[Gmsh] redundant nodes when using transfinite

[Thomas Unfer]

Hi there,

I am new to this list, so first how all greetings to everybody.
I am trying to mesh two adjacent boxes with hexaedra using transfinite 
(.geo attached) plus a few surfaces to apply different boundary 
conditions in my solver.
The meshing goes alright and the cells are (visually) conforming.
However in the .msh file the physical surfaces and volumes rely on 
different point ids which makes it impossible to retrieve proper 
connectivity. I tryed Coherence but it did no good. Does any one has any 
clue how to fix this?

Thanks for your help,

Thomas
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// geometry
h_die = 0.813e-3;
w_strip = 1.8e-3;
w_die = w_strip*5;
l_die = 0.1;
h_air = 1e-3;
w_air = w_die;
l_air = l_die;

h_port=h_die;
w_port=2*w_strip;

// meshing
nx_die   = 15;
nx_air   = 10;
ny_strip = 4;
ny_die   = ny_strip*5;
ny_port  = ny_strip*2;
ny_air   = ny_die;
nz_die   = 40;
nz_air   = nz_die;

// dielectric layer
Point(1) = {0, 0, 0};
Point(2) = {h_die, 0, 0};
Point(3) = {h_die, w_die, 0};
Point(4) = {0, w_die, 0};
Point(5) = {0, 0, l_die};
Point(6) = {h_die, 0, l_die};
Point(7) = {h_die, w_die, l_die};
Point(8) = {0, w_die, l_die};

// microstrip
Point(9) = {h_die,w_die/2-w_strip/2,0};
Point(10)= {h_die,w_die/2+w_strip/2,0};
Point(11)= {h_die,w_die/2+w_strip/2,l_die};
Point(12)= {h_die,w_die/2-w_strip/2,l_die};

// input port
Point(13)= {0,w_die/2-w_port/2,0};
Point(14)= {h_port,w_die/2-w_port/2,0};
Point(15)= {h_port,w_die/2+w_port/2,0};
Point(16)= {0,w_die/2+w_port/2,0};

// air volume
Point(101)={h_die+h_air, 0, 0};
Point(102)={h_die+h_air, w_air, 0};
Point(105)={h_die+h_air, 0, l_air};
Point(106)={h_die+h_air, w_air, l_air};

Line(1) = {1, 2};
Line(100)={2,101};
Line(2) = {2, 3};
Line(101)={101,102};
Line(3) = {3, 4};
Line(102)={102,3};
Line(4) = {4, 1};
Line(5) = {5, 6};
Line(104)={6,105};
Line(6) = {6, 7};
Line(105)={105,106};
Line(7) = {7, 8};
Line(106)={106,7};
Line(8) = {8, 5};
Line(9) = {3, 7};
Line(108)={102,106};
Line(10) = {4, 8};
Line(11) = {1, 5};
Line(12) = {2, 6};
Line(111)={101,105};
Line(13) = {9, 10};
Line(14) = {10,11};
Line(15) = {11,12};
Line(16) = {12, 9};
Line(17) = {13,14};
Line(18) = {14,15};
Line(19) = {15,16};
Line(20) = {16,13};
Line(21) = {4,16};
Line(22) = {13,1};
Line(23) = {14,2};
Line(24) = {3,15};


Line Loop(13) = {2, 9, -6, -12};
Line Loop(112)={101,108,-105,-111};
Plane Surface(14) = {13};
Plane Surface(113)={112};
Line Loop(15) = {9, 7, -10, -3};
Line Loop(114)={108,106,-9,-102};
Plane Surface(16) = {15};
Plane Surface(115)={114};
Line Loop(17) = {4, 11, -8, -10};
Line Loop(116)={-2,12,6,-9};
Plane Surface(18) = {17};
Plane Surface(117)={116};
Line Loop(19) = {4, 1, 2, 3};
Line Loop(118)={-2,100,101,102};
Plane Surface(20) = {19};
Plane Surface(119)={118};
Line Loop(21) = {1, 12, -5, -11};
Line Loop(120)={100,111,-104,-12};
Plane Surface(22) = {21};
Plane Surface(121)={120};
Line Loop(23) = {7, 8, 5, 6};
Line Loop(122)={106,-6,104,105};
Plane Surface(24) = {23};
Plane Surface(123)={122};
Surface Loop(25) = {14, 20, 18, 22, 24, 16};
Surface Loop(124)={113,119,117,121,123,115};
Volume(26) = {25};
Volume(125)={124};

Line Loop(24)={13,14,15,16};
Plane Surface(25)={24};
Line Loop(25)={17,18,19,20};
Plane Surface(26)={25};

Line Loop(26)={-22,17,23,-1};
Plane Surface(27)={26};
Line Loop(27)={-21,-3,24,19};
Plane Surface(28)={27};

Transfinite Line{1,3,5,7,17,19}=nx_die+1;
Transfinite Line{2,4,6,8,13,15}=ny_die+1;
Transfinite Line{13,15,18,20}=ny_strip+1;
Transfinite Line{21,22,23,24}=(ny_die-ny_port)/2+1;
Transfinite Line{9,10,11,12,14,16}=nz_die+1;


Transfinite Line{100,102,104,106}=nx_air+1;
Transfinite Line{101,105}=ny_air+1;
Transfinite Line{108,111}=nz_air+1;

Transfinite Surface{14};
Transfinite Surface{113};
Recombine Surface{14};
Recombine Surface{113};
Transfinite Surface{16};
Transfinite Surface{115};
Recombine Surface{16};
Recombine Surface{115};
Transfinite Surface{18};
Transfinite Surface{117};
Recombine Surface{18};
Recombine Surface{117};
Transfinite Surface{20};
Transfinite Surface{119};
Recombine Surface{20};
Recombine Surface{119};
Transfinite Surface{22};
Transfinite Surface{121};
Recombine Surface{22};
Recombine Surface{121};
Transfinite Surface{24};
Transfinite Surface{123};
Recombine Surface{24};
Recombine Surface{123};

Transfinite Surface{25};
Recombine Surface{25};
Transfinite Surface{26};
Recombine Surface{26};
Transfinite Surface{27};
Recombine Surface{27};
Transfinite Surface{28};
Recombine Surface{28};

Transfinite Volume{26};
Transfinite Volume{125};
Recombine Volume{26};
Recombine Volume{125};
Coherence;

Physical Volume(27)={125};
Physical Volume(28)={26};
Physical Surface(29)={26};
Physical Surface(30)={27,28,119,113,16,115,22,121,24,123};
Physical Surface(31)={25};
Physical Surface(32)={18};