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Add FATES land use change module to pass LUH2 data to FATES #5760

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merged 5 commits into from
Mar 6, 2024
Merged

Add FATES land use change module to pass LUH2 data to FATES #5760

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cbb0890
Add fates land use module
glemieux Mar 21, 2023
1bffbfe
add logic to avoid rho and tau calculation when fates is on
glemieux Oct 11, 2023
b559bd3
add fates landuse data default and update fates default paramfile
glemieux Feb 9, 2024
088b63f
remove depricated fates history variables from fates testmods
glemieux Feb 9, 2024
f09f5e3
add code comment describing variable short names
glemieux Feb 20, 2024
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1 change: 1 addition & 0 deletions cime_config/tests.py
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Expand Up @@ -415,6 +415,7 @@
"ERP_D_Ld3.f19_g16.IELMFATES.elm-fates_cold",
"ERS_D_Ld3_PS.f09_g16.IELMFATES.elm-fates_cold",
"ERS_D_Ld5.f45_g37.IELMFATES.elm-fates_cold",
"ERS_D_Ld30.f45_g37.IELMFATES.elm-fates_cold_landuse",
"ERS_Ld30.f45_g37.IELMFATES.elm-fates_satphen",
"ERS_Ld30.f45_g37.IELMFATES.elm-fates_cold_fixedbiogeo",
"ERS_Ld30.f45_g37.IELMFATES.elm-fates_cold_nocomp",
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44 changes: 42 additions & 2 deletions components/elm/bld/ELMBuildNamelist.pm
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Expand Up @@ -797,7 +797,8 @@ sub setup_cmdl_fates_mode {
"use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
"use_fates_inventory_init", "use_fates_fixed_biogeog", "use_fates_nocomp","use_fates_sp",
"fates_inventory_ctrl_filename","use_fates_logging", "use_fates_tree_damage",
"use_fates_parteh_mode","use_fates_cohort_age_tracking","use_snicar_ad");
"use_fates_parteh_mode","use_fates_cohort_age_tracking","use_snicar_ad", "use_fates_luh",
"fluh_timeseries");
foreach my $var ( @list ) {
if ( defined($nl->get_value($var)) ) {
$nl_flags->{$var} = $nl->get_value($var);
Expand Down Expand Up @@ -857,6 +858,10 @@ sub setup_cmdl_fates_mode {
if ( defined($nl->get_value($var)) ) {
fatal_error("$var is being set, but can ONLY be set when -bgc fates option is used.\n");
}
$var = "use_fates_luh";
if ( defined($nl->get_value($var)) ) {
fatal_error("$var is being set, but can ONLY be set when -bgc fates option is used.\n");
}
$var = "fates_inventory_ctrl_filename";
if ( defined($nl->get_value($var)) ) {
fatal_error("$var is being set, but can ONLY be set when -bgc fates option is used.\n");
Expand Down Expand Up @@ -3292,8 +3297,43 @@ sub setup_logic_fates {
add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'});
add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_tree_damage', 'use_fates'=>$nl_flags->{'use_fates'});
add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_seeddisp_cadence', 'use_fates'=>$nl_flags->{'use_fates'});
add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'});
add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});

add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fluh_timeseries', 'phys'=>$nl_flags->{'phys'});

# For FATES SP mode make sure no-competion, and fixed-biogeography are also set
# And also check for other settings that can't be trigged on as well
my $var = "use_fates_sp";
if ( defined($nl->get_value($var)) ) {
if ( &value_is_true($nl->get_value($var)) ) {
my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog" );
foreach my $var ( @list ) {
if ( ! &value_is_true($nl->get_value($var)) ) {
fatal_error("$var is required when FATES SP is on (use_fates_sp)" );
}
}
# spit-fire can't be on with FATES SP mode is active
if ( $nl->get_value('fates_spitfire_mode') > 0 ) {
fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true');
}
}
}
# check that fates landuse change mode has the necessary luh2 landuse timeseries data
my $var = "use_fates_luh";
if ( defined($nl->get_value($var)) ) {
if ( &value_is_true($nl->get_value($var)) ) {
$var = "fluh_timeseries";
add_default($test_files, $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)) ) {
fatal_error("$var is required when use_fates_luh is set" );
} elsif ( ! -f "$fname" ) {
fatal_error("$fname does NOT point to a valid filename" );
}
}
}
}
}

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8 changes: 7 additions & 1 deletion components/elm/bld/namelist_files/namelist_defaults.xml
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Expand Up @@ -127,7 +127,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<!-- ================================================================== -->
<!-- FATES default parameter file -->
<!-- ================================================================== -->
<fates_paramfile >lnd/clm2/paramdata/fates_params_api25.5.0_12pft_c230710.nc</fates_paramfile>
<fates_paramfile >lnd/clm2/paramdata/fates_params_api.32.0.0_12pft_c231215.nc</fates_paramfile>
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This file is not available on https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/paramdata/

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Thanks @bishtgautam I'll email you the file.

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The file is on the other server though. https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/paramdata/

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Oh, FATES also contributes code to CTSM, so it is on NCAR's server. In that case, we don't need to put on the E3SM server.

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Oh nice, I didn't realize that! Thanks @peterdschwartz


<!-- soil order related parameters (relative to {csmdata}) -->
<fsoilordercon >lnd/clm2/paramdata/CNP_parameters_c131108.nc</fsoilordercon>
Expand Down Expand Up @@ -565,6 +565,11 @@ lnd/clm2/surfdata_map/surfdata_conusx4v1_simyr2000_c160503.nc</fsurdat>
<flanduse_timeseries hgrid="ne30np4" rcp="2.6" sim_year_range="1850-2100"
use_crop=".false." >lnd/clm2/surfdata_map/surfdata.pftdyn_ne30np4_rcp2.6_simyr1850-2100_c130524.nc</flanduse_timeseries>

<!-- Land Use Harmonization unified data sets for dynamic FATES land use change -->
<fluh_timeseries hgrid="4x5" sim_year_range="1850-2015" 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>
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  1. This file is not on the E3SM input data server.
  2. FATES's SCI/API version number will continue to get updated. This would mean we would have many fates-sci* directories. How we have a single dir (e.g. lnd/clm2/surfdata_map/fates) and the metadata of the LUH2 file can include the information regarding the SCI/API version. In the F90 code, you can also include a sanity check regarding the SCI/API version.

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  1. @bishtgautam this file is fairly large. I submitted a request about 2 weeks ago to get access to the ANL servers using the procedure laid out on confluence so that I could load this and future updates directly. I haven't seen movement on that request. In the meantime, the data is on perlmutter; is this something you could upload for me via globus?
  2. That should work. The file structure here was the recommended by ctsm folks, although I can't remember the rationale currently. I'll definitely add the fates sci/api version to the data file meta data. That said, the meta data check isn't really needed for usage here.

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File is also on the other data server too https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/



<!-- GLC mask datasets (relative to {csmdata}) -->
<!-- Currently glc_grid is not being read from anywhere, so these rules are broken. -->
<!-- Until that is fixed, the first entry matching hgrid will be used. -->
Expand Down Expand Up @@ -2136,6 +2141,7 @@ this mask will have smb calculated over the entire global land surface
<use_fates_logging use_fates=".true.">.false.</use_fates_logging>
<use_fates_cohort_age_tracking use_fates=".true.">.false.</use_fates_cohort_age_tracking>
<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>
<use_fates_inventory_init use_fates=".true.">.false.</use_fates_inventory_init>
Expand Down
15 changes: 15 additions & 0 deletions components/elm/bld/namelist_files/namelist_definition.xml
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Expand Up @@ -381,6 +381,21 @@ Toggle to turn on inventory initialization(only relevant if FATES is being used)
Full pathname to the inventory initialization control file.
</entry>

<!-- This may eventually migrate to the dynamic_subgrid group-->
<entry id="use_fates_luh" type="logical" category="physics"
group="elm_inparm" valid_values="" >
If TRUE, enable use of land use state and transition data from luh_timeseries file.
(Only valid for fates land use change runs, where there is a luh_timeseries file.)
(Also, only valid for use_fates = true and is incompatible with transient runs currently.)
</entry>

<!-- This could eventually be included in the "dynamic_subgrid" -->
<entry id="fluh_timeseries" type="char*256" category="datasets"
input_pathname="abs" group="elm_inparm" valid_values="" >
Full pathname of unified land use harmonization data file. This causes the land-use
types to vary over time.
</entry>

<entry id="use_hydrstress" type="logical" category="physics"
group="elm_inparm" valid_values="" value=".false.">
Toggle to turn on if Kennedy et al plant hydraulics model is used.
Expand Down
7 changes: 3 additions & 4 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates/user_nl_elm
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Expand Up @@ -16,10 +16,8 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S',
'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE',
'FATES_HARVEST_CARBON_FLUX', 'FATES_DISTURBANCE_RATE_FIRE',
'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX',
'FATES_STOMATAL_COND', 'FATES_LBLAYER_COND', 'FATES_NPP', 'FATES_GPP',
'FATES_AUTORESP', 'FATES_GROWTH_RESP', 'FATES_MAINT_RESP', 'FATES_GPP_CANOPY',
'FATES_AUTORESP_CANOPY', 'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY',
Expand All @@ -28,4 +26,5 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL',
'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC',
'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC',
'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC'
'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC',
'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU'
1 change: 1 addition & 0 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_cold_landuse/include_user_mods
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@@ -0,0 +1 @@
../fates_cold
2 changes: 2 additions & 0 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_cold_landuse/user_nl_elm
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@@ -0,0 +1,2 @@
flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/landuse.timeseries_4x5_hist_simyr1850-2015_200311.nc'
do_harvest = .true.
1 change: 1 addition & 0 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_cold_luh2/include_user_mods
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@@ -0,0 +1 @@
../fates_cold
1 change: 1 addition & 0 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_cold_luh2/shell_commands
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@@ -0,0 +1 @@
./xmlchange TEST_MEMLEAK_TOLERANCE=0.2
1 change: 1 addition & 0 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_cold_luh2/user_nl_elm
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use_fates_luh = .true.
4 changes: 1 addition & 3 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_eca/user_nl_elm
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Expand Up @@ -19,10 +19,8 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S',
'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE',
'FATES_HARVEST_CARBON_FLUX', 'FATES_DISTURBANCE_RATE_FIRE',
'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX',
'FATES_STOMATAL_COND', 'FATES_LBLAYER_COND', 'FATES_NPP', 'FATES_GPP',
'FATES_AUTORESP', 'FATES_GROWTH_RESP', 'FATES_MAINT_RESP', 'FATES_GPP_CANOPY',
'FATES_AUTORESP_CANOPY', 'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY',
Expand Down
4 changes: 1 addition & 3 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_long/user_nl_elm
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Expand Up @@ -16,10 +16,8 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S',
'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE',
'FATES_HARVEST_CARBON_FLUX', 'FATES_DISTURBANCE_RATE_FIRE',
'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX',
'FATES_STOMATAL_COND', 'FATES_LBLAYER_COND', 'FATES_NPP', 'FATES_GPP',
'FATES_AUTORESP', 'FATES_GROWTH_RESP', 'FATES_MAINT_RESP', 'FATES_GPP_CANOPY',
'FATES_AUTORESP_CANOPY', 'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY',
Expand Down
4 changes: 1 addition & 3 deletions components/elm/cime_config/testdefs/testmods_dirs/elm/fates_rd/user_nl_elm
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Expand Up @@ -19,10 +19,8 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC',
'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND',
'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR',
'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S',
'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE',
'FATES_HARVEST_CARBON_FLUX', 'FATES_DISTURBANCE_RATE_FIRE',
'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL',
'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX',
'FATES_STOMATAL_COND', 'FATES_LBLAYER_COND', 'FATES_NPP', 'FATES_GPP',
'FATES_AUTORESP', 'FATES_GROWTH_RESP', 'FATES_MAINT_RESP', 'FATES_GPP_CANOPY',
'FATES_AUTORESP_CANOPY', 'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY',
Expand Down
15 changes: 9 additions & 6 deletions components/elm/src/biogeophys/SurfaceAlbedoMod.F90
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Expand Up @@ -754,13 +754,16 @@ subroutine SurfaceAlbedo(bounds, &
ws(p) = esai(p) / max( elai(p)+esai(p), mpe )
end do

do ib = 1, numrad
do fp = 1,num_vegsol
p = filter_vegsol(fp)
rho(p,ib) = max( rhol(veg_pp%itype(p),ib)*wl(p) + rhos(veg_pp%itype(p),ib)*ws(p), mpe )
tau(p,ib) = max( taul(veg_pp%itype(p),ib)*wl(p) + taus(veg_pp%itype(p),ib)*ws(p), mpe )
! rho and tau are not needed if fates is on
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if (.not. use_fates) then
do ib = 1, numrad
do fp = 1,num_vegsol
p = filter_vegsol(fp)
rho(p,ib) = max( rhol(veg_pp%itype(p),ib)*wl(p) + rhos(veg_pp%itype(p),ib)*ws(p), mpe )
tau(p,ib) = max( taul(veg_pp%itype(p),ib)*wl(p) + taus(veg_pp%itype(p),ib)*ws(p), mpe )
end do
end do
end do
end if

! Diagnose number of canopy layers for radiative transfer, in increments of dincmax.
! Add to number of layers so long as cumulative leaf+stem area does not exceed total
Expand Down
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