Merge branch 'b4b-dev' into PPE_b4b-dev

.git-blame-ignore-revs

@@ -26,6 +26,7 @@ d866510188d26d51bcd6d37239283db690af7e82
 0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7
 e096358c832ab292ddfd22dd5878826c7c788968
 475831f0fb0e31e97f630eac4e078c886558b61c
+fd5f177131d63d39e79a13918390bdfb642d781e
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
@@ -49,3 +50,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 665cf86102e09b4c4c5a140700676dca23bc55a9
 1a49e547ba3c48fa483f9ae81a8f05adcd6b888c
 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
+753fda3ff0147837231a73c9c728dd9ce47b5997

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.77.1_api.36.0.0
+fxtag = sci.1.77.2_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

bld/env_run.xml

@@ -9,6 +9,7 @@ Sample env_run.xml file that allows build-namelist to be run for testing in this
 -->
 <entry id="DIN_LOC_ROOT"         value="MYDINLOCROOT"  /> 
 <entry id="GLC_TWO_WAY_COUPLING" value="FALSE"         /> 
+<entry id="LND_SETS_DUST_EMIS_DRV_FLDS" value="TRUE"   /> 
 <entry id="NEONSITE"             value=""              /> 
 
 </config_definition>

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -351,6 +351,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <cmb_cmplt_fact_litter    fire_method="li2021gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
 <cmb_cmplt_fact_cwd       fire_method="li2021gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
 
+<rh_low                   fire_method="li2024gswpfrc" >30.0d00</rh_low>
+<rh_hgh                   fire_method="li2024gswpfrc" >80.0d00</rh_hgh>
+<bt_min                   fire_method="li2024gswpfrc" >0.85d00</bt_min>
+<bt_max                   fire_method="li2024gswpfrc" >0.98d00</bt_max>
+<cli_scale                fire_method="li2024gswpfrc" >0.025d00</cli_scale>
+<boreal_peatfire_c        fire_method="li2024gswpfrc" >0.09d-4</boreal_peatfire_c>
+<pot_hmn_ign_counts_alpha fire_method="li2024gswpfrc" >0.010d00</pot_hmn_ign_counts_alpha>
+<non_boreal_peatfire_c    fire_method="li2024gswpfrc" >0.17d-3</non_boreal_peatfire_c>
+<cropfire_a1              fire_method="li2024gswpfrc" >0.21d00</cropfire_a1>
+<occur_hi_gdp_tree        fire_method="li2024gswpfrc" >0.33d00</occur_hi_gdp_tree>
+<lfuel                    fire_method="li2024gswpfrc" >75.d00</lfuel>
+<ufuel                    fire_method="li2024gswpfrc" >1050.d00</ufuel>
+<cmb_cmplt_fact_litter    fire_method="li2024gswpfrc" >0.5d00</cmb_cmplt_fact_litter>
+<cmb_cmplt_fact_cwd       fire_method="li2024gswpfrc" >0.28d00</cmb_cmplt_fact_cwd>
+
 <!-- Canopy fluxes namelist defaults -->
 <use_undercanopy_stability               >.false.</use_undercanopy_stability>
 <use_undercanopy_stability phys="clm4_5" >.true.</use_undercanopy_stability>
@@ -1909,6 +1924,8 @@ lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240216.nc
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_C96_hist_1850_78pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="1x1_smallvilleIA" sim_year="1850" >
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_smallvilleIA_hist_1850_78pfts_c240221.nc</fsurdat>
+<fsurdat hgrid="1x1_cidadinhoBR" sim_year="2000" >
+lnd/clm2/surfdata_esmf/surfdata_1x1_cidadinhoBR_hist_2000_78pfts_c240613.nc</fsurdat>
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_1x1_brazil_hist_1850_78pfts_c240221.nc</fsurdat>
 
@@ -1980,11 +1997,14 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_C96_SSP2-4.5_1850-2100_78pfts_c240216.nc</flanduse_timeseries>
 
 
-<!-- Note that this transient file only goes up to year 1855.
+<!-- Note that these transient files only go up to year 1855.
      This is sufficient for testing purposes, but could cause problems if you try to run beyond 1855. -->
 <flanduse_timeseries hgrid="1x1_smallvilleIA" sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_1x1_smallvilleIA_SSP2-4.5_1850-1855_78pfts_c240221.nc</flanduse_timeseries>
 
+<!-- Cidadinho test site has no transient data. -->
+<flanduse_timeseries hgrid="1x1_cidadinhoBR" sim_year_range="1850-2000"></flanduse_timeseries>
+
 <!-- Future scenarios - landuse time series files with crop on -->
 
 <!-- SSP1-RCP2.6 - relative to {csmdata}) -->
@@ -2192,10 +2212,34 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <lai_mapalgo  hgrid="1x1_asphaltjungleNJ" >nn</lai_mapalgo>
 <lai_mapalgo  hgrid="5x5_amazon"          >nn</lai_mapalgo>
 
-<!-- crop calendar streams namelist defaults -->
-<stream_year_first_cropcal  >1850</stream_year_first_cropcal>
-<stream_year_last_cropcal   >2100</stream_year_last_cropcal>
-<model_year_align_cropcal   >1850</model_year_align_cropcal>
+<!-- crop calendars: default settings -->
+<cropcals_rx>.false.</cropcals_rx>
+<cropcals_rx_adapt>.true.</cropcals_rx_adapt>
+<cropcals_rx_adapt phys="clm4_5">.false.</cropcals_rx_adapt>
+<cropcals_rx_adapt phys="clm5_0">.false.</cropcals_rx_adapt>
+<cropcals_rx_adapt phys="clm5_1">.false.</cropcals_rx_adapt>
+<stream_gdd20_seasons>.false.</stream_gdd20_seasons>
+<flush_gdd20>.false.</flush_gdd20>
+<stream_year_first_cropcal_swindows  >2000</stream_year_first_cropcal_swindows>
+<stream_year_last_cropcal_swindows   >2000</stream_year_last_cropcal_swindows>
+<model_year_align_cropcal_swindows   >2000</model_year_align_cropcal_swindows>
+<stream_year_first_cropcal_cultivar_gdds  >2000</stream_year_first_cropcal_cultivar_gdds>
+<stream_year_last_cropcal_cultivar_gdds   >2000</stream_year_last_cropcal_cultivar_gdds>
+<model_year_align_cropcal_cultivar_gdds   >2000</model_year_align_cropcal_cultivar_gdds>
+
+<!-- crop calendars: default input files -->
+<stream_fldFileName_swindow_start cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_start>
+<stream_fldFileName_swindow_end cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_end>
+<stream_fldfilename_cultivar_gdds cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
+<stream_meshfile_cropcal cropcals_rx=".true.">lnd/clm2/cropdata/calendars/processed/360x720_120830_ESMFmesh_c20210507_cdf5.tweaked_latlons.nc</stream_meshfile_cropcal>
+<stream_fldFileName_swindow_start cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_start>
+<stream_fldFileName_swindow_end cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.tweaked_latlons.nc</stream_fldFileName_swindow_end>
+<stream_fldfilename_cultivar_gdds cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/gdds_20230829_161011.tweaked_latlons.nc</stream_fldfilename_cultivar_gdds>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".false.">lnd/clm2/cropdata/calendars/processed/20230714_cropcals_pr2_1deg.actually2deg.1980-2009.from_GDDB20.interpd_halfdeg.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_baseline cropcals_rx_adapt=".true." stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/gdd20bl.copied_from.gdds_20230829_161011.v2.tweaked_latlons.nc</stream_fldFileName_gdd20_baseline>
+<stream_fldFileName_gdd20_season_start stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_start>
+<stream_fldFileName_gdd20_season_end stream_gdd20_seasons=".true.">lnd/clm2/cropdata/calendars/processed/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-hcru_hcru_mt13.2000-2000.20230728_165845.tweaked_latlons.nc</stream_fldFileName_gdd20_season_end>
+<stream_meshfile_cropcal cropcals_rx_adapt=".true.">lnd/clm2/cropdata/calendars/processed/360x720_120830_ESMFmesh_c20210507_cdf5.tweaked_latlons.nc</stream_meshfile_cropcal>
 
 <!-- lightning streams namelist defaults -->
 
@@ -2459,8 +2503,6 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- Defaults for Zender's soil erodibility data  -->
 <!-- ===========================================  -->
 
-<dust_emis_method>Zender_2003</dust_emis_method>
-<zender_soil_erod_source dust_emis_method="Zender_2003">atm</zender_soil_erod_source>
 <zendersoilerod_mapalgo>bilinear</zendersoilerod_mapalgo>
 <stream_fldfilename_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd" lnd_tuning_mode="clm4_5_cam7.0"
 >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc</stream_fldfilename_zendersoilerod>
@@ -2538,6 +2580,17 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <stream_meshfile_zendersoilerod dust_emis_method="Zender_2003" zender_soil_erod_source="lnd"
 >lnd/clm2/dustemisdata/dust_2x2_ESMFmesh_cdf5_c230730.nc</stream_meshfile_zendersoilerod>
 
+<!-- =========================================  -->
+<!-- Defaults for Prigent's roughness data      -->
+<!-- =========================================  -->
+
+<use_prigent_roughness dust_emis_method="Leung_2023">.true.</use_prigent_roughness>
+<use_prigent_roughness                              >.false.</use_prigent_roughness>
+<stream_fldfilename_prigentroughness
+>lnd/clm2/dustemisdata/Prigent_2005_roughness_0.25x0.25_cdf5_c240127.nc</stream_fldfilename_prigentroughness>
+<stream_meshfile_prigentroughness
+>lnd/clm2/dustemisdata/dust_0.25x0.25_ESMFmesh_cdf5_c240222.nc</stream_meshfile_prigentroughness>
+
 <!-- =========================================  -->
 <!-- Defaults for different BGC/decomp modes    -->
 <!-- =========================================  -->
@@ -2608,7 +2661,10 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
 <!-- =========================================  -->
 
 <use_excess_ice>.false.</use_excess_ice>
-
+<excess_ice_coldstart_temp>-1.0</excess_ice_coldstart_temp>
+<excess_ice_coldstart_depth>0.5</excess_ice_coldstart_depth>
+<excess_ice_coldstart_temp use_excess_ice=".true.">-3.15</excess_ice_coldstart_temp>
+<excess_ice_coldstart_depth use_excess_ice=".true.">0.5</excess_ice_coldstart_depth>
 <stream_fldfilename_exice use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc</stream_fldfilename_exice>
 <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>

bld/namelist_files/namelist_defaults_dust_emis.xml

@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+
+<?xml-stylesheet type="text/xsl" href="namelist_defaults.xsl"?>
+
+<namelist_defaults>
+
+<!--
+Values to use by default for creation of CLM model driver namelists.
+The element names are the same as the corresponding namelist
+variables.  Values that depend on the model configuration use
+attributes to express the dependency.  The recognized attributes
+are: RESOLUTION, defaults, mask, ic_ymd, ic_tod, sim_year and all configuration
+attributes from the config_cache.xml file (with keys converted to upper-case).
+-->
+
+<!-- Defaults for dust_emis_inparm namelist  -->
+<dust_emis_method>Zender_2003</dust_emis_method>
+
+<zender_soil_erod_source>atm</zender_soil_erod_source>
+
+</namelist_defaults>

bld/namelist_files/namelist_defaults_overall.xml

@@ -62,6 +62,7 @@ determine default values for namelists.
 <res sitespf_pt="1x1_urbanc_alpha"   >1x1_urbanc_alpha</res>
 <res sitespf_pt="1x1_numaIA"         >1x1_numaIA</res>
 <res sitespf_pt="1x1_smallvilleIA"   >1x1_smallvilleIA</res>
+<res sitespf_pt="1x1_cidadinhoBR"    >1x1_cidadinhoBR</res>
 
 <!-- Default simulation year -->
 <sim_year>2000</sim_year>
@@ -110,6 +111,7 @@ determine default values for namelists.
 <mask hgrid="1x1_urbanc_alpha"    >test</mask>
 <mask hgrid="1x1_numaIA"          >navy</mask>
 <mask hgrid="1x1_smallvilleIA"    >test</mask>
+<mask hgrid="1x1_cidadinhoBR"     >test</mask>
 <mask                             >gx1v7</mask>
 
 <!-- Default glacier model options -->