ESCOMP · cacraigucar · Dec 3, 2020 · Sep 16, 2020 · Sep 16, 2020 · Sep 17, 2020
diff --git a/bld/build-namelist b/bld/build-namelist
@@ -3046,6 +3046,11 @@ if ($clubb_sgs  =~ /$TRUE/io) {
    add_default($nl, 'clubb_l_vert_avg_closure');
    add_default($nl, 'clubb_l_diag_Lscale_from_tau');
    add_default($nl, 'clubb_l_damp_wp2_using_em');
+   add_default($nl, 'do_clubb_mf');
+   add_default($nl, 'do_clubb_mf_diag');
+   add_default($nl, 'clubb_mf_L0');
+   add_default($nl, 'clubb_mf_ent0');
+   add_default($nl, 'clubb_mf_nup');
 }
 
 # Tuning for wet scavenging of modal aerosols

diff --git a/bld/namelist_files/namelist_defaults_cam.xml b/bld/namelist_files/namelist_defaults_cam.xml
@@ -1853,6 +1853,13 @@
 <clubb_l_diag_Lscale_from_tau           silhs="1" > .false. </clubb_l_diag_Lscale_from_tau>
 <clubb_l_damp_wp2_using_em              silhs="1" > .true.  </clubb_l_damp_wp2_using_em>
 
+<!-- CLUBB+MF options -->
+<do_clubb_mf                       > .false. </do_clubb_mf>
+<do_clubb_mf_diag                  > .false. </do_clubb_mf_diag>
+<clubb_mf_L0                       > 50.0    </clubb_mf_L0>
+<clubb_mf_ent0                     > 0.22    </clubb_mf_ent0>
+<clubb_mf_nup                      > 10      </clubb_mf_nup>
+
 <!-- Microphysics scheme -->
 <micro_mg_do_hail                       > .false. </micro_mg_do_hail>
 <micro_mg_do_graupel                    > .false. </micro_mg_do_graupel>

diff --git a/bld/namelist_files/namelist_definition.xml b/bld/namelist_files/namelist_definition.xml
@@ -3692,6 +3692,40 @@ energy.
 Default: true
 </entry>
 
+<!-- for CLUBB+MF -->
+<entry id="do_clubb_mf" type="logical" category="conv"
+       group="clubb_mf_nl" valid_values="" >
+If .true. add ensemble mass fluxes to CLUBB's higher-order equation set. 
+Together with CLUBB, this constitutes an eddy-diffusivity mass-flux approach. 
+Default: .false.
+</entry>
+
+<entry id="do_clubb_mf_diag" type="logical" category="conv"
+       group="clubb_mf_nl" valid_values="" >
+If .true. add detailed budget terms to output by default.  Note that do_clubb_mf must also be set to .true.
+Default: .false.
+</entry>
+
+<entry id="clubb_mf_L0" type="real" category="conv"
+       group="clubb_mf_nl" valid_values="" >
+Entrainment length scale in meters for individual plumes. Not used if
+do_clubb_mf=FALSE.
+Default: 50.0
+</entry>
+
+<entry id="clubb_mf_ent0" type="real" category="conv"
+       group="clubb_mf_nl" valid_values="" >
+Entrainment efficiency for individual plumes. Not used if
+do_clubb_mf=FALSE.
+Default: 0.22
+</entry>
+
+<entry id="clubb_mf_nup" type="integer" category="conv"
+       group="clubb_mf_nl" valid_values="" >
+Real: number of plumes in mass flux ensemble
+Default: 10
+</entry>
+
 <!-- CARMA Sectional Microphysics -->
 
 <entry id="carma_model" type="char*32" category="carma"

diff --git a/cime_config/testdefs/testlist_cam.xml b/cime_config/testdefs/testlist_cam.xml
@@ -174,6 +174,15 @@
     <options>
       <option name="wallclock">00:10:00</option>
     </options>
+<!--  Replace f10_f10_mg37 with CAM-SE-CSLAM grid when ready -->
+  </test>
+  <test compset="QPC6" grid="ne5pg3_ne5pg3_mg37" name="ERP_Ln9" testmods="cam/outfrq9s_clubbmf">
+    <machines>
+      <machine name="izumi" compiler="nag" category="aux_cam"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:10:00</option>
+    </options>
   </test>
   <test compset="QPRCEMIP" grid="ne30_ne30_mg17" name="ERP_Ln9" testmods="cam/outfrq9s">
     <machines>

diff --git a/cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/shell_commands b/cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/shell_commands
@@ -0,0 +1,2 @@
+./xmlchange ROF_NCPL=\$ATM_NCPL
+./xmlchange GLC_NCPL=\$ATM_NCPL
diff --git a/cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/user_nl_cam b/cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/user_nl_cam
@@ -0,0 +1,7 @@
+mfilt=1,1,1,1,1,1
+ndens=1,1,1,1,1,1
+nhtfrq=9,9,9,9,9,9
+inithist='ENDOFRUN'
+do_clubb_mf=.true.
+do_clubb_mf_diag=.true.
+deep_scheme='off'
diff --git a/cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/user_nl_clm b/cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/user_nl_clm
@@ -0,0 +1,27 @@
+!----------------------------------------------------------------------------------
+! 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 $inst_string for multi-ensemble cases)
+! Set glc_grid           with CISM_GRID                          option
+! Set glc_smb            with GLC_SMB                            option
+! Set maxpatch_glcmec    with GLC_NEC                            option
+! Set glc_do_dynglacier  with GLC_TWO_WAY_COUPLING               env variable
+!----------------------------------------------------------------------------------
+hist_nhtfrq = 9
+hist_mfilt  = 1
+hist_ndens  = 1
+
diff --git a/cime_config/usermods_dirs/scam_SAS/user_nl_cam b/cime_config/usermods_dirs/scam_SAS/user_nl_cam
@@ -1,6 +1,4 @@
 use_gw_front            = .false.
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/SAS_ideal_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-06-01-00000.nc"
 mfilt=30

diff --git a/cime_config/usermods_dirs/scam_arm95/user_nl_cam b/cime_config/usermods_dirs/scam_arm95/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-07-01-00000.nc"
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/ARM95_4scam.nc"
 mfilt=1500

diff --git a/cime_config/usermods_dirs/scam_arm97/user_nl_cam b/cime_config/usermods_dirs/scam_arm97/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/ARM97_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-06-01-00000.nc"
 mfilt=2088

diff --git a/cime_config/usermods_dirs/scam_atex/user_nl_cam b/cime_config/usermods_dirs/scam_atex/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/ATEX_48hr_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-02-01-00000.nc"
 mfilt=2088

diff --git a/cime_config/usermods_dirs/scam_bomex/user_nl_cam b/cime_config/usermods_dirs/scam_bomex/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/BOMEX_5day_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-06-01-00000.nc"
 mfilt=2088

diff --git a/cime_config/usermods_dirs/scam_cgilsS11/user_nl_cam b/cime_config/usermods_dirs/scam_cgilsS11/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/S11_CTL_MixedLayerInit_reduced.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-07-01-00000.nc"
 mfilt=2088

diff --git a/cime_config/usermods_dirs/scam_cgilsS12/user_nl_cam b/cime_config/usermods_dirs/scam_cgilsS12/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/S12_CTL_MixedLayerInit_reduced.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-07-01-00000.nc"
 mfilt=2088

diff --git a/cime_config/usermods_dirs/scam_cgilsS6/user_nl_cam b/cime_config/usermods_dirs/scam_cgilsS6/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/S6_CTL_reduced.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-07-01-00000.nc"
 mfilt=2088

diff --git a/cime_config/usermods_dirs/scam_dycomsRF01/user_nl_cam b/cime_config/usermods_dirs/scam_dycomsRF01/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/DYCOMSrf01_4day_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-07-01-00000.nc"
 mfilt=2088

diff --git a/cime_config/usermods_dirs/scam_dycomsRF02/user_nl_cam b/cime_config/usermods_dirs/scam_dycomsRF02/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/DYCOMSrf02_48hr_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-07-01-00000.nc"
 mfilt=2088

diff --git a/cime_config/usermods_dirs/scam_gateIII/user_nl_cam b/cime_config/usermods_dirs/scam_gateIII/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/GATEIII_4scam_c170809.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-08-01-00000.nc"
 mfilt=1440

diff --git a/cime_config/usermods_dirs/scam_mpace/user_nl_cam b/cime_config/usermods_dirs/scam_mpace/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/MPACE_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-10-01-00000.nc"
 mfilt=1242

diff --git a/cime_config/usermods_dirs/scam_rico/user_nl_cam b/cime_config/usermods_dirs/scam_rico/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/RICO_3day_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-07-01-00000.nc"
 mfilt=2088

diff --git a/cime_config/usermods_dirs/scam_sparticus/user_nl_cam b/cime_config/usermods_dirs/scam_sparticus/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/SPARTICUS_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-04-01-00000.nc"
 mfilt=2156

diff --git a/cime_config/usermods_dirs/scam_togaII/user_nl_cam b/cime_config/usermods_dirs/scam_togaII/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/TOGAII_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-12-01-00000.nc"
 mfilt=9

diff --git a/cime_config/usermods_dirs/scam_twp06/user_nl_cam b/cime_config/usermods_dirs/scam_twp06/user_nl_cam
@@ -1,5 +1,3 @@
-scmlon=$PTS_LON
-scmlat=$PTS_LAT
 iopfile="$DIN_LOC_ROOT/atm/cam/scam/iop/TWP06_4scam.nc"
 ncdata="$DIN_LOC_ROOT/atm/cam/scam/iop/CESM2.F2000climo.IOP_SITES.cam.i.0003-01-01-00000.nc"
 mfilt=1926

diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,5 +1,123 @@
 ===============================================================
 
+Tag name: cam6_3_006
+Originator(s): herrington, cacraig
+Date: Dec 2, 2020
+One-line Summary: Initial implementation of mass fluxes in CLUBB (CLUBB+MF) & scam bug-fix
+Github PR URL: https://github.com/ESCOMP/CAM/pull/221
+
+Purpose of changes (include the issue number and title text for each relevant GitHub issue):
+ - Implement CLUBB-MF functionality on trunk (#181)
+ - FSCAM is failing prealpha test (#213)
+ -   scmlat/scmlon nl's removed in prior tag, but still being set for scam cases
+ - Add back in TR8 and TGIT regression tests (#281)
+
+Describe any changes made to build system: NA
+
+Describe any changes made to the namelist:
+  - created namelist group clubb_mf_nl and added namelist variables: do_clubb_mf, do_clubb_mf_diag, lubb_mf_L0, 
+       clubb_mf_ent0 and clubb_mf_nup
+  - removed scmlat/scmlon declarations in user_nl_cam for scam cases in cime_config/usermods_dirs/scam_xxx
+
+List any changes to the defaults for the boundary datasets: NA
+
+Describe any substantial timing or memory changes: NA
+
+Code reviewed by: cacraig, goldy, eaton, nusbaume
+
+List all files eliminated:
+
+List all files added and what they do:
+A       src/physics/cam/clubb_mf.F90
+           - new mass flux subroutine
+
+A       cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/shell_commands
+A       cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/user_nl_cam
+A       cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/user_nl_clm
+           - settings for the clubbmf test
+
+List all existing files that have been modified, and describe the changes:
+
+M       bld/build-namelist
+           - added clubb_mf namelists in the do_clubb_sgs if statement
+
+M       bld/namelist_files/namelist_defaults_cam.xml
+           - added clubb_mf namelist defaults
+
+M       bld/namelist_files/namelist_definition.xml
+           - added clubb_mf namelist definitions
+
+M       cime_config/testdefs/testlist_cam.xml
+           - add new test for clubbmf
+
+M       cime_config/usermods_dirs/scam_SAS/user_nl_cam
+M       cime_config/usermods_dirs/scam_arm95/user_nl_cam
+M       cime_config/usermods_dirs/scam_arm97/user_nl_cam
+M       cime_config/usermods_dirs/scam_atex/user_nl_cam
+M       cime_config/usermods_dirs/scam_bomex/user_nl_cam
+M       cime_config/usermods_dirs/scam_cgilsS11/user_nl_cam
+M       cime_config/usermods_dirs/scam_cgilsS12/user_nl_cam
+M       cime_config/usermods_dirs/scam_cgilsS6/user_nl_cam
+M       cime_config/usermods_dirs/scam_dycomsRF01/user_nl_cam
+M       cime_config/usermods_dirs/scam_dycomsRF02/user_nl_cam
+M       cime_config/usermods_dirs/scam_gateIII/user_nl_cam
+M       cime_config/usermods_dirs/scam_mpace/user_nl_cam
+M       cime_config/usermods_dirs/scam_rico/user_nl_cam
+M       cime_config/usermods_dirs/scam_sparticus/user_nl_cam
+M       cime_config/usermods_dirs/scam_togaII/user_nl_cam
+M       cime_config/usermods_dirs/scam_twp06/user_nl_cam
+          - removed deprecated scm_lat/scm_lon entries from all scam user_nl_cam files
+
+M       src/dynamics/mpas/dp_coupling.F90
+M       src/dynamics/mpas/driver/cam_mpas_subdriver.F90
+          - fixed constants which needed an r8 or RKIND added to them
+
+M       src/physics/cam/clubb_intr.F90
+          - added call to mass flux routine (integrate_mf) defined in new module clubb_mf.F90
+          - additional variables required for input to mass flux routine have been defined
+          - added output fields for clubb_mf
+
+M       test/system/test_driver.sh
+          - add in TR8 and TGIT tests for izumi runs (output goes to the screen)
+
+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:
+
+izumi/nag/aux_cam:
+
+izumi/pgi/aux_cam:
+
+CAM tag used for the baseline comparison tests if different than previous
+tag:
+
+Summarize any changes to answers, i.e.,
+- what code configurations:
+- what platforms/compilers:
+- nature of change (roundoff; larger than roundoff but same climate; new
+  climate):
+ - namelist activating mass fluxes in this PR have been set to .false. in namelist_defaults
+ - so out of the box answers do not change. 
+
+If bitwise differences were observed, how did you show they were no worse
+than roundoff?
+
+If this tag changes climate describe the run(s) done to evaluate the new
+climate in enough detail that it(they) could be reproduced, i.e.,
+- source tag (all code used must be in the repository):
+- platform/compilers:
+- configure commandline:
+- build-namelist command (or complete namelist):
+- MSS location of output:
+
+MSS location of control simulations used to validate new climate:
+
+URL for AMWG diagnostics output used to validate new climate:
+===============================================================
+
 Tag name: cam6_3_005
 Originator(s): fvitt
 Date: 25 Nov 2020

diff --git a/src/dynamics/mpas/dp_coupling.F90 b/src/dynamics/mpas/dp_coupling.F90
@@ -740,8 +740,8 @@ subroutine dry_hydrostatic_pressure(nCells, nVertLevels, zz, zgrid, rho_zz, thet
    !
    ! TODO: Should temperature here be virtual temperature?
    !
-   ptop_int(:) = 2.0 * ptop_mid(:) &
-                 / (1.0 + exp( (zgrid(nVertLevels+1,:) - zgrid(nVertLevels,:)) * gravity / rgas / ttop_mid(:)))
+   ptop_int(:) = 2.0_r8 * ptop_mid(:) &
+                 / (1.0_r8 + exp( (zgrid(nVertLevels+1,:) - zgrid(nVertLevels,:)) * gravity / rgas / ttop_mid(:)))
 
 
    !
@@ -759,7 +759,7 @@ subroutine dry_hydrostatic_pressure(nCells, nVertLevels, zz, zgrid, rho_zz, thet
       pintdry(nVertLevels+1,iCell) = ptop_int(iCell)
       do k = nVertLevels, 1, -1
          pintdry(k,iCell) = pintdry(k+1,iCell) + gravity * zz(k,iCell) * rho_zz(k,iCell) * dz(k)
-         pmiddry(k,iCell) = 0.5 * (pintdry(k+1,iCell) + pintdry(k,iCell))
+         pmiddry(k,iCell) = 0.5_r8 * (pintdry(k+1,iCell) + pintdry(k,iCell))
       end do
    end do
 

diff --git a/src/dynamics/mpas/driver/cam_mpas_subdriver.F90 b/src/dynamics/mpas/driver/cam_mpas_subdriver.F90
@@ -1997,7 +1997,7 @@ subroutine cam_mpas_compute_unit_vectors()
 
           east(1,iCell) = -sin(lonCell(iCell))
           east(2,iCell) =  cos(lonCell(iCell))
-          east(3,iCell) =  0.0
+          east(3,iCell) =  0.0_RKIND
 
           ! Normalize
           east(1:3,iCell) = east(1:3,iCell) / sqrt(sum(east(1:3,iCell) * east(1:3,iCell)))
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		./xmlchange ROF_NCPL=\$ATM_NCPL
		./xmlchange GLC_NCPL=\$ATM_NCPL