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cam6_4_056: Nitrogen deposition fluxes #1216

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merged 16 commits into from
Jan 17, 2025
Merged

cam6_4_056: Nitrogen deposition fluxes #1216

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fa69b87
more sane way to control nitrogen deposition to surface models
fvitt Dec 11, 2024
b70cfea
fix some issues in derecho regression tests
fvitt Dec 19, 2024
24e012d
ChangeLog start; code clean up; add ndep diags to reg test
fvitt Dec 26, 2024
82a3c9c
fix restart problem with nitrogen flux history fields
fvitt Dec 26, 2024
bba4e59
add addfld calls to cam7 phys
fvitt Dec 26, 2024
9066aee
units correction in diagnostics
fvitt Dec 26, 2024
97fd801
set fldptr_ndep to zero for no flux cases
fvitt Dec 28, 2024
31796b2
namelist fixes
fvitt Dec 28, 2024
9848f15
use sim_year to determine stream_ndep settings; remove deprecated nde…
fvitt Jan 8, 2025
e106d4f
update ChangeLog
fvitt Jan 9, 2025
b30e948
add sim_year valid values of 2010 and 1850-2015
fvitt Jan 9, 2025
450312b
Add sim_year to geoschem use case files; ChangeLog updates
fvitt Jan 15, 2025
56e2c02
merge to head of ESCOMP/cam_development
fvitt Jan 15, 2025
c819813
adjust sim_years for co2_cycle file defaults
fvitt Jan 16, 2025
fa37cb5
ChangeLog update
fvitt Jan 17, 2025
4328f4e
ChangeLog update
fvitt Jan 17, 2025
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21 changes: 13 additions & 8 deletions bld/build-namelist
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Expand Up @@ -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 = $cfg->get('scam_iop');
Expand Down Expand Up @@ -705,6 +697,19 @@ if ($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');
Expand Down
33 changes: 26 additions & 7 deletions bld/namelist_files/namelist_defaults_cam.xml
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Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand Down
21 changes: 5 additions & 16 deletions bld/namelist_files/namelist_definition.xml
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Expand Up @@ -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"
Expand Down Expand Up @@ -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.
Expand Down
3 changes: 3 additions & 0 deletions bld/namelist_files/use_cases/1850_cam_lt.xml
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Expand Up @@ -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>
3 changes: 3 additions & 0 deletions bld/namelist_files/use_cases/1850_cam_mt.xml
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Expand Up @@ -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>
3 changes: 0 additions & 3 deletions bld/namelist_files/use_cases/2000_geoschem.xml
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Expand Up @@ -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>
Expand Down
2 changes: 0 additions & 2 deletions bld/namelist_files/use_cases/2000_trop_strat_vbs_cam6.xml
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Expand Up @@ -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>
Expand Down
3 changes: 3 additions & 0 deletions bld/namelist_files/use_cases/2010_cam6.xml
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Expand Up @@ -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>
3 changes: 2 additions & 1 deletion bld/namelist_files/use_cases/2010_geoschem.xml
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Expand Up @@ -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 -->

Expand Down Expand Up @@ -166,4 +165,6 @@
'so4_a3',
</fincl1>

<sim_year>2010</sim_year>

</namelist_defaults>
2 changes: 0 additions & 2 deletions bld/namelist_files/use_cases/2010_trop_strat_vbs_cam6.xml
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Expand Up @@ -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>
Expand Down
2 changes: 1 addition & 1 deletion bld/namelist_files/use_cases/hist_cam6.xml
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Expand Up @@ -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>
3 changes: 3 additions & 0 deletions bld/namelist_files/use_cases/hist_cam_lt.xml
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Expand Up @@ -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>
3 changes: 3 additions & 0 deletions bld/namelist_files/use_cases/hist_cam_mt.xml
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Expand Up @@ -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>
4 changes: 2 additions & 2 deletions bld/namelist_files/use_cases/hist_geoschem.xml
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Expand Up @@ -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>
Expand Down Expand Up @@ -163,4 +161,6 @@
'so4_a3',
</fincl1>

<sim_year>1850-2015</sim_year>

</namelist_defaults>
4 changes: 2 additions & 2 deletions bld/namelist_files/use_cases/hist_geoschem_nudged.xml
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Expand Up @@ -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>
Expand Down Expand Up @@ -218,4 +216,6 @@
'so4_a3',
</fincl1>

<sim_year>1850-2015</sim_year>

</namelist_defaults>
2 changes: 0 additions & 2 deletions bld/namelist_files/use_cases/hist_trop_strat_nudged_cam6.xml
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Expand Up @@ -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>
Expand Down
12 changes: 5 additions & 7 deletions bld/namelist_files/use_cases/hist_trop_strat_vbsext_cam6.xml
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Expand Up @@ -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>
Expand All @@ -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',
Expand Down Expand Up @@ -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',
Expand Down
2 changes: 0 additions & 2 deletions bld/namelist_files/use_cases/hist_trop_strat_vbsfire_cam6.xml
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Expand Up @@ -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>
Expand Down
4 changes: 3 additions & 1 deletion bld/namelist_files/use_cases/sd_cam6.xml
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Expand Up @@ -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>
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