phiFEM 0.7.2.dev2__py3-none-any.whl → 0.8.1.dev1__py3-none-any.whl

phifem/mesh_scripts.py

@@ -397,10 +397,50 @@ def _transfer_tags(
     return dest_entities_tags
 
 
+def _remove_isolated_cells(
+    mesh: dfx.mesh.Mesh,
+    exterior_indices: np.ndarray[np.int32],
+    cut_indices: np.ndarray[np.int32],
+    interior_indices: np.ndarray[np.int32],
+):
+    cdim = mesh.topology.dim
+    vdim = 0
+    # Create the cell to facet connectivity and reshape it into an array s.t. c2f_map[cell_index] = [facets of this cell index]
+    mesh.topology.create_connectivity(cdim, vdim)
+    c2v_connect = mesh.topology.connectivity(cdim, vdim)
+    num_vertices_per_cell = len(c2v_connect.links(0))
+    c2v_map = np.reshape(c2v_connect.array, (-1, num_vertices_per_cell))
+
+    mesh.topology.create_connectivity(vdim, cdim)
+    v2c_connect = mesh.topology.connectivity(vdim, cdim)
+    v2c_map, max_offset = _reshape_map(v2c_connect)
+
+    neighbor_cells = np.reshape(
+        v2c_map[c2v_map[cut_indices]], (-1, num_vertices_per_cell * max_offset)
+    )
+    mask_no_interior_connected = ~np.any(
+        np.isin(neighbor_cells, interior_indices), axis=1
+    )
+    mask_no_exterior_connected = ~np.any(
+        np.isin(neighbor_cells, exterior_indices), axis=1
+    )
+
+    cut_disconnected_interior = cut_indices[mask_no_interior_connected]
+    cut_disconnected_exterior = cut_indices[mask_no_exterior_connected]
+
+    cut_indices = np.setdiff1d(
+        cut_indices, np.union1d(cut_disconnected_interior, cut_disconnected_exterior)
+    )
+    exterior_indices = np.union1d(exterior_indices, cut_disconnected_interior)
+    interior_indices = np.union1d(interior_indices, cut_disconnected_exterior)
+
+    return exterior_indices, cut_indices, interior_indices
+
+
 def _tag_cells(
     mesh: Mesh,
     levelset_expression: Expression,
-    single_layer_cut: bool = False,
+    single_layer_cut: bool,
 ) -> MeshTags:
     """Tag the mesh cells by computing detection = Σ f(dof)/Σ|f(dof)| where 'dof' are coming from a custom quadrature rule with points on the boundary of the cell only.
         Strictly inside cell  => tag 1
@@ -431,26 +471,9 @@ def _tag_cells(
     cut_indices = np.where(cut)[0]
 
     if single_layer_cut:
-        vdim = 0
-        # Create the cell to facet connectivity and reshape it into an array s.t. c2f_map[cell_index] = [facets of this cell index]
-        mesh.topology.create_connectivity(cdim, vdim)
-        c2v_connect = mesh.topology.connectivity(cdim, vdim)
-        num_vertices_per_cell = len(c2v_connect.links(0))
-        c2v_map = np.reshape(c2v_connect.array, (-1, num_vertices_per_cell))
-
-        mesh.topology.create_connectivity(vdim, cdim)
-        v2c_connect = mesh.topology.connectivity(vdim, cdim)
-        v2c_map, max_offset = _reshape_map(v2c_connect)
-
-        neighbor_cells = np.reshape(
-            v2c_map[c2v_map[cut_indices]], (-1, num_vertices_per_cell * max_offset)
-        )
-        mask_connected_cut_cells = np.any(
-            np.isin(neighbor_cells, interior_indices), axis=1
+        exterior_indices, cut_indices, interior_indices = _remove_isolated_cells(
+            mesh, exterior_indices, cut_indices, interior_indices
         )
-        isolated_cut_cells = cut_indices[~mask_connected_cut_cells]
-        cut_indices = np.setdiff1d(cut_indices, isolated_cut_cells)
-        exterior_indices = np.union1d(exterior_indices, isolated_cut_cells)
 
     if debug_mode:
         if len(interior_indices) == 0:
@@ -480,7 +503,6 @@ def _tag_cells(
     cells_tags = dfx.mesh.meshtags(
         mesh, mesh.topology.dim, indices[sorted_indices], markers[sorted_indices]
     )
-
     return cells_tags
 
 
@@ -506,9 +528,9 @@ def _cells_facets_pairs(f2c_map, c2f_map, facets):
 def _tag_facets(
     mesh: Mesh,
     levelset_expression_facets: Expression,
+    single_layer_cut: bool,
     cells_tags: MeshTags | None = None,
     levelset_expression_cells: Expression | None = None,
-    single_layer_cut: bool = False,
 ) -> MeshTags:
     """Tag the mesh facets.
     Strictly interior facets  => tag 1
@@ -531,9 +553,7 @@ def _tag_facets(
         assert levelset_expression_cells is not None, (
             "You must either pass cells_tags or a levelset expression over the cells of the domain."
         )
-        cells_tags = _tag_cells(
-            mesh, levelset_expression_cells, single_layer_cut=single_layer_cut
-        )
+        cells_tags = _tag_cells(mesh, levelset_expression_cells, single_layer_cut)
 
     cdim = mesh.topology.dim
     fdim = cdim - 1
@@ -579,7 +599,10 @@ def _tag_facets(
     cut_indices = np.setdiff1d(cut_indices, direct_indices)
 
     # Compute the list of facets on the boundary of the union of cut cells
-    boundary_cut_indices = _compute_subdomain_exterior_facets(mesh, cells_tags, [2])
+    if len(cells_tags.find(2)) > 0:
+        boundary_cut_indices = _compute_subdomain_exterior_facets(mesh, cells_tags, [2])
+    else:
+        boundary_cut_indices = []
     boundary_exterior_indices = np.intersect1d(boundary_cut_indices, interior_indices)
     boundary_exterior_indices = np.setdiff1d(boundary_exterior_indices, direct_indices)
     interior_indices = np.setdiff1d(interior_indices, boundary_exterior_indices)
@@ -662,6 +685,60 @@ def _overwrite_tags(mesh, tags_to_overwrite, new_tags):
     return overwritten_tags
 
 
+def _compute_codim_interpolation_points(
+    space: dfx.fem.FunctionSpace,
+) -> np.ndarray[np.float64]:
+    """Compute the same FunctionSpace but defined over a submesh of codim 1.
+
+    Args:
+        space: the original space.
+
+    Return: a new space defined on a mesh of codim 1.
+    """
+    family_name = space.ufl_element().basix_element.family.name
+    degree = space.ufl_element().basix_element.degree
+    tdim = space.mesh.topology.dim
+    codim_mesh = dfx.mesh.create_submesh(space.mesh, tdim - 1, np.array([0.0]))[0]
+    codim_cell_name = codim_mesh.topology.cell_name()
+    new_elmt = element(family_name, codim_cell_name, degree)
+    new_space = dfx.fem.functionspace(codim_mesh, new_elmt)
+    return new_space.element.interpolation_points()
+
+
+def _levelset_expression(
+    mesh: dfx.mesh.Mesh,
+    levelset: Function | Callable,
+    interpolation_points: np.NDarray[np.float64],
+) -> Expression:
+    """Sanitize the levelset input by turning it into an Expression.
+
+    Args:
+        levelset: the levelset function.
+        detection_space: the detection space.
+
+    Return: the levelset as an Expression object.
+    """
+
+    # Sanitize levelset input
+    try:
+        # Test if levelset is a dolfinx.fem.Function
+        _ = levelset.function_space
+        levelset_expression = dfx.fem.Expression(
+            levelset, interpolation_points, comm=mesh.comm
+        )
+    except AttributeError:
+        try:
+            x = ufl.SpatialCoordinate(mesh)
+            levelset_expression = dfx.fem.Expression(
+                levelset(x), interpolation_points, comm=mesh.comm
+            )
+        except TypeError:
+            print(
+                "Invalid levelset type: must be either a dolfinx.fem.Function or a UFL based Callable."
+            )
+    return levelset_expression
+
+
 def compute_tags_measures(
     mesh: Mesh,
     levelset: Function | Callable,
@@ -692,27 +769,23 @@ def compute_tags_measures(
         The boundaries measure.
         Submesh c-map, v-map and n-map.
     """
+    interpolation_points = detection_space.element.interpolation_points()
+    levelset_expression = _levelset_expression(mesh, levelset, interpolation_points)
 
-    # Sanitize levelset input
-    try:
-        levelset_expression = dfx.fem.Expression(
-            levelset, detection_space.element.interpolation_points()
-        )
-    except AttributeError:
-        try:
-            x = mesh.SpatialCoordinate(mesh)
-            levelset_expression = dfx.fem.Expression(
-                levelset(x), detection_space.element.interpolation_points()
-            )
-        except TypeError:
-            print(
-                "Invalid levelset type: must be either a dolfinx.fem.Function or a UFL based Callable."
-            )
+    cells_tags = _tag_cells(mesh, levelset_expression, single_layer_cut)
 
-    cells_tags = _tag_cells(
-        mesh, levelset_expression, single_layer_cut=single_layer_cut
+    codim_interpolation_points = _compute_codim_interpolation_points(detection_space)
+    levelset_expression_facets = _levelset_expression(
+        mesh, levelset, codim_interpolation_points
+    )
+
+    facets_tags = _tag_facets(
+        mesh,
+        levelset_expression_facets,
+        single_layer_cut,
+        cells_tags=cells_tags,
+        levelset_expression_cells=levelset_expression,
     )
-    facets_tags = _tag_facets(mesh, cells_tags, discrete_levelset, detection_degree)
 
     if overwrite_tags is not None:
         if "cells" in overwrite_tags:

{phifem-0.7.2.dev2.dist-info → phifem-0.8.1.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: phiFEM
-Version: 0.7.2.dev2
+Version: 0.8.1.dev1
 Summary: phiFEM: convenience tools to use the phiFEM immersed boundary finite element method with dolfinx.
 Project-URL: Homepage, https://github.com/PhiFEM/phiFEM
 Project-URL: Issues, https://github.com/PhiFEM/phiFEM/issues

phifem-0.8.1.dev1.dist-info/RECORD

@@ -0,0 +1,7 @@
+phifem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+phifem/mesh_scripts.py,sha256=AAUsA75d8UVjKTcjbie9Ap9GS0zFBR2rvNPRiAfT9L0,33222
+phifem-0.8.1.dev1.dist-info/METADATA,sha256=9N9PgoSH6zNVh_jN3XSkp_QVseI74H8y-3yYRESOLRM,5606
+phifem-0.8.1.dev1.dist-info/WHEEL,sha256=W3fkpkm7-wf9vBI5Z-7s0eWkeM-spu78I8Neb98DeEg,87
+phifem-0.8.1.dev1.dist-info/licenses/COPYING,sha256=xTplwv1WHIfqq_EHLvXcq4ZTBCvBUwhGX1JBNYXrYnE,35146
+phifem-0.8.1.dev1.dist-info/licenses/COPYING.lesser,sha256=6or154nLLU6bELzjh0mCreFjt0m2v72zLi3yHE0QbeE,7650
+phifem-0.8.1.dev1.dist-info/RECORD,,

phifem-0.7.2.dev2.dist-info/RECORD

@@ -1,7 +0,0 @@
-phifem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-phifem/mesh_scripts.py,sha256=Im8vPg3NxA44qiynUmVkCvyu6C6tYcQLKhJpDY0FJbA,30820
-phifem-0.7.2.dev2.dist-info/METADATA,sha256=pggXcQxyYtwUxScyjZtHvFlmkiakNl8kLtbr9qCdj4s,5606
-phifem-0.7.2.dev2.dist-info/WHEEL,sha256=W3fkpkm7-wf9vBI5Z-7s0eWkeM-spu78I8Neb98DeEg,87
-phifem-0.7.2.dev2.dist-info/licenses/COPYING,sha256=xTplwv1WHIfqq_EHLvXcq4ZTBCvBUwhGX1JBNYXrYnE,35146
-phifem-0.7.2.dev2.dist-info/licenses/COPYING.lesser,sha256=6or154nLLU6bELzjh0mCreFjt0m2v72zLi3yHE0QbeE,7650
-phifem-0.7.2.dev2.dist-info/RECORD,,