[Gmsh] 3D Mesh of multiple volumes - only half of the mesh is made in 3D

Wed Feb 11 16:10:38 CET 2015

Hi all!

I'm currently working on meshing a geometry. The geometry (in words)
consists of a very small sphere found in a halfsphere. The halfcircle is
found in pretty much a rectangle. The rectangle is located in another
rectangle. After managing to get rid of problems with intersections I
managed to get the 3D meshing working. However, only a part of the geometry
is meshed in 3d, but I get no errors at all. In the case of the full
geometry the area inside the sphere and between the sphere and the
halfsphere are meshed in 3D, but not the region inside of the rectangles.
If I reduce the geometry and remove sphere and halfsphere I get a three
dimensional mesh in the rectangular volumes, but as soon as I add up a
circular component it will onlymesh inside the sphere. I'm sure I'm doing
something wrong, but the lack of an error message really confuses me...

Thanks in advance

The geometry is the following:

colloid = 1e-6;
polymer = 1e-6;
water = 1e-4;
cuvette = 5e-4;
p1 = newp; Point(p1) = {0, 0, 1e-6, colloid};
p2 = newp; Point(p2) = {125e-9, 0, 1e-6, colloid};
p3 = newp; Point(p3) = {-125e-9, 0, 1e-6, colloid};
p4 = newp; Point(p4) = {0, 125e-9, 1e-6, colloid};
p5 = newp; Point(p5) = {0, -125e-9, 1e-6, colloid};
p6 = newp; Point(p6) = {0, 0, 1125e-9, colloid};
p7 = newp; Point(p7) = {0, 0, 875e-9, colloid};
p37 = newp; Point(p37) = {0,0,-125e-9, colloid};
Circle(1) = {p7, p1, p4};
Circle(2) = {p4, p1, p6};
Circle(3) = {p6, p1, p5};
Circle(4) = {p5, p1, p3};
Circle(5) = {p5, p1, p7};
Circle(6) = {p7, p1, p3};
Circle(7) = {p3, p1, p4};
Circle(8) = {p4, p1, p2};
Circle(9) = {p2, p1, p6};
Circle(10) = {p5, p1, p2};
Circle(11) = {p2, p1, p7};
Circle(12) = {p6, p1, p3};
Line Loop(13) = {12, 7, 2};
Ruled Surface(14) = {-13};
Line Loop(15) = {2, -9, -8};
Ruled Surface(16) = {15};
Line Loop(17) = {10, 9, 3};
Ruled Surface(18) = {17};
Line Loop(19) = {12, -4, -3};
Ruled Surface(20) = {19};
Line Loop(21) = {5, 6, -4};
Ruled Surface(22) = {-21};
Line Loop(23) = {5, -11, -10};
Ruled Surface(24) = {23};
Line Loop(25) = {7, -1, 6};
Ruled Surface(26) = {25};
Line Loop(27) = {8, 11, 1};
Ruled Surface(28) = {27};
Physical Surface(1) = {26, 28, 16, 14, 24, 22, 20, 18};
p8 = newp; Point(p8) = {50e-6, 0, -125e-9, polymer};
p9 = newp; Point(p9) = {-50e-6, 0, -125e-9, polymer};
p10 = newp; Point(p10) = {0, 50e-6, -125e-9, polymer};
p11 = newp; Point(p11) = {0, -50e-6, -125e-9, polymer};
p12 = newp; Point(p12) = {0, 0, 49.875e-6, polymer};
Circle(29) = {p8, p37, p10};
Circle(30) = {p10, p37, p9};
Circle(31) = {p9, p37, p11};
Circle(32) = {p11, p37, p8};
Circle(33) = {p12, p37, p8};
Circle(34) = {p12, p37, p9};
Circle(35) = {p12, p37, p10};
Circle(36) = {p12, p37, p11};
Line Loop(37) = {35, 30, -34};
Ruled Surface(38) = {37};
Line Loop(39) = {29, -35, 33};
Ruled Surface(40) = {-39};
Line Loop(41) = {36, 32, -33};
Ruled Surface(42) = {41};
Line Loop(43) = {34, 31, -36};
Ruled Surface(44) = {43};
Line Loop(45) = {29, 30, 31, 32};
Plane Surface(46) = {-45};
Physical Surface(2) = {46, 44, 42, 40, 38, 26, 28, 16, 14, 24, 22, 20, 18};
p13 = newp; Point(p13) = {0.6e-2, 2.25e-2, -0.900125e-3, cuvette};
p14 = newp; Point(p14) = {0.6e-2, -2.25e-2, -0.900125e-3, cuvette};
p15 = newp; Point(p15) = {-0.6e-2, -2.25e-2, -0.900125e-3, cuvette};
p16 = newp; Point(p16) = {-0.6e-2, 2.25e-2, -0.900125e-3, cuvette};
p17 = newp; Point(p17) = {0.6e-2, 2.25e-2, 100e-6, cuvette};
p18 = newp; Point(p18) = {0.6e-2, -2.25e-2, 100e-6, cuvette};
p19 = newp; Point(p19) = {-0.6e-2, -2.25e-2, 100e-6, cuvette};
p20 = newp; Point(p20) = {-0.6e-2, 2.25e-2, 100e-6, cuvette};
p21 = newp; Point(p21) = {0.6e-2, 2.25e-2, 1.100e-3, cuvette};
p22 = newp; Point(p22) = {0.6e-2, -2.25e-2, 1.100e-3, cuvette};
p23 = newp; Point(p23) = {-0.6e-2, -2.25e-2, 1.100e-3, cuvette};
p24 = newp; Point(p24) = {-0.6e-2, 2.25e-2, 1.100e-3, cuvette};
p25 = newp; Point(p25) = {0.45e-2, 1e-2, -125e-9, water};
p26 = newp; Point(p26) = {0.45e-2, -1e-2, -125e-9, water};
p27 = newp; Point(p27) = {-0.45e-2, -1e-2, -125e-9, water};
p28 = newp; Point(p28) = {-0.45e-2, 1e-2, -125e-9, water};
p29 = newp; Point(p29) = {0.45e-2, 1e-2, 100e-6, water};
p30 = newp; Point(p30) = {0.45e-2, -1e-2, 100e-6, water};
p31 = newp; Point(p31) = {-0.45e-2, -1e-2, 100e-6, water};
p32 = newp; Point(p32) = {-0.45e-2, 1e-2, 100e-6, water};
p33 = newp; Point(p33) = {-0, 1.9e-2, -125e-9, water};
p34 = newp; Point(p34) = {-0, -1.9e-2, -125e-9, water};
p35 = newp; Point(p35) = {-0, -1.9e-2, 100e-6, water};
p36 = newp; Point(p36) = {-0, 1.9e-2, 100e-6, water};
Line(47) = {p23, p15};
Line(48) = {p15, p16};
Line(49) = {p16, p24};
Line(50) = {p24, p23};
Line(51) = {p23, p22};
Line(52) = {p22, p14};
Line(53) = {p14, p15};
Line(54) = {p22, p21};
Line(55) = {p21, p13};
Line(56) = {p13, p14};
Line(57) = {p13, p16};
Line(58) = {p24, p21};
Line(59) = {p27, p34};
Line(60) = {p34, p26};
Line(61) = {p27, p31};
Line(62) = {p31, p35};
Line(63) = {p35, p34};
Line(64) = {p35, p30};
Line(65) = {p30, p26};
Line(66) = {p31, p32};
Line(67) = {p28, p32};
Line(68) = {p28, p27};
Line(69) = {p32, p36};
Line(70) = {p33, p28};
Line(71) = {p36, p33};
Line(72) = {p36, p29};
Line(73) = {p25, p29};
Line(74) = {p25, p33};
Line(75) = {p29, p30};
Line(76) = {p26, p25};
Line Loop(77) = {72, 75, -64, -62, 66, 69};
Plane Surface(78) = {-77};
Line Loop(79) = {68, 59, 60, 76, 74, 70, 29, 30, 32, 31};
Plane Surface(80) = {79};
Line Loop(81) = {67, -66, -61, -68};
Plane Surface(82) = {-81};
Line Loop(83) = {61, 62, 63, -59};
Plane Surface(84) = {-83};
Line Loop(85) = {63, 60, -65, -64};
Plane Surface(86) = {85};
Line Loop(87) = {65, 76, 73, 75};
Plane Surface(88) = {87};
Line Loop(89) = {72, -73, 74, -71};
Plane Surface(90) = {89};
Line Loop(91) = {71, 70, 67, 69};
Plane Surface(92) = {91};
Physical Surface(3) = {78, 80, 82, 92, 84, 86, 88, 90, 44, 42, 40, 38, 46};
Line Loop(93) = {58, 55, 57, 49};
Plane Surface(94) = {93};
Line Loop(95) = {50, 51, 54, -58};
Plane Surface(96) = {95};
Line Loop(97) = {48, 49, 50, 47};
Plane Surface(98) = {-97};
Line Loop(99) = {53, -47, 51, 52};
Plane Surface(100) = {-99};
Line Loop(101) = {54, 55, 56, -52};
Plane Surface(102) = {-101};
Line Loop(103) = {57, -48, -53, -56};
Plane Surface(104) = {-103};
Physical Surface(4) = {94, 104, 102, 96, 98, 100, 78, 80, 84, 86, 88, 82,
92, 90};
Surface Loop(105) = {14, 16, 18, 24, 22, 20, 26, 28};
Volume(106) = {105};
Surface Loop(107) = {46, 44, 38, 40, 42};
Volume(108) = {107, 105};
Surface Loop(109) = {82, 80, 84, 86, 88, 90, 78, 92};
Volume(110) = {109, 107};
Surface Loop(111) = {104, 102, 100, 96, 98, 94};
Volume(112) = {111, 109};
Physical Volume(113) = {106};
Physical Volume(114) = {108};
Physical Volume(115) = {110};
Physical Volume(116) = {112};
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