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Message #24102
Fwd: [Merge] lp:~evanlezar/dolfin/elezar into lp:dolfin
Hi,
There has been no response on my earlier merge request, so I thought I would
just ping the list as well.
Would someone be able to merge these changes that extend the gmsh physical
region support of mesh-converter.py.
Thanks
Evan
--
www.evanlezar.com
GoogleTalk: evanlezar
Skype: evanlezar
---------- Forwarded message ----------
From: Evan Lezar <evanlezar@xxxxxxxxx>
Date: Thu, Jul 7, 2011 at 8:01 PM
Subject: [Merge] lp:~evanlezar/dolfin/elezar into lp:dolfin
To: mp+67168@xxxxxxxxxxxxxxxxxx
Evan Lezar has proposed merging lp:~evanlezar/dolfin/elezar into lp:dolfin.
Requested reviews:
DOLFIN Core Team (dolfin-core)
For more details, see:
https://code.launchpad.net/~evanlezar/dolfin/elezar/+merge/67168
Fixed a small bug in the facet marking section of mesh-convert and added a
simple 3D test case.
--
https://code.launchpad.net/~evanlezar/dolfin/elezar/+merge/67168
You are the owner of lp:~evanlezar/dolfin/elezar.
=== modified file 'site-packages/dolfin_utils/meshconvert.py'
--- site-packages/dolfin_utils/meshconvert.py 2011-07-01 15:46:37 +0000
+++ site-packages/dolfin_utils/meshconvert.py 2011-07-07 11:01:36 +0000
@@ -472,7 +472,7 @@
data = [int(0*k) for k in range(len(facets_to_check)) ]
for i, physical_region in enumerate(physical_regions):
- nodes = [n-1 for n in
vertices_used_for_dim[highest_dim-1][2*i:(2*i+highest_dim)]]
+ nodes = [n-1 for n in
vertices_used_for_dim[highest_dim-1][highest_dim*i:(highest_dim*i+highest_dim)]]
nodes.sort()
if physical_region != 0:
=== added file
'test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.geo'
--- test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.geo
1970-01-01 00:00:00 +0000
+++ test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.geo
2011-07-07 11:01:36 +0000
@@ -0,0 +1,39 @@
+cl1 = 1;
+Point(1) = {0, 0, 0, cl1};
+Point(2) = {1, 0, 0, cl1};
+Point(3) = {1, 1, 0, cl1};
+Point(4) = {0, 1, 0, cl1};
+Point(5) = {0, 0, 1, cl1};
+Point(6) = {1, 0, 1, cl1};
+Point(7) = {1, 1, 1, cl1};
+Point(8) = {0, 1, 1, cl1};
+Line(1) = {1, 2};
+Line(2) = {2, 3};
+Line(3) = {3, 4};
+Line(4) = {4, 1};
+Line(5) = {5, 6};
+Line(6) = {6, 7};
+Line(7) = {7, 8};
+Line(8) = {8, 5};
+Line(9) = {1, 5};
+Line(10) = {2, 6};
+Line(11) = {3, 7};
+Line(12) = {4, 8};
+Line Loop(15) = {1, 2, 3, 4};
+Plane Surface(15) = {15};
+Line Loop(17) = {5, 6, 7, 8};
+Plane Surface(17) = {17};
+Line Loop(19) = {10, -5, -9, 1};
+Plane Surface(19) = {19};
+Line Loop(21) = {2, 11, -6, -10};
+Plane Surface(21) = {21};
+Line Loop(22) = {7, -12, -3, 11};
+Plane Surface(22) = {22};
+Line Loop(24) = {4, 9, -8, -12};
+Plane Surface(24) = {24};
+Surface Loop(26) = {17, 19, 21, 15, 22, 24};
+Volume(26) = {26};
+PEC = 999;
+Physical Surface(PEC) = {17};
+cl1 = 0;
+Physical Volume(cl1) = {26};
=== added file
'test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.msh'
--- test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.msh
1970-01-01 00:00:00 +0000
+++ test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.msh
2011-07-07 11:01:36 +0000
@@ -0,0 +1,51 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$Nodes
+14
+1 0 0 0
+2 1 0 0
+3 1 1 0
+4 0 1 0
+5 0 0 1
+6 1 0 1
+7 1 1 1
+8 0 1 1
+9 0.5 0.5 0
+10 0.5 0.5 1
+11 0.5 0 0.5
+12 1 0.5 0.5
+13 0.5 1 0.5
+14 0 0.5 0.5
+$EndNodes
+$Elements
+28
+1 2 2 999 17 5 6 10
+2 2 2 999 17 7 8 10
+3 2 2 999 17 10 6 7
+4 2 2 999 17 10 8 5
+5 4 2 0 26 14 8 5 10
+6 4 2 0 26 3 9 13 4
+7 4 2 0 26 9 12 13 10
+8 4 2 0 26 6 11 5 10
+9 4 2 0 26 12 13 10 7
+10 4 2 0 26 14 9 13 10
+11 4 2 0 26 6 12 10 7
+12 4 2 0 26 12 9 2 11
+13 4 2 0 26 6 12 11 10
+14 4 2 0 26 14 11 5 1
+15 4 2 0 26 6 12 2 11
+16 4 2 0 26 13 8 10 7
+17 4 2 0 26 12 3 13 7
+18 4 2 0 26 14 8 13 4
+19 4 2 0 26 11 9 1 14
+20 4 2 0 26 9 14 4 1
+21 4 2 0 26 8 14 13 10
+22 4 2 0 26 11 14 5 10
+23 4 2 0 26 12 9 11 10
+24 4 2 0 26 14 9 4 13
+25 4 2 0 26 2 9 1 11
+26 4 2 0 26 12 9 3 2
+27 4 2 0 26 12 9 13 3
+28 4 2 0 26 11 9 14 10
+$EndElements
=== modified file 'test/unit/meshconvert/python/test.py'
--- test/unit/meshconvert/python/test.py 2011-06-24 09:25:10 +0000
+++ test/unit/meshconvert/python/test.py 2011-07-07 11:01:36 +0000
@@ -242,7 +242,7 @@
1 edge marked
"""
marked_facets = [7]
- self._facet_marker_driver(1, marked_facets, 8)
+ self._facet_marker_driver(2, 1, marked_facets, 8)
def test_2D_facet_markings_2 (self):
"""
@@ -250,7 +250,7 @@
2 edges marked
"""
marked_facets = [2,5]
- self._facet_marker_driver(2, marked_facets, 8)
+ self._facet_marker_driver(2, 2, marked_facets, 8)
def test_2D_facet_markings_3 (self):
"""
@@ -258,7 +258,7 @@
3 edges marked
"""
marked_facets = [5,6,7]
- self._facet_marker_driver(3, marked_facets, 8)
+ self._facet_marker_driver(2, 3, marked_facets, 8)
def test_2D_facet_markings_4 (self):
"""
@@ -266,20 +266,35 @@
4 edges marked
"""
marked_facets = [2,5,6,7]
- self._facet_marker_driver(4, marked_facets, 8)
-
- def _facet_marker_driver (self, id, marked_facets, size ):
- handler = self.__convert("gmsh_test_facet_regions_2D_%d.msh" % id,
DataHandler.CellType_Triangle, 2)
+ self._facet_marker_driver(2, 4, marked_facets, 8)
+
+ def test_3D_facet_markings_1 (self):
+ """
+ Test the marking of 3D facets
+ Unit cube, 1 Face marked
+ """
+# [0, 0, 0, 999, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 999, 0, 0, 0, 0,
0, 0, 0, 0, 999, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 999,
+# 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
+ marked_facets = [3, 15, 24, 39,]
+ self._facet_marker_driver(3, 1, marked_facets, 60)
+
+ def _facet_marker_driver (self, dim, id, marked_facets, size ):
+ if dim == 2:
+ cell_type = DataHandler.CellType_Triangle
+ elif dim == 3:
+ cell_type = DataHandler.CellType_Tetrahedron
+
+ handler = self.__convert("gmsh_test_facet_regions_%dD_%d.msh" %
(dim, id), cell_type, dim)
free_facets = range(size)
for i in marked_facets:
free_facets.remove(i)
- dim, sz, entries, ended = handler.functions["facet_region"]
+ function_dim, sz, entries, ended =
handler.functions["facet_region"]
# the dimension of the meshfunction should be 1
- self.assertEqual(dim, 1)
+ self.assertEqual(function_dim, dim-1)
# There should be 8 edges in the mesh function
self.assertEqual(len(entries), size)
self.assertEqual(sz, size)
=== modified file 'site-packages/dolfin_utils/meshconvert.py'
--- site-packages/dolfin_utils/meshconvert.py 2011-07-01 15:46:37 +0000
+++ site-packages/dolfin_utils/meshconvert.py 2011-07-07 11:01:36 +0000
@@ -472,7 +472,7 @@
data = [int(0*k) for k in range(len(facets_to_check)) ]
for i, physical_region in enumerate(physical_regions):
- nodes = [n-1 for n in vertices_used_for_dim[highest_dim-1][2*i:(2*i+highest_dim)]]
+ nodes = [n-1 for n in vertices_used_for_dim[highest_dim-1][highest_dim*i:(highest_dim*i+highest_dim)]]
nodes.sort()
if physical_region != 0:
=== added file 'test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.geo'
--- test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.geo 1970-01-01 00:00:00 +0000
+++ test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.geo 2011-07-07 11:01:36 +0000
@@ -0,0 +1,39 @@
+cl1 = 1;
+Point(1) = {0, 0, 0, cl1};
+Point(2) = {1, 0, 0, cl1};
+Point(3) = {1, 1, 0, cl1};
+Point(4) = {0, 1, 0, cl1};
+Point(5) = {0, 0, 1, cl1};
+Point(6) = {1, 0, 1, cl1};
+Point(7) = {1, 1, 1, cl1};
+Point(8) = {0, 1, 1, cl1};
+Line(1) = {1, 2};
+Line(2) = {2, 3};
+Line(3) = {3, 4};
+Line(4) = {4, 1};
+Line(5) = {5, 6};
+Line(6) = {6, 7};
+Line(7) = {7, 8};
+Line(8) = {8, 5};
+Line(9) = {1, 5};
+Line(10) = {2, 6};
+Line(11) = {3, 7};
+Line(12) = {4, 8};
+Line Loop(15) = {1, 2, 3, 4};
+Plane Surface(15) = {15};
+Line Loop(17) = {5, 6, 7, 8};
+Plane Surface(17) = {17};
+Line Loop(19) = {10, -5, -9, 1};
+Plane Surface(19) = {19};
+Line Loop(21) = {2, 11, -6, -10};
+Plane Surface(21) = {21};
+Line Loop(22) = {7, -12, -3, 11};
+Plane Surface(22) = {22};
+Line Loop(24) = {4, 9, -8, -12};
+Plane Surface(24) = {24};
+Surface Loop(26) = {17, 19, 21, 15, 22, 24};
+Volume(26) = {26};
+PEC = 999;
+Physical Surface(PEC) = {17};
+cl1 = 0;
+Physical Volume(cl1) = {26};
=== added file 'test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.msh'
--- test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.msh 1970-01-01 00:00:00 +0000
+++ test/unit/meshconvert/python/data/gmsh_test_facet_regions_3D_1.msh 2011-07-07 11:01:36 +0000
@@ -0,0 +1,51 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$Nodes
+14
+1 0 0 0
+2 1 0 0
+3 1 1 0
+4 0 1 0
+5 0 0 1
+6 1 0 1
+7 1 1 1
+8 0 1 1
+9 0.5 0.5 0
+10 0.5 0.5 1
+11 0.5 0 0.5
+12 1 0.5 0.5
+13 0.5 1 0.5
+14 0 0.5 0.5
+$EndNodes
+$Elements
+28
+1 2 2 999 17 5 6 10
+2 2 2 999 17 7 8 10
+3 2 2 999 17 10 6 7
+4 2 2 999 17 10 8 5
+5 4 2 0 26 14 8 5 10
+6 4 2 0 26 3 9 13 4
+7 4 2 0 26 9 12 13 10
+8 4 2 0 26 6 11 5 10
+9 4 2 0 26 12 13 10 7
+10 4 2 0 26 14 9 13 10
+11 4 2 0 26 6 12 10 7
+12 4 2 0 26 12 9 2 11
+13 4 2 0 26 6 12 11 10
+14 4 2 0 26 14 11 5 1
+15 4 2 0 26 6 12 2 11
+16 4 2 0 26 13 8 10 7
+17 4 2 0 26 12 3 13 7
+18 4 2 0 26 14 8 13 4
+19 4 2 0 26 11 9 1 14
+20 4 2 0 26 9 14 4 1
+21 4 2 0 26 8 14 13 10
+22 4 2 0 26 11 14 5 10
+23 4 2 0 26 12 9 11 10
+24 4 2 0 26 14 9 4 13
+25 4 2 0 26 2 9 1 11
+26 4 2 0 26 12 9 3 2
+27 4 2 0 26 12 9 13 3
+28 4 2 0 26 11 9 14 10
+$EndElements
=== modified file 'test/unit/meshconvert/python/test.py'
--- test/unit/meshconvert/python/test.py 2011-06-24 09:25:10 +0000
+++ test/unit/meshconvert/python/test.py 2011-07-07 11:01:36 +0000
@@ -242,7 +242,7 @@
1 edge marked
"""
marked_facets = [7]
- self._facet_marker_driver(1, marked_facets, 8)
+ self._facet_marker_driver(2, 1, marked_facets, 8)
def test_2D_facet_markings_2 (self):
"""
@@ -250,7 +250,7 @@
2 edges marked
"""
marked_facets = [2,5]
- self._facet_marker_driver(2, marked_facets, 8)
+ self._facet_marker_driver(2, 2, marked_facets, 8)
def test_2D_facet_markings_3 (self):
"""
@@ -258,7 +258,7 @@
3 edges marked
"""
marked_facets = [5,6,7]
- self._facet_marker_driver(3, marked_facets, 8)
+ self._facet_marker_driver(2, 3, marked_facets, 8)
def test_2D_facet_markings_4 (self):
"""
@@ -266,20 +266,35 @@
4 edges marked
"""
marked_facets = [2,5,6,7]
- self._facet_marker_driver(4, marked_facets, 8)
-
- def _facet_marker_driver (self, id, marked_facets, size ):
- handler = self.__convert("gmsh_test_facet_regions_2D_%d.msh" % id, DataHandler.CellType_Triangle, 2)
+ self._facet_marker_driver(2, 4, marked_facets, 8)
+
+ def test_3D_facet_markings_1 (self):
+ """
+ Test the marking of 3D facets
+ Unit cube, 1 Face marked
+ """
+# [0, 0, 0, 999, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 999, 0, 0, 0, 0, 0, 0, 0, 0, 999, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 999,
+# 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
+ marked_facets = [3, 15, 24, 39,]
+ self._facet_marker_driver(3, 1, marked_facets, 60)
+
+ def _facet_marker_driver (self, dim, id, marked_facets, size ):
+ if dim == 2:
+ cell_type = DataHandler.CellType_Triangle
+ elif dim == 3:
+ cell_type = DataHandler.CellType_Tetrahedron
+
+ handler = self.__convert("gmsh_test_facet_regions_%dD_%d.msh" % (dim, id), cell_type, dim)
free_facets = range(size)
for i in marked_facets:
free_facets.remove(i)
- dim, sz, entries, ended = handler.functions["facet_region"]
+ function_dim, sz, entries, ended = handler.functions["facet_region"]
# the dimension of the meshfunction should be 1
- self.assertEqual(dim, 1)
+ self.assertEqual(function_dim, dim-1)
# There should be 8 edges in the mesh function
self.assertEqual(len(entries), size)
self.assertEqual(sz, size)
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