Change paramter name and though up PR

Change "MLD_PHA_FIXED" to "MLD_PHA_CALC" which is default false.
Touch up a few formatting issues.
Add initialization and comment for mld_pha.

src/diagnostics/MOM_diagnose_MLD.F90

@@ -30,8 +30,7 @@ module MOM_diagnose_mld
 !> Diagnose a mixed layer depth (MLD) determined by a given density difference with the surface.
 !> This routine is appropriate in MOM_diabatic_aux due to its position within the time stepping.
 subroutine diagnoseMLDbyDensityDifference(id_MLD, h, tv, densityDiff, G, GV, US, diagPtr, &
-                                          ref_h_mld, id_ref_z, id_ref_rho, id_N2subML, id_MLDsq, dz_subML, &
-                                          MLD_out)
+                                          ref_h_mld, id_ref_z, id_ref_rho, id_N2subML, id_MLDsq, dz_subML, MLD_out)
   type(ocean_grid_type),   intent(in) :: G           !< Grid type
   type(verticalGrid_type), intent(in) :: GV          !< ocean vertical grid structure
   type(unit_scale_type),   intent(in) :: US          !< A dimensional unit scaling type
@@ -46,7 +45,7 @@ subroutine diagnoseMLDbyDensityDifference(id_MLD, h, tv, densityDiff, G, GV, US,
   integer,                 intent(in) :: id_ref_z    !< Handle (ID) of reference depth diagnostic
   integer,                 intent(in) :: id_ref_rho  !< Handle (ID) of reference density diagnostic
   real, dimension(SZI_(G),SZJ_(G)), &
-              optional, intent(inout) :: MLD_out  !< Send MLD to other routines [Z ~> m]
+              optional, intent(inout) :: MLD_out     !< Send MLD to other routines [Z ~> m]
   integer,       optional, intent(in) :: id_N2subML  !< Optional handle (ID) of subML stratification
   integer,       optional, intent(in) :: id_MLDsq    !< Optional handle (ID) of squared MLD
   real,          optional, intent(in) :: dz_subML    !< The distance over which to calculate N2subML
@@ -237,7 +236,7 @@ subroutine diagnoseMLDbyDensityDifference(id_MLD, h, tv, densityDiff, G, GV, US,
   if ((id_ref_z > 0) .and. (pRef_MLD(is)/=0.)) call post_data(id_ref_z, z_ref_diag , diagPtr)
   if (id_ref_rho > 0) call post_data(id_ref_rho, rhoSurf_2d , diagPtr)
 
-  if (present(MLD_out)) MLD_out(:,:)=MLD(:,:)
+  if (present(MLD_out)) MLD_out(:,:) = MLD(:,:)
 
 end subroutine diagnoseMLDbyDensityDifference
 
@@ -276,7 +275,7 @@ subroutine diagnoseMLDbyEnergy(id_MLD, h, tv, G, GV, US, Mixing_Energy, diagPtr,
                                                      !! available thermodynamic fields.
   type(diag_ctrl),         pointer    :: diagPtr     !< Diagnostics structure
   real, dimension(SZI_(G),SZJ_(G)), &
-              optional, intent(inout) :: MLD_out  !< Send MLD to other routines [Z ~> m]
+              optional, intent(inout) :: MLD_out     !< Send MLD to other routines [Z ~> m]
 
   ! Local variables
   real, dimension(SZI_(G),SZJ_(G),3) :: MLD  ! Diagnosed mixed layer depth [Z ~> m].
@@ -474,7 +473,7 @@ subroutine diagnoseMLDbyEnergy(id_MLD, h, tv, G, GV, US, Mixing_Energy, diagPtr,
   if (id_MLD(2) > 0) call post_data(id_MLD(2), MLD(:,:,2), diagPtr)
   if (id_MLD(3) > 0) call post_data(id_MLD(3), MLD(:,:,3), diagPtr)
 
-  if (present(MLD_out)) MLD_out(:,:)=MLD(:,:,1)
+  if (present(MLD_out)) MLD_out(:,:) = MLD(:,:,1)
 
 end subroutine diagnoseMLDbyEnergy
 

src/tracer/MOM_generic_tracer.F90

@@ -84,12 +84,11 @@ module MOM_generic_tracer
     logical :: tracers_may_reinit  !< If true, tracers may go through the
                                    !! initialization code if they are not found in the restart files.
 
-    !real, allocatable, dimension(:,:) :: mld_pha
-    logical :: mld_pha_fixed = .True.           !< If true, use a fixed value for photoacclimation MLD
+    logical :: mld_pha_calc = .False.           !< If true, use a fixed value for photoacclimation MLD
     real    :: mld_pha_val = 0.0                !< The value of fixed photoacclimation MLD
     logical :: mld_pha_use_delta_rho = .False.  !< If true, use a density diference to find the MLD
     real    :: mld_pha_href = 0.0               !< The reference depth for density difference based MLD
-    real    :: mld_pha_drho = 0.03              !< The density thershold for a density difference based MLD 
+    real    :: mld_pha_drho = 0.03              !< The density thershold for a density difference based MLD
     logical :: mld_pha_use_delta_eng = .False.  !< If true, use an energy diference to find the MLD
     real    :: mld_pha_deng = 25.0              !< The energy threshold for an energy d ifference based MLD
 
@@ -433,10 +432,11 @@ subroutine initialize_MOM_generic_tracer(restart, day, G, GV, US, h, tv, param_f
     enddo
     !! end section to re-initialize generic tracers
 
-    call get_param(param_file, "MOM", "PHA_MLD_FIXED", CS%mld_pha_fixed, &
-                 "If true, use a fixed value for the photoacclimation mixed layer depth within the "//&
-                 "generic tracer update. This MLD is only used for photoacclimation.", default=.true.)
-    if (CS%mld_pha_fixed) then
+    call get_param(param_file, "MOM", "PHA_MLD_CALC", CS%mld_pha_calc, &
+                 "If false, use a fixed value for the photoacclimation mixed layer depth within the "//&
+                 "generic tracer update. This MLD is only used for photoacclimation. This variable should "//&
+                 "be set to true if using COBALTv3 for the BGC.", default=.false.)
+    if (.not.CS%mld_pha_calc) then
       call get_param(param_file, "MOM", "PHA_MLD_VAL", CS%mld_pha_val, &
                    "The depth of photoacclimation if fixed depth is used [m].", &
                     units='m', default=0.0, scale=US%m_to_Z)
@@ -544,7 +544,8 @@ subroutine MOM_generic_tracer_column_physics(h_old, h_new, ea, eb, fluxes, Hml,
     real, dimension(SZI_(G),SZJ_(G),SZK_(GV)) :: rho_dzt ! Layer mass per unit area [kg m-2]
     real, dimension(SZI_(G),SZJ_(G),SZK_(GV)) :: dzt     ! Layer vertical extents [m]
     real, dimension(SZI_(G),SZJ_(G),SZK_(GV)) :: h_work  ! A work array of thicknesses [H ~> m or kg m-2]
-    real, dimension(SZI_(G),SZJ_(G)) :: mld_pha          ! 
+    real, dimension(SZI_(G),SZJ_(G)) :: mld_pha          ! The mixed layer depth calculated for photoacclimation
+                                                         ! that is used in COBALTv3
     integer :: i, j, k, isc, iec, jsc, jec, nk
 
     isc = G%isc ; iec = G%iec ; jsc = G%jsc ; jec = G%jec ; nk = GV%ke
@@ -610,7 +611,8 @@ subroutine MOM_generic_tracer_column_physics(h_old, h_new, ea, eb, fluxes, Hml,
     enddo ; enddo
     sosga = global_area_mean(surface_field, G, unscale=US%S_to_ppt)
 
-    if (CS%mld_pha_fixed) then
+    mld_pha(:,:) = 0.0          
+    if (.not.CS%mld_pha_calc) then
       mld_pha(:,:) = CS%mld_pha_val
     else
       if (CS%mld_pha_use_delta_rho) then