Exporting a hexahedral region into XDMF with meshio and importing it into dolfinx

General
1

Hexahedrons are exported to XDMF:

import sys 
import os 
sys.path.append(os.getcwd())
import meshio 
import numpy as np 
import HexRegion

# A hexahedron region is built by extusion of a rectangular plane that consists of sub-rectangles
# all with the same winding order... 10 segments are extruded with each segment having a length of 10 units
# in the case cm...
hex_reg = HexRegion(10, 10, 'rect_cross_section.json', isShaderActive=False)

# Gather all hexahedrons
hexahedrons = []
materials = []
for hex_index in range(hex_reg.num_hexas()):
    hexahedron = hex_reg.getHexaVerts(hex_index)
    material = hex_reg.TAGs[hex_index]
    hexahedrons.append(hexahedron)
    materials.append(material)

# Convert to numpy array for meshio
hexahedrons = np.array(hexahedrons)
# Create a mapping from material types to integers
material_mapping = {material: idx for idx, material in enumerate(set(materials))}
encoded_materials = np.array([material_mapping[mat] for mat in materials])
# Flatten the hexahedron vertices array for meshio
points = hexahedrons.reshape(-1, 3)
cells = [("hexahedron", np.arange(hexahedrons.shape[0] * 8).reshape(-1, 8))]
# Create the mesh
mesh = meshio.Mesh(points=points, cells=cells)
# Add material data as cell data
mesh.cell_data["material"] = [encoded_materials]
# Export to a file format suitable for dolfinx
mesh.write("hexahedrons.xdmf")
# Print material mapping for reference
print("Material mapping:", material_mapping)
print("Export complete.")

The XDMF files:

importing the hexahedrons.xdmf:

	import dolfinx
	from dolfinx import mesh
	from dolfinx.io import XDMFFile
	from mpi4py import MPI

	# Create an XDMFFile object for reading
	with XDMFFile(MPI.COMM_WORLD, "hexahedrons.xdmf", "r") as file:
		mesh_obj = mesh.create_mesh(MPI.COMM_WORLD, file.read_mesh())
		print("Mesh created successfully!")

	'''
	Traceback (most recent call last):
	  File "/home/prusso/dolfinx-hexahedron/main.py", line 8, in <module>
		mesh_obj = mesh.create_mesh(MPI.COMM_WORLD, file.read_mesh())
													^^^^^^^^^^^^^^^^
	  File "/home/prusso/spack/var/spack/environments/fenicsx-env/.spack-env/view/lib/python3.11/site-packages/dolfinx/io/utils.py", line 258, in read_mesh
		cell_shape, cell_degree = super().read_cell_type(name, xpath)
								  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	RuntimeError: <Grid> with name 'mesh' not found.
	'''

It seems that are some additional things to take into account when preparing an XDMF for the purposes of importing it into dolfinx.

So far I would like to do things in a way that will satisfy both dolfinx and PyVista.PyVista seems to squack a bit about timeframe data. Why this traceback about Grid from doflinx? How can I resolve the issue and get the XDMF file imported into dolfinx?

2

A bit later I found:

Mesh generation with Gmsh — DOLFINx 0.9.0.0 documentation (fenicsproject.org)

which maybe looks like a better approach to the problem of importing a custom hexahedron mesh.


gmsh.option.setNumber("Mesh.RecombinationAlgorithm", 2)
gmsh.option.setNumber("Mesh.RecombineAll", 2)

The above code is apparently what merges tetrahedrons into hexahedrons.