added some array intiailzaitons that resolves some of the issues

cime_config/testdefs/testmods_dirs/cam/outfrq9s/shell_commands

@@ -1,2 +1,3 @@
 ./xmlchange ROF_NCPL=\$ATM_NCPL
 ./xmlchange GLC_NCPL=\$ATM_NCPL
+./xmlchange CAM_CONFIG_OPTS='-phys cam_dev -microphys mg2' --append

cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/shell_commands

@@ -1,2 +1,3 @@
 ./xmlchange ROF_NCPL=\$ATM_NCPL
 ./xmlchange GLC_NCPL=\$ATM_NCPL
+./xmlchange CAM_CONFIG_OPTS='-phys cam6 -microphys mg2' --append

cime_config/testdefs/testmods_dirs/cam/outfrq9s_clubbmf/user_nl_cam

@@ -1,7 +1,9 @@
 mfilt=1,1,1,1,1,1
 ndens=1,1,1,1,1,1
 nhtfrq=9,9,9,9,9,9
+!nhtfrq=1,1,1,1,1,1
 inithist='ENDOFRUN'
+
 do_clubb_mf=.true.
 do_clubb_mf_diag=.true.
 do_clubb_mf_rad=.true.
@@ -10,15 +12,16 @@ deep_scheme='off'
 
 clubb_mf_nup = 25
 
-clubb_mf_Lopt = 6
-clubb_mf_up_ndt = 1
-clubb_mf_a0 = 2.0D0
-clubb_mf_b0 = 0.5D0
-clubb_mf_alphturb = 0.0D0
-clubb_mf_max_L0 = 733.34D0
+!clubb_mf_Lopt = 6
+!clubb_mf_up_ndt = 1
+!clubb_mf_a0 = 2.0D0
+!clubb_mf_b0 = 0.5D0
+!clubb_mf_max_L0 = 1000.0D0
+!clubb_mf_alphturb = 3.0D0
+!do_clubb_mf_rhtke = .true.
 
-clubb_mf_fdd = 0.5
-do_clubb_mf_coldpool = .true.
-clubb_mf_cp_ndt = 1
-clubb_mf_ddalph = 250.
-clubb_mf_ddbeta = 1.0
+!clubb_mf_fdd = 0.5
+!do_clubb_mf_coldpool = .true.
+!clubb_mf_cp_ndt = 1
+!clubb_mf_ddalph = 500.
+!clubb_mf_ddbeta = 1.0

src/control/cam_snapshot_common.F90

@@ -86,7 +86,10 @@ module cam_snapshot_common
 type (snapshot_type)    ::  tend_snapshot(6)
 type (snapshot_type)    ::  cam_in_snapshot(30)
 type (snapshot_type)    ::  cam_out_snapshot(30)
-type (snapshot_type_nd) ::  pbuf_snapshot(250)
+!+++ARH
+!type (snapshot_type_nd) ::  pbuf_snapshot(250)
+type (snapshot_type_nd) ::  pbuf_snapshot(350)
+!---ARH
 
 contains
 

src/cpl/nuopc/atm_comp_nuopc.F90

@@ -910,6 +910,14 @@ subroutine DataInitialize(gcomp, rc)
           call export_fields( gcomp, model_mesh, model_clock, cam_out, rc=rc )
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
        else
+!+++ARH
+       if (masterproc) then
+          write(iam+1000,*) '--------------'
+          write(iam+1000,*) 'DataInitialize'
+          write(iam+1000,*) '  cam_run1 sets cam_out'
+          write(iam+1000,*) '  nstep=',get_nstep()
+       end if
+!---ARH
           call cam_read_srfrest( gcomp, clock, rc=rc )
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
           call import_fields( gcomp, cam_in, restart_init=.true., rc=rc )
@@ -1093,6 +1101,14 @@ subroutine ModelAdvance(gcomp, rc)
        call import_fields( gcomp, cam_in, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
        call t_stopf  ('CAM_import')
+!+++ARH
+       if (masterproc) then
+          write(iam+1000,*) '--------------'
+          write(iam+1000,*) 'Model Advance'
+          write(iam+1000,*) '  CAM_import sets cam_in'
+          write(iam+1000,*) '  nstep=',get_nstep()
+       end if
+!---ARH
     end if
 
     dosend = .false.
@@ -1145,6 +1161,15 @@ subroutine ModelAdvance(gcomp, rc)
             yr_spec=yr_sync, mon_spec=mon_sync, day_spec=day_sync, sec_spec=tod_sync)
        call t_stopf  ('CAM_run4')
 
+!+++ARH
+       if (masterproc) then
+          write(iam+1000,*) '--------------'
+          write(iam+1000,*) 'ModelAdvance'
+          write(iam+1000,*) '  cam_run2,cam_run3,cam_run4'
+          write(iam+1000,*) '  nstep=',get_nstep()
+       end if
+!---ARH
+
        ! Advance cam time step
 
        call t_startf ('CAM_adv_timestep')
@@ -1157,6 +1182,15 @@ subroutine ModelAdvance(gcomp, rc)
        call cam_run1 ( cam_in, cam_out )
        call t_stopf  ('CAM_run1')
 
+!+++ARH
+       if (masterproc) then
+          write(iam+1000,*) '--------------'
+          write(iam+1000,*) 'ModelAdvance'
+          write(iam+1000,*) '  CAM_adv_timestep,cam_run1'
+          write(iam+1000,*) '  nstep=',get_nstep()
+       end if
+!---ARH
+
     end do
 
     if (mediator_present) then

src/physics/cam/clubb_intr.F90

@@ -2128,10 +2128,12 @@ subroutine clubb_ini_cam(pbuf2d)
          call add_default( 'edmf_uflx'     , 1, ' ')
          call add_default( 'edmf_vflx'     , 1, ' ')
          call add_default( 'edmf_qtflx'    , 1, ' ')
+!+++ARH - not bfb
          call add_default( 'edmf_thlforcup', 1, ' ')
          call add_default( 'edmf_qtforcup' , 1, ' ')
          call add_default( 'edmf_thlforcdn', 1, ' ')
          call add_default( 'edmf_qtforcdn' , 1, ' ')
+!---ARH
          call add_default( 'edmf_thlforc'  , 1, ' ')
          call add_default( 'edmf_qtforc'   , 1, ' ')
          call add_default( 'edmf_sqtup'    , 1, ' ')
@@ -3941,6 +3943,9 @@ subroutine clubb_tend_cam( state,   ptend_all,   pbuf,     hdtime, &
     ! pressure,exner on momentum grid needed for mass flux calc.
     if (do_clubb_mf) then
 
+      kappa_zt(:,:) = 0._r8
+      qc_zt(:,:) = 0._r8
+      invrs_exner_zt(:,:) = 0._r8
       do k=1,pver
         do i=1,ncol
           kappa_zt(i,k+1) = (rairv(i,pver-k+1,lchnk)/cpairv(i,pver-k+1,lchnk))
@@ -3953,15 +3958,19 @@ subroutine clubb_tend_cam( state,   ptend_all,   pbuf,     hdtime, &
       qc_zt(:ncol,1) = qc_zt(:ncol,2)
       invrs_exner_zt(:ncol,1) = invrs_exner_zt(:ncol,2)
 
+      kappa_zm(:,:) = 0._r8
       kappa_zm(1:ncol,:) = zt2zm_api(pverp+1-top_lev, ncol, gr, kappa_zt(1:ncol,:))
 
+      p_in_Pa_zm(:,:) = 0._r8
+      invrs_exner_zm(:,:) = 0._r8
       do k=1,pverp
         do i=1,ncol
           p_in_Pa_zm(i,k) = state1%pint(i,pverp-k+1)
           invrs_exner_zm(i,k) = 1._r8/((p_in_Pa_zm(i,k)/p0_clubb)**(kappa_zm(i,k)))
         end do
       end do
 
+      th_sfc(:) = 0._r8
       th_sfc(1:ncol) = cam_in%ts(1:ncol)*invrs_exner_zm(1:ncol,1)
 
       call calc_ustar( ncol, state1%t(:ncol,pver), state1%pmid(:ncol,pver), cam_in%wsx(:ncol), cam_in%wsy(:ncol), &
@@ -4121,15 +4130,23 @@ subroutine clubb_tend_cam( state,   ptend_all,   pbuf,     hdtime, &
       if (do_clubb_mf) then
 
 
+        dzt(:,:) = 0._r8
         do k=2,pverp
           do i=1, ncol
             dzt(i,k) = zi_g(i,k) - zi_g(i,k-1)
           end do
         end do
 
         dzt(:ncol,1) = dzt(:ncol,2)
+
+        invrs_dzt(:,:) = 0._r8
         invrs_dzt(:ncol,:) = 1._r8/dzt(:ncol,:)
 
+        rtm_zm_in(:,:) = 0._r8
+        thlm_zm_in(:,:) = 0._r8
+        th_zm(:,:) = 0._r8
+        qv_zm(:,:) = 0._r8
+        qc_zm(:,:) = 0._r8
         rtm_zm_in(1:ncol,:)  = zt2zm_api( pverp+1-top_lev, ncol, gr, rtm_in(1:ncol,:) )
         thlm_zm_in(1:ncol,:) = zt2zm_api( pverp+1-top_lev, ncol, gr, thlm_in(1:ncol,:) )
         th_zm(1:ncol,:)      = zt2zm_api( pverp+1-top_lev, ncol, gr, th_zt(1:ncol,:) )
@@ -4243,12 +4260,18 @@ subroutine clubb_tend_cam( state,   ptend_all,   pbuf,     hdtime, &
 
 
         ! pass MF turbulent advection term as CLUBB explicit forcing term
-        rtm_forcing(:ncol,1)  = 0._r8
-        thlm_forcing(:ncol,1) = 0._r8
-        mf_qtforcup(:ncol,1)  = 0._r8
-        mf_thlforcup(:ncol,1) = 0._r8
-        mf_qtforcdn(:ncol,1)  = 0._r8
-        mf_thlforcdn(:ncol,1) = 0._r8
+        !rtm_forcing(:ncol,1)  = 0._r8
+        !thlm_forcing(:ncol,1) = 0._r8
+        !mf_qtforcup(:ncol,1)  = 0._r8
+        !mf_thlforcup(:ncol,1) = 0._r8
+        !mf_qtforcdn(:ncol,1)  = 0._r8
+        !mf_thlforcdn(:ncol,1) = 0._r8
+        rtm_forcing(:ncol,:)  = 0._r8
+        thlm_forcing(:ncol,:) = 0._r8
+        mf_qtforcup(:ncol,:)  = 0._r8
+        mf_thlforcup(:ncol,:) = 0._r8
+        mf_qtforcdn(:ncol,:)  = 0._r8
+        mf_thlforcdn(:ncol,:) = 0._r8
 
         do k=2,pverp
           do i=1, ncol
@@ -4756,6 +4779,8 @@ subroutine clubb_tend_cam( state,   ptend_all,   pbuf,     hdtime, &
     wp2_zt  = zm2zt_api( pverp+1-top_lev, ncol, gr, wp2_in )
 
     ! Need moist_qc and cloudfrac on thermo grid for output
+    mf_qc_zt(:,:) = 0._r8
+    mf_cloudfrac_zt(:,:) = 0._r8
     mf_qc_zt = zm2zt_api( pverp+1-top_lev, ncol, gr, mf_qc)
     mf_cloudfrac_zt = zm2zt_api( pverp+1-top_lev, ncol, gr, mf_cloudfrac)
 
@@ -4908,9 +4933,15 @@ subroutine clubb_tend_cam( state,   ptend_all,   pbuf,     hdtime, &
             mf_sqtup_output(i,pverp-k+1)              = mf_sqtup(i,k)
             mf_sqtdn_output(i,pverp-k+1)              = mf_sqtdn(i,k)
 
+!+++ARH not bfb
             mf_cloudfrac_output(i,pverp-k+1)          = mf_cloudfrac_zt(i,k)
+            !mf_cloudfrac_output(i,pverp-k+1)          = mf_cloudfrac(i,k)
+
             mf_ent_output(i,pverp-k+1)                = mf_ent_nadv(i,k)
+
+!+++ARH not bfb
             mf_qc_output(i,pverp-k+1)                 = mf_qc_zt(i,k)
+            !mf_qc_output(i,pverp-k+1)                 = mf_qc(i,k)
           end if
 
           mf_upa_flip(i,pverp-k+1,:clubb_mf_nup)       = mf_upa(i,k,:clubb_mf_nup)
@@ -5486,7 +5517,9 @@ subroutine clubb_tend_cam( state,   ptend_all,   pbuf,     hdtime, &
 
     deepcu(:,:) = 0.0_r8
     shalcu(:,:) = 0.0_r8
-
+!+++ARH
+    sh_icwmr(:,:) = 0.0_r8
+!---ARH 
     do k=1,pver-1
       do i=1,ncol
          !  diagnose the deep convective cloud fraction, as done in macrophysics based on the 

src/physics/cam/clubb_mf.F90

@@ -567,6 +567,12 @@ subroutine integrate_mf( nz,
      dynamic_L0 = 0._r8
      ztop = 0._r8
 
+!+++ARH - uncomment to recover bgb restarts
+!     ddcp = 0._r8
+!     ztopm1 = zm(1)
+!     return
+!---ARH
+
      if (bsort) then
        niter_xc = 3
        limarea = .true.
@@ -1424,6 +1430,15 @@ subroutine integrate_mf( nz,
          vflx(k)    = vflxup(k) + vflxdn(k) 
        enddo
 
+!+++ARH - uncomment bfb restarts (state only, clubb+mf diags still not bfb)
+!       thlflx = 0._r8
+!       qtflx = 0._r8
+!       sqt = 0_r8
+!       sthl = 0._r8
+!       moist_a = 0._r8
+!       moist_qc = 0._r8
+!---ARH
+
      else
        ddcp = 0._r8
        ztopm1 = zm(1)