Only allow GCM to request certain output fields if base_bio_on is True

MARBL_tools/run_test_suite.sh

@@ -356,6 +356,12 @@ if [ "${STATUS}" == "PASS" ]; then
   STATUS=$(check_return $?)
   print_status "requested_tracers.py" >> ${RESULTS_CACHE}
 
+  # Print all output_for_GCM variables
+  cd ${MARBL_ROOT}/tests/regression_tests/available_output
+  (set -x ; ./available_output.py)
+  STATUS=$(check_return $?)
+  print_status "available_output.py" >> ${RESULTS_CACHE}
+
   # Initialize MARBL (with MPI)
   cd ${MARBL_ROOT}/tests/regression_tests/init
   (set -x ; ./init.py --mpitasks 2)

docs/py_requirements.txt

@@ -1,5 +1,6 @@
 pylint==2.10.2
 Sphinx==1.7.5
+alabaster==0.7.13
 sphinxcontrib-bibtex==0.4.0
 pybtex==0.22
 jinja2<3

docs/src/dev-guide/add-ofg.rst

@@ -0,0 +1,145 @@
+.. _add-ofg:
+
+============================
+Adding an Output for the GCM
+============================
+
+In addition to surface fluxes and interior tendencies, MARBL can provide :ref:`additional output <additional_output>` as well.
+These might be fluxes that feed back to the atmosphere, or tracer sums used for other physical properties.
+Adding a new output is a straightforward process.
+
+-------------------------------------------------
+Step 1. Add to MARBL output for GCM indexing type
+-------------------------------------------------
+
+MARBL tracks the internal index of each output for the GCM in the ``output_for_GCM_type`` components of the interface
+(``surface_flux_output`` and ``interior_tendency_output``).
+There is a module variable in ``marbl_interface_public_types.F90`` of type ``marbl_output_for_GCM_indexing_type``:
+
+.. code block from marbl_interface_public_types
+.. code-block:: fortran
+
+  type, public :: marbl_output_for_GCM_indexing_type
+    integer(int_kind) :: flux_o2_id = 0
+    integer(int_kind) :: flux_co2_id = 0
+    integer(int_kind) :: flux_nhx_id = 0
+    integer(int_kind) :: total_surfChl_id = 0
+    integer(int_kind) :: total_Chl_id = 0
+  end type marbl_output_for_GCM_indexing_type
+  type(marbl_output_for_GCM_indexing_type), target, public :: ofg_ind
+
+``ofg_ind`` is a target because there is a registry of all defined outputs for the GCM that use pointers to
+make sure the correct index is updated.
+Any new outputs for the GCM must have an index added to this indexing type.
+
+---------------------------------------------------
+Step 2. Add to MARBL output for GCM output registry
+---------------------------------------------------
+
+MARBL tracks what outputs are available via the ``marbl_output_for_GCM_registry_type``.
+When a GCM calls ``marbl_instance%add_output_for_GCM()``,
+MARBL checks the registry to see if it can provide the output.
+
+.. code block from marbl_interface_public_types
+.. code-block:: fortran
+
+  type, public :: marbl_output_for_GCM_linked_list_type
+    character(len=char_len)    :: short_name
+    character(len=char_len)    :: long_name
+    character(len=char_len)    :: units
+    character(len=char_len)    :: field_source
+    character(len=char_len)    :: err_message
+    integer(int_kind), pointer :: id
+    type(marbl_output_for_GCM_linked_list_type), pointer :: next => NULL()
+  end type marbl_output_for_GCM_linked_list_type
+
+  !*****************************************************************************
+
+  type, public :: marbl_output_for_GCM_registry_type
+    type(marbl_output_for_GCM_linked_list_type), pointer :: registered_outputs
+  contains
+    procedure, public  :: create_registry
+    procedure, private :: add_registry_entry
+  end type marbl_output_for_GCM_registry_type
+
+``create_registry()`` is called during MARBL initialization,
+and it makes repeated use of the ``add_registry_entry()`` subroutine.
+To add a new output to the registry, copy an existing block and modify appropriately:
+
+.. code block from marbl_interface_public_types
+.. code-block:: fortran
+
+    ! Surface Chlorophyll
+    err_message = ""
+    if (.not. base_bio_on) &
+      err_message = "requires base biotic tracers"
+    call this%add_registry_entry(short_name = "total_surfChl", &
+                                 long_name = "Total Surface Chlorophyll Concentration", &
+                                 units = "mg/m^3", &
+                                 field_source = "surface_flux", &
+                                 id = ofg_ind%total_surfChl_id, &
+                                 err_message = err_message)
+
+    ! Full Depth Chlorophyll
+    err_message = ""
+    if (.not. base_bio_on) &
+      err_message = "requires base biotic tracers"
+    call this%add_registry_entry(short_name = "total_Chl", &
+                                 long_name = "Total Chlorophyll Concentration", &
+                                 units = "mg/m^3", &
+                                 field_source = "interior_tendency", &
+                                 id = ofg_ind%total_Chl_id, &
+                                 err_message = err_message)
+
+* ``field_source`` will tell the GCM whether to look for updated values of this output
+  after calls to ``surface_flux_compute()`` or ``interior_tendency_compute()``.
+* If ``err_message`` is an empty string, then this output is available for the GCM.
+  If MARBL is configured in a way such that this output will not be computed,
+  ``err_message`` should give a concise explanation of why it is unavailable.
+  MARBL will return the error ``{short_name} {err_message}`` -- for example,
+  if ``base_bio_on = .false.`` and a GCM requests ``total_Chl`` then MARBL will abort with the message
+  ``total_Chl requires base biotic tracers``.
+
+------------------------------------------------
+Step 3. Copy Output into ``output_for_GCM_type``
+------------------------------------------------
+
+If ``field_source = "surface_flux"`` you need something like this inside ``surface_flux_compute()``:
+
+.. code block from marbl_surface_flux_mod
+.. code-block:: fortran
+
+    !-----------------------------------------------------------------------
+    !  Compute surface chlorophyll (if requested by GCM)
+    !-----------------------------------------------------------------------
+
+    if (ofg_ind%total_surfChl_id.ne.0) then
+      totalChl_loc = c0
+      do auto_ind = 1,autotroph_cnt
+        totalChl_loc = totalChl_loc +                                         &
+          max(c0, tracers_at_surface(:,marbl_tracer_indices%auto_inds(auto_ind)%Chl_ind))
+      end do
+      surface_flux_output%outputs_for_GCM(ofg_ind%total_surfChl_id)%forcing_field_0d(:) = totalChl_loc
+    end if
+
+Otherwise, ``field_source = "interior_tendency"`` and you need something like this inside ``interior_tendency_compute()``:
+
+.. code block from marbl_interior_tendency_mod
+.. code-block:: fortran
+
+    !-----------------------------------------------------------------------
+    !  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
+
+Note that, in both examples, the output is only computed and stored if the index is positive.
+If the GCM did not request this output,
+memory will not be allocated to store it and MARBL won't spend time computing it.

docs/src/dev-guide/development-examples.rst

@@ -12,4 +12,5 @@ Examples of common development tasks.
    add-diagnostic.rst
    add-settings-parameter.rst
    add-tracer.rst
+   add-ofg.rst
 

docs/src/dev-guide/marbl-interface.rst

@@ -32,6 +32,7 @@ The class definition is shown below:
      type(marbl_forcing_fields_type), allocatable       , public  :: interior_tendency_forcings(:) ! input
      real (r8), allocatable                             , public  :: interior_tendencies(:,:)      ! output
      type(marbl_interior_tendency_forcing_indexing_type), public  :: interior_tendency_forcing_ind ! FIXME #311: should be private
+     type(marbl_output_for_GCM_type)                    , public  :: interior_tendency_output      ! output
      type(marbl_diagnostics_type)                       , public  :: interior_tendency_diags       ! output
 
      ! public data related to computing surface fluxes
@@ -43,20 +44,20 @@ The class definition is shown below:
      type(marbl_diagnostics_type)                   , public               :: surface_flux_diags          ! output
 
      ! public data - global averages
-     real (r8)                                 , public, allocatable  :: glo_avg_fields_interior_tendency(:)   ! output (nfields)
-     real (r8)                                 , public, allocatable  :: glo_avg_averages_interior_tendency(:) ! input (nfields)
-     real (r8)                                 , public, allocatable  :: glo_avg_fields_surface_flux(:,:)      ! output (num_elements,nfields)
-     real (r8)                                 , public, allocatable  :: glo_avg_averages_surface_flux(:)      ! input (nfields)
+     real (r8), public, allocatable  :: glo_avg_fields_interior_tendency(:)   ! output (nfields)
+     real (r8), public, allocatable  :: glo_avg_averages_interior_tendency(:) ! input (nfields)
+     real (r8), public, allocatable  :: glo_avg_fields_surface_flux(:,:)      ! output (num_elements,nfields)
+     real (r8), public, allocatable  :: glo_avg_averages_surface_flux(:)      ! input (nfields)
 
      ! FIXME #77: for now, running means are being computed in the driver
      !            they will eventually be moved from the interface to inside MARBL
-     real (r8)                                 , public, allocatable  :: glo_scalar_interior_tendency(:)
-     real (r8)                                 , public, allocatable  :: glo_scalar_surface_flux(:)
+     real (r8), public, allocatable  :: glo_scalar_interior_tendency(:)
+     real (r8), public, allocatable  :: glo_scalar_surface_flux(:)
 
-     type(marbl_running_mean_0d_type)          , public, allocatable  :: glo_avg_rmean_interior_tendency(:)
-     type(marbl_running_mean_0d_type)          , public, allocatable  :: glo_avg_rmean_surface_flux(:)
-     type(marbl_running_mean_0d_type)          , public, allocatable  :: glo_scalar_rmean_interior_tendency(:)
-     type(marbl_running_mean_0d_type)          , public, allocatable  :: glo_scalar_rmean_surface_flux(:)
+     type(marbl_running_mean_0d_type), public, allocatable  :: glo_avg_rmean_interior_tendency(:)
+     type(marbl_running_mean_0d_type), public, allocatable  :: glo_avg_rmean_surface_flux(:)
+     type(marbl_running_mean_0d_type), public, allocatable  :: glo_scalar_rmean_interior_tendency(:)
+     type(marbl_running_mean_0d_type), public, allocatable  :: glo_scalar_rmean_surface_flux(:)
 
      ! private data
      type(unit_system_type),                   private :: unit_system
@@ -80,6 +81,7 @@ The class definition is shown below:
      type(marbl_internal_timers_type),         private :: timers
      type(marbl_timer_indexing_type),          private :: timer_ids
      type(marbl_settings_type),                private :: settings
+     type(marbl_output_for_GCM_registry_type), private :: output_for_gcm_registry
 
    contains
 
@@ -106,7 +108,6 @@ The class definition is shown below:
                                           get_string
      procedure, public  :: get_settings_var_cnt
      procedure, public  :: add_output_for_GCM
-     procedure, public  :: get_output_for_GCM
      procedure, private :: inquire_settings_metadata_by_name
      procedure, private :: inquire_settings_metadata_by_id
      procedure, private :: put_real

docs/src/implementations/pop/index.rst

@@ -4,6 +4,9 @@
 MARBL examples in POP
 =====================
 
+NOTE: POP is no longer being developed, and therefore is no longer keeping up with MARBL developments.
+All examples in this section refer to the `marbl0.43.0` tag of MARBL, from May 2023.
+
 .. toctree::
    :maxdepth: 1
    :caption: Contents:

docs/src/implementations/standalone/regression_tests.rst

@@ -36,12 +36,14 @@ to 0 may have relative errors that are O(1).
 Other Examples
 --------------
 
-There are five subdirectories that provide information on how MARBL is configured, and three are documented elsewhere on
+There are six subdirectories that provide information on how MARBL is configured, and three are documented elsewhere on
 on this site:
 
 #. ``gen_settings_file/`` generates a :ref:`settings file <marbl_settings.gen>` for a later MARBL run.
 #. ``requested_forcings/`` lists the :ref:`forcing fields MARBL needs <forcing_fields>` in a given configuration.
 #. ``requested_tracers/`` lists the :ref:`tracer tendencies computed <tracer_state>` in a given configuration.
+#. ``available_output/`` lists all the :ref:`additional output fields <additional_output>` available,
+   and also shows what is unavailable due to configuration settings.
 
 The stand-alone driver can also report what tracers are being restored
 (without :ref:`looking at the rest of the forcing fields <restoring_as_forcing>`)

docs/src/usr-guide/GCM-interface/additional_output.rst

@@ -0,0 +1,125 @@
+.. _additional_output:
+
+=================
+Additional Output
+=================
+
+MARBL can provide more output than just surface fluxes and interior tendencies.
+For example, MARBL can return the total chlorophyll concentration to the GCM,
+which can then be used to compute shortwave absorption.
+(MARBL can provide both surface chlorophyll and the full depth chlorophyll field,
+since difference shortwave absorption algorithms have different inputs.)
+MARBL can also provide the O2, CO2, and NHx fluxes at the surface if the GCM wants those to feedback to the atmosphere.
+
+----------------
+Available Fields
+----------------
+
+The full list of outputs is available from the ``available_output`` regression test.
+In the default configuration, the complete list is
+
+.. block comes from available_output test
+.. code-block:: none
+
+  ------------------------
+  Available output for GCM
+  ------------------------
+
+  1. Total Chlorophyll Concentration
+    short name: total_Chl
+    units: mg/m^3
+    field_source: interior_tendency
+  2. Total Surface Chlorophyll Concentration
+    short name: total_surfChl
+    units: mg/m^3
+    field_source: surface_flux
+  3. NHx Surface Emissions
+    short name: flux_nhx
+    units: nmol/cm^2/s
+    field_source: surface_flux
+  4. Carbon Dioxide Flux
+    short name: flux_co2
+    units: nmol/cm^2/s
+    field_source: surface_flux
+  5. Oxygen Flux
+    short name: flux_o2
+    units: nmol/cm^2/s
+    field_source: surface_flux
+
+-----------------
+Requesting Output
+-----------------
+
+By default, MARBL will not return any of the additional output.
+To request one or more of these fields,
+use the ``add_output_for_GCM()`` function on the MARBL interface:
+
+.. block comes from marbl_interface
+.. code-block:: fortran
+
+  subroutine add_output_for_GCM(this, num_elements, field_name, output_id, field_source, num_levels)
+    ! Check the registry to see if field_name is provided from surface_flux_compute() or interior_tendency_compute()
+    ! add it to the proper output_for_GCM type, or log a useful error message
+
+    use marbl_interface_public_types, only : marbl_output_for_GCM_linked_list_type
+
+    class (marbl_interface_class), intent(inout) :: this
+    character(len=*),     intent(in)    :: field_name
+    integer(int_kind),    intent(in)    :: num_elements
+    integer(int_kind),    intent(out)   :: output_id
+    character(len=*),     intent(out)   :: field_source
+    integer(int_kind),    optional, intent(in) :: num_levels
+
+The output field ``field_source`` will be  ``interior_tendency_output`` or ``surface_flux_output``
+component of the MARBL interface type.
+The following block of code from the stand-alone driver shows how to request both surface and total chlorophyll.
+Note that the driver tracks how many outputs are coming from ``field_source = "surface_flux"``
+and how many come from ``field_source = "interior_tendency"``.
+
+.. block comes from marbl_call_compute_subroutines_drv.F90
+.. code-block:: fortran
+
+    if (base_bio_on) then
+      do n=1, size(marbl_instances)
+        call marbl_instances(n)%add_output_for_GCM(num_elements=col_cnt(n), &
+                                                  field_name="total_surfChl", &
+                                                  output_id=total_surfChl_id, &
+                                                  field_source=field_source)
+        if (marbl_instances(n)%StatusLog%labort_marbl) then
+          call marbl_instances(n)%StatusLog%log_error_trace('marbl%add_output_for_GCM(total_surfChl)', subname)
+          return
+        end if
+      end do
+      if (trim(field_source) == "surface_flux") then
+        sfo_cnt = sfo_cnt+1
+      else if (trim(field_source) == "interior_tendency") then
+        ito_cnt = ito_cnt+1
+      else
+        write(log_message, "(3A)") "'", trim(field_source), "' is not a recognized field source (total_surfChl)"
+        call driver_status_log%log_error(log_message, subname)
+        return
+      end if
+    end if
+
+    if (base_bio_on) then
+      do n=1, size(marbl_instances)
+        call marbl_instances(n)%add_output_for_GCM(num_elements=col_cnt(n), &
+                                                  field_name="total_Chl", &
+                                                  output_id=total_Chl_id, &
+                                                  num_levels=num_levels, &
+                                                  field_source=field_source)
+        if (marbl_instances(n)%StatusLog%labort_marbl) then
+          call marbl_instances(n)%StatusLog%log_error_trace('marbl%add_output_for_GCM(total_Chl)', subname)
+          return
+        end if
+      end do
+      if (trim(field_source) == "surface_flux") then
+        sfo_cnt = sfo_cnt+1
+      else if (trim(field_source) == "interior_tendency") then
+        ito_cnt = ito_cnt+1
+      else
+        write(log_message, "(3A)") "'", trim(field_source), "' is not a recognized field source (total_Chl)"
+        call driver_status_log%log_error(log_message, subname)
+        return
+      end if
+    end if

docs/src/usr-guide/GCM-interface/index.rst

@@ -12,4 +12,5 @@ How to Use MARBL in a GCM
    GCM_requirements/index.rst
    surface_flux.rst
    interior_tend.rst
+   additional_output.rst
    shutdown.rst