hello sir , I’m using DOLFINx 0.7.3, and I’m encountering difficulties extracting boundaries from my MSH file. Below is my Python script:
from dolfinx import plot, mesh,fem
from mpi4py import MPI
from petsc4py import PETSc
import numpy as np
import ufl
from basix.ufl import element, mixed_element
from dolfinx import mesh, fem, plot, io
from dolfinx.fem import (Function, dirichletbc, form, functionspace,
locate_dofs_topological)
from dolfinx.fem.petsc import assemble_matrix_block, assemble_vector_block
from dolfinx.mesh import create_rectangle, locate_entities_boundary,CellType
from ufl import div, dx, grad, inner,as_vector,SpatialCoordinate,VectorElement, FiniteElement
import matplotlib.pyplot as plt
from dolfinx.io import XDMFFile
import pyvista
from dolfinx.plot import vtk_mesh
import warnings
from dolfinx.cpp.mesh import CellType
warnings.filterwarnings("ignore")
import meshio
import gmsh
import numpy as np
mesh, cell_markers, facet_markers = gmshio.read_from_msh("mesh_2.msh", MPI.COMM_WORLD, gdim=2)
def create_mesh(mesh, cell_type, prune_z=False):
cells = mesh.get_cells_type(cell_type)
cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
points = mesh.points[:, :2] if prune_z else mesh.points
out_mesh = meshio.Mesh(points=points, cells={cell_type: cells}, cell_data={"name_to_read": [cell_data.astype(np.int32)]})
return out_mesh
proc = MPI.COMM_WORLD.rank
if proc == 0:
# Read in mesh
msh = meshio.read("mesh_2.msh")
# Create and save one file for the mesh, and one file for the facets
triangle_mesh = create_mesh(msh, "triangle", prune_z=True)
line_mesh = create_mesh(msh, "line", prune_z=True)
meshio.write("mesh.xdmf", triangle_mesh)
meshio.write("mt.xdmf", line_mesh)
MPI.COMM_WORLD.barrier()
with XDMFFile(MPI.COMM_WORLD, "msh.xdmf", "r") as xdmf:
msh = xdmf.read_mesh(name="Grid")
ct = xdmf.read_meshtags(msh, name="Grid")
msh.topology.create_connectivity(msh.topology.dim, msh.topology.dim - 1)
with XDMFFile(MPI.COMM_WORLD, "mt.xdmf", "r") as xdmf:
ft = xdmf.read_meshtags(msh, name="Grid")
# in gmsh : inlet boundary=7, outlet_boundary=8, walls=9, obstacle_boundary=10
#Here, I aim to define Dirichlet boundaries to solve the Stokes problem. However, I'm unsure how to extract information from ct (or ft) to read the boundaries.
def u_expression(x):
return np.stack((4 * x[1] * (1.0 - x[1]), np.zeros(x.shape[1])))
P2 = element("Lagrange", msh.basix_cell(), 2, shape=(msh.geometry.dim,))
P1 = element("Lagrange", msh.basix_cell(), 1)
TH = mixed_element([P2, P1])
W = functionspace(msh, TH)
W0, _ = W.sub(0).collapse()
W1, W1_to_W = W.sub(1).collapse()
# Dirichlet conditions on the wall
u_wall=Function(W0)
facets_wall = locate_entities_boundary(msh, 1, ft.find(9))
dofs_wall = locate_dofs_topological((W.sub(0), W0), 1, facets_wall)
bc0 = dirichletbc(u_wall, dofs_wall, W.sub(0))
# Dirichlet conditions on the inlet
u_in=Function(W0)
u_in.interpolate(u_expression)
facets_in = locate_entities_boundary(msh, 1, ft.find(7))
dofs_in = locate_dofs_topological((W.sub(0), W0), 1, facets_in)
bc1 = dirichletbc(u_in, dofs_in, W.sub(0))
# Dirichlet conditions on the obstacle boundary
u_obst=Function(W0)
facets_obst = locate_entities_boundary(msh, 1, ft.find(10))
dofs_obst = locate_dofs_topological((W.sub(0), W0), 1, facets_obst)
bc2 = dirichletbc(u_in, dofs_obst, W.sub(0))
bcp=[bc0,bc1,bc2]
My msh file is :
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2.2 0 8
$EndMeshFormat
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2813 2 2 11 1 703 1409 1244
2814 2 2 11 1 210 1405 1022
2815 2 2 11 1 955 1408 956
2816 2 2 11 1 856 1428 158
2817 2 2 11 1 1357 1409 705
2818 2 2 11 1 1401 1431 989
2819 2 2 11 1 1059 1426 1060
2820 2 2 11 1 827 1403 1165
2821 2 2 11 1 829 1423 861
2822 2 2 11 1 662 1412 661
2823 2 2 11 1 142 1406 227
2824 2 2 11 1 1274 1422 1052
2825 2 2 11 1 1094 1413 192
2826 2 2 11 1 629 1410 627
2827 2 2 11 1 479 1414 231
2828 2 2 11 1 954 1419 181
2829 2 2 11 1 959 1421 1327
2830 2 2 11 1 85 1417 84
2831 2 2 11 1 1281 1374 664
2832 2 2 11 1 1074 1371 1291
2833 2 2 11 1 1091 1420 1092
2834 2 2 11 1 1115 1386 1366
2835 2 2 11 1 879 1416 815
2836 2 2 11 1 1040 1425 1039
2837 2 2 11 1 226 1423 1095
2838 2 2 11 1 989 1431 184
2839 2 2 11 1 701 1439 602
2840 2 2 11 1 756 1366 1340
2841 2 2 11 1 468 1427 547
2842 2 2 11 1 100 1433 99
2843 2 2 11 1 597 1422 1274
2844 2 2 11 1 131 1437 160
2845 2 2 11 1 814 1418 1192
2846 2 2 11 1 873 1436 845
2847 2 2 11 1 1155 1430 616
2848 2 2 11 1 544 1434 1148
2849 2 2 11 1 223 1395 1287
2850 2 2 11 1 225 1394 1288
2851 2 2 11 1 1210 1431 866
2852 2 2 11 1 661 1412 1345
2853 2 2 11 1 1343 1436 873
2854 2 2 11 1 224 1393 1289
2855 2 2 11 1 162 1392 1317
2856 2 2 11 1 1325 1370 860
2857 2 2 11 1 1299 1381 746
2858 2 2 11 1 1253 1429 717
2859 2 2 11 1 871 1424 1250
2860 2 2 11 1 1340 1366 1090
2861 2 2 11 1 840 1435 1386
2862 2 2 11 1 226 1397 1293
2863 2 2 11 1 992 1384 1316
2864 2 2 11 1 1293 1397 40
2865 2 2 11 1 1269 1435 840
2866 2 2 11 1 1304 1425 1040
2867 2 2 11 1 212 1407 1303
2868 2 2 11 1 1350 1406 802
2869 2 2 11 1 434 1404 1355
2870 2 2 11 1 1337 1403 827
2871 2 2 11 1 1378 1415 1003
2872 2 2 11 1 1338 1428 856
2873 2 2 11 1 1327 1421 741
2874 2 2 11 1 1355 1404 788
2875 2 2 11 1 828 1409 1357
2876 2 2 11 1 777 1438 1374
2877 2 2 11 1 1357 1429 838
2878 2 2 11 1 700 1415 1378
2879 2 2 11 1 1398 1426 1059
2880 2 2 11 1 540 1426 1398
$EndElements
Due to the large size of my MSH file, I have removed some lines to adhere to the maximum character limit.
I have the folowing error:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[30], line 11
9 # Dirichlet conditions on the wall
10 u_wall=Function(W0)
---> 11 facets_wall = locate_entities_boundary(msh, 1, ft.find(9))
12 dofs_wall = locate_dofs_topological((W.sub(0), W0), 1, facets_wall)
13 bc0 = dirichletbc(u_wall, dofs_wall, W.sub(0))
File ~/micromamba/envs/fenicsx/lib/python3.12/site-packages/dolfinx/mesh.py:233, in locate_entities_boundary(mesh, dim, marker)
208 def locate_entities_boundary(mesh: Mesh, dim: int, marker: typing.Callable) -> np.ndarray:
209 """Compute mesh entities that are connected to an owned boundary
210 facet and satisfy a geometric marking function.
211
(...)
231
232 """
--> 233 return _cpp.mesh.locate_entities_boundary(mesh._cpp_object, dim, marker)
TypeError: locate_entities_boundary(): incompatible function arguments. The following argument types are supported:
1. (mesh: dolfinx.cpp.mesh.Mesh_float32, dim: int, marker: Callable[[numpy.ndarray[numpy.float32]], numpy.ndarray[bool]]) -> numpy.ndarray[numpy.int32]
2. (mesh: dolfinx.cpp.mesh.Mesh_float64, dim: int, marker: Callable[[numpy.ndarray[numpy.float64]], numpy.ndarray[bool]]) -> numpy.ndarray[numpy.int32]
Invoked with: <dolfinx.cpp.mesh.Mesh_float64 object at 0x7f603c789a90>, 1, array([ 1, 3, 11, 26, 49, 69, 111, 157, 208, 267, 332,
407, 484, 568, 664, 766, 878, 995, 1117, 1245, 1287, 1371,
1373, 1497, 1499, 1620, 1622, 1747, 1753, 1865, 1874, 1973, 1985,
2073, 2088, 2177, 2195, 2282, 2302, 2390, 2411, 2504, 2527, 2623,
2646, 2753, 2776, 2887, 2910, 3009, 3132, 3249, 3353, 3455, 3554,
3639, 3720, 3794, 3855, 3916, 3967, 4013, 4052, 4083, 4109, 4131,
4148, 4158], dtype=int32)