'Add capability to read emissions datasets on unstructured grids

Imported from https://svn-ccsm-models.cgd.ucar.edu/cam1/trunk@91682 Committed by Francis Vitt <fvitt@ucar.edu> at 2019-09-12 09:07:16 -0600 Original svn commit message: Add capability to read emissions datasets on unstructured grids A + components/cam/test/system/nl_files/outfrq3s_unstr_emis M components/cam/test/system/input_tests_master M components/cam/test/system/tests_chem_mpi M components/cam/cime_config/config_pes.xml A + components/cam/cime_config/testdefs/testmods_dirs/cam/outfrq9s_refined_camchem A + components/cam/cime_config/testdefs/testmods_dirs/cam/outfrq1d_refined_camchem M components/cam/cime_config/testdefs/testlist_cam.xml M components/cam/doc/ChangeLog M components/cam/src/chemistry/utils/tracer_data.F90 M components/cam/src/chemistry/mozart/mo_srf_emissions.F90 M components/cam/src/chemistry/mozart/mo_extfrc.F90 '
mvertens · Oct 3, 2019 · 182906c · 182906c
1 parent c242f5b
commit 182906c
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Showing 15 changed files with 602 additions and 134 deletions.
diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml
@@ -325,6 +325,39 @@
 	  <rootpe_cpl>0</rootpe_cpl>                         
 	</rootpe>
       </pes>
+      <pes pesize="any" compset="_CAM60%CC">
+        <comment>none</comment>
+        <ntasks>
+          <ntasks_atm>-50</ntasks_atm>
+          <ntasks_lnd>-50</ntasks_lnd>
+          <ntasks_rof>-50</ntasks_rof>
+          <ntasks_ice>-50</ntasks_ice>
+          <ntasks_ocn>-50</ntasks_ocn>
+          <ntasks_glc>-50</ntasks_glc>
+          <ntasks_wav>-50</ntasks_wav>
+          <ntasks_cpl>-50</ntasks_cpl>
+        </ntasks>
+        <nthrds>
+          <nthrds_atm>1</nthrds_atm>
+          <nthrds_lnd>1</nthrds_lnd>
+          <nthrds_rof>1</nthrds_rof>
+          <nthrds_ice>1</nthrds_ice>
+          <nthrds_ocn>1</nthrds_ocn>
+          <nthrds_glc>1</nthrds_glc>
+          <nthrds_wav>1</nthrds_wav>
+          <nthrds_cpl>1</nthrds_cpl>
+        </nthrds>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_lnd>0</rootpe_lnd>
+          <rootpe_rof>0</rootpe_rof>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_ocn>0</rootpe_ocn>
+          <rootpe_glc>0</rootpe_glc>
+          <rootpe_wav>0</rootpe_wav>
+          <rootpe_cpl>0</rootpe_cpl>
+        </rootpe>
+      </pes>
     </mach>
   </grid>
   <grid name="a%ne16" >
@@ -439,37 +472,37 @@
     </mach>
     <mach name="cheyenne">
       <pes pesize="any" compset="_(CAM50|CAM60)%(CC|WC|CV|CF)">
-	<comment>none</comment>
- 	<ntasks>
-	  <ntasks_atm>1200</ntasks_atm> 
-	  <ntasks_lnd>1200</ntasks_lnd>           
-	  <ntasks_rof>1200</ntasks_rof> 
-	  <ntasks_ice>1200</ntasks_ice> 
-	  <ntasks_ocn>1200</ntasks_ocn> 
-	  <ntasks_glc>1200</ntasks_glc> 
-	  <ntasks_wav>1200</ntasks_wav> 
-	  <ntasks_cpl>1200</ntasks_cpl> 
-	</ntasks>
-	<nthrds>
-	  <nthrds_atm>3</nthrds_atm> 
-	  <nthrds_lnd>3</nthrds_lnd> 
-	  <nthrds_rof>3</nthrds_rof> 
-	  <nthrds_ice>3</nthrds_ice> 
-	  <nthrds_ocn>3</nthrds_ocn> 
-	  <nthrds_glc>3</nthrds_glc> 
-	  <nthrds_wav>3</nthrds_wav> 
-	  <nthrds_cpl>3</nthrds_cpl> 
-	</nthrds>
-	<rootpe>
-	  <rootpe_atm>0</rootpe_atm> 
-	  <rootpe_lnd>0</rootpe_lnd> 
-	  <rootpe_rof>0</rootpe_rof> 
-	  <rootpe_ice>0</rootpe_ice>    
-	  <rootpe_ocn>0</rootpe_ocn>   
-	  <rootpe_glc>0</rootpe_glc> 
-	  <rootpe_wav>0</rootpe_wav> 
-	  <rootpe_cpl>0</rootpe_cpl>                         
-	</rootpe>
+        <comment>none</comment>
+        <ntasks>
+          <ntasks_atm>-50</ntasks_atm>
+          <ntasks_lnd>-50</ntasks_lnd>
+          <ntasks_rof>-50</ntasks_rof>
+          <ntasks_ice>-50</ntasks_ice>
+          <ntasks_ocn>-50</ntasks_ocn>
+          <ntasks_glc>-50</ntasks_glc>
+          <ntasks_wav>-50</ntasks_wav>
+          <ntasks_cpl>-50</ntasks_cpl>
+        </ntasks>
+        <nthrds>
+          <nthrds_atm>1</nthrds_atm>
+          <nthrds_lnd>1</nthrds_lnd>
+          <nthrds_rof>1</nthrds_rof>
+          <nthrds_ice>1</nthrds_ice>
+          <nthrds_ocn>1</nthrds_ocn>
+          <nthrds_glc>1</nthrds_glc>
+          <nthrds_wav>1</nthrds_wav>
+          <nthrds_cpl>1</nthrds_cpl>
+        </nthrds>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_lnd>0</rootpe_lnd>
+          <rootpe_rof>0</rootpe_rof>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_ocn>0</rootpe_ocn>
+          <rootpe_glc>0</rootpe_glc>
+          <rootpe_wav>0</rootpe_wav>
+          <rootpe_cpl>0</rootpe_cpl>
+        </rootpe>
       </pes>
     </mach>
   </grid>

diff --git a/cime_config/testdefs/testlist_cam.xml b/cime_config/testdefs/testlist_cam.xml
@@ -354,7 +354,6 @@
   </test>
   <test compset="FCSD" grid="f05_f05_mg17" name="ERP_Ln9" testmods="cam/outfrq9s">
     <machines>
-      <machine name="cheyenne" compiler="intel" category="prealpha"/>
       <machine name="cheyenne" compiler="intel" category="camchem"/>
     </machines>
     <options>
@@ -403,8 +402,9 @@
       <machine name="cheyenne" compiler="intel" category="camchem"/>
     </machines>
   </test>
-  <test compset="FCHIST" grid="ne30_ne30_mg17" name="SMS_Ld1" testmods="cam/outfrq9s">
+  <test compset="FCHIST" grid="ne30_ne30_mg17" name="SMS_Ld1" testmods="cam/outfrq1d">
     <machines>
+      <machine name="cheyenne" compiler="intel" category="prebeta"/>
       <machine name="cheyenne" compiler="intel" category="camchem"/>
     </machines>
   </test>
@@ -417,6 +417,23 @@
       <option name="wallclock">00:30:00</option>
     </options>
   </test>
+  <test compset="FCHIST" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" name="SMS_D_Ln9" testmods="cam/outfrq9s_refined_camchem">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="aux_cam"/>
+      <machine name="cheyenne" compiler="intel" category="camchem"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:30:00</option>
+    </options>
+  </test>
+  <test compset="FCHIST" grid="ne0CONUSne30x8_ne0CONUSne30x8_mt12" name="ERS_Ld3" testmods="cam/outfrq1d_refined_camchem">
+    <machines>
+      <machine name="cheyenne" compiler="intel" category="camchem"/>
+    </machines>
+    <options>
+      <option name="wallclock">02:00:00</option>
+    </options>
+  </test>
   <test compset="FCvbsxHIST" grid="f09_f09_mg17" name="SMS_D_Ln9" testmods="cam/outfrq9s">
     <machines>
       <machine name="cheyenne" compiler="intel" category="camchem"/>

diff --git a/cime_config/testdefs/testmods_dirs/cam/outfrq1d_refined_camchem/shell_commands b/cime_config/testdefs/testmods_dirs/cam/outfrq1d_refined_camchem/shell_commands
@@ -0,0 +1,2 @@
+./xmlchange EPS_AAREA=1.e-4
+./xmlchange RUN_STARTDATE=2013-10-01
diff --git a/cime_config/testdefs/testmods_dirs/cam/outfrq1d_refined_camchem/user_nl_cam b/cime_config/testdefs/testmods_dirs/cam/outfrq1d_refined_camchem/user_nl_cam
@@ -0,0 +1,61 @@
+ se_phys_dyn_cp = 2
+ gw_polar_taper = .true.
+
+ mfilt=1,1,1,1,1,1,1,1,1
+ ndens=1,1,1,1,1,1,1,1,1
+ nhtfrq=-24,-24,-24,-24,-24,-24,-24,-24,-24
+
+ inithist='ENDOFRUN'
+
+ ncdata = '$DIN_LOC_ROOT/atm/cam/inic/se/fchist_ne0conus30x8_L32_2012-11-01_c190906.nc'
+
+ fincl2 = 'SFBENZENE','SFBIGALK','SFC2H2','SFCH2O','SFCH3COOH','SFCO','SFNO'
+
+ ext_frc_specifier =
+         'bc_a4  -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_bc_a4_aircraft_vertical_1750-2015_0.9x1.25_c20170608.nc',
+         'NO2    -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-EPA_NO2_vertical_anthro_201306-201310_conus_30x8_c190906.nc',
+         'num_a1 -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_so4_a1_anthro-ene_vertical_1750-2015_0.9x1.25_c20170616.nc',
+         'num_a1 -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_a1_so4_contvolcano_vertical_850-5000_0.9x1.25_c20170724.nc',
+         'num_a2 -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_a2_so4_contvolcano_vertical_850-5000_0.9x1.25_c20170724.nc',
+         'num_a4 -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_bc_a4_aircraft_vertical_1750-2015_0.9x1.25_c20170608.nc',
+         'SO2    -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-EPA_SO2_vertical_anthro_201306-201310_conus_30x8_c190906.nc',
+         'SO2    -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_SO2_contvolcano_vertical_850-5000_0.9x1.25_c20170724.nc',
+         'SO2    -> $DIN_LOC_ROOT/atm/cam/chem/stratvolc/VolcanEESMv3.11_SO2_850-2016_Mscale_Zreduc_1deg_c180812.nc',
+         'so4_a1 -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_so4_a1_anthro-ene_vertical_1750-2015_0.9x1.25_c20170616.nc',
+         'so4_a1 -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_so4_a1_contvolcano_vertical_850-5000_0.9x1.25_c20170724.nc',
+         'so4_a2 -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_so4_a2_contvolcano_vertical_850-5000_0.9x1.25_c20170724.nc'
+
+ srf_emis_specifier =         
+         'BENZENE  -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_BENZENE_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'BIGENE   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_BIGENE_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'C2H2     -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_C2H2_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'C2H4     -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_C2H4_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'C2H6     -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_C2H6_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'C3H6     -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_C3H6_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'C3H8     -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_C3H8_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'CH2O     -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_CH2O_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'CH3CHO   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_CH3CHO_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'CH3CN    -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_CH3CN_surface_anthro_2012-2014_conus_30x8_c190903.nc',
+         'CH3COOH  -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_CH3COOH_surface_anthro_2012-2014_conus_30x8_c190903.nc',
+         'CO       -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_CO_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'E90      -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions_E90global_surface_1750-2100_0.9x1.25_c20170322.nc',
+         'HCN      -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_HCN_surface_anthro_2012-2014_conus_30x8_c190903.nc',
+         'HCOOH    -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_HCOOH_surface_anthro_2012-2014_conus_30x8_c190903.nc',
+         'IVOC     -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_IVOC_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
+         'NH3      -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_NH3_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'NO       -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_NOx_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'SVOC     -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_SVOC_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
+         'TOLUENE  -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_TOLUENE_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'DMS      -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_DMS_other_surface_1750-2015_0.9x1.25_c20170322.nc',
+         'bc_a4    -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_BC_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'num_a1   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_so4_a1_bb_surface_1750-2015_0.9x1.25_c20170322.nc',
+         'num_a1   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_so4_a1_anthro-ag-ship_surface_1750-2015_0.9x1.25_c20170616.nc',
+         'num_a2   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_so4_a2_anthro-res_surface_1750-2015_0.9x1.25_c20170616.nc',
+         'num_a4   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_num_bc_a4_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'num_a4   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_num_pom_a4_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
+         'pom_a4   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_pom_a4_anthro_surface_1750-2015_0.9x1.25_c20170608.nc',
+         'SO2      -> $DIN_LOC_ROOT/atm/cam/chem/emis/CAM-SE_ne0conus_30x8/emissions-CMIP6_SO2_surface_anthro_2012-2014_masked_conus_30x8_c190903.nc',
+         'SO2      -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_SO2_anthro-ene_surface_1750-2015_0.9x1.25_c20170616.nc',
+         'so4_a1   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_so4_a1_anthro-ag-ship_surface_1750-2015_0.9x1.25_c20170616.nc',
+         'so4_a1   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_so4_a1_bb_surface_1750-2015_0.9x1.25_c20170322.nc',
+         'so4_a2   -> $DIN_LOC_ROOT/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions-cmip6_so4_a2_anthro-res_surface_1750-2015_0.9x1.25_c20170616.nc'
diff --git a/cime_config/testdefs/testmods_dirs/cam/outfrq1d_refined_camchem/user_nl_clm b/cime_config/testdefs/testmods_dirs/cam/outfrq1d_refined_camchem/user_nl_clm
@@ -0,0 +1,33 @@
+!----------------------------------------------------------------------------------
+! Users should add all user specific namelist changes below in the form of 
+! namelist_var = new_namelist_value 
+!
+! Include namelist variables for drv_flds_in ONLY if -megan and/or -drydep options
+! are set in the CLM_NAMELIST_OPTS env variable.
+!
+! EXCEPTIONS: 
+! Set use_cndv           by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting
+! Set use_vichydro       by the compset you use and the CLM_BLDNML_OPTS -vichydro           setting
+! Set use_cn             by the compset you use and CLM_BLDNML_OPTS -bgc  setting
+! Set use_crop           by the compset you use and CLM_BLDNML_OPTS -crop setting
+! Set spinup_state       by the CLM_BLDNML_OPTS -bgc_spinup      setting
+! Set irrigate           by the CLM_BLDNML_OPTS -irrig           setting
+! Set dtime              with L_NCPL                             option
+! Set fatmlndfrc         with LND_DOMAIN_PATH/LND_DOMAIN_FILE    options
+! Set finidat            with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases
+!                        (includes $inst_string for multi-ensemble cases)
+! Set glc_grid           with CISM_GRID                          option
+! Set glc_smb            with GLC_SMB                            option
+! Set maxpatch_glcmec    with GLC_NEC                            option
+! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
+!----------------------------------------------------------------------------------
+hist_nhtfrq = -24
+hist_mfilt  = 1
+hist_ndens  = 1
+
+finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata/opt_se_cslam_topo.FCHIST.ne30_ne30_mg17.default_spin_up_TS1.clm2.r.2012-11-01-00000_c190810.nc'
+use_init_interp = .true.
+
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_ne0CONUSne30x8_hist_16pfts_Irrig_CMIP6_simyr1850_c190814.nc'
+
+flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/landuse.timeseries_ne0CONUSne30x8_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c190815.nc'
diff --git a/cime_config/testdefs/testmods_dirs/cam/outfrq9s_refined_camchem/shell_commands b/cime_config/testdefs/testmods_dirs/cam/outfrq9s_refined_camchem/shell_commands
@@ -0,0 +1,2 @@
+./xmlchange EPS_AAREA=1.e-4
+./xmlchange RUN_STARTDATE=2013-10-01
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		./xmlchange EPS_AAREA=1.e-4
		./xmlchange RUN_STARTDATE=2013-10-01