[WIP] Add NVP (Non-Vascular Plant) Layer in CTSM

.gitmodules

@@ -27,8 +27,8 @@
 #
 [submodule "fates"]
 path = src/fates
-url = https://github.com/NGEET/fates
-fxtag = sci.1.91.1_api.43.1.0
+url = https://github.com/samsrabin/fates
+fxtag = 563e8f7b2a9d53ead5a0ea4e3c04bf809b0af305
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates
@@ -67,8 +67,8 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 
 [submodule "ccs_config"]
 path = ccs_config
-url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.77
+url = https://github.com/samsrabin/ccs_config_cesm.git
+fxtag = b6387972bba85d25b0e81ebc03035864e283823c
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
@@ -92,10 +92,10 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.93
+fxtag = 42f9a6b064ca8d1843a7849c58cc733b3994f94e
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
-fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
+fxDONOTUSEurl = https://github.com/samsrabin/CDEPS.git
 
 [submodule "share"]
 path = share

bld/CLMBuildNamelist.pm

@@ -823,7 +823,8 @@ sub setup_cmdl_fates_mode {
                       "use_fates_daylength_factor", "fates_photosynth_acclimation", "fates_stomatal_model",
                       "fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
                       "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model", "fates_electron_transport_model",
-		      "use_fates_managed_fire"
+                      "use_fates_managed_fire",
+                      "use_nvp", "use_nvp_undersnow", "nvp_rad_model_ground", "use_nvp_temp_for_patch_gas_params"
                    );
 
        # dis-allow fates specific namelist items with non-fates runs
@@ -4887,7 +4888,8 @@ sub setup_logic_fates {
                        "use_fates_daylength_factor", "fates_photosynth_acclimation", "fates_stomatal_model",
                        "fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
                        "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model", "fates_electron_transport_model",
-		       "use_fates_managed_fire"
+                       "use_fates_managed_fire",
+                       "use_nvp", "use_nvp_undersnow", "nvp_rad_model_ground", "use_nvp_temp_for_patch_gas_params"
                     );
 
         foreach my $var ( @list ) {
@@ -4910,6 +4912,7 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_spitfire_mode', 'use_fates'=>$nl_flags->{'use_fates'},
                     'use_fates_managed_fire'=>$nl->get_value('use_fates_managed_fire'),
                     'use_fates_sp'=>$nl_flags->{'use_fates_sp'} );
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_nvp');
 
         my $suplnitro = $nl->get_value('suplnitro');
         my $parteh_mode = $nl->get_value('fates_parteh_mode');

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -638,6 +638,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_luna                use_fates=".true." >.false.</use_luna>
 <use_luna phys="clm4_5"  use_fates=".false.">.false.</use_luna>
 
+<!-- NVP (non-vascular plant: moss/lichen) ground layer -->
+<!-- [PORTED by Hui Tang: NVP control flag defaults] -->
+<use_nvp              >.false.</use_nvp>
+<use_nvp_undersnow    >.false.</use_nvp_undersnow>
+<nvp_rad_model_ground >.false.</nvp_rad_model_ground>
+<use_nvp_temp_for_patch_gas_params >.true.</use_nvp_temp_for_patch_gas_params>
+
 <!-- Flexible CN options -->
 <MM_Nuptake_opt             use_flexibleCN=".true." >.true.</MM_Nuptake_opt>
 <CNratio_floating           use_flexibleCN=".true." >.true.</CNratio_floating>
@@ -1973,6 +1980,8 @@ lnd/clm2/surfdata_esmf/ctsm5.4.0/synthetic/surfdata_1x1_smallvilleIA_synth_hist_
 lnd/clm2/surfdata_esmf/ctsm5.4.0/synthetic/surfdata_1x1_cidadinhoBR_synth_hist_2000_78pfts_c251023.no_nan_fill.nc</fsurdat>
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.4.0/surfdata_1x1_brazil_hist_1850_78pfts_c251023.no_nan_fill.nc</fsurdat>
+<fsurdat hgrid="1x1_ALP2"         sim_year="2000" use_nvp=".true." use_fates_sp=".true.">
+lnd/clm2/surfdata_esmf/testdata/moss/surfdata_ALP2_hist_2000_16pfts_c260427.nc</fsurdat>
 
 <fsurdat hgrid="ne16np4.pg3"              sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.4.0/surfdata_ne16np4.pg3_hist_1850_78pfts_c251022.nc</fsurdat>

bld/namelist_files/namelist_defaults_overall.xml

@@ -61,6 +61,7 @@ determine default values for namelists.
 <res sitespf_pt="1x1_numaIA"         >1x1_numaIA</res>
 <res sitespf_pt="1x1_smallvilleIA"   >1x1_smallvilleIA</res>
 <res sitespf_pt="1x1_cidadinhoBR"    >1x1_cidadinhoBR</res>
+<res sitespf_pt="1x1_ALP2"           >1x1_ALP2</res>
 
 <!-- Default simulation year -->
 <sim_year>2000</sim_year>
@@ -110,6 +111,7 @@ determine default values for namelists.
 <mask hgrid="1x1_numaIA"          >navy</mask>
 <mask hgrid="1x1_smallvilleIA"    >test</mask>
 <mask hgrid="1x1_cidadinhoBR"     >test</mask>
+<mask hgrid="1x1_ALP2"            >test</mask>
 <mask                             >gx1v7</mask>
 
 <!-- Default glacier model options -->

bld/namelist_files/namelist_definition_ctsm.xml

@@ -946,6 +946,33 @@ LUNA operates on C3 and non-crop vegetation (see vcmax_opt for how other veg is
 LUNA: Leaf Utilization of Nitrogen for Assimilation
 </entry>
 
+<!-- NVP (non-vascular plant: moss/lichen) ground layer -->
+<!-- [PORTED by Hui Tang: NVP control flags] -->
+<entry id="use_nvp" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to activate the NVP (non-vascular plant: moss/lichen) ground layer.
+Requires use_fates=".true.".
+</entry>
+
+<entry id="use_nvp_undersnow" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Allow the NVP layer to remain active and exchange fluxes when covered by snow.
+Only relevant when use_nvp=".true.".
+</entry>
+
+<entry id="nvp_rad_model_ground" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Use FATES Beer's law radiation model for the NVP ground layer instead of
+the CLM bare-ground scheme.
+Only relevant when use_nvp=".true.".
+</entry>
+
+<entry id="use_nvp_temp_for_patch_gas_params" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".true.">
+Whether to use NVP temperature when getting entire patch's gas exchange parameters.
+Requires use_fates=".true.".
+</entry>
+
 <entry id="use_hillslope" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the hillslope model

cime_config/testdefs/ExpectedTestFails.xml

@@ -318,4 +318,17 @@
       <issue>#3507</issue>
     </phase>
   </test>  
+
+  <!-- other tests -->
+  <test name="SMS_Ld5_D_Mmpi-serial.1x1_ALP2.I2000Clm60Fates.derecho_intel.clm-FatesColdSatPhen--clm-FatesALP2Bare">
+    <phase name="RUN">
+      <status>FAIL</status>
+    </phase>
+  </test>
+  <test name="SMS_Ld5_D_Mmpi-serial.1x1_ALP2.I2000Clm60Fates.derecho_intel.clm-FatesColdSatPhen--clm-FatesALP2Grass">
+    <phase name="RUN">
+      <status>FAIL</status>
+    </phase>
+  </test>
+
 </expectedFails>

cime_config/testdefs/testlist_clm.xml

@@ -17,6 +17,7 @@
         decomp_init: Initialization tests specifically for examining the PE layout decomposition initialization
         uhr_decomp_init: Initialization tests at Ultra High Resolution - specifically for examining the PE layout decomposition initialization
         interim_restart: Tests having to do with interim restart capability.
+        fates_nvp: Tests of FATES non-vascular plant capability
       ROF model test lists: (in each component model)
         mosart: MOSART test list, run when MOSARt is updated
         rtm: RTM test list, run when RTM is updated
@@ -4901,5 +4902,56 @@
     </options>
   </test>
 
+<!-- Tests of FATES non-vascular plant capability -->
+
+<test name="SMS_Ld5_D_Mmpi-serial" grid="1x1_ALP2" compset="I2000Clm60Fates" testmods="clm/FatesColdSatPhen--clm/FatesALP2Moss">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates_nvp"/>
+      <machine name="izumi" compiler="nag" category="fates"/>
+      <machine name="izumi" compiler="nag" category="fates_nvp"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment">Test of FATES NVP at ALP2 (CRU-JRA climate) in SP mode, moss only, using moss temp for entire patch's gas params</option>
+    </options>
+  </test>
+<test name="SMS_Ld5_D_Mmpi-serial" grid="1x1_ALP2" compset="I2000Clm60Fates" testmods="clm/FatesColdSatPhen--clm/FatesALP2Moss_NoNvpTempForPatchGasParams">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates_nvp"/>
+      <machine name="izumi" compiler="nag" category="fates"/>
+      <machine name="izumi" compiler="nag" category="fates_nvp"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment">Test of FATES NVP at ALP2 (CRU-JRA climate) in SP mode, moss only, NOT using moss temp for entire patch's gas params </option>
+    </options>
+  </test>
+<test name="SMS_Ld5_D_Mmpi-serial" grid="1x1_ALP2" compset="I2000Clm60Fates" testmods="clm/FatesColdSatPhen--clm/FatesALP2Grass">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates_nvp"/>
+      <machine name="izumi" compiler="nag" category="fates"/>
+      <machine name="izumi" compiler="nag" category="fates_nvp"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment">Test of FATES NVP at ALP2 (CRU-JRA climate) in SP mode, grass only</option>
+    </options>
+  </test>
+<test name="SMS_Ld5_D_Mmpi-serial" grid="1x1_ALP2" compset="I2000Clm60Fates" testmods="clm/FatesColdSatPhen--clm/FatesALP2Bare">
+    <machines>
+      <machine name="derecho" compiler="intel" category="fates"/>
+      <machine name="derecho" compiler="intel" category="fates_nvp"/>
+      <machine name="izumi" compiler="nag" category="fates"/>
+      <machine name="izumi" compiler="nag" category="fates_nvp"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment">Test of FATES NVP at ALP2 (CRU-JRA climate) in SP mode, bare ground only</option>
+    </options>
+  </test>
+
 
 </testlist>

cime_config/testdefs/testmods_dirs/clm/FatesALP2Bare/shell_commands

@@ -0,0 +1 @@
+# ./xmlchange DATM_MODE=CLMCRUJRA2024b

cime_config/testdefs/testmods_dirs/clm/FatesALP2Bare/user_nl_clm

@@ -0,0 +1,9 @@
+fsurdat='$DIN_LOC_ROOT/lnd/clm2/testdata/moss/fsurdat/surfdata_ALP2_hist_2000_16pfts_c260427_bare.nc'
+use_fates = .true.
+use_fates_sp = .true.
+use_nvp = .true.
+use_nvp_undersnow = .true.
+nvp_rad_model_ground = .true.
+use_bedrock=.true.
+fates_paramfile = '$DIN_LOC_ROOT/lnd/clm2/testdata/moss/fates_paramfile/fates_params_default.c260717.45a9aaf3.json'
+

cime_config/testdefs/testmods_dirs/clm/FatesALP2Grass/shell_commands

@@ -0,0 +1 @@
+# ./xmlchange DATM_MODE=CLMCRUJRA2024b

cime_config/testdefs/testmods_dirs/clm/FatesALP2Grass/user_nl_clm

@@ -0,0 +1,9 @@
+fsurdat='$DIN_LOC_ROOT/lnd/clm2/testdata/moss/fsurdat/surfdata_ALP2_hist_2000_16pfts_c260427_grass.nc'
+use_fates = .true.
+use_fates_sp = .true.
+use_nvp = .true.
+use_nvp_undersnow = .true.
+nvp_rad_model_ground = .true.
+use_bedrock=.true.
+fates_paramfile = '$DIN_LOC_ROOT/lnd/clm2/testdata/moss/fates_paramfile/fates_params_default.c260717.45a9aaf3.json'
+

cime_config/testdefs/testmods_dirs/clm/FatesALP2Moss/shell_commands

@@ -0,0 +1 @@
+# ./xmlchange DATM_MODE=CLMCRUJRA2024b

cime_config/testdefs/testmods_dirs/clm/FatesALP2Moss/user_nl_clm

@@ -0,0 +1,10 @@
+fsurdat='$DIN_LOC_ROOT/lnd/clm2/testdata/moss/fsurdat/surfdata_ALP2_hist_2000_16pfts_c260427_moss.nc'
+use_fates = .true.
+use_fates_sp = .true.
+use_nvp = .true.
+use_nvp_undersnow = .true.
+nvp_rad_model_ground = .true.
+use_nvp_temp_for_patch_gas_params = .true.
+use_bedrock=.true.
+fates_paramfile = '$DIN_LOC_ROOT/lnd/clm2/testdata/moss/fates_paramfile/fates_params_default_moss.c260717.45a9aaf3.json'
+

cime_config/testdefs/testmods_dirs/clm/FatesALP2Moss_NoNvpTempForPatchGasParams/shell_commands

@@ -0,0 +1 @@
+# ./xmlchange DATM_MODE=CLMCRUJRA2024b

cime_config/testdefs/testmods_dirs/clm/FatesALP2Moss_NoNvpTempForPatchGasParams/user_nl_clm

@@ -0,0 +1,10 @@
+fsurdat='$DIN_LOC_ROOT/lnd/clm2/testdata/moss/fsurdat/surfdata_ALP2_hist_2000_16pfts_c260427_moss.nc'
+use_fates = .true.
+use_fates_sp = .true.
+use_nvp = .true.
+use_nvp_undersnow = .true.
+nvp_rad_model_ground = .true.
+use_nvp_temp_for_patch_gas_params = .false.
+use_bedrock=.true.
+fates_paramfile = '$DIN_LOC_ROOT/lnd/clm2/testdata/moss/fates_paramfile/fates_params_default_moss.c260717.45a9aaf3.json'
+

src/biogeophys/AerosolMod.F90

@@ -570,7 +570,11 @@ subroutine AerosolMasses(bounds, num_on, filter_on, num_off, filter_off, &
             ! layer mass of snow:
             snowmass = h2osoi_ice(c,j) + h2osoi_liq(c,j)
 
-            if (j >= snl(c)+1) then
+            ! [PORTED by Hui Tang: exclude NVP layer j=0 from aerosol snow calculation.
+            !  When NVP is active jbot_sno=-1 (bottom snow = j=-1); j=0 is NVP not snow.
+            !  Without this guard, j=0 satisfies j>=snl+1 and snowmass(j=0)≈0 → SIGFPE
+            !  divide-by-zero at the concentration lines below.]
+            if (j >= snl(c)+1 .and. j <= col%jbot_sno(c)) then
 
                mss_bctot(c,j)     = mss_bcpho(c,j) + mss_bcphi(c,j)
                mss_bc_col(c)      = mss_bc_col(c)  + mss_bctot(c,j)