Oops, more cleanup.

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
@@ -1750,21 +1749,9 @@ subroutine ModelAdvance(gcomp, rc)
         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
-        call ESMF_LogWrite("MOM_cap: Writing restart :  "//trim(restartname), ESMF_LOGMSG_INFO)
-        call write_stoch_restart_ocn('RESTART/'//trim(restartname))
      endif
 
      if (is_root_pe()) then

config_src/drivers/nuopc_cap/mom_ocean_model_nuopc.F90

@@ -62,8 +62,8 @@ 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>
 
@@ -177,8 +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
@@ -253,7 +255,9 @@ subroutine ocean_model_init(Ocean_sfc, OS, Time_init, Time_in, gas_fields_ocn, i
                       !! The actual depth over which melt potential is computed will
                       !! min(HFrz, OBLD), where OBLD is the boundary layer depth.
                       !! If HFrz <= 0 (default), melt potential will not be computed.
-  logical :: use_melt_pot!< If true, allocate melt_potential array
+  logical :: use_melt_pot !< If true, allocate melt_potential array
+  logical :: use_CFC  !< If true, allocated arrays for surface CFCs.
+
 
 ! This include declares and sets the variable "version".
 #include "version_variable.h"
@@ -425,10 +429,11 @@ 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, &

config_src/drivers/solo_driver/MOM_driver.F90

@@ -69,19 +69,6 @@ program MOM_main
   use MOM_write_cputime,   only : write_cputime, MOM_write_cputime_init
   use MOM_write_cputime,   only : write_cputime_start_clock, write_cputime_CS
 
-  use ensemble_manager_mod, only : ensemble_manager_init, get_ensemble_size
-  use ensemble_manager_mod, only : ensemble_pelist_setup
-  use mpp_mod, only : set_current_pelist => mpp_set_current_pelist
-  use time_interp_external_mod, only : time_interp_external_init
-  use fms_affinity_mod,     only : fms_affinity_init, fms_affinity_set,fms_affinity_get
-
-  use MOM_ice_shelf, only : initialize_ice_shelf, ice_shelf_end, ice_shelf_CS
-  use MOM_ice_shelf, only : shelf_calc_flux, add_shelf_forces, ice_shelf_save_restart
-! , add_shelf_flux_forcing, add_shelf_flux_IOB
-
-  use MOM_wave_interface, only: wave_parameters_CS, MOM_wave_interface_init
-  use MOM_wave_interface, only: MOM_wave_interface_init_lite, Update_Surface_Waves
-
   implicit none
 
 #include <MOM_memory.h>
@@ -91,7 +78,6 @@ program MOM_main
   ! A structure containing pointers to the thermodynamic forcing fields
   ! at the ocean surface.
   type(forcing) :: fluxes
-
   ! A structure containing pointers to the ocean surface state fields.
   type(surface) :: sfc_state
 

docs/conf.py

@@ -159,7 +159,7 @@ def latexPassthru(name, rawtext, text, lineno, inliner, options={}, content=[]):
 
 # General information about the project.
 project = u'MOM6'
-copyright = u'2017-2021, MOM6 developers'
+copyright = u'2017-2022, MOM6 developers'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

src/core/MOM.F90

@@ -132,7 +132,7 @@ module MOM
 use MOM_variables,             only : surface, allocate_surface_state, deallocate_surface_state
 use MOM_variables,             only : thermo_var_ptrs, vertvisc_type, porous_barrier_ptrs
 use MOM_variables,             only : accel_diag_ptrs, cont_diag_ptrs, ocean_internal_state
-use MOM_variables,             only : rotate_surface_state, stochastic_pattern
+use MOM_variables,             only : rotate_surface_state
 use MOM_verticalGrid,          only : verticalGrid_type, verticalGridInit, verticalGridEnd
 use MOM_verticalGrid,          only : fix_restart_scaling
 use MOM_verticalGrid,          only : get_thickness_units, get_flux_units, get_tr_flux_units
@@ -154,6 +154,8 @@ module MOM
 use MOM_offline_main,          only : offline_fw_fluxes_into_ocean, offline_fw_fluxes_out_ocean
 use MOM_offline_main,          only : offline_advection_layer, offline_transport_end
 use MOM_ALE,                   only : ale_offline_tracer_final, ALE_main_offline
+use MOM_ice_shelf,             only : ice_shelf_CS, ice_shelf_query, initialize_ice_shelf
+use MOM_particles_mod,         only : particles, particles_init, particles_run, particles_save_restart, particles_end
 
 implicit none ; private
 
@@ -402,6 +404,16 @@ module MOM
   type(ODA_CS), pointer :: odaCS => NULL() !< a pointer to the control structure for handling
                                 !! ensemble model state vectors and data assimilation
                                 !! increments and priors
+  type(porous_barrier_ptrs) :: pbv !< porous barrier fractional cell metrics
+  real ALLOCABLE_, dimension(NIMEMB_PTR_,NJMEM_,NKMEM_) &
+                            :: por_face_areaU !< fractional open area of U-faces [nondim]
+  real ALLOCABLE_, dimension(NIMEM_,NJMEMB_PTR_,NKMEM_) &
+                            :: por_face_areaV !< fractional open area of V-faces [nondim]
+  real ALLOCABLE_, dimension(NIMEMB_PTR_,NJMEM_,NK_INTERFACE_) &
+                            :: por_layer_widthU !< fractional open width of U-faces [nondim]
+  real ALLOCABLE_, dimension(NIMEM_,NJMEMB_PTR_,NK_INTERFACE_) &
+                            :: por_layer_widthV !< fractional open width of V-faces [nondim]
+  type(particles), pointer :: particles => NULL() !<Lagrangian particles
   type(stochastic_CS), pointer :: stoch_CS => NULL() !< a pointer to the stochastics control structure
 end type MOM_control_struct
 
@@ -1381,7 +1393,7 @@ subroutine step_MOM_thermo(CS, G, GV, US, u, v, h, tv, fluxes, dtdia, &
     call cpu_clock_begin(id_clock_diabatic)
 
     call diabatic(u, v, h, tv, CS%Hml, fluxes, CS%visc, CS%ADp, CS%CDp, dtdia, &
-                  Time_end_thermo, G, GV, US, CS%diabatic_CSp, CS%stoch_CS,OBC=CS%OBC, Waves=Waves)
+                  Time_end_thermo, G, GV, US, CS%diabatic_CSp, CS%stoch_CS, CS%OBC, Waves)
     fluxes%fluxes_used = .true.
 
     if (showCallTree) call callTree_waypoint("finished diabatic (step_MOM_thermo)")
@@ -1799,7 +1811,10 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
   integer :: nkml, nkbl, verbosity, write_geom
   integer :: dynamics_stencil  ! The computational stencil for the calculations
                                ! in the dynamic core.
-  real :: conv2watt, conv2salt
+  real :: conv2watt            ! A conversion factor from temperature fluxes to heat
+                               ! fluxes [J m-2 H-1 degC-1 ~> J m-3 degC-1 or J kg-1 degC-1]
+  real :: conv2salt            ! A conversion factor for salt fluxes [m H-1 ~> 1] or [kg m-2 H-1 ~> 1]
+  real :: RL2_T2_rescale, Z_rescale, QRZ_rescale ! Unit conversion factors
   character(len=48) :: flux_units, S_flux_units
 
   type(vardesc) :: vd_T, vd_S  ! Structures describing temperature and salinity variables.
@@ -2475,28 +2490,12 @@ subroutine initialize_MOM(Time, Time_init, param_file, dirs, CS, restart_CSp, &
     call callTree_waypoint("returned from ALE_init() (initialize_MOM)")
   endif
 
-  !   Shift from using the temporary dynamic grid type to using the final
-  ! (potentially static) ocean-specific grid type.
-  !   The next line would be needed if G%Domain had not already been init'd above:
-  !     call clone_MOM_domain(dG%Domain, G%Domain)
-  call MOM_grid_init(G, param_file, US, HI, bathymetry_at_vel=bathy_at_vel)
-  call copy_dyngrid_to_MOM_grid(dG, G, US)
-  call destroy_dyn_horgrid(dG)
-
   ! Set a few remaining fields that are specific to the ocean grid type.
   if (CS%rotate_index) then
     call set_first_direction(G, modulo(first_direction + turns, 2))
   else
     call set_first_direction(G, modulo(first_direction, 2))
   endif
-  call MOM_grid_init(G_in, param_file, US, HI_in, bathymetry_at_vel=bathy_at_vel)
-  call copy_dyngrid_to_MOM_grid(dG_in, G_in, US)
-  call destroy_dyn_horgrid(dG_in)
-
-  if (.not. CS%rotate_index) &
-    G => G_in
-  ! Set a few remaining fields that are specific to the ocean grid type.
-  call set_first_direction(G, first_direction)
   ! Allocate the auxiliary non-symmetric domain for debugging or I/O purposes.
   if (CS%debug .or. G%symmetric) then
     call clone_MOM_domain(G%Domain, G%Domain_aux, symmetric=.false.)

src/core/MOM_barotropic.F90

@@ -228,7 +228,7 @@ module MOM_barotropic
   logical :: tidal_sal_bug   !< If true, the tidal self-attraction and loading anomaly in the
                              !! barotropic solver has the wrong sign, replicating a long-standing
                              !! bug.
-  real    :: G_extra         !< A nondimensional factor by which gtot is enhanced.
+  real    :: G_extra         !< A nondimensional factor by which gtot is enhanced [nondim].
   integer :: hvel_scheme     !< An integer indicating how the thicknesses at
                              !! velocity points are calculated. Valid values are
                              !! given by the parameters defined below:
@@ -4302,7 +4302,9 @@ subroutine barotropic_init(u, v, h, eta, Time, G, GV, US, param_file, diag, CS,
   real :: det_de      ! The partial derivative due to self-attraction and loading of the reference
                       ! geopotential with the sea surface height when tides are enabled.
                       ! This is typically ~0.09 or less.
-  real, allocatable, dimension(:,:) :: lin_drag_h
+  real, allocatable :: lin_drag_h(:,:)  ! A spatially varying linear drag coefficient at tracer points
+                                        ! that acts on the barotropic flow [Z T-1 ~> m s-1].
+
   type(memory_size_type) :: MS
   type(group_pass_type) :: pass_static_data, pass_q_D_Cor
   type(group_pass_type) :: pass_bt_hbt_btav, pass_a_polarity

src/diagnostics/MOM_diagnostics.F90

@@ -1286,8 +1286,8 @@ subroutine post_surface_thermo_diags(IDs, G, GV, US, diag, dt_int, sfc_state, tv
   real,                     intent(in) :: dt_int !< total time step associated with these diagnostics [T ~> s].
   type(surface),            intent(in) :: sfc_state !< structure describing the ocean surface state
   type(thermo_var_ptrs),    intent(in) :: tv  !< A structure pointing to various thermodynamic variables
-  real, dimension(SZI_(G),SZJ_(G)), &
-                            intent(in) :: ssh !< Time mean surface height without corrections for ice displacement [m]
+  real, dimension(SZI_(G),SZJ_(G)), intent(in) :: ssh !< Time mean surface height without corrections
+                                              !! for ice displacement [Z ~> m]
   real, dimension(SZI_(G),SZJ_(G)), intent(in) :: ssh_ibc !< Time mean surface height with corrections
                                               !! for ice displacement and the inverse barometer [Z ~> m]