this PR includes: 1)vlab #69814: post update,2)ufs issue NCAR#3, Add …

…3D reflectivity to restart file and restart reproducibility for regional fv3,3)ufs issue NCAR#5, Updates to WW3, 4)vlab #69735, update netcdf time units attribute when iau_offset

.gitmodules

@@ -1,7 +1,7 @@
 [submodule "atmos_cubed_sphere"]
 	path = atmos_cubed_sphere
-	url = https://github.com/NOAA-EMC/GFDL_atmos_cubed_sphere
-	branch = dev/emc
+	url = https://github.com/junwang-noaa/GFDL_atmos_cubed_sphere
+	branch = regfv3_rst
 [submodule "ccpp/framework"]
 	path = ccpp/framework
 	url = https://github.com/NCAR/ccpp-framework

gfsphysics/GFS_layer/GFS_physics_driver.F90

@@ -1149,7 +1149,7 @@ subroutine GFS_physics_driver                                 &
             if (fice(i) < one) then
               wet(i) = .true.
 !             Sfcprop%tsfco(i) = tgice
-              Sfcprop%tsfco(i) = max(Sfcprop%tisfc(i), tgice)
+              if (.not. Model%cplflx) Sfcprop%tsfco(i) = max(Sfcprop%tisfc(i), tgice)
 !             Sfcprop%tsfco(i) = max((Sfcprop%tsfc(i) - fice(i)*sfcprop%tisfc(i)) &
 !                                     / (one - fice(i)), tgice)
             endif

gfsphysics/GFS_layer/GFS_restart.F90

@@ -117,6 +117,9 @@ subroutine GFS_restart_populate (Restart, Model, Statein, Stateout, Sfcprop, &
 #endif
 
     Restart%num3d = Model%ntot3d
+    if(Model%lrefres) then
+       Restart%num3d = Model%ntot3d+1
+    endif
 #ifdef CCPP
     ! GF
     if (Model%imfdeepcnv == 3) then
@@ -252,7 +255,13 @@ subroutine GFS_restart_populate (Restart, Model, Statein, Stateout, Sfcprop, &
         Restart%data(nb,num)%var3p => Tbd(nb)%phy_f3d(:,:,num)
       enddo
     enddo
-
+    if (Model%lrefres) then
+      num = Model%ntot3d+1
+      restart%name3d(num) = 'ref_f3d'
+      do nb = 1,nblks
+        Restart%data(nb,num)%var3p => IntDiag(nb)%refl_10cm(:,:)
+      enddo
+    endif
 #ifdef CCPP
     !--- RAP/HRRR-specific variables, 3D
     num = Model%ntot3d

gfsphysics/GFS_layer/GFS_typedefs.F90

@@ -701,6 +701,9 @@ module GFS_typedefs
     !--- GFDL microphysical paramters
     logical              :: lgfdlmprad      !< flag for GFDL mp scheme and radiation consistency 
 
+    !--- Thompson,GFDL mp parameter
+    logical              :: lrefres          !< flag for radar reflectivity in restart file
+
     !--- land/surface model parameters
     integer              :: lsm             !< flag for land surface model lsm=1 for noah lsm
     integer              :: lsm_noah=1      !< flag for NOAH land surface model
@@ -2740,6 +2743,9 @@ subroutine control_initialize (Model, nlunit, fn_nml, me, master, &
     !--- GFDL microphysical parameters
     logical              :: lgfdlmprad     = .false.            !< flag for GFDLMP radiation interaction 
 
+    !--- Thompson,GFDL microphysical parameter
+    logical              :: lrefres        = .false.            !< flag for radar reflectivity in restart file
+
     !--- land/surface model parameters
     integer              :: lsm            =  1              !< flag for land surface model to use =0  for osu lsm; =1  for noah lsm; =2  for noah mp lsm; =3  for RUC lsm
     integer              :: lsoil          =  4              !< number of soil layers
@@ -3023,7 +3029,7 @@ subroutine control_initialize (Model, nlunit, fn_nml, me, master, &
                                mg_do_graupel, mg_do_hail, mg_nccons, mg_nicons, mg_ngcons,  &
                                mg_ncnst, mg_ninst, mg_ngnst, sed_supersat, do_sb_physics,   &
                                mg_alf,   mg_qcmin, mg_do_ice_gmao, mg_do_liq_liu,           &
-                               ltaerosol, lradar, ttendlim, lgfdlmprad,                     &
+                               ltaerosol, lradar, lrefres, ttendlim, lgfdlmprad,            &
                           !--- max hourly
                                avg_max_length,                                              &
                           !--- land/surface model control
@@ -3312,6 +3318,8 @@ subroutine control_initialize (Model, nlunit, fn_nml, me, master, &
     Model%ttendlim         = ttendlim
 !--- gfdl  MP parameters
     Model%lgfdlmprad       = lgfdlmprad
+!--- Thompson,GFDL MP parameter
+    Model%lrefres          = lrefres
 
 !--- land/surface model parameters
     Model%lsm              = lsm
@@ -4310,6 +4318,7 @@ subroutine control_print(Model)
         print *, ' Thompson microphysical parameters'
         print *, ' ltaerosol         : ', Model%ltaerosol
         print *, ' lradar            : ', Model%lradar
+        print *, ' lrefres           : ', Model%lrefres
         print *, ' ttendlim          : ', Model%ttendlim
         print *, ' '
       endif
@@ -4327,6 +4336,7 @@ subroutine control_print(Model)
       if (Model%imp_physics == Model%imp_physics_gfdl) then
         print *, ' GFDL microphysical parameters'
         print *, ' GFDL MP radiation inter: ', Model%lgfdlmprad
+        print *, ' lrefres                : ', Model%lrefres
         print *, ' '
       endif
 

io/FV3GFS_io.F90

@@ -1119,15 +1119,10 @@ subroutine sfc_prop_restart_read (Sfcprop, Atm_block, Model, fv_domain)
           Sfcprop(nb)%zorll(ix) = Sfcprop(nb)%zorlo(ix)
           Sfcprop(nb)%zorl(ix)  = Sfcprop(nb)%zorlo(ix)
           Sfcprop(nb)%tsfc(ix)  = Sfcprop(nb)%tsfco(ix)
-          if (Sfcprop(nb)%slmsk(ix) < 0.1 .or. Sfcprop(nb)%slmsk(ix) > 1.9) then
+          if (Sfcprop(nb)%slmsk(ix) > 1.9) then
             Sfcprop(nb)%landfrac(ix) = 0.0
-            if (Sfcprop(nb)%oro_uf(ix) > 0.01) then
-              Sfcprop(nb)%lakefrac(ix) = 1.0        ! lake
-            else
-              Sfcprop(nb)%lakefrac(ix) = 0.0        ! ocean
-            endif
           else
-            Sfcprop(nb)%landfrac(ix) = 1.0          ! land
+            Sfcprop(nb)%landfrac(ix) = Sfcprop(nb)%slmsk(ix)
           endif
         enddo
       enddo

io/module_write_netcdf.F90

@@ -22,14 +22,15 @@ module module_write_netcdf
   contains
 
 !----------------------------------------------------------------------------------------
-  subroutine write_netcdf(fieldbundle, wrtfb, filename, mpi_comm, mype, im, jm, rc)
+  subroutine write_netcdf(fieldbundle, wrtfb, filename, mpi_comm, mype, im, jm, idate, rc)
 !
     type(ESMF_FieldBundle), intent(in) :: fieldbundle
     type(ESMF_FieldBundle), intent(in) :: wrtfb
     character(*), intent(in)           :: filename
     integer, intent(in)                :: mpi_comm
     integer, intent(in)                :: mype
     integer, intent(in)                :: im, jm
+    integer, intent(in)                :: idate(7)
     integer, optional,intent(out)      :: rc
 !
 !** local vars
@@ -146,7 +147,7 @@ subroutine write_netcdf(fieldbundle, wrtfb, filename, mpi_comm, mype, im, jm, rc
       call add_dim(ncid, "phalf", phalf_dimid, wrtgrid, rc)
     end if
 
-    call add_dim(ncid, "time", time_dimid, wrtgrid, rc)
+    call add_dim(ncid, "time", time_dimid, wrtgrid, rc, idate=idate)
 
     call get_global_attr(wrtfb, ncid, rc)
 
@@ -503,11 +504,12 @@ subroutine get_grid_attr(grid, prefix, ncid, varid, rc)
 
   end subroutine get_grid_attr
 
-  subroutine add_dim(ncid, dim_name, dimid, grid, rc)
+  subroutine add_dim(ncid, dim_name, dimid, grid, idate, rc)
     integer, intent(in)             :: ncid
     character(len=*), intent(in)    :: dim_name
-    integer, intent(inout) :: dimid
+    integer, intent(inout)          :: dimid
     type(ESMF_Grid), intent(in)     :: grid
+    integer, intent(in), optional   :: idate(7)
     integer, intent(out)            :: rc
 
 ! local variable
@@ -556,9 +558,38 @@ subroutine add_dim(ncid, dim_name, dimid, grid, rc)
 
     call get_grid_attr(grid, dim_name, ncid, dim_varid, rc)
 
+    ! if write grid comp changes time units
+    if ( present (idate) ) then
+      if ( trim(dim_name) == "time") then
+        ncerr = nf90_get_att(ncid, dim_varid, 'units', time_units); NC_ERR_STOP(ncerr)
+        time_units  = get_time_units_from_idate(idate)
+        ncerr = nf90_put_att(ncid, dim_varid, 'units', trim(time_units)); NC_ERR_STOP(ncerr)
+      endif
+    endif
+
   end subroutine add_dim
 !
 !----------------------------------------------------------------------------------------
+  function get_time_units_from_idate(idate, time_measure) result(time_units)
+      ! create time units attribute of form 'hours since YYYY-MM-DD HH:MM:SS'
+      ! from integer array with year,month,day,hour,minute,second
+      ! optional argument 'time_measure' can be used to change 'hours' to
+      ! 'days', 'minutes', 'seconds' etc.
+      character(len=*), intent(in), optional :: time_measure
+      integer, intent(in) ::  idate(7)
+      character(len=12) :: timechar
+      character(len=nf90_max_name) :: time_units
+      if (present(time_measure)) then
+         timechar = trim(time_measure)
+      else
+         timechar = 'hours'
+      endif
+      write(time_units,101) idate(1:6)
+101   format(' since ',i4.4,'-',i2.2,'-',i2.2,' ',&
+      i2.2,':',i2.2,':',i2.2)
+      time_units = trim(adjustl(timechar))//time_units
+  end function get_time_units_from_idate
+!
   subroutine nccheck(status)
     use netcdf
     implicit none

io/module_wrt_grid_comp.F90

@@ -1386,7 +1386,7 @@ subroutine wrt_run(wrt_comp, imp_state_write, exp_state_write,clock,rc)
 
               wbeg = MPI_Wtime()
               call write_netcdf(file_bundle,wrt_int_state%wrtFB(nbdl),trim(filename), &
-                               wrt_mpi_comm,wrt_int_state%mype,imo,jmo,rc)
+                               wrt_mpi_comm,wrt_int_state%mype,imo,jmo,idate,rc)
               wend = MPI_Wtime()
               if (lprnt) then
                 write(*,'(A,F10.5,A,I4.2,A,I2.2)')' netcdf      Write Time is ',wend-wbeg  &
@@ -1431,7 +1431,7 @@ subroutine wrt_run(wrt_comp, imp_state_write, exp_state_write,clock,rc)
 
               wbeg = MPI_Wtime()
               call write_netcdf(file_bundle,wrt_int_state%wrtFB(nbdl),trim(filename), &
-                                wrt_mpi_comm,wrt_int_state%mype,imo,jmo,rc)
+                                wrt_mpi_comm,wrt_int_state%mype,imo,jmo,idate,rc)
               wend = MPI_Wtime()
               if (mype == lead_write_task) then
                 write(*,'(A,F10.5,A,I4.2,A,I2.2)')' netcdf      Write Time is ',wend-wbeg  &

io/post_gfs.F90

@@ -451,8 +451,7 @@ subroutine set_postvars_gfs(wrt_int_state,mpicomp,setvar_atmfile,   &
       end do
 !
 ! GFS does not output PD
-!      pt    = 10000.          ! this is for 100 hPa added by Moorthi
-      pt    = 0.
+      pt    = ak5(1)
 
 ! GFS may not have model derived radar ref.
 !                        TKE
@@ -1296,7 +1295,7 @@ subroutine set_postvars_gfs(wrt_int_state,mpicomp,setvar_atmfile,   &
             endif
 
             ! inst incoming sfc longwave
-            if(trim(fieldname)=='dlwsf') then
+            if(trim(fieldname)=='dlwrf') then
               !$omp parallel do private(i,j)
               do j=jsta,jend
                 do i=ista, iend
@@ -1845,6 +1844,16 @@ subroutine set_postvars_gfs(wrt_int_state,mpicomp,setvar_atmfile,   &
 
             ! time averaged surface clear sky outgoing LW
             if(trim(fieldname)=='csulf') then
+              !$omp parallel do private(i,j)
+              do j=jsta,jend
+                do i=ista, iend
+                  alwoutc(i,j) = arrayr42d(i,j)
+                enddo
+              enddo
+            endif
+
+            ! time averaged TOA clear sky outgoing LW
+            if(trim(fieldname)=='csulftoa') then
               !$omp parallel do private(i,j)
               do j=jsta,jend
                 do i=ista, iend
@@ -1864,7 +1873,7 @@ subroutine set_postvars_gfs(wrt_int_state,mpicomp,setvar_atmfile,   &
             endif
 
             ! time averaged TOA clear sky outgoing SW
-            if(trim(fieldname)=='csusf') then
+            if(trim(fieldname)=='csusftoa') then
               !$omp parallel do private(i,j)
               do j=jsta,jend
                 do i=ista, iend
@@ -2271,7 +2280,6 @@ subroutine set_postvars_gfs(wrt_int_state,mpicomp,setvar_atmfile,   &
         enddo
       end do
 
-!??? reset pint(lev=1)
 !$omp parallel do private(i,j)
       do j=jsta,jend
         do i=1,im
@@ -2282,7 +2290,7 @@ subroutine set_postvars_gfs(wrt_int_state,mpicomp,setvar_atmfile,   &
 !      print *,'in setvar, pt=',pt,'ak5(lp1)=', ak5(lp1),'ak5(1)=',ak5(1)
 
 ! compute alpint
-      do l=lp1,2,-1
+      do l=lp1,1,-1
 !$omp parallel do private(i,j)
         do j=jsta,jend
           do i=1,im
@@ -2321,6 +2329,18 @@ subroutine set_postvars_gfs(wrt_int_state,mpicomp,setvar_atmfile,   &
         enddo
       enddo
 
+! compute cwm for gfdlmp
+      if(  imp_physics == 11 ) then
+        do l=1,lm
+!$omp parallel do private(i,j)
+          do j=jsta,jend
+            do i=ista,iend
+              cwm(i,j,l)=qqg(i,j,l)+qqs(i,j,l)+qqr(i,j,l)+qqi(i,j,l)+qqw(i,j,l)
+            enddo
+          enddo
+        enddo
+      endif
+
 ! estimate 2m pres and convert t2m to theta
 !$omp parallel do private(i,j)
       do j=jsta,jend