Merge pull request #81 from jiandewang/feature/update-to-main-20211220

update MOM6 to its main branch commit 20211220

Author: jiandewang

config_src/drivers/nuopc_cap/mom_cap.F90

@@ -98,7 +98,6 @@ module MOM_cap_mod
 use NUOPC_Model, only: model_label_Finalize       => label_Finalize
 use NUOPC_Model, only: SetVM
 
-use MOM_stochastics,         only : write_mom_restart_stoch
 !$use omp_lib             , only : omp_set_num_threads
 
 implicit none; private
@@ -1526,7 +1525,7 @@ subroutine ModelAdvance(gcomp, rc)
   integer                                :: nc
   type(ESMF_Time)                        :: MyTime
   integer                                :: seconds, day, year, month, hour, minute
-  character(ESMF_MAXSTR)                 :: restartname, cvalue
+  character(ESMF_MAXSTR)                 :: restartname, cvalue, stoch_restartname
   character(240)                         :: msgString
   character(ESMF_MAXSTR)                 :: casename
   integer                                :: iostat
@@ -1740,26 +1739,19 @@ subroutine ModelAdvance(gcomp, rc)
         ! write the final restart without a timestamp
         if (ESMF_AlarmIsRinging(stop_alarm, rc=rc)) then
            write(restartname,'(A)')"MOM.res"
+           write(stoch_restartname,'(A)')"ocn_stoch.res.nc"
         else
            write(restartname,'(A,I4.4,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2)') &
                 "MOM.res.", year, month, day, hour, minute, seconds
+           write(stoch_restartname,'(A,I4.4,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2,A)') &
+                "ocn_stoch.res.", year, month, day, hour, minute, seconds,".nc"
         endif
         call ESMF_LogWrite("MOM_cap: Writing restart :  "//trim(restartname), ESMF_LOGMSG_INFO)
 
         ! write restart file(s)
-        call ocean_model_restart(ocean_state, restartname=restartname)
+        call ocean_model_restart(ocean_state, restartname=restartname, &
+                                stoch_restartname=stoch_restartname)
 
-        if (ocean_state%do_sppt .OR. ocean_state%pert_epbl) then
-          if (ESMF_AlarmIsRinging(stop_alarm, rc=rc)) then
-             write(restartname,'(A)')"ocn_stoch.res.nc"
-          else
-             write(restartname,'(A,I4.4,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2,"-",I2.2,A)') &
-                  "ocn_stoch.res.", year, month, day, hour, minute, seconds,".nc"
-          endif
-          call ESMF_LogWrite("MOM_cap: Writing stoch restart :  "//trim(restartname), &
-                             ESMF_LOGMSG_INFO)
-          call write_mom_restart_stoch('RESTART/'//trim(restartname))
-        endif
      endif
 
      if (is_root_pe()) then

config_src/drivers/nuopc_cap/mom_ocean_model_nuopc.F90

@@ -62,8 +62,7 @@ module MOM_ocean_model_nuopc
 use MOM_surface_forcing_nuopc, only : convert_IOB_to_forces, ice_ocn_bnd_type_chksum
 use MOM_surface_forcing_nuopc, only : ice_ocean_boundary_type, surface_forcing_CS
 use MOM_surface_forcing_nuopc, only : forcing_save_restart
-use MOM_domains,               only : root_PE,num_PEs
-use MOM_coms,                  only : Get_PElist
+use get_stochy_pattern_mod,  only : write_stoch_restart_ocn
 use iso_fortran_env,           only : int64
 
 #include <MOM_memory.h>
@@ -178,8 +177,10 @@ module MOM_ocean_model_nuopc
                               !! steps can span multiple coupled time steps.
   logical :: diabatic_first   !< If true, apply diabatic and thermodynamic
                               !! processes before time stepping the dynamics.
-  logical,public :: do_sppt   !< If true, write stochastic physics restarts
-  logical,public :: pert_epbl !< If true, write stochastic physics restarts
+  logical :: do_sppt         !< If true, stochastically perturb the diabatic and
+                             !! write restarts
+  logical :: pert_epbl       !< If true, then randomly perturb the KE dissipation and
+                             !! genration termsand write restarts
 
   real :: eps_omesh           !< Max allowable difference between ESMF mesh and MOM6
                               !! domain coordinates
@@ -428,18 +429,18 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
 
   endif
 
-  ! check to see if stochastic physics is active
+  call extract_surface_state(OS%MOM_CSp, OS%sfc_state)
+! get number of processors and PE list for stocasthci physics initialization
   call get_param(param_file, mdl, "DO_SPPT", OS%do_sppt, &
                  "If true, then stochastically perturb the thermodynamic "//&
-                 "tendemcies of T,S, amd h.  Amplitude and correlations are "//&
+                 "tendencies of T,S, and h.  Amplitude and correlations are "//&
                  "controlled by the nam_stoch namelist in the UFS model only.", &
                  default=.false.)
   call get_param(param_file, mdl, "PERT_EPBL", OS%pert_epbl, &
                  "If true, then stochastically perturb the kinetic energy "//&
                  "production and dissipation terms.  Amplitude and correlations are "//&
                  "controlled by the nam_stoch namelist in the UFS model only.", &
                  default=.false.)
-  call extract_surface_state(OS%MOM_CSp, OS%sfc_state)
 
   call close_param_file(param_file)
   call diag_mediator_close_registration(OS%diag)
@@ -701,14 +702,17 @@ subroutine update_ocean_model(Ice_ocean_boundary, OS, Ocean_sfc, &
 end subroutine update_ocean_model
 
 !> This subroutine writes out the ocean model restart file.
-subroutine ocean_model_restart(OS, timestamp, restartname, num_rest_files)
+subroutine ocean_model_restart(OS, timestamp, restartname, stoch_restartname, num_rest_files)
   type(ocean_state_type),     pointer    :: OS !< A pointer to the structure containing the
                                                !! internal ocean state being saved to a restart file
   character(len=*), optional, intent(in) :: timestamp !< An optional timestamp string that should be
                                                !! prepended to the file name. (Currently this is unused.)
   character(len=*), optional, intent(in) :: restartname !< Name of restart file to use
                                                !! This option distinguishes the cesm interface from the
                                                !! non-cesm interface
+  character(len=*), optional, intent(in) :: stoch_restartname !< Name of restart file to use
+                                               !! This option distinguishes the cesm interface from the
+                                               !! non-cesm interface
   integer, optional, intent(out)         :: num_rest_files !< number of restart files written
 
   if (.not.MOM_state_is_synchronized(OS%MOM_CSp)) &
@@ -748,6 +752,11 @@ subroutine ocean_model_restart(OS, timestamp, restartname, num_rest_files)
         endif
      endif
   endif
+  if (present(stoch_restartname)) then
+      if (OS%do_sppt .OR. OS%pert_epbl) then
+         call write_stoch_restart_ocn('RESTART/'//trim(stoch_restartname))
+     endif
+  endif
 
 end subroutine ocean_model_restart
 ! </SUBROUTINE> NAME="ocean_model_restart"

config_src/external/OCEAN_stochastic_phyiscs/MOM_stochastics_stub.F90

@@ -0,0 +1,68 @@
+! The are stubs for ocean stochastic physics
+! the fully functional code is available at
+! http://github.com/noaa-psd/stochastic_physics
+module stochastic_physics
+
+implicit none
+
+private
+
+public :: init_stochastic_physics_ocn
+public :: run_stochastic_physics_ocn
+
+contains
+
+!!!!!!!!!!!!!!!!!!!!
+subroutine init_stochastic_physics_ocn(delt,geoLonT,geoLatT,nx,ny,nz,pert_epbl_in,do_sppt_in, &
+                                       mpiroot, mpicomm, iret)
+implicit none
+real,intent(in)       :: delt !< timestep in seconds between calls to run_stochastic_physics_ocn
+integer,intent(in)    :: nx   !< number of gridpoints in the x-direction of the compute grid
+integer,intent(in)    :: ny   !< number of gridpoints in the y-direction of the compute grid
+integer,intent(in)    :: nz   !< number of gridpoints in the z-direction of the compute grid
+real,intent(in)       :: geoLonT(nx,ny) !< Longitude in degrees
+real,intent(in)       :: geoLatT(nx,ny) !< Latitude in degrees
+logical,intent(in)    :: pert_epbl_in !< logical flag, if true generate random pattern for ePBL perturbations
+logical,intent(in)    :: do_sppt_in   !< logical flag, if true generate random pattern for SPPT perturbations
+integer,intent(in)    :: mpiroot !< root processor
+integer,intent(in)    :: mpicomm !< mpi communicator
+integer, intent(out)  :: iret    !< return code
+
+iret=0
+if (pert_epbl_in .EQV. .true. ) then
+   print*,'pert_epbl needs to be false if using the stub'
+   iret=-1
+endif
+if (do_sppt_in.EQV. .true. ) then
+   print*,'do_sppt needs to be false if using the stub'
+   iret=-1
+endif
+return
+end subroutine init_stochastic_physics_ocn
+
+subroutine run_stochastic_physics_ocn(sppt_wts,t_rp1,t_rp2)
+implicit none
+real, intent(inout) :: sppt_wts(:,:) !< array containing random weights for SPPT range [0,2]
+real, intent(inout) :: t_rp1(:,:)    !< array containing random weights for ePBL
+                                     !! perturbations (KE generation) range [0,2]
+real, intent(inout) :: t_rp2(:,:)    !< array containing random weights for ePBL
+                                     !! perturbations (KE dissipation) range [0,2]
+return
+end subroutine run_stochastic_physics_ocn
+
+end module stochastic_physics
+
+module get_stochy_pattern_mod
+
+private
+
+public  :: write_stoch_restart_ocn
+
+contains
+subroutine write_stoch_restart_ocn(sfile)
+
+character(len=*) :: sfile   !< name of restart file
+return
+end subroutine write_stoch_restart_ocn
+
+end module get_stochy_pattern_mod

config_src/external/stochastic_physics/stochastic_physics.F90

@@ -19,20 +19,20 @@ module MOM_stochastics
 use MOM_domains,             only : root_PE,num_PEs
 use MOM_coms,                only : Get_PElist
 use stochastic_physics,      only : init_stochastic_physics_ocn, run_stochastic_physics_ocn
-use get_stochy_pattern_mod, only: write_stoch_restart_ocn
 
 #include <MOM_memory.h>
 
 implicit none ; private
 
-public stochastics_init, update_stochastics, write_mom_restart_stoch
+public stochastics_init, update_stochastics
 
 !> This control structure holds parameters for the MOM_stochastics module
 type, public:: stochastic_CS
-  logical :: do_sppt                 !< If true, stochastically perturb the diabatic
-  logical :: pert_epbl       !! If true, then randomly perturb the KE dissipation and genration terms
-  integer :: id_sppt_wts  = -1
-  integer :: id_epbl1_wts=-1,id_epbl2_wts=-1
+  logical :: do_sppt         !< If true, stochastically perturb the diabatic
+  logical :: pert_epbl       !< If true, then randomly perturb the KE dissipation and genration terms
+  integer :: id_sppt_wts  = -1 !< Diagnostic id for SPPT
+  integer :: id_epbl1_wts=-1 !< Diagnostic id for epbl generation perturbation
+  integer :: id_epbl2_wts=-1 !< Diagnostic id for epbl dissipation perturbation
   ! stochastic patterns
   real, allocatable :: sppt_wts(:,:)  !< Random pattern for ocean SPPT
                                      !! tendencies with a number between 0 and 2
@@ -47,9 +47,9 @@ module MOM_stochastics
 !!   This subroutine initializes the stochastics physics control structure.
 subroutine stochastics_init(dt, grid, GV, CS, param_file, diag, Time)
   real, intent(in)                     :: dt       !< time step [T ~> s]
-  type(ocean_grid_type),   intent(in)  :: grid     ! horizontal grid information
-  type(verticalGrid_type), intent(in)  :: GV       ! vertical grid structure
-  type(stochastic_CS), pointer,     intent(inout):: CS
+  type(ocean_grid_type),   intent(in)  :: grid     !< horizontal grid information
+  type(verticalGrid_type), intent(in)  :: GV       !< vertical grid structure
+  type(stochastic_CS), pointer,     intent(inout):: CS !< stochastic control structure
   type(param_file_type),   intent(in)    :: param_file !< A structure to parse for run-time parameters
   type(diag_ctrl), target, intent(inout) :: diag             !< structure to regulate diagnostic output
   type(time_type), target                :: Time             !< model time
@@ -59,7 +59,7 @@ subroutine stochastics_init(dt, grid, GV, CS, param_file, diag, Time)
   integer :: num_procs         ! number of processors to pass to stochastic physics
   integer :: iret              ! return code from stochastic physics
   integer :: me                !  my pe
-  integer :: master            !  root pe
+  integer :: pe_zero           !  root pe
   integer :: nx                ! number of x-points including halo
   integer :: ny                ! number of x-points including halo
 
@@ -95,11 +95,11 @@ subroutine stochastics_init(dt, grid, GV, CS, param_file, diag, Time)
      num_procs=num_PEs()
      allocate(pelist(num_procs))
      call Get_PElist(pelist,commID = mom_comm)
-     master=root_PE()
+     pe_zero=root_PE()
      nx = grid%ied - grid%isd + 1
      ny = grid%jed - grid%jsd + 1
      call init_stochastic_physics_ocn(dt,grid%geoLonT,grid%geoLatT,nx,ny,GV%ke, &
-                                      CS%pert_epbl,CS%do_sppt,master,mom_comm,iret)
+                                      CS%pert_epbl,CS%do_sppt,pe_zero,mom_comm,iret)
      if (iret/=0)  then
          call MOM_error(FATAL, "call to init_stochastic_physics_ocn failed")
          return
@@ -140,16 +140,5 @@ subroutine update_stochastics(CS)
   return
 end subroutine update_stochastics
 
-!< wrapper to write ocean stochastic restarts
-subroutine write_mom_restart_stoch(filename)
-  character(len=*) :: filename
-
-  call callTree_enter("write_mom_restart_stoch(), MOM_stochastics.F90")
-
-  call write_stoch_restart_ocn(filename)
-
-  return
-end subroutine write_mom_restart_stoch
-
 end module MOM_stochastics
 

config_src/external/OCEAN_stochastic_phyiscs/MOM_stochastics.F90 src/parameterizations/stochastic/MOM_stochastics.F90

@@ -600,8 +600,8 @@ subroutine ePBL_column(h, u, v, T0, S0, dSV_dT, dSV_dS, TKE_forcing, B_flux, abs
                  optional, pointer       :: Waves  !< Wave CS for Langmuir turbulence
   type(ocean_grid_type), &
                  optional, intent(inout) :: G      !< The ocean's grid structure.
-  real,          optional, intent(in)    :: epbl1_wt ! random number to perturb KE generation
-  real,          optional, intent(in)    :: epbl2_wt ! random number to perturb KE dissipation
+  real,          optional, intent(in)    :: epbl1_wt !< random number to perturb KE generation
+  real,          optional, intent(in)    :: epbl2_wt !< random number to perturb KE dissipation
   integer,       optional, intent(in)    :: i      !< The i-index to work on (used for Waves)
   integer,       optional, intent(in)    :: j      !< The i-index to work on (used for Waves)