[BUG]
HGokcenGuner opened this issue · 0 comments
HGokcenGuner commented
Describe the bug
This is my error when I I run my meshio code as below. It does not show my physical groups when I open it on gmsh.
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
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_mapfile_format
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(
To Reproduce
This is my mesh:
2.2 0 8
$EndMeshFormat
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2
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2 2 "b2"
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128 2 2 0 1 76 170 120
129 2 2 0 1 90 177 118
130 2 2 0 1 107 179 130
131 2 2 0 1 122 173 139
132 2 2 0 1 130 179 101
133 2 2 0 1 13 135 69
134 2 2 0 1 14 135 13
135 2 2 0 1 135 136 134
136 2 2 0 1 138 163 109
137 2 2 0 1 104 164 146
138 2 2 0 1 93 98 82
139 2 2 0 1 105 131 83
140 2 2 0 1 7 93 82
141 2 2 0 1 71 150 107
142 2 2 0 1 100 101 81
143 2 2 0 1 102 105 83
144 2 2 0 1 93 114 98
145 2 2 0 1 100 117 101
146 2 2 0 1 102 116 105
147 2 2 0 1 111 115 110
148 2 2 0 1 137 139 138
149 2 2 0 1 129 130 78
150 2 2 0 1 106 118 108
151 2 2 0 1 111 148 122
152 2 2 0 1 84 102 83
153 2 2 0 1 87 92 5
154 2 2 0 1 7 82 81
155 2 2 0 1 8 84 83
156 2 2 0 1 25 123 77
157 2 2 0 1 27 125 73
158 2 2 0 1 32 127 96
159 2 2 0 1 36 129 78
160 2 2 0 1 61 150 71
161 2 2 0 1 71 107 106
162 2 2 0 1 108 109 80
163 2 2 0 1 101 149 81
164 2 2 0 1 84 103 102
165 2 2 0 1 86 111 110
166 2 2 0 1 104 119 103
167 2 2 0 1 127 132 128
168 2 2 0 1 79 139 137
169 2 2 0 1 86 110 87
170 2 2 0 1 12 133 11
171 2 2 0 1 46 137 45
172 2 2 0 1 51 140 50
173 2 2 0 1 69 133 12
174 2 2 0 1 37 129 36
175 2 2 0 1 45 137 72
176 2 2 0 1 97 140 51
177 2 2 0 1 60 150 61
178 2 2 0 1 123 124 77
179 2 2 0 1 127 128 96
180 2 2 0 1 97 141 140
181 2 2 0 1 119 120 103
182 2 2 0 1 11 65 10
183 2 2 0 1 11 133 65
184 2 2 0 1 13 69 12
185 2 2 0 1 16 75 15
186 2 2 0 1 17 145 16
187 2 2 0 1 16 145 75
188 2 2 0 1 18 68 17
189 2 2 0 1 68 145 17
190 2 2 0 1 43 94 42
191 2 2 0 1 44 147 43
192 2 2 0 1 43 147 94
193 2 2 0 1 45 72 44
194 2 2 0 1 72 147 44
195 2 2 0 1 47 79 46
196 2 2 0 1 50 70 49
197 2 2 0 1 50 140 70
198 2 2 0 1 52 97 51
199 2 2 0 1 55 143 91
200 2 2 0 1 63 151 148
201 2 2 0 1 64 148 86
202 2 2 0 1 82 100 81
203 2 2 0 1 111 121 115
204 2 2 0 1 64 86 5
205 2 2 0 1 86 87 5
206 2 2 0 1 6 88 62
207 2 2 0 1 55 91 8
208 2 2 0 1 79 137 46
209 2 2 0 1 53 89 54
210 2 2 0 1 54 143 55
211 2 2 0 1 89 143 54
212 2 2 0 1 140 142 70
213 2 2 0 1 137 138 72
214 2 2 0 1 145 146 75
215 2 2 0 1 87 99 92
216 2 2 0 1 143 144 91
217 2 2 0 1 148 151 122
218 2 2 0 1 111 122 121
219 2 2 0 1 71 80 6
220 2 2 0 1 62 151 63
221 2 2 0 1 63 148 64
222 2 2 0 1 106 108 80
223 2 2 0 1 141 142 140
224 2 2 0 1 99 113 92
225 2 2 0 1 81 149 59
226 2 2 0 1 88 151 62
227 2 2 0 1 71 106 80
228 2 2 0 1 61 71 6
229 2 2 0 1 7 81 59
230 2 2 0 1 8 83 56
231 2 2 0 1 21 95 20
232 2 2 0 1 23 76 22
233 2 2 0 1 25 77 24
234 2 2 0 1 26 123 25
235 2 2 0 1 27 73 26
236 2 2 0 1 73 123 26
237 2 2 0 1 28 125 27
238 2 2 0 1 29 67 28
239 2 2 0 1 67 125 28
240 2 2 0 1 32 96 31
241 2 2 0 1 33 127 32
242 2 2 0 1 34 74 33
243 2 2 0 1 74 127 33
244 2 2 0 1 36 78 35
245 2 2 0 1 38 90 37
246 2 2 0 1 90 129 37
247 2 2 0 1 40 66 39
248 2 2 0 1 56 131 57
249 2 2 0 1 83 131 56
250 2 2 0 1 57 85 58
251 2 2 0 1 59 149 60
252 2 2 0 1 149 150 60
253 2 2 0 1 74 132 127
254 2 2 0 1 84 104 103
255 2 2 0 1 108 112 109
256 2 2 0 1 86 148 111
257 2 2 0 1 57 131 85
258 2 2 0 1 14 152 135
259 2 2 0 1 133 190 65
260 2 2 0 1 67 189 125
261 2 2 0 1 154 187 66
262 2 2 0 1 153 188 68
263 2 2 0 1 75 152 15
264 2 2 0 1 132 191 100
265 2 2 0 1 110 193 142
266 2 2 0 1 77 195 116
267 2 2 0 1 78 196 117
268 2 2 0 1 121 192 79
269 2 2 0 1 118 194 90
270 2 2 0 1 135 152 136
271 2 2 0 1 15 152 14
272 2 2 0 1 144 180 136
273 2 2 0 1 66 187 178
274 2 2 0 1 120 188 95
275 2 2 0 1 117 191 74
276 2 2 0 1 70 193 115
277 2 2 0 1 139 192 122
278 2 2 0 1 105 195 124
279 2 2 0 1 101 196 130
280 2 2 0 1 144 164 91
281 2 2 0 1 10 156 9
282 2 2 0 1 19 153 18
283 2 2 0 1 30 155 29
284 2 2 0 1 41 154 40
285 2 2 0 1 65 190 157
286 2 2 0 1 158 189 67
287 2 2 0 1 136 165 144
288 2 2 0 1 65 156 10
289 2 2 0 1 18 153 68
290 2 2 0 1 29 155 67
291 2 2 0 1 40 154 66
292 2 2 0 1 146 165 75
293 2 2 0 1 129 168 130
294 2 2 0 1 105 167 131
295 2 2 0 1 82 166 100
296 2 2 0 1 150 179 107
297 2 2 0 1 21 174 95
298 2 2 0 1 23 175 76
299 2 2 0 1 34 176 74
300 2 2 0 1 38 177 90
301 2 2 0 1 102 170 116
302 2 2 0 1 70 171 49
303 2 2 0 1 47 169 79
304 2 2 0 1 101 179 149
305 2 2 0 1 120 170 103
306 2 2 0 1 110 172 87
307 2 2 0 1 118 178 108
308 2 2 0 1 76 174 22
309 2 2 0 1 77 175 24
310 2 2 0 1 78 176 35
311 2 2 0 1 66 177 39
312 2 2 0 1 151 173 122
313 2 2 0 1 143 180 144
314 2 2 0 1 2 181 41
315 2 2 0 1 3 183 30
316 2 2 0 1 31 183 3
317 2 2 0 1 20 184 4
318 2 2 0 1 42 181 2
319 2 2 0 1 4 184 19
320 2 2 0 1 9 182 1
321 2 2 0 1 1 182 52
322 2 2 0 1 107 194 106
323 2 2 0 1 58 185 7
324 2 2 0 1 7 185 93
325 2 2 0 1 92 186 5
326 2 2 0 1 5 186 53
327 2 2 0 1 138 160 72
328 2 2 0 1 68 159 145
329 2 2 0 1 145 159 146
330 2 2 0 1 72 160 147
331 2 2 0 1 152 165 136
332 2 2 0 1 134 161 113
333 2 2 0 1 104 159 119
334 2 2 0 1 112 160 109
335 2 2 0 1 162 185 85
336 2 2 0 1 109 197 80
337 2 2 0 1 84 198 104
338 2 2 0 1 163 173 88
339 2 2 0 1 89 186 161
340 2 2 0 1 168 194 107
341 2 2 0 1 119 188 120
342 2 2 0 1 114 189 98
343 2 2 0 1 99 190 113
344 2 2 0 1 114 162 126
345 2 2 0 1 113 161 92
346 2 2 0 1 93 162 114
347 2 2 0 1 30 183 155
348 2 2 0 1 156 182 9
349 2 2 0 1 19 184 153
350 2 2 0 1 41 181 154
351 2 2 0 1 103 170 102
352 2 2 0 1 90 168 129
353 2 2 0 1 98 166 82
354 2 2 0 1 87 172 99
355 2 2 0 1 149 179 150
356 2 2 0 1 48 169 47
357 2 2 0 1 49 171 48
358 2 2 0 1 88 173 151
359 2 2 0 1 48 171 169
360 2 2 0 1 22 174 21
361 2 2 0 1 24 175 23
362 2 2 0 1 35 176 34
363 2 2 0 1 39 177 38
364 2 2 0 1 108 178 112
365 2 2 0 1 131 167 85
366 2 2 0 1 89 180 143
367 2 2 0 1 75 165 152
368 2 2 0 1 53 186 89
369 2 2 0 1 85 185 58
370 2 2 0 1 95 184 20
371 2 2 0 1 94 181 42
372 2 2 0 1 52 182 97
373 2 2 0 1 96 183 31
374 2 2 0 1 124 195 77
375 2 2 0 1 130 196 78
376 2 2 0 1 115 193 110
377 2 2 0 1 79 192 139
378 2 2 0 1 100 191 117
379 2 2 0 1 8 198 84
380 2 2 0 1 80 197 6
381 2 2 0 1 91 198 8
382 2 2 0 1 6 197 88
383 2 2 0 1 117 196 101
384 2 2 0 1 116 195 105
385 2 2 0 1 106 194 118
386 2 2 0 1 142 193 70
387 2 2 0 1 122 192 121
388 2 2 0 1 74 191 132
389 2 2 0 1 163 197 109
390 2 2 0 1 104 198 164
391 2 2 0 1 98 189 158
392 2 2 0 1 157 190 99
393 2 2 0 1 155 183 96
394 2 2 0 1 154 181 94
395 2 2 0 1 153 184 95
396 2 2 0 1 97 182 156
397 2 2 0 1 94 187 154
398 2 2 0 1 95 188 153
399 2 2 0 1 178 187 112
400 2 2 0 1 161 186 92
401 2 2 0 1 93 185 162
402 2 2 0 1 90 194 168
403 2 2 0 1 164 198 91
404 2 2 0 1 88 197 163
405 2 2 0 2 204 205 200
406 2 2 0 2 204 207 202
407 2 2 0 2 200 208 204
408 2 2 0 2 204 208 207
409 2 2 0 2 199 205 204
410 2 2 0 2 203 204 202
411 2 2 0 2 207 208 201
412 2 2 0 2 55 199 54
413 2 2 0 2 58 200 57
414 2 2 0 2 61 201 60
415 2 2 0 2 64 202 63
416 2 2 0 2 206 208 200
417 2 2 0 2 54 203 53
418 2 2 0 2 57 205 56
419 2 2 0 2 60 206 59
420 2 2 0 2 63 207 62
421 2 2 0 2 199 204 203
422 2 2 0 2 199 203 54
423 2 2 0 2 200 205 57
424 2 2 0 2 201 206 60
425 2 2 0 2 202 207 63
426 2 2 0 2 5 209 64
427 2 2 0 2 6 212 61
428 2 2 0 2 7 211 58
429 2 2 0 2 8 210 55
430 2 2 0 2 53 209 5
431 2 2 0 2 62 212 6
432 2 2 0 2 59 211 7
433 2 2 0 2 56 210 8
434 2 2 0 2 203 209 53
435 2 2 0 2 205 210 56
436 2 2 0 2 206 211 59
437 2 2 0 2 207 212 62
438 2 2 0 2 55 210 199
439 2 2 0 2 58 211 200
440 2 2 0 2 61 212 201
441 2 2 0 2 64 209 202
442 2 2 0 2 199 210 205
443 2 2 0 2 200 211 206
444 2 2 0 2 201 212 207
445 2 2 0 2 202 209 203
446 2 2 0 2 201 208 206
$EndElements
Also, here is my .geo file:
// Gmsh project created on Mon May 8 00:21:34 2023
SetFactory("OpenCASCADE");
//+
Point(1) = {0, 0, 0, 1.0};
//+
Point(2) = {0, 6, 0, 1.0};
//+
Point(3) = {6, 6, 0, 1.0};
//+
Point(4) = {6, 0, 0, 1.0};
//+
Point(5) = {2, 2, 0, 1.0};
//+
Point(6) = {2, 4, 0, 1.0};
//+
Point(7) = {4, 4, 0, 1.0};
//+
Point(8) = {4, 2, 0, 1.0};
//+
Line(1) = {1, 4};
//+
Line(2) = {4, 3};
//+
Line(3) = {3, 2};
//+
Line(4) = {2, 1};
//+
Line(5) = {5, 8};
//+
Line(6) = {8, 7};
//+
Line(7) = {7, 6};
//+
Line(8) = {6, 5};
//+
Curve Loop(1) = {3, 4, 1, 2};
//+
Curve Loop(2) = {7, 8, 5, 6};
//+
Plane Surface(1) = {1, 2};
//+
Plane Surface(2) = {2};
//+
Physical Surface("b1") = {1,2};
//+
Physical Surface("b2") = {2};
This is my meshio code:
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)
Diagnose
I may ask you to cut and paste the output of the following command.
pip freeze | grep meshio
Did I help?
It did not help.