Hello dokken,
Based on the question you asked, I checked whether my format is correct and I solved my problem. When converting from gmsh to msh, I needed to select version II ASCII format, then I deleted the truss elements from the msh file. So my code worked.
Thank you so much
I was trying to run it, does not work now. Is there any updates how to convert msh to xdmf? Thank you!
The geo-file I am trying to convert:
Point(1) = {0.0, 0.0, 0, 0.1};
Point(2) = {1.0, 0.0, 0, 0.0001};
Point(3) = {0.0, 1.0, 0, 0.01};
Point(4) = {-1.0, 0.0, 0, 0.01};
Point(5) = {0.0, -1.0, 0, 0.01};
Circle(1) = {2, 1, 3};
Circle(2) = {3, 1, 4};
Circle(3) = {4, 1, 5};
Circle(4) = {5, 1, 2};
Line Loop(1) = {1, 2, 3, 4};
Plane Surface(1) = {1};
Point{1} In Surface{1};
from dolfin import *
from configparser import ConfigParser
import numpy as np
# Importing mesh from gmsh and defining surface and boundary markers
msh = meshio.read("mesh.msh")
# print(msh.cell_sets_dict)
print(msh.cell_data_dict)
for key in msh.cell_data_dict["gmsh:geometrical"].keys():
if key == "triangle":
triangle_data = msh.cell_data_dict["gmsh:geometrical"][key]
for cell in msh.cells:
if cell.type == "tetra":
tetra_cells = cell.data
elif cell.type == "triangle":
triangle_cells = cell.data
triangle_mesh =meshio.Mesh(points=msh.points,
cells=[("triangle", triangle_cells)],
cell_data={"name_to_read":[triangle_data]})
meshio.write("mesh.xdmf", triangle_mesh)
mesh = Mesh()
mvc = MeshValueCollection("size_t", mesh, mesh.topology().dim())
with XDMFFile("mesh.xdmf") as infile:
infile.read(mesh)
mvc = MeshValueCollection("size_t", mesh, mesh.topology().dim())
with XDMFFile("mesh.xdmf") as infile:
infile.read(mvc, "name_to_read")
mf = cpp.mesh.MeshFunctionSizet(mesh, mvc)
print(mesh.topology().dim() - 1)
boundary_markers = MeshFunction('size_t', mesh, mesh.topology().dim()-1, 0)
class Boundary(SubDomain):
def inside(self, x, on_boundary):
return on_boundary and near(x[1], 0.0)
b_c = Boundary()
b_c.mark(boundary_markers, 3)
# Compiling subdomains
ds = Measure('ds', domain=mesh, subdomain_data=boundary_markers)
dx = Measure("dx", domain=mesh, subdomain_data=mf, subdomain_id=1)
this works for me
1 Like
Hi, please make sure to select version II ASCII format when you export your gmsh as msh
1 Like
Hello Dokken,
I create a 2D mesh with an obstacle, the goal is to have different boundary conditions on all the walls and on the obstacle, when I get the mesh.msh and convert it through dolfin-convert, however, it only creates a file malla_physical_region.xml. When trying to impose the boundary conditions it gives me error. any suggestions?
Blockquote
def main():
#mesh = fe.UnitSquareMesh(N_POINTS_P_AXIS, N_POINTS_P_AXIS)
xml_file = “Malla1.xml”
mesh = fe.Mesh(xml_file)
n = fe.FacetNormal(mesh)
# Taylor-Hood Elements. The order of the function space for the pressure has
# to be one order lower than for the velocity
velocity_function_space = fe.VectorFunctionSpace(mesh, "Lagrange", 2)
pressure_function_space = fe.FunctionSpace(mesh, "Lagrange", 1)
u_trial = fe.TrialFunction(velocity_function_space)
p_trial = fe.TrialFunction(pressure_function_space)
v_test = fe.TestFunction(velocity_function_space)
q_test = fe.TestFunction(pressure_function_space)
# Define the Initial Value for velocity
u_0 = fe.Expression(('0.0', '0.0'), degree=2)
cd = fe.MeshFunction('size_t', mesh, "Malla1_physical_region.xml")
# Define the Boundary Condition for velocity
ymax = 2.0
Umax = 0.1
inflow = fe.Expression(('Umax*ymax*x[1]*(ymax - x[1])/(ymax*ymax)', '0.0'), degree=2, Umax=Umax, ymax=ymax)
u_in_boundary_condition = fe.DirichletBC(
velocity_function_space,
inflow,
cd,
12
)
Blockquote
Without supplying how you have generated the mesh, or the mesh itself, i cannot give any further guidance.
Please note that dolfin-convert is no longer maintained, and that it is recommended to use the xdmf format
Thank you very much. I created the mesh in gmsh with a .txt file and adding phishycal groups manually.
It is a very simple domain, as it is a first approximation to make a good labeling of the boundary conditions at entrance, walls and exit, as well as at the obstacle.Mallas
As I said, you should not use dolfin-convert (as it is no longer maintained).
The thread here has plenty of examples of how to use the newer and more supported framework. For instance
Sorry, I will try to use the one you recommend. However, when I want to use the code you mention, I get the following error. I have doubts about how to work with the “ds” since in my weak formulation I don’t consider them.
Blockquote
UserWarning: h5py is running against HDF5 1.10.7 when it was built against 1.12.2, this may cause problems
_warn(("h5py is running against HDF5 {0} when it was built against {1}, "
Warning! HDF5 library version mismatched error
1 Like
I am using this mesh and the recommended code.
Blockquote
Point(1) = { 0.000000, 0.000000, 0, 0.100000 };
Point(2) = { 2.000000, 0.000000, 0, 0.100000 };
Point(3) = { 2.000000, 1.000000, 0, 0.100000 };
Point(4) = { 0.000000, 1.000000, 0, 0.100000 };
Point(5) = { 0.500000, 0.2500000, 0, 0.100000 };
Point(6) = { 1.500000, 0.250000, 0, 0.100000 };
Point(7) = { 1.500000, 0.750000, 0, 0.100000 };
Point(8) = { 0.500000, 0.750000, 0, 0.100000 };
Line(1) = { 1, 2};
Line(2) = { 2, 3};
Line(3) = { 3, 4};
Line(4) = { 4, 1};
Line(5) = { 5, 6};
Line(6) = { 6, 7};
Line(7) = { 7, 8};
Line(8) = { 8, 5};
Curve Loop(9) = { 1, 2, 3, 4 };
Curve Loop(10) = { 5, 6, 7, 8 };
Plane Surface(11) = {9,10};
Physical Surface(“Obstaculo”) = {11}
Mesh 2;
Mesh.SurfaceFaces = 1;
Mesh.Points = 1;
When you install h5py, you need to build it against the allready installed HDF5 library.
This can be achieved by calling
pip3 uninstall h5py
pip3 install —no-binary=h5py h5py
How do I know how the walls are labeled to impose boundary conditions?
Tjue are label with integer markers, and you can visually inspect the files (mesh.xdmf for cell markers, and mf.xdmf for facet markers) to see what values you assigned them in GMSH.
Is it necessary to create pishycal groups in gmsh to extract them from the suggested code?
Blockquote
Point(1) = { 0.000000, 0.000000, 0, 0.100000 };
Point(2) = { 2.000000, 0.000000, 0, 0.100000 };
Point(3) = { 2.000000, 1.000000, 0, 0.100000 };
Point(4) = { 0.000000, 1.000000, 0, 0.100000 };
Point(5) = { 0.500000, 0.2500000, 0, 0.100000 };
Point(6) = { 1.500000, 0.250000, 0, 0.100000 };
Point(7) = { 1.500000, 0.750000, 0, 0.100000 };
Point(8) = { 0.500000, 0.750000, 0, 0.100000 };
Line(1) = { 1, 2};
Line(2) = { 2, 3};
Line(3) = { 3, 4};
Line(4) = { 4, 1};
Line(5) = { 5, 6};
Line(6) = { 6, 7};
Line(7) = { 7, 8};
Line(8) = { 8, 5};Curve Loop(9) = { 1, 2, 3, 4 };
Curve Loop(10) = { 5, 6, 7, 8 };Plane Surface(11) = {9,10};
Physical Surface(“Obstaculo”) = {11}
Mesh 2;
Mesh.SurfaceFaces = 1;
Mesh.Points = 1;
Is there a way to write pygmsh meshes with physical groups directly with meshio, without the intermediate step of writing the .msh using gmsh?
Consider the following MWE with the flag gmsh_workaround = True|False:
import meshio
import numpy as np
import pygmsh
def create_mesh(mesh, cell_type):
cells = mesh.get_cells_type(cell_type)
cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
out_mesh = meshio.Mesh(
points=mesh.points, cells={cell_type: cells}, cell_data={"markers": [cell_data]}
)
return out_mesh
gmsh_workaround = True
with pygmsh.geo.Geometry() as geom:
ny = 10
cylinder = geom.add_circle((0.2, 0, 0), 0.05, mesh_size=np.pi / ny / 30)
rectangle = geom.add_rectangle(
0.0, 2.2, -0.2, 0.21, 0, mesh_size=0.41 / ny, holes=[cylinder]
)
geom.add_physical(rectangle.lines[3], "inlet") # 1
geom.add_physical(rectangle.lines[1], "outlet") # 2
geom.add_physical(rectangle.lines[0::2], "walls") # 3
geom.add_physical(cylinder.curve_loop.curves, "cylinder") # 4
geom.add_physical(rectangle.surface, "domain") # 5
mesh = geom.generate_mesh(dim=2, verbose=True)
if gmsh_workaround:
import gmsh
gmsh.write("karm_test.msh")
gmsh.clear()
mesh = meshio.read("karm_test.msh")
triangle_mesh = create_mesh(mesh, "triangle")
line_mesh = create_mesh(mesh, "line")
meshio.write("mesh_2d.xdmf", triangle_mesh)
meshio.write("mesh_1d.xdmf", line_mesh)
Without writing the gmsh mesh, I get this error:
Traceback (most recent call last):
File "/home/david/work/FEniCS/NavierStokes/examples/scripts/test_genmesh.py", line 38, in <module>
triangle_mesh = create_mesh(mesh, "triangle")
File "/home/david/work/FEniCS/NavierStokes/examples/scripts/test_genmesh.py", line 8, in create_mesh
cell_data = mesh.get_cell_data("gmsh:physical", cell_type)
File "/usr/lib/python3.10/site-packages/meshio/_mesh.py", line 250, in get_cell_data
[d for c, d in zip(self.cells, self.cell_data[name]) if c.type == cell_type]
KeyError: 'gmsh:physical'
Thanks!
Bonus question: is there a way to force the integer IDs for physical groups? Some versions ago ints could be specified instead of string labels for add_physical().
This question is solely about pygmsh, and I would suggest asking the authors of the software at: Discussions · meshpro/pygmsh · GitHub
In the version of meshio that I am using (5.3.4), msh.cells is not a dictionary anymore. This part needs to be replaced by, e.g., msh.cells_dict["triangle"].
Hello @dokken,
I started to have an error with this code as below:
Traceback (most recent call last):
File "/home/hd/.local/lib/python3.10/site-packages/spyder_kernels/py3compat.py", line 356, in compat_exec
exec(code, globals, locals)
File "/home/hd/Desktop/work/readfromgmsh.py", line 26, in <module>
msh = meshio.read("mesh.msh")
File "/home/hd/.local/lib/python3.10/site-packages/meshio/_helpers.py", line 71, in read
return _read_file(Path(filename), file_format)
File "/home/hd.local/lib/python3.10/site-packages/meshio/_helpers.py", line 103, in _read_file
return reader_map[file_format](str(path))
File "/home/hd/.local/lib/python3.10/site-packages/meshio/gmsh/main.py", line 19, in read
mesh = read_buffer(f)
File "/home/hd/.local/lib/python3.10/site-packages/meshio/gmsh/main.py", line 48, in read_buffer
return reader.read_buffer(f, is_ascii, data_size)
File "/home/hd/.local/lib/python3.10/site-packages/meshio/gmsh/_gmsh22.py", line 59, in read_buffer
has_additional_tag_data, cell_tags = _read_cells(
File "/home/hd/.local/lib/python3.10/site-packages/meshio/gmsh/_gmsh22.py", line 135, in _read_cells
point_tags = np.asarray(point_tags, dtype=np.int32) - 1
TypeError: int() argument must be a string, a bytes-like object or a real number, not 'NoneType'
Is this a format problem?
Without supplying the mesh or the code you are running, your guess is as good as mine.
sorry, here it is:
$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
2
2 1 "b1"
2 2 "b2"
$EndPhysicalNames
$ParametricNodes
212
1 0 0 0 0 1
2 0 6 0 0 2
3 6 6 0 0 3
4 6 0 0 0 4
5 2 2 0 0 5
6 2 4 0 0 6
7 4 4 0 0 7
8 4 2 0 0 8
9 0.5 0 0 1 1 0.5
10 1 0 0 1 1 1
11 1.5 0 0 1 1 1.5
12 2 0 0 1 1 2
13 2.5 0 0 1 1 2.5
14 3 0 0 1 1 3
15 3.5 0 0 1 1 3.5
16 4 0 0 1 1 4
17 4.5 0 0 1 1 4.5
18 5 0 0 1 1 5
19 5.5 0 0 1 1 5.5
20 6 0.5 0 1 2 0.5
21 6 1 0 1 2 1
22 6 1.5 0 1 2 1.5
23 6 2 0 1 2 2
24 6 2.5 0 1 2 2.5
25 6 3 0 1 2 3
26 6 3.5 0 1 2 3.5
27 6 4 0 1 2 4
28 6 4.5 0 1 2 4.5
29 6 5 0 1 2 5
30 6 5.5 0 1 2 5.5
31 5.5 6 0 1 3 0.5
32 5 6 0 1 3 1
33 4.5 6 0 1 3 1.5
34 4 6 0 1 3 2
35 3.5 6 0 1 3 2.5
36 3 6 0 1 3 3
37 2.5 6 0 1 3 3.5
38 2 6 0 1 3 4
39 1.5 6 0 1 3 4.5
40 1 6 0 1 3 5
41 0.5 6 0 1 3 5.5
42 0 5.5 0 1 4 0.5
43 0 5 0 1 4 1
44 0 4.5 0 1 4 1.5
45 0 4 0 1 4 2
46 0 3.5 0 1 4 2.5
47 0 3 0 1 4 3
48 0 2.5 0 1 4 3.5
49 0 2 0 1 4 4
50 0 1.5 0 1 4 4.5
51 0 1 0 1 4 5
52 0 0.5 0 1 4 5.5
53 2.5 2 0 1 5 0.5
54 3 2 0 1 5 1
55 3.5 2 0 1 5 1.5
56 4 2.5 0 1 6 0.5
57 4 3 0 1 6 1
58 4 3.5 0 1 6 1.5
59 3.5 4 0 1 7 0.5
60 3 4 0 1 7 1
61 2.5 4 0 1 7 1.5
62 2 3.5 0 1 8 0.5
63 2 3 0 1 8 1
64 2 2.5 0 1 8 1.5
65 1.25 0.4330127018922192 0 2 1 -1.75 -2.566987298107781
66 1.25 5.566987298107781 0 2 1 -1.75 2.566987298107781
67 5.566987298107781 4.75 0 2 1 2.566987298107781 1.75
68 4.785698770022839 0.4946886104645802 0 2 1 1.785698770022839 -2.50531138953542
69 2.254496105780926 0.4612037892318082 0 2 1 -0.7455038942190743 -2.538796210768192
70 0.4419071631207996 1.801986396852013 0 2 1 -2.5580928368792 -1.198013603147987
71 2.25 4.433012701892219 0 2 1 -0.7499999999999999 1.433012701892219
72 0.424154499976745 4.244885714739565 0 2 1 -2.575845500023255 1.244885714739565
73 5.542555409831971 3.751214045741246 0 2 1 2.542555409831971 0.7512140457412455
74 4.198013603147987 5.558092836879201 0 2 1 1.198013603147987 2.5580928368792
75 3.749794349187955 0.4109272108559554 0 2 1 0.7497943491879548 -2.589072789144045
76 5.566987298107781 1.75 0 2 1 2.566987298107781 -1.25
77 5.561441691445058 2.710602528363683 0 2 1 2.561441691445058 -0.2893974716363172
78 3.289397471636317 5.561441691445058 0 2 1 0.2893974716363173 2.561441691445058
79 0.4385583085549416 3.210602528363683 0 2 1 -2.561441691445058 0.2106025283636827
80 1.769833736592407 4.450027367558652 0 2 1 -1.230166263407593 1.450027367558653
81 3.75 4.433012701892219 0 2 1 0.75 1.433012701892219
82 4.25 4.411827143433352 0 2 1 1.25 1.411827143433352
83 4.433012701892219 2.25 0 2 1 1.433012701892219 -0.7499999999999999
84 4.450027367558652 1.769833736592407 0 2 1 1.450027367558653 -1.230166263407593
85 4.380943079440677 3.260564491082436 0 2 1 1.380943079440677 0.2605644910824355
86 1.566987298107781 2.25 0 2 1 -1.433012701892219 -0.75
87 1.588172856566648 1.75 0 2 1 -1.411827143433352 -1.25
88 1.619672732565809 3.729960694538078 0 2 1 -1.380327267434191 0.7299606945380781
89 2.739631311553749 1.619187983641561 0 2 1 -0.2603686884462507 -1.380812016358439
90 2.194843539709156 5.57738249888757 0 2 1 -0.8051564602908443 2.57738249888757
91 3.729960694538078 1.598487174106941 0 2 1 0.729960694538078 -1.401512825893059
92 1.973824670666154 1.481059130458052 0 2 1 -1.026175329333846 -1.518940869541948
93 4.518955620286768 4.026371131970031 0 2 1 1.518955620286768 1.026371131970031
94 0.3977124653510797 5.277533144360017 0 2 1 -2.60228753464892 2.277533144360018
95 5.577380721241608 0.7975652546932412 0 2 1 2.577380721241608 -2.202434745306759
96 5.247881315359562 5.576613977472084 0 2 1 2.247881315359562 2.576613977472084
97 0.4233860225279162 0.7521186846404384 0 2 1 -2.576613977472084 -2.247881315359562
98 4.763602441325423 4.366598061914489 0 2 1 1.763602441325423 1.366598061914489
99 1.633434571858209 1.236400017132047 0 2 1 -1.366565428141791 -1.763599982867953
100 4.039397471636317 4.869409218767684 0 2 1 1.039397471636317 1.869409218767684
101 3.453641813381747 4.875403267153482 0 2 1 0.4536418133817469 1.875403267153482
102 4.847675622936643 2.003305622765402 0 2 1 1.847675622936643 -0.9966943772345985
103 4.844617326128677 1.503856559892968 0 2 1 1.844617326128677 -1.496143440107032
104 4.43301270189222 1.25 0 2 1 1.433012701892219 -1.75
105 4.872298467749047 2.552458628675642 0 2 1 1.872298467749048 -0.4475413713243582
106 1.980623085759417 4.855765412549202 0 2 1 -1.019376914240583 1.855765412549202
107 2.50964570037995 4.86745918732086 0 2 1 -0.4903542996200501 1.86745918732086
108 1.500076137058638 4.845965624397437 0 2 1 -1.499923862941362 1.845965624397438
109 1.25 4.433012701892221 0 2 1 -1.75 1.43301270189222
110 1.130590781232316 1.960602528363683 0 2 1 -1.869409218767684 -1.039397471636317
111 1.133410627051687 2.493433754727281 0 2 1 -1.866589372948313 -0.506566245272719
112 1.00978044413899 4.811716376621797 0 2 1 -1.99021955586101 1.811716376621797
113 2.018801111763219 0.9368273993501708 0 2 1 -0.9811988882367816 -2.063172600649829
114 5.065506773718249 3.986297989325121 0 2 1 2.065506773718249 0.986297989325121
115 0.700961894323342 2.250000000000001 0 2 1 -2.299038105676658 -0.7499999999999992
116 5.299038105676658 2.250000000000001 0 2 1 2.299038105676658 -0.7499999999999993
117 3.749999999999999 5.299038105676658 0 2 1 0.7499999999999993 2.299038105676658
118 1.742170209603563 5.293063027977954 0 2 1 -1.257829790396437 2.293063027977954
119 4.836791990489028 1.018249353596942 0 2 1 1.836791990489027 -1.981750646403058
120 5.268696212932559 1.266820846730809 0 2 1 2.268696212932559 -1.733179153269191
121 0.7253300846928736 2.777035804511485 0 2 1 -2.274669915307126 -0.2229641954885153
122 1.128480738016361 3.054910619600408 0 2 1 -1.871519261983639 0.05491061960040801
123 5.56440018511107 3.248123229382434 0 2 1 2.564400185111071 0.2481232293824344
124 5.16671580757486 2.956234933194443 0 2 1 2.16671580757486 -0.04376506680555695
125 5.563203307240025 4.227739259292114 0 2 1 2.563203307240025 1.227739259292114
126 5.13801503821123 3.436498477643077 0 2 1 2.13801503821123 0.4364984776430772
127 4.75 5.566987298107781 0 2 1 1.75 2.566987298107781
128 5 5.133974596215562 0 2 1 2 2.133974596215562
129 2.747373501890912 5.588981122252825 0 2 1 -0.2526264981090879 2.588981122252826
130 3 5.133974596215561 0 2 1 5.897316416670768e-16 2.133974596215561
131 4.404194383685529 2.760503853293013 0 2 1 1.404194383685529 -0.2394961467069871
132 4.467985229321447 5.157450585586439 0 2 1 1.467985229321447 2.157450585586438
133 1.766819683210608 0.4362336964008371 0 2 1 -1.233180316789392 -2.563766303599163
134 2.562557896604237 0.8701178554986022 0 2 1 -0.4374421033957626 -2.129882144501398
135 2.765041922468258 0.4379395999187623 0 2 1 -0.2349580775317417 -2.562060400081238
136 3.096060985700038 0.8117238386808792 0 2 1 0.09606098570003763 -2.188276161319121
137 0.4330127018922196 3.75 0 2 1 -2.56698729810778 0.7500000000000002
138 0.8755429280744131 3.997206851248701 0 2 1 -2.124457071925587 0.9972068512487008
139 0.8327000119036376 3.455550568711534 0 2 1 -2.167299988096362 0.4555505687115334
140 0.4330127018922196 1.25 0 2 1 -2.56698729810778 -1.75
141 0.8660254037844388 1 0 2 1 -2.133974596215561 -2
142 0.8425494144135626 1.532014770678553 0 2 1 -2.157450585586437 -1.467985229321447
143 3.244932001015305 1.602239262492889 0 2 1 0.2449320010153045 -1.397760737507111
144 3.513762402495052 1.164187780836219 0 2 1 0.5137624024950525 -1.835812219163781
145 4.25080123460803 0.4307529028994281 0 2 1 1.25080123460803 -2.569247097100572
146 3.991724016118942 0.8682567218111874 0 2 1 0.9917240161189418 -2.131743278188813
147 0.4938916050499853 4.786218630605578 0 2 1 -2.506108394950015 1.786218630605579
148 1.565977660213935 2.758057395721282 0 2 1 -1.434022339786065 -0.2419426042787184
149 3.242273635563625 4.413390120661525 0 2 1 0.2422736355636248 1.413390120661525
150 2.750319889323929 4.408795677150973 0 2 1 -0.2496801106760707 1.408795677150973
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