zoomy_core.mesh.base_mesh

zoomy_core.mesh.base_mesh#

BaseMesh: topology-only mesh (cells, faces, one ghost cell per boundary face) read from .msh via meshio or built from arrays, with geometry computed on the fly. The root of the BaseMesh -> FVMMesh -> LSQMesh hierarchy that every backend shares.

Module Contents#

Classes#

BaseMesh

Topology-only mesh with geometry computed on the fly.

API#

class zoomy_core.mesh.base_mesh.BaseMesh(**kwargs)#

Bases: param.Parameterized

Topology-only mesh with geometry computed on the fly.

Initialization

Create the mesh from its topology arrays and normalise boundary faces so face_cells[0] is the inner cell.

dimension#

‘Integer(…)’

type#

‘String(…)’

n_cells#

‘Integer(…)’

n_inner_cells#

‘Integer(…)’

n_faces#

‘Integer(…)’

n_vertices#

‘Integer(…)’

n_boundary_faces#

‘Integer(…)’

n_faces_per_cell#

‘Integer(…)’

vertex_coordinates#

‘Array(…)’

cell_vertices#

‘Array(…)’

cell_faces#

‘Array(…)’

face_cells#

‘Array(…)’

cell_neighbors#

‘Array(…)’

boundary_face_cells#

‘Array(…)’

boundary_face_ghosts#

‘Array(…)’

boundary_face_function_numbers#

‘Array(…)’

boundary_face_physical_tags#

‘Array(…)’

boundary_face_face_indices#

‘Array(…)’

boundary_conditions_sorted_physical_tags#

‘Array(…)’

boundary_conditions_sorted_names#

‘List(…)’

z_ordering#

‘Array(…)’

node_data#

‘Dict(…)’

cell_data#

‘Dict(…)’

cell_centers_computed() → numpy.ndarray#

Cell centres (3, n_cells); ghost centres are the inner centres mirrored across the boundary face.

cell_volumes_computed() → numpy.ndarray#

Cell volumes (n_cells,); a ghost takes its inner cell’s volume.

cell_inradius_computed() → numpy.ndarray#

Cell inradii (n_cells,): the minimum distance from the centre to the face planes (half the length in 1D).

face_normals_computed() → numpy.ndarray#

Unit face normals (3, n_faces) pointing from face_cells[0] to face_cells[1] (a sign in 1D).

face_volumes_computed() → numpy.ndarray#

Face areas (lengths in 2D) (n_faces,); 1.0 in 1D.

face_centers_computed() → numpy.ndarray#

Face centres (n_faces, 3).

face_subvolumes_computed() → numpy.ndarray#

Per face and side, the simplex (2D) or pyramid (3D) volume between the face and the cell centre, (n_faces, 2); a boundary face carries its inner side twice.

compute_derivatives(u: numpy.ndarray, degree: int = 1, derivatives_multi_index=None, *, u_boundary_face) → numpy.ndarray#

Derivatives of u from an LSQ stencil built on the fly (the cached variant lives on LSQMesh).

Args

  • u_boundary_face: (n_boundary_faces,) face values, or 'extrapolation' for Neumann-zero.

References

  • Mavriplis 2003, https://doi.org/10.2514/6.2003-3986

classmethod from_msh(filepath: str) → zoomy_core.mesh.base_mesh.BaseMesh#

Load a gmsh .msh file via meshio and build the topology, keeping node and cell data for mesh_ic.

classmethod from_arrays(vertex_coordinates, cell_vertices, mesh_type, *, face_tags=None, cell_face_tags=None, tag_names=None, default_tag=0, node_data=None, cell_data=None) → zoomy_core.mesh.base_mesh.BaseMesh#

Build a mesh from raw arrays of one cell type.

Args

  • vertex_coordinates: (dim, n_vertices).

  • cell_vertices: (verts_per_cell, n_cells).

  • face_tags: maps a boundary face (sorted vertex tuple) to its physical tag.

  • cell_face_tags: (faces_per_cell, n_cells) tag per local face (< 0: none), instead of face_tags.

  • tag_names: {tag: name}, default tag_<t>.

  • default_tag: tag of boundary faces without one.

classmethod create_1d(domain: tuple, n_inner_cells: int) → zoomy_core.mesh.base_mesh.BaseMesh#

Uniform 1D interval mesh on domain with two ghost cells; boundaries left and right.

classmethod create_2d(domain: tuple, nx: int, ny: int) → zoomy_core.mesh.base_mesh.BaseMesh#

Uniform quad mesh with boundaries left, right, bottom, top.

Args

  • domain: (x_min, x_max, y_min, y_max).

  • nx: inner cells in x; ny in y.

classmethod create_3d(domain: tuple, nx: int, ny: int, nz: int) → zoomy_core.mesh.base_mesh.BaseMesh#

Uniform hexahedral mesh with boundaries left, right, front, back, bottom, top.

Args

  • domain: (x_min, x_max, y_min, y_max, z_min, z_max).

  • nx: inner cells in x; ny, nz likewise.

classmethod extrude_2d(mesh2d, n_layers: int, height: float = 1.0) → zoomy_core.mesh.base_mesh.BaseMesh#

Extrude a 2D quad mesh into 3D hexahedra; shadowed by the later extrude_2d of this class, which is the one called.

write_to_hdf5(filepath: str)#

Write the topology fields to an HDF5 file (format version 2).

classmethod from_hdf5(filepath: str) → zoomy_core.mesh.base_mesh.BaseMesh#

Load a mesh written by write_to_hdf5.

resolve_periodic_bcs(bcs)#

Patch boundary_face_cells so Periodic boundaries read their partner’s cells. Idempotent: the remap source is face_cells[0] (never modified), not the possibly already patched array.

Contents