Merge branch 'even_moar_updates' of github.com:uramirez8707/FMS into …

…dmUpdate

diag_manager/diag_data.F90

@@ -335,6 +335,7 @@ MODULE diag_data_mod
     character(len=:), allocatable :: att_name     !< Name of the attribute
     contains
       procedure :: add => fms_add_attribute
+      procedure :: write_metadata
   end type fmsDiagAttribute_type
 ! Include variable "version" to be written to log file.
 #include<file_version.h>
@@ -562,8 +563,9 @@ function get_base_second() &
     res = base_second
   end function get_base_second
 
+  !> @brief Adds an attribute to the attribute type
   subroutine fms_add_attribute(this, att_name, att_value)
-    class(fmsDiagAttribute_type), intent(inout) :: this          !< Diag attribute type
+    class(fmsDiagAttribute_type), intent(inout) :: this         !< Diag attribute type
     character(len=*),             intent(in)    :: att_name     !< Name of the attribute
     class(*),                     intent(in)    :: att_value(:) !< The attribute value to add
 
@@ -589,6 +591,38 @@ subroutine fms_add_attribute(this, att_name, att_value)
       this%att_value = att_value
     end select
   end subroutine fms_add_attribute
+
+  !> @brief Writes out the attributes from an fmsDiagAttribute_type
+  subroutine write_metadata(this, fileobj, var_name, cell_methods)
+    class(fmsDiagAttribute_type),      intent(inout) :: this          !< Diag attribute type
+    class(FmsNetcdfFile_t),            INTENT(INOUT) :: fileobj       !< Fms2_io fileobj to write to
+    character(len=*),                  intent(in)    :: var_name      !< The name of the variable to write to
+    character(len=*),        optional, intent(inout) :: cell_methods  !< The cell methods attribute
+
+    select type (att_value =>this%att_value)
+    type is (character(len=*))
+      !< If the attribute is cell methods append to the current cell_methods attribute value
+      !! This will be writen once all of the cell_methods attributes are gathered ...
+      if (present(cell_methods)) then
+        if (trim(this%att_name) .eq. "cell_methods") then
+          cell_methods = trim(cell_methods)//" "//trim(att_value(1))
+          return
+        endif
+      endif
+
+      call register_variable_attribute(fileobj, var_name, this%att_name, trim(att_value(1)), &
+                                       str_len=len_trim(att_value(1)))
+    type is (real(kind=r8_kind))
+      call register_variable_attribute(fileobj, var_name, this%att_name, real(att_value, kind=r8_kind))
+    type is (real(kind=r4_kind))
+      call register_variable_attribute(fileobj, var_name, this%att_name, real(att_value, kind=r4_kind))
+    type is (integer(kind=i4_kind))
+      call register_variable_attribute(fileobj, var_name, this%att_name, int(att_value, kind=i4_kind))
+    type is (integer(kind=i8_kind))
+      call register_variable_attribute(fileobj, var_name, this%att_name, int(att_value, kind=i8_kind))
+    end select
+
+  end subroutine write_metadata
 END MODULE diag_data_mod
 !> @}
 ! close documentation grouping

diag_manager/diag_manager.F90

@@ -4432,6 +4432,11 @@ SUBROUTINE diag_field_add_cell_measures(diag_field_id, area, volume)
                & 'either area or volume arguments must be present', FATAL )
        END IF
 
+       if (use_modern_diag) then
+         call fms_diag_object%fms_diag_field_add_cell_measures(diag_field_id, area, volume)
+         return
+       ENDIF
+
        DO j=1, input_fields(diag_field_id)%num_output_fields
           ind = input_fields(diag_field_id)%output_fields(j)
           CALL init_field_cell_measures(output_fields(ind), area=area, volume=volume)

diag_manager/fms_diag_axis_object.F90

@@ -103,6 +103,7 @@ module fms_diag_axis_object_mod
        procedure :: add_structured_axis_ids
        procedure :: get_structured_axis
        procedure :: is_unstructured_grid
+       procedure :: get_edges_id
   END TYPE fmsDiagAxis_type
 
   !> @brief Type to hold the subaxis
@@ -152,6 +153,8 @@ module fms_diag_axis_object_mod
                                                                  !! or "UG_DOMAIN")
      INTEGER                        , private :: length          !< Global axis length
      INTEGER                        , private :: direction       !< Direction of the axis 0, 1, -1
+     INTEGER,            ALLOCATABLE, private :: edges_id        !< Axis ID for the edges axis
+                                                                 !! This axis will be written to the file
      CHARACTER(len=:),   ALLOCATABLE, private :: edges_name      !< Name for the previously defined "edges axis"
                                                                  !! This will be written as an attribute
      CHARACTER(len=:), ALLOCATABLE,   private :: aux             !< Auxiliary name, can only be <TT>geolon_t</TT>
@@ -169,7 +172,7 @@ module fms_diag_axis_object_mod
      PROCEDURE :: add_axis_attribute
      PROCEDURE :: register => register_diag_axis_obj
      PROCEDURE :: axis_length => get_axis_length
-     PROCEDURE :: set_edges_name
+     PROCEDURE :: set_edges
      PROCEDURE :: set_axis_id
      PROCEDURE :: get_compute_domain
      PROCEDURE :: get_indices
@@ -188,7 +191,7 @@ module fms_diag_axis_object_mod
   !> @brief Initialize the axis
   subroutine register_diag_axis_obj(this, axis_name, axis_data, units, cart_name, long_name, direction,&
   & set_name, Domain, Domain2, DomainU, aux, req, tile_count, domain_position, axis_length )
-    class(fmsDiagFullAxis_type),INTENT(out)  :: this            !< Diag_axis obj
+    class(fmsDiagFullAxis_type),INTENT(inout):: this            !< Diag_axis obj
     CHARACTER(len=*),   INTENT(in)           :: axis_name       !< Name of the axis
     class(*),           INTENT(in)           :: axis_data(:)    !< Array of coordinate values
     CHARACTER(len=*),   INTENT(in)           :: units           !< Units for the axis
@@ -299,6 +302,9 @@ subroutine write_axis_metadata(this, fileobj, parent_axis)
     type(fmsDiagFullAxis_type), pointer   :: diag_axis       !< Local pointer to the diag_axis
 
     integer :: type_of_domain !< The type of domain the current axis is in
+    logical :: is_subaxis     !< .true. if the axis is a subaxis
+
+    is_subaxis = .false.
 
     select type(this)
     type is (fmsDiagFullAxis_type)
@@ -307,6 +313,7 @@ subroutine write_axis_metadata(this, fileobj, parent_axis)
       diag_axis => this
       type_of_domain = this%type_of_domain
     type is (fmsDiagSubAxis_type)
+      is_subaxis = .true.
       axis_name => this%subaxis_name
       axis_length = this%ending_index - this%starting_index + 1
       !< Get all the other information from the parent axis (i.e the cart_name, units, etc)
@@ -373,7 +380,7 @@ subroutine write_axis_metadata(this, fileobj, parent_axis)
       call register_variable_attribute(fileobj, axis_name, "positive", "down", str_len=4)
     end select
 
-    if (allocated(diag_axis%edges_name)) then
+    if (allocated(diag_axis%edges_name) .and. .not. is_subaxis) then
       call register_variable_attribute(fileobj, axis_name, "edges", diag_axis%edges_name, &
         str_len=len_trim(diag_axis%edges_name))
     endif
@@ -521,6 +528,19 @@ pure function get_structured_axis(this) &
     end select
   end function get_structured_axis
 
+
+  !< @brief Get the edges_id of an axis_object
+  !! @return The edges_id of an axis object
+  pure integer function get_edges_id(this)
+    class(fmsDiagAxis_type), INTENT(in)    :: this        !< diag_axis obj
+
+    get_edges_id = diag_null
+    select type (this)
+    type is (fmsDiagFullAxis_type)
+      if (allocated(this%edges_id)) get_edges_id = this%edges_id
+    end select
+  end function
+
   !> @brief Get the starting and ending indices of the global io domain of the axis
   subroutine get_global_io_domain(this, global_io_index)
     class(fmsDiagFullAxis_type), intent(in)  :: this               !< diag_axis obj
@@ -593,13 +613,19 @@ subroutine set_axis_id(this, axis_id)
 
   end subroutine set_axis_id
 
-  !> @brief Set the name of the edges
-  subroutine set_edges_name(this, edges_name)
-    class(fmsDiagFullAxis_type), intent(inout) :: this !< diag_axis obj
-    CHARACTER(len=*),        intent(in)        :: edges_name !< Name of the edges
+    !> @brief Set the name and ids of the edges
+  subroutine set_edges(this, edges_name, edges_id)
+    class(fmsDiagFullAxis_type), intent(inout) :: this       !< diag_axis obj
+    CHARACTER(len=*),            intent(in)    :: edges_name !< Name of the edges
+    integer,                     intent(in)    :: edges_id   !< Axis id of the edges
 
+    !< Saving the name and the id of the edges axis because it will make it easier to use
+    !! downstream (i.e you need the edges name to write the attribute to the current axis,
+    !! and you need the edges id to add to the diag file object so that you can write the edges
+    !! to the file)
     this%edges_name = edges_name
-  end subroutine
+    this%edges_id = edges_id
+  end subroutine set_edges
 
   !> @brief Determine if the subRegion is in the current PE.
   !! If it is, determine the starting and ending indices of the current PE that belong to the subRegion

diag_manager/fms_diag_field_object.F90

@@ -147,6 +147,8 @@ module fms_diag_field_object_mod
      procedure :: write_field_metadata
      procedure :: write_coordinate_attribute
      procedure :: get_math_needs_to_be_done
+     procedure :: add_area_volume
+     procedure :: append_time_cell_methods
 end type fmsDiagField_type
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! variables !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 type(fmsDiagField_type) :: null_ob
@@ -671,11 +673,21 @@ end function get_vartype
 
 !> @brief Gets varname
 !! @return copy of the variable name
-pure function get_varname (this) &
+pure function get_varname (this, to_write) &
 result(rslt)
-     class (fmsDiagField_type), intent(in) :: this !< diag object
-     character(len=:), allocatable :: rslt
-     rslt = this%varname
+  class (fmsDiagField_type), intent(in) :: this     !< diag object
+  logical, optional,         intent(in) :: to_write !< .true. if getting the varname that will be writen to the file
+  character(len=:), allocatable :: rslt
+  rslt = this%varname
+
+  !< If writing the varname can be the outname which is defined in the yaml
+  if (present(to_write)) then
+    if (to_write) then
+    !TODO this is wrong
+    rslt = this%diag_field(1)%get_var_outname()
+    endif
+  endif
+
 end function get_varname
 
 !> @brief Gets longname
@@ -1082,13 +1094,15 @@ subroutine write_field_metadata(this, fileobj, file_id, yaml_id, diag_axis, unli
   class(fmsDiagAxisContainer_type),  intent(in)    :: diag_axis(:)  !< Diag_axis object
   character(len=*),                  intent(in)    :: unlim_dimname !< The name of the unlimited dimension
   logical,                           intent(in)    :: is_regional   !< Flag indicating if the field is regional
-  character(len=*),                  intent(inout) :: cell_measures
+  character(len=*),                  intent(in)    :: cell_measures !< The cell measures attribute to write
 
   type(diagYamlFilesVar_type), pointer     :: field_yaml  !< pointer to the yaml entry
   character(len=:),            allocatable :: var_name    !< Variable name
   character(len=:),            allocatable :: long_name   !< Longname to write
   character(len=:),            allocatable :: units       !< Units of the field to write
   character(len=120),          allocatable :: dimnames(:) !< Dimension names of the field
+  character(len=120)                       :: cell_methods!< Cell methods attribute to write
+  integer                                  :: i           !< For do loops
 
   field_yaml => diag_yaml%get_diag_field_from_id(yaml_id)
   var_name = field_yaml%get_var_outname()
@@ -1130,16 +1144,34 @@ subroutine write_field_metadata(this, fileobj, file_id, yaml_id, diag_axis, unli
       str_len=len_trim(this%get_interp_method()))
   endif
 
-  select case (field_yaml%get_var_reduction())
-  case (time_average, time_max, time_min)
-    call register_variable_attribute(fileobj, var_name, "time_avg_info", &
-      trim(avg_name)//'_T1,'//trim(avg_name)//'_T2,'//trim(avg_name)//'_DT', &
-      str_len=len(trim(avg_name)//'_T1,'//trim(avg_name)//'_T2,'//trim(avg_name)//'_DT'))
-  end select
+  if (.not. this%static) then
+    select case (field_yaml%get_var_reduction())
+    case (time_average, time_max, time_min, time_diurnal, time_power, time_rms, time_sum)
+      call register_variable_attribute(fileobj, var_name, "time_avg_info", &
+        trim(avg_name)//'_T1,'//trim(avg_name)//'_T2,'//trim(avg_name)//'_DT', &
+        str_len=len(trim(avg_name)//'_T1,'//trim(avg_name)//'_T2,'//trim(avg_name)//'_DT'))
+    end select
+  endif
 
-  call append_time_cell_measure(cell_measures, field_yaml)
-  if (trim(cell_measures) .ne. "") &
+  cell_methods = ""
+  !< Check if any of the attributes defined via a "diag_field_add_attribute" call
+  !! are the cell_methods, if so add to the "cell_methods" variable:
+  do i = 1, this%num_attributes
+    call this%attributes(i)%write_metadata(fileobj, var_name, &
+      cell_methods=cell_methods)
+  enddo
+
+  !< Append the time cell methods based on the variable's reduction
+  call this%append_time_cell_methods(cell_methods, field_yaml)
+  if (trim(cell_methods) .ne. "") &
     call register_variable_attribute(fileobj, var_name, "cell_methods", &
+      trim(adjustl(cell_methods)), str_len=len_trim(adjustl(cell_methods)))
+
+  !< Write out the cell_measures attribute (i.e Area, Volume)
+  !! The diag field ids for the Area and Volume are sent in the register call
+  !! This was defined in file object and passed in here
+  if (trim(cell_measures) .ne. "") &
+    call register_variable_attribute(fileobj, var_name, "cell_measures", &
       trim(adjustl(cell_measures)), str_len=len_trim(adjustl(cell_measures)))
 
   !< Write out the standard_name (this was defined in the register call)
@@ -1432,30 +1464,65 @@ PURE FUNCTION diag_field_id_from_name(this, module_name, field_name) &
   endif
 end function diag_field_id_from_name
 
-!> @brief Append the time cell measured based on the variable's reduction
-subroutine append_time_cell_measure(cell_measures, field_yaml)
-  character(len=*),            intent(inout) :: cell_measures !< The cell measures to append to
-  type(diagYamlFilesVar_type), intent(in)    :: field_yaml    !< The field's yaml
+!> @brief Adds the area and volume id to a field object
+subroutine add_area_volume(this, area, volume)
+  CLASS(fmsDiagField_type),          intent(inout) :: this   !< The field object
+  INTEGER,                 optional, INTENT(in)    :: area   !< diag ids of area
+  INTEGER,                 optional, INTENT(in)    :: volume !< diag ids of volume
+
+  if (present(area)) then
+    if (area > 0) then
+      this%area = area
+    else
+      call mpp_error(FATAL, "diag_field_add_cell_measures: the area id is not valid. "&
+                           &"Verify that the area_id passed in to the field:"//this%varname//&
+                           &" is valid and that the field is registered and in the diag_table.yaml")
+    endif
+  endif
+
+  if (present(volume)) then
+    if (volume > 0) then
+      this%volume = volume
+    else
+      call mpp_error(FATAL, "diag_field_add_cell_measures: the volume id is not valid. "&
+                           &"Verify that the volume_id passed in to the field:"//this%varname//&
+                           &" is valid and that the field is registered and in the diag_table.yaml")
+    endif
+  endif
+
+end subroutine add_area_volume
+
+!> @brief Append the time cell meathods based on the variable's reduction
+subroutine append_time_cell_methods(this, cell_methods, field_yaml)
+  class (fmsDiagField_type),   target, intent(inout) :: this          !< diag field
+  character(len=*),                    intent(inout) :: cell_methods  !< The cell methods var to append to
+  type(diagYamlFilesVar_type),         intent(in)    :: field_yaml    !< The field's yaml
+
+  if (this%static) then
+    cell_methods = trim(cell_methods)//" time: point "
+    return
+  endif
 
   select case (field_yaml%get_var_reduction())
   case (time_none)
-    cell_measures = trim(cell_measures)//" time: point "
+    cell_methods = trim(cell_methods)//" time: point "
   case (time_diurnal)
-    cell_measures = trim(cell_measures)//" time: mean"
+    cell_methods = trim(cell_methods)//" time: mean"
   case (time_power)
-    cell_measures = trim(cell_measures)//" time: mean_pow"//int2str(field_yaml%get_pow_value())
+    cell_methods = trim(cell_methods)//" time: mean_pow"//int2str(field_yaml%get_pow_value())
   case (time_rms)
-    cell_measures = trim(cell_measures)//" time: root_mean_square"
+    cell_methods = trim(cell_methods)//" time: root_mean_square"
   case (time_max)
-    cell_measures = trim(cell_measures)//" time: max"
+    cell_methods = trim(cell_methods)//" time: max"
   case (time_min)
-    cell_measures = trim(cell_measures)//" time: min"
+    cell_methods = trim(cell_methods)//" time: min"
   case (time_average)
-    cell_measures = trim(cell_measures)//" time: mean"
+    cell_methods = trim(cell_methods)//" time: mean"
   case (time_sum)
-    cell_measures = trim(cell_measures)//" time: sum"
+    cell_methods = trim(cell_methods)//" time: sum"
   end select
-end subroutine append_time_cell_measure
+end subroutine append_time_cell_methods
+
 !> Dumps any data from a given fmsDiagField_type object
 subroutine dump_field_obj (this, unit_num)
   class(fmsDiagField_type), intent(in) :: this

diag_manager/fms_diag_file_object.F90

@@ -1213,6 +1213,7 @@ subroutine write_axis_metadata(this, diag_axis)
   integer                              :: i,k            !< For do loops
   integer                              :: parent_axis_id !< Id of the parent_axis
   integer                              :: structured_ids(2) !< Ids of the uncompress axis
+  integer                              :: edges_id       !< Id of the axis edge
 
   class(fmsDiagAxisContainer_type), pointer :: axis_ptr !< pointer to the axis object currently writing
 
@@ -1234,6 +1235,12 @@ subroutine write_axis_metadata(this, diag_axis)
         call diag_axis(structured_ids(k))%axis%write_axis_metadata(fileobj)
       enddo
     endif
+
+    edges_id = axis_ptr%axis%get_edges_id()
+    if (edges_id .ne. diag_null) then
+      if (any(diag_file%axis_ids(1:diag_file%number_of_axis) .eq. edges_id)) return
+      call diag_axis(edges_id)%axis%write_axis_metadata(fileobj)
+    endif
   enddo
 
 end subroutine write_axis_metadata
@@ -1265,11 +1272,11 @@ subroutine write_field_metadata(this, diag_field, diag_axis)
     !the file that the fields are in needs to be added
     cell_measures = ""
     if (field_ptr%has_area()) then
-      cell_measures = "area:"//diag_field(field_ptr%get_area())%get_varname()
+      cell_measures = "area: "//diag_field(field_ptr%get_area())%get_varname(to_write=.true.)
     endif
 
     if (field_ptr%has_volume()) then
-      cell_measures = trim(cell_measures)//" volume:"//diag_field(field_ptr%get_volume())%get_varname()
+      cell_measures = trim(cell_measures)//" volume: "//diag_field(field_ptr%get_volume())%get_varname(to_write=.true.)
     endif
 
     call field_ptr%write_field_metadata(fileobj, diag_file%id, diag_file%yaml_ids(i), diag_axis, &