porepy.fracs.gmsh_interface module

Functionality to interface with Gmsh, mainly by translating information from a PorePy format to that used by the Gmsh Python API. For examples on how that can be used, see FractureNetwork2d and FractureNetwork3d.

Content:
Tags: Enum with fixed numerical representation of geometric objects. Used for tagging

geometric objects internally in PorePy.

PhysicalNames: Enum with fixed string representation of geometric objects. The

mesh generated by gmsh will use these to tag cells on geometric objcets.

GmshData1d, 2d, 3d: dataclasses for the specification of geometries in the various

dimensions.

GmshWriter: Interface to Gmsh. Takes a GmshData*d object and translates it to a

gmsh model. Can also mesh.

class GmshData1d(pts: 'np.ndarray', mesh_size: 'np.ndarray', lines: 'np.ndarray', physical_points: 'dict[int, Tags]', physical_lines: 'dict[int, Tags]', dim: 'int' = 1)[source]

Bases: _GmshData

Parameters
dim: int
class GmshData2d(pts: 'np.ndarray', mesh_size: 'np.ndarray', lines: 'np.ndarray', physical_points: 'dict[int, Tags]', physical_lines: 'dict[int, Tags]', dim: 'int' = 2)[source]

Bases: _GmshData

Parameters
dim: int
class GmshData3d(pts: 'np.ndarray', mesh_size: 'np.ndarray', lines: 'np.ndarray', physical_points: 'dict[int, Tags]', physical_lines: 'dict[int, Tags]', polygons: 'list[np.ndarray]', polygon_tags: 'dict[int, Tags]', physical_surfaces: 'dict[int, Tags]', lines_in_surface: 'list[list[int]]', dim: 'int' = 3)[source]

Bases: _GmshData

Parameters
dim: int
lines_in_surface: list[list[int]]
physical_surfaces: dict[int, porepy.fracs.gmsh_interface.Tags]
polygon_tags: dict[int, porepy.fracs.gmsh_interface.Tags]
polygons: list[numpy.ndarray]
class GmshWriter(data)[source]

Bases: object

Interface to Gmsh’s python API.

The geometry specification (in the form of a GmshData object) is converted to a model (in the Gmsh sense) upon initiation of a GmshWriter. A mesh can then be constructed either by the method generate, or by directly working with the gmsh api in a client script.

Parameters

data (Union[GmshData2d, GmshData3d]) –

define_geometry()[source]

Feed the geometry specified in self._data to gmsh.

Return type

None

generate(file_name, ndim=-1, write_geo=False, clear_gmsh=True, finalize=True)[source]

Make gmsh generate a mesh and write it to specified mesh size.

The mesh is generated from the geometry specified in gmsh.model.

NOTE: We have experienced issues relating to memory leakages in gmsh which manifest when gmsh is initialized and finalized several times in a session. In these situation, best practice seems to be not to finalize gmsh after mesh generation (set finalize=False, but rather clear the gmsh model by setting clear_gmsh=True), and finalize gmsh from the outside.

Parameters

  • file_name (str) – Name of the file. The suffix ‘.msh’ is added if necessary.

  • ndim (int, optional) – Dimension of the grid to be made. If not specified, the dimension of the data used to initialize this GmshWriter will be used.

  • write_geo (bool, optional) – If True, the geometry will be written before meshing. The name of the file will be file_name.geo_unrolled. Defaults to False.

  • clear_gmsh (bool, optional) – If True, the function gmsh.clear() is called after mesh generation. This will delete the geometry from gmsh.

  • finalize (bool, optional) – If True (default), the finalize method of the gmsh module is called after mesh generation. If set to False, gmsh should be finalized by a direct call to gmsh.finalize(); note however that if this is done, Gmsh cannot be accessed either from the outside or by an instance of the GmshWriter class before gmsh.initialize() is called.

Return type

None

set_gmsh_options(options=None)[source]

Set Gmsh options. See Gmsh documentation for choices available.

Parameters

options (dict) – Options to set. Keys should be recognizable for Gmsh.

Return type

None

gmsh_initialized
class PhysicalNames(value)[source]

Bases: Enum

String-based tags used to assign physical names (Gmsh jargon) to classes of objects in a mixed-dimensional geometry.

AUXILIARY_LINE
AUXILIARY_PLANE
DOMAIN
DOMAIN_BOUNDARY_LINE
DOMAIN_BOUNDARY_POINT
DOMAIN_BOUNDARY_SURFACE
FRACTURE
FRACTURE_BOUNDARY_LINE
FRACTURE_BOUNDARY_POINT
FRACTURE_CONSTRAINT_INTERSECTION_POINT
FRACTURE_INTERSECTION_LINE
FRACTURE_INTERSECTION_POINT
FRACTURE_TIP
class Tags(value)[source]

Bases: Enum

Numerical tags used to identify special objects in a mixed-dimensional geometry. These may be mapped to the string-based tag system used in Gmsh (see PhysicalNames)

AUXILIARY_LINE
AUXILIARY_PLANE
DOMAIN_BOUNDARY_LINE
DOMAIN_BOUNDARY_POINT
DOMAIN_BOUNDARY_SURFACE
FRACTURE
FRACTURE_BOUNDARY_LINE
FRACTURE_BOUNDARY_POINT
FRACTURE_CONSTRAINT_INTERSECTION_POINT
FRACTURE_INTERSECTION_LINE
FRACTURE_INTERSECTION_POINT
FRACTURE_TIP
NEUTRAL