diag_manifest patch

diag_manager/fms_diag_field_object.F90

@@ -344,6 +344,12 @@ subroutine fms_register_diag_field_obj &
 !> get the optional arguments if included and the diagnostic is in the diag table
   if (present(longname))      this%longname      = trim(longname)
   if (present(standname))     this%standname     = trim(standname)
+  do i=1, SIZE(diag_field_indices)
+    yaml_var_ptr => diag_yaml%get_diag_field_from_id(diag_field_indices(i))
+
+    !! Add standard name to the diag_yaml object, so that it can be used when writing the diag_manifest
+    call yaml_var_ptr%add_standname(standname)
+  enddo
 
   !> Ignore the units if they are set to "none". This is to reproduce previous diag_manager behavior
   if (present(units)) then

diag_manager/fms_diag_file_object.F90

@@ -49,7 +49,7 @@ module fms_diag_file_object_mod
 use fms_diag_field_object_mod, only: fmsDiagField_type
 use fms_diag_output_buffer_mod, only: fmsDiagOutputBuffer_type
 use mpp_mod, only: mpp_get_current_pelist, mpp_npes, mpp_root_pe, mpp_pe, mpp_error, FATAL, stdout, &
-                   uppercase, lowercase, NOTE
+                   uppercase, lowercase, NOTE, mpp_max
 use platform_mod, only: FMS_FILE_LEN
 use mpp_domains_mod, only: mpp_get_ntile_count, mpp_get_UG_domain_ntiles, mpp_get_io_domain_layout, &
                            mpp_get_io_domain_UG_layout
@@ -1615,12 +1615,21 @@ end subroutine init_unlim_dim
 
 !> \brief Get the number of time levels that were actually written to the file
 !! \return Number of time levels that were actually written to the file
-pure function get_num_time_levels(this) &
+function get_num_time_levels(this) &
 result(res)
   class(fmsDiagFileContainer_type), intent(in), target   :: this            !< The file object
   integer :: res
 
-  res = this%FMS_diag_file%num_time_levels
+  if (this%is_regional()) then
+    !! If this is a subregional file, num_time_levels will be set to 0 for
+    !! all PEs that are not in the subregion. If the root pe is not in the subregion
+    !! then the num_time_levels will not be correct, so this is just getting the max
+    !! from all PEs
+    res = this%FMS_diag_file%num_time_levels
+    call mpp_max(res)
+  else
+    res = this%FMS_diag_file%num_time_levels
+  endif
 end function
 
 !> \brief Get the number of tiles in the file's domain

diag_manager/fms_diag_yaml.F90

@@ -202,6 +202,7 @@ module fms_diag_yaml_mod
   character (len=:), private, allocatable :: var_outname !< Name of the variable as written to the file
   character (len=:), private, allocatable :: var_longname !< Overwrites the long name of the variable
   character (len=:), private, allocatable :: var_units !< Overwrites the units
+  character (len=:), private, allocatable :: standard_name !< Standard_name (saved from the register_diag_field call)
   real(kind=r4_kind), private             :: var_zbounds(2)  !< The z axis limits [vert_min, vert_max]
   integer          , private              :: n_diurnal !< Number of diurnal samples
                                                        !! 0 if var_reduction is not "diurnalXX"
@@ -243,8 +244,10 @@ module fms_diag_yaml_mod
   procedure :: has_var_attributes
   procedure :: has_n_diurnal
   procedure :: has_pow_value
+  procedure :: has_standname
   procedure :: add_axis_name
   procedure :: is_file_subregional
+  procedure :: add_standname
 
 end type diagYamlFilesVar_type
 
@@ -1453,6 +1456,12 @@ pure logical function has_pow_value(this)
   class(diagYamlFilesVar_type), intent(in) :: this !< diagYamlvar_type object to inquire
   has_pow_value = (this%pow_value .ne. 0)
 end function has_pow_value
+!> @brief Checks if diag_file_obj%standname is set
+!! @return true if diag_file_obj%standname is set
+pure logical function has_standname(this)
+  class(diagYamlFilesVar_type), intent(in) :: this !< diagYamlvar_type object to inquire
+  has_standname = (this%standard_name .ne. "")
+end function has_standname
 
 !> @brief Checks if diag_file_obj%diag_title is allocated
 !! @return true if diag_file_obj%diag_title is allocated
@@ -1814,6 +1823,7 @@ subroutine fms_diag_yaml_out(ntimes, ntiles, ndistributedfiles)
         call fms_f2c_string(keys3(key3_i)%key9, 'n_diurnal')
         call fms_f2c_string(keys3(key3_i)%key10, 'pow_value')
         call fms_f2c_string(keys3(key3_i)%key11, 'dimensions')
+        call fms_f2c_string(keys3(key3_i)%key12, 'standard_name')
         if (varptr%has_var_module())   call fms_f2c_string(vals3(key3_i)%val1, varptr%var_module)
         if (varptr%has_var_varname())  call fms_f2c_string(vals3(key3_i)%val2, varptr%var_varname)
         if (varptr%has_var_reduction()) then
@@ -1853,6 +1863,9 @@ subroutine fms_diag_yaml_out(ntimes, ntiles, ndistributedfiles)
 
         tmpstr1 = ''; tmpstr1 = varptr%var_axes_names
         call fms_f2c_string(vals3(key3_i)%val11, trim(adjustl(tmpstr1)))
+
+        if(diag_yaml%diag_fields(varnum_i)%has_standname())&
+          call fms_f2c_string(vals3(key3_i)%val12, diag_yaml%diag_fields(varnum_i)%standard_name)
       enddo
     endif
 
@@ -2080,6 +2093,18 @@ subroutine add_axis_name( this, axis_name )
 
 end subroutine add_axis_name
 
+!> @brief Adds the standname for the DiagYamlFilesVar_type
+subroutine add_standname (this, standard_name)
+  class(diagYamlFilesVar_type), intent(inout) :: this
+  character(len=*), optional, intent(in) :: standard_name
+
+  if (present(standard_name)) then
+    this%standard_name = standard_name(1:len_trim(standard_name))
+  else
+    this%standard_name = ""
+  endif
+end subroutine add_standname
+
 pure function is_file_subregional( this ) &
   result(res)
   class(diagYamlFilesVar_type), intent(in) :: this

test_fms/diag_manager/check_subregional.F90

@@ -19,10 +19,12 @@
 
 !> @brief Checks the output file after running test_subregional
 program check_subregional
+#ifdef use_yaml
   use fms_mod,           only: fms_init, fms_end, string
   use fms2_io_mod,       only: FmsNetcdfFile_t, read_data, close_file, open_file, get_dimension_size, file_exists
   use mpp_mod,           only: mpp_npes, mpp_error, FATAL, mpp_pe
   use platform_mod,      only: r4_kind, r8_kind
+  use yaml_parser_mod,   only: open_and_parse_file, get_num_blocks, get_block_ids, get_value_from_key
 
   implicit none
 
@@ -33,6 +35,7 @@ program check_subregional
   call check_subregional_file("test_subregional.nc")
   call check_subregional_file("test_subregional2.nc")
   call check_corner_files()
+  call check_manifest()
 
   call fms_end()
 
@@ -203,4 +206,31 @@ subroutine check_corner_files()
 
   end subroutine check_corner_files
 
+  !> @brief Check that the number of time levels was written correctly in the diag manifest yaml
+  subroutine check_manifest()
+    integer              :: diag_yaml_id !< Id for the diag manifest yaml
+    integer              :: nfiles       !< Number of diag files in the yaml
+    integer, allocatable :: file_ids(:)  !< Ids for all the diag files in the yaml
+    integer              :: i            !< For do loops
+    integer              :: ntime_levels !< Number of time levels are read from the yaml
+
+    if ( .not. file_exists("diag_manifest.yaml.0")) &
+      call mpp_error(FATAL, "diag manifest file does not exist!")
+
+    diag_yaml_id = open_and_parse_file("diag_manifest.yaml.0")
+
+    nfiles = get_num_blocks(diag_yaml_id, "diag_files")
+    allocate(file_ids(nfiles))
+    call get_block_ids(diag_yaml_id, "diag_files", file_ids)
+
+    do i = 1, nfiles
+      ntime_levels = -999
+      call get_value_from_key(diag_yaml_id, file_ids(i), "number_of_timelevels", ntime_levels)
+
+      if (ntime_levels .ne. 8)&
+        call mpp_error(FATAL, "The number of time levels is not correct:: "//string(ntime_levels))
+    enddo
+
+  end subroutine check_manifest
+#endif
 end program

test_fms/diag_manager/test_diag_manager2.sh

@@ -913,6 +913,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: z
+    standard_name:
   sub_region:
   - grid_type:
     tile:
@@ -948,6 +949,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time y x
+    standard_name:
   - module: ocn_mod
     var_name: var2
     reduction: average
@@ -959,6 +961,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time x y
+    standard_name:
   sub_region:
   - grid_type:
     tile:
@@ -993,6 +996,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time y3 x3
+    standard_name:
   - module: atm_mod
     var_name: var4
     reduction: average
@@ -1004,6 +1008,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time z y3 x3
+    standard_name:
   - module: atm_mod
     var_name: var6
     reduction: average
@@ -1015,6 +1020,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time z
+    standard_name: I hope this is the MDTF tables
   - module: atm_mod
     var_name: var4
     reduction: average
@@ -1026,6 +1032,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time z_sub01 y3 x3
+    standard_name:
   sub_region:
   - grid_type:
     tile:
@@ -1060,6 +1067,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time grid_index
+    standard_name:
   - module: atm_mod
     var_name: var7
     reduction: none
@@ -1071,6 +1079,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: z
+    standard_name:
   sub_region:
   - grid_type:
     tile:
@@ -1105,6 +1114,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time
+    standard_name: Land is important!
   sub_region:
   - grid_type:
     tile:
@@ -1139,6 +1149,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time z y3_sub01 x3_sub01
+    standard_name:
   sub_region:
   - grid_type: index
     tile: 1
@@ -1173,6 +1184,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time y x
+    standard_name:
   sub_region:
   - grid_type:
     tile:
@@ -1207,6 +1219,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time y x
+    standard_name:
   sub_region:
   - grid_type:
     tile:
@@ -1241,6 +1254,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time y x
+    standard_name:
   sub_region:
   - grid_type:
     tile:
@@ -1275,6 +1289,7 @@ diag_files:
     n_diurnal:
     pow_value:
     dimensions: time y x
+    standard_name:
   sub_region:
   - grid_type:
     tile:
@@ -1309,6 +1324,7 @@ diag_files:
     n_diurnal: 12
     pow_value:
     dimensions: time time_of_day_12 y x
+    standard_name:
   sub_region:
   - grid_type:
     tile:

test_fms/diag_manager/test_modern_diag.F90

@@ -161,11 +161,13 @@ program test_modern_diag
 id_var4 = register_diag_field  ('atm_mod', 'var4', (/id_x3, id_y3, id_z/), Time, &
                                 '3D var in a cube sphere domain', 'mullions')
 id_var5 = register_diag_field  ('lnd_mod', 'var5', (/id_ug/), Time, 'Var in a UG domain', 'mullions')
-id_var6 = register_diag_field  ('atm_mod', 'var6', (/id_z/), Time, 'Var not domain decomposed', 'mullions')
+id_var6 = register_diag_field  ('atm_mod', 'var6', (/id_z/), Time, 'Var not domain decomposed', 'mullions', &
+                                standard_name="I hope this is the MDTF tables")
 
 !< This has the same name as var1, but it should have a different id because the module is different
 !! so it should have its own diag_obj
-id_var7 = register_diag_field  ('lnd_mod', 'var1', Time, 'Some scalar var', 'mullions')
+id_var7 = register_diag_field  ('lnd_mod', 'var1', Time, 'Some scalar var', 'mullions', &
+                                 standard_name="Land is important!")
 id_var8 = register_static_field ('atm_mod', 'var7', (/id_z/), "Be static!", "none")
 
 if (.not. debug) then