Allow specifying dimension in Mesh.mesh_geometry

[paulromano]

This small change allows the dimension to be specified when meshing a geometry.

[akoen]

Looks good. If the codebase is to be refactored to allow other export formats other than MOAB, I would maybe find a way to refactor out some of the MOAB-specific logic, like this.
https://github.com/Thea-Energy/stellarmesh/blob/026acbef2b23f6e936ceb7ffea9c543432dba5a0/src/stellarmesh/mesh.py#L114

I would also double check that this logic still holds (normals aren't changed) when we mesh up to 3d.
https://github.com/Thea-Energy/stellarmesh/blob/28a27175ce17213a1825abb0de584a5a56688fbc/src/stellarmesh/moab.py#L234

Finally, I would clarify/assert that mesh refinement will discard all volume mesh data
https://github.com/Thea-Energy/stellarmesh/blob/28a27175ce17213a1825abb0de584a5a56688fbc/src/stellarmesh/mesh.py#L192

These are all minor points, otherwise this small change should be good.

[paulromano]

If the codebase is to be refactored to allow other export formats other than MOAB, I would maybe find a way to refactor out some of the MOAB-specific logic

Yes, I'm planning on continuing down this path. Specifically, in moab.py we need better separation between things that are MOAB-specific and things that are DAGMC-specific. This will be in a future PR.

I would also double check that this logic still holds (normals aren't changed) when we mesh up to 3d

I wasn't sure exactly how to check this -- appreciate any pointers you have in that regard. However, from what I can tell, when you ask gmsh to generate a mesh up to dim=3, it starts with the lower dimensions which proceed exactly the same as if you had requested dim=2.

I would clarify/assert that mesh refinement will discard all volume mesh data

In fact, we're actually discarding volume mesh data as soon as MOABModel.make_from_mesh is called. I added a warning in there to at least note in the log that volume data was discarded.

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Let me know if you think this is good to go!

[akoen]

If the codebase is to be refactored to allow other export formats other than MOAB, I would maybe find a way to refactor out some of the MOAB-specific logic

Yes, I'm planning on continuing down this path. Specifically, in moab.py we need better separation between things that are MOAB-specific and things that are DAGMC-specific. This will be in a future PR.

Great!

I would also double check that this logic still holds (normals aren't changed) when we mesh up to 3d

I wasn't sure exactly how to check this -- appreciate any pointers you have in that regard. However, from what I can tell, when you ask gmsh to generate a mesh up to dim=3, it starts with the lower dimensions which proceed exactly the same as if you had requested dim=2.

Yes, meshing up to dim=3 also meshes up to dim=2. I don't have any specific concerns about the codebase, but there could possibly be bugs for example in the way that physical groups are used. I don't think anything in this PR needs to be changed, but integration tests would be great to see in the future.

I would clarify/assert that mesh refinement will discard all volume mesh data

In fact, we're actually discarding volume mesh data as soon as MOABModel.make_from_mesh is called. I added a warning in there to at least note in the log that volume data was discarded.

Sound good!

You're welcome to merge the PR you like