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"""
This module test the utils.fenicsx class
"""
import pytest
from packaging.version import Version
def test_square_netgen():
"""
Testing FEniCSx interface with Netgen generating a square mesh
"""
try:
from mpi4py import MPI
import ngsPETSc.utils.fenicsx as ngfx
except ImportError:
pytest.skip("DOLFINx unavailable, skipping FENICSx test")
from netgen.geom2d import SplineGeometry
geo = SplineGeometry()
geo.AddRectangle((0, 0), (1, 1))
geoModel = ngfx.GeometricModel(geo, MPI.COMM_WORLD)
geoModel.model_to_mesh(hmax=0.1)
def test_poisson_netgen():
"""
Testing FEniCSx interface with Netgen generating a square mesh
"""
try:
import numpy as np
import ufl
from dolfinx import __version__ as dfx_version
from dolfinx import fem, mesh
from dolfinx.fem.petsc import LinearProblem
from ufl import dx, grad, inner
from mpi4py import MPI
from petsc4py.PETSc import ScalarType
import ngsPETSc.utils.fenicsx as ngfx
except ImportError:
pytest.skip("DOLFINx unavailable, skipping FENICSx test")
from netgen.geom2d import SplineGeometry
geo = SplineGeometry()
geo.AddRectangle((0, 0), (np.pi, np.pi))
geoModel = ngfx.GeometricModel(geo, MPI.COMM_WORLD)
msh, _, _ = geoModel.model_to_mesh(hmax=0.1)
V = fem.functionspace(msh, ("Lagrange", 2)) # pylint: disable=E1120
facetsLR = mesh.locate_entities_boundary(
msh,
dim=(msh.topology.dim - 1),
marker=lambda x: np.logical_or(np.isclose(x[0], 0.0), np.isclose(x[0], np.pi)),
)
facetsTB = mesh.locate_entities_boundary(
msh,
dim=(msh.topology.dim - 1),
marker=lambda x: np.logical_or(np.isclose(x[1], 0.0), np.isclose(x[1], np.pi)),
)
facets = np.append(facetsLR, facetsTB)
dofs = fem.locate_dofs_topological(V=V, entity_dim=1, entities=facets)
bc = fem.dirichletbc(value=ScalarType(0), dofs=dofs, V=V)
u = ufl.TrialFunction(V)
v = ufl.TestFunction(V)
x = ufl.SpatialCoordinate(msh)
f = ufl.exp(ufl.sin(x[0]) * ufl.sin(x[1]))
a = inner(grad(u), grad(v)) * dx
L = inner(f, v) * dx
# Backward compatibility
if Version(dfx_version) < Version("0.10.0"):
options = {}
else:
options = {"petsc_options_prefix": "test_solver"}
problem = LinearProblem(
a,
L,
bcs=[bc],
petsc_options={"ksp_type": "preonly", "pc_type": "lu"},
**options,
)
problem.solve()
@pytest.mark.parametrize("order", [1, 2, 3])
def test_markers(order):
"""Test cell and facet markers."""
try:
from mpi4py import MPI
import ngsPETSc.utils.fenicsx as ngfx
import dolfinx
import ufl
from netgen.occ import OCCGeometry, WorkPlane, Glue
import numpy as np
except ImportError:
pytest.skip("DOLFINx unavailable, skipping FENICSx test.")
wp = WorkPlane()
square = wp.Rectangle(1, 1).Face()
disk = wp.Circle(0.2, 0.2, 0.1).Face()
disk.edges.name = "circle"
disk.faces.name = "circle"
shape = Glue([square, disk])
geo = OCCGeometry(shape, dim=2)
geoModel = ngfx.GeometricModel(geo, MPI.COMM_WORLD)
gm = dolfinx.mesh.GhostMode.shared_facet
partitioner = dolfinx.mesh.create_cell_partitioner(gm)
_, (ct, _), region_map = geoModel.model_to_mesh(hmax=0.02, partitioner=partitioner)
curved_domain = geoModel.curveField(order)
steel_circle = region_map[(2, "circle")]
_, (ct_refined, ft_refined) = geoModel.refineMarkedElements(
ct.dim, ct.indices[np.isin(ct.values, steel_circle)]
)
curved_domain = geoModel.curveField(order)
# Integrate over interior marked interface
dS = ufl.Measure("dS", domain=curved_domain, subdomain_data=ft_refined)
crack_integer_marker = region_map[(1, "circle")]
local_interface = dolfinx.fem.assemble_scalar(
dolfinx.fem.form(1 * dS(crack_integer_marker))
)
interface = curved_domain.comm.allreduce(local_interface, op=MPI.SUM)
# Integrate over marked subdomain
dx = ufl.Measure("dx", domain=curved_domain, subdomain_data=ct_refined)
steel_circle = region_map[(2, "circle")]
local_area = dolfinx.fem.assemble_scalar(dolfinx.fem.form(1 * dx(steel_circle)))
area = curved_domain.comm.allreduce(local_area, op=MPI.SUM)
if order == 1:
tol = 5e-4
else:
tol = 1e-6
assert np.isclose(interface, 2 * np.pi * 0.1, atol=tol, rtol=tol)
assert np.isclose(area, np.pi * 0.1**2, atol=tol, rtol=tol)
@pytest.mark.parametrize("order", [1, 2, 3])
def test_refine(order):
"""Test mesh refinement (with curving)."""
try:
from mpi4py import MPI
import ngsPETSc.utils.fenicsx as ngfx
import dolfinx
import ufl
from netgen.csg import Sphere, Pnt, CSGeometry
import numpy as np
except ImportError:
pytest.skip("DOLFINx unavailable, skipping FENICSx test.")
center0 = Pnt(0, 0, 0)
center1 = Pnt(0.2, 0.2, 0)
radius0 = 1
radius1 = 0.3
sphere0 = Sphere(center0, radius0)
sphere0.bc("Outer")
sphere0.mat("Material")
sphere1 = Sphere(center1, radius1)
sphere1.bc("Inner")
shape = sphere0 - sphere1
geo = CSGeometry()
geo.Add(shape)
geoModel = ngfx.GeometricModel(geo, MPI.COMM_WORLD)
gm = dolfinx.mesh.GhostMode.shared_facet
partitioner = dolfinx.mesh.create_cell_partitioner(gm)
if order == 1:
hmax = 0.08
else:
hmax = 0.1
mesh, (_, _), region_map = geoModel.model_to_mesh(
hmax=hmax, partitioner=partitioner, gdim=3
)
mesh = geoModel.curveField(order)
def locate_facets(x):
return np.isclose(x[0] ** 2 + x[1] ** 2 + x[2] ** 2, radius0)
facets = dolfinx.mesh.locate_entities_boundary(
mesh, mesh.topology.dim - 1, locate_facets
)
refined_mesh, (_, ft_refined) = geoModel.refineMarkedElements(
mesh.topology.dim - 1, facets
)
refined_mesh = geoModel.curveField(order)
local_vol = dolfinx.fem.assemble_scalar(
dolfinx.fem.form(1 * ufl.dx(domain=refined_mesh))
)
vol = refined_mesh.comm.allreduce(local_vol, op=MPI.SUM)
ds = ufl.ds(domain=refined_mesh, subdomain_data=ft_refined)
inner_area = dolfinx.fem.form(1 * ds(region_map[(2, "Inner")]))
outer_area = dolfinx.fem.form(1 * ds(region_map[(2, "Outer")]))
local_inner = dolfinx.fem.assemble_scalar(inner_area)
local_outer = dolfinx.fem.assemble_scalar(outer_area)
inner = refined_mesh.comm.allreduce(local_inner, op=MPI.SUM)
outer = refined_mesh.comm.allreduce(local_outer, op=MPI.SUM)
if order == 1:
tol = 5e-3
else:
tol = 5e-5
assert np.isclose(
vol, 4 / 3 * np.pi * radius0**3 - 4 / 3 * np.pi * radius1**3, rtol=tol
)
assert np.isclose(inner, 4 * np.pi * radius1**2, rtol=tol)
assert np.isclose(outer, 4 * np.pi * radius0**2, rtol=tol)
@pytest.mark.parametrize("partitioner",
["partitioner", "partitioner_kahip", "partitioner_scotch"])
def test_mixed(partitioner):
"""
Testing FEniCSx interface with Netgen generating a square mesh
"""
try:
from mpi4py import MPI
import dolfinx
import ngsPETSc.utils.fenicsx as ngfx
except ImportError:
pytest.skip("DOLFINx unavailable, skipping FENICSx test")
if not hasattr(dolfinx.cpp.mesh.Topology, "original_cell_indices"):
pytest.skip("DOLFINx version does not support mixed meshes")
if hasattr(dolfinx.graph, partitioner):
partitioner_fn = getattr(dolfinx.graph, partitioner)
else:
pytest.skip(f"DOLFINx version does not support graph.{partitioner}")
from netgen.geom2d import SplineGeometry
geo = SplineGeometry()
geo.AddCircle((1, 1.2), 1)
geoModel = ngfx.GeometricModel(geo, MPI.COMM_WORLD)
part = dolfinx.mesh.create_cell_partitioner(
partitioner_fn(), dolfinx.mesh.GhostMode.none
)
domain, _, _ = geoModel.model_to_mesh(
hmax=0.4, meshing_options={"quad_dominated": True}, partitioner=part, gdim=2
)
assert len(domain.topology._cpp_object.cell_types) == 2 # pylint: disable=W0212
domain = geoModel.curveField(2)
from dolfinx.io.vtkhdf import write_mesh
write_mesh("mixed_mesh.vtkhdf", domain)
if __name__ == "__main__":
test_square_netgen()
test_poisson_netgen()
test_markers(2)
test_refine(3)
test_mixed()
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