Merge pull request #1216 from fvitt/nitro_dep_fluxes

cam6_4_056: Nitrogen deposition fluxes
ESCOMP · Jan 17, 2025 · ea101b3 · ea101b3
2 parents 7de26a3 + 4328f4e
commit ea101b3
Show file tree

Hide file tree

Showing 46 changed files with 540 additions and 341 deletions.
diff --git a/bld/build-namelist b/bld/build-namelist
@@ -509,14 +509,6 @@ if ($phys_mode_flags > 1) {
 my $simple_phys = 0;
 if ($adia_mode or $ideal_mode) { $simple_phys = 1; }
 
-# If running either a simple physics or an aquaplanet configuration, the nitrogen
-# deposition data is not used.  These files are set in buildnml and can't be overridden
-# via user_nl_cam.  So provide an override here.
-if ($simple_phys or $aqua_mode) {
-    $nl->set_variable_value('ndep_stream_nl', 'stream_ndep_data_filename', '" "');
-    $nl->set_variable_value('ndep_stream_nl', 'stream_ndep_mesh_filename', '" "');
-}
-
 # Single column mode
 my $scam = $cfg->get('scam');
 my $scam_iop = $cfg->get('scam_iop');
@@ -705,6 +697,19 @@ if ($sim_year =~ /(\d+)-(\d+)/) {
     $sim_year_start = $1;
 }
 
+# Setup default ndep streams only if not simple_phys or aqua_mode and
+# the chemistry cannot produce the nitrogen depostion fluxes
+if (!($simple_phys or $aqua_mode)) {
+  my $chem_nitrodep = chem_has_species($cfg, 'NO') and chem_has_species($cfg, 'NH3');
+  if ((!$chem_nitrodep) or ($chem =~ /geoschem/)) {
+    add_default($nl, 'stream_ndep_mesh_filename');
+    add_default($nl, 'stream_ndep_data_filename', 'sim_year'=>$sim_year);
+    add_default($nl, 'stream_ndep_year_first', 'sim_year'=>$sim_year);
+    add_default($nl, 'stream_ndep_year_last', 'sim_year'=>$sim_year);
+    add_default($nl, 'stream_ndep_year_align', 'sim_year'=>$sim_year);
+  }
+}
+
 # Topography
 add_default($nl, 'use_topo_file');
 my $use_topo_file = $nl->get_value('use_topo_file');

diff --git a/bld/namelist_files/namelist_defaults_cam.xml b/bld/namelist_files/namelist_defaults_cam.xml
@@ -690,13 +690,13 @@
 <flbc_file chem="ghg_mam4">atm/waccm/lb/LBC_17500116-20150116_CMIP6_0p5degLat_c180905.nc</flbc_file>
 
 <!-- Time-variant CO2 fossil fuel emissions -->
-<co2flux_fuel_file hgrid="0.9x1.25" sim_year="1850-2000">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_0.9x1.25_c20181011.nc</co2flux_fuel_file>
-<co2flux_fuel_file hgrid="1.9x2.5"  sim_year="1850-2000">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_1.9x2.5_c20181011.nc</co2flux_fuel_file>
-<co2flux_fuel_file hgrid="C384" sim_year="1850-2000">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_0.9x1.25_c20181011.nc</co2flux_fuel_file>
-<co2flux_fuel_file hgrid="C192" sim_year="1850-2000">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_0.9x1.25_c20181011.nc</co2flux_fuel_file>
-<co2flux_fuel_file hgrid="C96" sim_year="1850-2000">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_0.9x1.25_c20181011.nc</co2flux_fuel_file>
-<co2flux_fuel_file hgrid="C48" sim_year="1850-2000">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_1.9x2.5_c20181011.nc</co2flux_fuel_file>
-<co2flux_fuel_file hgrid="C24" sim_year="1850-2000">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_1.9x2.5_c20181011.nc</co2flux_fuel_file>
+<co2flux_fuel_file hgrid="0.9x1.25" sim_year="1850-2015">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_0.9x1.25_c20181011.nc</co2flux_fuel_file>
+<co2flux_fuel_file hgrid="1.9x2.5"  sim_year="1850-2015">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_1.9x2.5_c20181011.nc</co2flux_fuel_file>
+<co2flux_fuel_file hgrid="C384" sim_year="1850-2015">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_0.9x1.25_c20181011.nc</co2flux_fuel_file>
+<co2flux_fuel_file hgrid="C192" sim_year="1850-2015">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_0.9x1.25_c20181011.nc</co2flux_fuel_file>
+<co2flux_fuel_file hgrid="C96" sim_year="1850-2015">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_0.9x1.25_c20181011.nc</co2flux_fuel_file>
+<co2flux_fuel_file hgrid="C48" sim_year="1850-2015">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_1.9x2.5_c20181011.nc</co2flux_fuel_file>
+<co2flux_fuel_file hgrid="C24" sim_year="1850-2015">atm/cam/ggas/emissions-cmip6_CO2_anthro_surface_175001-201512_fv_1.9x2.5_c20181011.nc</co2flux_fuel_file>
 
 <ac_CO2_emis hgrid="0.9x1.25">ac_CO2_filelist_175001-201512_fv_0.9x1.25_c20181011.txt</ac_CO2_emis>
 <ac_CO2_emis hgrid="1.9x2.5" >ac_CO2_filelist_175001-201512_fv_1.9x2.5_c20181011.txt</ac_CO2_emis>
@@ -2058,6 +2058,25 @@
 <soil_erod_file phys="cam4"  >atm/cam/dst/dst_source2x2tuned-cam4-06132012.nc</soil_erod_file>
 <soil_erod_file phys="cam4" hgrid="0.9x1.25">atm/cam/dst/dst_source1x1tuned-cam4-06202012.nc</soil_erod_file>
 
+<!-- nitrogen deposition to surface models -->
+<stream_ndep_mesh_filename>share/meshes/fv0.9x1.25_141008_polemod_ESMFmesh.nc</stream_ndep_mesh_filename>
+
+<stream_ndep_data_filename >lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc</stream_ndep_data_filename>
+<stream_ndep_data_filename sim_year="1850">lnd/clm2/ndepdata/fndep_clm_WACCM6_CMIP6piControl001_y21-50avg_1850monthly_0.95x1.25_c180802.nc</stream_ndep_data_filename>
+
+<stream_ndep_year_first >2000</stream_ndep_year_first>
+<stream_ndep_year_first sim_year="1850">1850</stream_ndep_year_first>
+<stream_ndep_year_first sim_year="1850-2015">1850</stream_ndep_year_first>
+<stream_ndep_year_first sim_year="2010">2010</stream_ndep_year_first>
+
+<stream_ndep_year_last >2000</stream_ndep_year_last>
+<stream_ndep_year_last sim_year="1850">1850</stream_ndep_year_last>
+<stream_ndep_year_last sim_year="1850-2015">2015</stream_ndep_year_last>
+<stream_ndep_year_last sim_year="2010">2010</stream_ndep_year_last>
+
+<stream_ndep_year_align >1</stream_ndep_year_align>
+<stream_ndep_year_align sim_year="1850-2015">1850</stream_ndep_year_align>
+
 <!-- Turbulent Mountain Stress -->
 <do_tms                                                     > .false. </do_tms>
 <do_tms                   waccm_phys="1"      phys="cam4"   > .true.  </do_tms>

diff --git a/bld/namelist_files/namelist_definition.xml b/bld/namelist_files/namelist_definition.xml
@@ -7626,40 +7626,29 @@ Bubble-mediated sea-air transfer. See ocean_emis.F90 for details.
 Default: FALSE
 </entry>
 
-<entry id="ndep_list" type="char*16(2)" category="Nitrogen Deposition"
-       group="ndep_inparm" valid_values="" >
-List of nitrogen deposition fluxes to be sent from CAM to surface models.
-Default: set by build-namelist.
-</entry>
-
 <entry id="stream_ndep_year_first" type="integer" category="Nitrogen Deposition"
        group="ndep_stream_nl" valid_values="" >
-Year first to use in nitrogen deposition stream data. Set by case xml variable
-CAM_STREAM_NDEP_YEAR_FIRST
+Year first to use in nitrogen deposition stream data.
 </entry>
 
 <entry id="stream_ndep_year_last" type="integer" category="Nitrogen Deposition"
        group="ndep_stream_nl" valid_values="" >
 Year last to use in nitrogen deposition stream data.
-Set by case xml variable CAM_STREAM_NDEP_YEAR_LAST
 </entry>
 
 <entry id="stream_ndep_year_align" type="integer" category="Nitrogen Deposition"
        group="ndep_stream_nl" valid_values="" >
-Model year to align with CAM_STREAM_NDEP_YEAR_FIRST.
-Set by case xml variable CAM_STREAM_NDEP_YEAR_ALIGN
+Model year to align with stream_ndep_year_first.
 </entry>
 
 <entry id="stream_ndep_data_filename" type="char*256" input_pathname="abs" category="Nitrogen Deposition"
        group="ndep_stream_nl" valid_values="" >
-NDEP stream data filename.
-Set by case xml variable CAM_STREAM_NDEP_DATA_FILENAME.
+Nitrogen deposition stream data filename.
 </entry>
 
 <entry id="stream_ndep_mesh_filename" type="char*256" input_pathname="abs" category="Nitrogen Deposition"
        group="ndep_stream_nl" valid_values="" >
-NDEP mesh file corresponding to sream_ndep_data_filename.
-Set by case xml variable CAM_STREAM_NDEP_MESH_FILENAME.
+Grid mesh file corresponding to stream_ndep_data_filename.
 </entry>
 
 <entry id="megan_factors_file" type="char*256" input_pathname="abs" category="VOC_emissions"
@@ -8791,7 +8780,7 @@ Default: "."
 </entry>
 
 <entry id="sim_year" type="char*9" category="cam"
-       group="camexp" valid_values="1850,2000,1850-2000">
+       group="camexp" valid_values="1850,2000,2010,1850-2000,1850-2015">
 This varible is only used internally by build-namelist to determine
 appropriate defaults for climatological or transient forcing datasets.
 Default: set by build-namelist.

diff --git a/bld/namelist_files/use_cases/1850_cam_lt.xml b/bld/namelist_files/use_cases/1850_cam_lt.xml
@@ -61,4 +61,7 @@
 <csw_time_type>CYCLICAL</csw_time_type>
 <csw_cycle_yr>1850 </csw_cycle_yr>
 
+<!-- for prescribed nitrogen deposition fluxes -->
+<sim_year>1850</sim_year>
+
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/1850_cam_mt.xml b/bld/namelist_files/use_cases/1850_cam_mt.xml
@@ -56,4 +56,7 @@
 <csw_time_type>CYCLICAL</csw_time_type>
 <csw_cycle_yr>1850 </csw_cycle_yr>
 
+<!-- for prescribed nitrogen deposition fluxes -->
+<sim_year>1850</sim_year>
+
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/2000_geoschem.xml b/bld/namelist_files/use_cases/2000_geoschem.xml
@@ -36,9 +36,6 @@
 <!-- The below line is not commented out in 2000_trop_strat_vbs_cam6.xml -->
 <!-- <prescribed_strataero_cycle_yr>2000</prescribed_strataero_cycle_yr> -->
 
-<!-- The below line is not commented out in 2000_trop_strat_vbs_cam6.xml -->
-<!-- <ndep_list>'noy', 'nhx'</ndep_list> -->
-
 <!-- History Files -->
 
 <mfilt>           1,30,365,240,240,480,365,73,30  </mfilt>

diff --git a/bld/namelist_files/use_cases/2000_trop_strat_vbs_cam6.xml b/bld/namelist_files/use_cases/2000_trop_strat_vbs_cam6.xml
@@ -131,8 +131,6 @@
 <!-- HEMCO emissions -->
 <hemco_emission_year>2000</hemco_emission_year>
 
-<ndep_list>'noy', 'nhx'</ndep_list>
-
 <!-- History Files -->
 
 <mfilt>           1,30,365,240,240,480,365,73,30  </mfilt>

diff --git a/bld/namelist_files/use_cases/2010_cam6.xml b/bld/namelist_files/use_cases/2010_cam6.xml
@@ -83,4 +83,7 @@
 <flbc_type>      'CYCLICAL'                          </flbc_type>
 <flbc_cycle_yr>  2010                                </flbc_cycle_yr>
 
+<!-- sim_year -->
+<sim_year>2010</sim_year>
+
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/2010_geoschem.xml b/bld/namelist_files/use_cases/2010_geoschem.xml
@@ -34,7 +34,6 @@
 
 <!-- The below lines are not commented out in 2010_trop_strat_vbs_cam6.xml (*=many pointers) -->
 <!-- <prescribed_strataero_cycle_yr>2010</prescribed_strataero_cycle_yr> -->
-<!-- <ndep_list>'noy', 'nhx'</ndep_list>-->
 
 <!-- History Files -->
 
@@ -166,4 +165,6 @@
 'so4_a3',
 </fincl1>
 
+<sim_year>2010</sim_year>
+
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/2010_trop_strat_vbs_cam6.xml b/bld/namelist_files/use_cases/2010_trop_strat_vbs_cam6.xml
@@ -322,8 +322,6 @@
 <!-- HEMCO emissions -->
 <hemco_emission_year>2010</hemco_emission_year>
 
-<ndep_list>'noy', 'nhx'</ndep_list>
-
 <!-- History Files -->
 
 <mfilt>           1,30,365,240,240,480,365,73,30  </mfilt>

diff --git a/bld/namelist_files/use_cases/hist_cam6.xml b/bld/namelist_files/use_cases/hist_cam6.xml
@@ -31,6 +31,6 @@
   <flbc_list>'CO2','CH4','N2O','CFC11eq','CFC12'</flbc_list>
 
   <!-- sim_year used for CO2 cycle namelist settings -->
-  <sim_year>1850-2000</sim_year>
+  <sim_year>1850-2015</sim_year>
 
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/hist_cam_lt.xml b/bld/namelist_files/use_cases/hist_cam_lt.xml
@@ -42,4 +42,7 @@
 <srf_emis_type>INTERP_MISSING_MONTHS</srf_emis_type>
 <csw_time_type>SERIAL</csw_time_type>
 
+<!-- for prescribed nitrogen deposition fluxes -->
+<sim_year>1850-2015</sim_year>
+
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/hist_cam_mt.xml b/bld/namelist_files/use_cases/hist_cam_mt.xml
@@ -37,4 +37,7 @@
 <srf_emis_type>INTERP_MISSING_MONTHS</srf_emis_type>
 <csw_time_type>SERIAL</csw_time_type>
 
+<!-- for prescribed nitrogen deposition fluxes -->
+<sim_year>1850-2015</sim_year>
+
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/hist_geoschem.xml b/bld/namelist_files/use_cases/hist_geoschem.xml
@@ -31,8 +31,6 @@
 
 <prescribed_strataero_type>SERIAL</prescribed_strataero_type>
 
-<ndep_list>'noy', 'nhx'</ndep_list>
-
 <!-- History Files -->
 
 <mfilt>           1,30,365,240,240,480,365,73,30  </mfilt>
@@ -163,4 +161,6 @@
 'so4_a3',
 </fincl1>
 
+<sim_year>1850-2015</sim_year>
+
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/hist_geoschem_nudged.xml b/bld/namelist_files/use_cases/hist_geoschem_nudged.xml
@@ -31,8 +31,6 @@
 
 <prescribed_strataero_type>SERIAL</prescribed_strataero_type>
 
-<ndep_list>'noy', 'nhx'</ndep_list>
-
 <!-- nudging. this section is added over hist_geoschem.xml to match hist_trop_strat_nudged_cam6.xml -->
 
 <Nudge_Model>.true.</Nudge_Model>
@@ -218,4 +216,6 @@
 'so4_a3',
 </fincl1>
 
+<sim_year>1850-2015</sim_year>
+
 </namelist_defaults>
diff --git a/bld/namelist_files/use_cases/hist_trop_strat_nudged_cam6.xml b/bld/namelist_files/use_cases/hist_trop_strat_nudged_cam6.xml
@@ -127,8 +127,6 @@
          'so4_a2   -> $INPUTDATA_ROOT/atm/cam/chem/emis/emissions_ssp585/emissions-cmip6-ScenarioMIP_IAMC-REMIND-MAGPIE-ssp585-1-1_so4_a2_anthro-res_surface_mol_175001-210101_0.9x1.25_c20190224.nc'
 </srf_emis_specifier>
 
-<ndep_list>'noy', 'nhx'</ndep_list>
-
 <!-- nudging -->
 <Nudge_Model>.true.</Nudge_Model>
 <Nudge_Path hgrid="0.9x1.25" nlev="32">'atm/cam/met/nudging/MERRA2_fv09_32L/'</Nudge_Path>

diff --git a/bld/namelist_files/use_cases/hist_trop_strat_vbsext_cam6.xml b/bld/namelist_files/use_cases/hist_trop_strat_vbsext_cam6.xml
@@ -26,8 +26,6 @@
 
 <srf_emis_type>INTERP_MISSING_MONTHS</srf_emis_type>
 
-<ndep_list>'noy', 'nhx'</ndep_list>
-
 <!-- History Files -->
 
 <mfilt>           1,30,365,240,240,480,365,73,30  </mfilt>
@@ -44,9 +42,9 @@
 <history_cesm_forcing>.false.</history_cesm_forcing>
 <history_scwaccm_forcing>.false.</history_scwaccm_forcing>
 
-<!-- Monthly --> 
+<!-- Monthly -->
 <fincl1>
-         'CFC11STAR', 'AODDUST', 'AODDUST02', 'T', 'U', 'V', 'O3', 'OH', 'O3S',  
+         'CFC11STAR', 'AODDUST', 'AODDUST02', 'T', 'U', 'V', 'O3', 'OH', 'O3S',
          'NO3', 'HO2', 'LNO_COL_PROD', 'NO2_CLXF', 'SFNO', 'SFNH3', 'BRO', 'CH3CL',
          'CLO', 'CO2', 'HCL', 'HO2', 'HOCL', 'H2O', 'PHIS', 'Z3',
          'BENZENE', 'C2H2', 'C2H4', 'C2H6', 'C3H8', 'CCL4', 'CFC11', 'CFC113',
@@ -85,14 +83,14 @@
          'AODNIRstdn', 'AODUVstdn', 'AODdn_accum', 'AODdn_coarse', 'AODdnDUST01', 'AODdnDUST02', 'AODdnDUST03', 'AODVISstdn',
          'AODUVstdn', 'AODNIRstdn', 'AODNIRstdn', 'AODVISdn', 'AODUVdn', 'EXTINCTdn', 'EXTxASYMdn', 'EXTINCTNIRdn',
          'EXTINCTUVdn', 'WD_NC4CH2OH', 'WD_NC4CHO', 'WD_NDEP', 'WD_NH3', 'WD_NH4', 'WD_NHDEP',
-         'WD_NOA', 'WD_NTERPOOH', 'WD_ONITR', 'WD_PHENOOH', 'WD_POOH', 'WD_ROOH', 'WD_SO2', 
+         'WD_NOA', 'WD_NTERPOOH', 'WD_ONITR', 'WD_PHENOOH', 'WD_POOH', 'WD_ROOH', 'WD_SO2',
          'WD_SOAGbb0', 'WD_SOAGbb1', 'WD_SOAGbb2', 'WD_SOAGbb3', 'WD_SOAGbb4',
          'WD_SOAGbg0', 'WD_SOAGbg1', 'WD_SOAGbg2', 'WD_SOAGbg3', 'WD_SOAGbg4',
          'WD_SOAGff0', 'WD_SOAGff1', 'WD_SOAGff2', 'WD_SOAGff3', 'WD_SOAGff4',
          'WD_SVOCbb','WD_SVOCff', 'WD_TERP2OOH', 'WD_TERPNIT', 'WD_TERPOOH',
-         'DF_CO', 'DF_GLYALD', 
+         'DF_CO', 'DF_GLYALD',
          'dry_deposition_NHx_as_N', 'DF_NH3', 'DF_NH4', 'DF_NO', 'DF_NO2', 'DF_NOA', 'DF_NTERPOOH', 'DF_O3',
-         'DF_ONITR', 'DF_PAN', 'DF_PHENOOH', 'DF_POOH', 'DF_ROOH', 'DF_SO2', 
+         'DF_ONITR', 'DF_PAN', 'DF_PHENOOH', 'DF_POOH', 'DF_ROOH', 'DF_SO2',
          'DF_SOAGbb0', 'DF_SOAGbb1', 'DF_SOAGbb2', 'DF_SOAGbb3', 'DF_SOAGbb4',
          'DF_SOAGbg0', 'DF_SOAGbg1', 'DF_SOAGbg2', 'DF_SOAGbg3', 'DF_SOAGbg4', 'DF_SOAGff0', 'DF_SOAGff1', 'DF_SOAGff2', 'DF_SOAGff3', 'DF_SOAGff4',
          'DF_SVOCbb','DF_SVOCff', 'DF_TERP2OOH', 'DF_TERPNIT', 'DF_TERPOOH', 'DF_TERPROD1',

diff --git a/bld/namelist_files/use_cases/hist_trop_strat_vbsfire_cam6.xml b/bld/namelist_files/use_cases/hist_trop_strat_vbsfire_cam6.xml
@@ -67,8 +67,6 @@
 
 <srf_emis_type>INTERP_MISSING_MONTHS</srf_emis_type>
 
-<ndep_list>'noy', 'nhx'</ndep_list>
-
 <!-- History Files -->
 
 <mfilt>           1,30,365,240,240,480,365,73,30  </mfilt>

diff --git a/bld/namelist_files/use_cases/sd_cam6.xml b/bld/namelist_files/use_cases/sd_cam6.xml
@@ -28,12 +28,14 @@
 
   <prescribed_strataero_type    >     'SERIAL'                                                                     </prescribed_strataero_type>
   <prescribed_strataero_datapath>     'atm/cam/ozone_strataero'                                                    </prescribed_strataero_datapath>
-  <prescribed_strataero_file>         'ozone_strataero_WACCM_L70_zm5day_18500101-20150103_CMIP6ensAvg_c180923.nc'  </prescribed_strataero_file> 
+  <prescribed_strataero_file>         'ozone_strataero_WACCM_L70_zm5day_18500101-20150103_CMIP6ensAvg_c180923.nc'  </prescribed_strataero_file>
   <prescribed_strataero_use_chemtrop> .true.                                                                       </prescribed_strataero_use_chemtrop>
 
   <scenario_ghg            >    'CHEM_LBC_FILE'   </scenario_ghg>
   <flbc_file>atm/waccm/lb/LBC_1750-2015_CMIP6_GlobAnnAvg_c180926.nc</flbc_file>
   <flbc_type>'SERIAL'</flbc_type>
   <flbc_list>'CO2','CH4','N2O','CFC11eq','CFC12'</flbc_list>
 
+  <sim_year>1850-2015</sim_year>
+
 </namelist_defaults>