feat: add diag_yaml object (NOAA-GFDL#866)

rem1776 · Apr 30, 2024 · 1a7468f · 1a7468f
1 parent 35ccbe0
commit 1a7468f
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Showing 9 changed files with 470 additions and 311 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -130,6 +130,9 @@ list(APPEND fms_fortran_src_files
   diag_manager/fms_diag_elem_weight_procs.F90
   diag_manager/fms_diag_fieldbuff_update.F90
   diag_manager/fms_diag_bbox.F90
+  diag_manager/fms_diag_object.F90
+  diag_manager/fms_diag_yaml.F90
+  diag_manager/fms_diag_yaml_object.F90
   drifters/cloud_interpolator.F90
   drifters/drifters.F90
   drifters/drifters_comm.F90

diff --git a/diag_manager/Makefile.am b/diag_manager/Makefile.am
@@ -46,8 +46,6 @@ libdiag_manager_la_SOURCES = \
   include/fms_diag_fieldbuff_update.inc \
   include/fms_diag_fieldbuff_update.fh
   fms_diag_yaml.F90 \
-  diag_yaml.h \
-  diag_yaml.c \
   fms_diag_object.F90 \
   fms_diag_yaml_object.F90
 
@@ -56,21 +54,15 @@ diag_data_mod.$(FC_MODEXT): fms_diag_bbox_mod.$(FC_MODEXT)
 diag_axis_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT)
 diag_output_mod.$(FC_MODEXT): diag_axis_mod.$(FC_MODEXT) diag_data_mod.$(FC_MODEXT)
 diag_util_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) diag_axis_mod.$(FC_MODEXT) diag_output_mod.$(FC_MODEXT) \
-                  diag_grid_mod.$(FC_MODEXT) fms_diag_bbox_mod.$(FC_MODEXT)
+                            diag_grid_mod.$(FC_MODEXT)
 diag_table_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) diag_util_mod.$(FC_MODEXT)
-fms_diag_axis_object_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) fms_diag_time_utils_mod.$(FC_MODEXT)
-fms_diag_time_reduction_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT)
-fms_diag_elem_weight_procs_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT)
-fms_diag_outfield_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) fms_diag_elem_weight_procs_mod.$(FC_MODEXT)
-fms_diag_fieldbuff_update_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) diag_util_mod.$(FC_MODEXT) \
-                  fms_diag_outfield_mod.$(FC_MODEXT) fms_diag_elem_weight_procs_mod.$(FC_MODEXT) \
-                  fms_diag_bbox_mod.$(FC_MODEXT)
+fms_diag_yaml_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) diag_util_mod.$(FC_MODEXT) \
+                                  fms_diag_yaml_object_mod.$(FC_MODEXT)
+fms_diag_object_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) diag_axis_mod.$(FC_MODEXT) \
+                                  fms_diag_yaml_object_mod.$(FC_MODEXT)
 diag_manager_mod.$(FC_MODEXT): diag_axis_mod.$(FC_MODEXT) diag_data_mod.$(FC_MODEXT) diag_util_mod.$(FC_MODEXT) \
-                  diag_output_mod.$(FC_MODEXT) diag_grid_mod.$(FC_MODEXT) diag_table_mod.$(FC_MODEXT) \
-                  fms_diag_time_reduction_mod.$(FC_MODEXT) fms_diag_outfield_mod.$(FC_MODEXT) \
-                  fms_diag_fieldbuff_update_mod.$(FC_MODEXT) fms_diag_object_mod.$(FC_MODEXT)
-fms_diag_yaml_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) diag_util_mod.$(FC_MODEXT)
-fms_diag_object_mod.$(FC_MODEXT): diag_data_mod.$(FC_MODEXT) diag_axis_mod.$(FC_MODEXT) fms_diag_yaml_mod.$(FC_MODEXT)
+	                   diag_output_mod.$(FC_MODEXT) diag_grid_mod.$(FC_MODEXT) diag_table_mod.$(FC_MODEXT) \
+			   fms_diag_object_mod.$(FC_MODEXT) fms_diag_yaml_mod.$(FC_MODEXT)
 
 # Mod files are built and then installed as headers.
 MODFILES = \

diff --git a/diag_manager/diag_data.F90 b/diag_manager/diag_data.F90
@@ -104,33 +104,6 @@ MODULE diag_data_mod
 
   !> @}
 
-
-  !> @brief The files type matching a C struct containing diag_yaml information
-    !> @ingroup diag_data_mod
-type, bind(c) :: diag_files_type
-     character (kind=c_char) :: fname (20) !< file name
-     character (kind=c_char) :: frequnit (7) !< the frequency unit
-     integer (c_int)    :: freq !< the frequency of data
-     character (kind=c_char) :: timeunit(7) !< The unit of time
-     character (kind=c_char) :: unlimdim(8) !< The name of the unlimited dimension
-     character (kind=c_char) :: key(8) !< Storage for the key in the yaml file
-end type diag_files_type
-!> @brief The field type matching the C struct for diag_yaml information
-  !> @ingroup diag_data_mod
-type, bind(c) :: diag_fields_type
-     character (kind=c_char) :: fname (20) !< The field/diagnostic name
-     character (kind=c_char) :: var(20) !< The name of the variable
-     character (kind=c_char) :: files(20) !< The files that the diagnostic will be written to
-     integer (c_int)    :: ikind !< The type/kind of the variable
-     character (kind=c_char) :: skind(20) !< The type/kind of the variable
-     character (kind=c_char) :: reduction(20) !< IDK
-     character (kind=c_char) :: all_all(4) !< This has to be "all"
-     character (kind=c_char) :: region(50) !< The region
-     character (kind=c_char) :: regcoord(50) !< Coodinates of the region
-     character (kind=c_char) :: module_location(20) !< The module
-     character (kind=c_char) :: key(8) !< Storage for the key in the yaml file
-end type diag_fields_type
-
   !> @brief Contains the coordinates of the local domain to output.
   !> @ingroup diag_data_mod
   TYPE diag_grid

diff --git a/diag_manager/diag_manager.F90 b/diag_manager/diag_manager.F90
@@ -236,6 +236,9 @@ MODULE diag_manager_mod
   USE diag_table_mod, ONLY: parse_diag_table
   USE diag_output_mod, ONLY: get_diag_global_att, set_diag_global_att
   USE diag_grid_mod, ONLY: diag_grid_init, diag_grid_end
+#ifdef use_yaml
+  use fms_diag_yaml_mod, only: diag_yaml_object_init, diag_yaml_object_end
+#endif
   USE fms_diag_object_mod, ONLY: fms_diag_object, diag_object_placeholder
   USE constants_mod, ONLY: SECONDS_PER_DAY
   USE fms_diag_outfield_mod, ONLY: fmsDiagOutfieldIndex_type, fmsDiagOutfield_type
@@ -3706,6 +3709,10 @@ SUBROUTINE diag_manager_end(time)
     if (allocated(fileobj)) deallocate(fileobj)
     if (allocated(fileobjND)) deallocate(fileobjND)
     if (allocated(fnum_for_domain)) deallocate(fnum_for_domain)
+
+#ifdef use_yaml
+    if (use_modern_diag) call diag_yaml_object_end
+#endif
   END SUBROUTINE diag_manager_end
 
   !> @brief Replaces diag_manager_end; close just one file: files(file)
@@ -3803,12 +3810,8 @@ SUBROUTINE diag_manager_init(diag_model_subset, time_init, err_msg)
          & max_input_fields, max_axes, do_diag_field_log, write_bytes_in_file, debug_diag_manager,&
          & max_num_axis_sets, max_files, use_cmor, issue_oor_warnings,&
          & oor_warnings_fatal, max_out_per_in_field, flush_nc_files, region_out_use_alt_value, max_field_attributes,&
-<<<<<<< HEAD
          & max_file_attributes, max_axis_attributes, prepend_date, use_mpp_io, field_log_separator,&
-         & use_refactored_send
-=======
-         & max_file_attributes, max_axis_attributes, prepend_date, use_modern_diag, use_mpp_io
->>>>>>> 98bb81e0 (Adds  namelist variable)
+         & use_modern_diag
 
     ! If the module was already initialized do nothing
     IF ( module_is_initialized ) RETURN
@@ -3928,8 +3931,12 @@ SUBROUTINE diag_manager_init(diag_model_subset, time_init, err_msg)
        END IF
     END IF
 
-   CALL parse_diag_table(DIAG_SUBSET=diag_subset_output, ISTAT=mystat, ERR_MSG=err_msg_local)
-   IF ( mystat /= 0 ) THEN
+#ifdef use_yaml
+    if (use_modern_diag) CALL diag_yaml_object_init()
+#endif
+
+    CALL parse_diag_table(DIAG_SUBSET=diag_subset_output, ISTAT=mystat, ERR_MSG=err_msg_local)
+    IF ( mystat /= 0 ) THEN
        IF ( fms_error_handler('diag_manager_mod::diag_manager_init',&
             & 'Error parsing diag_table. '//TRIM(err_msg_local), err_msg) ) RETURN
    END IF

diff --git a/diag_manager/diag_yaml.c b/diag_manager/diag_yaml.c
diff --git a/diag_manager/diag_yaml.h b/diag_manager/diag_yaml.h
diff --git a/diag_manager/fms_diag_object.F90 b/diag_manager/fms_diag_object.F90
@@ -10,11 +10,9 @@ module fms_diag_object_mod
 use diag_data_mod,  only: diag_null
 use diag_data_mod,  only: r8, r4, i8, i4, string, null_type_int
 use diag_data_mod,  only: diag_null, diag_not_found, diag_not_registered, diag_registered_id
-use diag_data_mod,  only: diag_fields_type, diag_files_type
-use fms_diag_yaml_mod, only: is_field_type_null
-use fms_diag_yaml_mod, only: diag_yaml 
 use diag_axis_mod,  only: diag_axis_type
 use mpp_mod, only: fatal, note, warning, mpp_error
+use fms_diag_yaml_object_mod, only: diagYamlFiles_type, diagYamlFilesVar_type
 use time_manager_mod, ONLY: time_type
 !!!set_time, set_date, get_time, time_type, OPERATOR(>=), OPERATOR(>),&
 !!!       & OPERATOR(<), OPERATOR(==), OPERATOR(/=), OPERATOR(/), OPERATOR(+), ASSIGNMENT(=), get_date, &
@@ -59,8 +57,8 @@ module fms_diag_object_mod
 
 !> \brief Object that holds all variable information
 type fms_diag_object
-     type (diag_fields_type)                          :: diag_field        !< info from diag_table
-     type (diag_files_type),allocatable, dimension(:) :: diag_file         !< info from diag_table
+     type (diagYamlFilesVar_type), allocatable, dimension(:) :: diag_field !< info from diag_table
+     type (diagYamlFiles_type),     allocatable, dimension(:) :: diag_file  !< info from diag_table
      integer, allocatable, private                    :: diag_id           !< unique id for varable
      class(FmsNetcdfFile_t), dimension (:), pointer   :: fileob => NULL()  !< A pointer to all of the 
                                                                            !! file objects for this variable
@@ -238,13 +236,14 @@ subroutine fms_register_diag_field_obj &
   allocate(character(len=len(modname)) :: dobj%modname)
   dobj%modname = trim(modname)
 !> Grab the information from the diag_table
+!  TO DO:
 !  dobj%diag_field = get_diag_table_field(trim(varname))
 !  dobj%diag_field = diag_yaml%get_diag_field(
-  if (is_field_type_null(dobj%diag_field)) then
-     dobj%diag_id = diag_not_found
-     dobj%vartype = diag_null
-     return
-  endif
+!  if (is_field_type_null(dobj%diag_field)) then
+!     dobj%diag_id = diag_not_found
+!     dobj%vartype = diag_null
+!     return
+!  endif
 !> get the optional arguments if included and the diagnostic is in the diag table
   if (present(longname)) then
      allocate(character(len=len(longname)) :: dobj%longname)