Merge pull request #194 from gold2718/fix_dms

Summary: Fix SFDMS history output restart error
Contributors: gold2718
Reviewers: oyvindseland
Purpose of changes: FAIL ERR_Ld3.ne30pg3_tn14.N1850.betzy_intel.allactive-defaultio COMPARE_base_rest failing with latest alpha tag
Github PR URL: #194

Changes made to build system: None
Changes made to the namelist: None
Changes to the defaults for the boundary datasets: None]
Substantial timing or memory changes: None

    Add fdms, fbrf, fn2o_ocn and fnh3_ocn to the restart file
    Remove bad outfld call in atm_import_export

ERR_Ld3.ne30pg3_tn14.N1850.betzy_intel.allactive-defaultio
    Still fails COMPARE_base_rest but due only to a BLOM field

src/cpl/nuopc/atm_import_export.F90

@@ -15,7 +15,6 @@ module atm_import_export
   use cam_logfile       , only : iulog
   use cam_history       , only: outfld
   use spmd_utils        , only : masterproc, mpicom
-  use constituents      , only : cnst_get_ind, sflxnam
   use srf_field_check   , only : set_active_Sl_ram1
   use srf_field_check   , only : set_active_Sl_fv
   use srf_field_check   , only : set_active_Sl_soilw
@@ -555,7 +554,6 @@ subroutine import_fields( gcomp, cam_in, restart_init, rc)
     ! local variables
     type(ESMF_State)   :: importState
     integer            :: i,n,c,g, num  ! indices
-    integer            :: ncols         ! number of columns
     integer            :: nstep
     logical            :: overwrite_flds
     logical            :: exists
@@ -893,7 +891,6 @@ subroutine import_fields( gcomp, cam_in, restart_init, rc)
 
     call state_getfldptr(importState,  'Faoo_fdms_ocn', fldptr=fldptr1d, exists=exists, rc=rc)
     if (exists) then
-       call cnst_get_ind('DMS', pndx_fdms, abort=.true.)
        ! Ideally what should happen below is that
        ! cam_in%cflx(icol,pndx_fdms) should be set directly from
        ! fldptr1d. However, the code initializes the chemistry
@@ -908,8 +905,6 @@ subroutine import_fields( gcomp, cam_in, restart_init, rc)
              cam_in(c)%fdms(i) = -fldptr1d(g) * med2mod_areacor(g)
              g = g + 1
           end do
-          ncols = get_ncols_p(c)
-          call outfld( sflxnam(pndx_fdms), cam_in(c)%fdms, ncols, c)
        end do
     end if
 
@@ -1046,7 +1041,6 @@ subroutine export_fields( gcomp, model_mesh, model_clock, cam_out, rc)
     type(ESMF_State)  :: importState
     type(ESMF_Clock)  :: clock
     integer           :: i,m,c,n,g  ! indices
-    integer           :: ncols      ! Number of columns
     integer           :: nstep
     logical           :: exists
     real(r8)          :: scale_ndep

src/physics/cam/restart_physics.F90

@@ -46,6 +46,11 @@ module restart_physics
     type(var_desc_t) :: wsy_desc
     type(var_desc_t) :: shf_desc
 
+    type(var_desc_t) :: fdms_desc
+    type(var_desc_t) :: fbrf_desc
+    type(var_desc_t) :: fn2o_ocn_desc
+    type(var_desc_t) :: fnh3_ocn_desc
+
   CONTAINS
     subroutine init_restart_physics ( File, pbuf2d)
 
@@ -128,6 +133,11 @@ subroutine init_restart_physics ( File, pbuf2d)
     ierr = pio_def_var(File, 'wsy',  pio_double, hdimids, wsy_desc)
     ierr = pio_def_var(File, 'shf',  pio_double, hdimids, shf_desc)
 
+    ierr = pio_def_var(File, 'fdms',      pio_double, hdimids, fdms_desc)
+    ierr = pio_def_var(File, 'fbrf',      pio_double, hdimids, fbrf_desc)
+    ierr = pio_def_var(File, 'fn2o_ocn',  pio_double, hdimids, fn2o_ocn_desc)
+    ierr = pio_def_var(File, 'fnh3_ocn',  pio_double, hdimids, fnh3_ocn_desc)
+
     call radiation_define_restart(file)
 
     if (is_subcol_on()) then
@@ -328,6 +338,30 @@ subroutine write_restart_physics (File, cam_in, cam_out, pbuf2d)
       end do
       call pio_write_darray(File, shf_desc, iodesc, tmpfield, ierr)
 
+      do i = begchunk, endchunk
+        ncol = cam_in(i)%ncol
+        tmpfield(:ncol,i) = cam_in(i)%fdms(:ncol)
+      end do
+      call pio_write_darray(File, fdms_desc, iodesc, tmpfield, ierr)
+
+      do i = begchunk, endchunk
+        ncol = cam_in(i)%ncol
+        tmpfield(:ncol,i) = cam_in(i)%fbrf(:ncol)
+      end do
+      call pio_write_darray(File, fbrf_desc, iodesc, tmpfield, ierr)
+
+      do i = begchunk, endchunk
+        ncol = cam_in(i)%ncol
+        tmpfield(:ncol,i) = cam_in(i)%fn2o_ocn(:ncol)
+      end do
+      call pio_write_darray(File, fn2o_ocn_desc, iodesc, tmpfield, ierr)
+
+      do i = begchunk, endchunk
+        ncol = cam_in(i)%ncol
+        tmpfield(:ncol,i) = cam_in(i)%fnh3_ocn(:ncol)
+      end do
+      call pio_write_darray(File, fnh3_ocn_desc, iodesc, tmpfield, ierr)
+
       call radiation_write_restart(file)
 
     end subroutine write_restart_physics
@@ -583,7 +617,43 @@ subroutine read_restart_physics(File, cam_in, cam_out, pbuf2d)
            cam_in(c)%shf(i) = tmpfield2(i, c)
          end do
        end do
-     endif
+     end if
+     ierr = pio_inq_varid(File, 'fdms', vardesc)
+     if (ierr == PIO_NOERR) then ! variable found on restart file
+       call pio_read_darray(File, vardesc, iodesc, tmpfield2, ierr)
+       do c= begchunk, endchunk
+         do i = 1, pcols
+           cam_in(c)%fdms(i) = tmpfield2(i, c)
+         end do
+       end do
+     end if
+     ierr = pio_inq_varid(File, 'fbrf', vardesc)
+     if (ierr == PIO_NOERR) then ! variable found on restart file
+       call pio_read_darray(File, vardesc, iodesc, tmpfield2, ierr)
+       do c= begchunk, endchunk
+         do i = 1, pcols
+           cam_in(c)%fbrf(i) = tmpfield2(i, c)
+         end do
+       end do
+     end if
+     ierr = pio_inq_varid(File, 'fn2o_ocn', vardesc)
+     if (ierr == PIO_NOERR) then ! variable found on restart file
+       call pio_read_darray(File, vardesc, iodesc, tmpfield2, ierr)
+       do c= begchunk, endchunk
+         do i = 1, pcols
+           cam_in(c)%fn2o_ocn(i) = tmpfield2(i, c)
+         end do
+       end do
+     end if
+     ierr = pio_inq_varid(File, 'fnh3_ocn', vardesc)
+     if (ierr == PIO_NOERR) then ! variable found on restart file
+       call pio_read_darray(File, vardesc, iodesc, tmpfield2, ierr)
+       do c= begchunk, endchunk
+         do i = 1, pcols
+           cam_in(c)%fnh3_ocn(i) = tmpfield2(i, c)
+         end do
+       end do
+     end if
      call pio_seterrorhandling(File, err_handling)
 
      deallocate(tmpfield2)