Inheritance diagram for dolfin::HDF5File:

Collaboration diagram for dolfin::HDF5File:

Public Member Functions
	HDF5File (MPI_Comm comm, const std::string filename, const std::string file_mode)

	~HDF5File ()
	Destructor.

void	close ()
	Close file.

void	flush ()
	Flush buffered I/O to disk.

void	write (const std::vector< Point > &points, const std::string name)
	Write points to file.

void	write (const std::vector< double > &values, const std::string name)
	Write simple vector of double to file.

void	write (const GenericVector &x, const std::string name)
	Write Vector to file in a format suitable for re-reading.

void	read (GenericVector &x, const std::string dataset_name, const bool use_partition_from_file) const

void	write (const Mesh &mesh, const std::string name)
	Write Mesh to file in a format suitable for re-reading.

void	write (const Mesh &mesh, const std::size_t cell_dim, const std::string name)

void	write (const Function &u, const std::string name)
	Write Function to file in a format suitable for re-reading.

void	write (const Function &u, const std::string name, double timestamp)
	Write Function to file with a timestamp.

void	read (Function &u, const std::string name)

void	read (Mesh &mesh, const std::string data_path, bool use_partition_from_file) const

void	read (Mesh &input_mesh, const std::string topology_path, const std::string geometry_path, const int gdim, const CellType &cell_type, const std::int64_t expected_num_global_cells, const std::int64_t expected_num_global_points, bool use_partition_from_file) const

void	write (const MeshFunction< std::size_t > &meshfunction, const std::string name)
	Write MeshFunction to file in a format suitable for re-reading.

void	write (const MeshFunction< int > &meshfunction, const std::string name)
	Write MeshFunction to file in a format suitable for re-reading.

void	write (const MeshFunction< double > &meshfunction, const std::string name)
	Write MeshFunction to file in a format suitable for re-reading.

void	write (const MeshFunction< bool > &meshfunction, const std::string name)
	Write MeshFunction to file in a format suitable for re-reading.

void	read (MeshFunction< std::size_t > &meshfunction, const std::string name) const
	Read MeshFunction from file.

void	read (MeshFunction< int > &meshfunction, const std::string name) const
	Read MeshFunction from file.

void	read (MeshFunction< double > &meshfunction, const std::string name) const
	Read MeshFunction from file.

void	read (MeshFunction< bool > &meshfunction, const std::string name) const
	Read MeshFunction from file.

void	write (const MeshValueCollection< std::size_t > &mesh_values, const std::string name)
	Write MeshValueCollection to file.

void	write (const MeshValueCollection< double > &mesh_values, const std::string name)
	Write MeshValueCollection to file.

void	write (const MeshValueCollection< bool > &mesh_values, const std::string name)
	Write MeshValueCollection to file.

void	read (MeshValueCollection< std::size_t > &mesh_values, const std::string name) const
	Read MeshValueCollection from file.

void	read (MeshValueCollection< double > &mesh_values, const std::string name) const
	Read MeshValueCollection from file.

void	read (MeshValueCollection< bool > &mesh_values, const std::string name) const
	Read MeshValueCollection from file.

bool	has_dataset (const std::string dataset_name) const
	Check if dataset exists in HDF5 file.

HDF5Attribute	attributes (const std::string dataset_name)

void	set_mpi_atomicity (bool atomic)
	Set the MPI atomicity.

bool	get_mpi_atomicity () const
	Get the MPI atomicity.

hid_t	h5_id () const

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)

Friends
class	XDMFFile

class	TimeSeries

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

Constructor & Destructor Documentation

◆ HDF5File()

HDF5File::HDF5File	(	MPI_Comm	comm,
		const std::string	filename,
		const std::string	file_mode
	)

Constructor. file_mode should be "a" (append), "w" (write) or "r" (read).

Member Function Documentation

◆ read() [1/4]

void HDF5File::read	(	GenericVector &	x,
		const std::string	dataset_name,
		const bool	use_partition_from_file
	)		const

Read vector from file and optionally re-use any partitioning that is available in the file

◆ read() [2/4]

void HDF5File::read	(	Function &	u,
		const std::string	name
	)

Read Function from file and distribute data according to the Mesh and dofmap associated with the Function. If the 'name' refers to a HDF5 group, then it is assumed that the Function data is stored in the datasets within that group. If the 'name' refers to a HDF5 dataset within a group, then it is assumed that it is a Vector, and the Function will be filled from that Vector

◆ read() [3/4]

void HDF5File::read	(	Mesh &	mesh,
		const std::string	data_path,
		bool	use_partition_from_file
	)		const

Read Mesh from file, using attribute data (e.g., cell type) stored in the HDF5 file. Optionally re-use any partition data in the file. This function requires all necessary data for constructing a Mesh to be present in the HDF5 file.

◆ read() [4/4]

void HDF5File::read	(	Mesh &	input_mesh,
		const std::string	topology_path,
		const std::string	geometry_path,
		const int	gdim,
		const CellType &	cell_type,
		const std::int64_t	expected_num_global_cells,
		const std::int64_t	expected_num_global_points,
		bool	use_partition_from_file
	)		const

Construct Mesh with paths to topology and geometry datasets, and providing essential meta-data, e.g. geometric dimension and cell type. If this data is available in the HDF5 file, it will be checked for consistency. Set expected_num_global_cells to a negative value if not known.

This function is typically called when using the XDMF format, in which case the meta data has already been read from an XML file

◆ write()

void HDF5File::write	(	const Mesh &	mesh,
		const std::size_t	cell_dim,
		const std::string	name
	)

Write Mesh of given cell dimension to file in a format suitable for re-reading

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

/home/fenics/shared/dolfin/dolfin/io/HDF5File.h
/home/fenics/shared/dolfin/dolfin/io/HDF5File.cpp

Public Member Functions

Friends

Additional Inherited Members