XDMFFile Class Reference

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

#include <XDMFFile.h>

Public Types
enum class	Encoding : std::int8_t { HDF5 , ASCII }
	File encoding type.

Public Member Functions
	XDMFFile (MPI_Comm comm, const std::filesystem::path &filename, const std::string &file_mode, Encoding encoding=Encoding::HDF5)
	Constructor.
	XDMFFile (XDMFFile &&)=default
	Move constructor.
	~XDMFFile ()
	Destructor.
void	close ()
template<std::floating_point U>
void	write_mesh (const mesh::Mesh< U > &mesh, const std::string &xpath="/Xdmf/Domain")
void	write_geometry (const mesh::Geometry< double > &geometry, const std::string &name, const std::string &xpath="/Xdmf/Domain")
mesh::Mesh< double >	read_mesh (const fem::CoordinateElement< double > &element, mesh::GhostMode mode, const std::string &name, const std::string &xpath="/Xdmf/Domain") const
std::pair< std::vector< std::int64_t >, std::array< std::size_t, 2 > >	read_topology_data (const std::string &name, const std::string &xpath="/Xdmf/Domain") const
std::pair< std::variant< std::vector< float >, std::vector< double > >, std::array< std::size_t, 2 > >	read_geometry_data (const std::string &name, const std::string &xpath="/Xdmf/Domain") const
std::pair< mesh::CellType, int >	read_cell_type (const std::string &grid_name, const std::string &xpath="/Xdmf/Domain")
template<dolfinx::scalar T, std::floating_point U = scalar_value_t<T>>
void	write_function (const fem::Function< T, U > &u, double t, std::string mesh_xpath="/Xdmf/Domain/Grid[@GridType='Uniform'][1]")
	Write a fem::Function to file.
template<std::floating_point T>
void	write_meshtags (const mesh::MeshTags< std::int32_t > &meshtags, const mesh::Geometry< T > &x, const std::string &geometry_xpath, const std::string &xpath="/Xdmf/Domain")
mesh::MeshTags< std::int32_t >	read_meshtags (const mesh::Mesh< double > &mesh, const std::string &name, std::optional< std::string > attribute_name, const std::string &xpath="/Xdmf/Domain")
void	write_information (const std::string &name, const std::string &value, const std::string &xpath="/Xdmf/Domain/")
std::string	read_information (const std::string &name, const std::string &xpath="/Xdmf/Domain/")
MPI_Comm	comm () const

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; it 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	(	const std::string &	grid_name,
		const 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::variant< std::vector< float >, std::vector< double > >, std::array< std::size_t, 2 > > read_geometry_data	(	const std::string &	name,
		const 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	(	const std::string &	name,
		const std::string &	xpath = "/Xdmf/Domain/" )

Read Information

Parameters

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

read_mesh()

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

Read 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	(	const mesh::Mesh< double > &	mesh,
		const std::string &	name,
		std::optional< std::string >	attribute_name,
		const std::string &	xpath = "/Xdmf/Domain" )

Read MeshTags

Parameters

[in]	mesh	Mesh that the input data is defined on
[in]	name	Name of the grid node in the xml-scheme of the XDMF-file. E.g. "Material" in Grid Name="Material" GridType="Uniform"
[in]	attribute_name	Name of the attribute to read
[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	(	const std::string &	name,
		const 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()

template<dolfinx::scalar T, std::floating_point U>

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

Write a fem::Function to file.

Precondition

The fem::Function u must be (i) a lowest-order (P0) discontinuous Lagrange element or (ii) a continuous Lagrange element where the element 'nodes' are the same as the nodes of its mesh::Mesh. Otherwise an exception is raised.

Note

User interpolation to a suitable Lagrange space may be required to satisfy the precondition on u. The VTX output (io::VTXWriter) format is recommended over XDMF for discontinuous and/or high-order spaces.

Parameters

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

write_geometry()

void write_geometry	(	const mesh::Geometry< double > &	geometry,
		const std::string &	name,
		const 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	(	const std::string &	name,
		const std::string &	value,
		const 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()

template<std::floating_point U>

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

Save Mesh

Parameters

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

write_meshtags()

template<std::floating_point T>

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

Write MeshTags

Parameters

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

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

• /__w/dolfinx/dolfinx/cpp/dolfinx/io/XDMFFile.h
• /__w/dolfinx/dolfinx/cpp/dolfinx/io/XDMFFile.cpp