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Merge pull request #9 from samsrabin/hillslope_hydrology-ssr4
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Hillslope hydrology pre-merge changes
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@swensosc
swensosc authored Feb 7, 2024
2 parents 44d37e7 + dbae8b6 commit 220f314
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Showing 112 changed files with 3,509 additions and 863 deletions.
5 changes: 5 additions & 0 deletions .git-blame-ignore-revs
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Expand Up @@ -11,16 +11,21 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
b771971e3299c4fa56534b93421f7a2b9c7282fd
9de88bb57ea9855da408cbec1dc8acb9079eda47
8bc4688e52ea23ef688e283698f70a44388373eb
c8bd4c6f98c0b411391b4355da449507db3aab4e
4ee49e3e516ca7dee5df378f65664f93a7db4415
0207bc98dd5c75cd69a0e788bc53e41093712f5c
e4d38681df23ccca0ae29581a45f8362574e0630
0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
810cb346f05ac1aabfff931ab1a2b7b584add241
5933b0018f8e29413e30dda9b906370d147bad45
025d5e7c2e80263717fb029101d65cbbf261c3c4
a9d96219902cf609636886c7073a84407f450d9a
d866510188d26d51bcd6d37239283db690af7e82
# Ran SystemTests and python/ctsm through black python formatter
5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
8056ae649c1b37f5e10aaaac79005d6e3a8b2380
0bc3f00115d86d026a977918661c93779b3b19f9
540b256d1f3382f4619d7b0877c32d54ce5c40b6
8a168bb0895f4f2421608dd2589398e13a6663e6
183fc26a6691bbdf87f515dc47924a64be3ced9b
6fccf682eaf718615407d9bacdd3903b8786a03d
4 changes: 2 additions & 2 deletions Externals.cfg
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Expand Up @@ -59,7 +59,7 @@ tag = cdeps1.0.24
protocol = git
repo_url = https://github.com/ESCOMP/CDEPS.git
local_path = components/cdeps
externals = Externals_CDEPS.cfg
externals = Externals_CDEPS.cfg
required = True

[cpl7]
Expand Down Expand Up @@ -98,4 +98,4 @@ tag = v1.0.8
required = False

[externals_description]
schema_version = 1.0.0
schema_version = 1.0.0
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.1.68.2_api.31.0.0
tag = sci.1.71.0_api.33.0.0
required = True

[externals_description]
Expand Down
78 changes: 58 additions & 20 deletions bld/CLMBuildNamelist.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -784,7 +784,7 @@ sub setup_cmdl_fates_mode {
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_seeddisp_cadence" );
"fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries" );
# dis-allow fates specific namelist items with non-fates runs
foreach my $var ( @list ) {
if ( defined($nl->get_value($var)) ) {
Expand Down Expand Up @@ -1634,6 +1634,11 @@ sub process_namelist_inline_logic {
###############################
setup_logic_crop_inparm($opts, $nl_flags, $definition, $defaults, $nl);

###############################
# namelist group: tillage #
###############################
setup_logic_tillage($opts, $nl_flags, $definition, $defaults, $nl);

###############################
# namelist group: ch4par_in #
###############################
Expand Down Expand Up @@ -2236,12 +2241,28 @@ sub setup_logic_crop_inparm {
}
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "initial_seed_at_planting",
'use_crop'=>$nl->get_value('use_crop') );

my $crop_residue_removal_frac = $nl->get_value('crop_residue_removal_frac');
if ( $crop_residue_removal_frac < 0.0 or $crop_residue_removal_frac > 1.0 ) {
$log->fatal_error("crop_residue_removal_frac must be in range [0, 1]");
}
} else {
error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept" );
error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept", "crop_residue_removal_frac" );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_fsat_equals_zero' );
}
}

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

sub setup_logic_tillage {
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) );
if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) {
$log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." );
}
}

#-------------------------------------------------------------------------------
sub error_if_set {
# do a fatal_error and exit if any of the input variable names are set
Expand Down Expand Up @@ -2662,6 +2683,8 @@ sub setup_logic_do_transient_pfts {
$cannot_be_true = "$var cannot be combined with use_cndv";
} elsif (&value_is_true($nl->get_value('use_fates'))) {
$cannot_be_true = "$var cannot be combined with use_fates";
} elsif (&value_is_true($nl->get_value('use_hillslope'))) {
$cannot_be_true = "$var cannot be combined with use_hillslope";
}

if ($cannot_be_true) {
Expand Down Expand Up @@ -2737,6 +2760,8 @@ sub setup_logic_do_transient_crops {
# do_transient_crops. However, this hasn't been tested, so to be safe,
# we are not allowing this combination for now.
$cannot_be_true = "$var has not been tested with FATES, so for now these two options cannot be combined";
} elsif (&value_is_true($nl->get_value('use_hillslope'))) {
$cannot_be_true = "$var cannot be combined with use_hillslope";
}

if ($cannot_be_true) {
Expand Down Expand Up @@ -2832,6 +2857,8 @@ sub setup_logic_do_transient_lakes {
if (&value_is_true($nl->get_value($var))) {
if (&value_is_true($nl->get_value('collapse_urban'))) {
$log->fatal_error("$var cannot be combined with collapse_urban");
} elsif (&value_is_true($nl->get_value('use_hillslope'))) {
$log->fatal_error("$var cannot be combined with use_hillslope");
}
if ($n_dom_pfts > 0 || $n_dom_landunits > 0 || $toosmall_soil > 0 || $toosmall_crop > 0 || $toosmall_glacier > 0 || $toosmall_lake > 0 || $toosmall_wetland > 0 || $toosmall_urban > 0) {
$log->fatal_error("$var cannot be combined with any of the of the following > 0: n_dom_pfts > 0, n_dom_landunit > 0, toosmall_soil > 0._r8, toosmall_crop > 0._r8, toosmall_glacier > 0._r8, toosmall_lake > 0._r8, toosmall_wetland > 0._r8, toosmall_urban > 0._r8");
Expand Down Expand Up @@ -2895,6 +2922,8 @@ sub setup_logic_do_transient_urban {
if (&value_is_true($nl->get_value($var))) {
if (&value_is_true($nl->get_value('collapse_urban'))) {
$log->fatal_error("$var cannot be combined with collapse_urban");
} elsif (&value_is_true($nl->get_value('use_hillslope'))) {
$log->fatal_error("$var cannot be combined with use_hillslope");
}
if ($n_dom_pfts > 0 || $n_dom_landunits > 0 || $toosmall_soil > 0 || $toosmall_crop > 0 || $toosmall_glacier > 0 || $toosmall_lake > 0 || $toosmall_wetland > 0 || $toosmall_urban > 0) {
$log->fatal_error("$var cannot be combined with any of the of the following > 0: n_dom_pfts > 0, n_dom_landunit > 0, toosmall_soil > 0._r8, toosmall_crop > 0._r8, toosmall_glacier > 0._r8, toosmall_lake > 0._r8, toosmall_wetland > 0._r8, toosmall_urban > 0._r8");
Expand Down Expand Up @@ -3436,22 +3465,18 @@ sub setup_logic_hillslope {
#
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hillslope' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'downscale_hillslope_meteorology' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_head_gradient_method' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_transmissivity_method' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_pft_distribution_method' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_soil_profile_method' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hillslope_routing', 'use_hillslope'=>$nl_flags->{'use_hillslope'} );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hillslope' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'downscale_hillslope_meteorology' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_head_gradient_method' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_transmissivity_method' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_pft_distribution_method' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hillslope_soil_profile_method' );
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_hillslope_routing', 'use_hillslope'=>$nl_flags->{'use_hillslope'} );
my $use_hillslope = $nl->get_value('use_hillslope');
my $use_hillslope_routing = $nl->get_value('use_hillslope_routing');
if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
$log->fatal_error("Cannot turn on use_hillslope_routing when use_hillslope is off\n" );
}
my $downscale_hillslope_meteorology = $nl->get_value('use_hillslope_routing');
if ( (! &value_is_true($use_hillslope)) && &value_is_true($downscale_hillslope_meteorology) ) {
$log->fatal_error("Cannot turn on downscale_hillslope_meteorology when use_hillslope is off\n" );
}
if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
$log->fatal_error("Cannot turn on use_hillslope_routing when use_hillslope is off\n" );
}
}

#-------------------------------------------------------------------------------
Expand Down Expand Up @@ -4389,7 +4414,7 @@ sub setup_logic_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_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" );
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'} );
Expand Down Expand Up @@ -4417,21 +4442,34 @@ sub setup_logic_fates {
# spit-fire can't be on with FATES SP mode is active
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');
}
}
}
}
my $var = "use_fates_inventory_init";
if ( defined($nl->get_value($var)) ) {
if ( &value_is_true($nl->get_value($var)) ) {
$var = "fates_inventory_ctrl_filename";
my $fname = substr $nl->get_value($var), 1, -1; # ignore first and last positions of string because those are quote characters
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_inventory_init is set" );
} elsif ( ! -f "$fname" ) {
$log->fatal_error("$fname does NOT point to a valid filename" );
}
}
}
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 );
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" );
} elsif ( ! -f "$fname" ) {
$log->fatal_error("$fname does NOT point to a valid filename" );
}
}
}
}
}

Expand Down Expand Up @@ -4558,7 +4596,7 @@ sub write_output_files {
soil_resis_inparm bgc_shared canopyfluxes_inparm aerosol
clmu_inparm clm_soilstate_inparm clm_nitrogen clm_snowhydrology_inparm hillslope_hydrology_inparm hillslope_properties_inparm
cnprecision_inparm clm_glacier_behavior crop_inparm irrigation_inparm
surfacealbedo_inparm water_tracers_inparm);
surfacealbedo_inparm water_tracers_inparm tillage_inparm);

#@groups = qw(clm_inparm clm_canopyhydrology_inparm clm_soilhydrology_inparm
# finidat_consistency_checks dynpft_consistency_checks);
Expand Down
28 changes: 24 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 @@ -484,15 +484,15 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<!-- The default filenames are given relative to the root directory
for the CLM2 data in the CESM distribution -->
<!-- Plant function types (relative to {csmdata}) -->
<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c231117.nc</paramfile>
<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c231117.nc</paramfile>
<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c231117.nc</paramfile>
<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240105.nc</paramfile>
<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240105.nc</paramfile>
<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240105.nc</paramfile>

<!-- ================================================================== -->
<!-- FATES default parameter file -->
<!-- ================================================================== -->

<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230628.nc</fates_paramfile>
<fates_paramfile>lnd/clm2/paramdata/fates_params_api.32.0.0_12pft_c231215.nc</fates_paramfile>

<!-- ================================================================== -->
<!-- Default surface roughness parameterization -->
Expand Down Expand Up @@ -553,6 +553,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<use_grainproduct use_crop=".true." phys="clm5_0" >.true.</use_grainproduct> <!-- 1-year grain product pool default to on for clm50 if crop is turned on -->
<use_grainproduct use_crop=".true." phys="clm5_1" >.true.</use_grainproduct> <!-- 1-year grain product pool default to on for clm50 if crop is turned on -->

<crop_residue_removal_frac>0.d+0</crop_residue_removal_frac>

<!-- Crop model options -->
<baset_mapping use_crop=".true." phys="clm4_5" >constant</baset_mapping>
<baset_mapping use_crop=".true." phys="clm5_0" >varytropicsbylat</baset_mapping>
Expand Down Expand Up @@ -1584,6 +1586,15 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
<flanduse_timeseries hgrid="10x15" sim_year_range="1850-2100" ssp_rcp="SSP5-3.4"
use_crop=".false." >lnd/clm2/surfdata_map/release-clm5.0.18/landuse.timeseries_10x15_SSP5-3.4_16pfts_Irrig_CMIP6_simyr1850-2100_c190228.nc</flanduse_timeseries>

<!-- Land Use Harmonization unified 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>

<!-- 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>

<!-- Fixation and Uptake of Nitrogen Model (FUN2.0) -->
<use_fun phys="clm5_1" use_cn=".true." use_nitrif_denitrif=".true.">.true.</use_fun>
<use_fun phys="clm5_0" use_cn=".true." use_nitrif_denitrif=".true.">.true.</use_fun>
Expand Down Expand Up @@ -2767,6 +2778,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
<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>
<fates_parteh_mode use_fates=".true.">1</fates_parteh_mode>
<fates_seeddisp_cadence use_fates=".true.">0</fates_seeddisp_cadence>

Expand Down Expand Up @@ -2808,4 +2820,12 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
<stream_meshfile_exice use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_cdf5_c20220802.nc</stream_meshfile_exice>
<stream_mapalgo_exice use_excess_ice=".true.">bilinear</stream_mapalgo_exice>

<!-- ========================================= -->
<!-- Defaults for tillage -->
<!-- ========================================= -->

<tillage_mode>off</tillage_mode>
<use_original_tillage_phases>.false.</use_original_tillage_phases>
<max_tillage_depth>0.26d00</max_tillage_depth>

</namelist_defaults>
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