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Merged
thomas-robinson merged 4 commits into from
Apr 25, 2023
Merged

Modern diag_manager: Add standard_name and coordinates attributes + minor bug fixes #1176

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c68a925
make diag_table search not case sensitive
uramirez8707 Mar 29, 2023
e3ad056
Merge branch 'dmUpdate' of github.com:NOAA-GFDL/FMS into more_updates
uramirez8707 Mar 31, 2023
f59663b
Fix possible string issue in get_time_string
uramirez8707 Mar 31, 2023
d82d3f5
write the coordinate and standard name attribute to the field
uramirez8707 Mar 31, 2023
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26 changes: 25 additions & 1 deletion diag_manager/fms_diag_axis_object.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ module fms_diag_axis_object_mod
INTEGER , private :: direction !< Direction of the axis 0, 1, -1
CHARACTER(len=:), ALLOCATABLE, private :: edges_name !< Name for the previously defined "edges axis"
!! This will be written as an attribute
CHARACTER(len=128) , private :: aux !< Auxiliary name, can only be <TT>geolon_t</TT>
CHARACTER(len=:), ALLOCATABLE, private :: aux !< Auxiliary name, can only be <TT>geolon_t</TT>
!! or <TT>geolat_t</TT>
CHARACTER(len=128) , private :: req !< Required field names.
INTEGER , private :: tile_count !< The number of tiles
Expand All @@ -174,6 +174,8 @@ module fms_diag_axis_object_mod
PROCEDURE :: get_compute_domain
PROCEDURE :: get_indices
PROCEDURE :: get_global_io_domain
PROCEDURE :: get_aux
PROCEDURE :: has_aux
! TO DO:
! Get/has/is subroutines as needed
END TYPE fmsDiagFullAxis_type
Expand Down Expand Up @@ -560,6 +562,28 @@ function get_axis_length(this) &

end function


!> @brief Determine if an axis object has an auxiliary name
!! @return .true. if an axis object has an auxiliary name
pure function has_aux(this) &
result(rslt)
class(fmsDiagFullAxis_type), intent(in) :: this !< diag_axis obj
logical :: rslt

rslt = .false.
if (allocated(this%aux)) rslt = trim(this%aux) .ne. ""
end function has_aux

!> @brief Get the auxiliary name of an axis object
!! @return the auxiliary name of an axis object
pure function get_aux(this) &
result(rslt)
class(fmsDiagFullAxis_type), intent(in) :: this !< diag_axis obj
character(len=:), allocatable :: rslt

rslt = this%aux
end function get_aux

!> @brief Set the axis_id
subroutine set_axis_id(this, axis_id)
class(fmsDiagFullAxis_type), intent(inout) :: this !< diag_axis obj
Expand Down
41 changes: 41 additions & 0 deletions diag_manager/fms_diag_field_object.F90
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Expand Up @@ -145,6 +145,7 @@ module fms_diag_field_object_mod
procedure :: get_var_skind
procedure :: get_longname_to_write
procedure :: write_field_metadata
procedure :: write_coordinate_attribute
procedure :: get_math_needs_to_be_done
end type fmsDiagField_type
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! variables !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Expand Down Expand Up @@ -1141,7 +1142,47 @@ subroutine write_field_metadata(this, fileobj, file_id, yaml_id, diag_axis, unli
call register_variable_attribute(fileobj, var_name, "cell_methods", &
trim(adjustl(cell_measures)), str_len=len_trim(adjustl(cell_measures)))

!< Write out the standard_name (this was defined in the register call)
if (this%has_standname()) &
call register_variable_attribute(fileobj, var_name, "standard_name", &
trim(this%get_standname()), str_len=len_trim(this%get_standname()))

call this%write_coordinate_attribute(fileobj, var_name, diag_axis)
end subroutine write_field_metadata

!> @brief Writes the coordinate attribute of a field if any of the field's axis has an
!! auxiliary axis
subroutine write_coordinate_attribute (this, fileobj, var_name, diag_axis)
CLASS(fmsDiagField_type), intent(in) :: this !< The field object
class(FmsNetcdfFile_t), INTENT(INOUT) :: fileobj !< Fms2_io fileobj to write to
character(len=*), intent(in) :: var_name !< Variable name
class(fmsDiagAxisContainer_type), intent(in) :: diag_axis(:) !< Diag_axis object

integer :: i !< For do loops
character(len = 252) :: aux_coord !< Auxuliary axis name

!> If the variable is a scalar, go away
if (.not. allocated(this%axis_ids)) return

!> Determine if any of the field's axis has an auxiliary axis and the
!! axis_names as a variable attribute
aux_coord = ""
do i = 1, size(this%axis_ids)
select type (obj => diag_axis(this%axis_ids(i))%axis)
type is (fmsDiagFullAxis_type)
if (obj%has_aux()) then
aux_coord = trim(aux_coord)//" "//obj%get_aux()
endif
end select
enddo

if (trim(aux_coord) .eq. "") return

call register_variable_attribute(fileobj, var_name, "coordinates", &
trim(adjustl(aux_coord)), str_len=len_trim(adjustl(aux_coord)))

end subroutine write_coordinate_attribute

!> @brief Gets a fields data buffer
!! @return a pointer to the data buffer
function get_data_buffer (this) &
Expand Down
2 changes: 1 addition & 1 deletion diag_manager/fms_diag_time_utils.F90
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Expand Up @@ -195,7 +195,7 @@ END FUNCTION diag_forecast_time_inc
!! This string is used as suffix in output file name
!! @return Character(len=128) get_time_string
CHARACTER(len=128) FUNCTION get_time_string(filename, current_time)
CHARACTER(len=128), INTENT(in) :: filename !< File name.
CHARACTER(len=*), INTENT(in) :: filename !< File name.
TYPE(time_type), INTENT(in) :: current_time !< Current model time.

INTEGER :: yr1 !< get from current time
Expand Down
8 changes: 6 additions & 2 deletions diag_manager/fms_diag_yaml.F90
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Expand Up @@ -41,6 +41,7 @@ module fms_diag_yaml_mod
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
use platform_mod, only: r4_kind, i4_kind
use fms_mod, only: lowercase

implicit none

Expand Down Expand Up @@ -413,7 +414,8 @@ subroutine diag_yaml_object_init(diag_subset_output)
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
!! The diag_table is not case sensitive (so we are saving it as lowercase)
file_list%file_name(file_count) = lowercase(trim(diag_yaml%diag_files(file_count)%file_fname)//c_null_char)
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@thomas-robinson thomas-robinson Apr 21, 2023

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Why would we impose this? Why can't users have capital letters in the file names?

file_list%diag_file_indices(file_count) = file_count

nvars = 0
Expand Down Expand Up @@ -441,6 +443,8 @@ subroutine diag_yaml_object_init(diag_subset_output)
!> 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))
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@thomas-robinson thomas-robinson Apr 21, 2023

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Why can't users have a capital letter for the var name? I always think of temperature as T and time as t

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@uramirez8707 uramirez8707 Apr 21, 2023

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They can have capital letters.

This is for when we are searching for the variable name in the diag_table.yaml. The old diag manager was not case sensitive. So in the register_diag_field call the variable name could be "Temperature", and in the diag_table.yaml "TEMPERATURE" or whatever. Without this the code won't be able to find the variable because "Temperature" != "TEMPERATURE"

The variable_list is the sorted list of variables, in the diag_yaml it saved at whatever is in the diag_table.yaml

variable_list%diag_field_indices(var_count) = var_count
enddo nvars_loop
deallocate(var_ids)
Expand Down Expand Up @@ -1434,7 +1438,7 @@ function find_diag_field(diag_field_name, module_name) &
integer, allocatable :: indices(:)

indices = fms_find_my_string(variable_list%var_pointer, size(variable_list%var_pointer), &
& trim(diag_field_name)//":"//trim(module_name)//c_null_char)
& lowercase(trim(diag_field_name))//":"//lowercase(trim(module_name)//c_null_char))
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@thomas-robinson thomas-robinson Apr 21, 2023

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This one I actually agree with because the actual modules are all lower case (i think)

end function find_diag_field

!> @brief Gets the diag_field entries corresponding to the indices of the sorted variable_list
Expand Down