Detailed Description

HDF5 file manipulation for output and restart data.

Functions to write and read HDF5 data files and XDMF files for visit

Parallel restart file creation and read in
Data output for plotting
XDMF reference files for plot files

Author: Chris Hansen

Date: Summer 2010

Data Types
interface	hdf5_read
	Read data from an HDF5 file. More...
type	hdf5_rst
	HDF5 restart structure. More...
interface	hdf5_write
	Write data to an HDF5 file. More...
type	oft_bin_file
	Binary output file object. More...
type	xdmf_plot_file
	Information for XDMF plotting groups in HDF5 plot file. More...

Functions/Subroutines
subroutine	bin_file_add (self, fieldname, type_str, desc, fsize)
	Add field to Open FUSION Toolkit binary I/O file.
subroutine	bin_file_add_comm (self, comment)
	Add comment to Open FUSION Toolkit binary I/O file.
subroutine	bin_file_close (self)
	Close Open FUSION Toolkit binary I/O file.
subroutine	bin_file_flush (self)
	Flush I/O buffer for Open FUSION Toolkit binary I/O file.
subroutine	bin_file_header (self)
	Write header for Open FUSION Toolkit binary I/O file.
subroutine	bin_file_open (self)
	Open Open FUSION Toolkit binary I/O file.
subroutine	bin_file_setup (self, filename, desc)
	Setup Open FUSION Toolkit binary I/O file.
subroutine	bin_file_write (self, data_i4, data_i8, data_r4, data_r8)
	Write single set of data to Open FUSION Toolkit binary I/O file.
subroutine	hdf5_add_string_attribute (filename, objname, aname, attr_data)
	Add string attribute to existing object (group or dataset).
subroutine	hdf5_create_file (filename, persistent_space_tracking)
	Create an empty HDF5 output file.
subroutine	hdf5_create_group (filename, group_name)
	Create HDF5 group in existing file.
subroutine	hdf5_delete_obj (filename, obj_path)
	Delete HDF5 object in existing file.
logical function	hdf5_field_exist (filepath, path)
	Test for exitence of a field in a HDF5 file.
subroutine	hdf5_field_get_sizes (filepath, path, ndims, dim_sizes)
	Test for exitence of a field in a HDF5 file.
integer(hssize_t) function, dimension(2)	hdf5_file_size (filepath)
	Test for exitence of a field in a HDF5 file.
character(len=oft_mpi_plen) function	hdf5_proc_str (proc_ind)
	Get processor rank as string for HDF5 I/O.
subroutine	hdf5_read_1d_i4 (array, filename, path, success)
	integer(i8) 1D array implementation of hdf5_write
subroutine	hdf5_read_1d_r8 (array, filename, path, success)
	real(r8) 1D array implementation of hdf5_write
subroutine	hdf5_read_2d_i4 (array, filename, path, success)
	integer(i4) 2D array implementation of hdf5_write
subroutine	hdf5_read_2d_r8 (array, filename, path, success)
	real(r8) 2D array implementation of hdf5_write
subroutine	hdf5_read_rst (rst_info, filename, path, success)
	FE vector implementation of hdf5_write.
subroutine	hdf5_read_scalar_i4 (val, filename, path, success)
	integer(i4) scalar implementation of hdf5_read
subroutine	hdf5_read_scalar_r8 (val, filename, path, success)
	real(r8) scalar implementation of hdf5_read
subroutine	hdf5_rst_destroy (self)
	Deallocate internal storage fields created for HDF5 collective I/O.
character(len=oft_mpi_plen) function	hdf5_ts_str (ts_in)
	Get timestep index as string for HDF5 I/O.
subroutine	hdf5_write_1d_i4 (array, filename, path)
	integer(i4) 1D array implementation of hdf5_write
subroutine	hdf5_write_1d_r8 (array, filename, path, single_prec)
	real(r8) 1D array implementation of hdf5_write
subroutine	hdf5_write_2d_i4 (array, filename, path)
	integer(i4) 2D array implementation of hdf5_write
subroutine	hdf5_write_2d_r8 (array, filename, path, single_prec)
	real(r8) 2D array implementation of hdf5_write
subroutine	hdf5_write_rst (rst_info, filename, path)
	FE vector implementation of hdf5_write.
subroutine	hdf5_write_scalar_i4 (val, filename, path)
	integer(i4) scalar implementation of hdf5_write
subroutine	hdf5_write_scalar_r8 (val, filename, path, single_prec)
	real(r8) scalar implementation of hdf5_write
logical function	oft_file_exist (filepath)
	Test for exitence of a file.
subroutine	xdmf_add_mesh (self, mesh_type, pt_list, cell_list, grid_name)
	Needs docs.
subroutine	xdmf_add_timestep (self, t)
	Adds a timestep to the dump metadata file.
subroutine	xdmf_clear_timesteps (self, clear_static)
	Clear existing timesteps and reset to static fields.
subroutine	xdmf_write_scalar (self, data, grid_name, path, centering, single_prec)
	Write scalar field to plot file.
subroutine	xdmf_write_vector (self, data, grid_name, path, centering, single_prec)
	Write vector field to plot file.
subroutine	xmdf_setup (self, group_name, basepath, persistent_space_tracking)
	Needs docs.

Variables
integer(i4)	hdf5_fcount =0
	Number of HDF5 fields.
integer(i4), parameter	hdf5_flen =40
	Maximum size of HDF5 filenames.
integer(i4), parameter	hdf5_nl =800
	Maximum number of HDF5 fields.
integer(i4)	hdf5_ts =0
	Number of HDF5 time steps.

Function/Subroutine Documentation

◆ bin_file_add()

subroutine bin_file_add	(	class(oft_bin_file), intent(inout)	self,
		character(len=*), intent(in)	fieldname,
		character(len=2), intent(in)	type_str,
		character(len=*), intent(in), optional	desc,
		integer(i4), intent(in), optional	fsize )

Add field to Open FUSION Toolkit binary I/O file.

Parameters

[in,out]	self	File object
[in]	fieldname	Field name to add
[in]	type_str	Type of field
[in]	desc	Description of field
[in]	fsize	Size of field

◆ bin_file_add_comm()

subroutine bin_file_add_comm	(	class(oft_bin_file), intent(inout)	self,
		character(len=*), intent(in)	comment )

Add comment to Open FUSION Toolkit binary I/O file.

Parameters

[in,out]	self	File object
[in]	comment	Comment to add

◆ bin_file_close()

subroutine bin_file_close ( class(oft_bin_file), intent(inout) self )

Close Open FUSION Toolkit binary I/O file.

◆ bin_file_flush()

subroutine bin_file_flush ( class(oft_bin_file), intent(inout) self )

Flush I/O buffer for Open FUSION Toolkit binary I/O file.

◆ bin_file_header()

subroutine bin_file_header ( class(oft_bin_file), intent(inout) self )

Write header for Open FUSION Toolkit binary I/O file.

◆ bin_file_open()

subroutine bin_file_open ( class(oft_bin_file), intent(inout) self )

Open Open FUSION Toolkit binary I/O file.

◆ bin_file_setup()

subroutine bin_file_setup	(	class(oft_bin_file), intent(inout)	self,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in), optional	desc )

Setup Open FUSION Toolkit binary I/O file.

◆ bin_file_write()

subroutine bin_file_write	(	class(oft_bin_file), intent(inout)	self,
		integer(i4), dimension(:), intent(in), optional	data_i4,
		integer(i8), dimension(:), intent(in), optional	data_i8,
		real(r4), dimension(:), intent(in), optional	data_r4,
		real(r8), dimension(:), intent(in), optional	data_r8 )

Write single set of data to Open FUSION Toolkit binary I/O file.

Parameters

[in,out]	self	File object
[in]	data_i4	integer(i4) data
[in]	data_i8	integer(i8) data
[in]	data_r4	real(r4) data
[in]	data_r8	real(r8) data

◆ hdf5_add_string_attribute()

subroutine hdf5_add_string_attribute	(	character(len=*), intent(in)	filename,
		character(len=*), intent(in)	objname,
		character(len=*), intent(in)	aname,
		character(len=80), dimension(:), intent(in)	attr_data )

Add string attribute to existing object (group or dataset).

Parameters

[in]	filename	Name of HDF5 file
[in]	objname	Name of object (dataset or group)
[in]	aname	Attribute name
[in]	attr_data	Attribute data (80-character lines)

◆ hdf5_create_file()

subroutine hdf5_create_file	(	character(len=*), intent(in)	filename,
		logical, intent(in), optional	persistent_space_tracking )

Create an empty HDF5 output file.

Parameters

[in] filename Name of file to be created

◆ hdf5_create_group()

subroutine hdf5_create_group	(	character(len=*), intent(in)	filename,
		character(len=*), intent(in)	group_name )

Create HDF5 group in existing file.

Parameters

[in]	filename	Name of HDF5 file
[in]	group_name	Group path

◆ hdf5_delete_obj()

subroutine hdf5_delete_obj	(	character(len=*), intent(in)	filename,
		character(len=*), intent(in)	obj_path )

Delete HDF5 object in existing file.

Parameters

[in]	filename	Name of HDF5 file
[in]	obj_path	Object path

◆ hdf5_field_exist()

logical function hdf5_field_exist	(	character(len=*), intent(in)	filepath,
		character(len=*), intent(in)	path )

Test for exitence of a field in a HDF5 file.

Returns: Logical flag indicating existence of field and file

Parameters

[in]	filepath	Path to file
[in]	path	Path of field in file

◆ hdf5_field_get_sizes()

subroutine hdf5_field_get_sizes	(	character(len=*), intent(in)	filepath,
		character(len=*), intent(in)	path,
		integer(4), intent(out)	ndims,
		integer(4), dimension(:), intent(out), allocatable	dim_sizes )

Test for exitence of a field in a HDF5 file.

Returns: Logical flag indicating existence of field and file

Parameters

[in]	filepath	Path to file
[in]	path	Path of field in file
[out]	ndims	Number of dimensions in field
[out]	dim_sizes	Size of each dimension

◆ hdf5_file_size()

integer(hssize_t) function, dimension(2) hdf5_file_size ( character(len=*), intent(in) filepath )

Test for exitence of a field in a HDF5 file.

Returns: Logical flag indicating existence of field and file

Parameters

[in] filepath Path to file

◆ hdf5_proc_str()

character(len=oft_mpi_plen) function hdf5_proc_str ( integer(i4), intent(in), optional proc_ind )

Get processor rank as string for HDF5 I/O.

◆ hdf5_read_1d_i4()

subroutine hdf5_read_1d_i4	(	integer(i4), dimension(:), intent(inout)	array,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path,
		logical, intent(out), optional	success )

integer(i8) 1D array implementation of hdf5_write

Parameters

[in,out]	array	Values to read from file
[in]	filename	Path to file
[in]	path	Variable path in file
[out]	success	Successful read?

◆ hdf5_read_1d_r8()

subroutine hdf5_read_1d_r8	(	real(r8), dimension(:), intent(inout)	array,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path,
		logical, intent(out), optional	success )

real(r8) 1D array implementation of hdf5_write

Parameters

[in,out]	array	Values to read from file
[in]	filename	Path to file
[in]	path	Variable path in file
[out]	success	Successful read?

◆ hdf5_read_2d_i4()

subroutine hdf5_read_2d_i4	(	integer(i4), dimension(:,:), intent(inout)	array,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path,
		logical, intent(out), optional	success )

integer(i4) 2D array implementation of hdf5_write

Parameters

[in,out]	array	Values to read from file
[in]	filename	Path to file
[in]	path	Variable path in file
[out]	success	Successful read?

◆ hdf5_read_2d_r8()

subroutine hdf5_read_2d_r8	(	real(r8), dimension(:,:), intent(inout)	array,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path,
		logical, intent(out), optional	success )

real(r8) 2D array implementation of hdf5_write

Parameters

[in,out]	array	Values to read from file
[in]	filename	Path to file
[in]	path	Variable path in file
[out]	success	Successful read?

◆ hdf5_read_rst()

subroutine hdf5_read_rst	(	type(hdf5_rst), intent(inout)	rst_info,
		character(*), intent(in)	filename,
		character(*), intent(in)	path,
		logical, intent(out), optional	success )

FE vector implementation of hdf5_write.

Parameters

[in,out]	rst_info	Restart data (structure containing mapping and data holder)
[in]	filename	Path to file
[in]	path	Variable path in file
[out]	success	Successful read?

◆ hdf5_read_scalar_i4()

subroutine hdf5_read_scalar_i4	(	integer(i4), intent(out)	val,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path,
		logical, intent(out), optional	success )

integer(i4) scalar implementation of hdf5_read

Parameters

[out]	val	Value to read from file
[in]	filename	Path to file
[in]	path	Variable path in file
[out]	success	Successful read?

◆ hdf5_read_scalar_r8()

subroutine hdf5_read_scalar_r8	(	real(r8), intent(out)	val,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path,
		logical, intent(out), optional	success )

real(r8) scalar implementation of hdf5_read

Parameters

[out]	val	Value to read from file
[in]	filename	Path to file
[in]	path	Variable path in file
[out]	success	Successful read?

◆ hdf5_rst_destroy()

subroutine hdf5_rst_destroy ( type(hdf5_rst), intent(inout) self )

Deallocate internal storage fields created for HDF5 collective I/O.

◆ hdf5_ts_str()

character(len=oft_mpi_plen) function hdf5_ts_str ( integer(i4), intent(in), optional ts_in )

Get timestep index as string for HDF5 I/O.

◆ hdf5_write_1d_i4()

subroutine hdf5_write_1d_i4	(	integer(i4), dimension(:), intent(in)	array,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path )

integer(i4) 1D array implementation of hdf5_write

Parameters

[in]	array	Values to write to file
[in]	filename	Path to file
[in]	path	Variable path in file

◆ hdf5_write_1d_r8()

subroutine hdf5_write_1d_r8	(	real(r8), dimension(:), intent(in)	array,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path,
		logical, intent(in), optional	single_prec )

real(r8) 1D array implementation of hdf5_write

Parameters

[in]	array	Values to write to file
[in]	filename	Path to file
[in]	path	Variable path in file
[in]	single_prec	Save as single precision?

◆ hdf5_write_2d_i4()

subroutine hdf5_write_2d_i4	(	integer(i4), dimension(:,:), intent(in)	array,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path )

integer(i4) 2D array implementation of hdf5_write

Parameters

[in]	array	Values to write to file
[in]	filename	Path to file
[in]	path	Variable path in file

◆ hdf5_write_2d_r8()

subroutine hdf5_write_2d_r8	(	real(r8), dimension(:,:), intent(in)	array,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path,
		logical, intent(in), optional	single_prec )

real(r8) 2D array implementation of hdf5_write

Parameters

[in]	array	Values to write to file
[in]	filename	Path to file
[in]	path	Variable path in file
[in]	single_prec	Save as single precision?

◆ hdf5_write_rst()

subroutine hdf5_write_rst	(	type(hdf5_rst), intent(in)	rst_info,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path )

FE vector implementation of hdf5_write.

Parameters

[in]	rst_info	Restart data (structure containing data and mapping)
[in]	filename	Path to file
[in]	path	Variable path in file

◆ hdf5_write_scalar_i4()

subroutine hdf5_write_scalar_i4	(	integer(i4), intent(in)	val,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path )

integer(i4) scalar implementation of hdf5_write

Parameters

[in]	val	Value to write to file
[in]	filename	Path to file
[in]	path	Variable path in file

◆ hdf5_write_scalar_r8()

subroutine hdf5_write_scalar_r8	(	real(r8), intent(in)	val,
		character(len=*), intent(in)	filename,
		character(len=*), intent(in)	path,
		logical, intent(in), optional	single_prec )

real(r8) scalar implementation of hdf5_write

Parameters

[in]	val	Value to write to file
[in]	filename	Path to file
[in]	path	Variable path in file
[in]	single_prec	Save as single precision?

◆ oft_file_exist()

logical function oft_file_exist ( character(len=*), intent(in) filepath )

Test for exitence of a file.

Returns: Logical flag indicating existence

Parameters

[in] filepath Path to file

◆ xdmf_add_mesh()

subroutine xdmf_add_mesh	(	class(xdmf_plot_file), intent(inout)	self,
		integer(i4), intent(in)	mesh_type,
		real(r8), dimension(:,:), intent(in)	pt_list,
		integer(i4), dimension(:,:), intent(in)	cell_list,
		character(len=*), intent(in)	grid_name )

Needs docs.

Parameters

[in]	mesh_type	Mesh type flag (Tet/Tri or Hex/Quad)
[in]	pt_list	Point list [3,np]
[in]	cell_list	Cell list [:,nc]
[in]	grid_name	Path to mesh in HDF5 file

◆ xdmf_add_timestep()

subroutine xdmf_add_timestep	(	class(xdmf_plot_file), intent(inout)	self,
		real(r8), intent(in)	t )

Adds a timestep to the dump metadata file.

Subsequent output will be added to this timestep until another call to this subroutine

Parameters

[in] t Time value

◆ xdmf_clear_timesteps()

subroutine xdmf_clear_timesteps	(	class(xdmf_plot_file), intent(inout)	self,
		logical, intent(in), optional	clear_static )

Clear existing timesteps and reset to static fields.

Parameters

[in] clear_static Clear static fields as well?

◆ xdmf_write_scalar()

subroutine xdmf_write_scalar	(	class(xdmf_plot_file), intent(in)	self,
		real(r8), dimension(:), intent(in)	data,
		character(len=*), intent(in)	grid_name,
		character(len=*), intent(in)	path,
		integer(i4), intent(in)	centering,
		logical, intent(in), optional	single_prec )

Write scalar field to plot file.

Parameters

[in]	data	Scalar data
[in]	grid_name	Grid name
[in]	path	Name of the output field
[in]	centering	Centering of data (1-> vertex; 2-> cell)
[in]	single_prec	Save as single precision?

◆ xdmf_write_vector()

subroutine xdmf_write_vector	(	class(xdmf_plot_file), intent(in)	self,
		real(r8), dimension(:,:), intent(in)	data,
		character(len=*), intent(in)	grid_name,
		character(len=*), intent(in)	path,
		integer(i4), intent(in)	centering,
		logical, intent(in), optional	single_prec )

Write vector field to plot file.

Parameters

[in]	data	Vector data
[in]	grid_name	Grid name
[in]	path	Name of the output field
[in]	centering	Centering of data (1-> vertex; 2-> cell)
[in]	single_prec	Save as single precision?

◆ xmdf_setup()

subroutine xmdf_setup	(	class(xdmf_plot_file), intent(inout)	self,
		character(len=*), intent(in)	group_name,
		character(len=*), intent(in), optional	basepath,
		logical, intent(in), optional	persistent_space_tracking )

Needs docs.

Parameters

[in] group_name Path to mesh in HDF5 file

Variable Documentation

◆ hdf5_fcount

integer(i4) hdf5_fcount =0

Number of HDF5 fields.

◆ hdf5_flen

integer(i4), parameter hdf5_flen =40

Maximum size of HDF5 filenames.

◆ hdf5_nl

integer(i4), parameter hdf5_nl =800

Maximum number of HDF5 fields.

◆ hdf5_ts

integer(i4) hdf5_ts =0

Number of HDF5 time steps.

Detailed Description

Data Types

Functions/Subroutines

Variables

Function/Subroutine Documentation

◆ bin_file_add()

◆ bin_file_add_comm()

◆ bin_file_close()

◆ bin_file_flush()

◆ bin_file_header()

◆ bin_file_open()

◆ bin_file_setup()

◆ bin_file_write()

◆ hdf5_add_string_attribute()

◆ hdf5_create_file()

◆ hdf5_create_group()

◆ hdf5_delete_obj()

◆ hdf5_field_exist()

◆ hdf5_field_get_sizes()

◆ hdf5_file_size()

◆ hdf5_proc_str()

◆ hdf5_read_1d_i4()

◆ hdf5_read_1d_r8()

◆ hdf5_read_2d_i4()

◆ hdf5_read_2d_r8()

◆ hdf5_read_rst()

◆ hdf5_read_scalar_i4()

◆ hdf5_read_scalar_r8()

◆ hdf5_rst_destroy()

◆ hdf5_ts_str()

◆ hdf5_write_1d_i4()

◆ hdf5_write_1d_r8()

◆ hdf5_write_2d_i4()

◆ hdf5_write_2d_r8()

◆ hdf5_write_rst()

◆ hdf5_write_scalar_i4()

◆ hdf5_write_scalar_r8()

◆ oft_file_exist()

◆ xdmf_add_mesh()

◆ xdmf_add_timestep()

◆ xdmf_clear_timesteps()

◆ xdmf_write_scalar()

◆ xdmf_write_vector()

◆ xmdf_setup()

Variable Documentation

◆ hdf5_fcount

◆ hdf5_flen

◆ hdf5_nl

◆ hdf5_ts