sfepy.discrete.fem.meshio module¶
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class
sfepy.discrete.fem.meshio.
HDF5MeshIO
(filename, **kwargs)[source]¶ -
format
= 'hdf5'¶
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static
read_mesh_from_hdf5
(filename, group=None, mesh=None)[source]¶ Read the mesh from a HDF5 file.
- filename: str or tables.File
- The HDF5 file to read the mesh from.
- group: tables.group.Group or str, optional
- The HDF5 file group to read the mesh from. If None, the root group is used.
- mesh: sfepy.dicrete.fem.Mesh or None
- If None, the new mesh is created and returned, otherwise content of this argument is replaced by the read mesh.
Returns: sfepy.dicrete.fem.Mesh
readed mesh
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read_times
(filename=None)[source]¶ Read true time step data from individual time steps.
Returns: steps : array
The time steps.
times : array
The times of the time steps.
nts : array
The normalized times of the time steps, in [0, 1].
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string
= <module 'string' from '/usr/lib/python3.7/string.py'>¶
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static
write_mesh_to_hdf5
(filename, group, mesh)[source]¶ Write mesh to a hdf5 file.
- filename: str or tables.File
- The HDF5 file to write the mesh to.
- group: tables.group.Group or None or str
- The HDF5 file group to write the mesh to. If None, the root group is used. The group can be given as a path from root, e.g. /path/to/mesh
- mesh: sfepy.dicrete.fem.Mesh
- The mesh to write.
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class
sfepy.discrete.fem.meshio.
HypermeshAsciiMeshIO
(filename, **kwargs)[source]¶ -
format
= 'hmascii'¶
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class
sfepy.discrete.fem.meshio.
MeshIO
(filename, **kwargs)[source]¶ The abstract class for importing and exporting meshes.
Read the docstring of the Mesh() class. Basically all you need to do is to implement the read() method:
def read(self, mesh, **kwargs): nodes = ... ngroups = ... conns = ... mat_ids = ... descs = ... mesh._set_io_data(nodes, ngroups, conns, mat_ids, descs) return mesh
See the Mesh class’ docstring how the nodes, ngroups, conns, mat_ids and descs should look like. You just need to read them from your specific format from disk.
To write a mesh to disk, just implement the write() method and use the information from the mesh instance (e.g. nodes, conns, mat_ids and descs) to construct your specific format.
The methods read_dimension(), read_bounding_box() should be implemented in subclasses, as it is often possible to get that kind of information without reading the whole mesh file.
Optionally, subclasses can implement read_data() to read also computation results. This concerns mainly the subclasses with implemented write() supporting the ‘out’ kwarg.
The default implementation od read_last_step() just returns 0. It should be reimplemented in subclasses capable of storing several steps.
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static
any_from_filename
(filename, prefix_dir=None)¶ Create a MeshIO instance according to the kind of filename.
Parameters: filename : str, function or MeshIO subclass instance
The name of the mesh file. It can be also a user-supplied function accepting two arguments: mesh, mode, where mesh is a Mesh instance and mode is one of ‘read’,’write’, or a MeshIO subclass instance.
prefix_dir : str
The directory name to prepend to filename.
Returns: io : MeshIO subclass instance
The MeshIO subclass instance corresponding to the kind of filename.
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call_msg
= 'called an abstract MeshIO instance!'¶
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static
for_format
(filename, format=None, writable=False, prefix_dir=None)¶ Create a MeshIO instance for file filename with forced format.
Parameters: filename : str
The name of the mesh file.
format : str
One of supported formats. If None,
MeshIO.any_from_filename()
is called instead.writable : bool
If True, verify that the mesh format is writable.
prefix_dir : str
The directory name to prepend to filename.
Returns: io : MeshIO subclass instance
The MeshIO subclass instance corresponding to the format.
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format
= None¶
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static
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class
sfepy.discrete.fem.meshio.
Msh2MeshIO
(filename, **kwargs)[source]¶ Used to read and write data from .msh format used by GMSH, format 2.0 is currently partially supported allowing: mesh and ElementNodeData with InterpolationScheme to be written and read.
For details on format see [1].
For details on representing and visualization of DG FEM data using gmsh see [2].
[1] http://gmsh.info/doc/texinfo/gmsh.html#File-formats
[2] Remacle, J.-F., Chevaugeon, N., Marchandise, E., & Geuzaine, C. (2007). Efficient visualization of high-order finite elements. International Journal for Numerical Methods in Engineering, 69(4), 750-771. https://doi.org/10.1002/nme.1787
Attributes
msh20header : Header containing version number. msh_cells (dictionary) Mapping from msh to sfepy geometry. geo2msh_type (dictionary) Mapping from sfepy to msh geometry. -
format
= 'msh_v2'¶
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geo2msh_type
= {'1_2': 1, '2_3': 2, '2_4': 3, '3_4': 4, '3_8': 5}¶
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load_slices
= {'all': slice(0, None, None), 'first': slice(0, 1, None), 'last': slice(-1, None, None)}¶
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msh20header
= ['$MeshFormat\n', '2.0 0 8\n$EndMeshFormat\n']¶
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msh_cells
= {1: (2, 2), 2: (2, 3), 3: (2, 4), 4: (3, 4), 5: (3, 8), 6: (3, 6)}¶
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prism2hexa
= array([0, 1, 2, 2, 3, 4, 5, 5])¶
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read
(mesh, omit_facets=True, filename=None, drop_z=False, **kwargs)[source]¶ Reads mesh from msh v2.0 file returns it and also fills mesh parameter.
Parameters: mesh : Mesh instance
Empty sfepy.discrete.fem.mesh.Mesh instance to fill.
omit_facets : bool
Not used.
filename : string, optional
Name of the file to use if None file from object is used.
drop_z : bool, optional, default False
Drop Z coordinate if zero and return 2D mesh, 2D meshes are stored as 3D by msh.
Returns: mesh : Mesh instance
Computational mesh.
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read_data
(step=None, filename=None, cache=None, return_mesh=False, drop_z=True)[source]¶ Reads file or files with basename filename or self.filename, returns lists containing data. Considers all files to contain data from time steps of solution of single transient problem i.e. all data have the same shape, mesh and same interpolation scheme, if any. For stationary problems just reads one file with time 0.0 and time step 0.
Providing basename allows reading multiple files of format basename.*[0-9].msh
Parameters: step : String, int, optional
“all”, “last”, “first” or number of step to read: if “all” read all files with the basename varying step, if “last” read only last step of all files with the filename, if “first” reads step=0, if None reads file of filename provided or specified in object.
filename :string, optional
Basename of the files to use, if None file from object is used.
cache : object
Has no effect.
return_mesh : bool, optional, default True
Return mesh associated with data.
Returns: mesh : sfepy.discrete.fem.mesh.Mesh
Computational mesh.
out : dictionary
The output dictionary. Its keys represent name of data, values are Struct instances with the following attributes:
- data : array, contains ElementNodeData, shape is (len(time), n_cell, n_cell_dof).
- time : array, contains times.
- time_n : array, contains time step numbers.
- scheme : Struct, interpolation scheme used in data, only one
interpolation scheme is allowed. See
Msh2MeshIO._write_interpolation_scheme()
.
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write
(filename, mesh, out=None, ts=None, **kwargs)[source]¶ Writes mesh and data into msh v2.0 file, handles dg_cell_dofs data from DGField if provided in out.
Parameters: filename : string
Path to file.
mesh : sfepy.discrete.fem.mesh.Mesh
Computational mesh to write.
out : dictionary, optional
Dictionary containing data to write, expected to be in format generated by DGField.create_output(), key is name of data, value is Struct containing:
- mode : string, so far only dg_cell_dofs, representing modal data in cells is supported.
- data : array, DOFs as defined in DG Field.
- interpolation_scheme : Struct, interpolation scheme used in
data, only one interpolation scheme is allowed. See
Msh2MeshIO._write_interpolation_scheme()
.
ts : sfepy.solvers.ts.TimeStepper instance, optional
Provides data to write time step.
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class
sfepy.discrete.fem.meshio.
TetgenMeshIO
(filename, **kwargs)[source]¶ -
format
= 'tetgen'¶
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static
getele
(fele)[source]¶ Reads t.1.ele, returns a list of elements.
Example:
>>> elements, regions = self.getele("t.1.ele") >>> elements [(20, 154, 122, 258), (86, 186, 134, 238), (15, 309, 170, 310), (146, 229, 145, 285), (206, 207, 125, 211), (99, 193, 39, 194), (185, 197, 158, 225), (53, 76, 74, 6), (19, 138, 129, 313), (23, 60, 47, 96), (119, 321, 1, 329), (188, 296, 122, 322), (30, 255, 177, 256), ...] >>> regions {100: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 7, ...], ...}
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static
getnodes
(fnods)[source]¶ Reads t.1.nodes, returns a list of nodes.
Example:
>>> self.getnodes("t.1.node") [(0.0, 0.0, 0.0), (4.0, 0.0, 0.0), (0.0, 4.0, 0.0), (-4.0, 0.0, 0.0), (0.0, 0.0, 4.0), (0.0, -4.0, 0.0), (0.0, -0.0, -4.0), (-2.0, 0.0, -2.0), (-2.0, 2.0, 0.0), (0.0, 2.0, -2.0), (0.0, -2.0, -2.0), (2.0, 0.0, -2.0), (2.0, 2.0, 0.0), ... ]
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class
sfepy.discrete.fem.meshio.
UserMeshIO
(filename, **kwargs)[source]¶ Special MeshIO subclass that enables reading and writing a mesh using a user-supplied function.
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format
= 'function'¶
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class
sfepy.discrete.fem.meshio.
XYZMeshIO
(filename, **kwargs)[source]¶ Trivial XYZ format working only with coordinates (in a .XYZ file) and the connectivity stored in another file with the same base name and .IEN suffix.
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format
= 'xyz'¶
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sfepy.discrete.fem.meshio.
convert_complex_output
(out_in)[source]¶ Convert complex values in the output dictionary out_in to pairs of real and imaginary parts.
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sfepy.discrete.fem.meshio.
guess_format
(filename, ext, formats, io_table)[source]¶ Guess the format of filename, candidates are in formats.
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sfepy.discrete.fem.meshio.
mesh_from_groups
(mesh, ids, coors, ngroups, tris, mat_tris, quads, mat_quads, tetras, mat_tetras, hexas, mat_hexas, remap=None)[source]¶
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sfepy.discrete.fem.meshio.
split_conns_mat_ids
(conns_in)[source]¶ Split connectivities (columns except the last ones in conns_in) from cell groups (the last columns of conns_in).
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sfepy.discrete.fem.meshio.
var
(filename, ext, formats, io_table)¶ Guess the format of filename, candidates are in formats.