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change all fms2 fileobj instances to fms2io_fileobj #1327

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change all fms2 fileobj instances to fms2io_fileobj #1327

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ea0b2ea
change all fms2 fileobj instances to fms2io_fileobj
mcallic2 Aug 10, 2023
6b2848a
missed one
mcallic2 Aug 11, 2023
9e70819
Merge branch 'dmUpdate' into diag-changefileobj
mcallic2 Aug 14, 2023
bdb79b8
missed one
mcallic2 Aug 14, 2023
83cb6e1
fixes line count
mcallic2 Aug 14, 2023
95346e0
missing from merge
mcallic2 Aug 14, 2023
a8ea154
line count
mcallic2 Aug 14, 2023
9065b67
remove whitespace
mcallic2 Aug 14, 2023
ae290b8
merge dmUpdate
mcallic2 Aug 15, 2023
a6bff1c
forgot this file
mcallic2 Aug 15, 2023
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95 changes: 49 additions & 46 deletions diag_manager/fms_diag_axis_object.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -291,14 +291,15 @@ subroutine add_axis_attribute(this, att_name, att_value)
end subroutine add_axis_attribute

!> @brief Write the axis meta data to an open fileobj
subroutine write_axis_metadata(this, fileobj, edges_in_file, parent_axis)
class(fmsDiagAxis_type), target, INTENT(IN) :: this !< diag_axis obj
class(FmsNetcdfFile_t), INTENT(INOUT) :: fileobj !< Fms2_io fileobj to write the data to
logical, INTENT(IN) :: edges_in_file !< .True. if the edges to this axis are
!! already in the file
class(fmsDiagAxis_type), OPTIONAL, target, INTENT(IN) :: parent_axis !< If the axis is a subaxis, axis object
!! for the parent axis (this will be used
!! to get some of the metadata info)
subroutine write_axis_metadata(this, fms2io_fileobj, edges_in_file, parent_axis)
class(fmsDiagAxis_type), target, INTENT(IN) :: this !< diag_axis obj
class(FmsNetcdfFile_t), INTENT(INOUT) :: fms2io_fileobj !< Fms2_io fileobj to write the data to
logical, INTENT(IN) :: edges_in_file !< .True. if the edges to this axis are
!! already in the file
class(fmsDiagAxis_type), OPTIONAL, target, INTENT(IN) :: parent_axis !< If the axis is a subaxis, axis
!! object for the parent axis
!! (this will be used to get some
!! of the metadata info)
Comment on lines +294 to +302
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Why are there so many differences here?

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spacing, uriel told me I better keep everything looking pretty


character(len=:), ALLOCATABLE :: axis_edges_name !< Name of the edges, if it exist
character(len=:), pointer :: axis_name !< Name of the axis
Expand Down Expand Up @@ -330,106 +331,107 @@ subroutine write_axis_metadata(this, fileobj, edges_in_file, parent_axis)
endif
type_of_domain = NO_DOMAIN !< All subaxes are treated as non-domain decomposed (each rank writes it own file)
type is (fmsDiagDiurnalAxis_type)
call this%write_diurnal_metadata(fileobj)
call this%write_diurnal_metadata(fms2io_fileobj)
return
end select

!< Add the axis as a dimension in the netcdf file based on the type of axis_domain and the fileobj type
select type (fileobj)
select type (fms2io_fileobj)
!< The register_field calls need to be inside the select type block so that it can go inside the correct
!! register_field interface
type is (FmsNetcdfFile_t)
!< Here the axis is not domain decomposed (i.e z_axis)
call register_axis(fileobj, axis_name, axis_length)
call register_field(fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
call register_axis(fms2io_fileobj, axis_name, axis_length)
call register_field(fms2io_fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
type is (FmsNetcdfDomainFile_t)
select case (type_of_domain)
case (NO_DOMAIN)
!< Here the fileobj is domain decomposed, but the axis is not
!! Domain decomposed fileobjs can have axis that are not domain decomposed (i.e "Z" axis)
call register_axis(fileobj, axis_name, axis_length)
call register_field(fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
call register_axis(fms2io_fileobj, axis_name, axis_length)
call register_field(fms2io_fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
case (TWO_D_DOMAIN)
!< Here the axis is domain decomposed
call register_axis(fileobj, axis_name, diag_axis%cart_name, domain_position=diag_axis%domain_position)
call register_field(fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
call register_axis(fms2io_fileobj, axis_name, diag_axis%cart_name, domain_position=diag_axis%domain_position)
call register_field(fms2io_fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
end select
type is (FmsNetcdfUnstructuredDomainFile_t)
select case (type_of_domain)
case (UG_DOMAIN)
!< Here the axis is in a unstructured domain
call register_axis(fileobj, axis_name)
call register_field(fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
call register_axis(fms2io_fileobj, axis_name)
call register_field(fms2io_fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
case default
!< Here the fileobj is in the unstructured domain, but the axis is not
!< Unstructured domain fileobjs can have axis that are not domain decomposed (i.e "Z" axis)
call register_axis(fileobj, axis_name, axis_length)
call register_field(fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
call register_axis(fms2io_fileobj, axis_name, axis_length)
call register_field(fms2io_fileobj, axis_name, diag_axis%type_of_data, (/axis_name/))
end select
end select

!< Write its metadata
call register_variable_attribute(fileobj, axis_name, "long_name", diag_axis%long_name, &
call register_variable_attribute(fms2io_fileobj, axis_name, "long_name", diag_axis%long_name, &
str_len=len_trim(diag_axis%long_name))

if (diag_axis%cart_name .NE. "N") &
call register_variable_attribute(fileobj, axis_name, "axis", diag_axis%cart_name, str_len=1)
call register_variable_attribute(fms2io_fileobj, axis_name, "axis", diag_axis%cart_name, str_len=1)

if (trim(diag_axis%units) .NE. "none") &
call register_variable_attribute(fileobj, axis_name, "units", diag_axis%units, str_len=len_trim(diag_axis%units))
call register_variable_attribute(fms2io_fileobj, axis_name, "units", &
diag_axis%units, str_len=len_trim(diag_axis%units))

select case (diag_axis%direction)
case (direction_up)
call register_variable_attribute(fileobj, axis_name, "positive", "up", str_len=2)
call register_variable_attribute(fms2io_fileobj, axis_name, "positive", "up", str_len=2)
case (direction_down)
call register_variable_attribute(fileobj, axis_name, "positive", "down", str_len=4)
call register_variable_attribute(fms2io_fileobj, axis_name, "positive", "down", str_len=4)
end select

!< Ignore the edges attribute, if the edges are already in the file or if it is subaxis
if (.not. edges_in_file .and. allocated(diag_axis%edges_name) .and. .not. is_subaxis) then
call register_variable_attribute(fileobj, axis_name, "edges", diag_axis%edges_name, &
str_len=len_trim(diag_axis%edges_name))
call register_variable_attribute(fms2io_fileobj, axis_name, "edges", diag_axis%edges_name, &
str_len=len_trim(diag_axis%edges_name))
endif

if(allocated(diag_axis%attributes)) then
do i = 1, diag_axis%num_attributes
select type (att_value => diag_axis%attributes(i)%att_value)
type is (character(len=*))
call register_variable_attribute(fileobj, axis_name, diag_axis%attributes(i)%att_name, trim(att_value(1)), &
str_len=len_trim(att_value(1)))
call register_variable_attribute(fms2io_fileobj, axis_name, diag_axis%attributes(i)%att_name, &
trim(att_value(1)), str_len=len_trim(att_value(1)))
class default
call register_variable_attribute(fileobj, axis_name, diag_axis%attributes(i)%att_name, att_value)
call register_variable_attribute(fms2io_fileobj, axis_name, diag_axis%attributes(i)%att_name, att_value)
end select
enddo
endif

end subroutine write_axis_metadata

!> @brief Write the axis data to an open fileobj
subroutine write_axis_data(this, fileobj, parent_axis)
class(fmsDiagAxis_type), target, INTENT(IN) :: this !< diag_axis obj
class(FmsNetcdfFile_t), INTENT(INOUT) :: fileobj !< Fms2_io fileobj to write the data to
class(fmsDiagAxis_type), OPTIONAL, target, INTENT(IN) :: parent_axis !< The parent axis if this is a subaxis
subroutine write_axis_data(this, fms2io_fileobj, parent_axis)
class(fmsDiagAxis_type), target, INTENT(IN) :: this !< diag_axis obj
class(FmsNetcdfFile_t), INTENT(INOUT) :: fms2io_fileobj !< Fms2_io fileobj to write the data to
class(fmsDiagAxis_type), OPTIONAL, target, INTENT(IN) :: parent_axis !< The parent axis if this is a subaxis

integer :: i !< Starting index of a sub_axis
integer :: j !< Ending index of a sub_axis
integer :: global_io_index(2)!< Global io domain starting and ending index
select type(this)
type is (fmsDiagFullAxis_type)
call this%get_global_io_domain(global_io_index)
call write_data(fileobj, this%axis_name, this%axis_data(global_io_index(1):global_io_index(2)))
call write_data(fms2io_fileobj, this%axis_name, this%axis_data(global_io_index(1):global_io_index(2)))
type is (fmsDiagSubAxis_type)
i = this%starting_index
j = this%ending_index

if (present(parent_axis)) then
select type(parent_axis)
type is (fmsDiagFullAxis_type)
call write_data(fileobj, this%subaxis_name, parent_axis%axis_data(i:j))
call write_data(fms2io_fileobj, this%subaxis_name, parent_axis%axis_data(i:j))
end select
endif
type is (fmsDiagDiurnalAxis_type)
call write_data(fileobj, this%axis_name, this%diurnal_data)
call write_data(fms2io_fileobj, this%axis_name, this%diurnal_data)
end select
end subroutine write_axis_data

Expand Down Expand Up @@ -742,7 +744,8 @@ subroutine fill_subaxis(this, starting_index, ending_index, axis_id, parent_id,
integer , intent(in) :: starting_index !< Starting index of the subRegion for the PE
integer , intent(in) :: ending_index !< Ending index of the subRegion for the PE
integer , intent(in) :: axis_id !< Axis id to assign to the subaxis
integer , intent(in) :: parent_id !< The id of the parent axis, the subaxis belongs to
integer , intent(in) :: parent_id !< The id of the parent axis,
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Did you modify this?

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line count issue most likely

!! the subaxis belongs to
character(len=*) , intent(in) :: parent_axis_name !< Name of the parent_axis
real(kind=r4_kind), optional, intent(in) :: zbounds(2) !< Bounds of the z-axis

Expand Down Expand Up @@ -1263,18 +1266,18 @@ pure function get_diurnal_axis_samples(this) &
end function get_diurnal_axis_samples

!< @brief Writes out the metadata for a diurnal axis
subroutine write_diurnal_metadata(this, fileobj)
class(fmsDiagDiurnalAxis_type), intent(in) :: this !< Diurnal axis Object
class(FmsNetcdfFile_t), intent(inout) :: fileobj !< Fms2_io fileobj to write the data to
subroutine write_diurnal_metadata(this, fms2io_fileobj)
class(fmsDiagDiurnalAxis_type), intent(in) :: this !< Diurnal axis Object
class(FmsNetcdfFile_t), intent(inout) :: fms2io_fileobj !< Fms2_io fileobj to write the data to

call register_axis(fileobj, this%axis_name, size(this%diurnal_data))
call register_field(fileobj, this%axis_name, pack_size_str, (/trim(this%axis_name)/))
call register_variable_attribute(fileobj, this%axis_name, "units", &
call register_axis(fms2io_fileobj, this%axis_name, size(this%diurnal_data))
call register_field(fms2io_fileobj, this%axis_name, pack_size_str, (/trim(this%axis_name)/))
call register_variable_attribute(fms2io_fileobj, this%axis_name, "units", &
&trim(this%units), str_len=len_trim(this%units))
call register_variable_attribute(fileobj, this%axis_name, "long_name", &
call register_variable_attribute(fms2io_fileobj, this%axis_name, "long_name", &
&trim(this%long_name), str_len=len_trim(this%long_name))
if (this%edges_id .ne. diag_null) &
call register_variable_attribute(fileobj, this%axis_name, "edges", &
call register_variable_attribute(fms2io_fileobj, this%axis_name, "edges", &
&trim(this%edges_name), str_len=len_trim(this%edges_name))
end subroutine write_diurnal_metadata

Expand Down
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