def read_mesh_from_file():
comm = MPI.COMM_WORLD
# encoding = dolfinx.cpp.io.XDMFFile.Encoding.ASCII
encoding = XDMFFile.Encoding.HDF5
path = "square.xdmf"
infile = XDMFFile(comm, path, 'r', encoding)
fenics_mesh = infile.read_mesh(name='square')
print(fenics_mesh.name)
def load_virus():
path = "./1igt.xdmf"
comm = MPI.COMM_WORLD
encoding = XDMFFile.Encoding.HDF5
infile = XDMFFile(comm, path, 'r', encoding)
mesh = infile.read_mesh(name='Grid')
name = "virus"
mesh.name = name
return mesh
parser.add_argument("--out")
parser.add_argument("--steps", type=int)
parser.add_argument("--end", type=float)
parser.add_argument("--tp", type=float, help="Time at loading")
args = parser.parse_known_args()[0]
#
# Convert and read mesh and tags
#
meshname = args.mesh
filedir = os.path.dirname(__file__)
t0 = time()
infile = XDMFFile(MPI.COMM_WORLD,
os.path.join(filedir, "mesh/{}.xdmf".format(meshname)), "r")
mesh = infile.read_mesh(name="Grid")
mesh.topology.create_connectivity_all()
mt_cell = infile.read_meshtags(mesh, "Grid")
infile.close()
infile = XDMFFile(
MPI.COMM_WORLD,
os.path.join(filedir, "mesh/{}_triangle.xdmf".format(meshname)), "r")
mt_facet = infile.read_meshtags(mesh, "Grid")
infile.close()
# External boundary facets
ds = ufl.Measure("ds",
domain=mesh,
subdomain_data=mt_facet,
metadata={"quadrature_degree": 2})
# following way::
import matplotlib.pyplot as plt
import numpy as np
import dolfinx
from dolfinx import MPI, DirichletBC, Function, FunctionSpace, solve
from dolfinx.io import XDMFFile
from dolfinx.fem import locate_dofs_topological
from dolfinx.plotting import plot
from ufl import (FiniteElement, TestFunctions, TrialFunctions, VectorElement,
div, dx, grad, inner)
# Load mesh and subdomains
xdmf = XDMFFile(MPI.comm_world, "../dolfin_fine.xdmf")
mesh = xdmf.read_mesh(dolfinx.cpp.mesh.GhostMode.none)
sub_domains = xdmf.read_mf_size_t(mesh)
cmap = dolfinx.fem.create_coordinate_map(mesh.ufl_domain())
mesh.geometry.coord_mapping = cmap
# Next, we define a :py:class:`FunctionSpace
# <dolfinx.function.FunctionSpace>` built on a mixed finite element
# ``TH`` which consists of continuous piecewise quadratics and
# continuous piecewise linears::
# Define function spaces
P2 = VectorElement("Lagrange", mesh.ufl_cell(), 2)
P1 = FiniteElement("Lagrange", mesh.ufl_cell(), 1)
TH = P2 * P1
