[MOAB-dev] MOAB finding shells bounding closed regions in nonmanifold mesh

[Steve Hughey]

Hi Vijay,

Thank you for your detailed response. I looked into the discrete geometry
module and, while it is interesting, I unfortunately do not think it will
satisfy my needs. My meshes have sharp features and already largely use
quadratic elements for the smooth portions. I will keep it in mind for
future potential uses though!

I have thought some more about my problem and think I am closing in on a
solution that I hope MOAB can help with. I think the next step requires
defining or verifying the orientation of my surfaces in the usual way
(right-hand rule with surface always to the left of its boundary) to help
constrain a DFS of my surface-curve adjacency map. I'd like to update the
connectivity of each face to get a consistent normal over each surface and
to store a single sense for the entire surface rather than one for each
face. Is there an idiomatic way to deal with this in MOAB? Some of the
logic in GeomTopoTool::geometrize_surface_sets() looks relevant; perhaps I
just need to mimic that.

Also, given that I am trying to reconstruct geometry from the mesh, is
there an advantage to using MOAB's geometry set functionality? Because that
feature seems fairly closely associated with the now-defunct CGM project, I
have written my own containers to store relationships between the geometric
entities. I am always happier, of course, to take advantage of someone else
having already thought through my problem and written code.

Thanks,
Steve

On Wed, Jan 22, 2025 at 2:14 PM Vijay S. Mahadevan <vijay.m at gmail.com>
wrote:

> Dear Steve,
>
> > > However, I am now faced with the problem of finding closed regions. I
> have
> > > some ideas on how to do this based on concepts from half-facet data
> > > structures, but the MOAB classes FBEngine and GeomTopoTool caught my
> > > attention. I have tried reading the interface specification for these
> and
> > > have been unable to determine whether they could be useful for my
> closed
> > > regions problem. I have seen many allusions in the code to geometry and
> > > topology representation, but I haven’t been able to connect the dots.
> My
> > > hope is that someone has already thought through this problem and
> > > implemented a solution. I would appreciate any insight you can
> provide, and
> > > in the meantime I will continue testing things.
>
> You are correct in the assumption that some effort in MOAB exists
> along the lines of what you need. For example, FBiGeom is a
> Facet-based geometry interface that could be used to reconstruct a
> higher-order geometry representation from a bounded tesselation that
> can queried directly to compute normals and enclosed/connected
> regions. However, since we deprecated and removed support for ITAPS,
> none of this code is reusable.
>
> We also have an implementation of a WALF-based higher-order surface
> reconstruction method [1] that can generate feature-aware discrete
> geometry. This scheme can also be useful for constructing an enclosing
> boundary for a given mesh. However, I don't know how useful this might
> be for your case as there may be restrictions wrt
> regularity/smoothness of the boundary mesh that is being used to
> reconstruct the high-order surface.
>
> > I am hoping to take advantage of any extant machinery in MOAB for
> > addressing these problems. I have looked briefly at the CGM library, but
> > since it's no longer under development, I hesitate to adopt it.
>
> CGM would be appropriate if you had solid geometry that matched your
> mesh. However, due to funding and other constraints, we recently
> deprecated CGM and would not recommend it for what you need. We do not
> have the manpower to provide support or maintenance.
>
> My current suggestion would be to look at the DiscreteGeometry module
> [2] and reconstruction scheme [1] to see if they are useful. If not,
> we may have to custom write a boundary reconstruction scheme that
> satisfies your needs.
>
> Best,
> Vijay
>
> [1]
> https://web.cels.anl.gov/projects/sigma/docs/moab/HiReconstruction_8hpp.html
> [2]
> https://web.cels.anl.gov/projects/sigma/docs/moab/classmoab_1_1DGMSolver.html
>
> On Wed, Jan 22, 2025 at 1:16 PM Steve Hughey <hugheyst at gmail.com> wrote:
> >
> > Hi Paul,
> >
> > Thank you for your response and suggestions!
> >
> > In the terminology of the slides you sent, I am looking for a way to
> > construct from a raw mesh file the geometric Volumes, Surfaces, Curves,
> and
> > Nodes that make up the meshed geometry, similar to how CUBIT creates
> > mesh-based geometry from importing a mesh file. I've written a program
> that
> > uses the Skinner heavily to break the mesh down into connected meshed
> > Volumes, Surfaces, Curves, and Nodes; it also finds all of the
> > upward/downward adjacencies between these. If something equivalent to
> this
> > exists in MOAB, I am very interested to hear about it.
> >
> > Regardless, the next step I need to take is to find the empty Volumes
> > bounded by any subset of Surfaces in my geometry. These are important in
> > boundary-element codes because materially homogeneous regions of space
> are
> > represented by their boundaries only. Boundary-element meshes can contain
> > many of these unmeshed volumes and non-manifold curves where different
> > materials abut each other.
> >
> > I am hoping to take advantage of any extant machinery in MOAB for
> > addressing these problems. I have looked briefly at the CGM library, but
> > since it's no longer under development, I hesitate to adopt it.
> >
> > Thank you,
> >
> > Steve
> >
> > On Wed, Jan 22, 2025 at 11:24 AM Paul Wilson <paul.wilson at wisc.edu>
> wrote:
> >
> > > Hi Steve,
> > >
> > >
> > >
> > > The GeomTopoTool assumes that a mesh-based geometry follows the data
> model
> > > conventions described in slides 1-6 of this summary
> > > <
> https://urldefense.us/v3/__https://docs.google.com/presentation/d/10m8e6GN8DhLpNHHSOMniZ2pDU9DOAiD0xJF1Zyewzh8/edit*slide=id.g3b5f37914c_0_117__;Iw!!G_uCfscf7eWS!c1oZJ1JijGmIvdML0MotOwV3GWtr5fqBfxhmWMcy7yqyb53gbIG2AVFmXedMUDxrYu9Dm4Lak8QfebIWOqA9$
> >,
> > > and assumes that the relationships defined there are embedded when the
> > > mesh-based geometry is created.
> > >
> > >
> > >
> > > I’m not sure I fully understand your question/use case, but you may
> also
> > > be interested in the MOAB skinner
> > > <
> https://ftp.mcs.anl.gov/pub/fathom/moab-docs/classmoab_1_1Skinner.html>
> > > that is designed to identify boundary elements.
> > >
> > >
> > >
> > > I hope this is somewhat helpful,
> > >
> > > Paul
> > >
> > >
> > >
> > > --
> > > -- ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ --
> > > Paul P.H. Wilson (he/him/his)
> > > Grainger Professor of Nuclear Engineering
> > > Chair, Department of Nuclear Engineering & Engineering Physics
> > > o: 608-263-0807, c: 608-469-9615
> > > paul.wilson at wisc.edu
> > > 153 Engineering Research Bldg
> > > 1500 Engineering Dr, Madison, WI 53706
> > > Zoom Meeting Room:
> https://urldefense.us/v3/__https://uwmadison.zoom.us/j/6082630807__;!!G_uCfscf7eWS!c1oZJ1JijGmIvdML0MotOwV3GWtr5fqBfxhmWMcy7yqyb53gbIG2AVFmXedMUDxrYu9Dm4Lak8QfefhqeGPH$
> > > Zoom Phone Access: +1-929-205-6099, Access code: 6082630807
> > >
> > > Computational Nuclear Engineering Research Group
> > > <
> https://urldefense.us/v3/__http://cnerg.engr.wisc.edu__;!!G_uCfscf7eWS!c1oZJ1JijGmIvdML0MotOwV3GWtr5fqBfxhmWMcy7yqyb53gbIG2AVFmXedMUDxrYu9Dm4Lak8QfeRLDrXMw$
> >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > *From: *moab-dev <moab-dev-bounces at mcs.anl.gov> on behalf of Steve
> Hughey
> > > <hugheyst at gmail.com>
> > > *Date: *Wednesday, January 22, 2025 at 05:12
> > > *To: *moab-dev at mcs.anl.gov <moab-dev at mcs.anl.gov>
> > > *Subject: *[MOAB-dev] MOAB finding shells bounding closed regions in
> > > nonmanifold mesh
> > >
> > > Hello,
> > >
> > > I am using MOAB as the basis for a sort of mesh-based geometry model
> in a
> > > finite element/boundary element code. I must assume that the mesh
> > > connectivity and Exodus block specifications are the only information I
> > > have about the geometry. I have been able to use MOAB’s various
> adjacency
> > > queries to break the input mesh into connected components with
> adjacencies
> > > between them, largely along the lines of CUBIT’s mesh-based geometry
> > > engine. The meshes are pretty general, containing quads, tris, hexes,
> tets,
> > > prisms, and pyramids, and typically contain nonmanifold edges.
> > >
> > > However, I am now faced with the problem of finding closed regions. I
> have
> > > some ideas on how to do this based on concepts from half-facet data
> > > structures, but the MOAB classes FBEngine and GeomTopoTool caught my
> > > attention. I have tried reading the interface specification for these
> and
> > > have been unable to determine whether they could be useful for my
> closed
> > > regions problem. I have seen many allusions in the code to geometry and
> > > topology representation, but I haven’t been able to connect the dots.
> My
> > > hope is that someone has already thought through this problem and
> > > implemented a solution. I would appreciate any insight you can
> provide, and
> > > in the meantime I will continue testing things.
> > >
> > > Thanks,
> > > Steve
> > >
>