oft_io Module Reference

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 oft_io::hdf5_write
subroutine	hdf5_read_1d_r8 (array, filename, path, success)
	real(r8) 1D array implementation of oft_io::hdf5_write
subroutine	hdf5_read_2d_i4 (array, filename, path, success)
	integer(i4) 2D array implementation of oft_io::hdf5_write
subroutine	hdf5_read_2d_r8 (array, filename, path, success)
	real(r8) 2D array implementation of oft_io::hdf5_write
subroutine	hdf5_read_rst (rst_info, filename, path, success)
	FE vector implementation of oft_io::hdf5_write.
subroutine	hdf5_read_scalar_i4 (val, filename, path, success)
	integer(i4) scalar implementation of oft_io::hdf5_read
subroutine	hdf5_read_scalar_r8 (val, filename, path, success)
	real(r8) scalar implementation of oft_io::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 oft_io::hdf5_write
subroutine	hdf5_write_1d_r8 (array, filename, path, single_prec)
	real(r8) 1D array implementation of oft_io::hdf5_write
subroutine	hdf5_write_2d_i4 (array, filename, path)
	integer(i4) 2D array implementation of oft_io::hdf5_write
subroutine	hdf5_write_2d_r8 (array, filename, path, single_prec)
	real(r8) 2D array implementation of oft_io::hdf5_write
subroutine	hdf5_write_rst (rst_info, filename, path)
	FE vector implementation of oft_io::hdf5_write.
subroutine	hdf5_write_scalar_i4 (val, filename, path)
	integer(i4) scalar implementation of oft_io::hdf5_write
subroutine	hdf5_write_scalar_r8 (val, filename, path, single_prec)
	real(r8) scalar implementation of oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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 oft_io::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.