[Gmsh] Doubt about meshing closed STL shell

[MA Ariza-Gracia]

Dear Dr Geuzaine, Dr Remacle, and the Gmsh community,

first of all, thank you for sharing the software with us! I'm a postdoc 
working (mostly) in optics and I need to reconstruct some free-shape 
surfaces.

My final goal is to create a volume mesh enclosed by two discrete STL 
surfaces (given by a point cloud). The pipeline to do so is as follows:

1) Read point clouds and triangulate using Delaunay (scipy.spatial)

2) Create a 2 discrete surfaces giving the node coordinates and the 
connectivity of the triangles

3) Create a volume using a surface loop on both surfaces

4) Mesh the volume

5) Exporting the mesh to Abaqus/LS-Dyna (whatever software)


After reading the manual, tutorials and mailing list, the only 
approached that worked was the next one: having a single closed shell 
joining 'manually' the nodes in the boundary. I say manually because I 
needed to implement the substitution of the nodes myself and I couldn't 
do it using Gmsh using removeDuplicate and so on (i.e., I didn't know 
how to do it). After having a single closed shell without duplicate 
nodes and with the normals pointing outwards, I manage to mesh the 
volume inside the models (see manually-merged-thick.msh and 
manually-merged-thin.msh).


However, as this is my first approach to Gmsh, this is not efficient and 
I would like to know if:

1) *There is a more efficient procedure to, given two different STLs, 
mesh the volume enclosed by the two of them* (as I said, I tried may 
approaches including the ones regarding Earth topology reconstruction in 
the mail list, but I couldn't find a proper solution).

2) *There is a way of both remeshing the STLs AND meshing the volume at 
the same time*. In one of the approaches, I parameterized the discrete 
STL surfaces with /classifySurfaces/ and /createGeometry/ (see the 
Jupyter notebook, three first attempts). This allowed me to re-mesh the 
STL surfaces but, unfortunately, I could not mesh the volume after 
(complaining about 0 elements in the volume). As my Delaunay 
triangulation is quite ugly, this would be my preferred option if you 
could give me a hint on how to proceed.

3) In the end, I will have two surfaces: one main surface with one 
inclusion inside itself. From what I've read, I know I cannot do Boolean 
operations (as I'm using meshes and discrete elements), so I would 
appreciate any hint on how to proceed in this regard.


_Files enclosed in compressed folder 'inquiry-gmsh.zip':_

  * try-inquiry.ipynb: Jupyter notebook with the API code to create the
    surfaces
  * {anterior-lenticle-surface.txt, posterior-lenticle-surface.txt}:
    files containing the Cartesian point cloud
  * After running the code, it will generate:
      o thin-1.stl, thin-2.stl: surfaces used to generate the
        convex-convex thin lens
      o surface-1.stl, surface-2.stl: surfaces used to generate the
        concave-convex thick lens
      o shell-thin-lens.msh: attempt to mesh the volume of the thin mesh
        using: i) Two different STL surfaces (gmsh.merge); ii) remove
        duplicate coincident nodes (gmsh.removeDuplicateNodes); and iii)
        re-parameterizing
      o shell-concave2convex.msh: attempt to do the same as the previous
        one but with the thick lens (-> discard problems with sharp
        edges in the periphery)
      o merged-shell-concave2convex.msh: attempt to mesh the volume of
        the thick lens using: i) One single STL surface with duplicated
        nodes in the boundary; ii) Remove duplicated nodes using
        removeDuplicateNodes; iii) and classify surfaces + creating geometry
      o manually-merged-thick.msh and manually-merged-thin.msh: success
        BUT: i) I needed to remove myself the duplicated nodes; ii) If I
        try to parameterize the surface, I cannot mesh the volume inside
        but only the surfaces.


_Versions used:_

  - Ubuntu 18.04

- Gmsh 4.4.1 through the implementation in conda-forge

- Python 3.7 with Anaconda


Best regards,


MA

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