For the unit square domain defined as follows:
domain = mesh.create_unit_square(MPI.COMM_SELF, 8, 8, mesh.CellType.quadrilateral)
tdim = domain.topology.dim
If we want to display the mesh, we can use the code mentioned in here
That is:
topology, cell_types, geometry = plot.create_vtk_mesh(domain, tdim)
grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)
pyvista.set_jupyter_backend("pythreejs")
plotter = pyvista.Plotter()
plotter.add_mesh(grid, show_edges=True)
plotter.view_xy()
if not pyvista.OFF_SCREEN:
plotter.show()
else:
pyvista.start_xvfb()
figure = plotter.screenshot("fundamentals_mesh.png")
My intention is to draw a domain in the GMSH GUI and to display it as I did above.
For that purpose, I was going over this tutorial
Hence, I first created a mesh as below:
And then as mentioned in the tutorial:
from dolfinx.io.gmshio import model_to_mesh
from mpi4py import MPI
mesh, cell_tags, facet_tags = gmshio.read_from_msh("solving.msh", MPI.COMM_WORLD, 0, gdim=3)
But, it gave me an error: No module named 'dolfinx.io.gmshio'; 'dolfinx.io' is not a package
However, I did have the helper function file from somewhere. So, I thought if directly using the read_from_msh function:
def read_from_msh(filename: str, cell_data=False, facet_data=False, gdim=None): """ Reads a mesh from a msh-file and returns the dolfin-x mesh. Input: filename: Name of msh file cell_data: Boolean, True of a mesh tag for cell data should be returned (Default: False) facet_data: Boolean, True if a mesh tag for facet data should be returned (Default: False) gdim: Geometrical dimension of problem (Default: 3) """ if MPI.COMM_WORLD.rank == 0: # Check if gmsh is already initialized try: current_model = gmsh.model.getCurrent() except ValueError: current_model = None gmsh.initialize() gmsh.model.add("Mesh from file") gmsh.merge(filename) output = gmsh_model_to_mesh(gmsh.model, cell_data=cell_data, facet_data=facet_data, gdim=gdim) if MPI.COMM_WORLD.rank == 0: if current_model is None: gmsh.finalize() else: gmsh.model.setCurrent(current_model) return output def gmsh_model_to_mesh(model, cell_data=False, facet_data=False, gdim=None): """ Given a GMSH model, create a DOLFIN-X mesh and MeshTags. model: The GMSH model cell_data: Boolean, True of a mesh tag for cell data should be returned (Default: False) facet_data: Boolean, True if a mesh tag for facet data should be returned (Default: False) gdim: Geometrical dimension of problem (Default: 3) """ if gdim is None: gdim = 3 if MPI.COMM_WORLD.rank == 0: # Get mesh geometry x = extract_gmsh_geometry(model) # Get mesh topology for each element topologies = extract_gmsh_topology_and_markers(model) # Get information about each cell type from the msh files num_cell_types = len(topologies.keys()) cell_information = {} cell_dimensions = numpy.zeros(num_cell_types, dtype=numpy.int32) for i, element in enumerate(topologies.keys()): properties = model.mesh.getElementProperties(element) name, dim, order, num_nodes, local_coords, _ = properties cell_information[i] = {"id": element, "dim": dim, "num_nodes": num_nodes} cell_dimensions[i] = dim # Sort elements by ascending dimension perm_sort = numpy.argsort(cell_dimensions) # Broadcast cell type data and geometric dimension cell_id = cell_information[perm_sort[-1]]["id"] tdim = cell_information[perm_sort[-1]]["dim"] num_nodes = cell_information[perm_sort[-1]]["num_nodes"] cell_id, num_nodes = MPI.COMM_WORLD.bcast([cell_id, num_nodes], root=0) # Check for facet data and broadcast if found if facet_data: if tdim - 1 in cell_dimensions: num_facet_nodes = MPI.COMM_WORLD.bcast( cell_information[perm_sort[-2]]["num_nodes"], root=0) gmsh_facet_id = cell_information[perm_sort[-2]]["id"] marked_facets = numpy.asarray(topologies[gmsh_facet_id]["topology"], dtype=numpy.int64) facet_values = numpy.asarray(topologies[gmsh_facet_id]["cell_data"], dtype=numpy.int32) else: raise ValueError("No facet data found in file.") cells = numpy.asarray(topologies[cell_id]["topology"], dtype=numpy.int64) cell_values = numpy.asarray(topologies[cell_id]["cell_data"], dtype=numpy.int32) else: cell_id, num_nodes = MPI.COMM_WORLD.bcast([None, None], root=0) cells, x = numpy.empty([0, num_nodes], dtype=numpy.int32), numpy.empty([0, gdim]) cell_values = numpy.empty((0,), dtype=numpy.int32) if facet_data: num_facet_nodes = MPI.COMM_WORLD.bcast(None, root=0) marked_facets = numpy.empty((0, num_facet_nodes), dtype=numpy.int32) facet_values = numpy.empty((0,), dtype=numpy.int32) # Create distributed mesh ufl_domain = ufl_mesh_from_gmsh(cell_id, gdim) gmsh_cell_perm = perm_gmsh(to_type(str(ufl_domain.ufl_cell())), num_nodes) cells = cells[:, gmsh_cell_perm] mesh = create_mesh(MPI.COMM_WORLD, cells, x[:, :gdim], ufl_domain) # Create MeshTags for cells if cell_data: local_entities, local_values = distribute_entity_data( mesh, mesh.topology.dim, cells, cell_values) mesh.topology.create_connectivity(mesh.topology.dim, 0) adj = AdjacencyList_int32(local_entities) ct = create_meshtags(mesh, mesh.topology.dim, adj, local_values) ct.name = "Cell tags" # Create MeshTags for facets if facet_data: # Permute facets from MSH to Dolfin-X ordering # FIXME: This does not work for prism meshes facet_type = cell_entity_type(to_type(str(ufl_domain.ufl_cell())), mesh.topology.dim - 1, 0) gmsh_facet_perm = perm_gmsh(facet_type, num_facet_nodes) marked_facets = marked_facets[:, gmsh_facet_perm] local_entities, local_values = distribute_entity_data( mesh, mesh.topology.dim - 1, marked_facets, facet_values) mesh.topology.create_connectivity( mesh.topology.dim - 1, mesh.topology.dim) adj = AdjacencyList_int32(local_entities) ft = create_meshtags(mesh, mesh.topology.dim - 1, adj, local_values) ft.name = "Facet tags" if cell_data and facet_data: return mesh, ct, ft elif cell_data and not facet_data: return mesh, ct elif not cell_data and facet_data: return mesh, ft else: return mesh
But then, when I used: mesh, cell_tags, facet_tags = read_from_msh("solving.msh", MPI.COMM_WORLD, 0, gdim=2)
I get the following error:
Can someone please help me to properly handle this issue.
Furthermore, for from dolfinx.io import gmshio gives the error:
cannot import name 'gmshio' from 'dolfinx.io' (/usr/local/dolfinx-real/lib/python3.10/dist-packages/dolfinx/io.py)
I am using dolfinx through Docker and my version is :
0.4.2.0 0eab5343fe8674875f94d50706b033d84fa6d67b
