def test_save_2d_scalar(tempdir, cell_type):
mesh = UnitSquareMesh(MPI.COMM_WORLD, 16, 16, cell_type=cell_type)
u = Function(FunctionSpace(mesh, ("Lagrange", 2)))
with u.vector.localForm() as loc:
loc.set(1.0)
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(MPI.COMM_WORLD, filename, "w") as vtk:
vtk.write_function(u, 0.)
vtk.write_function(u, 1.)
def test_save_2d_tensor(tempdir):
mesh = UnitSquareMesh(MPI.COMM_WORLD, 16, 16)
u = Function(TensorFunctionSpace(mesh, ("Lagrange", 2)))
with u.vector.localForm() as loc:
loc.set(1.0)
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(mesh.mpi_comm(), filename, "w") as vtk:
vtk.write_function(u, 0.)
with u.vector.localForm() as loc:
loc.set(2.0)
vtk.write_function(u, 1.)
def test_save_1d_mesh(tempfile, file_options):
mesh = UnitIntervalMesh(MPI.COMM_WORLD, 32)
VTKFile(tempfile + "mesh.pvd").write(mesh)
f = VTKFile(tempfile + "mesh.pvd")
f.write(mesh, 0.)
f.write(mesh, 1.)
for file_option in file_options:
VTKFile(tempfile + "mesh.pvd", file_option).write(mesh)
def test_save_3d_mesh(tempfile, file_options):
mesh = UnitCubeMesh(MPI.COMM_WORLD, 8, 8, 8)
VTKFile(tempfile + "mesh.pvd").write(mesh)
f = VTKFile(tempfile + "mesh.pvd")
f.write(mesh, 0.)
f.write(mesh, 1.)
for file_option in file_options:
VTKFile(tempfile + "mesh.pvd", file_option).write(mesh)
def test_save_2d_mesh(tempfile, file_options):
mesh = UnitSquareMesh(MPI.comm_world, 32, 32)
VTKFile(tempfile + "mesh.pvd").write(mesh)
f = VTKFile(tempfile + "mesh.pvd")
f.write(mesh, 0.)
f.write(mesh, 1.)
for file_option in file_options:
VTKFile(tempfile + "mesh.pvd", file_option).write(mesh)
def test_save_1d_scalar(tempdir):
mesh = UnitIntervalMesh(MPI.COMM_WORLD, 32)
def f(x):
return x[0]
u = Function(FunctionSpace(mesh, ("CG", 2)))
u.interpolate(f)
u.vector.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(MPI.COMM_WORLD, filename, "w") as vtk:
vtk.write_function(u, 0.)
vtk.write_function(u, 1.)
def test_save_2d_vector(tempdir, cell_type):
mesh = UnitSquareMesh(MPI.COMM_WORLD, 16, 16, cell_type=cell_type)
u = Function(VectorFunctionSpace(mesh, ("Lagrange", 1)))
def f(x):
vals = np.zeros((2, x.shape[1]))
vals[0] = x[0]
vals[1] = 2 * x[0] * x[1]
return vals
u.interpolate(f)
u.vector.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(MPI.COMM_WORLD, filename, "w") as vtk:
vtk.write_function(u, 0.)
def test_save_1d_vector(tempdir):
mesh = create_unit_interval(MPI.COMM_WORLD, 32)
def f(x):
vals = np.zeros((2, x.shape[1]))
vals[0] = x[0]
vals[1] = 2 * x[0] * x[0]
return vals
element = ufl.VectorElement("Lagrange", mesh.ufl_cell(), 2, dim=2)
u = Function(FunctionSpace(mesh, element))
u.interpolate(f)
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(MPI.COMM_WORLD, filename, "w") as vtk:
vtk.write_function(u, 0.)
def test_save_2d_vector_CG2(tempdir):
points = np.array([[0, 0], [1, 0], [1, 2], [0, 2],
[1 / 2, 0], [1, 1], [1 / 2, 2],
[0, 1], [1 / 2, 1]])
points = np.array([[0, 0], [1, 0], [0, 2], [0.5, 1], [0, 1], [0.5, 0],
[1, 2], [0.5, 2], [1, 1]])
cells = np.array([[0, 1, 2, 3, 4, 5],
[1, 6, 2, 7, 3, 8]])
domain = ufl.Mesh(ufl.VectorElement("Lagrange", "triangle", 2))
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
u = Function(VectorFunctionSpace(mesh, ("Lagrange", 2)))
u.interpolate(lambda x: np.vstack((x[0], x[1])))
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(mesh.comm, filename, "w") as vtk:
vtk.write_function(u, 0.)
def test_save_2d_vector(tempdir, cell_type):
mesh = create_unit_square(MPI.COMM_WORLD, 16, 16, cell_type=cell_type)
u = Function(VectorFunctionSpace(mesh, ("Lagrange", 1)))
def f(x):
vals = np.zeros((2, x.shape[1]))
vals[0] = x[0]
vals[1] = 2 * x[0] * x[1]
return vals
u.interpolate(f)
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(MPI.COMM_WORLD, filename, "w") as vtk:
vtk.write_function(u, 0.)
vtk.write_function(u, 1.)
def test_save_1d_scalar(tempfile, file_options):
mesh = UnitIntervalMesh(MPI.comm_world, 32)
u = Function(FunctionSpace(mesh, ("Lagrange", 2)))
u.vector.set(1.0)
VTKFile(tempfile + "u.pvd").write(u)
f = VTKFile(tempfile + "u.pvd")
f.write(u, 0.)
f.write(u, 1.)
for file_option in file_options:
VTKFile(tempfile + "u.pvd", file_option).write(u)
def test_save_2d_scalar(tempfile, file_options):
mesh = UnitSquareMesh(MPI.COMM_WORLD, 16, 16)
u = Function(FunctionSpace(mesh, ("Lagrange", 2)))
u.vector.set(1.0)
VTKFile(tempfile + "u.pvd").write(u)
f = VTKFile(tempfile + "u.pvd")
f.write(u, 0.)
f.write(u, 1.)
for file_option in file_options:
VTKFile(tempfile + "u.pvd", file_option).write(u)
def test_save_2d_tensor(tempfile, file_options):
mesh = UnitSquareMesh(MPI.comm_world, 16, 16)
u = Function(TensorFunctionSpace(mesh, ("Lagrange", 2)))
u.vector.set(1)
VTKFile(tempfile + "u.pvd").write(u)
f = VTKFile(tempfile + "u.pvd")
f.write(u, 0.)
f.write(u, 1.)
for file_option in file_options:
VTKFile(tempfile + "u.pvd", file_option).write(u)
def test_save_3d_vector(tempfile, file_options):
mesh = UnitCubeMesh(MPI.comm_world, 8, 8, 8)
u = Function(VectorFunctionSpace(mesh, "Lagrange", 2))
u.vector.set(1)
VTKFile(tempfile + "u.pvd").write(u)
f = VTKFile(tempfile + "u.pvd")
f.write(u, 0.)
f.write(u, 1.)
for file_option in file_options:
VTKFile(tempfile + "u.pvd", file_option).write(u)
def test_save_3d_tensor(tempfile, file_options):
mesh = UnitCubeMesh(MPI.COMM_WORLD, 8, 8, 8)
u = Function(TensorFunctionSpace(mesh, ("Lagrange", 2)))
u.vector.set(1)
VTKFile(tempfile + "u.pvd").write(u)
f = VTKFile(tempfile + "u.pvd")
f.write(u, 0.)
f.write(u, 1.)
for file_option in file_options:
VTKFile(tempfile + "u.pvd", file_option).write(u)
def test_save_1d_vector(tempdir):
mesh = UnitIntervalMesh(MPI.COMM_WORLD, 32)
def f(x):
vals = np.zeros((2, x.shape[1]))
vals[0] = x[0]
vals[1] = 2 * x[0] * x[0]
return vals
element = ufl.VectorElement("Lagrange", mesh.ufl_cell(), 2, dim=2)
u = Function(FunctionSpace(mesh, element))
u.interpolate(f)
u.vector.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(MPI.COMM_WORLD, filename, "w") as vtk:
vtk.write_function(u, 0.)
def test_save_2d_vector_CG2(tempdir):
points = np.array([[0, 0], [1, 0], [1, 2], [0, 2],
[1 / 2, 0], [1, 2 / 2], [1 / 2, 2],
[0, 2 / 2], [1 / 2, 2 / 2]])
points = np.array([[0, 0], [1, 0], [0, 2], [0.5, 1], [0, 1], [0.5, 0],
[1, 2], [0.5, 2], [1, 1]])
cells = np.array([[0, 1, 2, 3, 4, 5],
[1, 6, 2, 7, 3, 8]])
domain = ufl.Mesh(ufl.VectorElement("Lagrange", "triangle", 2))
mesh = create_mesh(MPI.COMM_WORLD, cells, points, domain)
u = Function(VectorFunctionSpace(mesh, ("Lagrange", 2)))
def func(x):
vals = np.zeros((2, x.shape[1]))
vals[0] = x[0]
vals[1] = x[1]
return vals
u.interpolate(func)
filename = os.path.join(tempdir, "u.pvd")
with VTKFile(mesh.mpi_comm(), filename, "w") as vtk:
vtk.write_function(u, 0.)
def test_HDF5_io(tempdir, order, element):
pytest.importorskip("pygmsh")
h5py = pytest.importorskip("h5py")
from pygmsh.opencascade import Geometry
from pygmsh import generate_mesh
# Generate a sphere with gmsh with tetrahedral elements
geo = Geometry()
geo.add_raw_code("Mesh.Algorithm = 2;")
geo.add_raw_code("Mesh.Algorithm3D = 10;")
geo.add_raw_code("Mesh.ElementOrder = {0:d};".format(order))
geo.add_ball([0, 0, 0], 1, char_length=0.3)
geo.add_raw_code("Physical Volume (1) = {1};")
msh = generate_mesh(geo, verbose=False, dim=3)
# Write gmsh to HDF5
filename = os.path.join(tempdir, "mesh_order{0:d}.h5".format(order))
f = h5py.File(filename, "w", driver='mpio', comm=MPI4PY.COMM_WORLD)
grp = f.create_group("my_mesh")
grp.create_dataset("cell_indices",
data=range(msh.cells_dict[element].shape[0]))
grp.create_dataset("coordinates", data=msh.points)
top = grp.create_dataset("topology", data=msh.cells_dict[element])
top.attrs["celltype"] = np.bytes_('tetrahedron')
f.close()
# Read mesh from HDF5
mesh_file = HDF5File(MPI.comm_world, filename, "r")
mesh = mesh_file.read_mesh("/my_mesh", False, cpp.mesh.GhostMode.none)
mesh_file.close()
# Save mesh with VTK
outfile = os.path.join(tempdir, "mesh{0:d}.pvd".format(order))
VTKFile(outfile).write(mesh)
def test_save_1d_mesh(tempdir):
filename = os.path.join(tempdir, "mesh.pvd")
mesh = UnitIntervalMesh(MPI.COMM_WORLD, 32)
with VTKFile(MPI.COMM_WORLD, filename, "w") as vtk:
vtk.write_mesh(mesh)
vtk.write_mesh(mesh, 1)
def test_save_3d_mesh(tempdir, cell_type):
mesh = create_unit_cube(MPI.COMM_WORLD, 8, 8, 8, cell_type=cell_type)
filename = os.path.join(tempdir, f"mesh_{cell_type.name}.pvd")
with VTKFile(MPI.COMM_WORLD, filename, "w") as vtk:
vtk.write_mesh(mesh, 0.)
vtk.write_mesh(mesh, 2.)
def test_save_3d_mesh(tempdir, cell_type):
mesh = UnitCubeMesh(MPI.COMM_WORLD, 8, 8, 8, cell_type=cell_type)
filename = os.path.join(tempdir, f"mesh_{cpp.mesh.to_string(cell_type)}.pvd")
with VTKFile(MPI.COMM_WORLD, filename, "w") as vtk:
vtk.write_mesh(mesh, 0.)
vtk.write_mesh(mesh, 2.)
