Adjust to be closer to ESCOMP, remove accidental cam6_3_124 changes

bld/namelist_files/namelist_defaults_cam.xml

@@ -220,6 +220,7 @@
 <ncdata dyn="se" hgrid="ne3np4"   nlev="32"             ic_ymd="101" >atm/cam/inic/se/cam6_QPC6_topo_ne3pg3_mg37_L32_01-01-31_c221214.nc</ncdata>
 <ncdata dyn="se" hgrid="ne3np4"   nlev="58"             ic_ymd="101" >atm/cam/inic/se/cam6_QPC6_topo_ne3pg3_mg37_L58_01-01-31_c221214.nc</ncdata>
 <ncdata dyn="se" hgrid="ne3np4"   nlev="93"             ic_ymd="101" >atm/cam/inic/se/cam6_QPC6_topo_ne3pg3_mg37_L93_01-01-31_c221214.nc</ncdata>
+<ncdata dyn="se" hgrid="ne5np4"   nlev="30"             ic_ymd="101" >atm/cam/inic/homme/cami-mam3_0000-01_ne5np4_L30.140707.nc</ncdata>
 <ncdata dyn="se" hgrid="ne5np4"   nlev="32"             ic_ymd="101" >atm/cam/inic/se/F2000climo_ne5pg3_mg37_L32_01-01-31_c230520.nc</ncdata>
 <ncdata dyn="se" hgrid="ne5np4"   nlev="58"             ic_ymd="101" >atm/cam/inic/se/F2000climo_ne5pg3_mg37_L58_01-01-31_c230520.nc</ncdata>
 
@@ -2960,6 +2961,7 @@
 <fv3_nwat phys="adiabatic"                                                  > 1         </fv3_nwat>
 <fv3_nwat phys="kessler"                                                    > 3         </fv3_nwat>
 <fv3_nwat phys="tj2016"                                                     > 1         </fv3_nwat>
+<fv3_nwat phys="grayrad"                                                    > 1         </fv3_nwat>
 <fv3_fv_sg_adj                                                              > 0         </fv3_fv_sg_adj>
 <fv3_grid_type                                                              > 0         </fv3_grid_type>
 <fv3_hord_dp        dyn="fv3"                                               > -10        </fv3_hord_dp>
@@ -3185,7 +3187,6 @@
   'SolIonRate_Tot = jeuv_1 + jeuv_2 + jeuv_3 + jeuv_4 + jeuv_5 + jeuv_6 + jeuv_7 + jeuv_8 + jeuv_9 + jeuv_10 + jeuv_11 + ',
                    'jeuv_14 + jeuv_15 + jeuv_16 + jeuv_17 + jeuv_18 + jeuv_19 + jeuv_20 + jeuv_21 + jeuv_22 + jeuv_23',
 </rxn_rate_sums>
-
 <rxn_rate_sums chem="trop_strat_mam5_ts2">
     'O3_Prod = NO_HO2 + CH3O2_NO + HOCH2OO_NO + C2H5O2_NO + CH3CO3_NO + EO2_NO + C3H7O2_NO + PO2_NO + ',
                'RO2_NO + ENEO2_NO + MACRO2_NOa + jhonitr + ',

bld/namelist_files/namelist_definition.xml

@@ -53,6 +53,7 @@
           This is an optional attribute that is mainly useful for variables
           that have only a small number of allowed values.
                                                                         -->
+
 <!-- Frierson Simple Physics Parameters -->
 
 <entry id="frierson_Wind_min" type="real" category="frierson"
@@ -2951,7 +2952,7 @@ Default: .false.
 <entry id="hetfrz_bc_scalfac" type="real" category="microphys"
        group="hetfrz_classnuc_nl" valid_values="" >
 Heterogeneous freezing scaling factor for black carbon aerosols.
-Default: 0.0
+Default: 0.01
 </entry>
 
 <entry id="hetfrz_dust_scalfac" type="real" category="microphys"
@@ -5096,6 +5097,7 @@ Force emission year for HEMCO clock if positive. This will force cycling of data
 Default: set by build-namelist for climo cases, otherwise -1 to use model clock.
 </entry>
 
+
 <!-- Reference Pressures -->
 
 <entry id="trop_cloud_top_press" type="real" category="press_lim"

cime_config/config_component.xml

@@ -62,8 +62,8 @@
   <!--
     ===============
      HEMCO Options
-     ===============
-   -->
+    ===============
+  -->
     <desc option="HEMCO"        >With Harmonized Emissions Component (HEMCO) for chemistry:</desc>
 
   <!--
@@ -86,8 +86,8 @@
     <desc option="ADIAB"        >CAM dry adiabatic configurarion (no physics forcing):</desc>
     <desc option="DABIP04"      >CAM dry adiabatic baroclinic instability (Polvani et al., 2004):</desc>
     <desc option="TJ16"         >CAM moist Held-Suarez forcing (Thatcher and Jablonowski, 2016):</desc>
-    <desc option="HS94"         >CAM dry Held-Suarez forcing (Held and Suarez (1994)):</desc>
     <desc option="GRAYRAD"      >CAM moist simple model (Frierson, 2006):</desc>
+    <desc option="HS94"         >CAM dry Held-Suarez forcing (Held and Suarez (1994)):</desc>
     <desc option="KESSLER"      >CAM moist dynamical core test with Ullrich et al. (2014) baroclinic wave IC, Kessler physics and terminator chemistry:</desc>
 
   <!--
@@ -181,8 +181,8 @@
       <value compset="_CAM\d0%CC.*%SDYN">-nlev 56</value>
       <value compset="_CAM\d0%WC.*%SDYN">-nlev 88</value>
       <value compset="_CAM\d0%WX.*%SDYN">-nlev 145</value>
-      <value compset="_CAM.*%L58">-nlev 58 -model_top lt</value>
-      <value compset="_CAM.*%L93">-nlev 93 -model_top mt</value>
+      <value compset="_CAM.*%LT">-nlev 58 -model_top lt</value>
+      <value compset="_CAM.*%MT">-nlev 93 -model_top mt</value>
 
       <!-- Simple models -->
       <value compset="_CAM%ADIAB">-phys adiabatic</value>

cime_config/config_compsets.xml

@@ -86,7 +86,7 @@
 
   <compset>
     <alias>FLTHIST_v0d</alias>
-    <lname>HIST_CAM%DEV%GHGMAM4_CLM51%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
+    <lname>HIST_CAM%DEV%LT%GHGMAM4_CLM51%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
   </compset>
 
   <compset>
@@ -408,11 +408,6 @@
     <lname>HIST_CAM60%SDYN_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_SGLC_SWAV</lname>
   </compset>
 
-  <compset>
-    <alias>FGRAYRAD</alias>
-    <lname>2000_CAM%GRAYRAD_SLND_SICE_SOCN_SROF_SGLC_SWAV</lname>
-  </compset>
-
   <compset>
     <alias>FMOZ</alias>
     <lname>2000_CAM40%TMOZ_CLM45%SP_CICE%PRES_DOCN%DOM_RTM_SGLC_SWAV</lname>
@@ -428,6 +423,10 @@
     <lname>HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_SROF_SGLC_SWAV</lname>
   </compset>
 
+  <compset>
+    <alias>FGRAYRAD</alias>
+    <lname>2000_CAM%GRAYRAD_SLND_SICE_SOCN_SROF_SGLC_SWAV</lname>
+  </compset>
 
   <!-- ****************************** -->
   <!-- WACCM science supported compsets -->

cime_config/config_pes.xml

@@ -333,60 +333,6 @@
   </grid>
   <grid name="a%ne30" >
     <mach name="cheyenne">
-      <pes pesize="any" compset="_CAM%DEV%LT%GHGMAM4_">
-	<comment>none</comment>
-	<ntasks>
-	  <ntasks_atm>-8</ntasks_atm>
-	  <ntasks_lnd>-8</ntasks_lnd>
-	  <ntasks_rof>-8</ntasks_rof>
-	  <ntasks_ice>-8</ntasks_ice>
-	  <ntasks_ocn>-8</ntasks_ocn>
-	  <ntasks_cpl>-8</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_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_cpl>0</rootpe_cpl>
-	</rootpe>
-      </pes>
-      <pes pesize="any" compset="_CAM%DEV%MT%GHGMAM4_">
-	<comment>none</comment>
-	<ntasks>
-	  <ntasks_atm>-12</ntasks_atm>
-	  <ntasks_lnd>-12</ntasks_lnd>
-	  <ntasks_rof>-12</ntasks_rof>
-	  <ntasks_ice>-12</ntasks_ice>
-	  <ntasks_ocn>-12</ntasks_ocn>
-	  <ntasks_cpl>-12</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_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_cpl>0</rootpe_cpl>
-	</rootpe>
-      </pes>
       <pes pesize="any" compset="_CAM.*%(CC|WC|CV|CF)">
         <comment>none</comment>
         <ntasks>

doc/ChangeLog

@@ -1,94 +1,5 @@
 ===============================================================
 
-Tag name: cam6_3_124
-Originator(s): fvitt
-Date: 23 Aug 2023
-One-line Summary: Fix issues exposed by FMTHIST; add regression tests for FLTHIST and FMTHIST
-Github PR URL: https://github.com/ESCOMP/CAM/pull/872
-
-Purpose of changes (include the issue number and title text for each relevant GitHub issue):
-
- Fix memory issue in code that reads input data on the native unstructured model grid.
- Fix floating point exception issue in aerosol wet deposition caused by undefined values in
- BERGSO (conversion of cloud water to snow) above above pumus active region
-
- Address github issues:
-   Increase PE layout for MT runs #812
-   Introduce regression tests for FLTHIST and FMTHIST #841
-
-Describe any changes made to build system: n/a
-
-Describe any changes made to the namelist: n/a
-
-List any changes to the defaults for the boundary datasets: n/a
-
-Describe any substantial timing or memory changes: n/a
-
-Code reviewed by: cacraigucar nusbaume
-
-List all files eliminated: n/a
-
-List all files added and what they do: n/a
-
-List all existing files that have been modified, and describe the changes:
-M       Externals.cfg
-M       bld/namelist_files/namelist_defaults_cam.xml
- - default spun-up IC file for L93 ne30 CAM-Chem-SE
-
-M       cime_config/config_compsets.xml
- - remove "_v0d" from FLTHIST and FMTHIST compset short names
-
-M       cime_config/config_pes.xml
- - set default PE layouts for FLTHIST and FMTHIST compsets
-
-M       cime_config/testdefs/testlist_cam.xml
- - add cheyenne regression tests for FLTHIST and FMTHIST compsets
-
-M       src/chemistry/utils/tracer_data.F90
- - remove unused ps field that was allocated using undefined sizes when
-   the input file was on the native unsctructured model grid
-
-M       src/dynamics/se/dyn_comp.F90
- - write "Molecular viscosity" message only if masterproc
-
-M       src/physics/cam_dev/micro_pumas_cam.F90
- - zero bergo field above top_lev
-
-If there were any failures reported from running test_driver.sh on any test
-platform, and checkin with these failures has been OK'd by the gatekeeper,
-then copy the lines from the td.*.status files for the failed tests to the
-appropriate machine below.  All failed tests must be justified.
-
-cheyenne/intel/aux_cam:
-  ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq9s (Overall: FAIL) details:
-    FAIL ERP_Ln9_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq9s COMPARE_base_rest
-  SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h (Overall: DIFF) details:
-    FAIL SMS_Lh12_Vnuopc.f09_f09_mg17.FCSD_HCO.cheyenne_intel.cam-outfrq3h BASELINE /glade/p/cesm/amwg/cesm_baselines/cam6_3_123: DIFF
-  ERP_Ln9_Vnuopc.ne30pg3_ne30pg3_mg17.FW2000climo.cheyenne_intel.cam-outfrq9s_wcm_ne30 (Overall: FAIL) details:
-    FAIL ERP_Ln9_Vnuopc.ne30pg3_ne30pg3_mg17.FW2000climo.cheyenne_intel.cam-outfrq9s_wcm_ne30 RUN time=287
-    PEND ERP_Ln9_Vnuopc.ne30pg3_ne30pg3_mg17.FW2000climo.cheyenne_intel.cam-outfrq9s_wcm_ne30 COMPARE_base_rest
-  - pre-extisting failures
-
-  ERP_D_Ln9.ne30pg3_ne30pg3_mg17.FLTHIST.cheyenne_intel.cam-outfrq9s (Overall: DIFF) details:
-    FAIL ERP_D_Ln9.ne30pg3_ne30pg3_mg17.FLTHIST.cheyenne_intel.cam-outfrq9s NLCOMP
-    FAIL ERP_D_Ln9.ne30pg3_ne30pg3_mg17.FLTHIST.cheyenne_intel.cam-outfrq9s BASELINE /glade/p/cesm/amwg/cesm_baselines/cam6_3_123: ERROR BFAIL baseline directory '/glade/p/cesm/amwg/cesm_baselines/cam6_3_123/ERP_D_Ln9.ne30pg3_ne30pg3_mg17.FLTHIST.cheyenne_intel.cam-outfrq9s' does not exist
-  SMS_D_Ln9.ne30pg3_ne30pg3_mg17.FMTHIST.cheyenne_intel.cam-outfrq9s (Overall: DIFF) details:
-    FAIL SMS_D_Ln9.ne30pg3_ne30pg3_mg17.FMTHIST.cheyenne_intel.cam-outfrq9s NLCOMP
-    FAIL SMS_D_Ln9.ne30pg3_ne30pg3_mg17.FMTHIST.cheyenne_intel.cam-outfrq9s BASELINE /glade/p/cesm/amwg/cesm_baselines/cam6_3_123: ERROR BFAIL baseline directory '/glade/p/cesm/amwg/cesm_baselines/cam6_3_123/SMS_D_Ln9.ne30pg3_ne30pg3_mg17.FMTHIST.cheyenne_intel.cam-outfrq9s' does not exist
-  - new tests
-
-izumi/nag/aux_cam:
-  DAE_Vnuopc.f45_f45_mg37.FHS94.izumi_nag.cam-dae (Overall: FAIL) details:
-    FAIL DAE_Vnuopc.f45_f45_mg37.FHS94.izumi_nag.cam-dae RUN time=10
-  - pre-extisting failure
-
-izumi/gnu/aux_cam: All PASS
-
-Summarize any changes to answers: bit-for-bit unchanged
-
-===============================================================
-===============================================================
-
 Tag name: cam6_3_123
 Originator(s): cacraig, jedwards, fvitt
 Date: August 16, 2023

src/chemistry/utils/tracer_data.F90

@@ -92,10 +92,10 @@ module tracer_data
      real(r8) :: one_yr = 0
      real(r8) :: curr_mod_time ! model time - calendar day
      real(r8) :: next_mod_time ! model time - calendar day - next time step
-     integer :: nlon = 0
-     integer :: nlat = 0
-     integer :: nlev = 0
-     integer :: nilev = 0
+     integer :: nlon
+     integer :: nlat
+     integer :: nlev
+     integer :: nilev
      integer :: ps_coords(3) ! LATDIM | LONDIM | TIMDIM
      integer :: ps_order(3) ! LATDIM | LONDIM | TIMDIM
      real(r8), pointer, dimension(:) :: lons => null()
@@ -104,6 +104,7 @@ module tracer_data
      real(r8), pointer, dimension(:) :: ilevs => null()
      real(r8), pointer, dimension(:) :: hyam => null()
      real(r8), pointer, dimension(:) :: hybm => null()
+     real(r8), pointer, dimension(:,:) :: ps => null()
      real(r8), pointer, dimension(:) :: hyai => null()
      real(r8), pointer, dimension(:) :: hybi => null()
      real(r8), pointer, dimension(:,:) :: weight_x => null(), weight_y => null()
@@ -339,6 +340,12 @@ subroutine trcdata_init( specifier, filename, filelist, datapath, flds, file, &
        lat_dimid = old_dimid
     endif
 
+    allocate( file%ps(file%nlon,file%nlat), stat=astat )
+    if( astat /= 0 ) then
+       write(iulog,*) 'trcdata_init: file%ps allocation error = ',astat
+       call endrun('trcdata_init: failed to allocate x array')
+    end if
+
     call pio_seterrorhandling(File%curr_fileid, PIO_BCAST_ERROR, oldmethod=err_handling)
     ierr = pio_inq_varid( file%curr_fileid, 'PS', file%ps_id )
     file%has_ps = (ierr==PIO_NOERR)
@@ -428,6 +435,11 @@ subroutine trcdata_init( specifier, filename, filelist, datapath, flds, file, &
           ierr = pio_get_var( file%curr_fileid, varid, file%hybi )
        endif
 
+       allocate( file         %ps  (pcols,begchunk:endchunk), stat=astat   )
+       if( astat/= 0 ) then
+          write(iulog,*) 'trcdata_init: failed to allocate file%ps array; error = ',astat
+          call endrun
+       end if
        allocate( file%ps_in(1)%data(pcols,begchunk:endchunk), stat=astat   )
        if( astat/= 0 ) then
           write(iulog,*) 'trcdata_init: failed to allocate file%ps_in(1)%data array; error = ',astat

src/dynamics/se/dyn_comp.F90

@@ -763,10 +763,8 @@ subroutine dyn_init(dyn_in, dyn_out)
           (hvcoord%hyam(:)+hvcoord%hybm(:))*hvcoord%ps0,km_sponge_factor,&
           kmvis_ref,kmcnd_ref,rho_ref)
 
-     if (masterproc) then
-        write(iulog,*) "Molecular viscosity and thermal conductivity reference profile"
-        write(iulog,*) "k, p, z, km_sponge_factor, kmvis_ref/rho_ref, kmcnd_ref/(cp*rho_ref):"
-     end if
+     write(iulog,*) "Molecular viscoity and thermal conductivity reference profile"
+     write(iulog,*) "k, p, z, km_sponge_factor, kmvis_ref/rho_ref, kmcnd_ref/(cp*rho_ref):"
      do k=1,nlev
        ! only apply molecular viscosity where viscosity is > 1000 m/s^2
        if (MIN(kmvis_ref(k)/rho_ref(k),kmcnd_ref(k)/(cpair*rho_ref(k)))>1000.0_r8) then

src/physics/cam_dev/micro_pumas_cam.F90

@@ -2498,7 +2498,6 @@ subroutine micro_pumas_cam_tend(state, ptend, dtime, pbuf)
 
    !Copy pbuf field from proc_rates back to pbuf pointer
    bergstot(:ncol,top_lev:) = proc_rates%bergstot(:ncol,1:nlev)
-   bergstot(:ncol,1:top_lev-1) = 0._r8
 
    ! ------------------------------------------------------ !
    ! ------------------------------------------------------ !
@@ -2629,7 +2628,6 @@ subroutine micro_pumas_cam_tend(state, ptend, dtime, pbuf)
       nmultgo_grid(:ncol,:top_lev-1) = 0._r8
       nmultrgo_grid(:ncol,:top_lev-1) = 0._r8
       npsacwgo_grid(:ncol,:top_lev-1) = 0._r8
-      bergso_grid(:ncol,:top_lev-1) = 0._r8
 
       ! These pbuf fields need to be assigned.  There is no corresponding subcol_field_avg
       ! as they are reset before being used, so it would be a needless calculation