Read and write mesh::Mesh, fem::Function and other objects in XDMF. More...

#include <XDMFFile.h>

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

Public Member Functions
	XDMFFile (MPI_Comm comm, const std::filesystem::path &filename, std::string file_mode, Encoding encoding=default_encoding)
	Constructor.

	~XDMFFile ()
	Destructor.

void	close ()
	Close the file.

void	write_mesh (const mesh::Mesh &mesh, std::string xpath="/Xdmf/Domain")
	Save Mesh.

void	write_geometry (const mesh::Geometry &geometry, std::string name, std::string xpath="/Xdmf/Domain")
	Save Geometry.

mesh::Mesh	read_mesh (const fem::CoordinateElement &element, mesh::GhostMode mode, std::string name, std::string xpath="/Xdmf/Domain") const
	Read in Mesh.

std::pair< std::vector< std::int64_t >, std::array< std::size_t, 2 > >	read_topology_data (std::string name, std::string xpath="/Xdmf/Domain") const
	Read Topology data for Mesh.

std::pair< std::vector< double >, std::array< std::size_t, 2 > >	read_geometry_data (std::string name, std::string xpath="/Xdmf/Domain") const
	Read Geometry data for Mesh.

std::pair< mesh::CellType, int >	read_cell_type (std::string grid_name, std::string xpath="/Xdmf/Domain")
	Read information about cell type.

void	write_function (const fem::Function< double > &u, double t, std::string mesh_xpath="/Xdmf/Domain/Grid[@GridType='Uniform'][1]")
	Write Function.

void	write_function (const fem::Function< std::complex< double > > &u, double t, std::string mesh_xpath="/Xdmf/Domain/Grid[@GridType='Uniform'][1]")
	Write Function.

void	write_meshtags (const mesh::MeshTags< std::int32_t > &meshtags, std::string geometry_xpath, std::string xpath="/Xdmf/Domain")
	Write MeshTags.

mesh::MeshTags< std::int32_t >	read_meshtags (std::shared_ptr< const mesh::Mesh > mesh, std::string name, std::string xpath="/Xdmf/Domain")
	Read MeshTags.

void	write_information (std::string name, std::string value, std::string xpath="/Xdmf/Domain/")
	Write Information.

std::string	read_information (std::string name, std::string xpath="/Xdmf/Domain/")
	Read Information.

MPI_Comm	comm () const
	Get the MPI communicator.

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

Detailed Description

Read and write mesh::Mesh, fem::Function 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 higher order geometries, as their currently only supports 1st and 2nd order geometries.

Member Function Documentation

◆ close()

void close ( )

Close the file.

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

◆ comm()

MPI_Comm comm ( ) const

Get the MPI communicator.

Returns: The MPI communicator for the file object

◆ read_cell_type()

std::pair< mesh::CellType, int > read_cell_type	(	std::string	grid_name,
		std::string	xpath = `"/Xdmf/Domain"`
	)

Read information about cell type.

Parameters

[in]	grid_name	Name of Grid for which cell type is needed
[in]	xpath	XPath where Grid is stored

◆ read_geometry_data()

std::pair< std::vector< double >, std::array< std::size_t, 2 > > read_geometry_data	(	std::string	name,
		std::string	xpath = `"/Xdmf/Domain"`
	)		const

Read Geometry data for Mesh.

Parameters

[in]	name	Name of the mesh (Grid)
[in]	xpath	XPath where Mesh Grid data is located

Returns: points on each process

◆ read_information()

std::string read_information	(	std::string	name,
		std::string	xpath = `"/Xdmf/Domain/"`
	)

Read Information.

Parameters

[in]	name
[in]	xpath	XPath where Information is stored in file

◆ read_mesh()

mesh::Mesh read_mesh	(	const fem::CoordinateElement &	element,
		mesh::GhostMode	mode,
		std::string	name,
		std::string	xpath = `"/Xdmf/Domain"`
	)		const

Read in Mesh.

Parameters

[in]	element	Element that describes the geometry of a cell
[in]	mode	The type of ghosting/halo to use for the mesh when distributed in parallel
[in]	name
[in]	xpath	XPath where Mesh Grid is located

Returns: A Mesh distributed on the same communicator as the XDMFFile

◆ read_meshtags()

mesh::MeshTags< std::int32_t > read_meshtags	(	std::shared_ptr< const mesh::Mesh >	mesh,
		std::string	name,
		std::string	xpath = `"/Xdmf/Domain"`
	)

Read MeshTags.

Parameters

[in]	mesh	The Mesh that the data is defined on
[in]	name
[in]	xpath	XPath where MeshTags Grid is stored in file

◆ read_topology_data()

std::pair< std::vector< std::int64_t >, std::array< std::size_t, 2 > > read_topology_data	(	std::string	name,
		std::string	xpath = `"/Xdmf/Domain"`
	)		const

Read Topology data for Mesh.

Parameters

[in]	name	Name of the mesh (Grid)
[in]	xpath	XPath where Mesh Grid data is located

Returns: (Cell type, degree), and cells topology (global node indexing)

◆ write_function() [1/2]

void write_function	(	const fem::Function< double > &	u,
		double	t,
		std::string	mesh_xpath = `"/Xdmf/Domain/Grid[@GridType='Uniform'][1]"`
	)

Write Function.

Parameters

[in]	u	The Function to write to file
[in]	t	The time stamp to associate with the Function
[in]	mesh_xpath	XPath for a Grid under which Function will be inserted

◆ write_function() [2/2]

void write_function	(	const fem::Function< std::complex< double > > &	u,
		double	t,
		std::string	mesh_xpath = `"/Xdmf/Domain/Grid[@GridType='Uniform'][1]"`
	)

Write Function.

Parameters

[in]	u	The Function to write to file
[in]	t	The time stamp to associate with the Function
[in]	mesh_xpath	XPath for a Grid under which Function will be inserted

◆ write_geometry()

void write_geometry	(	const mesh::Geometry &	geometry,
		std::string	name,
		std::string	xpath = `"/Xdmf/Domain"`
	)

Save Geometry.

Parameters

[in]	geometry
[in]	name
[in]	xpath	XPath of a node where Geometry will be inserted

◆ write_information()

void write_information	(	std::string	name,
		std::string	value,
		std::string	xpath = `"/Xdmf/Domain/"`
	)

Write Information.

Parameters

[in]	name
[in]	value	String to store into Information tag
[in]	xpath	XPath where Information will be inserted

◆ write_mesh()

void write_mesh	(	const mesh::Mesh &	mesh,
		std::string	xpath = `"/Xdmf/Domain"`
	)

Save Mesh.

Parameters

[in]	mesh
[in]	xpath	XPath where Mesh Grid will be written

◆ write_meshtags()

void write_meshtags	(	const mesh::MeshTags< std::int32_t > &	meshtags,
		std::string	geometry_xpath,
		std::string	xpath = `"/Xdmf/Domain"`
	)

Write MeshTags.

Parameters

[in]	meshtags
[in]	geometry_xpath	XPath where Geometry is already stored in file
[in]	xpath	XPath where MeshTags Grid will be inserted

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

/build/reproducible-path/fenics-dolfinx-0.6.0/cpp/dolfinx/io/XDMFFile.h
/build/reproducible-path/fenics-dolfinx-0.6.0/cpp/dolfinx/io/XDMFFile.cpp

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

Member Function Documentation

◆ close()

◆ comm()

◆ read_cell_type()

◆ read_geometry_data()

◆ read_information()

◆ read_mesh()

◆ read_meshtags()

◆ read_topology_data()

◆ write_function() [1/2]

◆ write_function() [2/2]

◆ write_geometry()

◆ write_information()

◆ write_mesh()

◆ write_meshtags()