.. Documentation for the header file dolfin/io/HDF5File.h

.. _programmers_reference_cpp_io_hdf5file:

HDF5File.h
==========

.. note::
    
    The documentation on this page was automatically extracted from the
    DOLFIN C++ code and may need to be edited or expanded.
    

.. cpp:class:: HDF5File

    *Parent class(es)*
    
        * :cpp:class:`Variable`
        
    .. cpp:function:: 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).


    .. cpp:function:: void close()
    
        Close file


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


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


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


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


    .. cpp:function:: void 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


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


    .. cpp:function:: void 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


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


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


    .. cpp:function:: void 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


    .. cpp:function:: void 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.


    .. cpp:function:: 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
    
        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 alreayd been read from an XML
        file


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


    .. cpp:function:: void set_mpi_atomicity(bool atomic)
    
        Set the MPI atomicity


    .. cpp:function:: bool get_mpi_atomicity() const
    
        Get the MPI atomicity