methane Tech Note (ESCOMP#2091)
* Add is_doy_in_interval() function (ESCOMP#2158)
* Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125)

Closes issues:
* Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079)
* Rework master_list_(no)?fates.rst? (ESCOMP#2083)
* conda run -n can fail if a conda environment is already active (ESCOMP#2109)
* conda fails to load for SystemTests (ESCOMP#2111)
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@samsrabin
samsrabin committed Oct 5, 2023
2 parents 2bb68ad + 2e2434d commit d369f8d
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Showing 132 changed files with 8,077 additions and 6,254 deletions.
7 changes: 7 additions & 0 deletions .git-blame-ignore-revs
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@@ -1,4 +1,5 @@
# Ran python directory through black python formatter
d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
4cd83cb3ee6d85eb909403487abf5eeaf4d98911
0aa2957c1f8603c63fa30b11295c06cfddff44a5
2cdb380febb274478e84cd90945aee93f29fa2e6
Expand All @@ -10,5 +11,11 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
b771971e3299c4fa56534b93421f7a2b9c7282fd
9de88bb57ea9855da408cbec1dc8acb9079eda47
8bc4688e52ea23ef688e283698f70a44388373eb
0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
810cb346f05ac1aabfff931ab1a2b7b584add241
5933b0018f8e29413e30dda9b906370d147bad45
# Ran SystemTests and python/ctsm through black python formatter
5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
8056ae649c1b37f5e10aaaac79005d6e3a8b2380
540b256d1f3382f4619d7b0877c32d54ce5c40b6
8a168bb0895f4f2421608dd2589398e13a6663e6
18 changes: 17 additions & 1 deletion .github/workflows/black.yml
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Expand Up @@ -16,6 +16,22 @@ jobs:
# Use options and version identical to the conda environment
# Using pyproject.toml makes sure this testing is consistent with our python directory testing
options: "--check --config python/pyproject.toml"
src: "./python"
src: "./python"
# Version should be coordinated with the ctsm_pylib conda environment under the python directory
version: "22.3.0"
# Actions identical to above for each directory and source file we need to check (arrays aren't allowed for src: field)
- uses: psf/black@stable
with:
options: "--check --config python/pyproject.toml"
src: "./cime_config/SystemTests"
version: "22.3.0"
- uses: psf/black@stable
with:
options: "--check --config python/pyproject.toml"
src: "./cime_config/buildlib"
version: "22.3.0"
- uses: psf/black@stable
with:
options: "--check --config python/pyproject.toml"
src: "./cime_config/buildnml"
version: "22.3.0"
2 changes: 1 addition & 1 deletion Externals_CLM.cfg
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Expand Up @@ -2,7 +2,7 @@
local_path = src/fates
protocol = git
repo_url = https://github.com/NGEET/fates
tag = sci.1.67.1_api.26.0.0
tag = sci.1.67.2_api.27.0.0
required = True

[externals_description]
Expand Down
118 changes: 76 additions & 42 deletions bld/CLMBuildNamelist.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -91,11 +91,13 @@ OPTIONS
This toggles off the namelist variable: use_cn
bgc = Carbon Nitrogen with methane, nitrification, vertical soil C,
CENTURY or MIMICS decomposition
This toggles on the namelist variables:
This toggles on the namelist variables:
use_cn, use_lch4, use_nitrif_denitrif
fates = FATES/Ecosystem Demography with below ground BGC
This toggles on the namelist variables:
use_fates
fates = FATES/Ecosystem Demography with below ground BGC
CENTURY or MIMICS decomposition
This toggles on the namelist variables:
use_fates. use_lch4 and use_nitrif_denitrif are optional
(Only for CLM4.5/CLM5.0)
-[no-]chk_res Also check [do NOT check] to make sure the resolution and
land-mask is valid.
Expand Down Expand Up @@ -763,26 +765,12 @@ sub setup_cmdl_fates_mode {
}
}

# The following variables may be set by the user and are compatible with use_fates
# no need to set defaults, covered in a different routine
my @list = ( "use_lch4" );
foreach my $var ( @list ) {
if ( defined($nl->get_value($var)) ) {
$nl_flags->{$var} = $nl->get_value($var);
$val = $nl_flags->{$var};
my $group = $definition->get_group_name($var);
$nl->set_variable_value($group, $var, $val);
if ( ! $definition->is_valid_value( $var, $val ) ) {
my @valid_values = $definition->get_valid_values( $var );
$log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values");
}
}
}
} else {
# 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" );
"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" );
# dis-allow fates specific namelist items with non-fates runs
foreach my $var ( @list ) {
if ( defined($nl->get_value($var)) ) {
Expand Down Expand Up @@ -1592,6 +1580,7 @@ sub process_namelist_inline_logic {
setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl);
setup_logic_snowpack($opts, $nl_flags, $definition, $defaults, $nl);
setup_logic_fates($opts, $nl_flags, $definition, $defaults, $nl);
setup_logic_z0param($opts, $nl_flags, $definition, $defaults, $nl);
setup_logic_misc($opts, $nl_flags, $definition, $defaults, $nl);

#########################################
Expand Down Expand Up @@ -2990,24 +2979,30 @@ sub setup_logic_supplemental_nitrogen {
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" && &value_is_true($nl_flags->{'use_crop'}) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'});
}
# If this is non-fates, non-sp and crop is active
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'});

} elsif ( $nl_flags->{'bgc_mode'} eq "fates" && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) {
# Or... if its fates but not fates-sp
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
'suplnitro', 'use_fates'=>$nl_flags->{'use_fates'});
}

#
# Error checking for suplnitro
#
my $suplnitro = $nl->get_value('suplnitro');
if ( defined($suplnitro) ) {
if ( $nl_flags->{'bgc_mode'} eq "sp" ) {
$log->fatal_error("supplemental Nitrogen (suplnitro) is set, but neither CN nor CNDV is active!");
$log->fatal_error("supplemental Nitrogen (suplnitro) is set, but neither CN nor CNDV nor FATES is active!");
}
if ( ! &value_is_true($nl_flags->{'use_crop'}) && $suplnitro =~ /PROG_CROP_ONLY/i ) {
$log->fatal_error("supplemental Nitrogen is set to run over prognostic crops, but prognostic crop is NOT active!");
}

if ( $suplnitro =~ /ALL/i ) {
if ( $nl_flags->{'bgc_spinup'} eq "on" ) {
if ( $nl_flags->{'bgc_spinup'} eq "on" && $nl_flags->{'bgc_mode'} ne "fates" ) {
$log->warning("There is no need to use a bgc_spinup mode when supplemental Nitrogen is on for all PFT's, as these modes spinup Nitrogen" );
}
}
Expand Down Expand Up @@ -3324,6 +3319,12 @@ sub setup_logic_luna {
'use_cn'=>$nl_flags->{'use_cn'} );
}
$nl_flags->{'use_luna'} = $nl->get_value('use_luna');

# LUNA can NOT be on with FATES
if ( &value_is_true( $nl_flags->{'use_luna'} ) && &value_is_true( $nl_flags->{'use_fates'} )) {
$log->fatal_error("Cannot turn use_luna to true when bgc=fates" );
}

my $vcmax_opt= $nl->get_value('vcmax_opt');
# lnc_opt only applies if luna is on or for vcmax_opt=3/4
if ( &value_is_true( $nl_flags->{'use_luna'} ) || $vcmax_opt == 3 || $vcmax_opt == 4 ) {
Expand Down Expand Up @@ -3490,18 +3491,18 @@ sub setup_logic_nitrogen_deposition {
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

#
# Nitrogen deposition for bgc=CN
# Nitrogen deposition for bgc=CN or fates
#
if ( $nl_flags->{'bgc_mode'} =~/bgc/ ) {
if ( ($nl_flags->{'bgc_mode'} =~/bgc/) ) { # or ($nl_flags->{'bgc_mode'} =~/fates/) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'},
'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'},
'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_taxmode', 'phys'=>$nl_flags->{'phys'},
'use_cn'=>$nl_flags->{'use_cn'},
'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
'use_cn'=>$nl_flags->{'use_cn'},
'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_varlist', 'phys'=>$nl_flags->{'phys'},
'use_cn'=>$nl_flags->{'use_cn'},
'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
'use_cn'=>$nl_flags->{'use_cn'},
'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_ndep', 'phys'=>$nl_flags->{'phys'},
'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'},
'sim_year_range'=>$nl_flags->{'sim_year_range'});
Expand Down Expand Up @@ -3889,8 +3890,7 @@ sub setup_logic_lai_streams {
if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) {
$log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true.");
}
if ( $nl_flags->{'bgc_mode'} eq "sp" ) {

if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl->get_value('use_fates_sp')) )) {
if ( &value_is_true($nl->get_value('use_lai_streams')) ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams');
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo',
Expand All @@ -3916,15 +3916,20 @@ sub setup_logic_lai_streams {
}
}
} else {
# If bgc is CN/CNDV then make sure none of the LAI settings are set
if ( defined($nl->get_value('stream_year_first_lai')) ||
defined($nl->get_value('stream_year_last_lai')) ||
defined($nl->get_value('model_year_align_lai')) ||
defined($nl->get_value('lai_tintalgo' )) ||
# If bgc is BGC/BGCDV then make sure none of the LAI settings are set
if ( &value_is_true($nl->get_value('use_lai_streams'))) {
$log->fatal_error("When not in SP mode use_lai_streams cannot be .true.\n" .
"(eg. don't use this option with BGC or non-SP FATES), \n" .
"Update compset to use SP)");
}
if ( defined($nl->get_value('stream_year_first_lai')) ||
defined($nl->get_value('stream_year_last_lai')) ||
defined($nl->get_value('model_year_align_lai')) ||
defined($nl->get_value('lai_tintalgo' )) ||
defined($nl->get_value('stream_fldfilename_lai')) ) {
$log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" .
$log->fatal_error("When not in SP mode none of the following can be set: stream_year_first_lai,\n" .
"stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" .
"stream_fldfilename_lai (eg. don't use this option with BGC,CN,CNDV nor BGDCV).");
"stream_fldfilename_lai (eg. don't use this option with BGC or FATES-SP).");
}
}
}
Expand Down Expand Up @@ -4278,6 +4283,13 @@ sub setup_logic_fates {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
}
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 Down Expand Up @@ -4362,6 +4374,28 @@ sub setup_logic_exice {

#-------------------------------------------------------------------------------

sub setup_logic_z0param {
#
# Set default z0 paramterization
#
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'z0param_method');

my $z0param_method = remove_leading_and_trailing_quotes($nl->get_value('z0param_method' ));
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0m_snowmelt',
'z0param_method'=>$z0param_method );

my $use_z0m_snowmelt = $nl->get_value( 'use_z0m_snowmelt' );

if ( $z0param_method eq "ZengWang2007" && defined($use_z0m_snowmelt) && value_is_true($use_z0m_snowmelt)) {
$log->fatal_error("use_z0m_snowmelt must be .false. when z0param_method = $z0param_method.\n $@");
}

}

#-------------------------------------------------------------------------------

sub setup_logic_misc {
#
# Set some misc options
Expand All @@ -4379,7 +4413,7 @@ sub setup_logic_misc {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_use_second_grain_pool');
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_use_repr_structure_pool');
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_no_crop_seed_replenishment');
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_master_list_file');
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_fields_list_file');
}

#-------------------------------------------------------------------------------
Expand Down
22 changes: 18 additions & 4 deletions bld/namelist_files/namelist_defaults_ctsm.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -67,8 +67,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<for_testing_use_repr_structure_pool>.false.</for_testing_use_repr_structure_pool>
<for_testing_no_crop_seed_replenishment>.false.</for_testing_no_crop_seed_replenishment>

<!-- Set to .true. in namelist to write hist fields master list file -->
<hist_master_list_file>.false.</hist_master_list_file>
<!-- Set to .true. in namelist to write file with all history fields -->
<hist_fields_list_file>.false.</hist_fields_list_file>

<!-- In accelerated spinup mode reduce the amount of history output -->
<hist_empty_htapes clm_accelerated_spinup="on">.true.</hist_empty_htapes>
Expand Down Expand Up @@ -146,7 +146,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).

<!-- Supplmental Nitrogen mode -->
<suplnitro use_cn=".true." >NONE</suplnitro>
<suplnitro use_fates=".true." >NONE</suplnitro>
<suplnitro use_fates=".true." >ALL</suplnitro>

<!-- Albedo for glaciers -->
<albice phys="clm5_1" >0.50,0.30</albice>
Expand Down Expand Up @@ -213,7 +213,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<zetamaxstable use_biomass_heat_storage=".true." >2.0d00</zetamaxstable>
<zetamaxstable phys="clm4_5" >2.0d00</zetamaxstable>
<zetamaxstable phys="clm5_0" >0.5d00</zetamaxstable>
<zetamaxstable phys="clm5_1" >0.5d00</zetamaxstable>
<zetamaxstable phys="clm5_1" z0param_method="ZengWang2007" >0.5d00</zetamaxstable>
<zetamaxstable phys="clm5_1" z0param_method="Meier2022" >2.0d00</zetamaxstable>

<!-- atm2lnd defaults -->
<repartition_rain_snow phys="clm5_1" >.true.</repartition_rain_snow>
Expand Down Expand Up @@ -324,6 +325,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<itmax_canopy_fluxes structure="standard">40</itmax_canopy_fluxes>
<itmax_canopy_fluxes structure="fast" >3</itmax_canopy_fluxes>


<!-- Canopy hydrology namelist defaults -->
<use_clm5_fpi phys="clm5_1" >.true.</use_clm5_fpi>
<interception_fraction phys="clm5_1" >1.0</interception_fraction>
Expand Down Expand Up @@ -495,6 +497,15 @@ attributes from the config_cache.xml file (with keys converted to upper-case).

<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230628.nc</fates_paramfile>

<!-- ================================================================== -->
<!-- Default surface roughness parameterization -->
<!-- ================================================================== -->

<z0param_method>ZengWang2007</z0param_method>

<use_z0m_snowmelt z0param_method="Meier2022" >.true.</use_z0m_snowmelt>
<use_z0m_snowmelt >.false.</use_z0m_snowmelt>

<!-- ======================================================================================== -->
<!-- clm 5.0 BGC nitrogen model -->
<!-- ======================================================================================== -->
Expand All @@ -510,6 +521,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<use_luna phys="clm5_0" >.true.</use_luna>
<use_luna phys="clm5_0" use_fates=".true." >.false.</use_luna>
<use_luna phys="clm4_5" >.false.</use_luna>
<use_luna phys="clm4_5" use_fates=".true." >.false.</use_luna>

<!-- Flexible CN options -->
<MM_Nuptake_opt use_flexibleCN=".true." >.true.</MM_Nuptake_opt>
Expand Down Expand Up @@ -1128,6 +1140,8 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_C24_hist_78pfts_CMIP6_simyr2000
lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc</fsurdat>
<fsurdat hgrid="1.9x2.5" sim_year="2000" use_crop=".true." use_vichydro=".false.">
lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr2000_c190304.nc</fsurdat>
<fsurdat hgrid="hcru_hcru" sim_year="2000">
lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_360x720cru_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
<fsurdat hgrid="0.125x0.125" sim_year="2000" use_crop=".true." >
lnd/clm2/surfdata_map/release-clm5.0.24/surfdata_0.125x0.125_hist_78pfts_CMIP6_simyr2005_c190624.nc</fsurdat>
<fsurdat hgrid="10x15" sim_year="2000" use_crop=".true." use_vichydro=".false.">
Expand Down
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