import types
from collections.abc import Callable
import dolfinx
import numpy as np
from dolfinx import fem
from dolfinx.mesh import Mesh, locate_entities
from numpy import typing as npt
from scifem.mesh import transfer_meshtags_to_submesh
from festim.material import Material
# Define the appropriate method based on the version
try:
from dolfinx.mesh import EntityMap
entity_map_type = EntityMap
except ImportError:
entity_map_type = npt.NDArray[np.int32]
[docs]
class VolumeSubdomain:
"""
Volume subdomain class
Args:
id: the id of the volume subdomain
submesh: the submesh of the volume subdomain
cell_map: the cell map of the volume subdomain
parent_mesh: the parent mesh of the volume subdomain
parent_to_submesh: the parent to submesh map of the volume subdomain
v_map: the vertex map of the volume subdomain
n_map: the normal map of the volume subdomain
facet_to_parent: the facet to parent map of the volume subdomain
ft: the facet meshtags of the volume subdomain
padded: whether the subdomain is padded (for 0.9 compatibility)
u: the solution function of the subdomain
u_n: the previous solution function of the subdomain
material: the material assigned to the subdomain
sub_T: the sub temperature field in the subdomain
"""
id: int
submesh: dolfinx.mesh.Mesh
cell_map: "entity_map_type"
parent_mesh: dolfinx.mesh.Mesh
parent_to_submesh: "entity_map_type"
v_map: "entity_map_type"
n_map: np.ndarray
facet_to_parent: np.ndarray
ft: dolfinx.mesh.MeshTags
padded: bool # NOTE: Once 0.9 support is dropped, this can be removed
u: dolfinx.fem.Function
u_n: dolfinx.fem.Function
material: Material
sub_T: fem.Function | float
def __init__(
self, id, material, locator: Callable | None = None, name: str | None = None
):
self.id = id
self.material = material
self.locator = locator
self.name = name
@property
def name(self):
return self._name
@name.setter
def name(self, value):
if value is None:
self._name = None
elif isinstance(value, str):
self._name = value
else:
raise TypeError("Name must be a string")
[docs]
def create_subdomain(self, mesh: dolfinx.mesh.Mesh, marker: dolfinx.mesh.MeshTags):
"""
Creates the following attributes: ``.parent_mesh``, ``.submesh``, ``.cell_map``,
``.v_map``, ``padded``, and the entity map ``parent_to_submesh``.
Only used in ``festim.HydrogenTransportProblemDiscontinuous``
Args:
mesh (dolfinx.mesh.Mesh): the parent mesh
marker (dolfinx.mesh.MeshTags): the parent volume markers
"""
assert marker.dim == mesh.topology.dim
self.parent_mesh = (
mesh # NOTE: it doesn't seem like we use this attribute anywhere
)
entities = marker.find(self.id)
self.submesh, self.cell_map, self.v_map, self.n_map = (
dolfinx.mesh.create_submesh(mesh, marker.dim, entities)
)
if isinstance(entity_map_type, types.GenericAlias):
num_cells_local = (
mesh.topology.index_map(marker.dim).size_local
+ mesh.topology.index_map(marker.dim).num_ghosts
)
self.parent_to_submesh = np.full(num_cells_local, -1, dtype=np.int32)
self.parent_to_submesh[self.cell_map] = np.arange(
len(self.cell_map), dtype=np.int32
)
self.padded = False
def transfer_meshtag(self, mesh: dolfinx.mesh.Mesh, tag: dolfinx.mesh.MeshTags):
# Transfer meshtags to submesh
assert self.submesh is not None, "Need to call create_subdomain first"
self.ft, self.facet_to_parent = transfer_meshtags_to_submesh(
tag, self.submesh, self.v_map, self.cell_map
)
[docs]
def locate_subdomain_entities(self, mesh: Mesh) -> npt.NDArray[np.int32]:
"""Locates all cells in subdomain borders within domain
Args:
mesh: the mesh of the model
Returns:
entities: the entities of the subdomain
"""
if self.locator is None:
raise ValueError("No locator function provided for locating cells.")
entities = locate_entities(mesh, mesh.topology.dim, self.locator)
return entities
[docs]
class VolumeSubdomain1D(VolumeSubdomain):
"""
Volume subdomain class for 1D cases
Args:
id (int): the id of the volume subdomain
borders (list of float): the borders of the volume subdomain
material (festim.Material): the material of the volume subdomain
Attributes:
id (int): the id of the volume subdomain
borders (list of float): the borders of the volume subdomain
material (festim.Material): the material of the volume subdomain
Examples:
.. testsetup:: VolumeSubdomain1D
from festim import VolumeSubdomain1D, Material
my_mat = Material(D_0=1, E_D=1, name="test_mat")
.. testcode:: VolumeSubdomain1D
VolumeSubdomain1D(id=1, borders=[0, 1], material=my_mat)
"""
def __init__(self, id, borders, material) -> None:
super().__init__(
id,
material,
locator=lambda x: np.logical_and(x[0] >= borders[0], x[0] <= borders[1]),
)
self.borders = borders
def find_volume_from_id(id: int, volumes: list):
"""Returns the correct volume subdomain object from a list of volume ids
based on an int
Args:
id (int): the id of the volume subdomain
volumes (list): the list of volumes
Returns:
festim.VolumeSubdomain: the volume subdomain object with the correct id
Raises:
ValueError: if the volume name is not found in the list of volumes
"""
for vol in volumes:
if vol.id == id:
return vol
raise ValueError(f"id {id} not found in list of volumes")
