I intend to use the gmsh2nek tool from the Nek5000 library to convert a gmsh mesh to re2 format. So far I have been able to successfully use the gmsh2nek tool for the following cube.geo file.

//Sets the mesh element order
Mesh.ElementOrder = 2;

//Sets the mesh version for exporting the mesh
Mesh.MshFileVersion = 2.2;

Point(1) = {0, 0, 0, 1.0};
Point(2) = {1, 0, 0, 1.0};
Point(3) = {1, 1, 0, 1.0};
Point(4) = {0, 1, 0, 1.0};

Line(1) = {4, 3};
Line(2) = {3, 2};
Line(3) = {2, 1};
Line(4) = {1, 4};

Line Loop(5) = {1, 2, 3, 4};
Plane Surface(6) = {5};

Transfinite Line {1, 2, 3, 4} = 4 Using Progression 1;
Transfinite Surface {6};
Recombine Surface {6};

//+
Extrude {0, 0, 1} {
  Surface{6};
  Layers{3};
  Recombine;
}

Physical Surface("inlet", 29) = {15};
Physical Surface("outlet", 30) = {23};
Physical Surface("walls", 31) = {28, 27, 6, 19};
Physical Volume("fluid", 32) = {1};

I want to model a reactor fuel pin for which I started by sketching a cylinder inside a cylinder (pellet inside clad) for the time being in FreeCAD, exported it in the STEP format and opened it gmsh. The generated mesh seemed fine to me. However gmsh2nek didn’t work due to the following error:

only line3 and quad8/9 elements are accepted
please choose "set order 2" option to set all elements to 2nd order
please uncheck "save all elements" when exporting mesh
please see readme for more information

I have saved the generated mesh in the ASCII 2 format. The mesh appears fine to me.

However when I observe the .msh file for the cube (where gmsh2nek worked) and the file my 2 cylinders, I see that the section $Elements of cube.msh only has gmsh element types with element_ids 10 (Quadrilateral9 – (something called serendipity quadratic quadrilateral) & 12 (this I couldn’t figure out). I think this is somewhere correlated to the error which is asking me to use line3 or quad8/9 elements.

cube.msh snippet

// Comment - Each line is element_id element_type number_of_tags <tags> node_1 node_2 ... node_n. 
// Comment - 2nd digit is of our use - element_type

$Elements
81
1 10 2 31 6 4 9 69 25 11 73 74 28 75
2 10 2 31 6 25 69 70 24 74 76 77 27 78
3 10 2 31 6 24 70 20 1 77 79 23 26 80
4 10 2 31 6 9 10 71 69 12 81 82 73 83
....
55 12 2 32 1 69 9 4 25 219 94 49 171 73 74 227 11 98 28 51 181 228 229 99 189 75 230 231 100 190 232 233
56 12 2 32 1 219 94 49 171 220 95 50 172 228 229 234 99 101 189 52 184 235 236 102 191 232 237 238 103 192 239 240
....
$EndElements

OTOH, the $Elements of the my cylinders .msh file has all kinds of different gmsh element types – 5 -> Hexahedron8 (linear hexahedron), 3 -> Quadrilateral4 (linear quadrilateral), 1 -> Line2 (linear line) and 15.

How do I create a cylinder by using the gmsh element types which the error is indicating me to use?

What all I have tried so far?

• tried to make the cylinders using a .geo file – same error
• tried to make the cylinders using gmsh Python API – same error

I am quite the beginner in 3D modelling and all these softwares so I might be understanding something quite fundamental incorrectly. Please point me in the right direction.