phiFEM 0.8.0.dev1__py3-none-any.whl → 0.8.2.dev1__py3-none-any.whl

phifem/mesh_scripts.py

@@ -380,8 +380,9 @@ def _transfer_tags(
     # TODO: change this line to allow parallel computing
     source_tags = source_mesh_tags.values
 
-    dest_entities = np.arange(len(emap))
-    dest_tags = source_tags[emap]
+    num_entities = emap.topology.index_map(edim).size_local
+    dest_entities = np.arange(num_entities)
+    dest_tags = emap.sub_topology_to_topology(source_tags, False)
 
     dest_entities_indices = np.hstack(dest_entities).astype(np.int32)
     dest_entities_markers = np.hstack(dest_tags).astype(np.int32)
@@ -397,10 +398,50 @@ 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 +472,9 @@ 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 +504,6 @@ def _tag_cells(
     cells_tags = dfx.mesh.meshtags(
         mesh, mesh.topology.dim, indices[sorted_indices], markers[sorted_indices]
     )
-
     return cells_tags
 
 
@@ -506,9 +529,9 @@ 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 +554,7 @@ 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
@@ -550,21 +571,30 @@ def _tag_facets(
     interior_facets = np.setdiff1d(all_facets, boundary_facets)
 
     cell_facet_pairs = _cells_facets_pairs(f2c_map, c2f_map, interior_facets)
-    levelset_eval_int = levelset_expression_facets.eval(mesh, cell_facet_pairs)
+    levelset_eval_int = levelset_expression_facets.eval(
+        mesh, cell_facet_pairs.reshape(-1, 2)
+    )
 
-    exterior_int = np.min(levelset_eval_int, axis=1) > 0.0
-    interior_int = np.max(levelset_eval_int, axis=1) < 0.0
+    geq_zero_int = np.greater_equal(np.min(levelset_eval_int, axis=1), 0.0)
+    leq_zero_int = np.less_equal(np.max(levelset_eval_int, axis=1), 0.0)
     direct_int = np.isclose(np.sum(np.abs(levelset_eval_int), axis=1), 0.0)
+    exterior_int = np.logical_and(geq_zero_int, ~direct_int)
+    interior_int = np.logical_and(leq_zero_int, ~direct_int)
 
     connected_cells = f2c_map[boundary_facets][:, 0]
 
     cell_facet_pairs = _compute_integration_entities(
         mesh, connected_cells, boundary_facets, 0
     )[0][1]
-    levelset_eval_bdy = levelset_expression_facets.eval(mesh, cell_facet_pairs)
-    exterior_bdy = np.min(levelset_eval_bdy, axis=1) > 0.0
-    interior_bdy = np.max(levelset_eval_bdy, axis=1) < 0.0
+    levelset_eval_bdy = levelset_expression_facets.eval(
+        mesh, cell_facet_pairs.reshape(-1, 2)
+    )
+
+    geq_zero_bdy = np.greater_equal(np.min(levelset_eval_bdy, axis=1), 0.0)
+    leq_zero_bdy = np.less_equal(np.max(levelset_eval_bdy, axis=1), 0.0)
     direct_bdy = np.isclose(np.sum(np.abs(levelset_eval_bdy), axis=1), 0.0)
+    exterior_bdy = np.logical_and(geq_zero_bdy, ~direct_bdy)
+    interior_bdy = np.logical_and(leq_zero_bdy, ~direct_bdy)
 
     facets_indices = np.hstack([interior_facets, boundary_facets])
     exterior = np.hstack([exterior_int, exterior_bdy])
@@ -579,7 +609,10 @@ 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)
@@ -679,7 +712,7 @@ def _compute_codim_interpolation_points(
     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()
+    return new_space.element.interpolation_points
 
 
 def _levelset_expression(
@@ -746,12 +779,10 @@ def compute_tags_measures(
         The boundaries measure.
         Submesh c-map, v-map and n-map.
     """
-    interpolation_points = detection_space.element.interpolation_points()
+    interpolation_points = detection_space.element.interpolation_points
     levelset_expression = _levelset_expression(mesh, levelset, interpolation_points)
 
-    cells_tags = _tag_cells(
-        mesh, levelset_expression, single_layer_cut=single_layer_cut
-    )
+    cells_tags = _tag_cells(mesh, levelset_expression, single_layer_cut)
 
     codim_interpolation_points = _compute_codim_interpolation_points(detection_space)
     levelset_expression_facets = _levelset_expression(
@@ -761,9 +792,9 @@ def compute_tags_measures(
     facets_tags = _tag_facets(
         mesh,
         levelset_expression_facets,
-        cells_tags,
-        levelset_expression,
-        single_layer_cut=single_layer_cut,
+        single_layer_cut,
+        cells_tags=cells_tags,
+        levelset_expression_cells=levelset_expression,
     )
 
     if overwrite_tags is not None:

{phifem-0.8.0.dev1.dist-info → phifem-0.8.2.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: phiFEM
-Version: 0.8.0.dev1
+Version: 0.8.2.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
@@ -12,7 +12,7 @@ License-File: COPYING.lesser
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.9
-Requires-Dist: fenics-dolfinx==0.9.0
+Requires-Dist: fenics-dolfinx<0.11,>=0.9.0
 Description-Content-Type: text/markdown
 
 <p align="center" width="100%">

phifem-0.8.2.dev1.dist-info/RECORD

@@ -0,0 +1,7 @@
+phifem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+phifem/mesh_scripts.py,sha256=TIAGOjbfsHLrBFbNgvjs08iLEAPTabx-vrYUjmPcy0w,33678
+phifem-0.8.2.dev1.dist-info/METADATA,sha256=dQqGlLjoQ9B5uEGV9c_Gn-qZJeg-xsxQYyHUsceXlLY,5612
+phifem-0.8.2.dev1.dist-info/WHEEL,sha256=2iZrJkDIkeDh0k9SikKMqFuRP-ua6mb4Ir1AsER4BEw,87
+phifem-0.8.2.dev1.dist-info/licenses/COPYING,sha256=xTplwv1WHIfqq_EHLvXcq4ZTBCvBUwhGX1JBNYXrYnE,35146
+phifem-0.8.2.dev1.dist-info/licenses/COPYING.lesser,sha256=6or154nLLU6bELzjh0mCreFjt0m2v72zLi3yHE0QbeE,7650
+phifem-0.8.2.dev1.dist-info/RECORD,,

{phifem-0.8.0.dev1.dist-info → phifem-0.8.2.dev1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.32.4
+Generator: hatchling 1.33.0
 Root-Is-Purelib: true
 Tag: py3-none-any

phifem-0.8.0.dev1.dist-info/RECORD

@@ -1,7 +0,0 @@
-phifem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-phifem/mesh_scripts.py,sha256=g9G_QjgERcNNdo26tCGymidLYaCRzSvMYwVaCOmiDIs,32508
-phifem-0.8.0.dev1.dist-info/METADATA,sha256=jFmzNbqBlHFois1398voBC6m7rJyKoUpT_a6s_seKGI,5606
-phifem-0.8.0.dev1.dist-info/WHEEL,sha256=W3fkpkm7-wf9vBI5Z-7s0eWkeM-spu78I8Neb98DeEg,87
-phifem-0.8.0.dev1.dist-info/licenses/COPYING,sha256=xTplwv1WHIfqq_EHLvXcq4ZTBCvBUwhGX1JBNYXrYnE,35146
-phifem-0.8.0.dev1.dist-info/licenses/COPYING.lesser,sha256=6or154nLLU6bELzjh0mCreFjt0m2v72zLi3yHE0QbeE,7650
-phifem-0.8.0.dev1.dist-info/RECORD,,