Update to latest MOM6

- update patch files for updated MOM6 version

- Add new modules to MOM CMakeLists

Co-authored-by: Dougie Squire <42455466+dougiesquire@users.noreply.github.com>

Author: anton-seaice

MOM6/CMakeLists.txt

@@ -62,6 +62,7 @@ target_sources(OM3_mom6 PRIVATE
   MOM6/src/core/MOM_CoriolisAdv.F90
   MOM6/src/core/MOM_density_integrals.F90
   MOM6/src/core/MOM_dynamics_split_RK2.F90
+  MOM6/src/core/MOM_dynamics_split_RK2b.F90
   MOM6/src/core/MOM_dynamics_unsplit.F90
   MOM6/src/core/MOM_dynamics_unsplit_RK2.F90
   MOM6/src/core/MOM.F90
@@ -80,7 +81,9 @@ target_sources(OM3_mom6 PRIVATE
   MOM6/src/core/MOM_verticalGrid.F90
 
   MOM6/src/diagnostics/MOM_debugging.F90
+  MOM6/src/diagnostics/MOM_diagnose_MLD.F90
   MOM6/src/diagnostics/MOM_diagnostics.F90
+  MOM6/src/diagnostics/MOM_harmonic_analysis.F90
   MOM6/src/diagnostics/MOM_obsolete_diagnostics.F90
   MOM6/src/diagnostics/MOM_obsolete_params.F90
   MOM6/src/diagnostics/MOM_spatial_means.F90
@@ -97,6 +100,7 @@ target_sources(OM3_mom6 PRIVATE
   MOM6/src/equation_of_state/MOM_EOS_Wright.F90
   MOM6/src/equation_of_state/MOM_EOS_Wright_full.F90
   MOM6/src/equation_of_state/MOM_EOS_Wright_red.F90
+  MOM6/src/equation_of_state/MOM_EOS_base_type.F90
   MOM6/src/equation_of_state/MOM_temperature_convert.F90
   MOM6/src/equation_of_state/MOM_TFreeze.F90
 
@@ -201,7 +205,9 @@ target_sources(OM3_mom6 PRIVATE
   MOM6/src/parameterizations/lateral/MOM_MEKE.F90
   MOM6/src/parameterizations/lateral/MOM_MEKE_types.F90
   MOM6/src/parameterizations/lateral/MOM_mixed_layer_restrat.F90
+  MOM6/src/parameterizations/lateral/MOM_self_attr_load.F90
   MOM6/src/parameterizations/lateral/MOM_spherical_harmonics.F90
+  MOM6/src/parameterizations/lateral/MOM_streaming_filter.F90
   MOM6/src/parameterizations/lateral/MOM_thickness_diffuse.F90
   MOM6/src/parameterizations/lateral/MOM_tidal_forcing.F90
   MOM6/src/parameterizations/lateral/MOM_Zanna_Bolton.F90

MOM6/MOM6

@@ -1,24 +1,22 @@
---- ../MOM6/src/diagnostics/MOM_PointAccel.F90	2024-10-23 10:07:22.000000000 +1100
-+++ ../MOM6/src/diagnostics/MOM_PointAccel.F90.new	2024-10-23 10:15:54.000000000 +1100
-@@ -122,8 +122,8 @@
-     if (CS%u_file < 0) then
+diff --git a/MOM6/src/diagnostics/MOM_PointAccel.F90 b/MOM6/src/diagnostics/MOM_PointAccel.F90.new
+index 30f0803..7f91f79 100644
+--- a/MOM6/src/diagnostics/MOM_PointAccel.F90
++++ b/MOM6/src/diagnostics/MOM_PointAccel.F90.new
+@@ -124,7 +124,7 @@ subroutine write_u_accel(I, j, um, hin, ADp, CDp, dt, G, GV, US, CS, vel_rpt, st
+     if (CS%u_file == -1) then
        if (len_trim(CS%u_trunc_file) < 1) return
        call open_ASCII_file(CS%u_file, trim(CS%u_trunc_file), action=APPEND_FILE, &
 -                           threading=MULTIPLE, fileset=SINGLE_FILE)
--      if (CS%u_file < 0) then
 +                           threading=MULTIPLE, fileset=MULTIPLE)
-+      if (CS%u_file == -1) then
+       if (CS%u_file == -1) then
          call MOM_error(NOTE, 'Unable to open file '//trim(CS%u_trunc_file)//'.')
          return
-       endif
-@@ -461,8 +461,8 @@
-     if (CS%v_file < 0) then
+@@ -465,7 +465,7 @@ subroutine write_v_accel(i, J, vm, hin, ADp, CDp, dt, G, GV, US, CS, vel_rpt, st
+     if (CS%v_file == -1) then
        if (len_trim(CS%v_trunc_file) < 1) return
        call open_ASCII_file(CS%v_file, trim(CS%v_trunc_file), action=APPEND_FILE, &
 -                           threading=MULTIPLE, fileset=SINGLE_FILE)
--      if (CS%v_file < 0) then
 +                           threading=MULTIPLE, fileset=MULTIPLE)
-+      if (CS%v_file == -1) then
+       if (CS%v_file == -1) then
          call MOM_error(NOTE, 'Unable to open file '//trim(CS%v_trunc_file)//'.')
          return
-       endif

MOM6/patches/MOM_PointAccel.F90.patch

@@ -1,8 +1,8 @@
 diff --git a/MOM6/src/framework/MOM_coupler_types.F90 b/MOM6/src/framework/MOM_coupler_types.F90.new
-index f87b409..124d786 100644
+index b931a2d..cac9309 100644
 --- a/MOM6/src/framework/MOM_coupler_types.F90
 +++ b/MOM6/src/framework/MOM_coupler_types.F90.new
-@@ -8,7 +8,10 @@ use MOM_couplertype_infra, only : CT_set_diags, CT_send_data, CT_write_chksums,
+@@ -9,7 +9,10 @@ use MOM_couplertype_infra, only : CT_set_diags, CT_send_data, CT_write_chksums,
  use MOM_couplertype_infra, only : CT_copy_data, CT_increment_data, CT_rescale_data
  use MOM_couplertype_infra, only : CT_set_data, CT_extract_data, CT_redistribute_data
  use MOM_couplertype_infra, only : coupler_1d_bc_type, coupler_2d_bc_type, coupler_3d_bc_type
@@ -14,7 +14,7 @@ index f87b409..124d786 100644
  use MOM_domain_infra,      only : domain2D
  use MOM_time_manager,      only : time_type
 
-@@ -22,7 +25,10 @@ public :: atmos_ocn_coupler_flux, coupler_type_data_override
+@@ -23,7 +26,10 @@ public :: atmos_ocn_coupler_flux, coupler_type_data_override
  public :: coupler_1d_bc_type, coupler_2d_bc_type, coupler_3d_bc_type
  ! These are encoding constant parameters that indicate whether a flux, solubility or
  ! surface ocean concentration are being set or accessed with an inquiry.

MOM6/patches/MOM_coupler_types.F90.patch

@@ -1,8 +1,8 @@
 diff --git a/MOM6/src/core/MOM_forcing_type.F90 b/MOM6/src/core/MOM_forcing_type.F90.new
-index 200bbd7..fca9187 100644
+index 998713d..a2efcaa 100644
 --- a/MOM6/src/core/MOM_forcing_type.F90
 +++ b/MOM6/src/core/MOM_forcing_type.F90.new
-@@ -2080,6 +2080,11 @@ subroutine fluxes_accumulate(flux_tmp, fluxes, G, wt2, forces)
+@@ -2280,6 +2280,11 @@ subroutine fluxes_accumulate(flux_tmp, fluxes, G, wt2, forces)
 
      fluxes%salt_flux(i,j) = wt1*fluxes%salt_flux(i,j) + wt2*flux_tmp%salt_flux(i,j)
    enddo ; enddo

MOM6/patches/MOM_forcing_type.F90.patch

@@ -1,5 +1,5 @@
 diff --git a/MOM6/src/tracer/MOM_generic_tracer.F90 b/MOM6/src/tracer/MOM_generic_tracer.F90.new
-index 131110e..ae75b2e 100644
+index 6b10d15..e092aa7 100644
 --- a/MOM6/src/tracer/MOM_generic_tracer.F90
 +++ b/MOM6/src/tracer/MOM_generic_tracer.F90.new
 @@ -21,7 +21,7 @@ module MOM_generic_tracer
@@ -11,18 +11,7 @@ index 131110e..ae75b2e 100644
 
    use g_tracer_utils,   only: g_tracer_get_name,g_tracer_set_values,g_tracer_set_common,g_tracer_get_common
    use g_tracer_utils,   only: g_tracer_get_next,g_tracer_type,g_tracer_is_prog,g_tracer_flux_init
-@@ -352,7 +352,9 @@ contains
-           enddo ; enddo ; enddo
- 
-           !jgj: Reset CASED to 0 below K=1
--          if ( (trim(g_tracer_name) == 'cased') .or. (trim(g_tracer_name) == 'ca13csed') ) then
-+          ! dts: also WOMBAT sediment tracers
-+          if ( (trim(g_tracer_name) == 'cased') .or. (trim(g_tracer_name) == 'ca13csed') .or. &
-+            (trim(g_tracer_name) == 'det_sediment') .or. (trim(g_tracer_name) == 'caco3_sediment')) then
-             do k=2,nk ; do j=jsc,jec ; do i=isc,iec
-               if (tr_ptr(i,j,k) /= CS%tracer_land_val) then
-                 tr_ptr(i,j,k) = 0.0
-@@ -507,6 +509,11 @@ contains
+@@ -527,6 +527,11 @@ contains
      !      the fluxes without coming into this subroutine.
      !      MOM5 has to modified to conform.
 

MOM6/patches/MOM_generic_tracer.F90.patch

@@ -1,6 +1,8 @@
---- ../MOM6/config_src/infra/FMS2/MOM_io_infra.F90	2024-10-23 10:07:33.000000000 +1100
-+++ ../MOM6/config_src/infra/FMS2/MOM_io_infra.F90.new	2024-10-23 10:16:45.000000000 +1100
-@@ -376,8 +376,7 @@
+diff --git a/MOM6/config_src/infra/FMS2/MOM_io_infra.F90 b/MOM6/config_src/infra/FMS2/MOM_io_infra.F90.new
+index a43b4e9..169ed25 100644
+--- a/MOM6/config_src/infra/FMS2/MOM_io_infra.F90
++++ b/MOM6/config_src/infra/FMS2/MOM_io_infra.F90.new
+@@ -376,8 +376,7 @@ subroutine open_ASCII_file(unit, file, action, threading, fileset)
    logical :: exists
    logical :: is_open
    character(len=6) :: action_arg, position_arg
@@ -10,7 +12,7 @@
    ! NOTE: This function is written to emulate the original behavior of mpp_open
    !   from the FMS1 library, on which the MOM API is still based.  Much of this
    !   can be removed if we choose to drop this compatibility, but for now we
-@@ -433,12 +432,12 @@
+@@ -433,12 +432,12 @@ subroutine open_ASCII_file(unit, file, action, threading, fileset)
      endif
    endif
 

MOM6/patches/MOM_io_infra.F90.patch

@@ -1,5 +1,5 @@
 diff --git a/MOM6/config_src/drivers/nuopc_cap/mom_cap.F90 b/MOM6/config_src/drivers/nuopc_cap/mom_cap.F90.new
-index 3574943..f948684 100644
+index fab6fe1..541d7f1 100644
 --- a/MOM6/config_src/drivers/nuopc_cap/mom_cap.F90
 +++ b/MOM6/config_src/drivers/nuopc_cap/mom_cap.F90.new
 @@ -2,8 +2,9 @@
@@ -53,7 +53,7 @@ index 3574943..f948684 100644
  end type
 
  !>  Wrapper-derived type required to associate an internal state instance
-@@ -408,6 +422,10 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
+@@ -416,6 +430,10 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
    type (ocean_public_type),      pointer :: ocean_public => NULL()
    type (ocean_state_type),       pointer :: ocean_state => NULL()
    type(ice_ocean_boundary_type), pointer :: Ice_ocean_boundary => NULL()
@@ -64,15 +64,15 @@ index 3574943..f948684 100644
    type(ocean_internalstate_wrapper)      :: ocean_internalstate
    type(ocean_grid_type),         pointer :: ocean_grid => NULL()
    type(directories)                      :: dirs
-@@ -439,6 +457,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
+@@ -447,6 +465,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
    character(len=512)                     :: restartfile          ! Path/Name of restart file
    character(len=2048)                    :: restartfiles         ! Path/Name of restart files
                                                                   ! (same as restartfile if single restart file)
 +  character(240)                         :: additional_restart_dir
    character(len=*), parameter            :: subname='(MOM_cap:InitializeAdvertise)'
    character(len=32)                      :: calendar
    character(len=:), allocatable          :: rpointer_filename
-@@ -517,6 +536,8 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
+@@ -525,6 +544,8 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
    if (chkerr(rc,__LINE__,u_FILE_u)) return
    call MOM_infra_init(mpi_comm_mom)
 
@@ -81,7 +81,7 @@ index 3574943..f948684 100644
    ! determine the calendar
    if (cesm_coupled) then
      call NUOPC_CompAttributeGet(gcomp, name="calendar", value=cvalue, &
-@@ -648,13 +669,44 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
+@@ -656,13 +677,44 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
 
    endif
 
@@ -126,7 +126,7 @@ index 3574943..f948684 100644
 
    ! GMM, this call is not needed in CESM. Check with EMC if it can be deleted.
    call ocean_model_flux_init(ocean_state)
-@@ -721,6 +773,31 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
+@@ -729,6 +781,31 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
      Ice_ocean_boundary%hcond           = 0.0
    endif
 
@@ -158,7 +158,7 @@ index 3574943..f948684 100644
    call query_ocean_state(ocean_state, use_waves=use_waves, wave_method=wave_method)
    if (use_waves) then
      if (wave_method == "EFACTOR") then
-@@ -789,6 +866,15 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
+@@ -797,6 +874,15 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
      endif
    endif
 
@@ -174,7 +174,7 @@ index 3574943..f948684 100644
    !--------- export fields -------------
    call fld_list_add(fldsFrOcn_num, fldsFrOcn, "So_omask"   , "will provide")
    call fld_list_add(fldsFrOcn_num, fldsFrOcn, "So_t"       , "will provide")
-@@ -800,6 +886,8 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
+@@ -808,6 +894,8 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
    call fld_list_add(fldsFrOcn_num, fldsFrOcn, "Fioo_q"     , "will provide")
    call fld_list_add(fldsFrOcn_num, fldsFrOcn, "So_bldepth" , "will provide")
 
@@ -183,7 +183,7 @@ index 3574943..f948684 100644
    do n = 1,fldsToOcn_num
      call NUOPC_Advertise(importState, standardName=fldsToOcn(n)%stdname, name=fldsToOcn(n)%shortname, rc=rc)
      if (ChkErr(rc,__LINE__,u_FILE_u)) return
-@@ -1611,11 +1699,14 @@ subroutine ModelAdvance(gcomp, rc)
+@@ -1619,11 +1707,14 @@ subroutine ModelAdvance(gcomp, rc)
    type (ocean_public_type),      pointer :: ocean_public       => NULL()
    type (ocean_state_type),       pointer :: ocean_state        => NULL()
    type(ice_ocean_boundary_type), pointer :: Ice_ocean_boundary => NULL()
@@ -198,7 +198,7 @@ index 3574943..f948684 100644
    integer                                :: dth, dtm, dts
    integer                                :: nc
    type(ESMF_Time)                        :: MyTime
-@@ -1627,12 +1718,13 @@ subroutine ModelAdvance(gcomp, rc)
+@@ -1635,12 +1726,13 @@ subroutine ModelAdvance(gcomp, rc)
    integer                                :: writeunit
    integer                                :: localPet
    type(ESMF_VM)                          :: vm
@@ -213,15 +213,15 @@ index 3574943..f948684 100644
    integer                                :: num_rest_files
    real(8)                                :: MPI_Wtime, timers
    logical                                :: write_restart
-@@ -1673,6 +1765,7 @@ subroutine ModelAdvance(gcomp, rc)
+@@ -1683,6 +1775,7 @@ subroutine ModelAdvance(gcomp, rc)
 
    Time_step_coupled = esmf2fms_time(timeStep)
    Time = esmf2fms_time(currTime)
 +  Time_import = Time
 
    !---------------
    ! Apply ocean lag for startup runs:
-@@ -1748,8 +1841,39 @@ subroutine ModelAdvance(gcomp, rc)
+@@ -1758,8 +1851,39 @@ subroutine ModelAdvance(gcomp, rc)
      ! Import data
      !---------------
 
@@ -261,7 +261,7 @@ index 3574943..f948684 100644
 
      !---------------
      ! Update MOM6
-@@ -1811,7 +1935,7 @@ subroutine ModelAdvance(gcomp, rc)
+@@ -1831,7 +1955,7 @@ subroutine ModelAdvance(gcomp, rc)
        ! determine restart filename
        call ESMF_ClockGetNextTime(clock, MyTime, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -270,7 +270,7 @@ index 3574943..f948684 100644
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
        if (cesm_coupled) then
-@@ -1869,6 +1993,14 @@ subroutine ModelAdvance(gcomp, rc)
+@@ -1889,6 +2013,14 @@ subroutine ModelAdvance(gcomp, rc)
 
        endif
 
@@ -285,15 +285,15 @@ index 3574943..f948684 100644
        if (is_root_pe()) then
          write(stdout,*) subname//' writing restart file ',trim(restartname)
        endif
-@@ -2149,6 +2281,7 @@ subroutine ocean_model_finalize(gcomp, rc)
+@@ -2169,6 +2301,7 @@ subroutine ocean_model_finalize(gcomp, rc)
    integer                                :: alarmCount
    character(len=64)                      :: timestamp
    logical                                :: write_restart
 +  character(240)                         :: additional_restart_dir
    character(len=*),parameter  :: subname='(MOM_cap:ocean_model_finalize)'
    real(8)                                :: MPI_Wtime, timefs
 
-@@ -2182,6 +2315,18 @@ subroutine ocean_model_finalize(gcomp, rc)
+@@ -2202,6 +2335,18 @@ subroutine ocean_model_finalize(gcomp, rc)
 
    call ocean_model_end(ocean_public, ocean_State, Time, write_restart=write_restart)
 

MOM6/patches/mom_cap.F90.patch

@@ -1,5 +1,5 @@
 diff --git a/MOM6/config_src/drivers/nuopc_cap/mom_cap_methods.F90 b/MOM6/config_src/drivers/nuopc_cap/mom_cap_methods.F90.new
-index 125bae5..67f3314 100644
+index 125bae5..3f81f6a 100644
 --- a/MOM6/config_src/drivers/nuopc_cap/mom_cap_methods.F90
 +++ b/MOM6/config_src/drivers/nuopc_cap/mom_cap_methods.F90.new
 @@ -20,8 +20,15 @@ use MOM_ocean_model_nuopc,     only: ocean_public_type, ocean_state_type
@@ -18,25 +18,26 @@ index 125bae5..67f3314 100644
  ! By default make data private
  implicit none; private
 
-@@ -72,11 +79,16 @@ end subroutine mom_set_geomtype
+@@ -72,11 +79,17 @@ end subroutine mom_set_geomtype
  !> This function has a few purposes:
  !! (1) it imports surface fluxes using data from the mediator; and
  !! (2) it can apply restoring in SST and SSS.
 -subroutine mom_import(ocean_public, ocean_grid, importState, ice_ocean_boundary, rc)
-+!! (3) optional: if atm_fields is provided, it imports and sets the fields in atm_fields required for the
-+!! calculation of coupled generic tracer fluxes
++!! (3) optional: if atm_fields is provided, it imports and sets the fields in atm_fields required
++!! for the calculation of coupled generic tracer fluxes
 +subroutine mom_import(ocean_public, ocean_grid, importState, ice_ocean_boundary, atm_fields, rc)
    type(ocean_public_type)       , intent(in)    :: ocean_public       !< Ocean surface state
    type(ocean_grid_type)         , intent(in)    :: ocean_grid         !< Ocean model grid
    type(ESMF_State)              , intent(inout) :: importState        !< incoming data from mediator
    type(ice_ocean_boundary_type) , intent(inout) :: ice_ocean_boundary !< Ocean boundary forcing
-+  type(coupler_2d_bc_type), optional, intent(inout) :: atm_fields     !< If present, this type describes the atmospheric
-+                                                                      !! tracer fields to be imported for the calculation
-+                                                                      !! of generic tracer fluxes.
++  type(coupler_2d_bc_type), optional, intent(inout) :: atm_fields     !< If present, this type
++                                                       !! describes the atmospheric tracer fields to
++                                                       !! be imported for the calculation of generic
++                                                       !! tracer fluxes.
    integer                       , intent(inout) :: rc                 !< Return code
 
    ! Local Variables
-@@ -88,7 +100,10 @@ subroutine mom_import(ocean_public, ocean_grid, importState, ice_ocean_boundary,
+@@ -88,7 +101,10 @@ subroutine mom_import(ocean_public, ocean_grid, importState, ice_ocean_boundary,
    real(ESMF_KIND_R8), allocatable :: tauy(:,:)
    real(ESMF_KIND_R8), allocatable :: stkx(:,:,:)
    real(ESMF_KIND_R8), allocatable :: stky(:,:,:)
@@ -47,7 +48,7 @@ index 125bae5..67f3314 100644
 
    rc = ESMF_SUCCESS
 
-@@ -364,6 +379,48 @@ subroutine mom_import(ocean_public, ocean_grid, importState, ice_ocean_boundary,
+@@ -364,6 +380,48 @@ subroutine mom_import(ocean_public, ocean_grid, importState, ice_ocean_boundary,
        deallocate(stkx,stky)
    endif