Refactor fv3atm history & restart to reduce redundant code. Add rrfs-…

…sd and clm lake to quilt restart. (#660)

* move utility routines, data structures, and name generation out of FV3GFS_io.F90

* move RRFS SD state restart io to separate file and rename clm_lake_io.F90

* sfc array indices are calculated in FV3GFS_sfc_io.F90

* move rrfs sd emissions input code to FV3GFS_rrfs_sd_io.F90

* allocate sfc arrays in FV3GFS_sfc_io.F90

* define and write axes in FV3GFS_sfc_io.F90

* register sfc fields in FV3GFS_sfc_io.F90

* move sfc read loop to FV3GFS_sfc_io.F90

* Put post-read safeguards in FV3GFS_sfc_io.F90

* copy to grid in FV3GFS_sfc_io.F90 and make things private

* move oro reading to FV3GFS_oro_io.F90

* gwd I/O in FV3GFS_oro_io.F90

* store quilt restart data structures in FV3GFS_sfc_io types

* remove copy_from_GFS_Data calls from FV3GFS_restart_io.F90

* consistent naming and clm lake quilt restart

CMakeLists.txt

@@ -85,9 +85,13 @@ add_library(fv3atm
   cpl/module_block_data.F90
   cpl/module_cplfields.F90
   cpl/module_cap_cpl.F90
-  io/clm_lake_io.F90
-  io/FV3GFS_io.F90
-  io/FV3GFS_restart_io.F90
+  io/fv3atm_common_io.F90
+  io/fv3atm_clm_lake_io.F90
+  io/fv3atm_rrfs_sd_io.F90
+  io/fv3atm_sfc_io.F90
+  io/fv3atm_oro_io.F90
+  io/fv3atm_history_io.F90
+  io/fv3atm_restart_io.F90
   io/module_write_netcdf.F90
   io/module_write_restart_netcdf.F90
   io/module_fv3_io_def.F90

atmos_model.F90

@@ -90,13 +90,14 @@ module atmos_model_mod
 
 use stochastic_physics_wrapper_mod, only: stochastic_physics_wrapper,stochastic_physics_wrapper_end
 
-use FV3GFS_io_mod,      only: FV3GFS_restart_read, FV3GFS_restart_write, &
-                              FV3GFS_GFS_checksum,                       &
-                              FV3GFS_diag_register, FV3GFS_diag_output,  &
+use fv3atm_history_io_mod,    only: fv3atm_diag_register, fv3atm_diag_output,  &
                               DIAG_SIZE
-use FV3GFS_restart_io_mod,    only: FV3GFS_restart_register, &
+use fv3atm_restart_io_mod,    only: fv3atm_restart_register, &
+                                    fv3atm_checksum, &
                                     fv_phy_restart_output, &
-                                    fv_sfc_restart_output
+                                    fv_sfc_restart_output, &
+                                    fv3atm_restart_read, &
+                                    fv3atm_restart_write
 use fv_ufs_restart_io_mod,    only: fv_dyn_restart_register, &
                                     fv_dyn_restart_output
 use fv_iau_mod,         only: iau_external_data_type,getiauforcing,iau_initialize
@@ -369,7 +370,7 @@ subroutine update_atmos_radiation_physics (Atmos)
 
       if (chksum_debug) then
         if (mpp_pe() == mpp_root_pe()) print *,'RADIATION STEP  ', GFS_control%kdt, GFS_control%fhour
-        call FV3GFS_GFS_checksum(GFS_control, GFS_data, Atm_block)
+        call fv3atm_checksum(GFS_control, GFS_data, Atm_block)
       endif
 
       if (mpp_pe() == mpp_root_pe() .and. debug) write(6,*) "physics driver"
@@ -383,7 +384,7 @@ subroutine update_atmos_radiation_physics (Atmos)
 
       if (chksum_debug) then
         if (mpp_pe() == mpp_root_pe()) print *,'PHYSICS STEP1   ', GFS_control%kdt, GFS_control%fhour
-        call FV3GFS_GFS_checksum(GFS_control, GFS_data, Atm_block)
+        call fv3atm_checksum(GFS_control, GFS_data, Atm_block)
       endif
 
       if (GFS_Control%do_sppt .or. GFS_Control%do_shum .or. GFS_Control%do_skeb .or. &
@@ -402,7 +403,7 @@ subroutine update_atmos_radiation_physics (Atmos)
 
       if (chksum_debug) then
         if (mpp_pe() == mpp_root_pe()) print *,'PHYSICS STEP2   ', GFS_control%kdt, GFS_control%fhour
-        call FV3GFS_GFS_checksum(GFS_control, GFS_data, Atm_block)
+        call fv3atm_checksum(GFS_control, GFS_data, Atm_block)
       endif
       call getiauforcing(GFS_control,IAU_data)
       if (mpp_pe() == mpp_root_pe() .and. debug) write(6,*) "end of radiation and physics step"
@@ -736,15 +737,15 @@ subroutine atmos_model_init (Atmos, Time_init, Time, Time_step)
 !rab   call atmosphere_tracer_postinit (GFS_data, Atm_block)
 
    call atmosphere_nggps_diag (Time, init=.true.)
-   call FV3GFS_diag_register (GFS_Diag, Time, Atm_block, GFS_control, Atmos%lon, Atmos%lat, Atmos%axes)
+   call fv3atm_diag_register (GFS_Diag, Time, Atm_block, GFS_control, Atmos%lon, Atmos%lat, Atmos%axes)
    call GFS_restart_populate (GFS_restart_var, GFS_control, GFS_data%Statein, GFS_data%Stateout, GFS_data%Sfcprop, &
                               GFS_data%Coupling, GFS_data%Grid, GFS_data%Tbd, GFS_data%Cldprop,  GFS_data%Radtend, &
                               GFS_data%IntDiag, Init_parm, GFS_Diag)
    if (quilting_restart) then
       call fv_dyn_restart_register (Atm(mygrid))
-      call FV3GFS_restart_register (GFS_data%Sfcprop, GFS_restart_var, Atm_block, GFS_control)
+      call fv3atm_restart_register (GFS_data%Sfcprop, GFS_restart_var, Atm_block, GFS_control)
    endif
-   call FV3GFS_restart_read (GFS_data, GFS_restart_var, Atm_block, GFS_control, Atmos%domain_for_read, &
+   call fv3atm_restart_read (GFS_data, GFS_restart_var, Atm_block, GFS_control, Atmos%domain_for_read, &
                              Atm(mygrid)%flagstruct%warm_start, ignore_rst_cksum)
    if(GFS_control%do_ca .and. Atm(mygrid)%flagstruct%warm_start)then
       call read_ca_restart (Atmos%domain,GFS_control%ncells,GFS_control%nca,GFS_control%ncells_g,GFS_control%nca_g)
@@ -966,7 +967,7 @@ subroutine update_atmos_model_state (Atmos, rc)
     if (chksum_debug) then
       if (mpp_pe() == mpp_root_pe()) print *,'UPDATE STATE    ', GFS_control%kdt, GFS_control%fhour
       if (mpp_pe() == mpp_root_pe()) print *,'in UPDATE STATE    ', size(GFS_data(1)%SfcProp%tsfc),'nblks=',Atm_block%nblks
-      call FV3GFS_GFS_checksum(GFS_control, GFS_data, Atm_block)
+      call fv3atm_checksum(GFS_control, GFS_data, Atm_block)
     endif
 
     !--- advance time ---
@@ -995,7 +996,7 @@ subroutine update_atmos_model_state (Atmos, rc)
       endif
       if (mpp_pe() == mpp_root_pe()) write(6,*) ' gfs diags time since last bucket empty: ',time_int/3600.,'hrs'
       call atmosphere_nggps_diag(Atmos%Time)
-      call FV3GFS_diag_output(Atmos%Time, GFS_Diag, Atm_block, GFS_control%nx, GFS_control%ny, &
+      call fv3atm_diag_output(Atmos%Time, GFS_Diag, Atm_block, GFS_control%nx, GFS_control%ny, &
                             GFS_control%levs, 1, 1, 1.0_GFS_kind_phys, time_int, time_intfull, &
                             GFS_control%fhswr, GFS_control%fhlwr)
     endif
@@ -1109,7 +1110,7 @@ subroutine atmos_model_restart(Atmos, timestamp)
        call fv_dyn_restart_output(Atm(mygrid), timestamp)
     else
        call atmosphere_restart(timestamp)
-       call FV3GFS_restart_write (GFS_data, GFS_restart_var, Atm_block, &
+       call fv3atm_restart_write (GFS_data, GFS_restart_var, Atm_block, &
                                   GFS_control, Atmos%domain, timestamp)
     endif
     if(GFS_control%do_ca)then

fv3_cap.F90

@@ -1,4 +1,4 @@
-!--------------- FV3GFS solo model -----------------
+!--------------- FV3 ATM solo model ----------------
 !
 !*** The FV3 atmosphere grid component nuopc cap
 !
@@ -11,7 +11,7 @@
 ! 02 Nov 2017: J. Wang          Use Gerhard's transferable RouteHandle
 !
 
-module fv3gfs_cap_mod
+module fv3atm_cap_mod
 
   use ESMF
   use NUOPC
@@ -80,14 +80,14 @@ module fv3gfs_cap_mod
   contains
 
 !-----------------------------------------------------------------------
-!------------------- Solo fv3gfs code starts here ----------------------
+!------------------- Solo fv3atm code starts here ----------------------
 !-----------------------------------------------------------------------
 
   subroutine SetServices(gcomp, rc)
 
     type(ESMF_GridComp)  :: gcomp
     integer, intent(out) :: rc
-    character(len=*),parameter  :: subname='(fv3gfs_cap:SetServices)'
+    character(len=*),parameter  :: subname='(fv3atm_cap:SetServices)'
 
     rc = ESMF_SUCCESS
 
@@ -983,7 +983,7 @@ subroutine InitializeRealize(gcomp, rc)
     integer, intent(out) :: rc
 
     ! local variables
-    character(len=*),parameter :: subname='(fv3gfs_cap:InitializeRealize)'
+    character(len=*),parameter :: subname='(fv3atm_cap:InitializeRealize)'
     type(ESMF_Clock)           :: clock
     type(ESMF_State)           :: importState, exportState
     integer                    :: urc
@@ -1248,7 +1248,7 @@ subroutine fv3_checkimport(gcomp, rc)
     integer, intent(out)       :: rc
 
     ! local variables
-    character(len=*),parameter :: subname='(fv3gfs_cap:fv3_checkimport)'
+    character(len=*),parameter :: subname='(fv3atm_cap:fv3_checkimport)'
     integer                    :: n, nf
     type(ESMF_Clock)           :: clock
     type(ESMF_Time)            :: currTime, invalidTime
@@ -1335,7 +1335,7 @@ subroutine TimestampExport_phase1(gcomp, rc)
     integer, intent(out)       :: rc
 
     ! local variables
-    character(len=*),parameter :: subname='(fv3gfs_cap:TimestampExport_phase1)'
+    character(len=*),parameter :: subname='(fv3atm_cap:TimestampExport_phase1)'
     type(ESMF_Clock)           :: driverClock, modelClock
     type(ESMF_State)           :: exportState
 
@@ -1365,7 +1365,7 @@ subroutine ModelFinalize(gcomp, rc)
     integer, intent(out)       :: rc
 
     ! local variables
-    character(len=*),parameter :: subname='(fv3gfs_cap:ModelFinalize)'
+    character(len=*),parameter :: subname='(fv3atm_cap:ModelFinalize)'
     integer                    :: i, urc
     type(ESMF_VM)              :: vm
     real(kind=8)               :: MPI_Wtime, timeffs
@@ -1413,4 +1413,4 @@ end subroutine ModelFinalize
 !
 !-----------------------------------------------------------------------------
 
-end module fv3gfs_cap_mod
+end module fv3atm_cap_mod