Simplify changes to the generic tracer interface for cobalt-p4: ocean…

…_BGC side (#8)

* mod g_tracer_interface

* mod tracer interface

* Simplify g_tracer interface changes

* remove unused descriptions

* tmp changes in cobalt_ci.yml to pass ci test

* add optional for geolat and eqn_of_state

* Change branch back to dev/cefi

.github/workflows/cobalt_ci.yml

@@ -13,6 +13,9 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+env:
+  BRANCH_NAME: dev/cefi
+
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # This workflow contains a single job called "build"
@@ -46,7 +49,7 @@ jobs:
       - name: git clone MOM6_OBGC_examples and build mom6sis2-cobalt
         run: |
           cd ..
-          git clone https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6_OBGC_examples.git --recursive
+          git clone -b $BRANCH_NAME https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6_OBGC_examples.git --recursive
           rm -rf MOM6_OBGC_examples/src/ocean_BGC
           cp -r ocean_BGC MOM6_OBGC_examples/src
           cd MOM6_OBGC_examples/builds

generic_tracers/generic_COBALT.F90

@@ -144,8 +144,7 @@ module generic_COBALT
 #ifndef INTERNAL_FILE_NML
   use fms_mod,           only: open_namelist_file, close_file
 #endif
-  use MOM_EOS,           only: calculate_density
-  use MOM_variables,     only: thermo_var_ptrs
+  use MOM_EOS,           only: calculate_density, EOS_type
 
   use g_tracer_utils, only : g_tracer_type,g_tracer_start_param_list,g_tracer_end_param_list
   use g_tracer_utils, only : g_tracer_add,g_tracer_add_param, g_tracer_set_files
@@ -7853,13 +7852,12 @@ end subroutine generic_COBALT_update_from_bottom
   !subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,hblt_depth,&
   !     ilb,jlb,tau,dt,grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)
   ! If you'd like to pass the thermodynamic variables for a mld calculation
-  subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dzt,hblt_depth,&
-       ilb,jlb,tau,dt,grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)
+  subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,hblt_depth,&
+       ilb,jlb,tau,dt,grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff,geolat,eqn_of_state)
   !subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,hblt_depth,&
   !     ilb,jlb,tau,dt,grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)
 
     type(g_tracer_type),            pointer    :: tracer_list
-    type(thermo_var_ptrs),          intent(in) :: tv
     real, dimension(ilb:,jlb:,:),   intent(in) :: Temp,Salt,rho_dzt,dzt
     real, dimension(ilb:,jlb:),     intent(in) :: hblt_depth
     integer,                        intent(in) :: ilb,jlb,tau
@@ -7873,11 +7871,12 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz
     real, dimension(:,ilb:,jlb:,:), intent(in) :: opacity_band
     real, dimension(ilb:,jlb:),     intent(in) :: internal_heat
     real, dimension(ilb:,jlb:),     intent(in) :: frunoff
+    real, dimension(ilb:,jlb:), optional, intent(in) :: geolat
+    type(EOS_type),             optional, intent(in) :: eqn_of_state !< Equation of state structure
 
     character(len=fm_string_len), parameter :: sub_name = 'generic_COBALT_update_from_source'
     integer :: isc,iec, jsc,jec,isd,ied,jsd,jed,nk,ntau, i, j, k , m, n, k_100, k_200, kbot
     real, dimension(:,:,:) ,pointer :: grid_tmask
-    real, dimension(:,:), pointer :: geolon,geolat
     integer, dimension(:,:),pointer :: mask_coast,grid_kmt
     !
     !------------------------------------------------------------------------
@@ -7952,8 +7951,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz
     r_dt = 1.0 / dt
 
     call g_tracer_get_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,&
-         grid_tmask=grid_tmask,grid_mask_coast=mask_coast,grid_kmt=grid_kmt,&
-         geolon=geolon,geolat=geolat)
+         grid_tmask=grid_tmask,grid_mask_coast=mask_coast,grid_kmt=grid_kmt)
 
     call mpp_clock_begin(id_clock_carbon_calculations)
     !Get necessary fields
@@ -8317,7 +8315,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz
 
 
         ! calculate the mld for the photoacclimation calculations
-        call calculate_density(Temp(i,j,kmld_ref),Salt(i,j,kmld_ref),101325.0,rho_mld_ref,tv%eqn_of_state)
+        call calculate_density(Temp(i,j,kmld_ref),Salt(i,j,kmld_ref),101325.0,rho_mld_ref,eqn_of_state)
         !if ((i.eq.isc).and.(j.eq.jsc)) then
         !  write(outunit,*) 'rho_mld_ref = ',rho_mld_ref
         !endif
@@ -8332,7 +8330,7 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz
           deltaRhoAtKm1 = deltaRhoAtK
           dKm1 = dK
           dK = cobalt%mld_aclm(i,j) + 0.5*dzt(i,j,k)
-          call calculate_density(Temp(i,j,k),Salt(i,j,k),101325.0,rho_k,tv%eqn_of_state)
+          call calculate_density(Temp(i,j,k),Salt(i,j,k),101325.0,rho_k,eqn_of_state)
           cobalt%rho_test(i,j,k) = rho_k
           deltaRhoAtK = rho_k - rho_mld_ref
           if (deltaRhoAtK.lt.cobalt%densdiff_mld) then
@@ -8341,14 +8339,15 @@ subroutine generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dz
             afac = (cobalt%densdiff_mld - deltaRhoAtKm1)/(deltaRhoAtK - deltaRhoAtKm1)
             cobalt%mld_aclm(i,j) = afac*dK + (1.0-afac)*dKm1
             deltaRhoFlag = 1.0
-            !if ((i.eq.isc).and.(j.eq.jsc)) then
-            !   write(outunit,*) 'lat,lon=',geolat,geolon
-            !   write(outunit,*) 'kmld_ref, k = ',kmld_ref, k
-            !   write(outunit,*) 'rho_mld_ref = ',rho_mld_ref
-            !   write(outunit,*) 'rho_k = ',rho_k
-            !   write(outunit,*) 'deltaRhoAtK = ',deltaRhoAtK
-            !   write(outunit,*) 'mld_aclm = ',cobalt%mld_aclm(i,j)
-            !endif
+!            if ((i.eq.isc).and.(j.eq.jsc)) then
+!               write(outunit,*) 'i,j=',i,j
+!               write(outunit,*) 'lat,lon=',geolat(i,j)
+!               write(outunit,*) 'kmld_ref, k = ',kmld_ref, k
+!               write(outunit,*) 'rho_mld_ref = ',rho_mld_ref
+!               write(outunit,*) 'rho_k = ',rho_k
+!               write(outunit,*) 'deltaRhoAtK = ',deltaRhoAtK
+!               write(outunit,*) 'mld_aclm = ',cobalt%mld_aclm(i,j)
+!            endif
           endif
         enddo  !} k
 

generic_tracers/generic_tracer.F90

@@ -103,9 +103,9 @@ module generic_tracer
   use generic_COBALT,  only : generic_COBALT_init, generic_COBALT_update_from_source,generic_COBALT_register_diag
   use generic_COBALT,  only : generic_COBALT_update_from_bottom,generic_COBALT_update_from_coupler
   use generic_COBALT,  only : generic_COBALT_set_boundary_values, generic_COBALT_end, do_generic_COBALT
-  use generic_COBALT, only : as_param_cobalt
+  use generic_COBALT,  only : as_param_cobalt
 
-  use MOM_variables, only : thermo_var_ptrs
+  use MOM_EOS,         only: EOS_type
 
   implicit none ; private
 
@@ -248,17 +248,16 @@ end subroutine generic_tracer_register
   !   Grid mask
   !  </IN>
   ! </SUBROUTINE>
-  subroutine generic_tracer_init(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time,geolon,geolat)
+  subroutine generic_tracer_init(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time)
     integer,                       intent(in) :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes(3)
     type(time_type),               intent(in) :: init_time
     real, dimension(:,:,:),target, intent(in) :: grid_tmask
     integer, dimension(:,:)      , intent(in) :: grid_kmt
-    real, dimension(:,:),target,   intent(in) :: geolon,geolat
     type(g_tracer_type), pointer    :: g_tracer,g_tracer_next
 
     character(len=fm_string_len), parameter :: sub_name = 'generic_tracer_init'
 
-    call g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time,geolon,geolat) 
+    call g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time) 
 
     !Allocate and initialize all registered generic tracers
     !JGJ 2013/05/31  merged COBALT into siena_201303
@@ -505,11 +504,10 @@ end subroutine generic_tracer_diag
   !  </IN>
   ! </SUBROUTINE>
 
-  subroutine generic_tracer_source(Temp,Salt,tv,rho_dzt,dzt,hblt_depth,ilb,jlb,tau,dtts,&
+  subroutine generic_tracer_source(Temp,Salt,rho_dzt,dzt,hblt_depth,ilb,jlb,tau,dtts,&
        grid_dat,model_time,nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,&
-       frunoff,grid_ht, current_wave_stress, sosga)
+       frunoff,grid_ht, current_wave_stress, sosga, geolat, eqn_of_state)
     real, dimension(ilb:,jlb:,:),   intent(in) :: Temp,Salt,rho_dzt,dzt
-    type(thermo_var_ptrs),          intent(in) :: tv
     real, dimension(ilb:,jlb:),     intent(in) :: hblt_depth
     integer,                        intent(in) :: ilb,jlb,tau
     real,                           intent(in) :: dtts
@@ -524,7 +522,8 @@ subroutine generic_tracer_source(Temp,Salt,tv,rho_dzt,dzt,hblt_depth,ilb,jlb,tau
     real, dimension(ilb:,jlb:),optional,  intent(in) :: grid_ht
     real, dimension(ilb:,jlb:),optional , intent(in) :: current_wave_stress
     real,                      optional , intent(in) :: sosga ! global avg. sea surface salinity
-
+    real, dimension(ilb:,jlb:),optional,  intent(in) :: geolat 
+    type(EOS_type),            optional,  intent(in) :: eqn_of_state
 
 
     character(len=fm_string_len), parameter :: sub_name = 'generic_tracer_update_from_source'
@@ -554,9 +553,18 @@ subroutine generic_tracer_source(Temp,Salt,tv,rho_dzt,dzt,hblt_depth,ilb,jlb,tau
          hblt_depth,ilb,jlb,tau,dtts,grid_dat,model_time,&
          nbands,max_wavelength_band,sw_pen_band,opacity_band, grid_ht)
 
-    if(do_generic_COBALT)  call generic_COBALT_update_from_source(tracer_list,Temp,Salt,tv,rho_dzt,dzt,&
-         hblt_depth,ilb,jlb,tau,dtts,grid_dat,model_time,&
-         nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)
+    if (do_generic_COBALT) then
+       if (present(geolat) .and. present(eqn_of_state)) then
+          call generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,&
+            hblt_depth,ilb,jlb,tau,dtts,grid_dat,model_time,&
+            nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff,&
+            geolat,eqn_of_state)
+       else
+          call generic_COBALT_update_from_source(tracer_list,Temp,Salt,rho_dzt,dzt,&
+            hblt_depth,ilb,jlb,tau,dtts,grid_dat,model_time,&
+            nbands,max_wavelength_band,sw_pen_band,opacity_band,internal_heat,frunoff)
+       endif
+    endif
 
     if(do_generic_SF6)  call generic_SF6_update_from_source(tracer_list,rho_dzt,dzt,hblt_depth,&
          ilb,jlb,tau,dtts,grid_dat,model_time)

generic_tracers/generic_tracer_utils.F90

@@ -330,9 +330,6 @@ module g_tracer_utils
      !coast mask
      integer, _ALLOCATABLE, dimension(:,:):: grid_mask_coast    _NULL
 
-     real, _ALLOCATABLE, dimension(:,:) :: geolon  _NULL
-     real, _ALLOCATABLE, dimension(:,:) :: geolat  _NULL
-
      ! IN and OUT (restart) files
      character(len=fm_string_len) :: ice_restart_file, ocean_restart_file
   end type g_tracer_common
@@ -1600,19 +1597,18 @@ end subroutine g_tracer_set_csdiag
   !   grid_mask array and initial time.
   !  </DESCRIPTION>
   !  <TEMPLATE>
-  !   call g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time,geolon,geolat)
+  !   call g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time)
   !  </TEMPLATE>
   !  <IN NAME="" TYPE="">
   !   
   !  </IN>
   ! </SUBROUTINE>
 
-  subroutine g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time,geolon,geolat)
+  subroutine g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid_tmask,grid_kmt,init_time)
     integer,                     intent(in) :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes(3)
     real, dimension(isd:,jsd:,:),intent(in) :: grid_tmask
     integer,dimension(isd:,jsd:),intent(in) :: grid_kmt
     type(time_type),             intent(in) :: init_time
-    real, dimension(isd:,jsd:),  intent(in) :: geolon,geolat
 
     character(len=fm_string_len), parameter :: sub_name = 'g_tracer_set_common'
     integer :: i,j
@@ -1641,12 +1637,6 @@ subroutine g_tracer_set_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,axes,grid
 
     if(.NOT. _ALLOCATED(g_tracer_com%grid_mask_coast)) allocate(g_tracer_com%grid_mask_coast(isd:ied,jsd:jed))
 
-    if(.NOT. _ALLOCATED(g_tracer_com%geolon)) allocate(g_tracer_com%geolon(isd:ied,jsd:jed))
-    g_tracer_com%geolon = geolon
-
-    if(.NOT. _ALLOCATED(g_tracer_com%geolat)) allocate(g_tracer_com%geolat(isd:ied,jsd:jed))
-    g_tracer_com%geolat = geolat
-
     !Determine the coast line.
     !In order to that grid_tmask must have the proper value on the data domain boundaries isd,ied,jsd,jed
     !so that we can decide if the coast line coinsides with a point on the compute domain boundary
@@ -1681,16 +1671,14 @@ end subroutine g_tracer_set_common
   ! </SUBROUTINE>
 
   subroutine g_tracer_get_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,&
-       axes,grid_tmask,grid_mask_coast,grid_kmt,init_time,diag_CS,geolon,geolat)
+       axes,grid_tmask,grid_mask_coast,grid_kmt,init_time,diag_CS)
 
     integer,               intent(out) :: isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau
     integer,optional,      intent(out) :: axes(3)
     type(time_type), optional,      intent(out) :: init_time 
     real, optional, dimension(:,:,:),pointer    :: grid_tmask
     integer, optional, dimension(:,:),  pointer :: grid_mask_coast
     integer, optional, dimension(:,:),  pointer :: grid_kmt
-    real, optional, dimension(:,:), pointer :: geolon
-    real, optional, dimension(:,:), pointer :: geolat
     type(g_diag_ctrl), optional,        pointer :: diag_CS
 
     character(len=fm_string_len), parameter :: sub_name = 'g_tracer_get_common'
@@ -1713,8 +1701,6 @@ subroutine g_tracer_get_common(isc,iec,jsc,jec,isd,ied,jsd,jed,nk,ntau,&
     if(present(grid_mask_coast))  grid_mask_coast=> g_tracer_com%grid_mask_coast
     if(present(grid_kmt))         grid_kmt => g_tracer_com%grid_kmt
     if(present(diag_CS))          diag_CS => g_tracer_com%diag_CS
-    if(present(geolon))           geolon => g_tracer_com%geolon
-    if(present(geolat))           geolat => g_tracer_com%geolat
 !    if(present(ice_restart_file)) ice_restart_file    = g_tracer_com%ice_restart_file
 !    if(present(ocean_restart_file)) ocean_restart_file  = g_tracer_com%ocean_restart_file