[cig-commits] r21014 - in seismo/2D/SPECFEM2D/trunk: EXAMPLES/salt_dome EXAMPLES/salt_dome/CPML_normal EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec UTILS/cubit2specfem2d
dkomati1 at geodynamics.org
dkomati1 at geodynamics.org
Sun Nov 11 09:28:46 PST 2012
Author: dkomati1
Date: 2012-11-11 09:28:45 -0800 (Sun, 11 Nov 2012)
New Revision: 21014
Added:
seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/
seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/modelY1_ACIS_geometry_ascii_format.sat
seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/
seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1.cubit
seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML.cubit
seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_30.cubit
seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_50.cubit
seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_fine.cubit
seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d_original.py
seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d_with_routine_to_fix_negative_Jacobians_from_Ronan_Madec_2009.py
Removed:
seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d.py
Log:
added CUBIT and ACIS files for the salt dome model with CPML
Added: seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/modelY1_ACIS_geometry_ascii_format.sat
===================================================================
--- seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/modelY1_ACIS_geometry_ascii_format.sat (rev 0)
+++ seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/modelY1_ACIS_geometry_ascii_format.sat 2012-11-11 17:28:45 UTC (rev 21014)
@@ -0,0 +1,1705 @@
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\ No newline at end of file
Added: seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1.cubit
===================================================================
--- seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1.cubit (rev 0)
+++ seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1.cubit 2012-11-11 17:28:45 UTC (rev 21014)
@@ -0,0 +1,284 @@
+#!/opt/cubit/cubit
+
+create vertex 0.0 0.0 5200.0
+create vertex 6000.0 0.0 5200.0
+create vertex 0.0 0.0 0.0
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+create vertex 4324.3607 0.0 482.774
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+create vertex -200.0 0.0 5200.0
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+create vertex -200.0 0.0 1786.758
+create vertex -200.0 0.0 1262.1924
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+create vertex -200.0 0.0 0.0
+create vertex 6200.0 0.0 5200.0
+create vertex 6200.0 0.0 5000.0
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+create vertex 6200.0 0.0 0.0
+create vertex -200.0 0.0 -200.0
+create vertex 6200.0 0.0 -200.0
+
+create curve spline vertex 1 2
+create curve spline vertex 3 4
+create curve spline vertex 1 5
+create curve spline vertex 2 6
+create curve spline vertex 5 7 6
+create curve spline vertex 5 8
+create curve spline vertex 6 9
+create curve spline vertex 8 10 11 12 13 14 15 9
+create curve spline vertex 8 16
+create curve spline vertex 9 17
+create curve spline vertex 16 18 19 20
+create curve spline vertex 20 21 22 23 24 25 26 27 28 29
+create curve spline vertex 29 17
+create curve spline vertex 16 30
+create curve spline vertex 20 31 32
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+create curve spline vertex 36 35
+create curve spline vertex 30 37
+create curve spline vertex 32 38 39
+create curve spline vertex 37 40 41 42 39
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+create curve spline vertex 36 29
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+create curve spline vertex 45 36
+create curve spline vertex 44 46
+create curve spline vertex 45 47 48 49 46
+create curve spline vertex 37 50
+create curve spline vertex 39 51 52 53 54
+create curve spline vertex 50 55 56 57 58 54
+create curve spline vertex 54 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77
+create curve spline vertex 77 78 79 45
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+create curve spline vertex 77 81 82 83 84 85 86 80
+create curve spline vertex 50 87
+create curve spline vertex 87 3
+create curve spline vertex 80 88
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+create curve spline vertex 87 89 90 91 92 93 94 88
+create curve spline vertex 95 96
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+create curve spline vertex 97 98
+create curve spline vertex 98 99
+create curve spline vertex 99 100
+create curve spline vertex 100 101
+create curve spline vertex 101 102
+create curve spline vertex 102 103
+create curve spline vertex 1 95
+create curve spline vertex 103 3
+create curve spline vertex 96 5
+create curve spline vertex 97 8
+create curve spline vertex 98 16
+create curve spline vertex 99 30
+create curve spline vertex 100 37
+create curve spline vertex 101 50
+create curve spline vertex 102 87
+create curve spline vertex 104 105
+create curve spline vertex 105 106
+create curve spline vertex 106 107
+create curve spline vertex 107 108
+create curve spline vertex 108 109
+create curve spline vertex 109 110
+create curve spline vertex 110 111
+create curve spline vertex 111 112
+create curve spline vertex 104 2
+create curve spline vertex 112 4
+create curve spline vertex 105 6
+create curve spline vertex 106 9
+create curve spline vertex 107 17
+create curve spline vertex 108 35
+create curve spline vertex 109 46
+create curve spline vertex 110 80
+create curve spline vertex 111 88
+create curve spline vertex 113 103
+create curve spline vertex 114 112
+create curve spline vertex 113 114
+
+create surface curve 8 6 5 7
+create surface curve 9 8 10 11 12 13
+create surface curve 16 14 11 15
+create surface curve 12 15 20 29 31 32 25 23
+create surface curve 21 19 16 20
+create surface curve 13 18 17 23
+create surface curve 30 28 21 29
+create surface curve 18 25 27 26 24
+create surface curve 39 35 30 31 34 37
+create surface curve 27 32 34 33
+create surface curve 2 36 39 38
+create surface curve 40 36 39 38
+
+create surface curve 41 51 6 50
+create surface curve 42 52 9 51
+create surface curve 43 53 14 52
+create surface curve 44 54 19 53
+create surface curve 45 55 28 54
+create surface curve 46 56 35 55
+create surface curve 47 49 36 56
+create surface curve 7 68 58 67
+create surface curve 10 69 59 68
+create surface curve 17 70 60 69
+create surface curve 26 71 61 70 24
+create surface curve 33 72 62 71
+create surface curve 37 73 63 72
+create surface curve 38 66 64 73
+create surface curve 74 76 75 66 2 49
+
+merge vol all
+imprint vol all
+surface all size 40.0
+surface 4 size 60.
+
+#surface all size 30.0
+#surface 2 size 20.0
+#surface 6 size 20.0
+#surface 3 size 20.0
+#Surface 19 20 21 22 23 24 25 18 17 16 15 14 13 12 26 size 20
+surface all scheme pave
+mesh surface all
+
+#block 11 surface 1
+
+#block 10 surface 2
+
+#block 9 surface 3
+
+#block 8 surface 4
+
+#block 7 surface 5
+
+#block 6 surface 6
+
+#block 5 surface 7
+
+#block 4 surface 8
+
+#block 3 surface 9
+
+#block 2 surface 10
+
+#block 1 surface 11
+
+block 11 surface 1 12 19
+
+block 10 surface 2 13 20
+
+block 9 surface 3 14
+
+block 8 surface 4
+
+block 7 surface 5 15
+
+block 6 surface 6 21
+
+block 5 surface 7 16
+
+block 4 surface 8 22
+
+block 3 surface 9 17 24
+
+block 2 surface 10 23
+
+block 1 surface 11 18 25 26
+
+export Abaqus "modelY1_Abaqus_format" dimension 2 block all overwrite
+
+export Acis "modelY1_ACIS_ascii_format.sat" dimension 2 block all Ascii overwrite
+
Added: seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML.cubit
===================================================================
--- seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML.cubit (rev 0)
+++ seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML.cubit 2012-11-11 17:28:45 UTC (rev 21014)
@@ -0,0 +1,282 @@
+#!/opt/cubit/cubit
+
+create vertex 0.0 0.0 5200.0
+create vertex 6000.0 0.0 5200.0
+create vertex 0.0 0.0 0.0
+create vertex 6000.0 0.0 0.0
+create vertex 0.0 0.0 5000.0
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+create vertex 3000.0 0.0 5000.0
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+create vertex 4625.5924 0.0 3270.7763
+create vertex 0.0 0.0 2766.21
+create vertex 6000.0 0.0 2843.379
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+
+create curve spline vertex 1 2
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+create curve spline vertex 77 81 82 83 84 85 86 80
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+create curve spline vertex 1 95
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+create curve spline vertex 99 30
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+create curve spline vertex 104 2
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+create curve spline vertex 108 35
+create curve spline vertex 109 46
+create curve spline vertex 110 80
+create curve spline vertex 111 88
+create curve spline vertex 113 103
+create curve spline vertex 114 112
+create curve spline vertex 113 114
+
+create surface curve 8 6 5 7
+create surface curve 9 8 10 11 12 13
+create surface curve 16 14 11 15
+create surface curve 12 15 20 29 31 32 25 23
+create surface curve 21 19 16 20
+create surface curve 13 18 17 23
+create surface curve 30 28 21 29
+create surface curve 18 25 27 26 24
+create surface curve 39 35 30 31 34 37
+create surface curve 27 32 34 33
+create surface curve 2 36 39 38
+create surface curve 40 36 39 38
+
+create surface curve 41 51 6 50
+create surface curve 42 52 9 51
+create surface curve 43 53 14 52
+create surface curve 44 54 19 53
+create surface curve 45 55 28 54
+create surface curve 46 56 35 55
+create surface curve 47 49 36 56
+create surface curve 7 68 58 67
+create surface curve 10 69 59 68
+create surface curve 17 70 60 69
+create surface curve 26 71 61 70 24
+create surface curve 33 72 62 71
+create surface curve 37 73 63 72
+create surface curve 38 66 64 73
+create surface curve 74 76 75 66 2 49
+
+merge vol all
+imprint vol all
+surface all size 40.0
+surface 4 size 60.
+
+#surface all size 30.0
+#surface 2 size 20.0
+#surface 6 size 20.0
+#surface 3 size 20.0
+#Surface 19 20 21 22 23 24 25 18 17 16 15 14 13 12 26 size 20
+surface all scheme pave
+mesh surface all
+
+#block 11 surface 1
+
+#block 10 surface 2
+
+#block 9 surface 3
+
+#block 8 surface 4
+
+#block 7 surface 5
+
+#block 6 surface 6
+
+#block 5 surface 7
+
+#block 4 surface 8
+
+#block 3 surface 9
+
+#block 2 surface 10
+
+#block 1 surface 11
+
+block 8 surface 1 12 19
+
+block 7 surface 2 13 20
+
+block 6 surface 3 14 6 21
+
+block 5 surface 4
+
+#block 7 surface 5 15
+
+#block 6 surface 6 21
+
+#block 5 surface 7 16
+
+block 4 surface 8 22 5 15
+
+block 3 surface 9 17 24
+
+block 2 surface 10 23 7 16
+
+block 1 surface 11 18 25 26
+
+export Abaqus "modelY1_PML" dimension 2 block all overwrite
+
Added: seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_30.cubit
===================================================================
--- seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_30.cubit (rev 0)
+++ seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_30.cubit 2012-11-11 17:28:45 UTC (rev 21014)
@@ -0,0 +1,282 @@
+#!/opt/cubit/cubit
+
+create vertex 0.0 0.0 5200.0
+create vertex 6000.0 0.0 5200.0
+create vertex 0.0 0.0 0.0
+create vertex 6000.0 0.0 0.0
+create vertex 0.0 0.0 5000.0
+create vertex 6000.0 0.0 5000.0
+create vertex 3000.0 0.0 5000.0
+create vertex 0.0 0.0 3211.4155
+create vertex 6000.0 0.0 3276.7123
+create vertex 649.2891 0.0 3181.7352
+create vertex 1127.9621 0.0 3193.6073
+create vertex 1554.5024 0.0 3235.1598
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+create vertex 3502.3697 0.0 3276.7123
+create vertex 4625.5924 0.0 3270.7763
+create vertex 0.0 0.0 2766.21
+create vertex 6000.0 0.0 2843.379
+create vertex 341.2322 0.0 2754.3379
+create vertex 1421.8009 0.0 2760.274
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+create vertex 1767.7725 0.0 2944.2922
+create vertex 1985.782 0.0 3027.3973
+create vertex 2279.6209 0.0 3063.0137
+create vertex 2715.6398 0.0 3051.1416
+create vertex 3284.3602 0.0 3080.8219
+create vertex 3710.9005 0.0 3068.9498
+create vertex 3947.8673 0.0 2985.8447
+create vertex 3962.0853 0.0 2861.1872
+create vertex 3976.1985 0.0 2861.0639
+create vertex 0.0 0.0 2214.1553
+create vertex 1417.0616 0.0 2665.2968
+create vertex 1765.6054 0.0 2318.8245
+create vertex 687.2038 0.0 2231.9635
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+create vertex 6200.0 0.0 -200.0
+
+create curve spline vertex 1 2
+create curve spline vertex 3 4
+create curve spline vertex 1 5
+create curve spline vertex 2 6
+create curve spline vertex 5 7 6
+create curve spline vertex 5 8
+create curve spline vertex 6 9
+create curve spline vertex 8 10 11 12 13 14 15 9
+create curve spline vertex 8 16
+create curve spline vertex 9 17
+create curve spline vertex 16 18 19 20
+create curve spline vertex 20 21 22 23 24 25 26 27 28 29
+create curve spline vertex 29 17
+create curve spline vertex 16 30
+create curve spline vertex 20 31 32
+create curve spline vertex 30 33 34 32
+create curve spline vertex 17 35
+create curve spline vertex 36 35
+create curve spline vertex 30 37
+create curve spline vertex 32 38 39
+create curve spline vertex 37 40 41 42 39
+create curve spline vertex 43 36
+create curve spline vertex 36 29
+create curve spline vertex 35 44
+create curve spline vertex 45 36
+create curve spline vertex 44 46
+create curve spline vertex 45 47 48 49 46
+create curve spline vertex 37 50
+create curve spline vertex 39 51 52 53 54
+create curve spline vertex 50 55 56 57 58 54
+create curve spline vertex 54 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77
+create curve spline vertex 77 78 79 45
+create curve spline vertex 46 80
+create curve spline vertex 77 81 82 83 84 85 86 80
+create curve spline vertex 50 87
+create curve spline vertex 87 3
+create curve spline vertex 80 88
+create curve spline vertex 88 4
+create curve spline vertex 87 89 90 91 92 93 94 88
+create curve spline vertex 95 96
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+create curve spline vertex 99 100
+create curve spline vertex 100 101
+create curve spline vertex 101 102
+create curve spline vertex 102 103
+create curve spline vertex 1 95
+create curve spline vertex 103 3
+create curve spline vertex 96 5
+create curve spline vertex 97 8
+create curve spline vertex 98 16
+create curve spline vertex 99 30
+create curve spline vertex 100 37
+create curve spline vertex 101 50
+create curve spline vertex 102 87
+create curve spline vertex 104 105
+create curve spline vertex 105 106
+create curve spline vertex 106 107
+create curve spline vertex 107 108
+create curve spline vertex 108 109
+create curve spline vertex 109 110
+create curve spline vertex 110 111
+create curve spline vertex 111 112
+create curve spline vertex 104 2
+create curve spline vertex 112 4
+create curve spline vertex 105 6
+create curve spline vertex 106 9
+create curve spline vertex 107 17
+create curve spline vertex 108 35
+create curve spline vertex 109 46
+create curve spline vertex 110 80
+create curve spline vertex 111 88
+create curve spline vertex 113 103
+create curve spline vertex 114 112
+create curve spline vertex 113 114
+
+create surface curve 8 6 5 7
+create surface curve 9 8 10 11 12 13
+create surface curve 16 14 11 15
+create surface curve 12 15 20 29 31 32 25 23
+create surface curve 21 19 16 20
+create surface curve 13 18 17 23
+create surface curve 30 28 21 29
+create surface curve 18 25 27 26 24
+create surface curve 39 35 30 31 34 37
+create surface curve 27 32 34 33
+create surface curve 2 36 39 38
+create surface curve 40 36 39 38
+
+create surface curve 41 51 6 50
+create surface curve 42 52 9 51
+create surface curve 43 53 14 52
+create surface curve 44 54 19 53
+create surface curve 45 55 28 54
+create surface curve 46 56 35 55
+create surface curve 47 49 36 56
+create surface curve 7 68 58 67
+create surface curve 10 69 59 68
+create surface curve 17 70 60 69
+create surface curve 26 71 61 70 24
+create surface curve 33 72 62 71
+create surface curve 37 73 63 72
+create surface curve 38 66 64 73
+create surface curve 74 76 75 66 2 49
+
+merge vol all
+imprint vol all
+surface all size 30.0
+surface 4 size 30.
+
+#surface all size 30.0
+#surface 2 size 20.0
+#surface 6 size 20.0
+#surface 3 size 20.0
+#Surface 19 20 21 22 23 24 25 18 17 16 15 14 13 12 26 size 20
+surface all scheme pave
+mesh surface all
+
+#block 11 surface 1
+
+#block 10 surface 2
+
+#block 9 surface 3
+
+#block 8 surface 4
+
+#block 7 surface 5
+
+#block 6 surface 6
+
+#block 5 surface 7
+
+#block 4 surface 8
+
+#block 3 surface 9
+
+#block 2 surface 10
+
+#block 1 surface 11
+
+block 11 surface 1 12 19
+
+block 10 surface 2 13 20
+
+block 9 surface 3 14
+
+block 8 surface 4
+
+block 7 surface 5 15
+
+block 6 surface 6 21
+
+block 5 surface 7 16
+
+block 4 surface 8 22
+
+block 3 surface 9 17 24
+
+block 2 surface 10 23
+
+block 1 surface 11 18 25 26
+
+export Abaqus "modelY1_PML_30" dimension 2 block all overwrite
+
Added: seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_50.cubit
===================================================================
--- seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_50.cubit (rev 0)
+++ seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_50.cubit 2012-11-11 17:28:45 UTC (rev 21014)
@@ -0,0 +1,287 @@
+#!/opt/cubit/cubit
+
+create vertex 0.0 0.0 5200.0
+create vertex 6000.0 0.0 5200.0
+create vertex 0.0 0.0 0.0
+create vertex 6000.0 0.0 0.0
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+
+create curve spline vertex 1 2
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+create curve spline vertex 36 29
+#create curve spline vertex 35 44
+create curve spline vertex 35 46
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+create curve spline vertex 44 46
+create curve spline vertex 45 47 48 49 46
+create curve spline vertex 37 50
+create curve spline vertex 39 51 52 53 54
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+create curve spline vertex 110 80
+create curve spline vertex 111 88
+create curve spline vertex 113 103
+create curve spline vertex 114 112
+create curve spline vertex 113 114
+
+create surface curve 8 6 5 7
+create surface curve 9 8 10 11 12 13
+create surface curve 16 14 11 15
+create surface curve 12 15 20 29 31 32 25 23
+create surface curve 21 19 16 20
+create surface curve 13 18 17 23
+create surface curve 30 28 21 29
+create surface curve 18 25 27 24 #26 24
+create surface curve 39 35 30 31 34 37
+create surface curve 27 32 34 33
+create surface curve 2 36 39 38
+create surface curve 40 36 39 38
+
+create surface curve 41 51 6 50
+create surface curve 42 52 9 51
+create surface curve 43 53 14 52
+create surface curve 44 54 19 53
+create surface curve 45 55 28 54
+create surface curve 46 56 35 55
+create surface curve 47 49 36 56
+create surface curve 7 68 58 67
+create surface curve 10 69 59 68
+create surface curve 17 70 60 69
+create surface curve 71 61 70 24 #26
+create surface curve 33 72 62 71
+create surface curve 37 73 63 72
+create surface curve 38 66 64 73
+create surface curve 74 76 75 66 2 49
+
+surface 4 size 60.
+#surface all size 50.0
+surface 1 5 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 size 40.0
+
+#surface all size 30.0
+#surface 2 size 20.0
+#surface 6 size 20.0
+#surface 3 size 20.0
+#Surface 19 20 21 22 23 24 25 18 17 16 15 14 13 12 26 size 20
+surface all scheme pave
+mesh surface 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27
+surface 2 3 6 size 30.
+mesh surface 4
+merge vol all
+imprint vol all
+mesh surface 1 2 3 5 6 7 8 9 10 11 12
+
+#block 11 surface 1
+
+#block 10 surface 2
+
+#block 9 surface 3
+
+#block 8 surface 4
+
+#block 7 surface 5
+
+#block 6 surface 6
+
+#block 5 surface 7
+
+#block 4 surface 8
+
+#block 3 surface 9
+
+#block 2 surface 10
+
+#block 1 surface 11
+
+block 8 surface 1 12 19
+
+block 7 surface 2 13 20
+
+block 6 surface 3 14 6 21
+
+block 5 surface 4
+
+#block 7 surface 5 15
+
+#block 6 surface 6 21
+
+#block 5 surface 7 16
+
+block 4 surface 8 22 5 15
+
+block 3 surface 9 17 24
+
+block 2 surface 10 23 7 16
+
+block 1 surface 11 18 25 26
+
+export Abaqus "modelY1_PML_50" dimension 2 block all overwrite
+
Added: seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_fine.cubit
===================================================================
--- seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_fine.cubit (rev 0)
+++ seismo/2D/SPECFEM2D/trunk/EXAMPLES/salt_dome/CPML_normal/original_CUBIT_files_from_Ronan_Madec/modelY1_PML_fine.cubit 2012-11-11 17:28:45 UTC (rev 21014)
@@ -0,0 +1,282 @@
+#!/opt/cubit/cubit
+
+create vertex 0.0 0.0 5200.0
+create vertex 6000.0 0.0 5200.0
+create vertex 0.0 0.0 0.0
+create vertex 6000.0 0.0 0.0
+create vertex 0.0 0.0 5000.0
+create vertex 6000.0 0.0 5000.0
+create vertex 3000.0 0.0 5000.0
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+create vertex 4625.5924 0.0 3270.7763
+create vertex 0.0 0.0 2766.21
+create vertex 6000.0 0.0 2843.379
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+create vertex 1767.7725 0.0 2944.2922
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+create vertex 3876.7773 0.0 1596.8037
+create vertex 3919.4313 0.0 1602.7397
+create vertex 3919.4313 0.0 1785.6823
+create vertex 3919.4313 0.0 1798.6301
+create vertex 3971.564 0.0 1816.4384
+create vertex 6000.0 0.0 1157.4944
+create vertex 4037.6851 0.0 1762.4161
+create vertex 4320.323 0.0 1680.9843
+create vertex 4651.4132 0.0 1512.3043
+create vertex 4982.5034 0.0 1349.4407
+create vertex 5257.0659 0.0 1209.8434
+create vertex 5531.6285 0.0 1163.311
+create vertex 0.0 0.0 407.1588
+create vertex 6000.0 0.0 191.9463
+create vertex 520.8614 0.0 465.3244
+create vertex 1643.3378 0.0 529.3065
+create vertex 2398.3849 0.0 529.3065
+create vertex 3448.183 0.0 558.3893
+create vertex 4324.3607 0.0 482.774
+create vertex 5281.2921 0.0 261.745
+create vertex -200.0 0.0 5200.0
+create vertex -200.0 0.0 5000.0
+create vertex -200.0 0.0 3211.4155
+create vertex -200.0 0.0 2766.21
+create vertex -200.0 0.0 2214.1553
+create vertex -200.0 0.0 1786.758
+create vertex -200.0 0.0 1262.1924
+create vertex -200.0 0.0 407.1588
+create vertex -200.0 0.0 0.0
+create vertex 6200.0 0.0 5200.0
+create vertex 6200.0 0.0 5000.0
+create vertex 6200.0 0.0 3276.7123
+create vertex 6200.0 0.0 2843.379
+create vertex 6200.0 0.0 2605.9361
+create vertex 6200.0 0.0 1855.481
+create vertex 6200.0 0.0 1157.4944
+create vertex 6200.0 0.0 191.9463
+create vertex 6200.0 0.0 0.0
+create vertex -200.0 0.0 -200.0
+create vertex 6200.0 0.0 -200.0
+
+create curve spline vertex 1 2
+create curve spline vertex 3 4
+create curve spline vertex 1 5
+create curve spline vertex 2 6
+create curve spline vertex 5 7 6
+create curve spline vertex 5 8
+create curve spline vertex 6 9
+create curve spline vertex 8 10 11 12 13 14 15 9
+create curve spline vertex 8 16
+create curve spline vertex 9 17
+create curve spline vertex 16 18 19 20
+create curve spline vertex 20 21 22 23 24 25 26 27 28 29
+create curve spline vertex 29 17
+create curve spline vertex 16 30
+create curve spline vertex 20 31 32
+create curve spline vertex 30 33 34 32
+create curve spline vertex 17 35
+create curve spline vertex 36 35
+create curve spline vertex 30 37
+create curve spline vertex 32 38 39
+create curve spline vertex 37 40 41 42 39
+create curve spline vertex 43 36
+create curve spline vertex 36 29
+create curve spline vertex 35 44
+create curve spline vertex 45 36
+create curve spline vertex 44 46
+create curve spline vertex 45 47 48 49 46
+create curve spline vertex 37 50
+create curve spline vertex 39 51 52 53 54
+create curve spline vertex 50 55 56 57 58 54
+create curve spline vertex 54 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77
+create curve spline vertex 77 78 79 45
+create curve spline vertex 46 80
+create curve spline vertex 77 81 82 83 84 85 86 80
+create curve spline vertex 50 87
+create curve spline vertex 87 3
+create curve spline vertex 80 88
+create curve spline vertex 88 4
+create curve spline vertex 87 89 90 91 92 93 94 88
+create curve spline vertex 95 96
+create curve spline vertex 96 97
+create curve spline vertex 97 98
+create curve spline vertex 98 99
+create curve spline vertex 99 100
+create curve spline vertex 100 101
+create curve spline vertex 101 102
+create curve spline vertex 102 103
+create curve spline vertex 1 95
+create curve spline vertex 103 3
+create curve spline vertex 96 5
+create curve spline vertex 97 8
+create curve spline vertex 98 16
+create curve spline vertex 99 30
+create curve spline vertex 100 37
+create curve spline vertex 101 50
+create curve spline vertex 102 87
+create curve spline vertex 104 105
+create curve spline vertex 105 106
+create curve spline vertex 106 107
+create curve spline vertex 107 108
+create curve spline vertex 108 109
+create curve spline vertex 109 110
+create curve spline vertex 110 111
+create curve spline vertex 111 112
+create curve spline vertex 104 2
+create curve spline vertex 112 4
+create curve spline vertex 105 6
+create curve spline vertex 106 9
+create curve spline vertex 107 17
+create curve spline vertex 108 35
+create curve spline vertex 109 46
+create curve spline vertex 110 80
+create curve spline vertex 111 88
+create curve spline vertex 113 103
+create curve spline vertex 114 112
+create curve spline vertex 113 114
+
+create surface curve 8 6 5 7
+create surface curve 9 8 10 11 12 13
+create surface curve 16 14 11 15
+create surface curve 12 15 20 29 31 32 25 23
+create surface curve 21 19 16 20
+create surface curve 13 18 17 23
+create surface curve 30 28 21 29
+create surface curve 18 25 27 26 24
+create surface curve 39 35 30 31 34 37
+create surface curve 27 32 34 33
+create surface curve 2 36 39 38
+create surface curve 40 36 39 38
+
+create surface curve 41 51 6 50
+create surface curve 42 52 9 51
+create surface curve 43 53 14 52
+create surface curve 44 54 19 53
+create surface curve 45 55 28 54
+create surface curve 46 56 35 55
+create surface curve 47 49 36 56
+create surface curve 7 68 58 67
+create surface curve 10 69 59 68
+create surface curve 17 70 60 69
+create surface curve 26 71 61 70 24
+create surface curve 33 72 62 71
+create surface curve 37 73 63 72
+create surface curve 38 66 64 73
+create surface curve 74 76 75 66 2 49
+
+merge vol all
+imprint vol all
+surface all size 40.0
+surface 4 size 60.
+
+surface all size 40.0
+surface 2 size 10.0
+surface 6 size 20.0
+surface 3 size 20.0
+surface 19 20 21 22 23 24 25 18 17 16 15 14 13 12 26 size 20
+surface all scheme pave
+mesh surface all
+
+#block 11 surface 1
+
+#block 10 surface 2
+
+#block 9 surface 3
+
+#block 8 surface 4
+
+#block 7 surface 5
+
+#block 6 surface 6
+
+#block 5 surface 7
+
+#block 4 surface 8
+
+#block 3 surface 9
+
+#block 2 surface 10
+
+#block 1 surface 11
+
+block 8 surface 1 12 19
+
+block 7 surface 2 13 20
+
+block 6 surface 3 14 6 21
+
+block 5 surface 4
+
+#block 7 surface 5 15
+
+#block 6 surface 6 21
+
+#block 5 surface 7 16
+
+block 4 surface 8 22 5 15
+
+block 3 surface 9 17 24
+
+block 2 surface 10 23 7 16
+
+block 1 surface 11 18 25 26
+
+export Abaqus "modelY1_PML" dimension 2 block all overwrite
+
Deleted: seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d.py
===================================================================
--- seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d.py 2012-11-11 03:33:09 UTC (rev 21013)
+++ seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d.py 2012-11-11 17:28:45 UTC (rev 21014)
@@ -1,434 +0,0 @@
-#!/usr/bin/env python
-
-class mtools(object):
- """docstring for mtools"""
- def __init__(self,frequency,list_surf,list_vp):
- super(mtools, self).__init__()
- self.frequency = frequency
- self.list_surf = list_surf
- self.list_vp = list_vp
- self.ngll=5
- self.percent_gll=0.172
- self.point_wavelength=5
- def __repr__(self):
- txt='Meshing for frequency up to '+str(self.frequency)+'Hz\n'
- for surf,vp in zip(self.list_surf,self.list_vp):
- txt=txt+'surface '+str(surf)+', vp ='+str(vp)+' -> size '+str(self.freq2meshsize(vp)[0])+' -> dt '+str(self.freq2meshsize(vp)[0])+'\n'
- return txt
- def freq2meshsize(self,vp):
- velocity=vp*.5
- self.size=(1/2.5)*velocity/self.frequency*(self.ngll-1)/self.point_wavelength
- self.dt=.4*self.size/vp*self.percent_gll
- return self.size,self.dt
- def mesh_it(self):
- for surf,vp in zip(self.list_surf,self.list_vp):
- command = "surface "+str(surf)+" size "+str(self.freq2meshsize(vp)[0])
- cubit.cmd(command)
- command = "surface "+str(surf)+ 'scheme pave'
- cubit.cmd(command)
- command = "mesh surf "+str(surf)
- cubit.cmd(command)
-
-class block_tools:
- def __int__(self):
- pass
- def create_blocks(self,mesh_entity,list_entity=None,):
- if mesh_entity =='surface':
- txt=' face in surface '
- elif mesh_entity == 'curve':
- txt=' edge in curve '
- elif mesh_entity == 'group':
- txt=' face in group '
- if list_entity:
- if not isinstance(list_entity,list):
- list_entity=[list_entity]
- for entity in list_entity:
- iblock=cubit.get_next_block_id()
- command = "block "+str(iblock)+ txt +str(entity)
- cubit.cmd(command)
- def material_file(self,filename):
- matfile=open(filename,'w')
- material=[]
- for record in matfile:
- mat_name,vp_str=record.split()
- vp=float(vp_str)
- material.append([mat_name,vp])
- self.material=dict(material)
- def assign_block_material(self,id_block,mat_name,vp=None):
- try:
- material=self.material
- except:
- material=None
- cubit.cmd('block '+str(id_block)+' attribute count 2')
- cubit.cmd('block '+str(id_block)+' attribute index 1 '+str(id_block))
- if material:
- if material.has_key(mat_name):
- cubit.cmd('block '+str(id_block)+' attribute index 2 '+str(material[mat_name]))
- print 'block '+str(id_block)+' - material '+mat_name+' - vp '+str(material[mat_name])+' from database'
- elif vp:
- cubit.cmd('block '+str(id_block)+' attribute index 2 '+str(vp))
- print 'block '+str(id_block)+' - material '+mat_name+' - vp '+str(vp)
- else:
- print 'assignment impossible: check if '+mat_name+' is in the database or specify vp'
-
-class mesh_tools(block_tools):
- """Tools for the mesh
- #########
- dt,edge_dt,freq,edge_freq=seismic_resolution(edges,velocity,bins_d=None,bins_u=None,sidelist=None,ngll=5,np=8)
- Given the velocity of a list of edges, seismic_resolution provides the minimum Dt required for the stability condition (and the corrisponding edge).
- Furthermore, given the number of gll point in the element (ngll) and the number of GLL point for wavelength, it provide the maximum resolved frequency.
- #########
- length=edge_length(edge)
- return the length of a edge
- #########
- edge_min,length=edge_min_length(surface)
- given the cubit id of a surface, it return the edge with minimun length
- #########
- """
- def __int__(self):
- pass
- def seismic_resolution(self,edges,velocity,bins_d=None,bins_u=None,sidelist=None):
- """
- dt,edge_dt,freq,edge_freq=seismic_resolution(edges,velocity,bins_d=None,bins_u=None,sidelist=None,ngll=5,np=8)
- Given the velocity of a list of edges, seismic_resolution provides the minimum Dt required for the stability condition (and the corrisponding edge).
- Furthermore, given the number of gll point in the element (ngll) and the number of GLL point for wavelength, it provide the maximum resolved frequency.
- """
- ratiostore=1e10
- dtstore=1e10
- edgedtstore=-1
- edgeratiostore=-1
- for edge in edges:
- d=self.edge_length(edge)
- ratio=(1/2.5)*velocity/d*(self.ngll-1)/self.point_wavelength
- dt=.4*d/velocity*self.percent_gll
- if dt<dtstore:
- dtstore=dt
- edgedtstore=edge
- if ratio < ratiostore:
- ratiostore=ratio
- edgeratiostore=edge
- try:
- for bin_d,bin_u,side in zip(bins_d,bins_u,sidelist):
- if ratio >= bin_d and ratio < bin_u:
- command = "sideset "+str(side)+" edge "+str(edge)
- cubit.cmd(command)
- #print command
- break
- except:
- pass
- return dtstore,edgedtstore,ratiostore,edgeratiostore
- def edge_length(self,edge):
- """
- length=edge_length(edge)
- return the length of a edge
- """
- from math import sqrt
- nodes=cubit.get_connectivity('Edge',edge)
- x0,y0,z0=cubit.get_nodal_coordinates(nodes[0])
- x1,y1,z1=cubit.get_nodal_coordinates(nodes[1])
- d=sqrt((x1-x0)**2+(y1-y0)**2+(z1-z0)**2)
- return d
- def edge_min_length(self,surface):
- """
- edge_min,length=edge_min_length(surface)
- given the cubit id of a surface, it return the edge with minimun length
- """
- from math import sqrt
- self.dmin=99999
- edge_store=0
- command = "group 'list_edge' add edge in surf "+str(surface)
- command = command.replace("["," ").replace("]"," ")
- #print command
- cubit.cmd(command)
- group=cubit.get_id_from_name("list_edge")
- edges=cubit.get_group_edges(group)
- command = "delete group "+ str(group)
- cubit.cmd(command)
- for edge in edges:
- d=self.edge_length(edge)
- if d<dmin:
- self.dmin=d
- edge_store=edge
- self.edgemin=edge_store
- return self.edgemin,self.dmin
- def jac_check(self,nodes):
- x0=cubit.get_nodal_coordinates(nodes[0])
- x1=cubit.get_nodal_coordinates(nodes[1])
- x2=cubit.get_nodal_coordinates(nodes[2])
- xv1=x1[0]-x0[0]
- xv2=x2[0]-x1[0]
- zv1=x1[2]-x0[2]
- zv2=x2[2]-x1[2]
- jac=-xv2*zv1+xv1*zv2
- if jac > 0:
- return nodes
- elif jac < 0:
- return nodes[0],nodes[3],nodes[2],nodes[1]
- else:
- print 'error, jacobian=0'
- def mesh_analysis(self,frequency):
- cubit.cmd('set info off')
- cubit.cmd('set echo off')
- cubit.cmd('set journal off')
- bins_d=[0.0001]+range(0,int(frequency)+1)+[1000]
- bins_u=bins_d[1:]
- dt=[]
- ed_dt=[]
- r=[]
- ed_r=[]
- nstart=cubit.get_next_sideset_id()
- command = "del sideset all"
- cubit.cmd(command)
- for bin_d,bin_u in zip(bins_d,bins_u):
- nsideset=cubit.get_next_sideset_id()
- command='create sideset '+str(nsideset)
- cubit.cmd(command)
- command = "sideset "+str(nsideset)+ " name "+ "'ratio-["+str(bin_d)+"_"+str(bin_u)+"['"
- cubit.cmd(command)
- nend=cubit.get_next_sideset_id()
- sidelist=range(nstart,nend)
- for block in self.block_mat:
- name=cubit.get_exodus_entity_name('block',block)
- velocity=self.material[name][1]
- if velocity > 0:
- faces=cubit.get_block_faces(block)
- edges=[]
- for face in faces:
- es=cubit.get_sub_elements("face", face, 1)
- edges=edges+list(es)
- dtstore,edgedtstore,ratiostore,edgeratiostore=self.seismic_resolution(edges,velocity,bins_d,bins_u,sidelist)
- dt.append(dtstore)
- ed_dt.append(edgedtstore)
- r.append(ratiostore)
- ed_r.append(edgeratiostore)
- self.ddt=zip(ed_dt,dt)
- self.dr=zip(ed_r,r)
- def sorter(x, y):
- return cmp(x[1],y[1])
- self.ddt.sort(sorter)
- self.dr.sort(sorter)
- print self.ddt,self.dr
- print 'Deltat minimum => edge:'+str(self.ddt[0][0])+' dt: '+str(self.ddt[0][1])
- print 'minimum frequency resolved => edge:'+str(self.dr[0][0])+' frequency: '+str(self.dr[0][1])
- return self.ddt[0],self.dr[0]
-
-class mesh(object,mesh_tools):
- def __init__(self):
- super(mesh, self).__init__()
- self.mesh_name='mesh_file'
- self.nodecoord_name='nodes_coords_file'
- self.material_name='materials_file'
- self.nummaterial_name='nummaterial_velocity_file'
- self.absname='absorbing_surface_file'
- self.freename='free_surface_file'
- self.recname='STATIONS'
- self.face='QUAD4'
- self.edge='BAR2'
- self.topo='topo'
- self.rec='receivers'
- self.block_definition()
- self.ngll=5
- self.percent_gll=0.172
- self.point_wavelength=5
- cubit.cmd('compress')
- def __repr__(self):
- pass
- def block_definition(self):
- block_flag=[]
- block_mat=[]
- block_bc=[]
- block_bc_flag=[]
- material={}
- bc={}
- blocks=cubit.get_block_id_list()
- for block in blocks:
- name=cubit.get_exodus_entity_name('block',block)
- ty=cubit.get_block_element_type(block)
- if ty == self.face:
- flag=int(cubit.get_block_attribute_value(block,0))
- vel=cubit.get_block_attribute_value(block,1)
- block_flag.append(int(flag))
- block_mat.append(block)
- par=tuple([flag,vel])
- material[name]=par
- elif ty == self.edge:
- block_bc_flag.append(2)
- block_bc.append(block)
- bc[name]=2 #edge has connectivity = 2
- if name == self.topo: topography=block
- else:
- print 'blocks no properly defined'
- return None, None,None,None,None,None,None,None
- nsets=cubit.get_nodeset_id_list()
- if len(nsets) == 0: self.receivers=None
- for nset in nsets:
- name=cubit.get_exodus_entity_name('nodeset',nset)
- if name == self.rec:
- self.receivers=nset
- else:
- print 'nodeset '+name+' not defined'
- self.receivers=None
- try:
- self.block_mat=block_mat
- self.block_flag=block_flag
- self.block_bc=block_bc
- self.block_bc_flag=block_bc_flag
- self.material=material
- self.bc=bc
- self.topography=topography
- except:
- print 'blocks no properly defined'
- def tomo(self,flag,vel):
- vp=vel/1000
- rho=(1.6612*vp-0.472*vp**2+0.0671*vp**3-0.0043*vp**4+0.000106*vp**4)*1000
- txt='%3i %1i %20f %20f %20f %1i %1i\n' % (flag,1,rho,vel,vel/(3**.5),0,0)
- return txt
- def nummaterial_write(self,nummaterial_name):
- print 'Writing '+nummaterial_name+'.....'
- nummaterial=open(nummaterial_name,'w')
- for block in self.block_mat:
- name=cubit.get_exodus_entity_name('block',block)
- nummaterial.write(self.tomo(self.material[name][0],self.material[name][1]))
- nummaterial.close()
- print 'Ok'
- def mesh_write(self,mesh_name):
- meshfile=open(mesh_name,'w')
- print 'Writing '+mesh_name+'.....'
- num_elems=cubit.get_quad_count()
- meshfile.write(str(num_elems)+'\n')
- num_write=0
- for block,flag in zip(self.block_mat,self.block_flag):
- quads=cubit.get_block_faces(block)
- for inum,quad in enumerate(quads):
- nodes=cubit.get_connectivity('Face',quad)
- nodes=self.jac_check(nodes)
- txt=('%10i %10i %10i %10i\n')% nodes
- meshfile.write(txt)
- num_write=num_write+inum+1
- print inum
- meshfile.close()
- print 'Ok',str(num_elems), str(num_write)
- def material_write(self,mat_name):
- mat=open(mat_name,'w')
- print 'Writing '+mat_name+'.....'
- for block,flag in zip(self.block_mat,self.block_flag):
- quads=cubit.get_block_faces(block)
- for quad in quads:
- mat.write(('%10i\n') % flag)
- mat.close()
- print 'Ok'
- def nodescoord_write(self,nodecoord_name):
- nodecoord=open(nodecoord_name,'w')
- print 'Writing '+nodecoord_name+'.....'
- node_list=cubit.parse_cubit_list('node','all')
- num_nodes=len(node_list)
- nodecoord.write('%10i\n' % num_nodes)
- #
- for node in node_list:
- x,y,z=cubit.get_nodal_coordinates(node)
- txt=('%20f %20f\n') % (x,z)
- nodecoord.write(txt)
- nodecoord.close()
- print 'Ok'
- def free_write(self,freename=None):
- cubit.cmd('set info off')
- cubit.cmd('set echo off')
- cubit.cmd('set journal off')
- from sets import Set
- if not freename: freename=self.freename
- freeedge=open(freename,'w')
- print 'Writing '+freename+'.....'
- #
- #
- for block,flag in zip(self.block_bc,self.block_bc_flag):
- if block == self.topography:
- edges_all=Set(cubit.get_block_edges(block))
- freeedge.write('%10i\n' % len(edges_all))
- print len(edges_all)
- id_element=0
- for block,flag in zip(self.block_mat,self.block_flag):
- quads=cubit.get_block_faces(block)
- for quad in quads:
- id_element=id_element+1
- edges=Set(cubit.get_sub_elements("face", quad, 1))
- intersection=edges & edges_all
- if len(intersection) != 0:
- for e in intersection:
- node_edge=cubit.get_connectivity('Edge',e)
- nodes=cubit.get_connectivity('Face',quad)
- nodes=self.jac_check(list(nodes))
- nodes_ok=[]
- for i in nodes:
- if i in node_edge:
- nodes_ok.append(i)
- txt='%10i %10i %10i %10i\n' % (id_element,2,nodes_ok[0],nodes_ok[1])
- freeedge.write(txt)
- freeedge.close()
- print edges_all
- print 'Ok'
- cubit.cmd('set info on')
- cubit.cmd('set echo on')
- def abs_write(self,absname=None):
- cubit.cmd('set info off')
- cubit.cmd('set echo off')
- cubit.cmd('set journal off')
- from sets import Set
- if not absname: absname=self.absname
- absedge=open(absname,'w')
- print 'Writing '+absname+'.....'
- #
- #
- for block,flag in zip(self.block_bc,self.block_bc_flag):
- if block != self.topography:
- edges_all=Set(cubit.get_block_edges(block))
- absedge.write('%10i\n' % len(edges_all))
- print len(edges_all)
- id_element=0
- for block,flag in zip(self.block_mat,self.block_flag):
- quads=cubit.get_block_faces(block)
- for quad in quads:
- id_element=id_element+1
- edges=Set(cubit.get_sub_elements("face", quad, 1))
- intersection=edges & edges_all
- if len(intersection) != 0:
- for e in intersection:
- node_edge=cubit.get_connectivity('Edge',e)
- nodes=cubit.get_connectivity('Face',quad)
- nodes=self.jac_check(list(nodes))
- nodes_ok=[]
- for i in nodes:
- if i in node_edge:
- nodes_ok.append(i)
- txt='%10i %10i %10i %10i\n' % (id_element,2,nodes_ok[0],nodes_ok[1])
- absedge.write(txt)
- absedge.close()
- print edges_all,'- 2 corners'
- print 'Ok'
- cubit.cmd('set info on')
- cubit.cmd('set echo on')
- def rec_write(self,recname):
- print 'Writing '+self.recname+'.....'
- recfile=open(self.recname,'w')
- nodes=cubit.get_nodeset_nodes(self.receivers)
- for i,n in enumerate(nodes):
- x,y,z=cubit.get_nodal_coordinates(n)
- recfile.write('ST%i XX %20f %20f 0.0 0.0 \n' % (i,x,z))
- recfile.close()
- print 'Ok'
- def write(self,path=''):
- cubit.cmd('set info off')
- cubit.cmd('set echo off')
- cubit.cmd('set journal off')
- if len(path) != 0:
- if path[-1] != '/': path=path+'/'
- self.mesh_write(path+self.mesh_name)
- self.material_write(path+self.material_name)
- self.nodescoord_write(path+self.nodecoord_name)
- self.free_write(path+self.freename)
- self.abs_write(path+self.absname)
- self.nummaterial_write(path+self.nummaterial_name)
- if self.receivers: self.rec_write(path+self.recname)
- cubit.cmd('set info on')
- cubit.cmd('set echo on')
-
-profile=mesh()
\ No newline at end of file
Copied: seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d_original.py (from rev 21007, seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d.py)
===================================================================
--- seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d_original.py (rev 0)
+++ seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d_original.py 2012-11-11 17:28:45 UTC (rev 21014)
@@ -0,0 +1,434 @@
+#!/usr/bin/env python
+
+class mtools(object):
+ """docstring for mtools"""
+ def __init__(self,frequency,list_surf,list_vp):
+ super(mtools, self).__init__()
+ self.frequency = frequency
+ self.list_surf = list_surf
+ self.list_vp = list_vp
+ self.ngll=5
+ self.percent_gll=0.172
+ self.point_wavelength=5
+ def __repr__(self):
+ txt='Meshing for frequency up to '+str(self.frequency)+'Hz\n'
+ for surf,vp in zip(self.list_surf,self.list_vp):
+ txt=txt+'surface '+str(surf)+', vp ='+str(vp)+' -> size '+str(self.freq2meshsize(vp)[0])+' -> dt '+str(self.freq2meshsize(vp)[0])+'\n'
+ return txt
+ def freq2meshsize(self,vp):
+ velocity=vp*.5
+ self.size=(1/2.5)*velocity/self.frequency*(self.ngll-1)/self.point_wavelength
+ self.dt=.4*self.size/vp*self.percent_gll
+ return self.size,self.dt
+ def mesh_it(self):
+ for surf,vp in zip(self.list_surf,self.list_vp):
+ command = "surface "+str(surf)+" size "+str(self.freq2meshsize(vp)[0])
+ cubit.cmd(command)
+ command = "surface "+str(surf)+ 'scheme pave'
+ cubit.cmd(command)
+ command = "mesh surf "+str(surf)
+ cubit.cmd(command)
+
+class block_tools:
+ def __int__(self):
+ pass
+ def create_blocks(self,mesh_entity,list_entity=None,):
+ if mesh_entity =='surface':
+ txt=' face in surface '
+ elif mesh_entity == 'curve':
+ txt=' edge in curve '
+ elif mesh_entity == 'group':
+ txt=' face in group '
+ if list_entity:
+ if not isinstance(list_entity,list):
+ list_entity=[list_entity]
+ for entity in list_entity:
+ iblock=cubit.get_next_block_id()
+ command = "block "+str(iblock)+ txt +str(entity)
+ cubit.cmd(command)
+ def material_file(self,filename):
+ matfile=open(filename,'w')
+ material=[]
+ for record in matfile:
+ mat_name,vp_str=record.split()
+ vp=float(vp_str)
+ material.append([mat_name,vp])
+ self.material=dict(material)
+ def assign_block_material(self,id_block,mat_name,vp=None):
+ try:
+ material=self.material
+ except:
+ material=None
+ cubit.cmd('block '+str(id_block)+' attribute count 2')
+ cubit.cmd('block '+str(id_block)+' attribute index 1 '+str(id_block))
+ if material:
+ if material.has_key(mat_name):
+ cubit.cmd('block '+str(id_block)+' attribute index 2 '+str(material[mat_name]))
+ print 'block '+str(id_block)+' - material '+mat_name+' - vp '+str(material[mat_name])+' from database'
+ elif vp:
+ cubit.cmd('block '+str(id_block)+' attribute index 2 '+str(vp))
+ print 'block '+str(id_block)+' - material '+mat_name+' - vp '+str(vp)
+ else:
+ print 'assignment impossible: check if '+mat_name+' is in the database or specify vp'
+
+class mesh_tools(block_tools):
+ """Tools for the mesh
+ #########
+ dt,edge_dt,freq,edge_freq=seismic_resolution(edges,velocity,bins_d=None,bins_u=None,sidelist=None,ngll=5,np=8)
+ Given the velocity of a list of edges, seismic_resolution provides the minimum Dt required for the stability condition (and the corrisponding edge).
+ Furthermore, given the number of gll point in the element (ngll) and the number of GLL point for wavelength, it provide the maximum resolved frequency.
+ #########
+ length=edge_length(edge)
+ return the length of a edge
+ #########
+ edge_min,length=edge_min_length(surface)
+ given the cubit id of a surface, it return the edge with minimun length
+ #########
+ """
+ def __int__(self):
+ pass
+ def seismic_resolution(self,edges,velocity,bins_d=None,bins_u=None,sidelist=None):
+ """
+ dt,edge_dt,freq,edge_freq=seismic_resolution(edges,velocity,bins_d=None,bins_u=None,sidelist=None,ngll=5,np=8)
+ Given the velocity of a list of edges, seismic_resolution provides the minimum Dt required for the stability condition (and the corrisponding edge).
+ Furthermore, given the number of gll point in the element (ngll) and the number of GLL point for wavelength, it provide the maximum resolved frequency.
+ """
+ ratiostore=1e10
+ dtstore=1e10
+ edgedtstore=-1
+ edgeratiostore=-1
+ for edge in edges:
+ d=self.edge_length(edge)
+ ratio=(1/2.5)*velocity/d*(self.ngll-1)/self.point_wavelength
+ dt=.4*d/velocity*self.percent_gll
+ if dt<dtstore:
+ dtstore=dt
+ edgedtstore=edge
+ if ratio < ratiostore:
+ ratiostore=ratio
+ edgeratiostore=edge
+ try:
+ for bin_d,bin_u,side in zip(bins_d,bins_u,sidelist):
+ if ratio >= bin_d and ratio < bin_u:
+ command = "sideset "+str(side)+" edge "+str(edge)
+ cubit.cmd(command)
+ #print command
+ break
+ except:
+ pass
+ return dtstore,edgedtstore,ratiostore,edgeratiostore
+ def edge_length(self,edge):
+ """
+ length=edge_length(edge)
+ return the length of a edge
+ """
+ from math import sqrt
+ nodes=cubit.get_connectivity('Edge',edge)
+ x0,y0,z0=cubit.get_nodal_coordinates(nodes[0])
+ x1,y1,z1=cubit.get_nodal_coordinates(nodes[1])
+ d=sqrt((x1-x0)**2+(y1-y0)**2+(z1-z0)**2)
+ return d
+ def edge_min_length(self,surface):
+ """
+ edge_min,length=edge_min_length(surface)
+ given the cubit id of a surface, it return the edge with minimun length
+ """
+ from math import sqrt
+ self.dmin=99999
+ edge_store=0
+ command = "group 'list_edge' add edge in surf "+str(surface)
+ command = command.replace("["," ").replace("]"," ")
+ #print command
+ cubit.cmd(command)
+ group=cubit.get_id_from_name("list_edge")
+ edges=cubit.get_group_edges(group)
+ command = "delete group "+ str(group)
+ cubit.cmd(command)
+ for edge in edges:
+ d=self.edge_length(edge)
+ if d<dmin:
+ self.dmin=d
+ edge_store=edge
+ self.edgemin=edge_store
+ return self.edgemin,self.dmin
+ def jac_check(self,nodes):
+ x0=cubit.get_nodal_coordinates(nodes[0])
+ x1=cubit.get_nodal_coordinates(nodes[1])
+ x2=cubit.get_nodal_coordinates(nodes[2])
+ xv1=x1[0]-x0[0]
+ xv2=x2[0]-x1[0]
+ zv1=x1[2]-x0[2]
+ zv2=x2[2]-x1[2]
+ jac=-xv2*zv1+xv1*zv2
+ if jac > 0:
+ return nodes
+ elif jac < 0:
+ return nodes[0],nodes[3],nodes[2],nodes[1]
+ else:
+ print 'error, jacobian=0'
+ def mesh_analysis(self,frequency):
+ cubit.cmd('set info off')
+ cubit.cmd('set echo off')
+ cubit.cmd('set journal off')
+ bins_d=[0.0001]+range(0,int(frequency)+1)+[1000]
+ bins_u=bins_d[1:]
+ dt=[]
+ ed_dt=[]
+ r=[]
+ ed_r=[]
+ nstart=cubit.get_next_sideset_id()
+ command = "del sideset all"
+ cubit.cmd(command)
+ for bin_d,bin_u in zip(bins_d,bins_u):
+ nsideset=cubit.get_next_sideset_id()
+ command='create sideset '+str(nsideset)
+ cubit.cmd(command)
+ command = "sideset "+str(nsideset)+ " name "+ "'ratio-["+str(bin_d)+"_"+str(bin_u)+"['"
+ cubit.cmd(command)
+ nend=cubit.get_next_sideset_id()
+ sidelist=range(nstart,nend)
+ for block in self.block_mat:
+ name=cubit.get_exodus_entity_name('block',block)
+ velocity=self.material[name][1]
+ if velocity > 0:
+ faces=cubit.get_block_faces(block)
+ edges=[]
+ for face in faces:
+ es=cubit.get_sub_elements("face", face, 1)
+ edges=edges+list(es)
+ dtstore,edgedtstore,ratiostore,edgeratiostore=self.seismic_resolution(edges,velocity,bins_d,bins_u,sidelist)
+ dt.append(dtstore)
+ ed_dt.append(edgedtstore)
+ r.append(ratiostore)
+ ed_r.append(edgeratiostore)
+ self.ddt=zip(ed_dt,dt)
+ self.dr=zip(ed_r,r)
+ def sorter(x, y):
+ return cmp(x[1],y[1])
+ self.ddt.sort(sorter)
+ self.dr.sort(sorter)
+ print self.ddt,self.dr
+ print 'Deltat minimum => edge:'+str(self.ddt[0][0])+' dt: '+str(self.ddt[0][1])
+ print 'minimum frequency resolved => edge:'+str(self.dr[0][0])+' frequency: '+str(self.dr[0][1])
+ return self.ddt[0],self.dr[0]
+
+class mesh(object,mesh_tools):
+ def __init__(self):
+ super(mesh, self).__init__()
+ self.mesh_name='mesh_file'
+ self.nodecoord_name='nodes_coords_file'
+ self.material_name='materials_file'
+ self.nummaterial_name='nummaterial_velocity_file'
+ self.absname='absorbing_surface_file'
+ self.freename='free_surface_file'
+ self.recname='STATIONS'
+ self.face='QUAD4'
+ self.edge='BAR2'
+ self.topo='topo'
+ self.rec='receivers'
+ self.block_definition()
+ self.ngll=5
+ self.percent_gll=0.172
+ self.point_wavelength=5
+ cubit.cmd('compress')
+ def __repr__(self):
+ pass
+ def block_definition(self):
+ block_flag=[]
+ block_mat=[]
+ block_bc=[]
+ block_bc_flag=[]
+ material={}
+ bc={}
+ blocks=cubit.get_block_id_list()
+ for block in blocks:
+ name=cubit.get_exodus_entity_name('block',block)
+ ty=cubit.get_block_element_type(block)
+ if ty == self.face:
+ flag=int(cubit.get_block_attribute_value(block,0))
+ vel=cubit.get_block_attribute_value(block,1)
+ block_flag.append(int(flag))
+ block_mat.append(block)
+ par=tuple([flag,vel])
+ material[name]=par
+ elif ty == self.edge:
+ block_bc_flag.append(2)
+ block_bc.append(block)
+ bc[name]=2 #edge has connectivity = 2
+ if name == self.topo: topography=block
+ else:
+ print 'blocks no properly defined'
+ return None, None,None,None,None,None,None,None
+ nsets=cubit.get_nodeset_id_list()
+ if len(nsets) == 0: self.receivers=None
+ for nset in nsets:
+ name=cubit.get_exodus_entity_name('nodeset',nset)
+ if name == self.rec:
+ self.receivers=nset
+ else:
+ print 'nodeset '+name+' not defined'
+ self.receivers=None
+ try:
+ self.block_mat=block_mat
+ self.block_flag=block_flag
+ self.block_bc=block_bc
+ self.block_bc_flag=block_bc_flag
+ self.material=material
+ self.bc=bc
+ self.topography=topography
+ except:
+ print 'blocks no properly defined'
+ def tomo(self,flag,vel):
+ vp=vel/1000
+ rho=(1.6612*vp-0.472*vp**2+0.0671*vp**3-0.0043*vp**4+0.000106*vp**4)*1000
+ txt='%3i %1i %20f %20f %20f %1i %1i\n' % (flag,1,rho,vel,vel/(3**.5),0,0)
+ return txt
+ def nummaterial_write(self,nummaterial_name):
+ print 'Writing '+nummaterial_name+'.....'
+ nummaterial=open(nummaterial_name,'w')
+ for block in self.block_mat:
+ name=cubit.get_exodus_entity_name('block',block)
+ nummaterial.write(self.tomo(self.material[name][0],self.material[name][1]))
+ nummaterial.close()
+ print 'Ok'
+ def mesh_write(self,mesh_name):
+ meshfile=open(mesh_name,'w')
+ print 'Writing '+mesh_name+'.....'
+ num_elems=cubit.get_quad_count()
+ meshfile.write(str(num_elems)+'\n')
+ num_write=0
+ for block,flag in zip(self.block_mat,self.block_flag):
+ quads=cubit.get_block_faces(block)
+ for inum,quad in enumerate(quads):
+ nodes=cubit.get_connectivity('Face',quad)
+ nodes=self.jac_check(nodes)
+ txt=('%10i %10i %10i %10i\n')% nodes
+ meshfile.write(txt)
+ num_write=num_write+inum+1
+ print inum
+ meshfile.close()
+ print 'Ok',str(num_elems), str(num_write)
+ def material_write(self,mat_name):
+ mat=open(mat_name,'w')
+ print 'Writing '+mat_name+'.....'
+ for block,flag in zip(self.block_mat,self.block_flag):
+ quads=cubit.get_block_faces(block)
+ for quad in quads:
+ mat.write(('%10i\n') % flag)
+ mat.close()
+ print 'Ok'
+ def nodescoord_write(self,nodecoord_name):
+ nodecoord=open(nodecoord_name,'w')
+ print 'Writing '+nodecoord_name+'.....'
+ node_list=cubit.parse_cubit_list('node','all')
+ num_nodes=len(node_list)
+ nodecoord.write('%10i\n' % num_nodes)
+ #
+ for node in node_list:
+ x,y,z=cubit.get_nodal_coordinates(node)
+ txt=('%20f %20f\n') % (x,z)
+ nodecoord.write(txt)
+ nodecoord.close()
+ print 'Ok'
+ def free_write(self,freename=None):
+ cubit.cmd('set info off')
+ cubit.cmd('set echo off')
+ cubit.cmd('set journal off')
+ from sets import Set
+ if not freename: freename=self.freename
+ freeedge=open(freename,'w')
+ print 'Writing '+freename+'.....'
+ #
+ #
+ for block,flag in zip(self.block_bc,self.block_bc_flag):
+ if block == self.topography:
+ edges_all=Set(cubit.get_block_edges(block))
+ freeedge.write('%10i\n' % len(edges_all))
+ print len(edges_all)
+ id_element=0
+ for block,flag in zip(self.block_mat,self.block_flag):
+ quads=cubit.get_block_faces(block)
+ for quad in quads:
+ id_element=id_element+1
+ edges=Set(cubit.get_sub_elements("face", quad, 1))
+ intersection=edges & edges_all
+ if len(intersection) != 0:
+ for e in intersection:
+ node_edge=cubit.get_connectivity('Edge',e)
+ nodes=cubit.get_connectivity('Face',quad)
+ nodes=self.jac_check(list(nodes))
+ nodes_ok=[]
+ for i in nodes:
+ if i in node_edge:
+ nodes_ok.append(i)
+ txt='%10i %10i %10i %10i\n' % (id_element,2,nodes_ok[0],nodes_ok[1])
+ freeedge.write(txt)
+ freeedge.close()
+ print edges_all
+ print 'Ok'
+ cubit.cmd('set info on')
+ cubit.cmd('set echo on')
+ def abs_write(self,absname=None):
+ cubit.cmd('set info off')
+ cubit.cmd('set echo off')
+ cubit.cmd('set journal off')
+ from sets import Set
+ if not absname: absname=self.absname
+ absedge=open(absname,'w')
+ print 'Writing '+absname+'.....'
+ #
+ #
+ for block,flag in zip(self.block_bc,self.block_bc_flag):
+ if block != self.topography:
+ edges_all=Set(cubit.get_block_edges(block))
+ absedge.write('%10i\n' % len(edges_all))
+ print len(edges_all)
+ id_element=0
+ for block,flag in zip(self.block_mat,self.block_flag):
+ quads=cubit.get_block_faces(block)
+ for quad in quads:
+ id_element=id_element+1
+ edges=Set(cubit.get_sub_elements("face", quad, 1))
+ intersection=edges & edges_all
+ if len(intersection) != 0:
+ for e in intersection:
+ node_edge=cubit.get_connectivity('Edge',e)
+ nodes=cubit.get_connectivity('Face',quad)
+ nodes=self.jac_check(list(nodes))
+ nodes_ok=[]
+ for i in nodes:
+ if i in node_edge:
+ nodes_ok.append(i)
+ txt='%10i %10i %10i %10i\n' % (id_element,2,nodes_ok[0],nodes_ok[1])
+ absedge.write(txt)
+ absedge.close()
+ print edges_all,'- 2 corners'
+ print 'Ok'
+ cubit.cmd('set info on')
+ cubit.cmd('set echo on')
+ def rec_write(self,recname):
+ print 'Writing '+self.recname+'.....'
+ recfile=open(self.recname,'w')
+ nodes=cubit.get_nodeset_nodes(self.receivers)
+ for i,n in enumerate(nodes):
+ x,y,z=cubit.get_nodal_coordinates(n)
+ recfile.write('ST%i XX %20f %20f 0.0 0.0 \n' % (i,x,z))
+ recfile.close()
+ print 'Ok'
+ def write(self,path=''):
+ cubit.cmd('set info off')
+ cubit.cmd('set echo off')
+ cubit.cmd('set journal off')
+ if len(path) != 0:
+ if path[-1] != '/': path=path+'/'
+ self.mesh_write(path+self.mesh_name)
+ self.material_write(path+self.material_name)
+ self.nodescoord_write(path+self.nodecoord_name)
+ self.free_write(path+self.freename)
+ self.abs_write(path+self.absname)
+ self.nummaterial_write(path+self.nummaterial_name)
+ if self.receivers: self.rec_write(path+self.recname)
+ cubit.cmd('set info on')
+ cubit.cmd('set echo on')
+
+profile=mesh()
\ No newline at end of file
Added: seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d_with_routine_to_fix_negative_Jacobians_from_Ronan_Madec_2009.py
===================================================================
--- seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d_with_routine_to_fix_negative_Jacobians_from_Ronan_Madec_2009.py (rev 0)
+++ seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d_with_routine_to_fix_negative_Jacobians_from_Ronan_Madec_2009.py 2012-11-11 17:28:45 UTC (rev 21014)
@@ -0,0 +1,368 @@
+#!/usr/bin/python
+
+#last modified: Juin 2009
+
+#script to convert format Abaqus generated by Cubit in format Specfem2D
+
+#usage : python Cubit2Specfem2D.py input_file
+
+
+import sys, os
+from scipy import *
+
+
+def readAbaqus(file):
+ if os.path.exists(file) :
+ infile=open(file,'r')
+ lines=infile.readlines()
+ line=lines[0].split(',')
+ label=0
+ coords=[]
+ elem=[]
+ i=0
+ #read nodes coordinates
+ while line[0].strip()!='*NODE' and i<len(lines)-1:
+ i+=1
+ line=lines[i].split(',')
+ i+=1
+ line=lines[i].split(',')
+ while line[0].rstrip()!='*ELEMENT' and i<len(lines)-1:
+ #coords=[...,[i,x(i),y(i),z(i)],...]
+ coords.append([int(line[0]),[float(line[1]),float(line[2]),float(line[3])]])
+ i+=1
+ line=lines[i].split(',')
+
+ #read elements with their label
+ while i<len(lines)-1:
+ i+=1
+ line=lines[i].split(',')
+ label+=1
+ while line[0].rstrip()!='*ELEMENT' and i<len(lines):
+ #elem=[...,[i,label,[node(1),node(2),node(3),node(4)]],...]
+ elem.append([int(line[0]),label,[int(line[1]),int(line[2]),int(line[3]),int(line[4])]])
+ i+=1
+ if i!=len(lines):
+ line=lines[i].split(',')
+
+ infile.close()
+ return [coords,elem]
+
+ else:
+ print file,': file not found'
+ sys.exit(-1)
+
+#write mesh file
+def writeMesh(elem,jacob,outfile,ifirst):
+ file=open(outfile,'w')
+ file.write(str(len(elem))+'\n')
+ for i in range(len(elem)):
+ if jacob[i]==1:
+ file.write(str(elem[i][2][ifirst[i]%4])+' '+str(elem[i][2][(ifirst[i]+1)%4])+
+ ' '+str(elem[i][2][(ifirst[i]+2)%4])+' '+str(elem[i][2][(ifirst[i]+3)%4])+'\n')
+ elif jacob[i]==-1:
+ file.write(str(elem[i][2][ifirst[i]%4])+' '+str(elem[i][2][(ifirst[i]+3)%4])+
+ ' '+str(elem[i][2][(ifirst[i]+2)%4])+' '+str(elem[i][2][(ifirst[i]+1)%4])+'\n')
+ else:
+ print 'wrong jacobian direction parameter (must be 1 or -1):', jacob[i]
+ sys.exit(-1)
+ file.close()
+
+#write coords file
+def writeNodes(coords,col,outfile):
+ file=open(outfile,'w')
+ file.write(str(len(coords))+'\n')
+ for i in coords:
+ file.write(' ')
+ for j in col:
+ file.write(' '+str(i[1][j]))
+ file.write('\n')
+ file.close()
+ return
+
+#write file with label of each element
+def writeMaterials(elem,outfile):
+ file=open(outfile,'w')
+ for i in elem:
+ file.write(str(i[1])+'\n')
+ file.close()
+ return
+
+#write file after finding free surface boundary edges
+def writeFree(coords,elem,abs,outfile):
+ x=[]
+ z=[]
+ for i in coords:
+ x.append(i[1][0])
+ z.append(i[1][2])
+
+ xmin=min(x[:])
+ xmax=max(x[:])
+ zmin=min(z[:])
+ zmax=max(z[:])
+
+#structure:
+# edges=[...,[[node1,node2],ielem,label],...]
+# bound=[...,[node1,node2],...]
+ edges=[]
+ bound=[]
+ for ielem in elem:
+ for k in range(4):
+ p1=ielem[2][k]
+ p2=ielem[2][(k+1)%4]
+ edges.append([[min(p1,p2),max(p1,p2)],ielem[0],ielem[1]])
+
+ #an edge on the boundary is only in one element
+ #and an edge on the interior is in two elements
+ while len(edges)>0:
+ k=1
+ count=1
+ while k<len(edges) and edges[0][0]!=edges[k][0]:
+ k+=1
+ if k==len(edges):
+ #right
+ if x[edges[0][0][0]-1]==x[edges[0][0][1]-1] and x[edges[0][0][0]-1]==xmax:
+ if abs[1]==0:
+ bound.append(edges[0])
+ #bottom
+ elif z[edges[0][0][0]-1]==z[edges[0][0][1]-1] and z[edges[0][0][0]-1]==zmin:
+ if abs[2]==0:
+ bound.append(edges[0])
+ #left
+ elif x[edges[0][0][0]-1]==x[edges[0][0][1]-1] and x[edges[0][0][0]-1]==xmin:
+ if abs[3]==0:
+ bound.append(edges[0])
+ #top
+ elif abs[0]==0:
+ bound.append(edges[0])
+ else:
+ count+=1
+ del edges[k]
+ del edges[0]
+
+ file=open(outfile,'w')
+ file.write(str(len(bound))+'\n')
+ for i in bound:
+ file.write(str(i[1])+' 2 '+str(i[0][0])+' '+str(i[0][1])+'\n')
+ file.close()
+ return
+
+#write file after finding absorbing boundary edges
+def writeAbsorbing(coords,elem,abs,outfile):
+ x=[]
+ z=[]
+ for i in coords:
+ x.append(i[1][0])
+ z.append(i[1][2])
+
+ xmin=min(x[:])
+ xmax=max(x[:])
+ zmin=min(z[:])
+ zmax=max(z[:])
+
+
+#structure:
+# edges=[...,[[node1,node2],ielem,label],...]
+# bound=[...,[node1,node2],...]
+ edges=[]
+ bound=[]
+ for ielem in elem:
+ for k in range(4):
+ p1=ielem[2][k]
+ p2=ielem[2][(k+1)%4]
+ edges.append([[min(p1,p2),max(p1,p2)],ielem[0],ielem[1]])
+
+ #an edge on the boundary is only in one element
+ #and an edge on the interior is in two elements
+ while len(edges)>0:
+ k=1
+ count=1
+ while k<len(edges) and edges[0][0]!=edges[k][0]:
+ k+=1
+ if k==len(edges):
+ #right
+ if x[edges[0][0][0]-1]==x[edges[0][0][1]-1] and x[edges[0][0][0]-1]==xmax:
+ if abs[1]==1:
+ bound.append(edges[0])
+ #bottom
+ elif z[edges[0][0][0]-1]==z[edges[0][0][1]-1] and z[edges[0][0][0]-1]==zmin:
+ if abs[2]==1:
+ bound.append(edges[0])
+ #left
+ elif x[edges[0][0][0]-1]==x[edges[0][0][1]-1] and x[edges[0][0][0]-1]==xmin:
+ if abs[3]==1:
+ bound.append(edges[0])
+ #top
+ elif abs[0]==1:
+ bound.append(edges[0])
+ else:
+ count+=1
+ del edges[k]
+ del edges[0]
+
+ file=open(outfile,'w')
+ file.write(str(len(bound))+'\n')
+ for i in bound:
+ file.write(str(i[1])+' 2 '+str(i[0][0])+' '+str(i[0][1])+'\n')
+ file.close()
+ return
+
+#check if jacobian of elements are
+def check_jacobian(coords,elem):
+ jacobian=[]
+ positif=0
+ negatif=0
+ xi=[-1.,1.,1.,-1.]
+ gamma=[-1.,-1.,1.,1.]
+ for i in range(len(elem)):
+ sign_jac=[]
+ for k in range(len(elem[i][2])):
+ xxi=0.
+ zxi=0.
+ xgamma=0.
+ zgamma=0.
+ for ia in range(len(elem[i][2])):
+ x=coords[elem[i][2][ia]-1][1][0]
+ z=coords[elem[i][2][ia]-1][1][2]
+ dershape=der_shape_function(xi[k],gamma[k],ia)
+ xxi += dershape[0]*x
+ zxi += dershape[0]*z
+ xgamma += dershape[1]*x
+ zgamma += dershape[1]*z
+
+ if xxi*zgamma - xgamma*zxi == 0:
+ print 'error jacobian null on element :', i, 'point :', k
+ sys.exit(-1)
+ elif xxi*zgamma - xgamma*zxi < 0:
+ sign_jac.append(-1)
+ else:
+ sign_jac.append(1)
+
+ if sign_jac[0]==1:
+ if sign_jac[1]!=1 or sign_jac[2]!=1 or sign_jac[3]!=1:
+ print 'elem ', i, ' with jacobian not all positif'
+ sys.exit(-1)
+ jacobian.append(1)
+ positif+=1
+ elif sign_jac[0]==-1:
+ if sign_jac[1]!=-1 or sign_jac[2]!=-1 or sign_jac[3]!=-1:
+ print 'elem ', i, ' with jacobian not all negatif'
+ sys.exit(-1)
+ jacobian.append(-1)
+ negatif+=1
+ else:
+ print 'pb with jacobian in elem :', i
+
+ print 'on the mesh, there is '+str(positif)+' positive jacobian elements (unchanged)'
+ print ' and '+str(negatif)+' negative jacobian elements (re-ordered)'
+
+ return jacobian
+
+def der_shape_function(xi,gamma,inode):
+ sm=xi-1.
+ sp=xi+1.
+ tm=gamma-1.
+ tp=gamma+1.
+
+ if inode==0:
+ dershape=[.25*tm,.25*sm]
+ elif inode==1:
+ dershape=[-.25*tm,-.25*sp]
+ elif inode==2:
+ dershape=[.25*tp,.25*sp]
+ elif inode==3:
+ dershape=[-.25*tp,-.25*sm]
+ else:
+ print 'unknown inode for shape function (0,1,2 or 3):', inode
+ return dershape
+
+#check if jacobian of elements are
+def find_first(coords,elem):
+ ifirst=[]
+ imin=-1
+ for i in range(len(elem)):
+ min_sum=1.e100
+ for k in range(len(elem[i][2])):
+ if (min_sum>(coords[elem[i][2][k]-1][1][0]+coords[elem[i][2][k]-1][1][2])):
+ imin=k
+ min_sum=coords[elem[i][2][k]-1][1][0]+coords[elem[i][2][k]-1][1][2]
+ if (imin>3 or imin<0):
+ print 'pb in the detection of best first node element'+str(i)+': ifirst =', imin
+ sys.exit(-1)
+ ifirst.append(imin)
+ return ifirst
+
+#
+#
+#
+#
+#----------------------------Script beginning
+#
+#
+#
+#
+
+if len(sys.argv)<2:
+ print 'usage: python Cubit2Specfem2D.py input_file'
+ print ' to change absorbing conditions and precise label of the fluid'
+ print ' you have to change vector abs and vector label explicitely given'
+ print ' in the script (search "Parameters" in script to find it)'
+ print ''
+ sys.exit(-1)
+
+inputfile=sys.argv[1]
+temp=inputfile.split('.')
+name_root_file=temp[0]
+
+#Parameters
+#we only need X and Z coordinates
+col=[0,2]
+#model5
+#label=[7]
+#bathy
+label=[9]
+
+#absorbing conditions: if 0 false, if 1 true
+abs_top=0
+abs_rig=1
+abs_bot=1
+abs_lef=1
+
+abs=[abs_top,abs_rig,abs_bot,abs_lef]
+
+
+mesh_meshfem2D_file=name_root_file+'_mesh_file'
+nodes_meshfem2D_file=name_root_file+'_nodes_coords_file'
+materials_meshfem2D_file=name_root_file+'_materials_file'
+free_surface_meshfem2D_file=name_root_file+'_free_surface_file'
+absorbing_surface_meshfem2D_file=name_root_file+'_absorbing_surface_file'
+
+[coords,elem]=readAbaqus(inputfile)
+#structures:
+#
+# coords=[...,[i,[x(i),y(i),z(i)]],...]
+# elem=[...,[i,label,[node(1)+1,node(2)+1,node(3)+1,node(4)+1]],...]
+
+#jacobian :
+# if it is 1, the element nodes will be written in the same order as Cubit
+# if it is -1, the element nodes will be written in the oposite order as Cubit
+jacobian_direction=check_jacobian(coords,elem)
+
+#Find good first element (sum of coordinates the smallest)
+ifirst=find_first(coords,elem)
+
+print 'creating mesh file...'
+writeMesh(elem,jacobian_direction,mesh_meshfem2D_file,ifirst)
+
+print 'creating nodes file...'
+writeNodes(coords,col,nodes_meshfem2D_file)
+
+print 'creating materials file...'
+writeMaterials(elem,materials_meshfem2D_file)
+
+print 'creating free surface file... (can be long)'
+writeFree(coords,elem,abs,free_surface_meshfem2D_file)
+
+print 'creating absorbing condition file... (can be long)'
+writeAbsorbing(coords,elem,abs,absorbing_surface_meshfem2D_file)
+
+sys.exit(0)
Property changes on: seismo/2D/SPECFEM2D/trunk/UTILS/cubit2specfem2d/cubit2specfem2d_with_routine_to_fix_negative_Jacobians_from_Ronan_Madec_2009.py
___________________________________________________________________
Name: svn:executable
+ *
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