zoomy-core 0.1.1__py3-none-any.whl → 0.1.2__py3-none-any.whl

zoomy_core/mesh/mesh_extrude.py

@@ -0,0 +1,168 @@
+import numpy as np
+
+
+def extrude_points(points, Z):
+    n_points = points.shape[0]
+    dim = points.shape[1]
+    Nz = Z.shape[0]
+    points_ext = np.empty((n_points * (Nz), dim + 1), dtype=float)
+    for i in range(n_points):
+        for iz, z in enumerate(Z):
+            offset = iz * n_points
+            points_ext[i + offset, :dim] = points[i]
+            points_ext[i + offset, -1] = z
+    return points_ext
+
+
+def extrude_element_vertices(element_vertices, n_vertices, Nz):
+
+    n_elements = element_vertices.shape[0]
+    n_vertices_per_element = element_vertices.shape[1]
+    if n_vertices_per_element == 2:
+        return extrude_element_vertices_line(element_vertices, n_vertices, Nz)
+    element_vertices_ext = np.empty(
+        (n_elements * Nz, 2 * n_vertices_per_element), dtype=int
+    )
+    for i in range(n_elements):
+        for iz in range(Nz):
+            offset = iz * n_elements
+            element_vertices_ext[i + offset, :n_vertices_per_element] = (
+                element_vertices[i, :] + iz * n_vertices
+            )
+            element_vertices_ext[i + offset, n_vertices_per_element:] = (
+                element_vertices[i, :] + (iz + 1) * n_vertices
+            )
+    return element_vertices_ext
+
+def extrude_element_vertices_line(element_vertices, n_vertices, Nz):
+    n_elements = element_vertices.shape[0]
+    n_vertices_per_element = 2
+    element_vertices_ext = np.empty(
+        (n_elements * Nz, 2 * n_vertices_per_element), dtype=int
+    )
+    for i in range(n_elements):
+        for iz in range(Nz):
+            offset = iz * n_elements
+            element_vertices_ext[i + offset, [0, 3]] = (
+                element_vertices[i, :] + iz * n_vertices
+            )
+            element_vertices_ext[i + offset, [1,2]] = (
+                element_vertices[i, :] + (iz + 1) * n_vertices
+            )
+    return element_vertices_ext
+
+
+def extrude_boundary_face_vertices(msh, Nz):
+    """
+    convenction: 1. bottom 2. sides 3. top
+    """
+    n_boundary_elements = msh.n_boundary_elements * Nz + 2 * msh.n_elements
+    n_vertices_per_face = msh.boundary_face_vertices.shape[1]
+    n_vertices_per_face_ext = 2 * n_vertices_per_face
+    boundary_face_vertices = np.empty(
+        (n_boundary_elements, n_vertices_per_face_ext), dtype=int
+    )
+
+    # for wface, boundary elements may have 3 or 4 vertices. In case of 3, I want to overwrite the other entries to be dublicates of existing entries
+    side_offset = 0
+    # bottom
+    for i in range(msh.n_elements):
+        boundary_face_vertices[i, : msh.element_vertices[i].shape[0]] = (
+            msh.element_vertices[i]
+        )
+        boundary_face_vertices[i, msh.element_vertices[i].shape[0] :] = (
+            msh.element_vertices[i][-1]
+        )
+    side_offset += msh.n_elements
+
+    n_vertices_per_layer = msh.n_vertices
+    # sides
+    for i in range(msh.n_boundary_elements):
+        face_vertices = msh.boundary_face_vertices[i]
+        for iz in range(Nz):
+            offset = iz * msh.n_boundary_elements + side_offset
+            boundary_face_vertices[i + offset, :n_vertices_per_face] = (
+                face_vertices + iz * n_vertices_per_layer
+            )
+            boundary_face_vertices[i + offset, n_vertices_per_face:] = (
+                face_vertices + (iz + 1) * n_vertices_per_layer
+            )
+    side_offset += Nz * msh.n_boundary_elements
+
+    # top
+    for i in range(msh.n_elements):
+        # boundary_face_vertices[i + side_offset] = msh.element_vertices[i] + Nz * msh.n_vertices
+        boundary_face_vertices[i + side_offset, : msh.element_vertices[i].shape[0]] = (
+            msh.element_vertices[i] + Nz * msh.n_vertices
+        )
+        boundary_face_vertices[i + side_offset, msh.element_vertices[i].shape[0] :] = (
+            msh.element_vertices[i][-1] + Nz * msh.n_vertices
+        )
+
+    return boundary_face_vertices
+
+
+def extrude_boundary_face_corresponding_element(msh, Nz):
+    """
+    convenction: 1. bottom 2. sides 3. top
+    """
+    n_boundary_elements = msh.n_boundary_elements * Nz + 2 * msh.n_elements
+    boundary_face_corresponding_element = np.empty((n_boundary_elements), dtype=int)
+
+    side_offset = 0
+    # bottom
+    for i in range(msh.n_elements):
+        boundary_face_corresponding_element[i] = i
+    side_offset += msh.n_elements
+
+    # sides
+    for i in range(msh.n_boundary_elements):
+        i_elem = msh.boundary_face_corresponding_element[i]
+        for iz in range(Nz):
+            offset_boundary = iz * msh.n_boundary_elements + side_offset
+            offset_elements = iz * msh.n_elements
+            boundary_face_corresponding_element[i + offset_boundary] = (
+                i_elem + offset_elements
+            )
+    side_offset += Nz * msh.n_boundary_elements
+
+    # top
+    for i in range(msh.n_elements):
+        boundary_face_corresponding_element[i + side_offset] = (
+            i + (Nz - 1) * msh.n_elements
+        )
+
+    return boundary_face_corresponding_element
+
+
+def extrude_boundary_face_tags(msh, Nz):
+    """
+    convenction: 1. bottom 2. sides 3. top
+    """
+    n_boundary_elements = msh.n_boundary_elements * Nz + 2 * msh.n_elements
+    boundary_face_tags = np.empty((n_boundary_elements), int)
+
+    n_existing_tags = len(msh.boundary_tag_names)
+    tag_bottom = n_existing_tags
+    tag_top = n_existing_tags + 1
+
+    side_offset = 0
+    # bottom
+    for i in range(msh.n_elements):
+        boundary_face_tags[i] = tag_bottom
+    side_offset += msh.n_elements
+
+    # sides
+    for i in range(msh.n_boundary_elements):
+        i_elem = msh.boundary_face_corresponding_element[i]
+        for iz in range(Nz):
+            offset_boundary = iz * msh.n_boundary_elements + side_offset
+            offset_elements = iz * msh.n_elements
+            boundary_face_tags[i + offset_boundary] = msh.boundary_face_tag[i]
+    side_offset += Nz * msh.n_boundary_elements
+
+    # top
+    for i in range(msh.n_elements):
+        boundary_face_tags[i + side_offset] = tag_top
+
+    return boundary_face_tags

zoomy_core/mesh/mesh_util.py

@@ -0,0 +1,487 @@
+import numpy as np
+
+def convert_mesh_type_to_meshio_mesh_type(mesh_type: str) -> str:
+    if mesh_type == "triangle":
+        return "triangle"
+    elif mesh_type == "hexahedron":
+        return "hexahedron"
+    elif mesh_type == "line":
+        return "line"
+    elif mesh_type == "quad":
+        return "quad"
+    elif mesh_type == "wface":
+        return "wedge"
+    elif mesh_type == "tetra":
+        return "tetra"
+    else:
+        assert False
+
+def _get_n_nodes_per_element(mesh_type: str) -> int:
+    if (mesh_type) == "quad":
+        return 4
+    elif (mesh_type) == "triangle":
+        return 3
+    elif (mesh_type) == "wface":
+        return 6
+    elif (mesh_type) == "hexahedron":
+        return 8
+    elif (mesh_type) == "tetra":
+        return 4
+    else:
+        assert False
+
+def get_extruded_mesh_type(mesh_type: str) -> str:
+    if (mesh_type) == "quad":
+        return "hexahedron"
+    elif (mesh_type) == "triangle":
+        return "wface"
+    elif (mesh_type) == "line":
+        return "quad"
+    else:
+        assert False
+
+
+def get_global_cell_index_from_vertices(
+    cells, coordinates, return_first=True, offset=0
+):
+    hits = []
+    for index, cell in enumerate(cells):
+        if set(coordinates).issubset(set(cell)):
+            hits.append(offset + index)
+            if return_first:
+                return offset + index
+    # if hits == []:
+    #     assert False
+    return hits
+
+
+def get_element_neighbors(element_vertices, current_elem, mesh_type):
+    num_vertices_per_face = _get_num_vertices_per_face(mesh_type)
+    max_num_neighbors = _get_faces_per_element(mesh_type)
+    element_neighbor_indices = np.zeros((max_num_neighbors), dtype=int)
+    element_neighbor_face_index = np.zeros((max_num_neighbors), dtype=int)
+    n_found_neighbors = 0
+    for i_elem, elem in enumerate(element_vertices):
+        found_overlapping_vertices = set(elem).intersection(set(current_elem))
+        n_found_overlapping_vertices = len(found_overlapping_vertices)
+
+        if n_found_overlapping_vertices == np.min(num_vertices_per_face):
+            for i_elem_face_index, edge in enumerate(
+                _face_order(current_elem, mesh_type)
+            ):
+                if set(edge).issubset(found_overlapping_vertices):
+                    element_neighbor_face_index[n_found_neighbors] = i_elem_face_index
+                    break
+            element_neighbor_indices[n_found_neighbors] = i_elem
+            n_found_neighbors += 1
+            if n_found_neighbors == max_num_neighbors:
+                break
+    return n_found_neighbors, element_neighbor_indices, element_neighbor_face_index
+
+
+def face_normals(coordinates, element, mesh_type) -> float:
+    if mesh_type == "triangle":
+        return _face_normals_2d(coordinates, element, mesh_type)
+    elif mesh_type == "quad":
+        return _face_normals_2d(coordinates, element, mesh_type)
+    elif mesh_type == "tetra":
+        return _face_normals_3d(coordinates, element, mesh_type)
+    elif mesh_type == "hexahedron":
+        return _face_normals_3d(coordinates, element, mesh_type)
+    elif mesh_type == "wface":
+        return _face_normals_3d(coordinates, element, mesh_type)
+    assert False
+
+
+def _face_normals_2d(coordinates, element, mesh_type) -> float:
+    edges = _face_order(element, mesh_type)
+    ez = np.array([0, 0, 1], dtype=float)
+    normals = np.zeros((len(edges), 3), dtype=float)
+    for i_edge, edge in enumerate(edges):
+        edge_direction = coordinates[edge[1]] - coordinates[edge[0]]
+        normals[i_edge, :] = -np.cross(edge_direction, ez)
+        normals[i_edge, :] /= np.linalg.norm(normals[i_edge, :])
+
+    # DEBUG: check that the normal goes into the right direction
+    # center_point = center(coordinates, element)
+    # ec = coordinates[edges]
+    # edge_centers = [np.mean(ec[i], axis=0) for i in range(4)]
+    # for i in range(4):
+    #     assert np.allclose(center_point + 0.125 * normals[i], edge_centers[i])
+
+    return normals
+
+
+def _face_normals_3d(coordinates, element, mesh_type) -> float:
+    faces = _face_order(element, mesh_type)
+    boundary_mesh_type = _get_boundary_element_type(mesh_type)
+    normals = np.zeros((len(faces), 3), dtype=float)
+    for i_face, face in enumerate(faces):
+        # I will only consider the first 2 edges, regardless of the element type.
+        # flat elements, where 2 edges already span the plane and normal
+        edges = _face_order(face, boundary_mesh_type[i_face])
+        edge_1 = edges[0]
+        edge_2 = edges[1]
+        edge_direction_1 = coordinates[edge_1[1]] - coordinates[edge_1[0]]
+        edge_direction_2 = coordinates[edge_2[1]] - coordinates[edge_2[0]]
+        normals[i_face, :] = -np.cross(edge_direction_1, edge_direction_2)
+        normals[i_face, :] /= np.linalg.norm(normals[i_face, :])
+    return normals
+
+
+def _face_normals_wface(coordinates, element, mesh_type) -> float:
+    faces = _face_order(element, mesh_type)
+    boundary_mesh_type = _get_boundary_element_type(mesh_type)
+    normals = np.zeros((len(faces), 3), dtype=float)
+    for i_face, face in enumerate(faces):
+        # I will only consider the first 2 edges, regardless of the element type.
+        # flat elements, where 2 edges already span the plane and normal
+        edges = _face_order(face, boundary_mesh_type[i_face])
+        edge_1 = edges[0]
+        edge_2 = edges[1]
+        edge_direction_1 = coordinates[edge_1[1]] - coordinates[edge_1[0]]
+        edge_direction_2 = coordinates[edge_2[1]] - coordinates[edge_2[0]]
+        normals[i_face, :] = -np.cross(edge_direction_1, edge_direction_2)
+        normals[i_face, :] /= np.linalg.norm(normals[i_face, :])
+    return normals
+
+
+def face_areas(coordinates, element, mesh_type) -> float:
+    num_faces = _get_faces_per_element(mesh_type)
+    faces = _face_order(element, mesh_type)
+    boundary_mesh_type = _get_boundary_element_type(mesh_type)
+    face_areas = np.zeros(num_faces, dtype=float)
+
+    for i_face, face in enumerate(faces):
+        face_areas[i_face] = volume(coordinates, face, boundary_mesh_type[i_face])
+
+    return face_areas
+
+
+def center(coordinates, element) -> float:
+    center = np.zeros(3, dtype=float)
+    dim = coordinates.shape[1]
+    for vertex_coord in coordinates[np.array(element)]:
+        center[:dim] += vertex_coord
+    center /= np.array(element).shape[0]
+    return center[:dim]
+
+
+def volume(coordinates, element, mesh_type) -> float:
+    if mesh_type == "line":
+        return edge_length(coordinates, element)
+    elif mesh_type == "triangle":
+        return _area_triangle(coordinates, element)
+    elif mesh_type == "quad":
+        return _area_quad(coordinates, element)
+    elif mesh_type == "tetra":
+        return _volume_tetra(coordinates, element)
+    elif mesh_type == "hexahedron":
+        return _volume_hex(coordinates, element)
+    elif mesh_type == "wface":
+        return _volume_wface(coordinates, element)
+    assert False
+
+
+def _area_triangle(coordinates, element) -> float:
+    edges = _edge_order_triangle(element)
+    return _area_triangle_heron_formula(coordinates, edges)
+
+
+def _area_triangle_heron_formula(coordinates, edges):
+    perimeter = 0.0
+    for edge in edges:
+        perimeter += edge_length(coordinates, edge)
+    s = perimeter / 2
+    a = edge_length(coordinates, edges[0])
+    b = edge_length(coordinates, edges[1])
+    c = edge_length(coordinates, edges[2])
+    return np.sqrt(s * (s - a) * (s - b) * (s - c))
+
+
+def _area_quad(coordinates, element) -> float:
+    # compute area by splitting in 2 triangles.
+    edges_tri_1 = [
+        (element[0], element[1]),
+        (element[1], element[2]),
+        (element[2], element[0]),
+    ]
+    edges_tri_2 = [
+        (element[2], element[3]),
+        (element[3], element[0]),
+        (element[0], element[2]),
+    ]
+    return _area_triangle_heron_formula(
+        coordinates, edges_tri_1
+    ) + _area_triangle_heron_formula(coordinates, edges_tri_2)
+
+
+# formula from https://en.wikipedia.org/wiki/Tetrahedron, section 'general properties'
+def _volume_tetra(coordinates, element) -> float:
+    a = coordinates[element[0]]
+    b = coordinates[element[1]]
+    c = coordinates[element[2]]
+    d = coordinates[element[3]]
+    volume = np.abs(np.dot((a - d), np.cross((b - d), (c - d)))) / 6
+    return volume
+
+
+def _volume_hex(coordinates, element) -> float:
+    # devide into tetraheda and use formula above
+    # e.g. make up a point in the middle
+    volume = 0
+    center_point = center(coordinates, element)
+    faces = _face_order_hex(element)
+    for face in faces:
+        a = coordinates[face[0]]
+        b = coordinates[face[1]]
+        c = coordinates[face[2]]
+        d = center_point
+        volume += np.abs(np.dot((a - d), np.cross((b - d), (c - d)))) / 6
+    return volume
+
+
+def _volume_wface(coordinates, element) -> float:
+    volume = 0
+    faces = _face_order_wface(element)
+    area_triangle = _area_triangle(coordinates, faces[0])
+    height = np.linalg.norm(coordinates[element[0]] - coordinates[element[3]])
+    return area_triangle * height
+
+
+def inradius(coordinates, element, mesh_type) -> float:
+    if mesh_type == "triangle":
+        return _inradius_triangle(coordinates, element)
+    elif mesh_type == "quad":
+        return _inradius_quad(coordinates, element)
+    elif mesh_type == "tetra":
+        return _inradius_tetra(coordinates, element)
+    elif mesh_type == "hexahedron":
+        return _inradius_generic(coordinates, element, "hexahedron")
+    elif mesh_type == "wface":
+        return _inradius_generic(coordinates, element, "wface")
+    assert False
+
+
+def _inradius_triangle(coordinates, element) -> float:
+    area = _area_triangle(coordinates, element)
+    edges = _edge_order_triangle(element)
+    perimeter = 0.0
+    for edge in edges:
+        perimeter += edge_length(coordinates, edge)
+    s = perimeter / 2
+    result = 1.0
+    for edge in edges:
+        result *= s - edge_length(coordinates, edge)
+    result /= s
+    return float(np.sqrt(result))
+
+
+def _inradius_quad(coordinates, element) -> float:
+    area = _area_quad(coordinates, element)
+    edges = _edge_order_quad(element)
+    perimeter = 0.0
+    for edge in edges:
+        perimeter += edge_length(coordinates, edge)
+    s = perimeter / 2
+    return float(area / s)
+
+
+# see https://en.wikipedia.org/wiki/Tetrahedron, "Inradius"
+def _inradius_tetra(coordinates, element) -> float:
+    faces = _face_order_tetra(element)
+    area = 0
+    for face in faces:
+        area += _area_triangle(coordinates, face)
+    volume = _volume_tetra(coordinates, element)
+    return 3 * volume / area
+
+
+def _inradius_generic(coordinates, element, mesh_type) -> float:
+    """
+    strategy: find the shortest path from the center to each side (defined by face center and normal)
+    use the minimum of all these shortest paths
+    """
+    faces = _face_order(element, mesh_type)
+    normals = face_normals(coordinates, element, mesh_type)
+    element_center = center(coordinates, element)
+    n_faces = len(faces)
+    distances = np.empty(n_faces, dtype=float)
+    for i_face, face in enumerate(faces):
+        face_center = center(coordinates, face)
+        face_normal = normals[i_face]
+        distances[i_face] = np.abs(np.dot(face_center - element_center, face_normal))
+    return np.min(distances)
+
+
+def edge_length(coordinates, edge) -> float:
+    x0 = coordinates[edge[0]]
+    x1 = coordinates[edge[1]]
+    return np.linalg.norm(x1 - x0, 2)
+
+
+def _face_order(element, mesh_type):
+    if mesh_type == "triangle":
+        return _edge_order_triangle(element)
+    elif mesh_type == "quad":
+        return _edge_order_quad(element)
+    elif mesh_type == "tetra":
+        return _face_order_tetra(element)
+    elif mesh_type == "hexahedron":
+        return _face_order_hex(element)
+    elif mesh_type == "wface":
+        return _face_order_wface(element)
+    else:
+        assert False
+
+
+def _edge_order_triangle(element):
+    return [
+        (element[0], element[1]),
+        (element[1], element[2]),
+        (element[2], element[0]),
+    ]
+
+
+def _edge_order_quad(element):
+    return [
+        (element[0], element[1]),
+        (element[1], element[2]),
+        (element[2], element[3]),
+        (element[3], element[0]),
+    ]
+
+
+def _face_order_tetra(element):
+    return [
+        (element[0], element[1], element[2]),
+        (element[0], element[1], element[3]),
+        (element[1], element[2], element[3]),
+        (element[2], element[0], element[3]),
+    ]
+
+
+def _face_order_hex(element):
+    return [
+        (element[0], element[1], element[2], element[3]),
+        (element[4], element[5], element[6], element[7]),
+        (element[0], element[1], element[5], element[4]),
+        (element[1], element[2], element[6], element[5]),
+        (element[2], element[3], element[7], element[6]),
+        (element[3], element[0], element[4], element[7]),
+    ]
+
+
+def _face_order_wface(element):
+    return [
+        (element[0], element[1], element[2]),
+        (element[3], element[4], element[5]),
+        (element[0], element[3], element[4], element[1]),
+        (element[1], element[4], element[5], element[2]),
+        (element[2], element[5], element[3], element[0]),
+    ]
+
+
+def _get_num_vertices_per_face(mesh_type) -> float:
+    if mesh_type == "triangle":
+        return [2, 2, 2]
+    elif mesh_type == "quad":
+        return [2, 2, 2, 2]
+    elif mesh_type == "tetra":
+        return [3, 3, 3, 3]
+    elif mesh_type == "hexahedron":
+        return [4, 4, 4, 4, 4, 4]
+    elif mesh_type == "wface":
+        return [3, 3, 4, 4, 4]
+    assert False
+
+
+def _get_dimension(mesh_type):
+    if mesh_type == "triangle":
+        return 2
+    elif mesh_type == "quad":
+        return 2
+    elif mesh_type == "tetra":
+        return 3
+    elif mesh_type == "hexahedron":
+        return 3
+    else:
+        assert False
+
+
+def _get_faces_per_element(mesh_type):
+    if mesh_type == "line":
+        return 2
+    elif mesh_type == "triangle":
+        return 3
+    elif mesh_type == "quad":
+        return 4
+    elif mesh_type == "tetra":
+        return 4
+    elif mesh_type == "hexahedron":
+        return 6
+    elif mesh_type == "wface":
+        return 5
+    else:
+        assert False
+
+
+def _get_boundary_element_type(mesh_type):
+    if mesh_type == "triangle":
+        return ["line", "line", "line"]
+    elif mesh_type == "quad":
+        return ["line", "line", "line", "line"]
+    elif mesh_type == "tetra":
+        return ["triangle", "triangle", "triangle", "triangle"]
+    elif mesh_type == "hexahedron":
+        return ["quad", "quad", "quad", "quad", "quad", "quad"]
+    elif mesh_type == "wface":
+        return ["triangle", "triangle", "quad", "quad", "quad"]
+    else:
+        assert False
+
+
+def find_edge_index(element, edge_vertices, element_type):
+    edges = _face_order(element, element_type)
+    for i_edge, edge in enumerate(edges):
+        if set(edge).issubset(edge_vertices):
+            return i_edge
+    assert False
+
+
+def compute_subvolume(face_vertices, cell_center, dim):
+    """
+    Computes the subvolume of a face given its vertices and the cell center.
+
+    Parameters:
+    face_vertices (np.ndarray): The coordinates of the vertices of the face.
+    cell_center (np.ndarray): The coordinates of the cell center.
+    dim (int): The dimensionality of the problem (1, 2, or 3).
+
+    Returns:
+    float: The subvolume of the face.
+    """
+    if dim == 1:
+        # 1D: Length of the line segment
+        return np.abs(face_vertices[1] - face_vertices[0])
+
+    elif dim == 2:
+        # 2D: Area of the triangle
+        v0, v1 = face_vertices
+        return 0.5 * np.abs(np.cross(v1 - v0, cell_center - v0))
+
+    elif dim == 3:
+        if face_vertices.shape[0] == 3:
+            # 3D: Volume of the tetrahedron
+            v0, v1, v2 = face_vertices
+            return np.abs(np.dot(np.cross(v1 - v0, v2 - v0), cell_center - v0)) / 6.0
+        elif face_vertices.shape[0] == 4:
+            # 3D: Volume of the pyramid
+            # WARNING crude approximation
+            v0, v1, v2 = face_vertices
+            return np.abs(np.dot(np.cross(v1 - v0, v2 - v0), cell_center - v0)) / 6.0
+        else:
+            assert False
+
+    else:
+        raise ValueError("Unsupported dimensionality")

zoomy_core/misc/custom_types.py

@@ -0,0 +1,6 @@
+import numpy as np
+import numpy.typing as npt
+
+FArray = npt.NDArray[np.float64]
+IArray = npt.NDArray[np.int64]
+CArray = npt.NDArray[np.str_]