fms_diag_yaml.F90

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!*
!* This file is part of the GFDL Flexible Modeling System (FMS).
!*
!* Licensed under the Apache License, Version 2.0 (the "License");
!* you may not use this file except in compliance with the License.
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!> @defgroup fms_diag_yaml_mod fms_diag_yaml_mod
!> @ingroup diag_manager
!! @brief fms_diag_yaml_mod is an integral part of
!!   diag_manager_mod. Its function is to read the diag_table.yaml to fill in
!!   the diag_yaml_object
 
!> @file
!> @brief File for @ref diag_yaml_mod
 
!> @addtogroup fms_diag_yaml_mod
!> @{
module fms_diag_yaml_mod
#ifdef use_yaml
use diag_data_mod,   only: diag_null, diag_ocean, diag_all, diag_other, set_base_time, latlon_gridtype, &
                           index_gridtype, null_gridtype, diag_seconds, diag_minutes, diag_hours, diag_days, &
                           diag_months, diag_years, time_average, time_rms, time_max, time_min, time_sum, &
                           time_diurnal, time_power, time_none, r8, i8, r4, i4, diag_not_registered, &
                           middle_time, begin_time, end_time, max_str_len, max_dimensions
use yaml_parser_mod, only: open_and_parse_file, get_value_from_key, get_num_blocks, get_nkeys, &
                           get_block_ids, get_key_value, get_key_ids, get_key_name, missing_file_error_code
use fms_yaml_output_mod, only: fmsyamloutkeys_type, fmsyamloutvalues_type, write_yaml_from_struct_3, &
                               yaml_out_add_level2key, initialize_key_struct, initialize_val_struct
use mpp_mod,         only: mpp_error, fatal, note, mpp_pe, mpp_root_pe, stdout
use, intrinsic :: iso_c_binding, only : c_ptr, c_null_char
use fms_string_utils_mod, only: fms_array_to_pointer, fms_find_my_string, fms_sort_this, fms_find_unique, string, &
                                fms_f2c_string
use platform_mod, only: r4_kind, i4_kind, r8_kind, i8_kind, fms_file_len
use fms_mod, only: lowercase
use fms_diag_time_utils_mod, only: set_time_type
use time_manager_mod, only: time_type, date_to_string
use fms2_io_mod, only: file_exists, get_instance_filename
 
implicit none
 
private
 
public :: diag_yaml
public :: diag_yaml_object_init, diag_yaml_object_end
public :: diagyamlobject_type, get_diag_yaml_obj, subregion_type
public :: diagyamlfiles_type, diagyamlfilesvar_type
public :: get_num_unique_fields, find_diag_field, get_diag_fields_entries, get_diag_files_id
public :: get_diag_field_ids
public :: dump_diag_yaml_obj
public :: fms_diag_yaml_out
public :: max_subaxes
!> @}
 
integer, parameter :: basedate_size = 6
integer, parameter :: NUM_SUB_REGION_ARRAY = 8
integer, parameter :: MAX_FREQ = 12
integer            :: MAX_SUBAXES = 0 !< Max number of subaxis, set in diag_yaml_object_init depending on
                                      !! what is in the diag yaml
 
 
!> @brief type to hold an array of sorted diag_fiels
type varlist_type
  character(len=255), allocatable :: var_name(:) !< Array of diag_field
  type(c_ptr), allocatable :: var_pointer(:) !< Array of pointers
  integer, allocatable :: diag_field_indices(:) !< Index of the field in the diag_field array
end type
 
!> @brief type to hold an array of sorted diag_files
type filelist_type
  character(len=FMS_FILE_LEN), allocatable :: file_name(:) !< Array of diag_field
  type(c_ptr), allocatable :: file_pointer(:) !< Array of pointers
  integer, allocatable :: diag_file_indices(:)  !< Index of the file in the diag_file array
end type
 
!> @brief type to hold the sub region information about a file
type subregion_type
  INTEGER                        :: grid_type   !< Flag indicating the type of region,
                                                !! acceptable values are latlon_gridtype, index_gridtype,
                                                !! null_gridtype
  class(*),          allocatable :: corners(:,:)!< (x, y) coordinates of the four corner of the region
  integer                        :: tile        !< Tile number of the sub region
                                                !! required if using the "index" grid type
 
end type subregion_type
 
!> @brief type to hold the diag_file information
type diagyamlfiles_type
  private
  character (len=:),    allocatable :: file_fname                        !< file name
  integer                           :: file_frequnit(max_freq)           !< the frequency unit (DIAG_SECONDS,
                                                                         !! DIAG_MINUTES, DIAG_HOURS, DIAG_DAYS,
                                                                         !! DIAG_YEARS)
  integer                           :: file_freq(max_freq)               !< the frequency of data
  integer                           :: file_timeunit                     !< The unit of time (DIAG_SECONDS,
                                                                         !! DIAG_MINUTES, DIAG_HOURS, DIAG_DAYS,
                                                                         !! DIAG_YEARS)
  character (len=:),   allocatable :: file_unlimdim                      !< The name of the unlimited dimension
  type(subregion_type)             :: file_sub_region                    !< type containing info about the subregion
  integer                          :: file_new_file_freq(max_freq)       !< Frequency for closing the existing file
  integer                          :: file_new_file_freq_units(max_freq) !< Time units for creating a new file.
                                                                         !! Required if “new_file_freq” used
                                                                         !! (DIAG_SECONDS, DIAG_MINUTES, &
                                                                         !! DIAG_HOURS, DIAG_DAYS, DIAG_YEARS)
  type(time_type)                  :: file_start_time                    !< Time to start the file for the
                                                                         !! first time.
  logical                          :: file_start_time_set                !< .True. if file_start_time has been set
  integer                          :: filename_time                      !< The time to use when setting the name of
                                                                         !! new files: begin, middle, or end of the
                                                                         !! time_bounds
  integer                          :: file_duration(max_freq)            !< How long the file should receive data
                                                                         !! after start time in file_duration_units.
                                                                         !! This optional field can only be used if
                                                                         !! the start_time field is present.  If this
                                                                         !! field is absent, then the file duration
                                                                         !! will be equal to the frequency for
                                                                         !! creating new files. NOTE: The
                                                                         !! file_duration_units field must also
                                                                         !! be present if this field is present.
  integer                          :: file_duration_units(max_freq)      !< The file duration units
                                                                         !! (DIAG_SECONDS, DIAG_MINUTES, &
                                                                         !! DIAG_HOURS, DIAG_DAYS, DIAG_YEARS)
  integer                          :: current_new_file_freq_index        !< The index of the new_file_freq array
  !< Need to use `MAX_STR_LEN` because not all filenames/global attributes are the same length
  character (len=MAX_STR_LEN), allocatable :: file_varlist(:)            !< An array of variable names
                                                                         !! within a file
  character (len=MAX_STR_LEN), allocatable :: file_outlist(:)            !< An array of variable output names
                                                                         !! within a file, used to distinguish
                                                                         !! varlist names for yaml output
  character (len=MAX_STR_LEN), allocatable :: file_global_meta(:,:)      !< Array of key(dim=1)
                                                                         !! and values(dim=2) to be
                                                                         !! added as global meta data to
                                                                         !! the file
  character (len=:),    allocatable :: default_var_precision !< The precision for all of the variables in the file
                                                             !! This may be overridden if the precison was defined
                                                             !! at the variable level
  character (len=:),    allocatable :: default_var_reduction !< The reduction for all of the variables in the file
                                                             !! This may be overridden if the reduction was defined at
                                                             !! the variable level
  character (len=:),    allocatable :: default_var_module    !< The module for all of the variables in the file
                                                             !! This may be overridden if the modules was defined at the
                                                             !! variable level
  logical                           :: use_collective_writes !< True if using collective writes, default is false
  integer, dimension(MAX_DIMENSIONS):: default_chunksizes    !< Specified chunksizes to use by default
 contains
 
 !> All getter functions (functions named get_x(), for member field named x)
 !! return copies of the member variables unless explicitly noted.
 procedure, public :: size_file_varlist
 procedure, public :: get_file_fname
 procedure, public :: get_file_frequnit
 procedure, public :: get_file_freq
 procedure, public :: get_file_timeunit
 procedure, public :: get_file_unlimdim
 procedure, public :: get_file_sub_region
 procedure, public :: get_file_new_file_freq
 procedure, public :: get_file_new_file_freq_units
 procedure, public :: get_file_start_time
 procedure, public :: get_file_duration
 procedure, public :: get_file_duration_units
 procedure, public :: get_file_varlist
 procedure, public :: get_file_global_meta
 procedure, public :: get_filename_time
 procedure, public :: is_using_collective_writes
 procedure, public :: is_global_meta
 !> Has functions to determine if allocatable variables are true.  If a variable is not an allocatable
 !! then is will always return .true.
 procedure, public :: has_file_fname
 procedure, public :: has_file_frequnit
 procedure, public :: has_file_freq
 procedure, public :: has_file_timeunit
 procedure, public :: has_file_unlimdim
 procedure, public :: has_file_sub_region
 procedure, public :: has_file_new_file_freq
 procedure, public :: has_file_new_file_freq_units
 procedure, public :: has_file_start_time
 procedure, public :: has_file_duration
 procedure, public :: has_file_duration_units
 procedure, public :: has_file_varlist
 procedure, public :: has_file_global_meta
 procedure, public :: increase_new_file_freq_index
end type diagyamlfiles_type
 
!> @brief type to hold the info a diag_field
type diagyamlfilesvar_type
  character (len=:), private, allocatable :: var_fname !< The field/diagnostic name
  character (len=:), private, allocatable :: var_varname !< The name of the variable
  integer          , private, allocatable :: var_reduction !< Reduction to be done on var
                                                           !! time_average, time_rms, time_max,
                                                           !! time_min, time_sum, time_diurnal, time_power
  character (len=:), private, allocatable :: var_module !< The module that th variable is in
  integer          , private, allocatable :: var_kind !< The type/kind of the variable
  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"
  integer          , private              :: pow_value !< The power value
                                                       !! 0 if pow_value is not "powXX"
  integer, dimension(MAX_DIMENSIONS), private :: chunksizes !< Specified chunksize for each axis in the field
  logical          , private              :: var_file_is_subregional !< true if the file this entry
                                                                     !! belongs to is subregional
 
  !< Need to use `MAX_STR_LEN` because not all filenames/global attributes are the same length
  character (len=MAX_STR_LEN), dimension (:, :), private, allocatable :: var_attributes !< Attributes to overwrite or
                                                                                        !! add from diag_yaml
  character(len=:), allocatable :: var_axes_names !< list of axes names
 contains
 !> All getter functions (functions named get_x(), for member field named x)
 !! return copies of the member variables unless explicitly noted.
  procedure :: get_var_fname
  procedure :: get_var_varname
  procedure :: get_var_reduction
  procedure :: get_var_module
  procedure :: get_var_kind
  procedure :: get_var_outname
  procedure :: get_var_longname
  procedure :: get_var_units
  procedure :: get_var_zbounds
  procedure :: get_var_attributes
  procedure :: get_n_diurnal
  procedure :: get_pow_value
  procedure :: get_chunksizes
  procedure :: is_var_attributes
 
  procedure :: has_var_fname
  procedure :: has_var_varname
  procedure :: has_var_reduction
  procedure :: has_var_module
  procedure :: has_var_kind
  procedure :: has_var_outname
  procedure :: has_var_longname
  procedure :: has_var_units
  procedure :: has_var_zbounds
  procedure :: has_var_attributes
  procedure :: has_n_diurnal
  procedure :: has_pow_value
  procedure :: has_standname
  procedure :: has_chunksizes
  procedure :: add_axis_name
  procedure :: is_file_subregional
  procedure :: add_standname
 
end type diagyamlfilesvar_type
 
!> @brief Object that holds the information of the diag_yaml
!> @ingroup fms_diag_yaml_mod
type diagyamlobject_type
  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, public, dimension (:) :: diag_fields !< Diag fields info
  contains
  procedure :: size_diag_files
 
  procedure :: get_title        !< Returns the title
  procedure :: get_basedate     !< Returns the basedate array
  procedure :: get_diag_files   !< Returns the diag_files array
  procedure :: get_diag_fields  !< Returns the diag_field array
  procedure :: get_diag_field_from_id
 
  procedure :: has_diag_title
  procedure :: has_diag_basedate
  procedure :: has_diag_files
  procedure :: has_diag_fields
 
end type diagyamlobject_type
 
type (diagyamlobject_type), target :: diag_yaml  !< Obj containing the contents of the diag_table.yaml
type (varlist_type),  save :: variable_list !< List of all the variables in the diag_table.yaml
type (filelist_type), save :: file_list !< List of all files in the diag_table.yaml
 
logical, private :: diag_yaml_module_initialized = .false.
 
 
!> @addtogroup fms_diag_yaml_mod
!> @{
contains
 
!> @brief gets the diag_yaml module variable
!! @return a copy of the diag_yaml module variable
function get_diag_yaml_obj() &
result(res)
  type (diagyamlobject_type), pointer :: res
 
  res => diag_yaml
end function get_diag_yaml_obj
 
!> @brief get the basedate of a diag_yaml type
!! @return the basedate as an integer array
pure function get_basedate (this) &
result(diag_basedate)
  class(diagyamlobject_type), intent(in) :: this          !< The diag_yaml
  integer, dimension (basedate_size)      :: diag_basedate !< Basedate array result to return
 
  diag_basedate = this%diag_basedate
end function get_basedate
 
!> @brief Find the number of files listed in the diag yaml
!! @return the number of files in the diag yaml
pure integer function size_diag_files(this)
  class(diagyamlobject_type), intent(in) :: this      !< The diag_yaml
  if (this%has_diag_files()) then
    size_diag_files = size(this%diag_files)
  else
    size_diag_files = 0
  endif
end function size_diag_files
 
!> @brief get the title of a diag_yaml type
!! @return the title of the diag table as an allocated string
pure function get_title (this) &
  result(diag_title)
  class(diagyamlobject_type), intent(in) :: this       !< The diag_yaml
  character(len=:),allocatable            :: diag_title !< Basedate array result to return
 
  diag_title = this%diag_title
end function get_title
 
!> @brief get the diag_files of a diag_yaml type
!! @return the diag_files
function get_diag_files(this) &
result(diag_files)
  class(diagyamlobject_type), intent(in)              :: this       !< The diag_yaml
  type(diagyamlfiles_type), allocatable, dimension (:) :: diag_files !< History file info
 
  diag_files = this%diag_files
end function get_diag_files
 
!> @brief Get the diag_field yaml corresponding to a yaml_id
!! @return Pointer to the diag_field yaml entry
function get_diag_field_from_id(this, yaml_id) &
  result(diag_field)
    class(diagyamlobject_type), target, intent(in) :: this      !< The diag_yaml
    integer,                             intent(in) :: yaml_id   !< Yaml id
 
    type(diagyamlfilesvar_type), pointer :: diag_field !< Diag fields info
 
    if (yaml_id .eq. diag_not_registered) call mpp_error(fatal, &
      "Diag_manager: The yaml id for this field is not is not set")
 
    diag_field => this%diag_fields(variable_list%diag_field_indices(yaml_id))
 
end function get_diag_field_from_id
 
!> @brief get the diag_fields of a diag_yaml type
!! @return the diag_fields
pure function get_diag_fields(this) &
result(diag_fields)
  class(diagyamlobject_type), intent(in)                 :: this        !< The diag_yaml
  type(diagyamlfilesvar_type), allocatable, dimension (:) :: diag_fields !< Diag fields info
 
  diag_fields = this%diag_fields
end function get_diag_fields
 
!> @brief Uses the yaml_parser_mod to read in the diag_table and fill in the
!! diag_yaml object
subroutine diag_yaml_object_init(diag_subset_output)
  integer, intent(in)  :: diag_subset_output !< DIAG_ALL   - Current PE is in the one and only pelist
                                             !! DIAG_OTHER - Current PE is not in the ocean pelist
                                             !! and there are multiple pelists
                                             !! DIAG_OCEAN - Current PE is in the ocean pelist
                                             !! and there are multiple pelists
  integer              :: diag_yaml_id     !< Id for the diag_table yaml
  integer              :: nfiles           !< Number of files in the diag_table yaml
  integer, allocatable :: diag_file_ids(:) !< Ids of the files in the diag_table yaml
  integer              :: i, j             !< For do loops
  integer              :: total_nvars      !< The total number of variables in the diag_table yaml
  integer              :: var_count        !< The current number of variables added to the diag_yaml obj
  integer              :: file_var_count   !< The current number of variables added in the diag_file
  integer              :: nvars            !< The number of variables in the current file
  integer, allocatable :: var_ids(:)       !< Ids of the variables in diag_table yaml
  logical              :: is_ocean         !< Flag indicating if it is an ocean file
  logical, allocatable :: ignore(:)        !< Flag indicating if the diag_file is going to be ignored
  integer              :: actual_num_files !< The actual number of files that were saved
  integer              :: file_count       !! The current number of files added to the diag_yaml obj
  logical              :: write_file       !< Flag indicating if the user wants the file to be written
  logical              :: write_var        !< Flag indicating if the user wants the variable to be written
  logical              :: allow_averages   !< .True. if averages are allowed (the file is not static of you are
                                           !! outputing data at every frequency)
  character(len=:), allocatable :: filename!< Diag file name (for error messages)
  logical              :: is_instantaneous !< .True. if the file is instantaneous (i.e no averaging)
  character(len=FMS_FILE_LEN)   :: yamlfilename     !< Name of the expected diag_table.yaml
 
  integer                                  :: nmods              !< Number of module block in a file
  integer,                     allocatable :: mod_ids(:)         !< Ids for each module block in a file
  integer,                     allocatable :: nvars_per_file(:)  !< Number of variables in each file that are actually
                                                                 !! being written
  logical,                     allocatable :: has_module_block(:)!< True if each file is using the module block
  character(len=FMS_FILE_LEN), allocatable :: mod_name(:)        !< Buffer to store module name
  character(len=FMS_FILE_LEN)              :: buffer             !< Buffer to stote string variables
  integer                                  :: istart, iend       !< Starting and ending indices of the file block
 
  if (diag_yaml_module_initialized) return
 
  ! If doing and ensemble or nest run add the filename appendix (ens_XX or nest_XX) to the filename
  call get_instance_filename("diag_table.yaml", yamlfilename)
  if (index(trim(yamlfilename), "ens_") .ne. 0) then
    if (file_exists(yamlfilename) .and. file_exists("diag_table.yaml")) &
      call mpp_error(fatal, "Both diag_table.yaml and "//trim(yamlfilename)//" exists, pick one!")
    !< If the end_* file does not exist, revert back to "diag_table.yaml"
    !! where every ensemble is using the same yaml
    if (.not. file_exists(yamlfilename)) yamlfilename = "diag_table.yaml"
  endif
  diag_yaml_id = open_and_parse_file(trim(yamlfilename))
  if (diag_yaml_id .eq. missing_file_error_code) &
    call mpp_error(fatal, "The "//trim(yamlfilename)//" is not present and it is required!")
 
  call diag_get_value_from_key(diag_yaml_id, 0, "title", diag_yaml%diag_title)
  call get_value_from_key(diag_yaml_id, 0, "base_date", diag_yaml%diag_basedate)
  call set_base_time(diag_yaml%diag_basedate)
 
  nfiles = get_num_blocks(diag_yaml_id, "diag_files")
  allocate(diag_file_ids(nfiles))
  allocate(ignore(nfiles))
 
  call get_block_ids(diag_yaml_id, "diag_files", diag_file_ids)
 
  ignore = .false.
  total_nvars = 0
  !< If you are on two separate pelists
  if(diag_subset_output .ne. diag_all) then
    do i = 1, nfiles
      is_ocean = .false.
      call get_value_from_key(diag_yaml_id, diag_file_ids(i), "is_ocean", is_ocean, is_optional=.true.)
      !< If you are on the ocean pelist and the file is not an ocean file, skip the file
      if (diag_subset_output .eq. diag_ocean .and. .not. is_ocean) ignore(i) = .true.
 
      !< If you are not on the ocean pelist and the file is ocean, skip the file
      if(diag_subset_output .eq. diag_other .and. is_ocean) ignore(i) = .true.
    enddo
  endif
 
  !< Determine how many files are in the diag_yaml, ignoring those with write_file = False
  actual_num_files = 0
  allocate(nvars_per_file(nfiles))
  allocate(has_module_block(nfiles))
  do i = 1, nfiles
    write_file = .true.
    call get_value_from_key(diag_yaml_id, diag_file_ids(i), "write_file", write_file, is_optional=.true.)
    if(.not. write_file) ignore(i) = .true.
 
    !< If ignoring the file, ignore the fields in that file too!
    if (.not. ignore(i)) then
        ! Determine if the file has defined a module block
        nmods = 0
        nmods = get_num_blocks(diag_yaml_id, "modules", parent_block_id=diag_file_ids(i))
 
        nvars_per_file(i) = get_num_blocks(diag_yaml_id, "varlist", parent_block_id=diag_file_ids(i))
        if (nmods .ne. 0) then
          has_module_block(i) = .true.
          ! Get the total number of variables in each module block, ignoring those with write_var = .false.
          if (nvars_per_file(i) .ne. 0) &
            call mpp_error(fatal, "diag_manager_mod:: the file:"//trim(filename)//" has a 'modules' block defined "//&
                                  "and a 'module' key defined at the file level. This is not allowed!")
 
          allocate(mod_ids(nmods))
          call get_block_ids(diag_yaml_id, "modules", mod_ids, parent_block_id=diag_file_ids(i))
 
          nvars = 0
          do j =  1, nmods
            nvars_per_file(i) = nvars_per_file(i) + get_num_blocks(diag_yaml_id, "varlist", parent_block_id=mod_ids(j))
            nvars = nvars + get_total_num_vars(diag_yaml_id, mod_ids(j))
          enddo
          deallocate(mod_ids)
        else
          nvars = get_total_num_vars(diag_yaml_id, diag_file_ids(i))
          has_module_block(i) = .false.
        endif
        total_nvars = total_nvars + nvars
        if (nvars .ne. 0) then
          actual_num_files = actual_num_files + 1
        else
          call diag_get_value_from_key(diag_yaml_id, diag_file_ids(i), "file_name", filename)
          call mpp_error(note, "diag_manager_mod:: the file:"//trim(filename)//" has no variables defined. Ignoring!")
          if (allocated(filename)) deallocate(filename)
          ignore(i) = .true.
        endif
    endif
  enddo
 
  allocate(diag_yaml%diag_files(actual_num_files))
  allocate(diag_yaml%diag_fields(total_nvars))
  allocate(variable_list%var_name(total_nvars))
  allocate(variable_list%diag_field_indices(total_nvars))
  allocate(file_list%file_name(actual_num_files))
  allocate(file_list%diag_file_indices(actual_num_files))
 
  var_count = 0
  file_count = 0
  !> Loop through the number of nfiles and fill in the diag_yaml obj
  nfiles_loop: do i = 1, nfiles
    if(ignore(i)) cycle
    file_count = file_count + 1
    call diag_yaml_files_obj_init(diag_yaml%diag_files(file_count))
    call fill_in_diag_files(diag_yaml_id, diag_file_ids(i), diag_yaml%diag_files(file_count))
 
    !> Save the file name in the file_list
    file_list%file_name(file_count) = trim(diag_yaml%diag_files(file_count)%file_fname)//c_null_char
    file_list%diag_file_indices(file_count) = file_count
 
    if (has_module_block(i)) then
      allocate(var_ids(nvars_per_file(i)))
      allocate(mod_name(nvars_per_file(i)))
      nmods = get_num_blocks(diag_yaml_id, "modules", parent_block_id=diag_file_ids(i))
      allocate(mod_ids(nmods))
      call get_block_ids(diag_yaml_id, "modules", mod_ids, parent_block_id=diag_file_ids(i))
 
      istart = 1
      nvars_per_file(i) = 0
      do j = 1, nmods
        iend = istart + get_num_blocks(diag_yaml_id, "varlist", parent_block_id=mod_ids(j)) - 1
        call get_block_ids(diag_yaml_id, "varlist", var_ids(istart:iend), parent_block_id=mod_ids(j))
 
        ! Update nvars_per_file to only include those are actually being written
        nvars_per_file(i) = nvars_per_file(i) + get_total_num_vars(diag_yaml_id, mod_ids(j))
 
        call get_value_from_key(diag_yaml_id, mod_ids(j), "module", buffer)
        mod_name(istart:iend) = trim(buffer)
 
        istart  = iend + 1
      enddo
 
      deallocate(mod_ids)
    else
      allocate(var_ids(get_num_blocks(diag_yaml_id, "varlist", parent_block_id=diag_file_ids(i))))
      allocate(mod_name(size(var_ids)))
      call get_block_ids(diag_yaml_id, "varlist", var_ids, parent_block_id=diag_file_ids(i))
      nvars_per_file(i) = get_total_num_vars(diag_yaml_id, diag_file_ids(i))
    endif
 
    file_var_count = 0
    allocate(diag_yaml%diag_files(file_count)%file_varlist(nvars_per_file(i)))
    allocate(diag_yaml%diag_files(file_count)%file_outlist(nvars_per_file(i)))
 
    allow_averages = .not. diag_yaml%diag_files(file_count)%file_freq(1) < 1
    is_instantaneous = .false.
    nvars_loop: do j = 1, size(var_ids)
      write_var = .true.
      call get_value_from_key(diag_yaml_id, var_ids(j), "write_var", write_var, is_optional=.true.)
      if (.not. write_var) cycle
 
      var_count = var_count + 1
      file_var_count = file_var_count + 1
 
      !> Save the filename in the diag_field type
      diag_yaml%diag_fields(var_count)%var_fname = diag_yaml%diag_files(file_count)%file_fname
 
      !> initialize axes string
      diag_yaml%diag_fields(var_count)%var_axes_names = ""
      diag_yaml%diag_fields(var_count)%var_file_is_subregional = diag_yaml%diag_files(file_count)%has_file_sub_region()
 
      call fill_in_diag_fields(diag_yaml_id, diag_yaml%diag_files(file_count), var_ids(j), &
        diag_yaml%diag_fields(var_count), allow_averages, has_module_block(i), mod_name(j))
 
      !> Save the variable name in the diag_file type
      diag_yaml%diag_files(file_count)%file_varlist(file_var_count) = diag_yaml%diag_fields(var_count)%var_varname
      if(diag_yaml%diag_fields(var_count)%has_var_outname()) then
        diag_yaml%diag_files(file_count)%file_outlist(file_var_count) = diag_yaml%diag_fields(var_count)%var_outname
      else
        diag_yaml%diag_files(file_count)%file_outlist(file_var_count) = ""
      endif
 
      !> Save the variable name and the module name in the variable_list
      variable_list%var_name(var_count) = trim(diag_yaml%diag_fields(var_count)%var_varname)//&
                                        ":"//trim(diag_yaml%diag_fields(var_count)%var_module)//c_null_char
      !! The diag_table is not case sensitive (so we are saving it as lowercase)
      variable_list%var_name(var_count) = lowercase(variable_list%var_name(var_count))
      variable_list%diag_field_indices(var_count) = var_count
    enddo nvars_loop
    deallocate(var_ids)
    deallocate(mod_name)
  enddo nfiles_loop
 
  !> Sort the file list in alphabetical order
  file_list%file_pointer = fms_array_to_pointer(file_list%file_name)
  call fms_sort_this(file_list%file_pointer, actual_num_files, file_list%diag_file_indices)
 
  variable_list%var_pointer = fms_array_to_pointer(variable_list%var_name)
  call fms_sort_this(variable_list%var_pointer, total_nvars, variable_list%diag_field_indices)
 
  deallocate(diag_file_ids)
  diag_yaml_module_initialized = .true.
end subroutine
 
!> @brief Destroys the diag_yaml object
subroutine diag_yaml_object_end()
  integer :: i !< For do loops
 
  do i = 1, size(diag_yaml%diag_files, 1)
    if(allocated(diag_yaml%diag_files(i)%file_varlist)) deallocate(diag_yaml%diag_files(i)%file_varlist)
    if(allocated(diag_yaml%diag_files(i)%file_outlist)) deallocate(diag_yaml%diag_files(i)%file_outlist)
    if(allocated(diag_yaml%diag_files(i)%file_global_meta)) deallocate(diag_yaml%diag_files(i)%file_global_meta)
    if(allocated(diag_yaml%diag_files(i)%file_sub_region%corners)) &
      deallocate(diag_yaml%diag_files(i)%file_sub_region%corners)
  enddo
  if(allocated(diag_yaml%diag_files)) deallocate(diag_yaml%diag_files)
 
  do i = 1, size(diag_yaml%diag_fields, 1)
    if(allocated(diag_yaml%diag_fields(i)%var_attributes)) deallocate(diag_yaml%diag_fields(i)%var_attributes)
  enddo
  if(allocated(diag_yaml%diag_fields)) deallocate(diag_yaml%diag_fields)
 
  if(allocated(file_list%file_pointer)) deallocate(file_list%file_pointer)
  if(allocated(file_list%file_name)) deallocate(file_list%file_name)
  if(allocated(file_list%diag_file_indices)) deallocate(file_list%diag_file_indices)
 
  if(allocated(variable_list%var_pointer)) deallocate(variable_list%var_pointer)
  if(allocated(variable_list%var_name)) deallocate(variable_list%var_name)
  if(allocated(variable_list%diag_field_indices)) deallocate(variable_list%diag_field_indices)
 
end subroutine diag_yaml_object_end
 
!> @brief Fills in a diagYamlFiles_type with the contents of a file block in diag_table.yaml
subroutine fill_in_diag_files(diag_yaml_id, diag_file_id, yaml_fileobj)
  integer,                    intent(in)    :: diag_yaml_id !< Id of the diag_table.yaml
  integer,                    intent(in)    :: diag_file_id !< Id of the file block to read
  type(diagyamlfiles_type), intent(inout) :: yaml_fileobj   !< diagYamlFiles_type obj to read the contents into
 
  integer :: nsubregion       !< Flag indicating of there any regions (0 or 1)
  integer :: sub_region_id(1) !< Id of the sub_region block
  integer :: natt             !< Number of global attributes in the current file
  integer :: global_att_id(1) !< Id of the global attributes block
  integer :: nkeys            !< Number of key/value global attributes pair
  integer :: j                !< For do loops
 
  integer, allocatable :: key_ids(:) !< Id of the gloabl atttributes key/value pairs
  character(len=:), ALLOCATABLE :: grid_type !< grid_type as it is read in from the yaml
  character(len=:), ALLOCATABLE :: buffer      !< buffer to store any *_units as it is read from the yaml
  integer :: start_time_int(6) !< The start_time as read in from the diag_table yaml
 
  yaml_fileobj%file_frequnit = 0
 
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "file_name", yaml_fileobj%file_fname)
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "freq", buffer)
  call parse_key(yaml_fileobj%file_fname, buffer, yaml_fileobj%file_freq, yaml_fileobj%file_frequnit, "freq")
  deallocate(buffer)
 
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "unlimdim", yaml_fileobj%file_unlimdim)
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "time_units", buffer)
  call set_file_time_units(yaml_fileobj, buffer)
  deallocate(buffer)
 
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "new_file_freq", buffer, is_optional=.true.)
  call parse_key(yaml_fileobj%file_fname, buffer, yaml_fileobj%file_new_file_freq, &
       yaml_fileobj%file_new_file_freq_units, "new_file_freq")
  deallocate(buffer)
 
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "filename_time", buffer, is_optional=.true.)
  call set_filename_time(yaml_fileobj, buffer)
  deallocate(buffer)
 
  start_time_int = diag_null
  yaml_fileobj%file_start_time_set = .false.
  call get_value_from_key(diag_yaml_id, diag_file_id, "start_time", &
    start_time_int, is_optional=.true.)
  if (any(start_time_int .ne. diag_null)) then
    yaml_fileobj%file_start_time_set = .true.
    call set_time_type(start_time_int, yaml_fileobj%file_start_time)
   endif
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "file_duration", buffer, is_optional=.true.)
  call parse_key(yaml_fileobj%file_fname, buffer, yaml_fileobj%file_duration, yaml_fileobj%file_duration_units, &
    "file_duration")
 
  nsubregion = 0
  nsubregion = get_num_blocks(diag_yaml_id, "sub_region", parent_block_id=diag_file_id)
  if (nsubregion .eq. 1) then
    max_subaxes = max_subaxes + 1
    call get_block_ids(diag_yaml_id, "sub_region", sub_region_id, parent_block_id=diag_file_id)
    call diag_get_value_from_key(diag_yaml_id, sub_region_id(1), "grid_type", grid_type)
    call get_sub_region(diag_yaml_id, sub_region_id(1), yaml_fileobj%file_sub_region, grid_type, &
         yaml_fileobj%file_fname)
  elseif (nsubregion .eq. 0) then
    yaml_fileobj%file_sub_region%grid_type = null_gridtype
  else
    call mpp_error(fatal, "diag_yaml_object_init: file "//trim(yaml_fileobj%file_fname)//" has multiple region blocks")
  endif
 
  natt = 0
  natt = get_num_blocks(diag_yaml_id, "global_meta", parent_block_id=diag_file_id)
  if (natt .eq. 1) then
    call get_block_ids(diag_yaml_id, "global_meta", global_att_id, parent_block_id=diag_file_id)
    nkeys = get_nkeys(diag_yaml_id, global_att_id(1))
    allocate(key_ids(nkeys))
    call get_key_ids(diag_yaml_id, global_att_id(1), key_ids)
 
    allocate(yaml_fileobj%file_global_meta(nkeys, 2))
    do j = 1, nkeys
      call get_key_name(diag_yaml_id,  key_ids(j), yaml_fileobj%file_global_meta(j, 1))
      call get_key_value(diag_yaml_id, key_ids(j), yaml_fileobj%file_global_meta(j, 2))
    enddo
    deallocate(key_ids)
  elseif (natt .ne. 0) then
    call mpp_error(fatal, "diag_yaml_object_init: file "//trim(yaml_fileobj%file_fname)//&
                         &" has multiple global_meta blocks")
  endif
 
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "reduction", yaml_fileobj%default_var_reduction, &
    is_optional=.true.)
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "kind", yaml_fileobj%default_var_precision, &
    is_optional=.true.)
  call diag_get_value_from_key(diag_yaml_id, diag_file_id, "module", yaml_fileobj%default_var_module, &
    is_optional=.true.)
 
  yaml_fileobj%use_collective_writes = .false.
  call get_value_from_key(diag_yaml_id, diag_file_id, "use_collective_writes", &
    yaml_fileobj%use_collective_writes, is_optional=.true.)
 
  yaml_fileobj%default_chunksizes = diag_null
  call get_value_from_key(diag_yaml_id, diag_file_id, "chunksizes", &
    yaml_fileobj%default_chunksizes, is_optional=.true.)
 
end subroutine
 
!> @brief Fills in a diagYamlFilesVar_type with the contents of a variable block in
!! diag_table.yaml
subroutine fill_in_diag_fields(diag_file_id, yaml_fileobj, var_id, field, allow_averages, &
                               has_module_block, mod_name)
  integer,                        intent(in)  :: diag_file_id !< Id of the file block in the yaml file
  type(diagyamlfiles_type),       intent(in)  :: yaml_fileobj !< The yaml file obj for the variables
  integer,                        intent(in)  :: var_id       !< Id of the variable block in the yaml file
  type(diagyamlfilesvar_type), intent(inout)  :: field        !< diagYamlFilesVar_type obj to read the contents into
  logical,                        intent(in)  :: allow_averages !< .True. if averages are allowed for this file
  logical,                        intent(in)  :: has_module_block
  character(len=*),               intent(in)  :: mod_name
 
  integer :: natt          !< Number of attributes in variable
  integer :: var_att_id(1) !< Id of the variable attribute block
  integer :: nkeys         !< Number of key/value pairs of attributes
  integer :: j             !< For do loops
 
  integer, allocatable :: key_ids(:) !< Id of each attribute key/value pair
  character(len=:), ALLOCATABLE :: buffer    !< buffer to store the reduction method as it is read from the yaml
 
  call diag_get_value_from_key(diag_file_id, var_id, "var_name", field%var_varname)
 
  if (yaml_fileobj%default_var_reduction .eq. "") then
    !! If there is no default, the reduction method is required
    call diag_get_value_from_key(diag_file_id, var_id, "reduction", buffer)
  else
    call diag_get_value_from_key(diag_file_id, var_id, "reduction", buffer, is_optional=.true.)
    !! If the reduction was not set for the variable, override it with the default
    if (trim(buffer) .eq. "") buffer = yaml_fileobj%default_var_reduction
  endif
  call set_field_reduction(field, buffer)
  deallocate(buffer)
 
  if (.not. allow_averages) then
    if (field%var_reduction .ne. time_none) &
      call mpp_error(fatal, "The file "//field%var_fname//" can only have variables that have none as "//&
        "the reduction method because the frequency is either -1 or 0. "//&
        "Check your diag_table.yaml for the field:"//trim(field%var_varname))
  endif
 
  if (yaml_fileobj%default_var_module .eq. "" .and. .not. has_module_block) then
    call diag_get_value_from_key(diag_file_id, var_id, "module", field%var_module)
 else
    call diag_get_value_from_key(diag_file_id, var_id, "module", buffer, is_optional=.true.)
    !! If the module was set for the variable, override it with the default
    if (trim(buffer) .eq. "") then
      if (has_module_block) then
        field%var_module = trim(mod_name)
      else
        field%var_module = yaml_fileobj%default_var_module
      endif
    else
      field%var_module = trim(buffer)
    endif
    deallocate(buffer)
  endif
 
  if (yaml_fileobj%default_var_precision .eq. "") then
    !! If there is no default, the kind is required
    call diag_get_value_from_key(diag_file_id, var_id, "kind", buffer)
  else
    call diag_get_value_from_key(diag_file_id, var_id, "kind", buffer, is_optional=.true.)
    !! If the kind was set for the variable, override it with the default
    if (trim(buffer) .eq. "") buffer = yaml_fileobj%default_var_precision
  endif
  call set_field_kind(field, buffer)
 
  call diag_get_value_from_key(diag_file_id, var_id, "output_name", field%var_outname, is_optional=.true.)
  call diag_get_value_from_key(diag_file_id, var_id, "long_name", field%var_longname, is_optional=.true.)
  !! VAR_UNITS !!
 
  natt = 0
  natt = get_num_blocks(diag_file_id, "attributes", parent_block_id=var_id)
  if (natt .eq. 1) then
    call get_block_ids(diag_file_id, "attributes", var_att_id, parent_block_id=var_id)
    nkeys = get_nkeys(diag_file_id, var_att_id(1))
    allocate(key_ids(nkeys))
    call get_key_ids(diag_file_id, var_att_id(1), key_ids)
 
    allocate(field%var_attributes(nkeys, 2))
    do j = 1, nkeys
      call get_key_name(diag_file_id,  key_ids(j), field%var_attributes(j, 1))
      call get_key_value(diag_file_id, key_ids(j), field%var_attributes(j, 2))
    enddo
    deallocate(key_ids)
  elseif (natt .ne. 0) then
      call mpp_error(fatal, "diag_yaml_object_init: variable "//trim(field%var_varname)//&
                            " has multiple attribute blocks")
  endif
 
  !> Set the zbounds if they exist
  field%var_zbounds = diag_null
  call get_value_from_key(diag_file_id, var_id, "zbounds", field%var_zbounds, is_optional=.true.)
  if (field%has_var_zbounds()) max_subaxes = max_subaxes + 1
 
  field%chunksizes = diag_null
  call get_value_from_key(diag_file_id, var_id, "chunksizes", field%chunksizes, is_optional=.true.)
  if (.not. field%has_chunksizes()) then
    field%chunksizes = yaml_fileobj%default_chunksizes
  endif
end subroutine
 
!> @brief diag_manager wrapper to get_value_from_key to use for allocatable
!! string variables
subroutine diag_get_value_from_key(diag_file_id, par_id, key_name, value_name, is_optional)
  integer,           intent(in) :: diag_file_id!< Id of the file block in the yaml file
  integer,           intent(in) :: par_id      !< Id of the parent block in the yaml file
  character(len=*),  intent(in) :: key_name    !< Key to look for in the parent block
  character(len=:), allocatable :: value_name  !< Value of the key
  logical, intent(in), optional :: is_optional !< Flag indicating if the key is optional
 
  character(len=255) :: buffer !< String buffer to read in to
 
  buffer = "" !< Needs to be initialized for optional keys that are not present
  call get_value_from_key(diag_file_id, par_id, trim(key_name), buffer, is_optional= is_optional)
  allocate(character(len=len_trim(buffer)) :: value_name)
  value_name = trim(buffer)
 
end subroutine diag_get_value_from_key
 
!> @brief gets the lat/lon of the sub region to use in a diag_table yaml
subroutine get_sub_region(diag_yaml_id, sub_region_id, sub_region, grid_type, fname)
  integer,             intent(in)    :: diag_yaml_id       !< Id of the diag_table yaml file
  integer,             intent(in)    :: sub_region_id      !< Id of the region block to read from
  type(subregion_type),intent(inout) :: sub_region         !< Type that stores the sub_region
  character(len=*),    intent(in)    :: grid_type          !< The grid_type as it is read from the file
  character(len=*),    intent(in)    :: fname              !< filename of the subregion (for error messages)
 
  select case (trim(grid_type))
  case ("latlon")
    sub_region%grid_type = latlon_gridtype
    allocate(real(kind=r4_kind) :: sub_region%corners(4,2))
  case ("index")
    sub_region%grid_type = index_gridtype
    allocate(integer(kind=i4_kind) :: sub_region%corners(4,2))
 
    call get_value_from_key(diag_yaml_id, sub_region_id, "tile", sub_region%tile, is_optional=.true.)
    if (sub_region%tile .eq. diag_null) call mpp_error(fatal, &
      "The tile number is required when defining a "//&
      "subregion. Check your subregion entry for "//trim(fname))
  case default
    call mpp_error(fatal, trim(grid_type)//" is not a valid region type. &
    &The acceptable values are latlon and index. &
    &Check your entry for file:"//trim(fname))
  end select
 
  call get_value_from_key(diag_yaml_id, sub_region_id, "corner1", sub_region%corners(1,:))
  call get_value_from_key(diag_yaml_id, sub_region_id, "corner2", sub_region%corners(2,:))
  call get_value_from_key(diag_yaml_id, sub_region_id, "corner3", sub_region%corners(3,:))
  call get_value_from_key(diag_yaml_id, sub_region_id, "corner4", sub_region%corners(4,:))
 
end subroutine get_sub_region
 
!> @brief gets the total number of variables in the diag_table yaml file
!! @return total number of variables
function get_total_num_vars(diag_yaml_id, diag_file_id) &
result(total_nvars)
 
  integer, intent(in) :: diag_yaml_id     !< Id for the diag_table yaml
  integer, intent(in) :: diag_file_id     !< Id of the file in the diag_table yaml
  integer :: total_nvars
 
  integer :: i !< For do loop
  integer :: nvars !< Number of variables in a file
  integer, allocatable :: var_ids(:) !< Id of the variables in the file block of the yaml file
  logical :: var_write !< Flag indicating if the user wants the variable to be written
 
  nvars = get_num_blocks(diag_yaml_id, "varlist", parent_block_id=diag_file_id)
  allocate(var_ids(nvars))
  call get_block_ids(diag_yaml_id, "varlist", var_ids, parent_block_id=diag_file_id)
 
  !< Loop through all the variables in the diag_file block and only count those that don't have write_var=false
  total_nvars = 0
  do i = 1, nvars
    var_write = .true.
    call get_value_from_key(diag_yaml_id, var_ids(i), "write_var", var_write, is_optional=.true.)
    if (var_write) total_nvars = total_nvars + 1
  end do
end function
 
!> @brief This parses the freq, new_file_freq, or file_duration keys which are read in as a comma list
subroutine parse_key(filename, buffer, file_freq, file_frequnit, var)
  character(len=*),         intent(in)     :: filename         !< The name of the file (for error messages)
  character(len=*),         intent(inout)  :: buffer           !< Buffer that was read in from the yaml
  integer,                  intent(out)    :: file_freq(:)     !< buffer to store the freq, new_file_freq, or
                                                               !! file_duration after it is parsed
  integer,                  intent(out)    :: file_frequnit(:) !< buffer to store the freq units, new_file_freq units,
                                                               !! or file_duration units after it is parsed
  character(len=*),         intent(in)     :: var              !< Name of the key parsing
 
  integer            :: j           !< location of the ",' in the buffer
  integer            :: k           !< location of the " " that separated the units
  logical            :: finished    !< .true. if the parsing is complete
  integer            :: count       !< Number of keys that have been parsed
  character(len=255) :: str         !< Member of the comma separated list
  character(len=10)  :: units       !< String to hold the units
  integer            :: err_unit    !< Error key
 
  if (buffer .eq. "") return
 
  finished = .false.
  j = 0
  count = 0
  do while (.not. finished)
    count = count + 1
    buffer = buffer(j+1:len_trim(buffer))
    j = index(buffer, ",")
    if (j == 0) then
      !< There is only 1 member in the list
      j = len_trim(buffer)+1
      finished = .true.
    endif
 
    str = adjustl(buffer(1:j-1))
 
    k = index(str, " ")
    read(str(1:k-1), *, iostat=err_unit) file_freq(count)
    units = str(k+1:len_trim(str))
 
    if (err_unit .ne. 0) &
      call mpp_error(fatal, "Error parsing "//trim(var)//". Check your entry for file"//&
        trim(filename))
 
    if (file_freq(count) .lt. -1) &
        call mpp_error(fatal, trim(var)//" is not valid. &
        &Check your entry for file:"//trim(filename))
 
    if (file_freq(count) .eq. -1 .or. file_freq(count) .eq. 0) then
      !! The file is static so no need to read the units
      file_frequnit(count) = diag_days
    else
      if (trim(units) .eq. "") &
        call mpp_error(fatal, trim(var)//" units is required. &
        &Check your entry for file:"//trim(filename))
 
      file_frequnit(count) = set_valid_time_units(units, &
        trim(var)//" for file:"//trim(filename))
    endif
  enddo
end subroutine parse_key
 
!> @brief This checks if the time unit in a diag file is valid and sets the integer equivalent
subroutine set_file_time_units (yaml_fileobj, file_timeunit)
  type(diagyamlfiles_type), intent(inout) :: yaml_fileobj  !< diagYamlFiles_type obj to checK
  character(len=*),         intent(in)    :: file_timeunit !< file_timeunit as it is read from the diag_table
 
 yaml_fileobj%file_timeunit = set_valid_time_units(file_timeunit, "timeunit for file:"//trim(yaml_fileobj%file_fname))
end subroutine set_file_time_units
 
!> @brief This checks if the filename_time in a diag file is correct and sets the integer equivalent
subroutine set_filename_time(yaml_fileobj, filename_time)
  type(diagyamlfiles_type), intent(inout) :: yaml_fileobj        !< diagYamlFiles_type obj to check
  character(len=*),         intent(in)    :: filename_time       !< filename_time as it is read from the yaml
 
  select case (trim(filename_time))
  case ("")
    yaml_fileobj%filename_time = middle_time !< This is the default
  case ("begin")
    yaml_fileobj%filename_time = begin_time
  case ("middle")
    yaml_fileobj%filename_time = middle_time
  case ("end")
    yaml_fileobj%filename_time = end_time
  case default
    call mpp_error(fatal, trim(filename_time)//" is an invalid filename_time &
    &The acceptable values are begin, middle, and end. &
    &Check your entry for file "//trim(yaml_fileobj%file_fname))
  end select
end subroutine set_filename_time
 
!> @brief This checks if the kind of a diag field is valid and sets it
subroutine set_field_kind(field, skind)
  type(diagyamlfilesvar_type), intent(inout) :: field        !< diagYamlFilesVar_type obj to read the contents into
  character(len=*),            intent(in)    :: skind        !< The variable kind as read from diag_yaml
 
  select case (trim(skind))
  case ("r4")
    field%var_kind = r4
  case ("r8")
    field%var_kind = r8
  case ("i4")
    field%var_kind = i4
  case ("i8")
    field%var_kind = i8
  case default
    call mpp_error(fatal, trim(skind)//" is an invalid kind! &
      &The acceptable values are r4, r8, i4, i8. &
      &Check your entry for file:"//trim(field%var_varname)//" in file "//trim(field%var_fname))
  end select
 
end subroutine set_field_kind
 
!> @brief This checks if the reduction of a diag field is valid and sets it
!! If the reduction method is diurnalXX or powXX, it gets the number of diurnal sample and the power value
subroutine set_field_reduction(field, reduction_method)
  type(diagyamlfilesvar_type), intent(inout) :: field           !< diagYamlFilesVar_type obj to read the contents into
  character(len=*)           , intent(in)    :: reduction_method!< reduction method as read from the yaml
 
  integer :: n_diurnal !< number of diurnal samples
  integer :: pow_value !< The power value
  integer :: ioerror   !< io error status after reading in the diurnal samples
 
  n_diurnal = 0
  pow_value = 0
  ioerror = 0
  if (index(reduction_method, "diurnal") .ne. 0) then
    READ (reduction_method(8:len_trim(reduction_method)), fmt=*, iostat=ioerror) n_diurnal
    if (ioerror .ne. 0) &
      call mpp_error(fatal, "Error getting the number of diurnal samples from "//trim(reduction_method))
    if (n_diurnal .le. 0) &
      call mpp_error(fatal, "Diurnal samples should be greater than 0. &
        & Check your entry for file:"//trim(field%var_varname)//" in file "//trim(field%var_fname))
    field%var_reduction = time_diurnal
  elseif (index(reduction_method, "pow") .ne. 0) then
    READ (reduction_method(4:len_trim(reduction_method)), fmt=*, iostat=ioerror) pow_value
    if (ioerror .ne. 0) &
      call mpp_error(fatal, "Error getting the power value from "//trim(reduction_method))
      if (pow_value .le. 0) &
      call mpp_error(fatal, "The power value should be greater than 0. &
        & Check your entry for file:"//trim(field%var_varname)//" in file "//trim(field%var_fname))
    field%var_reduction = time_power
  else
    select case (reduction_method)
    case ("none")
      field%var_reduction = time_none
    case ("average")
      field%var_reduction = time_average
    case ("min")
      field%var_reduction = time_min
    case ("max")
      field%var_reduction = time_max
    case ("rms")
      field%var_reduction = time_rms
    case ("sum")
      field%var_reduction = time_sum
    case default
      call mpp_error(fatal, trim(reduction_method)//" is an invalid reduction method! &
        &The acceptable values are none, average, pow##, diurnal##, min, max, and rms. &
        &Check your entry for file:"//trim(field%var_varname)//" in file "//trim(field%var_fname))
    end select
  endif
 
  field%n_diurnal = n_diurnal
  field%pow_value = pow_value
end subroutine set_field_reduction
 
!> @brief This checks if a time unit is valid and if it is, it assigns the integer equivalent
!! @return The integer equivalent to the time units
function set_valid_time_units(time_units, error_msg) &
result(time_units_int)
 
  character(len=*), intent(in)  :: time_units      !< The time_units as a string
  character(len=*), intent(in)  :: error_msg       !< Error message to append
 
  integer                       :: time_units_int  !< The integer equivalent of the time_units
 
  select case (trim(time_units))
  case ("seconds")
    time_units_int = diag_seconds
  case ("minutes")
    time_units_int = diag_minutes
  case ("hours")
    time_units_int = diag_hours
  case ("days")
    time_units_int = diag_days
  case ("months")
    time_units_int = diag_months
  case ("years")
    time_units_int = diag_years
  case default
    time_units_int =diag_null
    call mpp_error(fatal, trim(error_msg)//" is not valid. Acceptable values are &
                          &seconds, minutes, hours, days, months, years")
  end select
end function set_valid_time_units
 
!!!!!!! YAML FILE INQUIRIES !!!!!!!
!> @brief Finds the number of variables in the file_varlist
!! @return the size of the diag_files_obj%file_varlist array
integer pure function size_file_varlist (this)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 size_file_varlist = size(this%file_varlist)
end function size_file_varlist
 
!> @brief Inquiry for diag_files_obj%file_fname
!! @return file_fname of a diag_yaml_file obj
pure function get_file_fname (this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 character (len=:), allocatable :: res !< What is returned
  res = this%file_fname
end function get_file_fname
!> @brief Inquiry for diag_files_obj%file_frequnit
!! @return file_frequnit of a diag_yaml_file_obj
pure function get_file_frequnit (this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 integer :: res !< What is returned
  res = this%file_frequnit(this%current_new_file_freq_index)
end function get_file_frequnit
!> @brief Inquiry for diag_files_obj%file_freq
!! @return file_freq of a diag_yaml_file_obj
pure function get_file_freq(this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 integer :: res !< What is returned
  res = this%file_freq(this%current_new_file_freq_index)
end function get_file_freq
!> @brief Inquiry for diag_files_obj%file_timeunit
!! @return file_timeunit of a diag_yaml_file_obj
pure function get_file_timeunit (this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 integer :: res !< What is returned
  res = this%file_timeunit
end function get_file_timeunit
!> @brief Inquiry for diag_files_obj%file_unlimdim
!! @return file_unlimdim of a diag_yaml_file_obj
pure function get_file_unlimdim(this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 character (len=:), allocatable :: res !< What is returned
  res = this%file_unlimdim
end function get_file_unlimdim
!> @brief Inquiry for diag_files_obj%file_subregion
!! @return file_sub_region of a diag_yaml_file_obj
function get_file_sub_region (this) &
result(res)
 class(diagyamlfiles_type), target, intent(in) :: this !< The object being inquiried
 type(subregion_type), pointer :: res !< What is returned
  res => this%file_sub_region
end function get_file_sub_region
!> @brief Inquiry for diag_files_obj%file_new_file_freq
!! @return file_new_file_freq of a diag_yaml_file_obj
pure function get_file_new_file_freq(this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 integer :: res !< What is returned
  res = this%file_new_file_freq(this%current_new_file_freq_index)
end function get_file_new_file_freq
!> @brief Inquiry for diag_files_obj%file_new_file_freq_units
!! @return file_new_file_freq_units of a diag_yaml_file_obj
pure function get_file_new_file_freq_units (this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 integer :: res !< What is returned
  res = this%file_new_file_freq_units(this%current_new_file_freq_index)
end function get_file_new_file_freq_units
!> @brief Inquiry for diag_files_obj%file_start_time
!! @return file_start_time of a diag_yaml_file_obj
pure function get_file_start_time (this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 type(time_type) :: res !< What is returned
  res = this%file_start_time
end function get_file_start_time
!> @brief Inquiry for diag_files_obj%file_duration
!! @return file_duration of a diag_yaml_file_obj
pure function get_file_duration (this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 integer :: res !< What is returned
  res = this%file_duration(this%current_new_file_freq_index)
end function get_file_duration
!> @brief Inquiry for diag_files_obj%file_duration_units
!! @return file_duration_units of a diag_yaml_file_obj
pure function get_file_duration_units (this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
  integer :: res !< What is returned
  res = this%file_duration_units(this%current_new_file_freq_index)
end function get_file_duration_units
!> @brief Inquiry for diag_files_obj%file_varlist
!! @return file_varlist of a diag_yaml_file_obj
pure function get_file_varlist (this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 character (:), allocatable :: res(:) !< What is returned
  res = this%file_varlist
end function get_file_varlist
!> @brief Inquiry for diag_files_obj%file_global_meta
!! @return file_global_meta of a diag_yaml_file_obj
pure function get_file_global_meta (this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 character (len=MAX_STR_LEN), allocatable :: res(:,:) !< What is returned
  res = this%file_global_meta
end function get_file_global_meta
!> @brief Get the integer equivalent of the time to use to determine the filename,
!! if using a wildcard file name (i.e ocn%4yr%2mo%2dy%2hr)
!! @return the integer equivalent of the time to use to determine the filename
pure function get_filename_time(this) &
result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 integer :: res !< What is returned
  res = this%filename_time
end function
!> @brief Inquiry for whether file_global_meta is allocated
!! @return Flag indicating if file_global_meta is allocated
function is_global_meta(this) &
  result(res)
 class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 logical :: res
 res = .false.
 if (allocated(this%file_global_meta)) &
   res = .true.
end function
 
!> \brief Determines whether or not the file is using netcdf collective writes
!! \return logical indicating whether or not the file is using netcdf collective writes
pure function is_using_collective_writes(this) &
  result(res)
  class(diagyamlfiles_type), intent(in) :: this !< The object being inquiried
 
  logical :: res
  res = this%use_collective_writes
end function
 
!> @brief Increate the current_new_file_freq_index by 1
subroutine increase_new_file_freq_index(this)
  class(diagyamlfiles_type), intent(inout) :: this !< The file object
  this%current_new_file_freq_index = this%current_new_file_freq_index + 1
end subroutine
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!! VARIABLES ROUTINES AND FUNCTIONS !!!!!!!
 
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!! YAML VAR INQUIRIES !!!!!!!
!> @brief Inquiry for diag_yaml_files_var_obj%var_fname
!! @return var_fname of a diag_yaml_files_var_obj
pure function get_var_fname (this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 character (len=:), allocatable :: res !< What is returned
  res = this%var_fname
end function get_var_fname
!> @brief Inquiry for diag_yaml_files_var_obj%var_varname
!! @return var_varname of a diag_yaml_files_var_obj
pure function get_var_varname (this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 character (len=:), allocatable :: res !< What is returned
  res = this%var_varname
end function get_var_varname
!> @brief Inquiry for diag_yaml_files_var_obj%var_reduction
!! @return var_reduction of a diag_yaml_files_var_obj
pure function get_var_reduction (this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 integer, allocatable :: res !< What is returned
  res = this%var_reduction
end function get_var_reduction
!> @brief Inquiry for diag_yaml_files_var_obj%var_module
!! @return var_module of a diag_yaml_files_var_obj
pure function get_var_module (this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 character (len=:), allocatable :: res !< What is returned
  res = this%var_module
end function get_var_module
!> @brief Inquiry for diag_yaml_files_var_obj%var_kind
!! @return var_kind of a diag_yaml_files_var_obj
pure function get_var_kind (this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 integer, allocatable :: res !< What is returned
  res = this%var_kind
end function get_var_kind
!> @brief Inquiry for diag_yaml_files_var_obj%var_outname
!! @return var_outname of a diag_yaml_files_var_obj
pure function get_var_outname (this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 character (len=:), allocatable :: res !< What is returned
 
 if (this%has_var_outname()) then
   res = this%var_outname
 else
   res = this%var_varname !< If outname is not set, the variable name will be used
 endif
end function get_var_outname
!> @brief Inquiry for diag_yaml_files_var_obj%var_longname
!! @return var_longname of a diag_yaml_files_var_obj
pure function get_var_longname (this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 character (len=:), allocatable :: res !< What is returned
  res = this%var_longname
end function get_var_longname
!> @brief Inquiry for diag_yaml_files_var_obj%var_units
!! @return var_units of a diag_yaml_files_var_obj
pure function get_var_units (this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 character (len=:), allocatable :: res !< What is returned
  res = this%var_units
end function get_var_units
!> @brief Inquiry for diag_yaml_files_var_obj%var_zbounds
!! @return var_zbounds of a diag_yaml_files_var_obj
pure function get_var_zbounds (this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 real(kind=r4_kind) :: res(2) !< What is returned
  res = this%var_zbounds
end function get_var_zbounds
!> @brief Inquiry for diag_yaml_files_var_obj%var_attributes
!! @return var_attributes of a diag_yaml_files_var_obj
pure function get_var_attributes(this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 character (len=MAX_STR_LEN), allocatable :: res (:,:) !< What is returned
 res = this%var_attributes
end function get_var_attributes
!> @brief Inquiry for diag_yaml_files_var_obj%n_diurnal
!! @return the number of diurnal samples of a diag_yaml_files_var_obj
pure function get_n_diurnal(this) &
result(res)
  class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
  integer :: res !< What is returned
  res = this%n_diurnal
end function get_n_diurnal
!> @brief Inquiry for diag_yaml_files_var_obj%pow_value
!! @return the pow_value of a diag_yaml_files_var_obj
pure function get_pow_value(this) &
result(res)
  class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
  integer :: res !< What is returned
  res = this%pow_value
end function get_pow_value
 
!> @brief Inquiry for chunksizes
!! @return the chunksizes for the fiel
pure function get_chunksizes(this) &
result(res)
  class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
  integer :: res(max_dimensions) !< What is returned
 
  res = this%chunksizes
end function get_chunksizes
 
!> @brief Inquiry for whether var_attributes is allocated
!! @return Flag indicating if var_attributes is allocated
function is_var_attributes(this) &
result(res)
 class(diagyamlfilesvar_type), intent(in) :: this !< The object being inquiried
 logical :: res
 res = .false.
 if (allocated(this%var_attributes)) &
   res = .true.
end function is_var_attributes
 
!> @brief Initializes the non string values of a diagYamlFiles_type to its
!! default values
subroutine diag_yaml_files_obj_init(obj)
  type(diagyamlfiles_type), intent(out) :: obj !< diagYamlFiles_type object to initialize
 
  obj%file_freq           = diag_null
  obj%file_sub_region%tile = diag_null
  obj%file_new_file_freq = diag_null
  obj%file_duration = diag_null
  obj%file_new_file_freq_units = diag_null
  obj%file_duration_units = diag_null
  obj%current_new_file_freq_index = 1
end subroutine diag_yaml_files_obj_init
 
!> @brief Checks if diag_file_obj%file_fname is allocated
!! @return true if diag_file_obj%file_fname is allocated
pure logical function has_file_fname (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_fname = allocated(this%file_fname)
end function has_file_fname
!> @brief Checks if diag_file_obj%file_frequnit is allocated
!! @return true if diag_file_obj%file_frequnit is allocated
pure logical function has_file_frequnit (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_frequnit = this%file_frequnit(this%current_new_file_freq_index) .NE. diag_null
end function has_file_frequnit
!> @brief diag_file_obj%file_freq is on the stack, so the object always has it
!! @return true if diag_file_obj%file_freq is allocated
pure logical function has_file_freq (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_freq = .true.
end function has_file_freq
!> @brief Checks if diag_file_obj%file_timeunit is allocated
!! @return true if diag_file_obj%file_timeunit is allocated
pure logical function has_file_timeunit (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_timeunit = this%file_timeunit .ne. diag_null
end function has_file_timeunit
!> @brief Checks if diag_file_obj%file_unlimdim is allocated
!! @return true if diag_file_obj%file_unlimdim is allocated
pure logical function has_file_unlimdim (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_unlimdim = allocated(this%file_unlimdim)
end function has_file_unlimdim
!> @brief Checks if diag_file_obj%file_write is on the stack, so this will always be true
!! @return true
pure logical function has_file_write (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_write = .true.
end function has_file_write
!> @brief Checks if diag_file_obj%file_sub_region is being used and has the sub region variables allocated
!! @return true if diag_file_obj%file_sub_region sub region variables are allocated
pure logical function has_file_sub_region (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  if ( this%file_sub_region%grid_type .eq. latlon_gridtype .or. this%file_sub_region%grid_type .eq. index_gridtype) then
       has_file_sub_region = .true.
  else
       has_file_sub_region = .false.
  endif
end function has_file_sub_region
!> @brief diag_file_obj%file_new_file_freq is defined on the stack, so this will return true
!! @return true
pure logical function has_file_new_file_freq (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_new_file_freq = this%file_new_file_freq(this%current_new_file_freq_index) .ne. diag_null
end function has_file_new_file_freq
!> @brief Checks if diag_file_obj%file_new_file_freq_units is allocated
!! @return true if diag_file_obj%file_new_file_freq_units is allocated
pure logical function has_file_new_file_freq_units (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_new_file_freq_units = this%file_new_file_freq_units(this%current_new_file_freq_index) .ne. diag_null
end function has_file_new_file_freq_units
!> @brief Checks if diag_file_obj%file_start_time is allocated
!! @return true if diag_file_obj%file_start_time is allocated
pure logical function has_file_start_time (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_start_time = this%file_start_time_set
end function has_file_start_time
!> @brief diag_file_obj%file_duration is allocated on th stack, so this is always true
!! @return true
pure logical function has_file_duration (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_duration = this%file_duration(this%current_new_file_freq_index) .ne. diag_null
end function has_file_duration
!> @brief diag_file_obj%file_duration_units is on the stack, so this will retrun true
!! @return true
pure logical function has_file_duration_units (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_duration_units = this%file_duration_units(this%current_new_file_freq_index) .ne. diag_null
end function has_file_duration_units
!> @brief Checks if diag_file_obj%file_varlist is allocated
!! @return true if diag_file_obj%file_varlist is allocated
pure logical function has_file_varlist (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_varlist = allocated(this%file_varlist)
end function has_file_varlist
!> @brief Checks if diag_file_obj%file_global_meta is allocated
!! @return true if diag_file_obj%file_global_meta is allocated
pure logical function has_file_global_meta (this)
  class(diagyamlfiles_type), intent(in) :: this !< diagYamlFiles_type object to initialize
  has_file_global_meta = allocated(this%file_global_meta)
end function has_file_global_meta
 
!> @brief Checks if diag_file_obj%var_fname is allocated
!! @return true if diag_file_obj%var_fname is allocated
pure logical function has_var_fname (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_fname = allocated(this%var_fname)
end function has_var_fname
!> @brief Checks if diag_file_obj%var_varname is allocated
!! @return true if diag_file_obj%var_varname is allocated
pure logical function has_var_varname (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_varname = allocated(this%var_varname)
end function has_var_varname
!> @brief Checks if diag_file_obj%var_reduction is allocated
!! @return true if diag_file_obj%var_reduction is allocated
pure logical function has_var_reduction (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_reduction = allocated(this%var_reduction)
end function has_var_reduction
!> @brief Checks if diag_file_obj%var_module is allocated
!! @return true if diag_file_obj%var_module is allocated
pure logical function has_var_module (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_module = allocated(this%var_module)
end function has_var_module
!> @brief Checks if diag_file_obj%var_kind is allocated
!! @return true if diag_file_obj%var_kind is allocated
pure logical function has_var_kind (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_kind = allocated(this%var_kind)
end function has_var_kind
!> @brief diag_file_obj%var_write is on the stack, so this returns true
!! @return true
pure logical function has_var_write (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_write = .true.
end function has_var_write
!> @brief Checks if diag_file_obj%var_outname is allocated
!! @return true if diag_file_obj%var_outname is allocated
pure logical function has_var_outname (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  if (allocated(this%var_outname)) then
    if (trim(this%var_outname) .ne. "") then
      has_var_outname = .true.
    else
      has_var_outname = .false.
    endif
  else
    has_var_outname = .true.
  endif
end function has_var_outname
!> @brief Checks if diag_file_obj%var_longname is allocated
!! @return true if diag_file_obj%var_longname is allocated
pure logical function has_var_longname (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_longname = allocated(this%var_longname)
end function has_var_longname
!> @brief Checks if diag_file_obj%var_units is allocated
!! @return true if diag_file_obj%var_units is allocated
pure logical function has_var_units (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_units = allocated(this%var_units)
end function has_var_units
!> @brief Checks if diag_file_obj%var_zbounds is allocated
!! @return true if diag_file_obj%var_zbounds is allocated
pure logical function has_var_zbounds (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_zbounds = any(this%var_zbounds .ne. diag_null)
end function has_var_zbounds
!> @brief Checks if diag_file_obj%var_attributes is allocated
!! @return true if diag_file_obj%var_attributes is allocated
pure logical function has_var_attributes (this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to initialize
  has_var_attributes = allocated(this%var_attributes)
end function has_var_attributes
!> @brief Checks if diag_file_obj%n_diurnal is set
!! @return true if diag_file_obj%n_diurnal is set
pure logical function has_n_diurnal(this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to inquire
  has_n_diurnal = (this%n_diurnal .ne. 0)
end function has_n_diurnal
!> @brief Checks if diag_file_obj%pow_value is set
!! @return true if diag_file_obj%pow_value is set
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 chunksizes is set for the diag field
!! @return true if chunksizes is set for the diag field
pure logical function has_chunksizes(this)
  class(diagyamlfilesvar_type), intent(in) :: this !< diagYamlvar_type object to inquire
  has_chunksizes = any(this%chunksizes .ne. diag_null)
end function has_chunksizes
 
!> @brief Checks if diag_file_obj%diag_title is allocated
!! @return true if diag_file_obj%diag_title is allocated
pure logical function has_diag_title (this)
  class(diagyamlobject_type), intent(in) :: this !< diagYamlObject_type object to inquire
  has_diag_title = allocated(this%diag_title)
end function has_diag_title
!> @brief diag_file_obj%diag_basedate is on the stack, so this is always true
!! @return true
pure logical function has_diag_basedate (this)
  class(diagyamlobject_type), intent(in) :: this !< diagYamlObject_type object to initialize
  has_diag_basedate = .true.
end function has_diag_basedate
!> @brief Checks if diag_file_obj%diag_files is allocated
!! @return true if diag_file_obj%diag_files is allocated
pure logical function has_diag_files (this)
  class(diagyamlobject_type), intent(in) :: this !< diagYamlObject_type object to initialize
  has_diag_files = allocated(this%diag_files)
end function has_diag_files
!> @brief Checks if diag_file_obj%diag_fields is allocated
!! @return true if diag_file_obj%diag_fields is allocated
pure logical function has_diag_fields (this)
  class(diagyamlobject_type), intent(in) :: this !< diagYamlObject_type object to initialize
  has_diag_fields = allocated(this%diag_fields)
end function has_diag_fields
 
!> @brief Determine the number of unique diag_fields in the diag_yaml_object
!! @return The number of unique diag_fields
function get_num_unique_fields() &
  result(nfields)
  integer :: nfields
  nfields = fms_find_unique(variable_list%var_pointer, size(variable_list%var_pointer))
 
end function get_num_unique_fields
 
!> @brief Determines if a diag_field is in the diag_yaml_object
!! @return Indices of the locations where the field was found
function find_diag_field(diag_field_name, module_name) &
result(indices)
 
  character(len=*), intent(in) :: diag_field_name !< diag_field name to search for
  character(len=*), intent(in) :: module_name     !< Name of the module, the variable is in
 
  integer, allocatable :: indices(:)
 
  indices = fms_find_my_string(variable_list%var_pointer, size(variable_list%var_pointer), &
                               & lowercase(trim(diag_field_name))//":"//lowercase(trim(module_name)//c_null_char))
end function find_diag_field
 
!> @brief Gets the diag_field entries corresponding to the indices of the sorted variable_list
!! @return Array of diag_fields
function get_diag_fields_entries(indices) &
  result(diag_field)
 
  integer, intent(in) :: indices(:) !< Indices of the field in the sorted variable_list array
  type(diagyamlfilesvar_type), dimension (:), allocatable :: diag_field
 
  integer :: i !< For do loops
  integer :: field_id !< Indices of the field in the diag_yaml array
 
  allocate(diag_field(size(indices)))
 
  do i = 1, size(indices)
    field_id = variable_list%diag_field_indices(indices(i))
    diag_field(i) = diag_yaml%diag_fields(field_id)
  end do
 
end function get_diag_fields_entries
 
!> @brief Gets field indices corresponding to the indices (input argument) in the sorted variable_list
!! @return Copy of array of field indices
function get_diag_field_ids(indices) result(field_ids)
 
  integer, intent(in) :: indices(:) !< Indices of the fields in the sorted variable_list array
  integer, allocatable :: field_ids(:)
  integer :: i !< For do loop
 
  allocate(field_ids(size(indices)))
 
  do i = 1, size(indices)
    field_ids(i) = variable_list%diag_field_indices(indices(i))
  end do
 
end function get_diag_field_ids
 
!> @brief Finds the indices of the diag_yaml%diag_files(:) corresponding to fields in variable_list(indices)
!! @return indices of the diag_yaml%diag_files(:)
function get_diag_files_id(indices) &
  result(file_id)
 
  integer, intent(in) :: indices(:) !< Indices of the field in the sorted variable_list
  integer, allocatable :: file_id(:)
 
  integer :: field_id !< Indices of the field in the diag_yaml field array
  integer :: i !< For do loops
  character(len=FMS_FILE_LEN) :: filename !< Filename of the field
  integer, allocatable :: file_indices(:) !< Indices of the file in the sorted variable_list
 
  allocate(file_id(size(indices)))
 
  do i = 1, size(indices)
    field_id = variable_list%diag_field_indices(indices(i))
    !< Get the filename of the field
    filename = diag_yaml%diag_fields(field_id)%var_fname
 
    !< File indice of that file in the array of list of sorted files
    file_indices = fms_find_my_string(file_list%file_pointer, size(file_list%file_pointer), &
      & trim(filename)//c_null_char)
 
    if (size(file_indices) .ne. 1) &
      & call mpp_error(fatal, "get_diag_files_id: Error getting the correct number of file indices!"//&
                              " The diag file "//trim(filename)//" was defined "//string(size(file_indices))&
                              // " times")
 
    if (file_indices(1) .eq. diag_null) &
      & call mpp_error(fatal, "get_diag_files_id: Error finding the file "//trim(filename)//" in the diag_files yaml")
 
    !< Get the index of the file in the diag_yaml file
    file_id(i) = file_list%diag_file_indices(file_indices(1))
  end do
 
end function get_diag_files_id
 
!> Prints out values from diag_yaml object for debugging.
!! Only writes on root.
subroutine dump_diag_yaml_obj( filename )
  character(len=*), optional, intent(in)        :: filename !< optional name of logfile to write to, otherwise
                                                            !! prints to stdout
  type(diagyamlfilesvar_type), allocatable      :: fields(:)
  type(diagyamlfiles_type), pointer :: files(:)
  integer                                       :: i, unit_num
  if( present(filename)) then
    open(newunit=unit_num, file=trim(filename), action='WRITE')
  else
    unit_num = stdout()
  endif
  !! TODO write to log
  if( mpp_pe() .eq. mpp_root_pe()) then
    write(unit_num, *) '**********Dumping diag_yaml object**********'
    if( diag_yaml%has_diag_title())    write(unit_num, *) 'Title:', diag_yaml%diag_title
    if( diag_yaml%has_diag_basedate()) write(unit_num, *) 'basedate array:', diag_yaml%diag_basedate
    write(unit_num, *) 'FILES'
    allocate(fields(SIZE(diag_yaml%get_diag_fields())))
    files => diag_yaml%diag_files
    fields = diag_yaml%get_diag_fields()
    do i=1, SIZE(files)
      write(unit_num, *) 'File: ', files(i)%get_file_fname()
      if(files(i)%has_file_frequnit()) write(unit_num, *) 'file_frequnit:', files(i)%get_file_frequnit()
      if(files(i)%has_file_freq()) write(unit_num, *) 'freq:', files(i)%get_file_freq()
      if(files(i)%has_file_timeunit()) write(unit_num, *) 'timeunit:', files(i)%get_file_timeunit()
      if(files(i)%has_file_unlimdim()) write(unit_num, *) 'unlimdim:', files(i)%get_file_unlimdim()
      !if(files(i)%has_file_sub_region()) write(unit_num, *) 'sub_region:', files(i)%get_file_sub_region()
      if(files(i)%has_file_new_file_freq()) write(unit_num, *) 'new_file_freq:', files(i)%get_file_new_file_freq()
      if(files(i)%has_file_new_file_freq_units()) write(unit_num, *) 'new_file_freq_units:', &
                                                         & files(i)%get_file_new_file_freq_units()
      if(files(i)%has_file_start_time()) write(unit_num, *) 'start_time:', &
                                                         & date_to_string(files(i)%get_file_start_time())
      if(files(i)%has_file_duration()) write(unit_num, *) 'duration:', files(i)%get_file_duration()
      if(files(i)%has_file_duration_units()) write(unit_num, *) 'duration_units:', files(i)%get_file_duration_units()
      if(files(i)%has_file_varlist()) write(unit_num, *) 'varlist:', files(i)%get_file_varlist()
      if(files(i)%has_file_global_meta()) write(unit_num, *) 'global_meta:', files(i)%get_file_global_meta()
      if(files(i)%is_global_meta()) write(unit_num, *) 'global_meta:', files(i)%is_global_meta()
      write(unit_num, *) ''
    enddo
    write(unit_num, *) 'FIELDS'
    do i=1, SIZE(fields)
      write(unit_num, *) 'Field: ', fields(i)%get_var_fname()
      if(fields(i)%has_var_fname()) write(unit_num, *) 'fname:', fields(i)%get_var_fname()
      if(fields(i)%has_var_varname()) write(unit_num, *) 'varname:', fields(i)%get_var_varname()
      if(fields(i)%has_var_reduction()) write(unit_num, *) 'reduction:', fields(i)%get_var_reduction()
      if(fields(i)%has_var_module()) write(unit_num, *) 'module:', fields(i)%get_var_module()
      if(fields(i)%has_var_kind()) write(unit_num, *) 'kind:', fields(i)%get_var_kind()
      if(fields(i)%has_var_outname()) write(unit_num, *) 'outname:', fields(i)%get_var_outname()
      if(fields(i)%has_var_longname()) write(unit_num, *) 'longname:', fields(i)%get_var_longname()
      if(fields(i)%has_var_units()) write(unit_num, *) 'units:', fields(i)%get_var_units()
      if(fields(i)%has_var_zbounds()) write(unit_num, *) 'zbounds:', fields(i)%get_var_zbounds()
      if(fields(i)%has_var_attributes()) write(unit_num, *) 'attributes:', fields(i)%get_var_attributes()
      if(fields(i)%has_n_diurnal()) write(unit_num, *) 'n_diurnal:', fields(i)%get_n_diurnal()
      if(fields(i)%has_pow_value()) write(unit_num, *) 'pow_value:', fields(i)%get_pow_value()
      if(fields(i)%has_var_attributes()) write(unit_num, *) 'is_var_attributes:', fields(i)%is_var_attributes()
    enddo
    deallocate(fields)
    nullify(files)
    if( present(filename)) then
      close(unit_num)
    endif
  endif
end subroutine
 
!> Writes an output yaml with all available information on the written files.
!! Will only write with root pe.
!! Global attributes are limited to 16 per file.
subroutine fms_diag_yaml_out(ntimes, ntiles, ndistributedfiles)
  integer, intent(in) :: ntimes(:)            !< The number of time levels that were written for each file
  integer, intent(in) :: ntiles(:)            !< The number of tiles for each file domain
  integer, intent(in) :: ndistributedfiles(:) !< The number of distributed files
 
  type(diagyamlfiles_type), pointer :: fileptr !< pointer for individual variables
  type(diagyamlfilesvar_type), pointer :: varptr !< pointer for individual variables
  type (fmsyamloutkeys_type), allocatable :: keys(:), keys2(:), keys3(:)
  type (fmsyamloutvalues_type), allocatable :: vals(:), vals2(:), vals3(:)
  integer :: i, j, k
  character(len=128) :: tmpstr1, tmpstr2 !< string to store output fields
  integer, parameter :: tier1size = 3 !< size of first tier, will always be 3 for basedate, title and diag_files
  integer :: tier2size, tier3size !< size of each 'tier'(based one numbers of tabs) in the yaml
  integer, allocatable :: tier3each(:) !< tier 3 list sizes corresponding to where they are in the second tier
  integer, dimension(basedate_size) :: basedate_loc !< local copy of basedate to loop through
  integer :: varnum_i, key3_i, gm
  character(len=32), allocatable :: st_vals(:) !< start times for gcc bug
  character(len=FMS_FILE_LEN) :: filename !< Name of the diag manifest file
                                !! When there are more than 1 ensemble the filename is
                                !! diag_manifest_ens_xx.yaml.yy (where xx is the ensembles number, yy is the root pe)
                                !! otherwhise the filename is diag_manifest.yaml.yy
 
  if( mpp_pe() .ne. mpp_root_pe()) return
 
  allocate(tier3each(SIZE(diag_yaml%diag_files) * 3))
  tier3size = 0; tier3each = 0
 
  !! allocations for key+val structs
  allocate(keys(1))
  allocate(vals(1))
  allocate(keys2(SIZE(diag_yaml%diag_files)))
  allocate(vals2(SIZE(diag_yaml%diag_files)))
  allocate(st_vals(SIZE(diag_yaml%diag_files)))
  do i=1, SIZE(diag_yaml%diag_files)
    call initialize_key_struct(keys2(i))
    call initialize_val_struct(vals2(i))
    if (allocated(diag_yaml%diag_files(i)%file_varlist) ) then
      do j=1, SIZE(diag_yaml%diag_files(i)%file_varlist)
        tier3size = tier3size + 1
      enddo
    endif
    tier3size = tier3size + 2
  enddo
  allocate(keys3(tier3size))
  allocate(vals3(tier3size))
 
  !! tier 1 - title, basedate, diag_files
  call initialize_key_struct(keys(1))
  call initialize_val_struct(vals(1))
  call fms_f2c_string( keys(1)%key1, 'title')
  call fms_f2c_string( vals(1)%val1, diag_yaml%diag_title)
  call fms_f2c_string( keys(1)%key2, 'base_date')
  basedate_loc = diag_yaml%get_basedate()
  tmpstr1 = ''; tmpstr2 = ''
  tmpstr1 = string(basedate_loc(1))
  tmpstr2 = trim(tmpstr1)
  do i=2, basedate_size
    tmpstr1 = string(basedate_loc(i))
    tmpstr2 = trim(tmpstr2) // ' ' // trim(tmpstr1)
  enddo
  call fms_f2c_string(vals(1)%val2, trim(tmpstr2))
  call yaml_out_add_level2key('diag_files', keys(1))
  key3_i = 0
  !! tier 2 - diag files
  do i=1, SIZE(diag_yaml%diag_files)
    fileptr => diag_yaml%diag_files(i)
 
    call fms_f2c_string(keys2(i)%key1, 'file_name')
    call fms_f2c_string(keys2(i)%key2, 'freq')
    call fms_f2c_string(keys2(i)%key3, 'freq_units')
    call fms_f2c_string(keys2(i)%key4, 'time_units')
    call fms_f2c_string(keys2(i)%key5, 'unlimdim')
    call fms_f2c_string(keys2(i)%key6, 'new_file_freq')
    call fms_f2c_string(keys2(i)%key7, 'new_file_freq_units')
    call fms_f2c_string(keys2(i)%key8, 'start_time')
    call fms_f2c_string(keys2(i)%key9, 'file_duration')
    call fms_f2c_string(keys2(i)%key10, 'file_duration_units')
 
    !! The number of timelevels that were written for the file
    call fms_f2c_string(keys2(i)%key11, 'number_of_timelevels')
 
    !! The number of tiles in the file's domain
    !! When the number of tiles is greater than 1, the name of the diag file
    !! is filename_tileXX.nc, where XX is the tile number, (1 to the number of tiles)
    call fms_f2c_string(keys2(i)%key12, 'number_of_tiles')
 
    !! This is the number of distributed files
    !! If the diag files were not combined, the name of the diag file is going to be
    !! filename_tileXX.nc.YY, where YY is the distributed file number
    !! (1 to the number of distributed files)
    call fms_f2c_string(keys2(i)%key13, 'number_of_distributed_files')
 
    call fms_f2c_string(vals2(i)%val1, fileptr%file_fname)
    call fms_f2c_string(vals2(i)%val5, fileptr%file_unlimdim)
    call fms_f2c_string(vals2(i)%val4, get_diag_unit_string((/fileptr%file_timeunit/)))
    tmpstr1 = ''
    do k=1, SIZE(fileptr%file_freq)
        if(fileptr%file_freq(k) .eq. diag_null) exit
        tmpstr2 = ''
        tmpstr2 = string(fileptr%file_freq(k))
        tmpstr1 = trim(tmpstr1)//" "//trim(tmpstr2)
    enddo
    call fms_f2c_string(vals2(i)%val2, adjustl(tmpstr1))
    call fms_f2c_string(vals2(i)%val3, get_diag_unit_string(fileptr%file_frequnit))
    tmpstr1 = ''
    do k=1, SIZE(fileptr%file_new_file_freq)
        if(fileptr%file_new_file_freq(k) .eq. diag_null) exit
        tmpstr2 = ''
        tmpstr2 = string(fileptr%file_new_file_freq(k))
        tmpstr1 = trim(tmpstr1)//" "//trim(tmpstr2)
    enddo
    call fms_f2c_string(vals2(i)%val6, adjustl(tmpstr1))
    call fms_f2c_string(vals2(i)%val7, get_diag_unit_string(fileptr%file_new_file_freq_units))
    if (fileptr%has_file_start_time()) then
      call fms_f2c_string(vals2(i)%val8, trim(date_to_string(fileptr%get_file_start_time())))
    else
      call fms_f2c_string(vals2(i)%val8, "")
    endif
    tmpstr1 = ''
    do k=1, SIZE(fileptr%file_duration)
        if(fileptr%file_duration(k) .eq. diag_null) exit
        tmpstr2 = ''
        tmpstr2 = string(fileptr%file_duration(k))
        tmpstr1 = trim(tmpstr1)//" "//trim(tmpstr2)
    enddo
    call fms_f2c_string(vals2(i)%val9, adjustl(tmpstr1))
    call fms_f2c_string(vals2(i)%val10, get_diag_unit_string(fileptr%file_duration_units))
    call fms_f2c_string(vals2(i)%val11, string(ntimes(i)))
    call fms_f2c_string(vals2(i)%val12, string(ntiles(i)))
    call fms_f2c_string(vals2(i)%val13, string(ndistributedfiles(i)))
 
    !! tier 3 - varlists, subregion, global metadata
    call yaml_out_add_level2key('varlist', keys2(i))
    j = 0
    if( SIZE(fileptr%file_varlist) .gt. 0) then
      do j=1, SIZE(fileptr%file_varlist)
        key3_i = key3_i + 1
        call initialize_key_struct(keys3(key3_i))
        call initialize_val_struct(vals3(key3_i))
        !! find the variable object from the list
        varptr => null()
        do varnum_i=1, SIZE(diag_yaml%diag_fields)
          if( trim(diag_yaml%diag_fields(varnum_i)%var_varname ) .eq. trim(fileptr%file_varlist(j)) .and. &
              trim(diag_yaml%diag_fields(varnum_i)%var_fname) .eq. trim(fileptr%file_fname)) then
            ! if theres a output name, that should match as well
            if(diag_yaml%diag_fields(varnum_i)%has_var_outname()) then
              if(trim(diag_yaml%diag_fields(varnum_i)%var_outname) .eq. trim(fileptr%file_outlist(j))) then
                varptr => diag_yaml%diag_fields(varnum_i)
                exit
              endif
            else
              varptr => diag_yaml%diag_fields(varnum_i)
              exit
            endif
          endif
        enddo
        if( .not. associated(varptr)) call mpp_error(fatal, "diag_yaml_output: could not find variable in list."//&
                                                            " var: "// trim(fileptr%file_varlist(j)))
        call fms_f2c_string(keys3(key3_i)%key1, 'module')
        call fms_f2c_string(keys3(key3_i)%key2, 'var_name')
        call fms_f2c_string(keys3(key3_i)%key3, 'reduction')
        call fms_f2c_string(keys3(key3_i)%key4, 'kind')
        call fms_f2c_string(keys3(key3_i)%key5, 'output_name')
        call fms_f2c_string(keys3(key3_i)%key6, 'long_name')
        call fms_f2c_string(keys3(key3_i)%key7, 'units')
        call fms_f2c_string(keys3(key3_i)%key8, 'zbounds')
        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
            call fms_f2c_string(vals3(key3_i)%val3, &
                    get_diag_reduction_string((/varptr%var_reduction/)))
        endif
        if (varptr%has_var_outname())  call fms_f2c_string(vals3(key3_i)%val5, varptr%var_outname)
        if (varptr%has_var_longname()) call fms_f2c_string(vals3(key3_i)%val6, varptr%var_longname)
        if (varptr%has_var_units()) call fms_f2c_string(vals3(key3_i)%val7, varptr%var_units)
        if (varptr%has_var_kind()) then
          select case(varptr%var_kind)
            case(i4)
              call fms_f2c_string(vals3(key3_i)%val4, 'i4')
            case(i8)
              call fms_f2c_string(vals3(key3_i)%val4, 'i8')
            case(r4)
              call fms_f2c_string(vals3(key3_i)%val4, 'r4')
            case(r8)
              call fms_f2c_string(vals3(key3_i)%val4, 'r8')
          end select
        endif
 
        if( abs(varptr%var_zbounds(1) - real(diag_null, r4_kind)) .gt. 1.0e-5 ) then
          tmpstr2 = string(varptr%var_zbounds(1), "F8.2") // ' ' // string(varptr%var_zbounds(2), "F8.2")
          call fms_f2c_string(vals3(key3_i)%val8, trim(tmpstr2))
        endif
 
        if( varptr%n_diurnal .gt. 0) then
          tmpstr1 = ''; tmpstr1 = string(varptr%n_diurnal)
          call fms_f2c_string(vals3(key3_i)%val9, tmpstr1)
        endif
 
        if( varptr%pow_value .gt. 0) then
          tmpstr1 = ''; tmpstr1 = string(varptr%pow_value)
          call fms_f2c_string(vals3(key3_i)%val10, tmpstr1)
        endif
 
        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
 
    key3_i = key3_i + 1
    tier3each(i*3-2) = j-1 ! j-1 structs to print for varlist keys
    tier3each(i*3-1) = 1   ! 1 struct per sub_region key
    tier3each(i*3) = 1     ! 1 struct per global metadata key
    call initialize_key_struct(keys3(key3_i))
    call initialize_val_struct(vals3(key3_i))
    !! sub region
    call yaml_out_add_level2key('sub_region', keys2(i))
    call fms_f2c_string(keys3(key3_i)%key1, 'grid_type')
    call fms_f2c_string(keys3(key3_i)%key2, 'tile')
    call fms_f2c_string(keys3(key3_i)%key3, 'corner1')
    call fms_f2c_string(keys3(key3_i)%key4, 'corner2')
    call fms_f2c_string(keys3(key3_i)%key5, 'corner3')
    call fms_f2c_string(keys3(key3_i)%key6, 'corner4')
 
    select case (fileptr%file_sub_region%grid_type)
      case(latlon_gridtype)
        call fms_f2c_string(vals3(key3_i)%val1, 'latlon')
      case(index_gridtype)
        call fms_f2c_string(vals3(key3_i)%val1, 'index')
    end select
    if(fileptr%file_sub_region%tile .ne. diag_null) then
      tmpstr1 = ''; tmpstr1 = string(fileptr%file_sub_region%tile)
      call fms_f2c_string(vals3(key3_i)%val2, tmpstr1)
    endif
    if(fileptr%has_file_sub_region()) then
      if( allocated(fileptr%file_sub_region%corners)) then
        select type (corners => fileptr%file_sub_region%corners)
        type is (real(r8_kind))
          tmpstr1 = ''; tmpstr1 = string(corners(1,1))
          tmpstr2 = ''; tmpstr2 = string(corners(1,2))
          call fms_f2c_string(vals3(key3_i)%val3, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(2,1))
          tmpstr2 = ''; tmpstr2 = string(corners(2,2))
          call fms_f2c_string(vals3(key3_i)%val4, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(3,1))
          tmpstr2 = ''; tmpstr2 = string(corners(3,2))
          call fms_f2c_string(vals3(key3_i)%val5, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(4,1))
          tmpstr2 = ''; tmpstr2 = string(corners(4,2))
          call fms_f2c_string(vals3(key3_i)%val6, trim(tmpstr1)//' '//trim(tmpstr2))
        type is (real(r4_kind))
          tmpstr1 = ''; tmpstr1 = string(corners(1,1))
          tmpstr2 = ''; tmpstr2 = string(corners(1,2))
          call fms_f2c_string(vals3(key3_i)%val3, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(2,1))
          tmpstr2 = ''; tmpstr2 = string(corners(2,2))
          call fms_f2c_string(vals3(key3_i)%val4, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(3,1))
          tmpstr2 = ''; tmpstr2 = string(corners(3,2))
          call fms_f2c_string(vals3(key3_i)%val5, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(4,1))
          tmpstr2 = ''; tmpstr2 = string(corners(4,2))
          call fms_f2c_string(vals3(key3_i)%val6, trim(tmpstr1)//' '//trim(tmpstr2))
        type is (integer(i4_kind))
          tmpstr1 = ''; tmpstr1 = string(corners(1,1))
          tmpstr2 = ''; tmpstr2 = string(corners(1,2))
          call fms_f2c_string(vals3(key3_i)%val3, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(2,1))
          tmpstr2 = ''; tmpstr2 = string(corners(2,2))
          call fms_f2c_string(vals3(key3_i)%val4, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(3,1))
          tmpstr2 = ''; tmpstr2 = string(corners(3,2))
          call fms_f2c_string(vals3(key3_i)%val5, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(4,1))
          tmpstr2 = ''; tmpstr2 = string(corners(4,2))
          call fms_f2c_string(vals3(key3_i)%val6, trim(tmpstr1)//' '//trim(tmpstr2))
        type is (integer(i8_kind))
          tmpstr1 = ''; tmpstr1 = string(corners(1,1))
          tmpstr2 = ''; tmpstr2 = string(corners(1,2))
          call fms_f2c_string(vals3(key3_i)%val3, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(2,1))
          tmpstr2 = ''; tmpstr2 = string(corners(2,2))
          call fms_f2c_string(vals3(key3_i)%val4, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(3,1))
          tmpstr2 = ''; tmpstr2 = string(corners(3,2))
          call fms_f2c_string(vals3(key3_i)%val5, trim(tmpstr1)//' '//trim(tmpstr2))
          tmpstr1 = ''; tmpstr1 = string(corners(4,1))
          tmpstr2 = ''; tmpstr2 = string(corners(4,2))
          call fms_f2c_string(vals3(key3_i)%val6, trim(tmpstr1)//' '//trim(tmpstr2))
        end select
      endif
    endif
    !! global metadata
    key3_i = key3_i + 1
    call initialize_key_struct(keys3(key3_i))
    call initialize_val_struct(vals3(key3_i))
    call yaml_out_add_level2key('global_meta', keys2(i))
    if ( fileptr%has_file_global_meta()) then
      do gm=1, SIZE(fileptr%file_global_meta, 1)
        select case(gm)
          case (1)
            call fms_f2c_string(keys3(key3_i)%key1, fileptr%file_global_meta(1,1))
            call fms_f2c_string(vals3(key3_i)%val1, fileptr%file_global_meta(1,2))
          case (2)
            call fms_f2c_string(keys3(key3_i)%key2, fileptr%file_global_meta(2,1))
            call fms_f2c_string(vals3(key3_i)%val2, fileptr%file_global_meta(2,2))
          case (3)
            call fms_f2c_string(keys3(key3_i)%key3, fileptr%file_global_meta(3,1))
            call fms_f2c_string(vals3(key3_i)%val3, fileptr%file_global_meta(3,2))
          case (4)
            call fms_f2c_string(keys3(key3_i)%key4, fileptr%file_global_meta(4,1))
            call fms_f2c_string(vals3(key3_i)%val4, fileptr%file_global_meta(4,2))
          case (5)
            call fms_f2c_string(keys3(key3_i)%key5, fileptr%file_global_meta(5,1))
            call fms_f2c_string(vals3(key3_i)%val5, fileptr%file_global_meta(5,2))
          case (6)
            call fms_f2c_string(keys3(key3_i)%key6, fileptr%file_global_meta(6,1))
            call fms_f2c_string(vals3(key3_i)%val6, fileptr%file_global_meta(6,2))
          case (7)
            call fms_f2c_string(keys3(key3_i)%key7, fileptr%file_global_meta(7,1))
            call fms_f2c_string(vals3(key3_i)%val7, fileptr%file_global_meta(7,2))
          case (8)
            call fms_f2c_string(keys3(key3_i)%key8, fileptr%file_global_meta(8,1))
            call fms_f2c_string(vals3(key3_i)%val8, fileptr%file_global_meta(8,2))
          case (9)
            call fms_f2c_string(keys3(key3_i)%key9, fileptr%file_global_meta(9,1))
            call fms_f2c_string(vals3(key3_i)%val9, fileptr%file_global_meta(9,2))
          case (10)
            call fms_f2c_string(keys3(key3_i)%key10, fileptr%file_global_meta(10,1))
            call fms_f2c_string(vals3(key3_i)%val10, fileptr%file_global_meta(10,2))
          case (11)
            call fms_f2c_string(keys3(key3_i)%key11, fileptr%file_global_meta(11,1))
            call fms_f2c_string(vals3(key3_i)%val11, fileptr%file_global_meta(11,2))
          case (12)
            call fms_f2c_string(keys3(key3_i)%key12, fileptr%file_global_meta(12,1))
            call fms_f2c_string(vals3(key3_i)%val12, fileptr%file_global_meta(12,2))
          case (13)
            call fms_f2c_string(keys3(key3_i)%key13, fileptr%file_global_meta(13,1))
            call fms_f2c_string(vals3(key3_i)%val13, fileptr%file_global_meta(13,2))
          case (14)
            call fms_f2c_string(keys3(key3_i)%key14, fileptr%file_global_meta(14,1))
            call fms_f2c_string(vals3(key3_i)%val14, fileptr%file_global_meta(14,2))
          case (15)
            call fms_f2c_string(keys3(key3_i)%key15, fileptr%file_global_meta(15,1))
            call fms_f2c_string(vals3(key3_i)%val15, fileptr%file_global_meta(15,2))
          case (16)
            call fms_f2c_string(keys3(key3_i)%key16, fileptr%file_global_meta(16,1))
            call fms_f2c_string(vals3(key3_i)%val16, fileptr%file_global_meta(16,2))
        end select
      enddo
    endif
  enddo
  tier2size = i
 
  call get_instance_filename('diag_manifest.yaml.'//string(mpp_pe()), filename)
  call write_yaml_from_struct_3( trim(filename)//c_null_char,  1, keys, vals, &
                                 SIZE(diag_yaml%diag_files), keys2, vals2, &
                                 tier3size, tier3each, keys3, vals3,       &
                                 (/size(diag_yaml%diag_files), 0, 0, 0, 0, 0, 0, 0/))
  deallocate( keys, keys2, keys3, vals, vals2, vals3)
 
end subroutine
 
!> private function for getting unit string from diag_data parameter values
pure function get_diag_unit_string( unit_param )
    integer, intent(in) :: unit_param(:) !< diag unit parameter values from diag_data_mod.
                                      !! <br>eg. DIAG_SECONDS, DIAG_MINUTES,DIAG_HOURS, DIAG_DAYS, DIAG_YEARS
    character(len=8 * SIZE(unit_param)) :: get_diag_unit_string
    character(len=7) :: tmp
    integer :: i
    get_diag_unit_string = ' '
    do i=1, SIZE(unit_param)
        select case(unit_param(i))
            case (diag_seconds)
                tmp = 'seconds'
            case (diag_minutes)
                tmp = 'minutes'
            case (diag_hours)
                tmp = 'hours'
            case (diag_days)
                tmp = 'days'
            case (diag_months)
                tmp = 'months'
            case (diag_years)
                tmp = 'years'
            case default
                exit
        end select
        get_diag_unit_string = trim(get_diag_unit_string)//" "//trim(tmp)
    enddo
    get_diag_unit_string = adjustl(get_diag_unit_string)
end function
 
!> private function for getting reduction type string from parameter values
pure function get_diag_reduction_string( reduction_val )
    integer, intent(in) :: reduction_val(:) !< reduction types (eg. time_average)
    integer :: i
    character(len=8 * MAX_FREQ) :: get_diag_reduction_string
    character(len=7) :: tmp
    get_diag_reduction_string = ''
    do i=1, SIZE(reduction_val)
        select case (reduction_val(i))
            case (time_none)
                tmp = 'none'
            case (time_average)
                tmp = 'average'
            case (time_min)
                tmp = 'min'
            case (time_max)
                tmp = 'max'
            case (time_rms)
                tmp = 'rms'
            case (time_sum)
                tmp = 'sum'
            case (time_diurnal)
                tmp = 'diurnal'
            case default
                exit
        end select
        get_diag_reduction_string = trim(get_diag_reduction_string) //" "//trim(tmp)
    enddo
    get_diag_reduction_string = adjustl(get_diag_reduction_string)
end function
 
subroutine add_axis_name( this, axis_name )
    class(diagyamlfilesvar_type), intent(inout) :: this
    character(len=:), allocatable, intent(in)   :: axis_name
    character(len=:), allocatable   :: tmp_str
 
    this%var_axes_names = trim(axis_name)//" "//trim(this%var_axes_names)
 
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
  logical                                  :: res
 
  res = this%var_file_is_subregional
end function is_file_subregional
 
#endif
end module fms_diag_yaml_mod
!> @}
! close documentation grouping