zoomy_core.mesh.base_mesh module

zoomy_core.mesh.base_mesh module#

BaseMesh — topology-only mesh loaded from .msh via meshio (no PETSc).

All geometric quantities (volumes, normals, centers, …) are computed on the fly from the stored topology. Derived classes (FVMMesh, LSQMesh, …) cache selected quantities for performance.

class zoomy_core.mesh.base_mesh.BaseMesh(*, boundary_conditions_sorted_names, boundary_conditions_sorted_physical_tags, boundary_face_cells, boundary_face_face_indices, boundary_face_function_numbers, boundary_face_ghosts, boundary_face_physical_tags, cell_faces, cell_neighbors, cell_vertices, dimension, face_cells, n_boundary_faces, n_cells, n_faces, n_faces_per_cell, n_inner_cells, n_vertices, type, vertex_coordinates, z_ordering, name)#

Bases: Parameterized

Topology-only mesh. Geometry computed on the fly.

dimension = 2#
type = 'triangle'#
n_cells = 0#
n_inner_cells = 0#
n_faces = 0#
n_vertices = 0#
n_boundary_faces = 0#
n_faces_per_cell = 0#
vertex_coordinates = array([], shape=(0, 0), dtype=float64)#
cell_vertices = array([], shape=(0, 0), dtype=int64)#
cell_faces = array([], shape=(0, 0), dtype=int64)#
face_cells = array([], shape=(0, 0), dtype=int64)#
cell_neighbors = array([], shape=(0, 0), dtype=int64)#
boundary_face_cells = array([], dtype=int64)#
boundary_face_ghosts = array([], dtype=int64)#
boundary_face_function_numbers = array([], dtype=int64)#
boundary_face_physical_tags = array([], dtype=int64)#
boundary_face_face_indices = array([], dtype=int64)#
boundary_conditions_sorted_physical_tags = array([], dtype=int64)#
boundary_conditions_sorted_names = []#
z_ordering = array([-1])#
cell_centers_computed()#

Compute cell centers from vertex coordinates. Shape (3, n_cells).

Return type:

ndarray

cell_volumes_computed()#

Compute cell volumes. Shape (n_cells,).

Return type:

ndarray

cell_inradius_computed()#

Compute cell inradius (min distance from center to face plane).

Uses the same projection-based approach as PETSc’s computeCellGeometryFVM for consistency.

Return type:

ndarray

face_normals_computed()#

Compute face normals. Shape (3, n_faces).

For 1D meshes all normals point in the +x direction (convention).

Return type:

ndarray

face_volumes_computed()#

Compute face areas/lengths. Shape (n_faces,).

For 1D meshes, face ‘volumes’ are 1.0 (point has no area).

Return type:

ndarray

face_centers_computed()#

Compute face centers. Shape (n_faces, 3).

Return type:

ndarray

face_subvolumes_computed()#

Compute face subvolumes. Shape (n_faces, 2).

Return type:

ndarray

compute_derivatives(u, degree=1, derivatives_multi_index=None)#

Compute derivatives using on-the-fly LSQ reconstruction.

Parameters:

  • u (ndarray) –

  • degree (int) –

Return type:

ndarray

classmethod from_msh(filepath)#

Load a .msh file via meshio and build topology (no PETSc).

Parameters:

filepath (str) –

Return type:

BaseMesh

classmethod create_1d(domain, n_inner_cells)#

Build a uniform 1D interval mesh.

Parameters:

  • domain (tuple) –

  • n_inner_cells (int) –

Return type:

BaseMesh

classmethod create_2d(domain, nx, ny)#

Build a uniform 2D quad mesh.

Parameters:

  • domain ((x_min, x_max, y_min, y_max)) –

  • nx (number of inner cells in x and y directions) –

  • ny (number of inner cells in x and y directions) –

Return type:

BaseMesh

classmethod create_3d(domain, nx, ny, nz)#

Build a uniform 3D hexahedral mesh.

Parameters:

  • domain ((x_min, x_max, y_min, y_max, z_min, z_max)) –

  • nx (number of inner cells in each direction) –

  • ny (number of inner cells in each direction) –

  • nz (number of inner cells in each direction) –

Return type:

BaseMesh

write_to_hdf5(filepath)#

Serialize topology-only fields to HDF5.

Parameters:

filepath (str) –

classmethod from_hdf5(filepath)#

Load a BaseMesh from HDF5.

Parameters:

filepath (str) –

Return type:

BaseMesh

classmethod extrude_2d(mesh_2d, n_layers, height)#

Extrude a 2D mesh into 3D by stacking layers in the z-direction.

Parameters:

  • mesh_2d (BaseMesh) – A 2D mesh (type "quad" or "triangle").

  • n_layers (int) – Number of layers in the z-direction.

  • height (float or array-like) – Total extrusion height (uniform layers), or a list/array of n_layers individual layer heights.

Returns:

A 3D mesh of type "hexahedron" (from quads) or "wface" (from triangles).

Return type:

BaseMesh

name = 'BaseMesh'#
resolve_periodic_bcs(bcs)#

Patch boundary_face_cells for periodic boundary conditions.