[Gmsh] Identical Points in Triangulation

[Alex Lindsay]

I have a mesh that is a repeating lattice of unit cells. When I use a 
relatively small lattice, say 10x10, the mesh is always created without 
error. However, for larger lattices, say 25x25, I commonly get the error 
`Identical points in triangulation: increase element size or 
Mesh.RandomFactor`. I've looked at the documentation, and the ratio of 
my smallest element size to model size is 1e-3 at worst. Regardless, 
I've increased Mesh.RandomFactor to 1e-6 and I still get errors. I can't 
really increase my characteristic length any larger because it's already 
around the order of the smallest geometric feature. Does anyone have any 
other troubleshooting suggestions? I've attached my `geo` file in case 
it's helpful.
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Mesh.RandomFactor = 1e-6;
graph_sqc_rad = 2.54; // MSRE (cm) unless otherwise noted
fuel_sqc_rad = 2.8847; // See N and O columns of MSRE-properties.ods. Ensures correct volume fraction of .229
pitch = 2 * fuel_sqc_rad;
num_cells = 28;
height = 162.56; // p. 101 robertson design report part 1: 162.56
lc = .3;

Point(1) = {-graph_sqc_rad, -graph_sqc_rad, 0, lc};
Point(2) = {graph_sqc_rad, -graph_sqc_rad, 0, lc};
Point(3) = {graph_sqc_rad, graph_sqc_rad, 0, lc};
Point(4) = {-graph_sqc_rad, graph_sqc_rad, 0, lc};
Line(1) = {4, 1};
Line(2) = {1, 2};
Line(3) = {3, 2};
Line(4) = {3, 4};
Point(5) = {-fuel_sqc_rad, -fuel_sqc_rad, 0, lc};
Point(6) = {-fuel_sqc_rad, fuel_sqc_rad, 0, lc};
Point(7) = {fuel_sqc_rad, fuel_sqc_rad, 0, lc};
Point(8) = {fuel_sqc_rad, -fuel_sqc_rad, 0, lc};
Line(5) = {6, 7};
Line(6) = {7, 8};
Line(7) = {8, 5};
Line(8) = {5, 6};
Line Loop(9) = {5, 6, 7, 8};
Line Loop(10) = {4, 1, 2, -3};
Plane Surface(11) = {9, 10};
Plane Surface(12) = {10};
fuel_surfaces[] = {11};
moder_surfaces[] = {12};
For xindex In {1:num_cells-1}
new_f_surface = Translate {xindex*pitch, 0, 0} {
  Duplicata { Surface{11}; }
};
fuel_surfaces += new_f_surface;
new_m_surface = Translate {xindex*pitch, 0, 0} {
  Duplicata { Surface{12}; }
};
moder_surfaces += new_m_surface;
EndFor // xindex

For yindex In {1:num_cells-1}
new_f_surface = Translate {0, yindex*pitch, 0} {
  Duplicata { Surface{11}; }
};
fuel_surfaces += new_f_surface;
new_m_surface = Translate {0, yindex*pitch, 0} {
  Duplicata { Surface{12}; }
};
moder_surfaces += new_m_surface;
EndFor // yindex

For xindex In {1:num_cells-1}
For yindex In {1:num_cells-1}
new_f_surface = Translate {xindex*pitch, yindex*pitch, 0} {
  Duplicata { Surface{11}; }
};
fuel_surfaces += new_f_surface;
new_m_surface = Translate {xindex*pitch, yindex*pitch, 0} {
  Duplicata { Surface{12}; }
};
moder_surfaces += new_m_surface;
EndFor // xindex
EndFor // yindex

fuel_volumes[] = {};
moder_volumes[] = {};
fuel_tops[] = {};
fuel_sides[] = {};
moder_tops[] = {};
For index In {0:num_cells*num_cells-1}
// For index In {3:5}
fuel_out[] = Extrude {0, 0, height} { Surface{fuel_surfaces[index]}; };
fuel_volumes += fuel_out[1];
fuel_tops += fuel_out[0];
If (index == 0)
fuel_sides += fuel_out[4];
fuel_sides += fuel_out[5];
ElseIf (index == num_cells * num_cells - 1)
fuel_sides += fuel_out[2];
fuel_sides += fuel_out[3];
ElseIf (index == num_cells -1)
fuel_sides += fuel_out[3];
fuel_sides += fuel_out[4];
ElseIf (index == 2 * num_cells - 2)
fuel_sides += fuel_out[5];
fuel_sides += fuel_out[2];
ElseIf (index < num_cells) // -y side
fuel_sides += fuel_out[4];
ElseIf (index < 2 * num_cells - 2) // -x side
fuel_sides += fuel_out[5];
ElseIf ((index - 2 * (num_cells - 1)) % (num_cells - 1) == 0)
fuel_sides += fuel_out[2];
ElseIf (index >= num_cells * num_cells - num_cells + 1 && index < num_cells * num_cells - 1)
fuel_sides += fuel_out[3];
EndIf
// If (index >= num_cells * (num_cells - 1) && index < num_cells * num_cells)// +y side
// fuel_sides += fuel_out[2];
// EndIf
// If (index % num_cells == num_cells - 1) // +x side
// fuel_sides += fuel_out[3];
// EndIf
moder_out[] = Extrude {0, 0, height} { Surface{moder_surfaces[index]}; };
moder_volumes += moder_out[1];
moder_tops += moder_out[0];
EndFor // index

Physical Volume ("fuel") = { fuel_volumes[] };
Physical Volume ("moder") = { moder_volumes[] };
tot_volumes = {};
tot_volumes[] = fuel_volumes[];
tot_volumes += moder_volumes[];
bound_surfs = {};
bound_surfs[] = fuel_surfaces[];
bound_surfs += moder_surfaces[];
bound_surfs += fuel_tops[];
bound_surfs += moder_tops[];
bound_surfs += fuel_sides[];

temp_diri_surfs = {};
temp_diri_surfs[] = fuel_surfaces[];
temp_diri_surfs += moder_surfaces[];
temp_diri_surfs += fuel_sides[];

temp_outflow_surfs = {};
temp_outflow_surfs[] = fuel_tops[];

temp_inflow_surfs = {};
temp_inflow_surfs[] = fuel_surfaces[];

// Physical Surface ("boundary") = { bound_surfs[] };
// Physical Surface ("temp_diri_bnd") = { temp_diri_surfs[] };
// Physical Surface ("temp_outflow_bnd") = { temp_outflow_surfs[] };
// Physical Surface ("temp_inflow_bnd") = { temp_inflow_surfs[] };
Physical Surface ("fuel_bottoms") = { fuel_surfaces[] };
Physical Surface ("fuel_tops") = { fuel_tops[] };
Physical Surface ("moder_bottoms") = { moder_surfaces[] };
Physical Surface ("moder_tops") = { moder_tops[] };
Physical Surface ("fuel_sides") = { fuel_sides[] };