cam6_4_023: SCAM-SE feature addition plus bugfixes and some refactoring.

bld/build-namelist

@@ -4017,7 +4017,7 @@ if ($cfg->get('scam')) {
     if ($chem =~ /_mam/) {
 	add_default($nl, 'scm_relax_fincl');
     }
-    if ($cfg->get('scam_iop')) {
+    if ($scam_iop) {
 	add_default($nl, 'iopfile');
     }
     if ($scam_iop eq 'SAS') {

bld/config_files/definition.xml

@@ -147,7 +147,7 @@ Turn on CO2 cycle in biogeochemistry model: 0 => no, 1 => yes.
 Modifications that allow perturbation growth testing: 0=off, 1=on.
 </entry>
 <entry id="scam" valid_values="0,1" value="0">
-Configure CAM for single column mode and specify an IOP.
+Configure CAM for single column mode and specify an IOP: 0=no, 1=yes.
 This option only supported for the Eulerian and SE dycores.
 </entry>
 <entry id="scam_iop" valid_values="arm95,arm97,atex,bomex,cgilss11,cgilss12,cgilss6,dycomsrf01,dycomsrf02,gateiii,mpace,rico,sas,sparticus,togaii,twp06,camfrc,none" value="none">

bld/namelist_files/namelist_defaults_cam.xml

@@ -2884,6 +2884,7 @@
 <scm_use_obs_uv                  scam="1"                   > .true.    </scm_use_obs_uv>
 <scale_dry_air_mass              scam="1"        dyn="se"   > 0.0D0     </scale_dry_air_mass>
 <scm_relaxation                  scam="1"                   > .true.    </scm_relaxation>
+<scm_relax_tau_sec               scam="1"                   > 10800._r8 </scm_relax_tau_sec>
 <scm_relax_fincl   phys="cam6"   scam="1"  >
   'T', 'bc_a1', 'bc_a4', 'dst_a1', 'dst_a2', 'dst_a3', 'ncl_a1', 'ncl_a2', 'ncl_a3',
   'num_a1', 'num_a2', 'num_a3', 'num_a4', 'pom_a1', 'pom_a4', 'so4_a1', 'so4_a2', 'so4_a3', 'soa_a1', 'soa_a2'
@@ -2905,56 +2906,64 @@
 
 <!-- iop spefic defaults for SCAM mode -->
 
-<!-- "IOP: ARM 1995 (18 Jul 1995 - 2 Aug 1995)" -->
+<!-- IOP ARM95/ARM Southern Great Plains/lat:36/lon:263/Jul 1995/18d/M. Zhang et al. (2016)/Land convection -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="arm95"     >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-06-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="arm95"     >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-06-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="arm95"     >atm/cam/scam/iop/ARM95_4scam.nc</iopfile>
 <co2vmr                                               scam_iop="arm95"     > 368.9e-6  </co2vmr>
 
-<!-- "IOP: ARM 1997 (18 Jun 1997 - 17 Jul 1997)" -->
+<!-- IOP ARM97/ARM Southern Great Plains/lat:36/lon:263/Jun 1997/30d/M. Zhang et al. (2016) Land convection -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="arm95"     >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-06-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="arm95"     >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-06-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="arm97"     >atm/cam/scam/iop/ARM97_4scam.nc</iopfile>
 <co2vmr                                               scam_iop="arm97"     > 368.9e-6  </co2vmr>
 
+<!-- IOP ATEX/Atlantic Trade Wind Exp/lat:15/lon:345/Feb 1969/2d/Augstein et al. (1973) Shallow cumulus -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="atex"      >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-02-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="atex"      >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-02-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="atex"      >atm/cam/scam/iop/ATEX_48hr_4scam.nc</iopfile>
 
+<!-- IOP BOMEX/Barbados Ocean and Met Exp/lat:15/lon:300/Jun 1969/5d/Holland and Rasmusson (1973) Shallow cumulus -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="bomex"     >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-06-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="bomex"     >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-06-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="bomex"     >atm/cam/scam/iop/BOMEX_5day_4scam.nc</iopfile>
 
+<!-- IOP CGILSS11/CFMIP-GASS SCM/LES Intercomparison/lat:32/lon:231/Jul 1997/30d/M. Zhang et al. (2013) Stratocumulus -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="cgilsS11"  >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-07-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="cgilsS11"  >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-07-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="cgilsS11"  >atm/cam/scam/iop/S11_CTL_MixedLayerInit_reduced.nc</iopfile>
 
+<!-- IOP CGILSS12/CFMIP-GASS SCM/LES Intercomparison/lat:35/lon:235/Jul 1997/30d/M. Zhang et al. (2013) Stratus -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="cgilsS12"  >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-07-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="cgilsS12"  >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-07-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="cgilsS12"  >atm/cam/scam/iop/S12_CTL_MixedLayerInit_reduced.nc</iopfile>
 
+<!-- IOP CGILSS6/CFMIP-GASS SCM/LES Intercomparison/lat:17/lon:211/Jul 1997/30d/M. Zhang et al. (2013) Shallow cumulus -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="cgilsS6"   >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-07-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="cgilsS6"  >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-07-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="cgilsS6"   >atm/cam/scam/iop/S6_CTL_reduced.nc</iopfile>
 
+<!-- IOP DYCOMSRF01/Dynamics of Marine StratoCu/lat:32/lon:239/Jul 15/2001/2d Stevens et al. (2003) Stratocumulus -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="dycomsRF01">atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-07-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="dycomsRF01"  >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-07-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="dycomsRF01">atm/cam/scam/iop/DYCOMSrf01_4day_4scam.nc</iopfile>
 
+<!-- IOP DYCOMSRF02/Dynamics of Marine StratoCu/lat:32/lon:239/Jul 11/2001/2d Stevens et al. (2003) Stratocumulus -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="dycomsRF02">atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-07-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="dycomsRF02"  >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-07-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="dycomsRF02">atm/cam/scam/iop/DYCOMSrf02_48hr_4scam.nc</iopfile>
 
-<!-- "IOP: GARP Atlantic Tropical Experiment 1974 (30 Aug. 1974 - 18 Sept. 1974)" -->
+<!-- IOP GATEIII/GARP Atlantic Tropical Experiment Phase III/lat:9/lon:336/Aug 1974/20d/Thompson et al.(1979) Tropical convection -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="gateiii"   >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-08-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="gateIII"   >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-08-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="gateiii"   >atm/cam/scam/iop/GATEIII_4scam_c170809.nc</iopfile>
 
+<!-- IOP MICRE/Macquarie Island Cloud Radiation Experiment/lat:-56/lon:141/2017/90d/Marchand R. 2020/Marine -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="micre2017" >atm/cam/scam/iop/micre2017_3mo.cam.i.2017-01-01-00000.regrid.ne3np4.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="micre2017" >atm/cam/scam/iop/micre2017_3mo.cam.i.2017-01-01-00000.regrid.Gaus_64x128.nc</ncdata>
 <iopfile                                              scam_iop="micre2017" >atm/cam/scam/iop/micre2017_3mo.macquarie2017.iop.nc</iopfile>
 
-<!-- "IOP: MPACE 2004 (05 Oct 2004 - 22 Oct  2004)" -->
+<!-- IOP MPACE/Mixed Phase Arctic Clouds Exp/lat:71/lon:206/Oct 2004/17d/Verlinde et al. (2007)/Arctic -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="mpace"     >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-10-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="mpace"  >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-10-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="mpace"     >atm/cam/scam/iop/MPACE_4scam.nc</iopfile>
@@ -2971,35 +2980,37 @@
         'TGCLDLWP','GCLDLWP'
 </fincl1>
 
+<!-- IOP RICO/Rain and Cumulus over Oceans/lat:18/lon:299/Dec 2004/3d/Rauber et al. (2007)/Shallow cumulus -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="rico"      >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-07-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="rico"      >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-07-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="rico"      >atm/cam/scam/iop/RICO_3day_4scam.nc</iopfile>
 
+<!-- IOP SAS/The Southeast Atmosphere Study (SAS) campaign/lat:32/lon:272/June 2013/30d/Carlton (2018)/Southeast US Air Chemistry -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="SAS"       >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-06-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="SAS"       >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-06-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="SAS"       >atm/cam/scam/iop/SAS_ideal_4scam.nc</iopfile>
 <co2vmr                                               scam_iop="SAS"       > 368.9e-6  </co2vmr>
 <use_gw_front                                         scam_iop="SAS"       > .false.   </use_gw_front>
 <scm_backfill_iop_w_init                              scam_iop="SAS"       > .true.    </scm_backfill_iop_w_init>
 
-<!-- "IOP: Small Particles in Cirrus  2010 (01 April 2010 - 30 April 2010)" -->
+<!-- IOP SPARTICUS/Small Particles in Cirrus/lat:37/lon:263/Apr 2010/30d/Mace et al. (2009)/Cirrus, convection -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="sparticus" >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-04-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="sparticus" >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-04-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="sparticus" >atm/cam/scam/iop/SPARTICUS_4scam.nc</iopfile>
 
-<!-- "IOP: TOGA COARE IOP2 1992 ( 18 Dec. 1992 - 08 Jan. 1993)" -->
+<!-- IOP TOGAII/Tropical Ocean Global Atmosphere IOP2/lat:-2/lon:154/Dec 1992/21d/Webster and Lukas (1992)/Tropical convection -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="togaII" >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-12-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="togaII" >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-12-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="togaII" >atm/cam/scam/iop/TOGAII_4scam.nc</iopfile>
 
-<!-- "IOP: TWP-ICE 2006 (17 Jan 2006 - 12 Feb 2006)" -->
+<!-- IOP TWP06/Tropical W. Pacific Convection/lat:-12/lon:131/Jan 2006/26d/May et al. (2008)/Tropical convection -->
 <ncdata             hgrid="ne3np4"    nlev="32"       scam_iop="twp06" >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-01-01-00000.nc</ncdata>
 <ncdata             hgrid="64x128"    nlev="32"       scam_iop="twp06" >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-01-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="twp06" >atm/cam/scam/iop/TWP06_4scam.nc</iopfile>
 <iradlw                                               scam_iop="twp06" > 1  </iradlw>
 <iradsw                                               scam_iop="twp06" > 1  </iradsw>
 
-<!-- "IOP: CAM Forcing file" -->
+<!-- IOP USER/User specified IOP forcing/lat:yy/lon:xx/Date:Any/Length:Any/SCAM Forcing -->
 <ncdata            hgrid="ne3np4"    nlev="32"        scam_iop="camfrc"     >atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-06-01-00000.nc</ncdata>
 <ncdata            hgrid="64x128"    nlev="32"        scam_iop="camfrc"     >atm/cam/inic/gaus/CESM2.F2000climo.64x128.cam.i.0003-06-01-00000.nc</ncdata>
 <iopfile                                              scam_iop="camfrc"     >atm/cam/scam/iop/ARM97_4scam.nc</iopfile>

bld/namelist_files/namelist_definition.xml

@@ -5863,7 +5863,7 @@ Default: FALSE
 <entry id="scm_use_3dfrc" type="logical" category="scam"
        group="scam_nl" valid_values="">
 Use the SCAM-IOP 3d forcing if true, use combination of dycore vertical advection and iop horiz advection if false
-Default:
+Default:False
 </entry>
 
 <entry id="scm_force_latlon" type="logical" category="scam"

cime_config/SystemTests/sct.py

@@ -62,14 +62,13 @@ def _case_two_setup(self):
         self._case.set_value("BFBFLAG","TRUE")
 
         CAM_CONFIG_OPTS = self._case1.get_value("CAM_CONFIG_OPTS").replace('-camiop','')
+        self._case.set_value("CAM_CONFIG_OPTS","{} -scam camfrc ".format(CAM_CONFIG_OPTS))
         if self._case.get_value("CAM_DYCORE") == "se":
-            self._case.set_value("CAM_CONFIG_OPTS","{} -scam camfrc ".format(CAM_CONFIG_OPTS))
             self._case.set_value("PTS_LAT",44.80320177421346)
             self._case.set_value("PTS_LON",276.7082039324993)
             append_to_user_nl_files(caseroot = self._get_caseroot(), component = "cam", contents = "scale_dry_air_mass     = 0.0D0")
         else:
             append_to_user_nl_files(caseroot = self._get_caseroot(), component = "cam", contents = "ncdata = '../"+case_name+".cam.i."+RUN_STARTDATE+"-00000.nc'")
-            self._case.set_value("CAM_CONFIG_OPTS","{} -scam camfrc ".format(CAM_CONFIG_OPTS))
             self._case.set_value("PTS_LAT",-20.0)
             self._case.set_value("PTS_LON",140.0)
 

cime_config/config_component.xml

@@ -192,7 +192,6 @@
       <value compset="_CAM.*%SCAMRICO">-scam rico</value>
       <value compset="_CAM.*%SCAMSPARTICUS">-scam sparticus</value>
       <value compset="_CAM.*%SCAMTOGA2">-scam togaII</value>
-      <value compset="_CAM.*%SCAMTOGA2">-scam user</value>
       <value compset="_CAM.*%SCAMTWP06">-scam twp06</value>
       <value compset="_CAM.*%SCAMCAMFRC">-scam camfrc</value>
 

cime_config/config_compsets.xml

@@ -158,7 +158,7 @@
 
   <compset>
     <alias>FSCAMCGILSS6</alias>
-    <lname>2000_CAM60%SCAMCgilss6_CLM50%SP_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV</lname>
+    <lname>2000_CAM60%SCAMCGILSS6_CLM50%SP_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV</lname>
     <science_support grid="T42_T42"/>
   </compset>
 

cime_config/testdefs/testlist_cam.xml

@@ -1156,6 +1156,7 @@
       <machine name="izumi" compiler="gnu" category="aux_cam"/>
     </machines>
     <options>
+      <option name="comment" >Spectral Element SCAM BFB test with CAM w GNU</option>
       <option name="wallclock">00:30:00</option>
     </options>
   </test>
@@ -1349,7 +1350,8 @@
     </machines>
     <options>
       <option name="wallclock">00:30:00</option>
-    </options>
+      <option name="comment" >Derecho Spectral Element SCAM BFB test with CAM (Intel)</option>
+   </options>
   </test>
 <!--              001                        -->
   <test compset="QPC5" grid="T42_T42_mg17" name="SCT_D_Ln7_Vnuopc" testmods="cam/scm_prep">
@@ -1468,6 +1470,7 @@
       <machine name="derecho" compiler="intel" category="test_scam"/>
     </machines>
     <options>
+      <option name="comment" >Eulerian ARM97 IOP SCAM Smoke test</option>
       <option name="wallclock">00:10:00</option>
     </options>
   </test>
@@ -1477,6 +1480,7 @@
       <machine name="derecho" compiler="intel" category="test_scam"/>
     </machines>
     <options>
+      <option name="comment" >pre_alpha Eulerian MPACE IPO SCAM Smoke test</option>
       <option name="wallclock">00:10:00</option>
     </options>
   </test>

cime_config/usermods_dirs/scam_mandatory/shell_commands

@@ -9,7 +9,7 @@
 ./xmlchange REST_OPTION=never
 
 # Note that clm cannot use initial conditions with SCAM -so will only use specified phenology
-# Only change if CLM_FORCE_COLDSTART exists and dycore is eularian
+# Only change if CLM_FORCE_COLDSTART exists and dycore is eulerian
 if [ `./xmlquery --value CAM_DYCORE` == 'eul' ] && [ `./xmlquery --value CLM_FORCE_COLDSTART |& grep -c 'ERROR'` -eq 0 ]; then
 ./xmlchange CLM_FORCE_COLDSTART='on'
 fi

src/control/cam_history.F90

@@ -919,8 +919,6 @@ subroutine history_readnl(nlfile)
     end if
     if (inithist == 'CAMIOP') then
        write_camiop=.true.
-    else
-       write_camiop=.false.
     end if
     ! separate namelist reader for the satellite history file
     call sat_hist_readnl(nlfile, hfilename_spec, mfilt, fincl, nhtfrq, avgflag_pertape)