Adopt progsigma (#1)

* Adopt progsigma "Add prognostic cumulus closure description in saSAS NCAR#903"
https://github.com/NCAR/ccpp-physics/pull/903/files
	modified:   GFS_DCNV_generic_post.F90
	modified:   GFS_DCNV_generic_post.meta
	modified:   GFS_DCNV_generic_pre.F90
	modified:   GFS_DCNV_generic_pre.meta
	modified:   GFS_MP_generic_post.F90
	modified:   GFS_MP_generic_post.meta
	modified:   GFS_SCNV_generic_post.F90
	modified:   GFS_SCNV_generic_post.meta
	modified:   GFS_SCNV_generic_pre.F90
	modified:   GFS_SCNV_generic_pre.meta
	modified:   GFS_suite_interstitial_3.F90
	modified:   GFS_suite_interstitial_3.meta
	new file:   progsigma_calc.f90
	modified:   samfdeepcnv.f
	modified:   samfdeepcnv.meta
	modified:   samfshalcnv.f
	modified:   samfshalcnv.meta
	modified:   satmedmfvdifq.F
	modified:   satmedmfvdifq.meta

* Adopt bugfixed progsigma "Bugfix and optimization of prognostic closure for the P8 physics suite NCAR#967"
https://github.com/NCAR/ccpp-physics/pull/967/files
	modified:   GFS_MP_generic_pre.F90
	modified:   GFS_MP_generic_pre.meta
	modified:   progsigma_calc.f90
	modified:   samfdeepcnv.f
	modified:   samfshalcnv.f

	modified:   physics/GFS_MP_generic_pre.F90
	modified:   physics/GFS_MP_generic_pre.meta
	modified:   physics/progsigma_calc.f90
	modified:   physics/samfdeepcnv.f
	modified:   physics/samfshalcnv.f

physics/GFS_DCNV_generic_post.F90

@@ -15,7 +15,7 @@ subroutine GFS_DCNV_generic_post_run (im, levs, lssav, ldiag3d, qdiag3d, ras, &
       index_of_temperature, index_of_x_wind, index_of_y_wind, ntqv, gq0, save_q,  &
       cnvw, cnvc, cnvw_phy_f3d, cnvc_phy_f3d, flag_for_dcnv_generic_tend,         &
       ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,                               &
-      ntgnc, nthl, nthnc, nthv, ntgv, ntrac,clw,                                  &
+      ntgnc, nthl, nthnc, nthv, ntgv, ntsigma, ntrac,clw,                                  &
       satmedmf, trans_trac, errmsg, errflg)
 
 
@@ -45,7 +45,7 @@ subroutine GFS_DCNV_generic_post_run (im, levs, lssav, ldiag3d, qdiag3d, ras, &
       integer, intent(in) :: dtidx(:,:), index_of_process_dcnv, index_of_temperature, &
            index_of_x_wind, index_of_y_wind, ntqv
       integer, intent(in) :: ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,   &
-                             ntgnc, nthl, nthnc, nthv, ntgv, ntrac
+                             ntgnc, nthl, nthnc, nthv, ntgv, ntsigma, ntrac
       real(kind=kind_phys), dimension(:,:,:), intent(in) :: clw
 
 
@@ -112,7 +112,7 @@ subroutine GFS_DCNV_generic_post_run (im, levs, lssav, ldiag3d, qdiag3d, ras, &
                      n /= ntrw  .and. n /= ntsw  .and. n /= ntrnc   .and. &
                      n /= ntsnc .and. n /= ntgl  .and. n /= ntgnc   .and. &
                      n /= nthl  .and. n /= nthnc .and. n /= nthv    .and. &
-                     n /= ntgv ) then
+                     n /= ntgv  .and. n /= ntsigma) then
                    tracers = tracers + 1
                    idtend = dtidx(100+n,index_of_process_dcnv)
                    if(idtend>0) then

physics/GFS_DCNV_generic_post.meta

@@ -356,6 +356,13 @@
   dimensions = ()
   type = logical
   intent = in
+[ntsigma]
+  standard_name = index_of_updraft_area_fraction_in_tracer_concentration_array
+  long_name = tracer index of updraft_area_fraction
+  units = index
+  dimensions = ()
+  type = integer
+  intent = in
 [ntcw]
   standard_name = index_of_cloud_liquid_water_mixing_ratio_in_tracer_concentration_array
   long_name = tracer index for cloud condensate (or liquid water)

physics/GFS_DCNV_generic_pre.F90

@@ -13,7 +13,7 @@ subroutine GFS_DCNV_generic_pre_run (im, levs, ldiag3d, qdiag3d, do_cnvgwd, cplc
                                          gu0, gv0, gt0, gq0, nsamftrac, ntqv,            &
                                          save_u, save_v, save_t, save_q, clw,            &
                                          ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,   &
-                                         ntgnc, nthl, nthnc, nthv, ntgv,                 &
+                                         ntgnc, nthl, nthnc, nthv, ntgv, ntsigma,        &
                                          cscnv, satmedmf, trans_trac, ras, ntrac,        &
                                          dtidx, index_of_process_dcnv, errmsg, errflg)
 
@@ -22,7 +22,7 @@ subroutine GFS_DCNV_generic_pre_run (im, levs, ldiag3d, qdiag3d, do_cnvgwd, cplc
       implicit none
 
       integer, intent(in) :: im, levs, nsamftrac, ntqv, index_of_process_dcnv, dtidx(:,:), &
-           ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,ntrac,ntgnc,nthl,nthnc,nthv,ntgv
+           ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,ntrac,ntgnc,nthl,nthnc,nthv,ntgv,ntsigma
       logical, intent(in) :: ldiag3d, qdiag3d, do_cnvgwd, cplchm
       real(kind=kind_phys), dimension(:,:),   intent(in)    :: gu0
       real(kind=kind_phys), dimension(:,:),   intent(in)    :: gv0
@@ -68,7 +68,7 @@ subroutine GFS_DCNV_generic_pre_run (im, levs, ldiag3d, qdiag3d, do_cnvgwd, cplc
                     n /= ntrw  .and. n /= ntsw  .and. n /= ntrnc   .and. &
                     n /= ntsnc .and. n /= ntgl  .and. n /= ntgnc   .and. &
                     n /= nthl  .and. n /= nthnc .and. n /= nthv    .and. &
-                    n /= ntgv ) then
+                    n /= ntgv  .and. n /= ntsigma) then
                   tracers = tracers + 1
                   if(dtidx(100+n,index_of_process_dcnv)>0) then
                      save_q(:,:,n) = clw(:,:,tracers)
@@ -87,4 +87,4 @@ subroutine GFS_DCNV_generic_pre_run (im, levs, ldiag3d, qdiag3d, do_cnvgwd, cplc
 
     end subroutine GFS_DCNV_generic_pre_run
 
-    end module GFS_DCNV_generic_pre
+    end module GFS_DCNV_generic_pre

physics/GFS_DCNV_generic_pre.meta

@@ -169,6 +169,13 @@
   dimensions = ()
   type = logical
   intent = in
+[ntsigma]
+  standard_name = index_of_updraft_area_fraction_in_tracer_concentration_array
+  long_name = tracer index of updraft_area_fraction
+  units = index
+  dimensions = ()
+  type = integer
+  intent = in
 [ntcw]
   standard_name = index_of_cloud_liquid_water_mixing_ratio_in_tracer_concentration_array
   long_name = tracer index for cloud condensate (or liquid water)
@@ -289,4 +296,4 @@
   units = 1
   dimensions = ()
   type = integer
-  intent = out
+  intent = out

physics/GFS_MP_generic_post.F90

@@ -20,14 +20,15 @@ module GFS_MP_generic_post
 !> @{
       subroutine GFS_MP_generic_post_run(                                                                                 &
         im, levs, kdt, nrcm, nncl, ntcw, ntrac, imp_physics, imp_physics_gfdl, imp_physics_thompson, imp_physics_nssl,    &
-        imp_physics_mg, imp_physics_fer_hires, cal_pre, cplflx, cplchm, con_g, rainmin, dtf, frain, rainc,                &
+        imp_physics_mg, imp_physics_fer_hires, cal_pre, cplflx, cplchm, progsigma, con_g, rainmin, dtf, frain, rainc,     &
         rain1, rann, xlat, xlon, gt0, gq0, prsl, prsi, phii, tsfc, ice, snow, graupel, save_t, save_q, rain0, ice0, snow0,&
         graupel0, del, rain, domr_diag, domzr_diag, domip_diag, doms_diag, tprcp, srflag, sr, cnvprcp, totprcp, totice,   &
         totsnw, totgrp, cnvprcpb, totprcpb, toticeb, totsnwb, totgrpb, rain_cpl, rainc_cpl, snow_cpl, pwat,               &
         drain_cpl, dsnow_cpl, lsm, lsm_ruc, lsm_noahmp, raincprv, rainncprv, iceprv, snowprv,                             &
         graupelprv, draincprv, drainncprv, diceprv, dsnowprv, dgraupelprv, dtp, dfi_radar_max_intervals,                  &
-        dtend, dtidx, index_of_temperature, index_of_process_mp,ldiag3d, qdiag3d, lssav, num_dfi_radar, fh_dfi_radar,     &
-        index_of_process_dfi_radar, ix_dfi_radar, dfi_radar_tten, radar_tten_limits, fhour, errmsg, errflg)
+        dtend, dtidx, index_of_temperature, index_of_process_mp,ldiag3d,qdiag3d,dqdt_qmicro, lssav, num_dfi_radar,        &
+        fh_dfi_radar,index_of_process_dfi_radar, ix_dfi_radar,dfi_radar_tten, radar_tten_limits, fhour, prevsq,           &
+        errmsg, errflg)
 !
       use machine, only: kind_phys
 
@@ -36,7 +37,7 @@ subroutine GFS_MP_generic_post_run(
       integer, intent(in) :: im, levs, kdt, nrcm, nncl, ntcw, ntrac, num_dfi_radar, index_of_process_dfi_radar
       integer, intent(in) :: imp_physics, imp_physics_gfdl, imp_physics_thompson, imp_physics_mg, imp_physics_fer_hires
       integer, intent(in) :: imp_physics_nssl
-      logical, intent(in) :: cal_pre, lssav, ldiag3d, qdiag3d, cplflx, cplchm
+      logical, intent(in) :: cal_pre, lssav, ldiag3d, qdiag3d, cplflx, cplchm, progsigma
       integer, intent(in) :: index_of_temperature,index_of_process_mp
 
       integer                                                :: dfi_radar_max_intervals
@@ -80,7 +81,8 @@ subroutine GFS_MP_generic_post_run(
       real(kind=kind_phys), dimension(:),      intent(inout) :: diceprv
       real(kind=kind_phys), dimension(:),      intent(inout) :: dsnowprv
       real(kind=kind_phys), dimension(:),      intent(inout) :: dgraupelprv
-
+      real(kind=kind_phys), dimension(:,:),    intent(inout) :: dqdt_qmicro
+      real(kind=kind_phys), dimension(:,:),    intent(inout) :: prevsq
       real(kind=kind_phys),                    intent(in)    :: dtp
 
       ! CCPP error handling
@@ -352,6 +354,15 @@ subroutine GFS_MP_generic_post_run(
         endif if_tendency_diagnostics
       endif if_save_fields
 
+      !If prognostic updraft area fraction is used in saSAS
+      if(progsigma)then
+         do k=1,levs
+            do i=1,im
+               dqdt_qmicro(i,k)=(gq0(i,k,1)-save_q(i,k,1))/dtp
+            enddo
+         enddo
+      endif
+
       if (cplflx .or. cplchm) then
         do i = 1, im
           dsnow_cpl(i)= max(zero, rain(i) * srflag(i))
@@ -387,7 +398,13 @@ subroutine GFS_MP_generic_post_run(
         pwat(i) = pwat(i) * onebg
       enddo
 
-
+      if(progsigma)then      
+         do k = 1, levs
+            do i=1, im
+               prevsq(i,k) = gq0(i,k,1)
+            enddo
+         enddo
+      endif
       end subroutine GFS_MP_generic_post_run
 !> @}
 

physics/GFS_MP_generic_post.meta

@@ -128,6 +128,13 @@
   dimensions = ()
   type = logical
   intent = in
+[progsigma]
+  standard_name = do_prognostic_updraft_area_fraction
+  long_name = flag for prognostic sigma in cumulus scheme
+  units = flag
+  dimensions = ()
+  type = logical
+  intent = in
 [con_g]
   standard_name = gravitational_acceleration
   long_name = gravitational acceleration
@@ -724,6 +731,22 @@
   dimensions = ()
   type = logical
   intent = in
+[dqdt_qmicro]
+  standard_name = instantaneous_tendency_of_specific_humidity_due_to_microphysics
+  long_name = moisture tendency due to microphysics
+  units = kg kg-1 s-1
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension)
+  type = real
+  kind = kind_phys
+  intent = inout
+[prevsq]
+  standard_name = specific_humidity_on_previous_timestep
+  long_name = specific_humidity_on_previous_timestep
+  units = kg kg-1
+  dimensions = (horizontal_loop_extent,vertical_layer_dimension)
+  type = real
+  kind = kind_phys
+  intent = inout
 [lssav]
   standard_name = flag_for_diagnostics
   long_name = logical flag for storing diagnostics

physics/GFS_MP_generic_pre.F90

@@ -9,14 +9,14 @@ module GFS_MP_generic_pre
 !> \section arg_table_GFS_MP_generic_pre_run Argument Table
 !! \htmlinclude GFS_MP_generic_pre_run.html
 !!
-      subroutine GFS_MP_generic_pre_run(im, levs, ldiag3d, qdiag3d, do_aw, ntcw, nncl, &
+      subroutine GFS_MP_generic_pre_run(im, levs, ldiag3d, qdiag3d, do_aw, progsigma, ntcw, nncl, &
                                         ntrac, gt0, gq0, save_t, save_q, num_dfi_radar, errmsg, errflg)
 !
       use machine,               only: kind_phys
 
       implicit none
       integer,                                intent(in) :: im, levs, ntcw, nncl, ntrac, num_dfi_radar
-      logical,                                intent(in) :: ldiag3d, qdiag3d, do_aw
+      logical,                                intent(in) :: ldiag3d, qdiag3d, do_aw, progsigma
       real(kind=kind_phys), dimension(:,:),   intent(in) :: gt0
       real(kind=kind_phys), dimension(:,:,:), intent(in) :: gq0
 
@@ -39,7 +39,7 @@ subroutine GFS_MP_generic_pre_run(im, levs, ldiag3d, qdiag3d, do_aw, ntcw, nncl,
           enddo
         enddo
       endif
-      if (ldiag3d .or. do_aw) then
+      if (ldiag3d .or. do_aw .or. progsigma) then
         if(qdiag3d) then
            do n=1,ntrac
               do k=1,levs
@@ -48,7 +48,7 @@ subroutine GFS_MP_generic_pre_run(im, levs, ldiag3d, qdiag3d, do_aw, ntcw, nncl,
                  enddo
               enddo
            enddo
-        else if(do_aw) then
+        else if(do_aw .or. progsigma) then
            ! if qdiag3d, all q are saved already
            save_q(1:im,:,1) = gq0(1:im,:,1)
            do n=ntcw,ntcw+nncl-1
@@ -59,4 +59,4 @@ subroutine GFS_MP_generic_pre_run(im, levs, ldiag3d, qdiag3d, do_aw, ntcw, nncl,
 
       end subroutine GFS_MP_generic_pre_run
 
-      end module GFS_MP_generic_pre
+      end module GFS_MP_generic_pre

physics/GFS_MP_generic_pre.meta

@@ -42,6 +42,13 @@
   dimensions = ()
   type = logical
   intent = in
+[progsigma]
+  standard_name = do_prognostic_updraft_area_fraction
+  long_name = flag for prognostic area fraction in cumulus convection
+  units = flag
+  dimensions = ()
+  type = logical
+  intent = in
 [ntcw]
   standard_name = index_of_cloud_liquid_water_mixing_ratio_in_tracer_concentration_array
   long_name = tracer index for cloud condensate (or liquid water)
@@ -116,4 +123,4 @@
   units = 1
   dimensions = ()
   type = integer
-  intent = out
+  intent = out

physics/GFS_SCNV_generic_post.F90

@@ -14,7 +14,7 @@ subroutine GFS_SCNV_generic_post_run (im, levs, nn, lssav, ldiag3d, qdiag3d, &
         rainc, cnvprcp, cnvprcpb, cnvw_phy_f3d, cnvc_phy_f3d,                      &
         dtend, dtidx, index_of_temperature, index_of_x_wind, index_of_y_wind,      &
         index_of_process_scnv, ntqv, flag_for_scnv_generic_tend,                   &
-        ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,ntgnc,                        &
+        ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,ntgnc,ntsigma,                &
         imfshalcnv, imfshalcnv_sas, imfshalcnv_samf, ntrac,                        &
         cscnv, satmedmf, trans_trac, ras, errmsg, errflg)
 
@@ -23,7 +23,7 @@ subroutine GFS_SCNV_generic_post_run (im, levs, nn, lssav, ldiag3d, qdiag3d, &
       implicit none
 
       integer, intent(in) :: im, levs, nn, ntqv, nsamftrac
-      integer, intent(in) :: ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,ntgnc,ntrac
+      integer, intent(in) :: ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,ntgnc,ntsigma,ntrac
       logical, intent(in) :: lssav, ldiag3d, qdiag3d, flag_for_scnv_generic_tend
       real(kind=kind_phys),                     intent(in) :: frain
       real(kind=kind_phys), dimension(:,:), intent(in) :: gu0, gv0, gt0
@@ -103,7 +103,7 @@ subroutine GFS_SCNV_generic_post_run (im, levs, nn, lssav, ldiag3d, qdiag3d, &
              do n=2,ntrac
                 if ( n /= ntcw  .and. n /= ntiw  .and. n /= ntclamt .and. &
                      n /= ntrw  .and. n /= ntsw  .and. n /= ntrnc   .and. &
-                     n /= ntsnc .and. n /= ntgl  .and. n /= ntgnc) then
+                     n /= ntsnc .and. n /= ntgl  .and. n /= ntgnc   .and. n /= ntsigma) then
                    tracers = tracers + 1
                    idtend = dtidx(100+n,index_of_process_scnv)
                    if(idtend>0) then

physics/GFS_SCNV_generic_post.meta

@@ -335,6 +335,13 @@
   dimensions = ()
   type = logical
   intent = in
+[ntsigma]
+  standard_name = index_of_updraft_area_fraction_in_tracer_concentration_array
+  long_name = tracer index of updraft_area_fraction
+  units = index
+  dimensions = ()
+  type = integer
+  intent = in
 [ntcw]
   standard_name = index_of_cloud_liquid_water_mixing_ratio_in_tracer_concentration_array
   long_name = tracer index for cloud condensate (or liquid water)

physics/GFS_SCNV_generic_pre.F90

@@ -11,14 +11,14 @@ module GFS_SCNV_generic_pre
       subroutine GFS_SCNV_generic_pre_run (im, levs, ldiag3d, qdiag3d, gu0, gv0, gt0, gq0, &
         save_u, save_v, save_t, save_q, ntqv, nsamftrac, flag_for_scnv_generic_tend,       &
         dtidx, index_of_process_scnv, ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,ntgnc,  &
-        cscnv, satmedmf, trans_trac, ras, ntrac, clw, errmsg, errflg)
+        ntsigma, cscnv, satmedmf, trans_trac, ras, ntrac, clw, errmsg, errflg)
 
         use machine,               only: kind_phys
 
         implicit none
 
         integer, intent(in) :: im, levs, ntqv, nsamftrac, index_of_process_scnv, dtidx(:,:)
-        integer, intent(in) :: ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,ntgnc,ntrac
+        integer, intent(in) :: ntcw,ntiw,ntclamt,ntrw,ntsw,ntrnc,ntsnc,ntgl,ntgnc,ntsigma,ntrac
         logical, intent(in) :: ldiag3d, qdiag3d, flag_for_scnv_generic_tend
         real(kind=kind_phys), dimension(:,:),   intent(in) :: gu0, gv0, gt0
         real(kind=kind_phys), dimension(:,:,:), intent(in) :: gq0
@@ -49,7 +49,7 @@ subroutine GFS_SCNV_generic_pre_run (im, levs, ldiag3d, qdiag3d, gu0, gv0, gt0,
                 do n=2,ntrac
                    if ( n /= ntcw  .and. n /= ntiw  .and. n /= ntclamt .and. &
                         n /= ntrw  .and. n /= ntsw  .and. n /= ntrnc   .and. &
-                        n /= ntsnc .and. n /= ntgl  .and. n /= ntgnc) then
+                        n /= ntsnc .and. n /= ntgl  .and. n /= ntgnc   .and. n /= ntsigma) then
                       tracers = tracers + 1
                       if(dtidx(100+n,index_of_process_scnv)>0) then
                          save_q(:,:,n) = clw(:,:,tracers)
@@ -69,5 +69,4 @@ subroutine GFS_SCNV_generic_pre_run (im, levs, ldiag3d, qdiag3d, gu0, gv0, gt0,
 
     end subroutine GFS_SCNV_generic_pre_run
 
-
-    end module GFS_SCNV_generic_pre
+    end module GFS_SCNV_generic_pre

physics/GFS_SCNV_generic_pre.meta

@@ -162,6 +162,13 @@
   dimensions = ()
   type = logical
   intent = in
+[ntsigma]
+  standard_name = index_of_updraft_area_fraction_in_tracer_concentration_array
+  long_name = tracer index of updraft_area_fraction
+  units = index
+  dimensions = ()
+  type = integer
+  intent = in
 [ntcw]
   standard_name = index_of_cloud_liquid_water_mixing_ratio_in_tracer_concentration_array
   long_name = tracer index for cloud condensate (or liquid water)
@@ -254,4 +261,4 @@
   units = 1
   dimensions = ()
   type = integer
-  intent = out
+  intent = out