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	(	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

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

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

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.

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

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

Public Member Functions

Friends

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation