dolfinx.io

Tools for file input/output (IO).

Functions

distribute_entity_data(mesh, entity_dim, ...)

Given a set of mesh entities and values, distribute them to the process that owns the entity.

Classes

VTKFile(self, comm, filename, mode)

Interface to VTK files.

XDMFFile(self, comm, filename, file_mode[, ...])

VTXWriter(comm, filename, output[, engine, ...])

Writer for VTX files, using ADIOS2 to create the files.

VTXMeshPolicy(*values)

class dolfinx.io.VTKFile(self, comm: MPICommWrapper, filename: str | os.PathLike, mode: str)[source]

Bases: VTKFile

Interface to VTK files.

VTK supports arbitrary order Lagrange finite elements for the geometry description. XDMF is the preferred format for geometry order <= 2.

write_function(u: list[Function] | Function, t: float = 0.0) → None[source]

Write a single function or a list of functions to file for a given time (default 0.0)

write_mesh(mesh: Mesh, t: float = 0.0) → None[source]

Write mesh to file for a given time (default 0.0)

class dolfinx.io.VTXMeshPolicy(*values)

Bases: Enum

reuse = 1
update = 0
class dolfinx.io.VTXWriter(comm: Comm, filename: str | Path, output: Mesh | Function | list[Function] | tuple[Function], engine: str = 'BPFile', mesh_policy: VTXMeshPolicy = VTXMeshPolicy.update)[source]

Bases: object

Writer for VTX files, using ADIOS2 to create the files.

VTX supports arbitrary order Lagrange finite elements for the geometry description and arbitrary order (discontinuous) Lagrange finite elements for Functions.

The files can be viewed using Paraview.

Initialize a writer for outputting data in the VTX format.

Parameters:

  • comm – The MPI communicator

  • filename – The output filename

  • output – The data to output. Either a mesh, a single (discontinuous) Lagrange Function or list of (discontinuous) Lagrange Functions.

  • engine – ADIOS2 engine to use for output. See ADIOS2 documentation for options.

  • mesh_policy – Controls if the mesh is written to file at the first time step only when a Function is written to file, or is re-written (updated) at each time step. Has an effect only for Function output.

Note

All Functions for output must share the same mesh and have the same element type.

close()[source]
write(t: float)[source]
class dolfinx.io.XDMFFile(self, comm: MPICommWrapper, filename: str | os.PathLike, file_mode: str, encoding: dolfinx.cpp.io.XDMFFile.Encoding = Encoding.HDF5)[source]

Bases: XDMFFile

read_mesh(ghost_mode=GhostMode.shared_facet, name='mesh', xpath='/Xdmf/Domain') → Mesh[source]

Read mesh data from file.

read_meshtags(mesh: Mesh, name: str, attribute_name: str | None = None, xpath: str = '/Xdmf/Domain') → MeshTags[source]

Read MeshTags with a specific name as specified in the XMDF file.

Parameters:

  • mesh – Mesh that the input data is defined on.

  • name – Name of the grid node in the xml-scheme of the XDMF-file.

  • attribute_name – The name of the attribute to read. If attribute_name is empty, reads the first attribute in the file. If attribute_name is not empty but no attributes have the provided name, throws an error. If multiple attributes have the provided name, reads the first one found.

  • xpath – XPath where MeshTags Grid is stored in file.

Returns:

A MeshTags object containing the requested data read from file.

write_function(u: Function, t: float = 0.0, mesh_xpath="/Xdmf/Domain/Grid[@GridType='Uniform'][1]")[source]

Write function to file for a given time.

Note

Function is interpolated onto the mesh nodes, as a Nth order Lagrange function, where N is the order of the coordinate map. If the Function is a cell-wise constant, it is saved as a cell-wise constant.

Parameters:

  • u – Function to write to file.

  • t – Time associated with Function output.

  • mesh_xpath – Path to mesh associated with the Function in the XDMFFile.

write_mesh(mesh: Mesh, xpath: str = '/Xdmf/Domain') → None[source]

Write mesh to file

write_meshtags(tags: MeshTags, x: Geometry, geometry_xpath: str = '/Xdmf/Domain/Grid/Geometry', xpath: str = '/Xdmf/Domain') → None[source]

Write mesh tags to file

dolfinx.io.distribute_entity_data(mesh: Mesh, entity_dim: int, entities: ndarray[Any, dtype[int64]], values: ndarray) → tuple[ndarray[Any, dtype[int64]], ndarray][source]

Given a set of mesh entities and values, distribute them to the process that owns the entity.

The entities are described by the global vertex indices of the mesh. These entity indices are using the original input ordering.

Returns:

Entities owned by the process (and their local entity-to-vertex indices) and the corresponding values.