[petsc-users] orientation of DMPLEX for tetrehedral meshes

[Matteo Semplice]

Thanks!

     is there a document explaining the DMPLex internal ordering?

(and by the way what's the reason to have the factors 0.5 in the 
jacobians? I would not expect them if the reference tet is (0,0,0), 
(1,0,0), etc

if (J) {
           for (d = 0; d < dim; d++) {
             /* I orient with outward face normals */
             J[d * dim + 0] =*0.5* * (PetscRealPart(coords[2 * dim + d]) -
     PetscRealPart(coords[0 * dim + d]));
             J[d * dim + 1] =*0.5* * (PetscRealPart(coords[1 * dim + d]) -
     PetscRealPart(coords[0 * dim + d]));
             J[d * dim + 2] =*0.5* * (PetscRealPart(coords[3 * dim + d]) -
     PetscRealPart(coords[0 * dim + d]));
           }
     }

Thanks

     Matteo

Il 02/07/26 17:22, Jed Brown ha scritto:
> DMPlex internal ordering is not the same as VTK ordering. The code you supply will have an inward-facing normal (as evaluated by DMPlex geometry routines). The IO routines translate to the internal ordering convention. If you are creating a mesh manually or writing a new file reader, you should use (or convert to) the DMPlex convention.
>
> Matteo Semplice via petsc-users<petsc-users at mcs.anl.gov> writes:
>
>> Dear PETSc,
>>
>>       I am a bit puzzled by the 3d tet mesh representations as DMPlex. I
>> boiled it down to a mesh of a single tet. More specifically,
>>
>>    * if a I create the mesh as
>>
>>             const PetscInt dim=3;
>>             const PetscInt numCells=1; // The number of cells, only on
>>          process 0
>>             const PetscInt numVertices=4; // The number of vertices owned
>>          by this process, or PETSC_DECIDE, only on process 0
>>             const PetscInt numCorners=4; // The number of vertices for
>>          each cell, only on process 0
>>             const PetscBool interpolate=PETSC_TRUE; // should
>>          intermediate mesh entities (faces, edges) be created?
>>             // An array of numCells×numCornersnumCells×numCorners
>>          numbers, the vertices for each cell, only on process 0
>>             const PetscInt cells[] = {0,1,2,3 };
>>             const PetscInt spaceDim=3; // The spatial dimension used for
>>          coordinates
>>             // An array of numVertices×spaceDimnumVertices×spaceDim
>>          numbers, the coordinates of each vertex, only on process 0
>>             const PetscReal vertexCoords[] = { 0,0,0,
>>                                                1,0,0,
>>                                                0,1,0,
>>                                                0,0,1 };
>>             PetscCall( DMPlexCreateFromCellListPetsc(MPI_COMM_WORLD, dim,
>>                        numCells, numVertices, numCorners, interpolate, cells,
>>                        spaceDim, vertexCoords, dmMesh) );
>>
>>      I get the representation that I would expect:
>>
>>      DM Object: Mesh 1 MPI process
>>        type: plex
>>      Mesh in 3 dimensions:
>>        Number of 0-cells per rank: 4
>>        Number of 1-cells per rank: 6
>>        Number of 2-cells per rank: 4
>>        Number of 3-cells per rank: 1
>>      Labels:
>>        celltype: 4 strata with value/size (0 (4), 1 (6), 3 (4), 6 (1))
>>        depth: 4 strata with value/size (0 (4), 1 (6), 2 (4), 3 (1))
>>      Mesh with 1 cells
>>
>>      with DMPlexGetCellCoordinates giving me the coordinates
>>
>>      CELL 0 with vertices at
>>      ( 0.000,     0, 0.000 )
>>      ( 1.000,     0, 0.000 )
>>      ( 0.000,     1, 0.000 )
>>      ( 0.000,     0, 1.000 )
>>
>>    * on the other hand, if I load the MSH file
>>
>>          $MeshFormat
>>          2.2 0 8
>>          $EndMeshFormat
>>          $Nodes
>>          4
>>          1 0.0 0.0 0.0
>>          2 1.0 0.0 0.0
>>          3 0.0 1.0 0.0
>>          4 0.0 0.0 1.0
>>          $EndNodes
>>          $Elements
>>          1
>>          1 4 2 0 1 1 2 3 4
>>          $EndElements
>>
>>      with DMPlexCreateGmshFromFile, the first and second vertices are
>>      swapped and I get
>>
>>      DM Object: Mesh 1 MPI process
>>        type: plex
>>      Mesh in 3 dimensions:
>>        Number of 0-cells per rank: 4
>>        Number of 1-cells per rank: 6
>>        Number of 2-cells per rank: 4
>>        Number of 3-cells per rank: 1
>>      Labels:
>>        celltype: 4 strata with value/size (0 (4), 1 (6), 3 (4), 6 (1))
>>        depth: 4 strata with value/size (0 (4), 1 (6), 2 (4), 3 (1))
>>        Cell Sets: 1 strata with value/size (0 (1))
>>      Mesh with 1 cells
>>
>>      with DMPlexGetCellCoordinates giving me
>>
>>      CELL 0 with vertices at
>>      ( 1.000,     0, 0.000 )
>>      ( 0.000,     0, 0.000 )
>>      ( 0.000,     1, 0.000 )
>>      ( 0.000,     0, 1.000 )
>>
>> I understand that this behaviour is somehow consistent with the formulas
>> in DMPlexComputeTetrahedronGeometry_Internal, where you compute the
>> Jacobians swappnig the order of vertices (and with 0.5 factors that I do
>> not understand at all... it looks as if your reference element was not
>> the unit simplex)
>>
>>      if (J) {
>>            for (d = 0; d < dim; d++) {
>>              /* I orient with outward face normals */
>>              J[d * dim + 0] = 0.5 * (PetscRealPart(coords[2 * dim + d]) -
>>      PetscRealPart(coords[0 * dim + d]));
>>              J[d * dim + 1] = 0.5 * (PetscRealPart(coords[1 * dim + d]) -
>>      PetscRealPart(coords[0 * dim + d]));
>>              J[d * dim + 2] = 0.5 * (PetscRealPart(coords[3 * dim + d]) -
>>      PetscRealPart(coords[0 * dim + d]));
>>            }
>>      }
>>
>> but still I am worried by this fact that different ways of creating a
>> mesh gives a DMPlex with different orientations.
>>
>> Can you explain the rationale behind this or refer me to some
>> documentation?
>>
>> Best
>>
>>       Matteo
>>
>> -- 
>> Prof. Matteo Semplice
>> Università degli Studi dell’Insubria
>> Dipartimento di Scienza e Alta Tecnologia – DiSAT
>> Professore Associato
>> Via Valleggio, 11 – 22100 Como (CO) – Italia
>> tel.: +39 031 2386316

-- 
Prof. Matteo Semplice
Università degli Studi dell’Insubria
Dipartimento di Scienza e Alta Tecnologia – DiSAT
Professore Associato
Via Valleggio, 11 – 22100 Como (CO) – Italia
tel.: +39 031 2386316
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