Read and write Mesh, Function, MeshFunction and other objects in XDMF. More...

#include <XDMFFile.h>

Inheritance diagram for dolfin::XDMFFile:

Collaboration diagram for dolfin::XDMFFile:

Public Types
enum	Encoding { HDF5, ASCII }
	File encoding type.

Public Member Functions
	XDMFFile (const std::string filename)
	Constructor.

	XDMFFile (MPI_Comm comm, const std::string filename)
	Constructor.

	~XDMFFile ()
	Destructor.

void	close ()

void	write (const Mesh &mesh, Encoding encoding=default_encoding)

void	write_checkpoint (const Function &u, std::string function_name, double time_step=0.0, Encoding encoding=default_encoding, bool append=false)

void	write (const Function &u, Encoding encoding=default_encoding)

void	write (const Function &u, double t, Encoding encoding=default_encoding)

void	write (const MeshFunction< bool > &meshfunction, Encoding encoding=default_encoding)

void	write (const MeshFunction< int > &meshfunction, Encoding encoding=default_encoding)

void	write (const MeshFunction< std::size_t > &meshfunction, Encoding encoding=default_encoding)

void	write (const MeshFunction< double > &meshfunction, Encoding encoding=default_encoding)

void	write (const MeshValueCollection< bool > &mvc, Encoding encoding=default_encoding)

void	write (const MeshValueCollection< int > &mvc, Encoding encoding=default_encoding)

void	write (const MeshValueCollection< std::size_t > &mvc, Encoding encoding=default_encoding)

void	write (const MeshValueCollection< double > &mvc, Encoding encoding=default_encoding)

void	write (const std::vector< Point > &points, Encoding encoding=default_encoding)

void	write (const std::vector< Point > &points, const std::vector< double > &values, Encoding encoding=default_encoding)

void	read (Mesh &mesh) const

void	read_checkpoint (Function &u, std::string func_name, std::int64_t counter=-1)

void	read (MeshFunction< bool > &meshfunction, std::string name="")

void	read (MeshFunction< int > &meshfunction, std::string name="")

void	read (MeshFunction< std::size_t > &meshfunction, std::string name="")

void	read (MeshFunction< double > &meshfunction, std::string name="")

void	read (MeshValueCollection< bool > &mvc, std::string name="")

void	read (MeshValueCollection< int > &mvc, std::string name="")

void	read (MeshValueCollection< std::size_t > &mvc, std::string name="")

void	read (MeshValueCollection< double > &mvc, std::string name="")

template<>
void	add_data_item (MPI_Comm comm, pugi::xml_node &xml_node, hid_t h5_id, const std::string h5_path, const std::vector< bool > &x, const std::vector< std::int64_t > shape, const std::string number_type)

Public Member Functions inherited from dolfin::Variable
	Variable ()
	Create unnamed variable.

	Variable (const std::string name, const std::string label)
	Create variable with given name and label.

	Variable (const Variable &variable)
	Copy constructor.

virtual	~Variable ()
	Destructor.

const Variable &	operator= (const Variable &variable)
	Assignment operator.

void	rename (const std::string name, const std::string label)
	Rename variable.

std::string	name () const
	Return name.

std::string	label () const
	Return label (description)

std::size_t	id () const

virtual std::string	str (bool verbose) const
	Return informal string representation (pretty-print)

Static Public Attributes
static const Encoding	default_encoding = Encoding::HDF5
	Default encoding type.

Additional Inherited Members
Public Attributes inherited from dolfin::Variable
Parameters	parameters
	Parameters.

Detailed Description

Read and write Mesh, Function, MeshFunction and other objects in XDMF.

This class supports the output of meshes and functions in XDMF (http://www.xdmf.org) format. It creates an XML file that describes the data and points to a HDF5 file that stores the actual problem data. Output of data in parallel is supported.

XDMF is not suitable for checkpointing as it may decimate some data.

Member Function Documentation

◆ close()

void XDMFFile::close ( )

Close the file

This closes any open HDF5 files. In ASCII mode the XML file is closed each time it is written to or read from, so close() has no effect.

From Python you can also use XDMFFile as a context manager:

with XDMFFile(mpi_comm_world(), 'name.xdmf') as xdmf:
    xdmf.write(mesh)

The file is automatically closed at the end of the with block

◆ read() [1/9]

void XDMFFile::read ( Mesh & mesh ) const

Read in the first Mesh in XDMF file

Parameters

mesh	(Mesh) Mesh to fill from XDMF file

◆ read() [2/9]

void XDMFFile::read	(	MeshFunction< bool > &	meshfunction,
		std::string	name = `""`
	)

Read first MeshFunction from file

Parameters

meshfunction	(MeshFunction<bool>) MeshFunction to restore
name	(std::string) Name of data attribute in XDMF file

◆ read() [3/9]

void XDMFFile::read	(	MeshFunction< int > &	meshfunction,
		std::string	name = `""`
	)

Read first MeshFunction from file

Parameters

meshfunction	(MeshFunction<int>) MeshFunction to restore
name	(std::string) Name of data attribute in XDMF file

◆ read() [4/9]

void XDMFFile::read	(	MeshFunction< std::size_t > &	meshfunction,
		std::string	name = `""`
	)

Read MeshFunction from file, optionally specifying dataset name

Parameters

meshfunction	(MeshFunction<std::size_t>) MeshFunction to restore
name	(std::string) Name of data attribute in XDMF file

◆ read() [5/9]

void XDMFFile::read	(	MeshFunction< double > &	meshfunction,
		std::string	name = `""`
	)

Read MeshFunction from file, optionally specifying dataset name

Parameters

meshfunction	(MeshFunction<double>) MeshFunction to restore
name	(std::string) Name of data attribute in XDMF file

◆ read() [6/9]

void XDMFFile::read	(	MeshValueCollection< bool > &	mvc,
		std::string	name = `""`
	)

Read MeshValueCollection from file, optionally specifying dataset name

Parameters

mvc	(MeshValueCollection<bool>) MeshValueCollection to restore
name	(std::string) Name of data attribute in XDMF file

◆ read() [7/9]

void XDMFFile::read	(	MeshValueCollection< int > &	mvc,
		std::string	name = `""`
	)

Read MeshValueCollection from file, optionally specifying dataset name

Parameters

mvc	(MeshValueCollection<int>) MeshValueCollection to restore
name	(std::string) Name of data attribute in XDMF file

◆ read() [8/9]

void XDMFFile::read	(	MeshValueCollection< std::size_t > &	mvc,
		std::string	name = `""`
	)

Read MeshValueCollection from file, optionally specifying dataset name

Parameters

mvc	(MeshValueCollection<std::size_t>) MeshValueCollection to restore
name	(std::string) Name of data attribute in XDMF file

◆ read() [9/9]

void XDMFFile::read	(	MeshValueCollection< double > &	mvc,
		std::string	name = `""`
	)

Read MeshValueCollection from file, optionally specifying dataset name

Parameters

mvc	(MeshValueCollection<double>) MeshValueCollection to restore
name	(std::string) Name of data attribute in XDMF file

◆ read_checkpoint()

void XDMFFile::read_checkpoint	(	Function &	u,
		std::string	func_name,
		std::int64_t	counter = `-1`
	)

Read a function from the XDMF file. Supplied function must come with already initialized and compatible function space.

Functions saved as time-series must be addressed through (integer) internal counter and function name. Function name is a name of function that was saved. Counter stands for the number of function from time-series, e.g. counter=0 refers to first saved function regardless of its time-step value.

Parameters

u	(Function) A function to read.
func_name	(string) A name of a function to read. Must be the same on all processes in parallel.
counter	(int64_t) Internal integer counter - used in time-series. Default value is -1 which points to last saved function. Counter works same as python array position key, i.e. counter = -2 points to the function before the last one.

◆ write() [1/13]

void XDMFFile::write	(	const Mesh &	mesh,
		Encoding	encoding = `default_encoding`
	)

Save a mesh to XDMF format, either using an associated HDF5 file, or storing the data inline as XML Create function on given function space

Parameters

mesh	(Mesh) A mesh to save.
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [2/13]

void XDMFFile::write	(	const Function &	u,
		Encoding	encoding = `default_encoding`
	)

Save a Function to XDMF file for visualisation, using an associated HDF5 file, or storing the data inline as XML.

Parameters

u	(Function) A function to save.
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [3/13]

void XDMFFile::write	(	const Function &	u,
		double	t,
		Encoding	encoding = `default_encoding`
	)

Save a Function with timestamp to XDMF file for visualisation, using an associated HDF5 file, or storing the data inline as XML.

You can control the output with the following boolean parameters on the XDMFFile class:

rewrite_function_mesh (default true): Controls whether the mesh will be rewritten every timestep. If the mesh does not change this can be turned off to create smaller files.
functions_share_mesh (default false): Controls whether all functions on a single time step share the same mesh. If true the files created will be smaller and also behave better in Paraview, at least in version 5.3.0

Parameters

u	(Function) A function to save.
t	(double) Timestep
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [4/13]

void XDMFFile::write	(	const MeshFunction< bool > &	meshfunction,
		Encoding	encoding = `default_encoding`
	)

Save MeshFunction to file using an associated HDF5 file, or storing the data inline as XML.

Parameters

meshfunction	(MeshFunction) A meshfunction to save.
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [5/13]

void XDMFFile::write	(	const MeshFunction< int > &	meshfunction,
		Encoding	encoding = `default_encoding`
	)

Save MeshFunction to file using an associated HDF5 file, or storing the data inline as XML.

Parameters

meshfunction	(MeshFunction) A meshfunction to save.
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [6/13]

void XDMFFile::write	(	const MeshFunction< std::size_t > &	meshfunction,
		Encoding	encoding = `default_encoding`
	)

Save MeshFunction to file using an associated HDF5 file, or storing the data inline as XML.

Parameters

meshfunction	(MeshFunction) A meshfunction to save.
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [7/13]

void XDMFFile::write	(	const MeshFunction< double > &	meshfunction,
		Encoding	encoding = `default_encoding`
	)

Save MeshFunction to file using an associated HDF5 file, or storing the data inline as XML.

Parameters

meshfunction	(MeshFunction) A meshfunction to save.
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [8/13]

void XDMFFile::write	(	const MeshValueCollection< bool > &	mvc,
		Encoding	encoding = `default_encoding`
	)

Write out mesh value collection (subset) using an associated HDF5 file, or storing the data inline as XML.

Parameters

mvc	(MeshValueCollection<bool>) MeshValueCollection to save
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [9/13]

void XDMFFile::write	(	const MeshValueCollection< int > &	mvc,
		Encoding	encoding = `default_encoding`
	)

Write out mesh value collection (subset) using an associated HDF5 file, or storing the data inline as XML.

Parameters

mvc	(MeshValueCollection<int>) MeshValueCollection to save
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [10/13]

void XDMFFile::write	(	const MeshValueCollection< std::size_t > &	mvc,
		Encoding	encoding = `default_encoding`
	)

Write out mesh value collection (subset) using an associated HDF5 file, or storing the data inline as XML.

Parameters

mvc	(MeshValueCollection<int>) MeshValueCollection to save
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [11/13]

void XDMFFile::write	(	const MeshValueCollection< double > &	mvc,
		Encoding	encoding = `default_encoding`
	)

Write out mesh value collection (subset) using an associated HDF5 file, or storing the data inline as XML.

Parameters

mvc	(MeshValueCollection<double>) MeshValueCollection to save
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [12/13]

void XDMFFile::write	(	const std::vector< Point > &	points,
		Encoding	encoding = `default_encoding`
	)

Save a cloud of points to file using an associated HDF5 file, or storing the data inline as XML.

Parameters

points	(std::vector<Point>) A list of points to save.
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write() [13/13]

void XDMFFile::write	(	const std::vector< Point > &	points,
		const std::vector< double > &	values,
		Encoding	encoding = `default_encoding`
	)

Save a cloud of points, with scalar values using an associated HDF5 file, or storing the data inline as XML.

Parameters

points	(std::vector<Point>) A list of points to save.
values	(std::vector<double>) A list of values at each point.
encoding	(Encoding) Encoding to use: HDF5 or ASCII

◆ write_checkpoint()

void XDMFFile::write_checkpoint	(	const Function &	u,
		std::string	function_name,
		double	time_step = `0.0`,
		Encoding	encoding = `default_encoding`,
		bool	append = `false`
	)

Save a Function to XDMF file for checkpointing, using an associated HDF5 file, or storing the data inline as XML.

If the file where we would like to write exists, then the function is appended to the file.

Parameters

u	(Function) A function to save.
function_name	(string) Name of the function used in XDMF XML and HDF file (if encoding = HDF). The string is used to fill value for XML attribute Name of Grid node. It is also used in HDF file in path to datasets. Must be the same on all processes in parallel.
time_step	(double) Time step. It is saved only in XDMF file. The function could be saved with the same time step several times. There is an internal "counter" value stored in XDMF which differentiates the same time steps.
encoding	(Encoding) Encoding to use: HDF5 or ASCII
append	(default false) If set (default) to false, then XDMF and HDF files (if encoding = HDF) are overwritten. If set to true, then both XDMF and HDF (if encoding = HDF) files are appended at end. Set append to true when saving timeseries.

The documentation for this class was generated from the following files:

/home/fenics/shared/dolfin/dolfin/io/XDMFFile.h
/home/fenics/shared/dolfin/dolfin/io/XDMFFile.cpp

Public Types

Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ close()

◆ read() [1/9]

◆ read() [2/9]

◆ read() [3/9]

◆ read() [4/9]

◆ read() [5/9]

◆ read() [6/9]

◆ read() [7/9]

◆ read() [8/9]

◆ read() [9/9]

◆ read_checkpoint()

◆ write() [1/13]

◆ write() [2/13]

◆ write() [3/13]

◆ write() [4/13]

◆ write() [5/13]

◆ write() [6/13]

◆ write() [7/13]

◆ write() [8/13]

◆ write() [9/13]

◆ write() [10/13]

◆ write() [11/13]

◆ write() [12/13]

◆ write() [13/13]

◆ write_checkpoint()