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Vertex submesh support #3455

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merged 8 commits into from
Oct 7, 2024
Merged

Vertex submesh support #3455

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2d6b40e
Add tests for submesh of vertices
jorgensd Oct 5, 2024
2d19c4d
Redirect basix branch
jorgensd Oct 5, 2024
50f48f6
Ruff formatting
jorgensd Oct 5, 2024
9fa907d
Add fixes and simplifications for submesh of vertices
jorgensd Oct 5, 2024
a602cc2
Tidy up test
jorgensd Oct 5, 2024
965b7f3
Ignore when edim becomes negative by setting to zero in parametrized …
jorgensd Oct 5, 2024
809db42
Revert branches
jorgensd Oct 7, 2024
e86432c
Remove formatting error
jorgensd Oct 7, 2024
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6 changes: 3 additions & 3 deletions .github/workflows/ccpp.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ jobs:
if: github.event_name != 'workflow_dispatch'
run: |
pip install git+https://github.com/FEniCS/ufl.git
pip install git+https://github.com/FEniCS/basix.git
pip install git+https://github.com/FEniCS/basix.git@dokken/vertex-submesh
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pip install git+https://github.com/FEniCS/ffcx.git
- name: Install FEniCS Python components
if: github.event_name == 'workflow_dispatch'
Expand Down Expand Up @@ -173,7 +173,7 @@ jobs:
if: github.event_name != 'workflow_dispatch'
run: |
pip install git+https://github.com/FEniCS/ufl.git
pip install git+https://github.com/FEniCS/basix.git
pip install git+https://github.com/FEniCS/basix.git@dokken/vertex-submesh
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pip install git+https://github.com/FEniCS/ffcx.git

- name: Install FEniCS Python components
Expand Down Expand Up @@ -251,7 +251,7 @@ jobs:
if: github.event_name != 'workflow_dispatch'
run: |
pip install git+https://github.com/FEniCS/ufl.git
pip install git+https://github.com/FEniCS/basix.git
pip install git+https://github.com/FEniCS/basix.git@dokken/vertex-submesh
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pip install git+https://github.com/FEniCS/ffcx.git
- name: Install FEniCS Python components
if: github.event_name == 'workflow_dispatch'
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/macos.yml
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Expand Up @@ -62,7 +62,7 @@ jobs:

- name: Install FEniCSx dependencies
run: |
python -m pip install git+https://github.com/FEniCS/basix.git
python -m pip install git+https://github.com/FEniCS/basix.git@dokken/vertex-submesh
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python -m pip install git+https://github.com/FEniCS/ufl.git
python -m pip install git+https://github.com/FEniCS/ffcx.git

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2 changes: 1 addition & 1 deletion .github/workflows/oneapi.yml
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Expand Up @@ -52,7 +52,7 @@ jobs:
conda list

- name: Install Basix
run: pip install --no-build-isolation git+https://github.com/FEniCS/basix.git
run: pip install --no-build-isolation git+https://github.com/FEniCS/basix.git@dokken/vertex-submesh
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- name: Clone FFCx
uses: actions/checkout@v4
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2 changes: 1 addition & 1 deletion .github/workflows/pyvista.yml
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Expand Up @@ -39,7 +39,7 @@ jobs:
- name: Install FEniCS Python components
run: |
pip install git+https://github.com/FEniCS/ufl.git
pip install git+https://github.com/FEniCS/basix.git
pip install git+https://github.com/FEniCS/basix.git@dokken/vertex-submesh
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pip install git+https://github.com/FEniCS/ffcx.git
apt-get update
apt-get install -y --no-install-recommends libgl1-mesa-dev xvfb # pyvista
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/redhat.yml
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Expand Up @@ -31,7 +31,7 @@ jobs:
- name: Install FEniCS Python components
run: |
python3 -m pip install git+https://github.com/FEniCS/ufl.git
python3 -m pip install git+https://github.com/FEniCS/basix.git
python3 -m pip install git+https://github.com/FEniCS/basix.git@dokken/vertex-submesh
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python3 -m pip install git+https://github.com/FEniCS/ffcx.git

- name: Configure C++
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2 changes: 1 addition & 1 deletion .github/workflows/sonarcloud.yml
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Expand Up @@ -59,7 +59,7 @@ jobs:
- name: Install FEniCS Python components
run: |
python3 -m pip install git+https://github.com/FEniCS/ufl.git
python3 -m pip install git+https://github.com/FEniCS/basix.git
python3 -m pip install git+https://github.com/FEniCS/basix.git@dokken/vertex-submesh
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python3 -m pip install git+https://github.com/FEniCS/ffcx.git
- name: Run build-wrapper
run: |
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7 changes: 6 additions & 1 deletion cpp/dolfinx/mesh/utils.h
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Expand Up @@ -1250,7 +1250,12 @@ create_subgeometry(const Mesh<T>& mesh, int dim,
// Create sub-geometry coordinate element
CellType sub_coord_cell
= cell_entity_type(geometry.cmap().cell_shape(), dim, 0);
fem::CoordinateElement<T> sub_cmap(sub_coord_cell, geometry.cmap().degree(),
// Special handling if point meshes, as they only support constant basis
// functions
int degree = geometry.cmap().degree();
if (sub_coord_cell == CellType::point)
degree = 0;
fem::CoordinateElement<T> sub_cmap(sub_coord_cell, degree,
geometry.cmap().variant());

// Sub-geometry input_global_indices
Expand Down
3 changes: 1 addition & 2 deletions python/dolfinx/mesh.py
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Expand Up @@ -675,11 +675,10 @@ def create_submesh(
submsh, entity_map, vertex_map, geom_map = _cpp.mesh.create_submesh(
msh._cpp_object, dim, entities
)
submsh_ufl_cell = ufl.Cell(to_string(submsh.topology.cell_type))
submsh_domain = ufl.Mesh(
basix.ufl.element(
"Lagrange",
submsh_ufl_cell.cellname(),
to_string(submsh.topology.cell_type),
submsh.geometry.cmap.degree,
basix.LagrangeVariant(submsh.geometry.cmap.variant),
shape=(submsh.geometry.dim,),
Expand Down
16 changes: 9 additions & 7 deletions python/test/unit/mesh/test_mesh.py
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Expand Up @@ -503,35 +503,37 @@ def boundary_2(x):


# TODO Test that submesh of full mesh is a copy of the mesh
@pytest.mark.parametrize("d", [2, 3])
@pytest.mark.parametrize("d", [1, 2, 3])
@pytest.mark.parametrize("n", [3, 6])
@pytest.mark.parametrize("codim", [0, 1, 2])
@pytest.mark.parametrize("marker", [lambda x: x[0] >= 0.5, lambda x: x[0] >= -1])
@pytest.mark.parametrize("ghost_mode", [GhostMode.none, GhostMode.shared_facet])
@pytest.mark.parametrize("simplex", [True, False])
def test_submesh_full(d, n, codim, marker, ghost_mode, simplex):
if d == codim:
pytest.xfail("Cannot create vertex submesh")
if d == 2:
if d == 1:
mesh = create_unit_interval(MPI.COMM_WORLD, n, ghost_mode=ghost_mode)
elif d == 2:
ct = CellType.triangle if simplex else CellType.quadrilateral
mesh = create_unit_square(MPI.COMM_WORLD, n, n, ghost_mode=ghost_mode, cell_type=ct)
else:
ct = CellType.tetrahedron if simplex else CellType.hexahedron
mesh = create_unit_cube(MPI.COMM_WORLD, n, n, n, ghost_mode=ghost_mode, cell_type=ct)

edim = mesh.topology.dim - codim
edim = max(mesh.topology.dim - codim, 0)
entities = locate_entities(mesh, edim, marker)
submesh, entity_map, vertex_map, geom_map = create_submesh(mesh, edim, entities)
submesh_topology_test(mesh, submesh, entity_map, vertex_map, edim)
submesh_geometry_test(mesh, submesh, entity_map, geom_map, edim)


@pytest.mark.parametrize("d", [2, 3])
@pytest.mark.parametrize("d", [1, 2, 3])
@pytest.mark.parametrize("n", [3, 6])
@pytest.mark.parametrize("boundary", [boundary_0, boundary_1, boundary_2])
@pytest.mark.parametrize("ghost_mode", [GhostMode.none, GhostMode.shared_facet])
def test_submesh_boundary(d, n, boundary, ghost_mode):
if d == 2:
if d == 1:
mesh = create_unit_interval(MPI.COMM_WORLD, n, ghost_mode=ghost_mode)
elif d == 2:
mesh = create_unit_square(MPI.COMM_WORLD, n, n, ghost_mode=ghost_mode)
else:
mesh = create_unit_cube(MPI.COMM_WORLD, n, n, n, ghost_mode=ghost_mode)
Expand Down
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