HDF5File

class dolfin.cpp.io.HDF5File(comm, filename, file_mode)

Bases: dolfin.cpp.common.Variable

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

attributes()
close()

Close file

flush()

Flush buffered I/O to disk

get_mpi_atomicity()

Get the MPI atomicity

h5_id()
has_dataset()

Check if dataset exists in HDF5 file

read()

Overloaded versions

  • read(x, dataset_name, use_partition_from_file)

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

  • read(u, 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(mesh, data_path, use_partition_from_file)

    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(input_mesh, topology_path, geometry_path, gdim, cell_type, expected_num_global_cells, expected_num_global_points, use_partition_from_file)

    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

  • read(meshfunction, name)

    Read MeshFunction from file

  • read(meshfunction, name)

    Read MeshFunction from file

  • read(meshfunction, name)

    Read MeshFunction from file

  • read(meshfunction, name)

    Read MeshFunction from file

  • read(mesh_values, name)

    Read MeshValueCollection from file

  • read(mesh_values, name)

    Read MeshValueCollection from file

  • read(mesh_values, name)

    Read MeshValueCollection from file

set_mpi_atomicity()

Set the MPI atomicity

thisown

The membership flag

write()

Overloaded versions

  • write(points, name)

    Write points to file

  • write(values, name)

    Write simple vector of double to file

  • write(x, name)

    Write Vector to file in a format suitable for re-reading

  • write(mesh, name)

    Write Mesh to file in a format suitable for re-reading

  • write(mesh, cell_dim, name)

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

  • write(u, name)

    Write Function to file in a format suitable for re-reading

  • write(u, name, timestamp)

    Write Function to file with a timestamp

  • write(meshfunction, name)

    Write MeshFunction to file in a format suitable for re-reading

  • write(meshfunction, name)

    Write MeshFunction to file in a format suitable for re-reading

  • write(meshfunction, name)

    Write MeshFunction to file in a format suitable for re-reading

  • write(meshfunction, name)

    Write MeshFunction to file in a format suitable for re-reading

  • write(mesh_values, name)

    Write MeshValueCollection to file

  • write(mesh_values, name)

    Write MeshValueCollection to file

  • write(mesh_values, name)

    Write MeshValueCollection to file