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# Copyright (C) 2012-2019 Garth N. Wells
#
# This file is part of DOLFINx (https://www.fenicsproject.org)
#
# SPDX-License-Identifier: LGPL-3.0-or-later
from pathlib import Path
from mpi4py import MPI
import numpy as np
import pytest
import basix
from dolfinx import default_real_type
from dolfinx.fem import Function, functionspace
from dolfinx.io import XDMFFile
from dolfinx.mesh import CellType, create_unit_cube, create_unit_interval, create_unit_square
# Supported XDMF file encoding
if MPI.COMM_WORLD.size > 1:
encodings = [XDMFFile.Encoding.HDF5]
else:
encodings = [XDMFFile.Encoding.HDF5, XDMFFile.Encoding.ASCII]
celltypes_2D = [CellType.triangle, CellType.quadrilateral]
celltypes_3D = [CellType.tetrahedron, CellType.hexahedron]
def mesh_factory(tdim, n):
if tdim == 1:
return create_unit_interval(MPI.COMM_WORLD, n)
elif tdim == 2:
return create_unit_square(MPI.COMM_WORLD, n, n)
elif tdim == 3:
return create_unit_cube(MPI.COMM_WORLD, n, n, n)
# --- Function
@pytest.mark.parametrize("use_pathlib", [True, False])
@pytest.mark.parametrize("encoding", encodings)
@pytest.mark.parametrize("dtype", [np.double, np.complex128])
def test_save_1d_scalar(tempdir, encoding, dtype, use_pathlib):
xtype = np.real(dtype(0)).dtype
filename2 = Path(tempdir).joinpath("u1_.xdmf") if use_pathlib else Path(tempdir, "u1_.xdmf")
mesh = create_unit_interval(MPI.COMM_WORLD, 32, dtype=xtype)
V = functionspace(mesh, ("Lagrange", 2))
u = Function(V, dtype=dtype)
u.x.array[:] = 1.0 + (1j if np.issubdtype(dtype, np.complexfloating) else 0)
with pytest.raises(RuntimeError):
with XDMFFile(mesh.comm, filename2, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u)
V1 = functionspace(mesh, ("Lagrange", 1))
u1 = Function(V1, dtype=dtype)
u1.interpolate(u)
with XDMFFile(mesh.comm, filename2, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u1)
@pytest.mark.parametrize("cell_type", celltypes_2D)
@pytest.mark.parametrize("encoding", encodings)
@pytest.mark.parametrize("dtype", [np.double, np.complex128])
def test_save_2d_scalar(tempdir, encoding, dtype, cell_type):
xtype = np.real(dtype(0)).dtype
filename = Path(tempdir, "u2.xdmf")
mesh = create_unit_square(MPI.COMM_WORLD, 12, 12, cell_type, dtype=xtype)
V = functionspace(mesh, ("Lagrange", 2))
u = Function(V, dtype=dtype)
u.x.array[:] = 1.0
V1 = functionspace(mesh, ("Lagrange", 1))
u1 = Function(V1, dtype=dtype)
u1.interpolate(u)
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u1)
# Discontinuous (degree == 0)
V = functionspace(mesh, ("Discontinuous Lagrange", 0))
u = Function(V, dtype=dtype)
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u)
# Discontinuous (degree > 0) should raise exception
V = functionspace(mesh, ("Discontinuous Lagrange", 1))
u = Function(V, dtype=dtype)
with pytest.raises(RuntimeError):
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u)
@pytest.mark.parametrize("cell_type", celltypes_3D)
@pytest.mark.parametrize("encoding", encodings)
@pytest.mark.parametrize("dtype", [np.double, np.complex128])
def test_save_3d_scalar(tempdir, encoding, dtype, cell_type):
xtype = np.real(dtype(0)).dtype
filename = Path(tempdir, "u3.xdmf")
mesh = create_unit_cube(MPI.COMM_WORLD, 4, 3, 4, cell_type, dtype=xtype)
V = functionspace(mesh, ("Lagrange", 2))
u = Function(V, dtype=dtype)
u.x.array[:] = 1.0
V1 = functionspace(mesh, ("Lagrange", 1))
u1 = Function(V1, dtype=dtype)
u1.interpolate(u)
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u1)
@pytest.mark.parametrize("cell_type", celltypes_2D)
@pytest.mark.parametrize("encoding", encodings)
@pytest.mark.parametrize("dtype", [np.double, np.complex128])
def test_save_2d_vector(tempdir, encoding, dtype, cell_type):
xtype = np.real(dtype(0)).dtype
filename = Path(tempdir, "u_2dv.xdmf")
mesh = create_unit_square(MPI.COMM_WORLD, 12, 13, cell_type, dtype=xtype)
gdim = mesh.geometry.dim
V = functionspace(mesh, ("Lagrange", 2, (gdim,)))
u = Function(V, dtype=dtype)
u.x.array[:] = 1.0 + (1j if np.issubdtype(dtype, np.complexfloating) else 0)
V1 = functionspace(mesh, ("Lagrange", 1, (gdim,)))
u1 = Function(V1, dtype=dtype)
u1.interpolate(u)
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u1)
@pytest.mark.parametrize("cell_type", celltypes_3D)
@pytest.mark.parametrize("encoding", encodings)
@pytest.mark.parametrize("dtype", [np.double, np.complex128])
def test_save_3d_vector(tempdir, encoding, dtype, cell_type):
xtype = np.real(dtype(0)).dtype
filename = Path(tempdir, "u_3Dv.xdmf")
mesh = create_unit_cube(MPI.COMM_WORLD, 2, 2, 2, cell_type, dtype=xtype)
gdim = mesh.geometry.dim
u = Function(functionspace(mesh, ("Lagrange", 1, (gdim,))), dtype=dtype)
u.x.array[:] = 1.0 + (1j if np.issubdtype(dtype, np.complexfloating) else 0)
V1 = functionspace(mesh, ("Lagrange", 1, (gdim,)))
u1 = Function(V1, dtype=dtype)
u1.interpolate(u)
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u1)
V2 = functionspace(mesh, ("RT", 1))
u2 = Function(V2, dtype=dtype)
u2.interpolate(u)
with pytest.raises(RuntimeError):
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u2)
@pytest.mark.parametrize("cell_type", celltypes_2D)
@pytest.mark.parametrize("encoding", encodings)
@pytest.mark.parametrize("dtype", [np.double, np.complex128])
def test_save_2d_tensor(tempdir, encoding, dtype, cell_type):
xtype = np.real(dtype(0)).dtype
filename = Path(tempdir, "tensor.xdmf")
mesh = create_unit_square(MPI.COMM_WORLD, 16, 16, cell_type, dtype=xtype)
gdim = mesh.geometry.dim
u = Function(functionspace(mesh, ("Lagrange", 2, (gdim, gdim))), dtype=dtype)
u.x.array[:] = 1.0 + (1j if np.issubdtype(dtype, np.complexfloating) else 0)
u1 = Function(functionspace(mesh, ("Lagrange", 1, (gdim, gdim))), dtype=dtype)
u1.interpolate(u)
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u1)
@pytest.mark.parametrize("cell_type", celltypes_3D)
@pytest.mark.parametrize("encoding", encodings)
@pytest.mark.parametrize("dtype", [np.float32, np.float64, np.complex64, np.complex128])
def test_save_3d_tensor(tempdir, encoding, dtype, cell_type):
xtype = np.real(dtype(0)).dtype
filename = Path(tempdir, "u3t.xdmf")
mesh = create_unit_cube(MPI.COMM_WORLD, 4, 4, 4, cell_type, dtype=xtype)
gdim = mesh.geometry.dim
u = Function(functionspace(mesh, ("Lagrange", 2, (gdim, gdim))), dtype=dtype)
u.x.array[:] = 1.0 + (1j if np.issubdtype(dtype, np.complexfloating) else 0)
u1 = Function(functionspace(mesh, ("Lagrange", 1, (gdim, gdim))), dtype=dtype)
u1.interpolate(u)
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
file.write_function(u1)
@pytest.mark.parametrize("cell_type", celltypes_3D)
@pytest.mark.parametrize("encoding", encodings)
@pytest.mark.parametrize("dtype", [np.float32, np.float64, np.complex64, np.complex128])
def test_save_3d_vector_series(tempdir, encoding, dtype, cell_type):
filename = Path(tempdir, "u_3D.xdmf")
xtype = np.real(dtype(0)).dtype
mesh = create_unit_cube(MPI.COMM_WORLD, 2, 2, 2, cell_type, dtype=xtype)
gdim = mesh.geometry.dim
u = Function(functionspace(mesh, ("Lagrange", 1, (gdim,))), dtype=dtype)
with XDMFFile(mesh.comm, filename, "w", encoding=encoding) as file:
file.write_mesh(mesh)
u.x.array[:] = 1.0 + (1j if np.issubdtype(dtype, np.complexfloating) else 0)
file.write_function(u, 0.1)
u.x.array[:] = 2.0 + (2j if np.issubdtype(dtype, np.complexfloating) else 0)
file.write_function(u, 0.2)
with XDMFFile(mesh.comm, filename, "a", encoding=encoding) as file:
u.x.array[:] = 3.0 + (3j if np.issubdtype(dtype, np.complexfloating) else 0)
file.write_function(u, 0.3)
def test_higher_order_function(tempdir):
"""Test Function output for higher-order meshes."""
gmsh = pytest.importorskip("gmsh")
from dolfinx.io import gmshio
gmsh.initialize()
def gmsh_tet_model(order):
gmsh.option.setNumber("General.Terminal", 0)
model = gmsh.model()
comm = MPI.COMM_WORLD
if comm.rank == 0:
model.add("Sphere minus box")
model.setCurrent("Sphere minus box")
model.occ.addSphere(0, 0, 0, 1)
model.occ.synchronize()
volume_entities = [model[1] for model in model.getEntities(3)]
model.addPhysicalGroup(3, volume_entities, tag=2)
model.mesh.generate(3)
gmsh.option.setNumber("General.Terminal", 1)
model.mesh.setOrder(order)
gmsh.option.setNumber("General.Terminal", 0)
msh, _, _ = gmshio.model_to_mesh(model, comm, 0)
return msh
def gmsh_hex_model(order):
model = gmsh.model()
gmsh.option.setNumber("General.Terminal", 0)
model.add("Hexahedral mesh")
model.setCurrent("Hexahedral mesh")
comm = MPI.COMM_WORLD
if comm.rank == 0:
gmsh.option.setNumber("Mesh.RecombinationAlgorithm", 2)
gmsh.option.setNumber("Mesh.RecombineAll", 2)
gmsh.option.setNumber("Mesh.CharacteristicLengthFactor", 1)
circle = model.occ.addDisk(0, 0, 0, 1, 1)
circle_inner = model.occ.addDisk(0, 0, 0, 0.5, 0.5)
cut = model.occ.cut([(2, circle)], [(2, circle_inner)])[0]
extruded_geometry = model.occ.extrude(cut, 0, 0, 0.5, numElements=[5], recombine=True)
model.occ.synchronize()
model.addPhysicalGroup(2, [cut[0][1]], tag=1)
model.setPhysicalName(2, 1, "2D cylinder")
boundary_entities = model.getEntities(2)
other_boundary_entities = []
for entity in boundary_entities:
if entity != cut[0][1]:
other_boundary_entities.append(entity[1])
model.addPhysicalGroup(2, other_boundary_entities, tag=3)
model.setPhysicalName(2, 3, "Remaining boundaries")
model.mesh.generate(3)
model.mesh.setOrder(order)
volume_entities = []
for entity in extruded_geometry:
if entity[0] == 3:
volume_entities.append(entity[1])
model.addPhysicalGroup(3, volume_entities, tag=1)
model.setPhysicalName(3, 1, "Mesh volume")
msh, _, _ = gmshio.model_to_mesh(gmsh.model, comm, 0)
return msh
# -- Degree 1 mesh (tet)
msh = gmsh_tet_model(1)
gdim = msh.geometry.dim
assert msh.geometry.cmap.degree == 1
# Write P1 Function
u = Function(functionspace(msh, ("Lagrange", 1, (gdim,))))
filename = Path(tempdir, "u3D_P1.xdmf")
with XDMFFile(msh.comm, filename, "w") as file:
file.write_mesh(msh)
file.write_function(u)
# Write P2 Function (exception expected)
u = Function(functionspace(msh, ("Lagrange", 2, (gdim,))))
filename = Path(tempdir, "u3D_P2.xdmf")
with pytest.raises(RuntimeError):
with XDMFFile(msh.comm, filename, "w") as file:
file.write_mesh(msh)
file.write_function(u)
# -- Degree 2 mesh (tet)
msh = gmsh_tet_model(2)
gdim = msh.geometry.dim
assert msh.geometry.cmap.degree == 2
# Write P1 Function (exception expected)
u = Function(functionspace(msh, ("Lagrange", 1, (gdim,))))
with pytest.raises(RuntimeError):
filename = Path(tempdir, "u3D_P1.xdmf")
with XDMFFile(msh.comm, filename, "w") as file:
file.write_mesh(msh)
file.write_function(u)
# Write P2 Function
u = Function(functionspace(msh, ("Lagrange", 2, (gdim,))))
filename = Path(tempdir, "u3D_P2.xdmf")
with XDMFFile(msh.comm, filename, "w") as file:
file.write_mesh(msh)
file.write_function(u)
# -- Degree 3 mesh (tet)
# NOTE: XDMF/ParaView does not support TETRAHEDRON_20
msh = gmsh_tet_model(3)
gdim = msh.geometry.dim
assert msh.geometry.cmap.degree == 3
# Write P2 Function (exception expected)
u = Function(functionspace(msh, ("Lagrange", 2, (gdim,))))
with pytest.raises(RuntimeError):
filename = Path(tempdir, "u3D_P3.xdmf")
with XDMFFile(msh.comm, filename, "w") as file:
file.write_mesh(msh)
file.write_function(u)
# Write P3 GLL Function (exception expected)
ufl_e = basix.ufl.element(
basix.ElementFamily.P,
basix.CellType.tetrahedron,
3,
basix.LagrangeVariant.gll_warped,
dtype=default_real_type,
)
u = Function(functionspace(msh, ufl_e))
with pytest.raises(RuntimeError):
filename = Path(tempdir, "u3D_P3.xdmf")
with XDMFFile(msh.comm, filename, "w") as file:
file.write_mesh(msh)
file.write_function(u)
# Write P3 equispaced Function
ufl_e = basix.ufl.element(
basix.ElementFamily.P,
basix.CellType.tetrahedron,
3,
basix.LagrangeVariant.equispaced,
dtype=default_real_type,
)
u1 = Function(functionspace(msh, ufl_e))
u1.interpolate(u)
filename = Path(tempdir, "u3D_P3.xdmf")
with XDMFFile(msh.comm, filename, "w") as file:
file.write_mesh(msh)
file.write_function(u1)
# -- Degree 2 mesh (hex)
msh = gmsh_hex_model(2)
gdim = msh.geometry.dim
assert msh.geometry.cmap.degree == 2
# Write Q1 Function (exception expected)
u = Function(functionspace(msh, ("Lagrange", 1, (gdim,))))
with pytest.raises(RuntimeError):
filename = Path(tempdir, "u3D_Q1.xdmf")
with XDMFFile(msh.comm, filename, "w") as file:
file.write_mesh(msh)
file.write_function(u)
# Write Q2 Function
u = Function(functionspace(msh, ("Lagrange", 2, (gdim,))))
filename = Path(tempdir, "u3D_Q2.xdmf")
with XDMFFile(msh.comm, filename, "w") as file:
file.write_mesh(msh)
file.write_function(u)
# TODO: Higher-order gmsh hex meshes not yet supported by DOLFINx
#
# # Degree 3 mesh (hex)
# msh = gmsh_hex_model(3)
# assert msh.geometry.cmap.degree == 3
# gdim = msh.geometry.dim
# u = Function(functionspace(msh, ("Lagrange", 1, (gdim,))))
# with pytest.raises(RuntimeError):
# filename = Path(tempdir, "u3D_Q1.xdmf")
# with XDMFFile(msh.comm, filename, "w") as file:
# file.write_mesh(msh)
# file.write_function(u)
# u = Function(functionspace(msh, ("Lagrange", 2, (gdim,))))
# filename = Path(tempdir, "u3D_Q2.xdmf")
# with XDMFFile(msh.comm, filename, "w") as file:
# file.write_mesh(msh)
# file.write_function(u)
gmsh.finalize()
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