[petsc-users] DMPlexComputeCellGeometryFVM: "Cannot handle faces with 1 vertices"

[Matthew Knepley]

On Tue, Mar 12, 2019 at 11:20 AM <finnkochinski at keemail.me> wrote:

> I think I found a hint in src/dm/impls/plex/examples/tests/ex5.c to get my
> code corrected.
>
> Apparently the contiguous numbering is
> NOT: cells, vertices, edges, faces (as you said),
> BUT: cells, vertices, faces, edges.
>

There is an easy way to check. We can output the whole DAG for a single
cell using the ASCII viewer:

cd $PETSC_DIR/src/dm/impls/plex/examples/tests
make ex1
./ex1 -dim 3 -cell_simplex 0 -domain_box_sizes 1,1,1 -interpolate -dm_view
::ascii_info_detail

and yes, faces are numbered before edges. Sorry about the flip.


> Then in numPoints, you don't put depth 0..3 or depth 3..0,
> BUT: #vertices, #faces, #edges, #cells.
>

Actually the order in numPoints does not matter beyond having vertices
first, so the documentation is correct:


https://bitbucket.org/petsc/petsc/src/e551bc0b4a184f2209a31a59ea3fbdc3edbf3863/src/dm/impls/plex/plexcreate.c#lines-3066


> This seems completely random, but works in the attached example.
> Maybe you should finally take the time to document this mess if even the
> developers no longer understand it.
>

There is a chapter in the manual and many manpages.

  Thanks,

     Matt


> regards
> Chris
>
> Mar 12, 2019, 1:38 PM by knepley at gmail.com:
>
> On Tue, Mar 12, 2019 at 9:25 AM <finnkochinski at keemail.me> wrote:
>
> Thank you,
> I added DMPlexInterpolate(). Now I get a different error in
> DMPlexInterpolate():
> ...
>
>
> Okay, you did not need interpolate. You already specified all the levels.
> However, your orientations are wrong.
> Get rid of that code.
>
>
>
> [0]PETSC ERROR: Dimension 0 not supported
> ...
>
> The source code and full output are attached. Anybody able to fix this?
>
>
> The problem is a numbering convention in the library. Plex will accept any
> consistent DAG. However, if you
> want to use other things in the library, like geometry routines, then
> there is a convention on numbering (which
> makes many things simpler). We require that you number contiguously:
>
>   Cells:      [0, Nc)
>   Vertices: [Nc, Nc+Nv)
>   Edges:    [Nc+Nv, Nc+Nv+Ne)
>   Faces:    [Nc+Nv+Ne, Nc+Nv+Ne+Nf)
>
> You numbered the faces in the vertices slot,  so the geometry routines got
> confused.
>
>   Thanks,
>
>     Matt
>
>
>
> regards
> Chris
>
> --
> Securely sent with Tutanota. Get your own encrypted, ad-free mailbox:
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>
>
> Mar 12, 2019, 1:08 PM by knepley at gmail.com:
>
> On Tue, Mar 12, 2019 at 9:03 AM Chris Finn via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
> Hello,
> with the code below, I create a tetrahedron using DMPlexCreateFromDAG,
> then I try to run DMPlexComputeCellGeometryFVM on this cell. The latter
> call fails with output:
>
>
> All the geometry stuff requires that you interpolate the mesh I think,
> Just use DMPlexInterpolate().
>
>   Thanks,
>
>     Matt
>
>
>
> ...
> [0]PETSC ERROR: --------------------- Error Message -----------------
> [0]PETSC ERROR: Argument out of range
> [0]PETSC ERROR: Cannot handle faces with 1 vertices
> ...
> (full output is attached).
>
> What am I doing wrong?
> regards
> Chris
>
> Here is the code:
> static char help[] = "No help \n";
>
> #include <petscdmplex.h>
>
> #undef __FUNCT__
> #define __FUNCT__ "main"
> int main(int argc,char **args)
> {
>   PetscErrorCode ierr;
>   PetscInitialize(&argc,&args,(char*)0,help);
>
>   DM                dm;
>   int cStart,cEnd;
>   int fStart,fEnd;
>
>   int depth = 3;
>   int dim = 3;
>
>   PetscInt    numPoints[4]        = {1,4,6,4};
>   PetscInt    coneSize[15]         = {4,3,3,3,3,2,2,2,2,2,2,0,0,0,0};
>   PetscInt    cones[28]            = {1,2,3,4, 5,9,8, 9,6,10, 10,8,7,
> 5,6,7, 11,12, 12,13, 13,11, 11,14, 12,14, 13,14};
>   PetscInt    coneOrientations[28] = {0 };
>   PetscScalar vertexCoords[12]     = {0,0,0, 1,0,0, 0,1,0, 0,0,1};
>
>   DMCreate(PETSC_COMM_WORLD, &dm);
>   DMSetType(dm, DMPLEX);
>   DMSetDimension(dm,dim);
>   DMPlexCreateFromDAG(dm, depth, numPoints, coneSize, cones,
> coneOrientations, vertexCoords);
>
>   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
>   DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);
>
>   for (int k =cStart;k<cEnd;k++){
>     double vol;
>     double centroid[3];
>     double normal[3];
>     ierr = DMPlexComputeCellGeometryFVM(dm, k, &vol,
> centroid,NULL);CHKERRQ(ierr);
>     printf("FVM: V=%f c=(%f %f %f) n=(%f %f
> %f)\n",vol,centroid[0],centroid[1],centroid[2],
>       normal[0],normal[1],normal[2]);
>   }
>   ierr = PetscFinalize();
>   return 0;
> }
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
>
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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