feat: modern diag fix and add calls to allocate_diag_field_output_buf…

…fers (NOAA-GFDL#1314)

diag_manager/fms_diag_field_object.F90

@@ -75,7 +75,7 @@ module fms_diag_field_object_mod
                                                                            !! been allocated
      logical, allocatable, private                    :: math_needs_to_be_done !< If true, do math
                                                                            !! functions. False when done.
-     logical, allocatable, dimension(:)               :: buffer_allocated  !< True if a buffer pointed by
+     logical, allocatable                             :: buffer_allocated  !< True if a buffer pointed by
                                                                            !! the corresponding index in
                                                                            !! buffer_ids(:) is allocated.
   contains
@@ -146,6 +146,7 @@ module fms_diag_field_object_mod
      procedure :: get_missing_value
      procedure :: get_data_RANGE
      procedure :: get_axis_id
+     procedure :: get_data_buffer
      procedure :: dump_field_obj
      procedure :: get_domain
      procedure :: get_type_of_domain
@@ -629,7 +630,8 @@ end function diag_obj_is_registered
 function diag_obj_is_static (this) result (rslt)
     class(fmsDiagField_type), intent(in) :: this
     logical :: rslt
-    rslt = this%static
+    rslt = .false.
+    if (allocated(this%static)) rslt = this%static
 end function diag_obj_is_static
 
 !> @brief Determine if the field is a scalar
@@ -1276,38 +1278,13 @@ function get_data_buffer (this) &
   else
     rslt => null()
   endif
-!  select type (db => this%data_buffer)
-!    type is (real(kind=r4_kind))
-!      allocate (real(kind=r4_kind) :: rslt(size(this%data_buffer,1), &
-!                                      size(this%data_buffer,2), &
-!                                      size(this%data_buffer,3), &
-!                                      size(this%data_buffer,4) ))
-!      rslt = this%data_buffer
-!    type is (real(kind=r8_kind))
-!      allocate (real(kind=r8_kind) :: rslt(size(this%data_buffer,1), &
-!                                      size(this%data_buffer,2), &
-!                                      size(this%data_buffer,3), &
-!                                      size(this%data_buffer,4) ))
-!      rslt = this%data_buffer
-!    type is (integer(kind=i4_kind))
-!      allocate (integer(kind=i4_kind) :: rslt(size(this%data_buffer,1), &
-!                                      size(this%data_buffer,2), &
-!                                      size(this%data_buffer,3), &
-!                                      size(this%data_buffer,4) ))
-!      rslt = this%data_buffer
-!    type is (integer(kind=i8_kind))
-!      allocate (integer(kind=i8_kind) :: rslt(size(this%data_buffer,1), &
-!                                      size(this%data_buffer,2), &
-!                                      size(this%data_buffer,3), &
-!                                      size(this%data_buffer,4) ))
-!      rslt = this%data_buffer
-!  end select
 end function get_data_buffer
 !> Gets the flag telling if the math functions need to be done
 !! \return Copy of math_needs_to_be_done flag
 pure logical function get_math_needs_to_be_done(this)
   class (fmsDiagField_type), intent(in) :: this !< diag object
-  get_math_needs_to_be_done = this%math_needs_to_be_done
+  get_math_needs_to_be_done = .false.
+  if (allocated(this%math_needs_to_be_done)) get_math_needs_to_be_done = this%math_needs_to_be_done
 end function get_math_needs_to_be_done
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !!!!! Allocation checks
@@ -1494,10 +1471,10 @@ function get_default_missing_value(var_type) &
 
   select case(var_type)
   case (r4)
-    allocate(integer(kind=r4_kind) :: rslt)
+    allocate(real(kind=r4_kind) :: rslt)
     rslt = real(CMOR_MISSING_VALUE, kind=r4_kind)
   case (r8)
-    allocate(integer(kind=r8_kind) :: rslt)
+    allocate(real(kind=r8_kind) :: rslt)
     rslt = real(CMOR_MISSING_VALUE, kind=r8_kind)
   case default
   end select

diag_manager/fms_diag_file_object.F90

@@ -760,7 +760,6 @@ subroutine add_axes(this, axis_ids, diag_axis, naxis, yaml_id, buffer_id, output
         this%axis_ids = diag_null
       endif
     endif
-    return
   type is (fmsDiagFile_type)
     do i = 1, size(var_axis_ids)
       axis_found = .false.

diag_manager/fms_diag_object.F90

@@ -231,7 +231,6 @@ integer function fms_register_diag_field_obj &
   enddo
 
 !> Allocate and initialize member buffer_allocated of this field
-  allocate(fieldptr%buffer_allocated(size(diag_field_indices)))
   fieldptr%buffer_allocated = .false.
 
 !> Register the data for the field
@@ -575,6 +574,8 @@ logical function fms_diag_accept_data (this, diag_field_id, field_data, time, is
     return
   else
 !!TODO: Loop through fields and do averages/math functions
+
+    call this%allocate_diag_field_output_buffers(field_data, diag_field_id)
     do i = 1, size(this%FMS_diag_fields(diag_field_id)%buffer_ids)
       buffer_id = this%FMS_diag_fields(diag_field_id)%buffer_ids(i)
 
@@ -662,9 +663,9 @@ subroutine fms_diag_send_complete(this, time_step)
 
         diag_field => this%FMS_diag_fields(file_field_ids(ifield))
         !> Check if math needs to be done
-        ! math = diag_field%get_math_needs_to_be_done()
-        math = .false. !TODO: replace this with real thing
+        math = diag_field%get_math_needs_to_be_done()
         calling_math: if (math) then
+          call this%allocate_diag_field_output_buffers(diag_field%get_data_buffer(), file_field_ids(ifield))
           !!TODO: call math functions !!
         endif calling_math
         !> Clean up, clean up, everybody everywhere
@@ -1004,9 +1005,12 @@ subroutine allocate_diag_field_output_buffers(this, field_data, field_id)
   class(DiagYamlFilesVar_type), pointer :: ptr_diag_field_yaml !< Pointer to a field from yaml fields
   integer, allocatable :: axis_ids(:) !< Pointer to indices of axes of the field variable
   integer :: var_type !< Stores type of the field data (r4, r8, i4, i8, and string) represented as an integer.
-  real :: missing_value !< Fill value to initialize output buffers
+  class(*), allocatable :: missing_value !< Missing value to initialize the data to
   character(len=128), allocatable :: var_name !< Field name to initialize output buffers
   logical :: is_scalar !< Flag indicating that the variable is a scalar
+  integer :: yaml_id
+
+  if (this%FMS_diag_fields(field_id)%buffer_allocated) return
 
   ! Determine the type of the field data
   var_type = get_var_type(field_data(1, 1, 1, 1))
@@ -1015,12 +1019,14 @@ subroutine allocate_diag_field_output_buffers(this, field_data, field_id)
   var_name = this%Fms_diag_fields(field_id)%get_varname()
 
   ! Get missing value for the field
+  !TODO class (*) is weird missing_value = this%FMS_diag_fields(field_id)%get_missing_value(var_type)
+  !!should work ...
   if (this%FMS_diag_fields(field_id)%has_missing_value()) then
     select type (my_type => this%FMS_diag_fields(field_id)%get_missing_value(var_type))
       type is (real(kind=r4_kind))
-        missing_value = my_type
+        missing_value = real(my_type, kind=r4_kind)
       type is (real(kind=r8_kind))
-        missing_value = real(my_type)
+        missing_value = real(my_type, kind=r8_kind)
       class default
         call mpp_error( FATAL, 'fms_diag_object_mod:allocate_diag_field_output_buffers Invalid type')
     end select
@@ -1036,10 +1042,7 @@ subroutine allocate_diag_field_output_buffers(this, field_data, field_id)
   endif
 
   ! Determine dimensions of the field
-  is_scalar = .True.
-  if (this%FMS_diag_fields(field_id)%has_axis_ids()) then
-    is_scalar = .False.
-  endif
+  is_scalar = this%FMS_diag_fields(field_id)%is_scalar()
 
   ! Loop over a number of fields/buffers where this variable occurs
   do i = 1, size(this%FMS_diag_fields(field_id)%buffer_ids)
@@ -1051,16 +1054,23 @@ subroutine allocate_diag_field_output_buffers(this, field_data, field_id)
       ndims = size(axis_ids)
     endif
 
-    ptr_diag_field_yaml => diag_yaml%get_diag_field_from_id(buffer_id)
+    yaml_id = this%FMS_diag_output_buffers(buffer_id)%get_yaml_id()
+
+    ptr_diag_field_yaml => diag_yaml%diag_fields(yaml_id)
     num_diurnal_samples = ptr_diag_field_yaml%get_n_diurnal() !< Get number of diurnal samples
 
     ! If diurnal axis exists, fill lengths of axes.
     if (num_diurnal_samples .ne. 0) then
       allocate(axes_length(ndims + 1)) !< Include extra length for the diurnal axis
-      do j = 1, ndims
-        axes_length(j) = this%fms_get_axis_length(axis_ids(j))
-      enddo
-      !TODO This is going to require more work for when we have subRegion variables
+    else
+      allocate(axes_length(ndims))
+    endif
+
+    do j = 1, ndims
+      axes_length(j) = this%fms_get_axis_length(axis_ids(j))
+    enddo
+
+    if (num_diurnal_samples .ne. 0) then
       axes_length(ndims + 1) = num_diurnal_samples
       ndims = ndims + 1 !< Add one more dimension for the diurnal axis
     endif
@@ -1069,7 +1079,7 @@ subroutine allocate_diag_field_output_buffers(this, field_data, field_id)
     ! outputBuffer0d_type, outputBuffer1d_type, outputBuffer2d_type, outputBuffer3d_type,
     ! outputBuffer4d_type or outputBuffer5d_type.
     if (.not. allocated(this%FMS_diag_output_buffers(buffer_id)%diag_buffer_obj)) then
-      this%FMS_diag_output_buffers(buffer_id) = fms_diag_output_buffer_create_container(ndims)
+      call fms_diag_output_buffer_create_container(ndims, this%FMS_diag_output_buffers(buffer_id))
     end if
 
     ptr_diag_buffer_obj => this%FMS_diag_output_buffers(buffer_id)%diag_buffer_obj
@@ -1108,7 +1118,12 @@ subroutine allocate_diag_field_output_buffers(this, field_data, field_id)
       class default
         call mpp_error( FATAL, 'allocate_diag_field_output_buffers: invalid buffer type')
     end select
+
+    if (allocated(axis_ids)) deallocate(axis_ids)
+    deallocate(axes_length)
   enddo
+
+  this%FMS_diag_fields(field_id)%buffer_allocated = .true.
 #else
   call mpp_error( FATAL, "allocate_diag_field_output_buffers: "//&
     "you can not use the modern diag manager without compiling with -Duse_yaml")

diag_manager/fms_diag_output_buffer.F90

@@ -174,33 +174,32 @@ end function fms_diag_output_buffer_init
 !> Creates a container type encapsulating a new buffer object for the given dimensions.
 !! The buffer object will still need to be allocated to a type via allocate_buffer() before use.
 !> @result A fmsDiagBufferContainer_type that holds a bufferNd_type, where N is buff_dims
-function fms_diag_output_buffer_create_container(buff_dims) &
-result(rslt)
-  integer, intent(in)                            :: buff_dims !< dimensions
-  type(fmsDiagOutputBufferContainer_type), allocatable :: rslt
+subroutine fms_diag_output_buffer_create_container(buff_dims, buffer_obj)
+  integer,                                 intent(in)     :: buff_dims !< dimensions
+  type(fmsDiagOutputBufferContainer_type), intent(inout)  :: buffer_obj
+
   character(len=5) :: dim_output !< string to output buff_dims on error
 
-  allocate(rslt)
   select case (buff_dims)
     case (0)
-      allocate(outputBuffer0d_type :: rslt%diag_buffer_obj)
+      allocate(outputBuffer0d_type :: buffer_obj%diag_buffer_obj)
     case (1)
-      allocate(outputBuffer1d_type :: rslt%diag_buffer_obj)
+      allocate(outputBuffer1d_type :: buffer_obj%diag_buffer_obj)
     case (2)
-      allocate(outputBuffer2d_type :: rslt%diag_buffer_obj)
+      allocate(outputBuffer2d_type :: buffer_obj%diag_buffer_obj)
     case (3)
-      allocate(outputBuffer3d_type :: rslt%diag_buffer_obj)
+      allocate(outputBuffer3d_type :: buffer_obj%diag_buffer_obj)
     case (4)
-      allocate(outputBuffer4d_type :: rslt%diag_buffer_obj)
+      allocate(outputBuffer4d_type :: buffer_obj%diag_buffer_obj)
     case (5)
-      allocate(outputBuffer5d_type :: rslt%diag_buffer_obj)
+      allocate(outputBuffer5d_type :: buffer_obj%diag_buffer_obj)
     case default
       write( dim_output, *) buff_dims
       dim_output = adjustl(dim_output)
       call mpp_error(FATAL, 'fms_diag_buffer_create_container: invalid number of dimensions given:' // dim_output //&
                             '. Must be 0-5')
   end select
-end function fms_diag_output_buffer_create_container
+end subroutine fms_diag_output_buffer_create_container
 
 !!--------generic routines for any fmsDiagBuffer_class objects
 

diag_manager/fms_diag_yaml.F90

@@ -226,7 +226,7 @@ module fms_diag_yaml_mod
   character(len=:), allocatable, private :: diag_title                   !< Experiment name
   integer, private, dimension (basedate_size) :: diag_basedate           !< basedate array
   type(diagYamlFiles_type), allocatable, public, dimension (:) :: diag_files!< History file info
-  type(diagYamlFilesVar_type), allocatable, private, dimension (:) :: diag_fields !< Diag fields info
+  type(diagYamlFilesVar_type), allocatable, public, dimension (:) :: diag_fields !< Diag fields info
   contains
   procedure :: size_diag_files