Hey all,
I believe there is a bug somewhere in the read-in portion for .xda
files. I have not been able to track it down, but the code having
problems. To be sure this wasn't a fixed problem I downloaded the most
recent version on the sourceforge svn server today.
I generated a tetrahedral mesh using another program and converted it to
.xda format using a script, based on the answers benkirk gave to my
question about the format. I have attached the file, but here is the
header and the first few lines of the connectivity array:
\begin{verbatim}
libMesh-0.7.0+
1143 # number of elements
222 # number of nodes
. # boundary condition specification file
n/a # subdomain id specification file
n/a # processor id specification file
n/a # p-level specification file
1143 # n_elem at level 0, [type (n0 ... nN-1) ]
8 85 19 80 93
8 2 1 26 49
8 77 55 58 17
8 44 57 49 15
\end{verbatim}
I then used the file in a modified version of example 3 (single
processor) which worked just fine in 3d using using
\begin{verbatim}
MeshTools::Generation::build_cube (mesh,
20, 20, 20,
-1., 1.,
-1., 1.,
-1., 1.,
HEX20);
\end{verbatim}
However, when attempting to use this mesh I get the following error
messages:
\begin{verbatim}
ERROR: Finite element LAGRANGE on geometric element TET
only supports FEInterface::max_order = 1, not fe_type.order = 2
WARNING: Finite element LAGRANGE on geometric element TET
could not be p refined past FEInterface::max_order = 1
ERROR: unsigned char too small to hold Elem::_p_level!
Recompile with Elem:_p_level set to something bigger!
[0] /home/bkraczek/codes-lnx/libmesh/include/geom/elem.h, line 1574,
compiled Jan 29 2009 at 16:23:47
terminate called after throwing an instance of 'libMesh::LogicError'
what(): Error in libMesh internal logic
Aborted
\end{verbatim}
What I have found through digging is that when it goes to reinitialize
the mesh (DofMap::reinit) it finds that fe_type.order == 2;
elem->p_level()==255 .
Any help would be appreciated,
Brent
Kirk, Benjamin (JSC-EG) wrote:
Connectivity:
The header is followed immediately by the connectivity. Are blank or
commented lines ignored? (i.e. can I put a blank line anywhere?)
I think so, I'll check... if not I will fix the code because that is a
perfectly reasonable request. Certainly a comment can follow data on a
line, see for example reference_elements/3D/one_hex20.xda
In connectivity section, it appears that the first number is the element
type. I want to use tetrahedra, so it looks like this number should be 8
for a tet4 and 9 for a tet10. The rest of the numbers are the node index
numbers, starting from zero.
Right.
Nodes:
Next come the node locations in Cartesian coordinates. Their order
should correspond to the indices used by the connectivity and the
possibly the boundary conditions.
Right.
Boundary conditions (where I have the most questions):
First, is this section necessary if I intend to use the same boundary
condition on all external elements? In the examples I've been working
from (primarily #3, which uses a penalty method), the code checks to see
if the element has a neighbor and applies the BC if it does not. In my
application I need to use a special mixed ("Robin") BC, so I don't to
use a pure Dirichlet condition.
Correct. The boundary conditions are only there for your convenience. If
you do not need to
Second, how is the side index determined? Specifically, If I have a
tetrahedron with arbitrary position in space, how do I know which index
a side gets?
The side indices is dependent on the node ordering. see for example
src/geom/cell_tet4.C:
const unsigned int Tet4::side_nodes_map[4][3] =
{
{0, 2, 1}, // Side 0
{0, 1, 3}, // Side 1
{1, 2, 3}, // Side 2
{2, 0, 3} // Side 3
};
So side 0 is the triangle defined by nodes (0,2,1) from the tet.
Third, how is the number for the boundary condition used? Is this index
the same as used in something like 'elem->neighbor(side)'?
It is not used at all. It is inserted into the BoundaryInfo object
('mesh.boundary_info') and you can get access to it to set different BCs on
different parts of the domain.
-Ben
libMesh-0.7.0+
1143 # number of elements
222 # number of nodes
. # boundary condition specification file
n/a # subdomain id specification file
n/a # processor id specification file
n/a # p-level specification file
1143 # n_elem at level 0, [type (n0 ... nN-1) ]
8 85 19 80 93
8 2 1 26 49
8 77 55 58 17
8 44 57 49 15
8 17 47 26 59
8 85 26 78 75
8 41 28 21 36
8 44 47 15 31
8 97 35 93 82
8 31 20 37 21
8 39 34 41 51
8 66 57 26 49
8 33 18 14 31
8 63 29 50 52
8 1 81 71 10
8 4 41 54 46
8 29 28 46 40
8 90 9 68 27
8 13 11 74 27
8 39 34 51 48
8 83 1 89 12
8 64 29 52 43
8 84 11 16 27
8 33 14 47 31
8 41 21 18 39
8 78 66 26 91
8 35 12 87 98
8 29 50 46 4
8 74 60 27 67
8 7 80 82 70
8 7 6 9 76
8 1 66 73 91
8 56 13 27 4
8 33 39 45 48
8 6 88 76 7
8 33 17 32 58
8 12 13 81 10
8 85 19 96 91
8 50 56 13 60
8 13 63 10 5
8 53 64 43 10
8 3 41 18 34
8 47 57 26 59
8 77 55 17 75
8 30 53 43 10
8 95 12 98 87
8 35 87 16 92
8 84 11 74 87
8 7 8 70 32
8 9 32 76 65
8 1 19 91 0
8 64 29 43 10
8 19 85 96 93
8 4 69 54 9
8 90 9 27 6
8 90 9 6 76
8 11 94 74 87
8 29 28 4 46
8 62 1 2 49
8 33 39 34 18
8 63 64 81 10
8 39 33 31 18
8 1 12 81 10
8 40 28 46 36
8 96 19 0 91
8 69 68 27 86
8 64 29 10 63
8 4 69 9 27
8 20 30 42 43
8 29 40 52 43
8 63 29 10 5
8 63 29 5 50
8 17 77 32 58
8 29 40 43 20
8 90 9 76 68
8 88 6 16 7
8 1 83 81 12
8 14 17 47 15
8 13 94 79 74
8 88 35 16 92
8 13 50 63 5
8 220 198 208 217
8 72 88 82 7
8 4 41 46 28
8 56 46 4 54
8 19 8 75 80
8 32 72 76 61
8 217 220 221 203
8 66 1 62 49
8 85 26 75 19
8 35 8 19 80
8 44 31 30 37
8 35 80 93 82
8 90 88 16 92
8 30 2 53 10
8 51 68 9 54
8 83 1 81 71
8 35 19 96 93
8 30 44 42 49
8 50 29 46 40
8 6 88 16 90
8 4 69 27 56
8 94 12 95 87
8 84 90 16 92
8 32 72 61 70
8 29 30 43 10
8 68 69 27 9
8 8 17 26 75
8 18 41 3 28
8 51 34 41 54
8 57 47 26 15
8 39 31 38 21
8 41 34 3 54
8 78 75 26 59
8 50 29 5 4
8 32 61 76 65
8 85 26 19 91
8 78 66 57 26
8 46 28 41 36
8 77 17 32 8
8 1 19 26 91
8 27 90 6 16
8 58 61 32 48
8 29 28 40 20
8 68 69 9 54
8 51 34 54 9
8 84 92 16 87
8 77 58 70 32
8 11 94 13 74
8 8 77 70 32
8 2 62 53 71
8 88 7 16 35
8 16 87 35 11
8 90 27 86 84
8 94 13 79 81
8 30 44 49 15
8 220 198 189 202
8 94 11 12 87
8 34 39 41 18
8 27 60 74 13
8 30 29 43 20
8 34 51 48 65
8 57 44 47 15
8 94 83 95 12
8 19 85 80 75
8 66 1 73 62
8 83 1 73 89
8 11 84 16 87
8 12 83 95 89
8 28 18 21 31
8 97 35 92 98
8 34 33 32 48
8 55 17 75 59
8 4 41 28 3
8 35 97 93 98
8 47 14 15 31
8 57 78 26 59
8 32 72 70 7
8 44 47 31 38
8 9 34 32 65
8 33 45 58 48
8 7 80 70 8
8 32 72 7 76
8 3 9 4 54
8 18 21 41 28
8 62 1 73 71
8 33 39 38 45
8 217 189 220 198
8 30 20 42 37
8 33 45 38 47
8 30 31 44 15
8 12 94 81 13
8 31 37 38 21
8 33 55 45 47
8 50 29 40 52
8 68 51 9 65
8 20 30 31 37
8 30 44 37 42
8 87 12 35 11
8 11 94 12 13
8 72 7 82 70
8 12 95 98 96
8 77 17 8 75
8 220 189 194 202
8 221 176 177 164
8 57 15 26 49
8 30 42 43 53
8 28 40 20 36
8 30 42 53 49
8 34 3 54 9
8 19 35 80 93
8 7 80 8 35
8 50 56 46 4
8 88 35 97 82
8 9 68 65 76
8 90 27 84 16
8 67 69 27 86
8 217 185 180 191
8 39 33 38 31
8 1 62 2 71
8 17 55 47 59
8 35 12 98 96
8 75 17 26 59
8 4 69 56 54
8 221 220 217 163
8 92 35 87 98
8 90 27 68 86
8 33 17 47 14
8 48 61 32 65
8 33 47 38 31
8 2 30 53 49
8 1 2 10 71
8 67 84 86 27
8 9 7 76 32
8 7 80 35 82
8 33 58 32 48
8 47 17 26 15
8 13 79 60 74
8 11 84 74 27
8 19 8 26 75
8 84 67 74 27
8 28 29 30 20
8 13 56 27 60
8 35 12 96 19
8 221 177 163 164
8 30 2 15 49
8 13 63 81 10
8 2 53 10 71
8 50 13 63 60
8 13 79 63 60
8 34 48 32 65
8 88 72 76 7
8 30 28 20 31
8 67 56 27 69
8 13 79 81 63
8 28 36 20 21
8 8 77 80 70
8 96 35 93 98
8 51 34 9 65
8 89 1 91 0
8 1 83 73 71
8 1 66 26 49
8 12 89 95 96
8 28 20 31 21
8 56 50 13 4
8 12 1 89 0
8 89 96 0 91
8 56 67 27 60
8 83 94 81 12
8 88 6 76 90
8 89 1 73 91
8 7 88 82 35
8 81 64 71 10
8 35 88 97 92
8 15 2 26 49
8 39 33 34 48
8 89 12 0 96
8 85 26 91 78
8 12 19 0 96
8 8 77 75 80
8 4 41 3 54
8 64 29 63 52
8 13 50 5 4
8 62 2 53 49
8 44 31 37 38
8 58 61 70 32
8 217 180 183 191
8 33 55 47 17
8 18 39 21 31
8 66 1 26 91
8 53 64 10 71
8 33 55 17 58
8 33 55 58 45
8 116 64 71 129
8 67 132 142 130
8 124 76 127 138
8 124 61 48 65
8 75 131 55 122
8 111 51 114 65
8 124 76 65 127
8 127 133 147 68
8 105 112 53 49
8 126 91 134 139
8 61 72 128 70
8 57 78 59 120
8 103 50 110 46
8 139 89 148 135
8 138 72 141 128
8 85 75 134 146
8 80 150 82 70
8 154 85 96 153
8 97 151 93 98
8 46 40 36 103
8 42 105 53 49
8 55 131 58 119
8 151 144 97 141
8 110 121 56 50
8 68 149 147 90
8 50 121 56 60
8 220 163 221 177
8 81 63 125 115
8 22 36 103 99
8 104 36 41 23
8 134 91 85 153
8 68 51 65 114
8 217 183 198 191
8 103 52 106 113
8 55 131 119 122
8 56 121 67 60
8 55 122 59 75
8 136 87 145 143
8 105 22 42 43
8 58 77 70 131
8 126 73 91 139
8 136 87 143 74
8 75 59 134 122
8 111 127 124 65
8 67 121 130 60
8 145 94 136 140
8 47 57 59 120
8 37 105 100 42
8 154 85 153 146
8 39 41 23 102
8 136 87 94 145
8 101 21 39 38
8 85 154 80 146
8 154 96 148 153
8 121 130 60 125
8 84 149 142 86
8 88 144 97 92
8 217 189 198 183
8 154 85 93 96
8 100 20 21 37
8 52 103 50 113
8 52 106 64 43
8 116 43 64 106
8 55 45 108 119
8 61 58 124 48
8 88 144 92 90
8 22 100 42 20
8 22 105 42 100
8 50 121 60 125
8 56 110 46 118
8 124 76 138 61
8 132 67 142 86
8 95 94 87 145
8 105 116 106 43
8 129 73 62 123
8 23 41 39 21
8 111 39 51 48
8 88 144 141 97
8 128 61 70 58
8 56 132 69 67
8 62 116 71 129
8 154 150 80 146
8 145 95 140 148
8 117 45 119 109
8 145 95 98 87
8 64 43 116 53
8 62 73 129 71
8 221 220 177 176
8 132 121 67 56
8 83 73 129 135
8 136 87 74 94
8 105 42 53 43
8 129 73 83 71
8 137 79 136 125
8 174 219 221 176
8 132 67 86 69
8 146 122 131 75
8 66 112 123 126
8 89 140 148 135
8 84 149 152 142
8 134 75 85 78
8 67 74 60 130
8 134 122 146 75
8 134 59 75 78
8 85 80 75 146
8 41 51 54 114
8 99 110 46 103
8 85 134 153 146
8 41 23 102 104
8 112 57 107 120
8 132 133 69 86
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8 141 93 154 150
8 41 114 54 104
8 99 46 36 103
8 39 111 102 109
8 151 154 93 98
8 121 110 56 118
8 151 145 148 98
8 36 40 20 103
8 117 111 124 48
8 104 36 23 99
8 174 219 176 184
8 50 110 46 56
8 50 63 113 125
8 85 154 93 80
8 71 64 116 53
8 37 105 42 44
8 39 45 48 109
8 88 138 141 144
8 84 143 74 142
8 74 143 136 130
8 55 131 77 58
8 88 97 141 82
8 114 118 54 104
8 45 39 38 101
8 103 50 46 40
8 63 52 115 64
8 116 62 53 112
8 132 133 118 69
8 73 89 139 135
8 72 88 141 82
8 37 105 44 107
8 51 111 114 102
8 93 151 141 154
8 68 90 147 76
8 103 52 43 106
8 117 128 131 58
8 133 149 147 68
8 72 61 128 138
8 123 112 66 62
8 57 78 120 126
8 139 134 153 91
8 129 83 135 137
8 50 52 113 63
8 103 36 22 20
8 131 80 70 150
8 68 127 76 147
8 58 117 124 48
8 112 57 120 126
8 154 151 148 98
8 88 90 76 147
8 56 132 118 69
8 143 145 152 87
8 20 100 42 37
8 112 66 62 49
8 84 90 92 152
8 137 79 94 136
8 94 83 137 140
8 149 144 90 152
8 151 145 92 152
8 138 127 147 76
8 221 176 165 174
8 127 133 68 114
8 127 111 114 65
8 96 89 148 91
8 121 50 113 125
8 62 66 123 73
8 116 105 53 43
8 50 103 52 40
8 221 163 156 164
8 80 150 93 82
8 99 22 36 23
8 104 36 99 46
8 129 64 71 81
8 78 134 59 120
8 57 107 120 47
8 108 47 59 120
8 129 83 137 81
8 129 83 81 71
8 217 221 161 162
8 89 73 139 91
8 83 89 73 135
8 101 21 23 39
8 55 45 119 58
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8 144 88 147 90
8 79 63 125 81
8 52 106 115 64
8 149 144 147 90
8 38 100 21 37
8 221 158 160 170
8 101 45 108 38
8 141 93 150 82
8 116 106 64 115
8 117 45 48 58
8 105 44 49 42
8 39 111 51 102
8 37 105 107 100
8 89 139 148 91
8 137 79 125 81
8 102 41 104 114
8 139 91 153 148
8 101 21 38 100
8 46 41 54 104
8 80 150 131 146
8 126 73 139 123
8 105 116 53 112
8 151 145 98 92
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8 221 24 159 155
8 154 150 93 80
8 83 94 137 81
8 55 47 59 108
8 108 45 55 47
8 116 62 112 123
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8 138 88 147 144
8 94 140 137 136
8 122 108 59 120
8 84 149 90 152
8 67 84 142 86
8 112 66 57 126
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8 150 128 82 70
8 145 95 148 98
8 107 100 38 37
8 128 72 82 70
8 91 96 153 148
8 112 62 53 49
8 95 96 148 98
8 126 73 123 66
8 221 160 172 170
8 81 125 137 115
8 101 100 38 107
8 74 143 130 142
8 127 68 76 65
8 39 45 109 101
8 85 91 134 78
8 66 78 57 126
8 94 95 140 145
8 149 84 90 86
8 128 58 70 131
8 67 74 130 142
8 110 46 118 104
8 46 56 118 54
8 133 149 68 86
8 133 68 69 86
8 64 63 81 115
8 143 84 152 142
8 44 107 38 37
8 149 68 86 90
8 78 134 120 126
8 92 145 98 87
8 113 63 115 125
8 39 23 101 102
8 138 61 128 124
8 73 139 123 135
8 121 110 113 50
8 45 117 119 58
8 111 39 48 109
8 62 116 129 123
8 61 128 124 58
8 47 107 120 108
8 44 107 47 38
8 84 143 87 74
8 132 121 56 118
8 107 47 38 108
8 152 145 92 87
8 129 81 137 115
8 84 152 92 87
8 96 154 148 98
8 118 133 54 69
8 116 62 71 53
8 45 101 108 109
8 101 107 38 108
8 138 88 76 147
8 214 221 217 169
8 79 94 136 74
8 105 112 49 107
8 112 66 49 57
8 39 51 41 102
8 58 117 119 131
8 44 105 49 107
8 112 57 49 107
8 45 108 119 109
8 80 77 75 131
8 172 221 188 215
8 51 111 48 65
8 146 80 75 131
8 103 50 113 110
8 215 166 221 203
8 104 36 46 41
8 130 79 125 136
8 73 123 129 135
8 45 117 48 109
8 57 44 49 107
8 79 74 136 130
8 197 214 186 215
8 129 116 64 115
8 111 124 48 65
8 70 80 131 77
8 126 91 66 78
8 74 79 60 130
8 126 91 78 134
8 63 50 60 125
8 150 128 70 131
8 149 132 142 86
8 106 52 115 113
8 117 111 48 109
8 79 130 125 60
8 55 122 119 108
8 94 83 140 95
8 90 144 92 152
8 85 96 153 91
8 140 83 137 135
8 217 216 220 203
8 217 220 216 208
8 89 83 95 140
8 126 73 66 91
8 20 23 36 22
8 20 23 22 100
8 101 21 100 23
8 141 93 82 97
8 144 151 97 92
8 89 95 96 148
8 45 47 108 38
8 208 198 220 202
8 20 23 100 21
8 20 23 21 36
8 128 117 124 58
8 214 186 215 178
8 55 131 75 77
8 118 56 69 54
8 41 23 36 21
8 22 105 106 43
8 22 20 42 43
8 40 20 103 43
8 103 52 40 43
8 88 72 141 138
8 44 57 47 107
8 51 41 102 114
8 20 22 103 43
8 22 106 103 43
8 221 174 165 167
8 134 122 59 120
8 121 132 67 130
8 67 84 74 142
8 133 68 54 69
8 128 150 82 141
8 51 68 54 114
8 133 118 54 114
8 68 133 54 114
8 72 88 76 138
8 124 76 61 65
8 221 165 158 167
8 151 144 152 92
8 72 128 82 141
8 63 79 125 60
8 141 151 93 97
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8 214 166 215 203
8 72 61 138 76
8 84 143 152 87
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8 95 89 140 148
8 129 64 81 115
8 214 178 179 190
8 39 101 109 102
8 52 63 115 113
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8 100 24 156 25
8 138 141 192 196
8 198 135 148 204
8 183 123 180 168
8 117 119 174 109
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8 101 23 157 102
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8 105 100 24 161
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8 151 212 203 141
8 117 187 174 184
8 187 150 196 200
8 24 100 105 22
8 177 122 120 108
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8 105 161 162 173
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8 122 176 184 119
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8 122 194 131 184
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8 162 106 159 103
8 157 108 164 101
8 165 176 108 119
8 217 193 182 201
8 152 203 151 211
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8 193 179 130 190
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8 99 22 24 103
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8 115 129 173 185
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8 107 101 164 108
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8 150 154 141 207
8 147 144 197 192
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8 146 134 153 202
8 160 99 104 23
8 123 139 191 135
8 120 112 126 175
8 201 140 136 137
8 150 141 196 207
8 221 159 166 155
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8 199 143 205 210
8 158 111 109 102
8 106 113 159 103
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8 154 150 146 207
8 102 25 23 157
8 102 160 114 104
8 176 122 184 194
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8 166 121 178 118
8 111 167 181 170
8 201 182 185 137
8 168 183 126 175
8 217 182 185 201
8 132 178 186 190
8 157 108 101 109
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8 189 177 120 175
8 101 156 164 157
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8 204 198 135 191
8 122 176 177 194
8 22 23 25 100
8 171 113 169 159
8 110 155 166 103
8 161 105 168 173
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8 99 22 23 25
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8 100 101 156 107
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8 140 135 137 201
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8 129 201 135 191
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8 105 22 106 162
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8 153 207 154 146
8 143 199 152 210
8 108 107 163 164
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8 22 105 24 162
8 123 129 191 180
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8 104 166 155 172
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