Physical region and facet not read by meshconvert

Hello, i’m doing a project that requires the legacy dolfin xml format and i’ve recently asked about dolfin-convert to create xml files from gmsh mesh file. I tried making a simple 2D box with a rectangular hole inside. I used the dolfin-convert on terminal.
It works as intended, except it didn’t read my physical and facet region. So it only produced the mesh .xml, no physical or facet xml produced. Here is the said .msh file :

Simple box mesh

Why is it not reading my physical and facet region? Thank you for your help!

Additional information
Mesh created on Gmsh 4.8.4
Fenics version 2019.2.0dev0

Please add the msh file directly to the question using 3x` encapsulation.
It would be even better if you could supply the geo file

Hi, dokken. Thanks for replying! I did try using the 3x` encapsulation but it was over the limit of characters allowed. Also .geo file :

// Gmsh project created on Tue Aug 03 16:46:33 2021
Point(1) = {10, 10, 0, 1.0};
Point(2) = {0, 0, 0, 1.0};
Point(3) = {10, 0, 0, 1.0};
Point(4) = {0, 10, 0, 1.0};
Line(1) = {4, 2};
Line(2) = {2, 3};
Line(3) = {3, 1};
Line(4) = {1, 4};
Curve Loop(1) = {4, 1, 2, 3};
Point(5) = {2.5, 2.5, 0, 1.0};
Point(6) = {2.5, 7.5, 0, 1.0};
Point(7) = {7.5, 7.5, 0, 1.0};
Point(8) = {7.5, 2.5, 0, 1.0};
Line(5) = {7, 6};
Line(6) = {6, 5};
Line(7) = {5, 8};
Line(8) = {8, 7};
Physical Curve("outer", 15) = {5, 8, 7, 6};
Physical Curve("inner", 16) = {1, 4, 3, 2};
Curve Loop(3) = {8, 5, 6, 7};
Plane Surface(1) = {1, 3};
Plane Surface(2) = {3};
Physical Surface("inner", 17) = {2};

Pardon the messiness of the GEO files because i am using the GUI for the test and it records anything i do in the GUI

EDIT : i simplified the GEO file from text editor

Have you tried not using strings for tagging your region and facets?

i.e.

// Gmsh project created on Tue Aug 03 16:46:33 2021
Point(1) = {10, 10, 0, 1.0};
Point(2) = {0, 0, 0, 1.0};
Point(3) = {10, 0, 0, 1.0};
Point(4) = {0, 10, 0, 1.0};
Line(1) = {4, 2};
Line(2) = {2, 3};
Line(3) = {3, 1};
Line(4) = {1, 4};
Curve Loop(1) = {4, 1, 2, 3};
Point(5) = {2.5, 2.5, 0, 1.0};
Point(6) = {2.5, 7.5, 0, 1.0};
Point(7) = {7.5, 7.5, 0, 1.0};
Point(8) = {7.5, 2.5, 0, 1.0};
Line(5) = {7, 6};
Line(6) = {6, 5};
Line(7) = {5, 8};
Line(8) = {8, 7};
Physical Curve(15) = {5, 8, 7, 6};
Physical Curve(16) = {1, 4, 3, 2};
Curve Loop(3) = {8, 5, 6, 7};
Plane Surface(1) = {1, 3};
Plane Surface(2) = {3};
Physical Surface(17) = {2};

I tried your configuration and it still doesn’t produce the physical and facet region xmls, i wonder what’s wrong

I have added another physical surface to the outer part of the mesh. Running the dolfin-convert command in the terminal now produces no error. Maybe this helps?

// Gmsh project created on Tue Aug 03 16:46:33 2021
Point(1) = {10, 10, 0, 1.0};
Point(2) = {0, 0, 0, 1.0};
Point(3) = {10, 0, 0, 1.0};
Point(4) = {0, 10, 0, 1.0};
Line(1) = {4, 2};
Line(2) = {2, 3};
Line(3) = {3, 1};
Line(4) = {1, 4};
Curve Loop(1) = {4, 1, 2, 3};
Point(5) = {2.5, 2.5, 0, 1.0};
Point(6) = {2.5, 7.5, 0, 1.0};
Point(7) = {7.5, 7.5, 0, 1.0};
Point(8) = {7.5, 2.5, 0, 1.0};
Line(5) = {7, 6};
Line(6) = {6, 5};
Line(7) = {5, 8};
Line(8) = {8, 7};
Physical Curve(15) = {5, 8, 7, 6};
Physical Curve(16) = {1, 4, 3, 2};
Curve Loop(3) = {8, 5, 6, 7};
Plane Surface(1) = {1, 3};
Plane Surface(2) = {3};
Physical Surface(17) = {2};
Physical Surface(18) = {1};

Thank you for your replies! It is indeed running with no errors, yet dolfin-convert still didn’t make any physical region or facet region xmls…

This is strange because those files were created when I ran the command on my computer. I’m out of ideas now, sorry.

No worries! Having people notice my thread is helpful enough.
Also, i read that the format for elements in gmsh .msh are :
element number - element type - number of tags - tag(s) - node(s)
And i checked with the exported .msh :

$MeshFormat
2.2 0 8
$EndMeshFormat
$Nodes
64
1 10 10 0
2 0 0 0
3 10 0 0
4 0 10 0
5 2.5 2.5 0
6 2.5 7.5 0
7 7.5 7.5 0
8 7.5 2.5 0
9 0 8.333333333333334 0
10 0 6.666666666666667 0
11 0 5 0
12 0 3.333333333333334 0
13 0 1.666666666666666 0
14 1.666666666664462 0 0
15 3.333333333326262 0 0
16 4.999999999992399 0 0
17 6.666666666661599 0 0
18 8.333333333330799 0 0
19 10 1.666666666664462 0
20 10 3.333333333326262 0
21 10 4.999999999992399 0
22 10 6.666666666661599 0
23 10 8.333333333330799 0
24 8.333333333333334 10 0
25 6.666666666666667 10 0
26 5 10 0
27 3.333333333333334 10 0
28 1.666666666666666 10 0
29 5.833333333333334 7.5 0
30 4.166666666666667 7.5 0
31 2.5 5.833333333333334 0
32 2.5 4.166666666666667 0
33 4.166666666666666 2.5 0
34 5.833333333333333 2.5 0
35 7.5 4.166666666666666 0
36 7.5 5.833333333333333 0
37 9.035714285714677 2.575396825392835 0
38 2.575396825392914 0.9642857142852637 0
39 4.166666666659331 1.1111111111112 0
40 8.8888888888888 4.166666666659331 0
41 1.220238095238095 7.159391534391533 0
42 2.575396825396826 9.035714285714285 0
43 7.1593915343916 8.779761904761854 0
44 5.765211640211653 9.033730158730149 0
45 4.166666666666669 8.888888888888889 0
46 0.9642857142851252 2.575396825396358 0
47 0.9662698412698414 5.76521164021164 0
48 1.111111111111111 4.166666666666667 0
49 5.833333333326999 1.111111111110688 0
50 8.88888888888931 5.833333333326999 0
51 8.77976190476204 7.159391534389162 0
52 7.159391534389552 1.220238095237467 0
53 1.210317460314515 1.210317460315119 0
54 1.240703967041952 8.758894322765279 0
55 8.758894322766613 1.240703967039182 0
56 8.747789905294024 8.747789905293287 0
57 5 6.024041468517416 0
58 4.999999999999999 3.974746876424108 0
59 6.262800408580524 4.999798057490253 0
60 3.737199591419476 4.999798057490253 0
61 6.28840122574157 6.288401225741572 0
62 3.711598774258427 3.711598774258428 0
63 3.711598774258426 6.288401225741571 0
64 6.288401225741574 3.711598774258428 0
$EndNodes
$Elements
146
1 15 2 0 1 1
2 15 2 0 2 2
3 15 2 0 3 3
4 15 2 0 4 4
5 15 2 0 5 5
6 15 2 0 6 6
7 15 2 0 7 7
8 15 2 0 8 8
9 1 2 0 1 4 9
10 1 2 0 1 9 10
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20 1 2 0 2 18 3
21 1 2 0 3 3 19
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25 1 2 0 3 22 23
26 1 2 0 3 23 1
27 1 2 0 4 1 24
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31 1 2 0 4 27 28
32 1 2 0 4 28 4
33 1 2 0 5 7 29
34 1 2 0 5 29 30
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36 1 2 0 6 6 31
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38 1 2 0 6 32 5
39 1 2 0 7 5 33
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43 1 2 0 8 35 36
44 1 2 0 8 36 7
45 2 2 0 1 42 6 45
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48 2 2 0 1 31 6 41
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50 2 2 0 1 5 32 48
51 2 2 0 1 46 5 48
52 2 2 0 1 31 41 47
53 2 2 0 1 31 47 48
54 2 2 0 1 29 44 45
55 2 2 0 1 32 31 48
56 2 2 0 1 30 29 45
57 2 2 0 1 7 36 51
58 2 2 0 1 8 34 52
59 2 2 0 1 36 50 51
60 2 2 0 1 34 49 52
61 2 2 0 1 8 37 40
62 2 2 0 1 5 38 39
63 2 2 0 1 33 39 49
64 2 2 0 1 35 40 50
65 2 2 0 1 34 33 49
66 2 2 0 1 36 35 50
67 2 2 0 1 35 8 40
68 2 2 0 1 33 5 39
69 2 2 0 1 38 5 53
70 2 2 0 1 37 8 55
71 2 2 0 1 5 46 53
72 2 2 0 1 8 52 55
73 2 2 0 1 2 14 53
74 2 2 0 1 28 4 54
75 2 2 0 1 6 42 54
76 2 2 0 1 41 6 54
77 2 2 0 1 4 9 54
78 2 2 0 1 23 1 56
79 2 2 0 1 3 19 55
80 2 2 0 1 43 7 56
81 2 2 0 1 1 24 56
82 2 2 0 1 7 51 56
83 2 2 0 1 13 2 53
84 2 2 0 1 18 3 55
85 2 2 0 1 20 21 40
86 2 2 0 1 15 16 39
87 2 2 0 1 37 20 40
88 2 2 0 1 38 15 39
89 2 2 0 1 39 16 49
90 2 2 0 1 40 21 50
91 2 2 0 1 19 20 37
92 2 2 0 1 14 15 38
93 2 2 0 1 21 22 50
94 2 2 0 1 16 17 49
95 2 2 0 1 50 22 51
96 2 2 0 1 49 17 52
97 2 2 0 1 27 42 45
98 2 2 0 1 43 25 44
99 2 2 0 1 47 11 48
100 2 2 0 1 12 13 46
101 2 2 0 1 24 25 43
102 2 2 0 1 12 46 48
103 2 2 0 1 27 28 42
104 2 2 0 1 41 10 47
105 2 2 0 1 11 12 48
106 2 2 0 1 26 27 45
107 2 2 0 1 10 11 47
108 2 2 0 1 25 26 44
109 2 2 0 1 9 10 41
110 2 2 0 1 44 26 45
111 2 2 0 1 22 23 51
112 2 2 0 1 17 18 52
113 2 2 0 1 14 38 53
114 2 2 0 1 19 37 55
115 2 2 0 1 46 13 53
116 2 2 0 1 52 18 55
117 2 2 0 1 9 41 54
118 2 2 0 1 42 28 54
119 2 2 0 1 51 23 56
120 2 2 0 1 24 43 56
121 2 2 0 2 57 58 59
122 2 2 0 2 58 57 60
123 2 2 0 2 33 34 58
124 2 2 0 2 29 30 57
125 2 2 0 2 35 36 59
126 2 2 0 2 31 32 60
127 2 2 0 2 36 7 61
128 2 2 0 2 7 29 61
129 2 2 0 2 5 33 62
130 2 2 0 2 30 6 63
131 2 2 0 2 32 5 62
132 2 2 0 2 6 31 63
133 2 2 0 2 34 8 64
134 2 2 0 2 8 35 64
135 2 2 0 2 57 30 63
136 2 2 0 2 58 34 64
137 2 2 0 2 29 57 61
138 2 2 0 2 33 58 62
139 2 2 0 2 60 57 63
140 2 2 0 2 57 59 61
141 2 2 0 2 58 60 62
142 2 2 0 2 59 58 64
143 2 2 0 2 59 36 61
144 2 2 0 2 35 59 64
145 2 2 0 2 60 32 62
146 2 2 0 2 31 60 63
$EndElements

So i wonder does this mean my exported .msh file somehow doesn’t recognize the physical entity from .geo file?

EDIT : i tried changing some of the zeros to one (manually) and it indeed being read as physical region by dolfin-convert, yet i still don’t know which part is being read as facet region by dolfin-convert and why does exporting the mesh to version 2 from gmsh doesn’t include the physical entity label. Also, which part of this mesh is supposed to be recognized as facets?

Using gmsh 4.6.0 and the following command:

 gmsh -3 dconvert.geo -format msh2

I am able to convert the msh file to xml (including physical and facet regions) using

 dolfin-convert dconvert.msh mesh.xml
2 Likes

when I tried converting your .msh file, I also get no physical or facet .xml files. What happens when you try the mesh I created from your .geo file? Here is my .msh file:

$MeshFormat
2.2 0 8
$EndMeshFormat
$Nodes
148
1 10 10 0
2 0 0 0
3 10 0 0
4 0 10 0
5 2.5 2.5 0
6 2.5 7.5 0
7 7.5 7.5 0
8 7.5 2.5 0
9 0 8.999999999999998 0
10 0 7.999999999999996 0
11 0 6.999999999999994 0
12 0 5.999999999999991 0
13 0 4.999999999999989 0
14 0 3.999999999999988 0
15 0 2.999999999999985 0
16 0 1.999999999999982 0
17 0 0.9999999999999911 0
18 0.9999999999991893 0 0
19 1.999999999996827 0 0
20 2.99999999999391 0 0
21 3.999999999991027 0 0
22 4.999999999992411 0 0
23 5.999999999993932 0 0
24 6.999999999995455 0 0
25 7.999999999996978 0 0
26 8.99999999999849 0 0
27 10 0.9999999999991893 0
28 10 1.999999999996827 0
29 10 2.99999999999391 0
30 10 3.999999999991027 0
31 10 4.999999999992411 0
32 10 5.999999999993932 0
33 10 6.999999999995455 0
34 10 7.999999999996978 0
35 10 8.99999999999849 0
36 8.999999999999998 10 0
37 7.999999999999996 10 0
38 6.999999999999994 10 0
39 5.999999999999991 10 0
40 4.999999999999989 10 0
41 3.999999999999988 10 0
42 2.999999999999985 10 0
43 1.999999999999982 10 0
44 0.9999999999999911 10 0
45 6.499999999999998 7.5 0
46 5.499999999999996 7.5 0
47 4.499999999999994 7.5 0
48 3.499999999999991 7.5 0
49 2.5 6.499999999999998 0
50 2.5 5.499999999999996 0
51 2.5 4.499999999999994 0
52 2.5 3.499999999999991 0
53 3.500000000000002 2.5 0
54 4.500000000000004 2.5 0
55 5.500000000000006 2.5 0
56 6.500000000000009 2.5 0
57 7.5 3.500000000000002 0
58 7.5 4.500000000000004 0
59 7.5 5.500000000000006 0
60 7.5 6.500000000000009 0
61 1.504237369278822 0.8437935400932353 0
62 9.09742746643666 1.569695173660743 0
63 1.552867838065872 9.052119733802147 0
64 8.447132161933904 9.052119733801668 0
65 9.076579026614752 3.383820427574388 0
66 3.499999999992468 0.8660254037819272 0
67 0.8159800986278851 2.565090298183414 0
68 3.03474995713471 8.35680591780779 0
69 1.666666666666666 4.013743614618013 0
70 1.654494632043742 6.995091566207847 0
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72 5.499999999999991 9.158248672024422 0
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75 8.345505367955765 4.995091566207249 0
76 8.36602540378443 7.000000000000005 0
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147 4.791009322085348 4.051515143830581 0
148 4.790616148109524 5.948751121073604 0
$EndNodes
$Elements
314
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2 1 2 16 1 9 10
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4 1 2 16 1 11 12
5 1 2 16 1 12 13
6 1 2 16 1 13 14
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$EndElements

This does work. I guess the export function from the GUI is not as reliable as Ubuntu packages. I tried dokken’s method and it works. Huh, weird gmsh stuff i guess :laughing:

1 Like

Thanks, it works! I guess i’ll just use terminal to export .geo files from now on instead of the GUI.