Merge tag 'marbl0.48.2' into fe_updates_from_uci

MARBL_tools/run_test_suite.sh

@@ -136,6 +136,9 @@ if [ "${STATUS}" == "PASS" ]; then
   print_status "init.py" >> ${RESULTS_CACHE}
   # Initialize MARBL with settings from tests/input_files/settings/
   for settingsfile in `find ../../input_files/settings -type f`; do
+    if [ "`basename $settingsfile`" == "marbl_with_ladjust_bury_coeff.settings" ]; then
+      continue
+    fi
     (set -x ; ./init.py -s $settingsfile)
     STATUS=$(check_return $?)
     print_status "init.py ($(basename ${settingsfile}))" >> ${RESULTS_CACHE}
@@ -362,6 +365,12 @@ if [ "${STATUS}" == "PASS" ]; then
   STATUS=$(check_return $?)
   print_status "requested_tracers.py" >> ${RESULTS_CACHE}
 
+  # Print all fields MARBL needs running means of
+  cd ${MARBL_ROOT}/tests/regression_tests/bury_coeff
+  (set -x ; ./bury_coeff.py)
+  STATUS=$(check_return $?)
+  print_status "bury_coeff.py" >> ${RESULTS_CACHE}
+
   # Print all output_for_GCM variables
   cd ${MARBL_ROOT}/tests/regression_tests/available_output
   (set -x ; ./available_output.py)

defaults/diagnostics_latest.yaml

@@ -236,7 +236,7 @@ DUST_FLUX :
    longname : Atmospheric Dust Flux
    units : g/cm^2/s
    vertical_grid : none
-   frequency : never
+   frequency : medium
    operator : average
    diag_mode : minimal
 NOx_FLUX :
@@ -839,7 +839,7 @@ dustToSed :
    vertical_grid : none
    frequency : medium
    operator : average
-   diag_mode : full
+   diag_mode : minimal
 pfeToSed :
    dependencies :
       base_bio_on : .true.
@@ -848,7 +848,7 @@ pfeToSed :
    vertical_grid : none
    frequency : medium
    operator : average
-   diag_mode : full
+   diag_mode : minimal
 CaCO3_form_zint :
    dependencies :
       base_bio_on : .true.
@@ -1407,7 +1407,7 @@ POC_FLUX_IN :
    vertical_grid : layer_avg
    frequency : medium
    operator : average
-   diag_mode : full
+   diag_mode : minimal
 POC_sFLUX_IN :
    dependencies :
       base_bio_on : .true.

defaults/json/diagnostics_latest.json

@@ -1686,7 +1686,7 @@
          "base_bio_on": ".true."
       },
       "diag_mode": "minimal",
-      "frequency": "never",
+      "frequency": "medium",
       "longname": "Atmospheric Dust Flux",
       "operator": "average",
       "units": "g/cm^2/s",
@@ -2210,7 +2210,7 @@
       "dependencies": {
          "base_bio_on": ".true."
       },
-      "diag_mode": "full",
+      "diag_mode": "minimal",
       "frequency": "medium",
       "longname": "POC Flux into Cell",
       "operator": "average",
@@ -2736,7 +2736,7 @@
       "dependencies": {
          "base_bio_on": ".true."
       },
-      "diag_mode": "full",
+      "diag_mode": "minimal",
       "frequency": "medium",
       "longname": "dust Flux to Sediments",
       "operator": "average",
@@ -3053,7 +3053,7 @@
       "dependencies": {
          "base_bio_on": ".true."
       },
-      "diag_mode": "full",
+      "diag_mode": "minimal",
       "frequency": "medium",
       "longname": "pFe Flux to Sediments",
       "operator": "average",

src/marbl_interface.F90

@@ -151,6 +151,7 @@ module marbl_interface
      procedure, public  :: extract_timing
      procedure, private :: glo_vars_init
      procedure, public  :: get_tracer_index
+     procedure, public  :: compute_totChl
      procedure, public  :: interior_tendency_compute
      procedure, public  :: surface_flux_compute
      procedure, public  :: set_global_scalars
@@ -188,6 +189,7 @@ module marbl_interface
   private :: reset_timers
   private :: extract_timing
   private :: glo_vars_init
+  private :: compute_totChl
   private :: interior_tendency_compute
   private :: surface_flux_compute
   private :: shutdown
@@ -972,6 +974,18 @@ end subroutine glo_vars_init
 
   !***********************************************************************
 
+  subroutine compute_totChl(this)
+
+    use marbl_interior_tendency_mod, only : marbl_interior_tendency_compute_totChl
+
+    class(marbl_interface_class), intent(inout) :: this
+
+    call marbl_interior_tendency_compute_totChl(this%tracers, this%tracer_indices, this%interior_tendency_output)
+
+  end subroutine compute_totChl
+
+  !***********************************************************************
+
   subroutine interior_tendency_compute(this)
 
     use marbl_interior_tendency_mod, only : marbl_interior_tendency_compute

src/marbl_interior_tendency_mod.F90

@@ -90,6 +90,7 @@ module marbl_interior_tendency_mod
 
   public  :: marbl_interior_tendency_compute
   public  :: marbl_interior_tendency_adjust_bury_coeff
+  public  :: marbl_interior_tendency_compute_totChl
 
 contains
 
@@ -135,7 +136,6 @@ subroutine marbl_interior_tendency_compute( &
     use marbl_interface_private_types, only : marbl_internal_timers_type
     use marbl_interface_private_types, only : marbl_timer_indexing_type
     use marbl_interface_private_types, only : marbl_interior_tendency_saved_state_indexing_type
-    use marbl_interface_public_types, only : ofg_ind
     use marbl_interface_public_types, only : marbl_diagnostics_type
     use marbl_interior_tendency_share_mod, only : marbl_interior_tendency_share_export_variables
     use marbl_interior_tendency_share_mod, only : marbl_interior_tendency_share_export_zooplankton
@@ -183,7 +183,7 @@ subroutine marbl_interior_tendency_compute( &
     real(r8), dimension(size(tracers,1), domain%km) :: interior_restore
     real(r8), dimension(size(tracers,1), domain%km) :: tracer_local
 
-    integer (int_kind) :: auto_ind, k        ! indices for loops
+    integer (int_kind) :: k                  ! index for loops
 
     real (r8) :: surf_press(domain%km)       ! pressure in surface layer
     real (r8) :: temperature(domain%km)      ! in situ temperature
@@ -275,14 +275,7 @@ subroutine marbl_interior_tendency_compute( &
     !  Compute Chlorophyll (if requested by GCM)
     !-----------------------------------------------------------------------
 
-    if (ofg_ind%total_Chl_id.ne.0) then
-      interior_tendency_output%outputs_for_GCM(ofg_ind%total_Chl_id)%forcing_field_1d(1,:) = c0
-      do auto_ind = 1,autotroph_cnt
-        interior_tendency_output%outputs_for_GCM(ofg_ind%total_Chl_id)%forcing_field_1d(1,:) = &
-            interior_tendency_output%outputs_for_GCM(ofg_ind%total_Chl_id)%forcing_field_1d(1,:) &
-            + tracer_local(marbl_tracer_indices%auto_inds(auto_ind)%Chl_ind,:)
-      end do
-    end if
+    call marbl_interior_tendency_compute_totChl(tracer_local, marbl_tracer_indices, interior_tendency_output)
 
     ! Verify forcing is consistent
     if (lcheck_forcing) &
@@ -774,6 +767,29 @@ end subroutine marbl_interior_tendency_adjust_bury_coeff
 
   !***********************************************************************
 
+  subroutine marbl_interior_tendency_compute_totChl(tracer_local, marbl_tracer_indices, interior_tendency_output)
+
+    use marbl_interface_public_types, only : ofg_ind
+
+    real(r8), dimension(:,:),        intent(in)    :: tracer_local
+    type(marbl_tracer_index_type),   intent(in)    :: marbl_tracer_indices
+    type(marbl_output_for_GCM_type), intent(inout) :: interior_tendency_output
+
+    integer (int_kind) :: auto_ind
+
+    if (ofg_ind%total_Chl_id.ne.0) then
+      interior_tendency_output%outputs_for_GCM(ofg_ind%total_Chl_id)%forcing_field_1d(1,:) = c0
+      do auto_ind = 1,autotroph_cnt
+        interior_tendency_output%outputs_for_GCM(ofg_ind%total_Chl_id)%forcing_field_1d(1,:) = &
+            interior_tendency_output%outputs_for_GCM(ofg_ind%total_Chl_id)%forcing_field_1d(1,:) &
+            + tracer_local(marbl_tracer_indices%auto_inds(auto_ind)%Chl_ind,:)
+      end do
+    end if
+
+  end subroutine marbl_interior_tendency_compute_totChl
+
+  !***********************************************************************
+
   subroutine setup_local_tracers(column_kmt, marbl_tracer_indices, tracers, &
        autotroph_local, tracer_local, zooplankton_local)
 

src/marbl_nhx_surface_emis_mod.F90

@@ -72,7 +72,7 @@ subroutine marbl_nhx_surface_emis_compute( &
 
     call marbl_comp_Hstar_nhx(num_elements, ph, sst, sss, Hstar_nhx)
 
-    K(:) = c1 / (c1 / kg_nh3(:) + Hstar_nhx / kw_nh3(:))
+    K(:) = (kg_nh3(:) * kw_nh3(:)) / (kw_nh3(:) + Hstar_nhx * kg_nh3(:))
     nhx_surface_emis(:) = (c1 - ifrac(:)) * K(:) * Hstar_nhx(:) * max(nh4(:),c0)
 
   end subroutine marbl_nhx_surface_emis_compute

tests/driver_src/marbl.F90

@@ -410,7 +410,6 @@ Program marbl
                ' (units: ', trim(marbl_instances(1)%interior_tendency_forcings(n)%metadata%field_units),')'
           call driver_status_log%log_noerror(log_message, subname)
         end do
-
         call marbl_instances(1)%shutdown()
       end if
 
@@ -439,6 +438,66 @@ Program marbl
         call marbl_instances(1)%shutdown()
       end if
 
+    ! -- bury_coeff test -- !
+    case ('bury_coeff')
+      call verify_single_instance(num_inst, trim(testname))
+      lprint_marbl_log = .false.
+      call marbl_init_test(marbl_instances(1), unit_system_opt, lshutdown = .false., lhas_global_ops=.true.)
+      if (.not. marbl_instances(1)%StatusLog%labort_marbl) then
+        ! Log requested surface forcing fields
+        call driver_status_log%log_header('Requested surface forcing fields', subname)
+        do n=1,size(marbl_instances(1)%surface_flux_forcings)
+          write(log_message, "(I0, 5A)") n, '. ', &
+                trim(marbl_instances(1)%surface_flux_forcings(n)%metadata%varname), &
+                ' (units: ', trim(marbl_instances(1)%surface_flux_forcings(n)%metadata%field_units),')'
+          call driver_status_log%log_noerror(log_message, subname)
+        end do
+
+        ! Log requested interior forcing fields
+        call driver_status_log%log_header('Requested interior forcing fields', subname)
+        ! Provide message if no itnerior tendency forcings are requested
+        if (size(marbl_instances(1)%interior_tendency_forcings) == 0) &
+          call driver_status_log%log_noerror('No forcing fields requested for interior_tendency_compute()!', subname)
+        do n=1,size(marbl_instances(1)%interior_tendency_forcings)
+          write(log_message, "(I0, 5A)") n, '. ', &
+               trim(marbl_instances(1)%interior_tendency_forcings(n)%metadata%varname), &
+               ' (units: ', trim(marbl_instances(1)%interior_tendency_forcings(n)%metadata%field_units),')'
+          call driver_status_log%log_noerror(log_message, subname)
+        end do
+
+        ! Print info about burial coefficient vars as well
+        call driver_status_log%log_header('Size of arrays for running means', subname)
+        write(log_message, "(A, I0)") "size(glo_avg_rmean_interior_tendency): ", &
+                                      size(marbl_instances(1)%glo_avg_rmean_interior_tendency)
+        call driver_status_log%log_noerror(log_message, subname)
+        do n=1,size(marbl_instances(1)%glo_avg_rmean_interior_tendency)
+          write(log_message, "(2A)") "  -- ", trim(marbl_instances(1)%glo_avg_rmean_interior_tendency(n)%sname)
+          call driver_status_log%log_noerror(log_message, subname)
+        end do
+        write(log_message, "(A, I0)") "size(glo_avg_rmean_surface_flux): ", &
+                                      size(marbl_instances(1)%glo_avg_rmean_surface_flux)
+        call driver_status_log%log_noerror(log_message, subname)
+        do n=1,size(marbl_instances(1)%glo_avg_rmean_surface_flux)
+          write(log_message, "(2A)") "  -- ", trim(marbl_instances(1)%glo_avg_rmean_surface_flux(n)%sname)
+          call driver_status_log%log_noerror(log_message, subname)
+        end do
+        write(log_message, "(A, I0)") "size(glo_scalar_rmean_interior_tendency): ", &
+                                      size(marbl_instances(1)%glo_scalar_rmean_interior_tendency)
+        call driver_status_log%log_noerror(log_message, subname)
+        do n=1,size(marbl_instances(1)%glo_scalar_rmean_interior_tendency)
+          write(log_message, "(2A)") "  -- ", trim(marbl_instances(1)%glo_scalar_rmean_interior_tendency(n)%sname)
+          call driver_status_log%log_noerror(log_message, subname)
+        end do
+        write(log_message, "(A, I0)") "size(glo_scalar_rmean_surface_flux): ", &
+                                      size(marbl_instances(1)%glo_scalar_rmean_surface_flux)
+        call driver_status_log%log_noerror(log_message, subname)
+        do n=1,size(marbl_instances(1)%glo_scalar_rmean_surface_flux)
+          write(log_message, "(2A)") "  -- ", trim(marbl_instances(1)%glo_scalar_rmean_surface_flux(n)%sname)
+          call driver_status_log%log_noerror(log_message, subname)
+        end do
+        call marbl_instances(1)%shutdown()
+      end if
+
     ! -- available_output test -- !
     case ('available_output')
       call verify_single_instance(num_inst, trim(testname))

tests/driver_src/marbl_init_drv.F90

@@ -14,17 +14,18 @@ module marbl_init_drv
 
 Contains
 
-  subroutine test(marbl_instance, unit_system_opt, lshutdown, num_PAR_subcols)
+  subroutine test(marbl_instance, unit_system_opt, lshutdown, num_PAR_subcols, lhas_global_ops)
 
     type(marbl_interface_class), intent(inout) :: marbl_instance
     character(len=*),            intent(in)    :: unit_system_opt
     logical, optional,           intent(in)    :: lshutdown
     integer, optional,           intent(in)    :: num_PAR_subcols
+    logical, optional,           intent(in)    :: lhas_global_ops
 
     character(*), parameter      :: subname = 'marbl_init_drv:test'
     real(kind=r8), dimension(km) :: delta_z, zw, zt
     integer                      :: k, num_PAR_subcols_loc
-    logical                      :: lshutdown_loc
+    logical                      :: lshutdown_loc, lhas_global_ops_loc
 
     ! Run marbl_instance%shutdown? (Skip when running get_setting() from driver)
     if (present(lshutdown)) then
@@ -39,6 +40,12 @@ subroutine test(marbl_instance, unit_system_opt, lshutdown, num_PAR_subcols)
       num_PAR_subcols_loc = 1
     end if
 
+    if (present(lhas_global_ops)) then
+      lhas_global_ops_loc = lhas_global_ops
+    else
+      lhas_global_ops_loc = .false.
+    end if
+
     ! Initialize levels
     delta_z = c1
     zw(1) = delta_z(1)
@@ -57,7 +64,8 @@ subroutine test(marbl_instance, unit_system_opt, lshutdown, num_PAR_subcols)
                              gcm_delta_z = delta_z,                     &
                              gcm_zw = zw,                               &
                              gcm_zt = zt,                               &
-                             unit_system_opt = unit_system_opt)
+                             unit_system_opt = unit_system_opt,         &
+                             lgcm_has_global_ops=lhas_global_ops_loc)
     if (marbl_instance%StatusLog%labort_marbl) then
       call marbl_instance%StatusLog%log_error_trace('marbl%init', subname)
       return

tests/input_files/settings/marbl_with_ladjust_bury_coeff.settings

@@ -0,0 +1 @@
+ladjust_bury_coeff = .true.

tests/regression_tests/bury_coeff/bury_coeff.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+
+from sys import path
+import os
+
+path.insert(0, os.path.join('..', '..', 'python_for_tests'))
+from marbl_testing_class import MARBL_testcase
+
+mt = MARBL_testcase()
+
+mt.parse_args(desc='Run full MARBL setup (config, init, and complete) and print '
+                   'output relating to burial coefficients',
+                   DefaultSettingsFile='../../input_files/settings/marbl_with_ladjust_bury_coeff.settings')
+
+mt.build_exe()
+
+mt.run_exe()

tests/regression_tests/bury_coeff/test.nml

@@ -0,0 +1,3 @@
+&marbl_driver_nml
+testname="bury_coeff"
+/