#include <petsc/private/dmpleximpl.h> /*I      "petscdmplex.h"   I*/

#ifdef PETSC_HAVE_EGADS
  #include <egads.h>
/* Need to make EGADSLite header compatible */
extern "C" int EGlite_getTopology(const ego, ego *, int *, int *, double *, int *, ego **, int **);
extern "C" int EGlite_inTopology(const ego, const double *);
#endif

#if defined(PETSC_HAVE_TETGEN_TETLIBRARY_NEEDED)
  #define TETLIBRARY
#endif
#if defined(__clang__)
  #pragma clang diagnostic push
  #pragma clang diagnostic ignored "-Wunused-parameter"
  #pragma clang diagnostic ignored "-Wzero-as-null-pointer-constant"
#elif defined(__GNUC__) || defined(__GNUG__)
  #pragma GCC diagnostic push
  #pragma GCC diagnostic ignored "-Wunused-parameter"
#endif
#include <tetgen.h>
#if defined(__clang__)
  #pragma clang diagnostic pop
#elif defined(__GNUC__) || defined(__GNUG__)
  #pragma GCC diagnostic pop
#endif

/* This is to fix the tetrahedron orientation from TetGen */
static PetscErrorCode DMPlexInvertCells_Tetgen(PetscInt numCells, PetscInt numCorners, PetscInt cells[])
{
  PetscInt bound = numCells * numCorners, coff;

  PetscFunctionBegin;
#define SWAP(a, b) \
  do { \
    PetscInt tmp = (a); \
    (a)          = (b); \
    (b)          = tmp; \
  } while (0)
  for (coff = 0; coff < bound; coff += numCorners) SWAP(cells[coff], cells[coff + 1]);
#undef SWAP
  PetscFunctionReturn(PETSC_SUCCESS);
}

PETSC_EXTERN PetscErrorCode DMPlexGenerate_Tetgen(DM boundary, PetscBool interpolate, DM *dm)
{
  MPI_Comm               comm;
  const PetscInt         dim = 3;
  ::tetgenio             in;
  ::tetgenio             out;
  PetscContainer         modelObj;
  DMUniversalLabel       universal;
  PetscInt               vStart, vEnd, v, eStart, eEnd, e, fStart, fEnd, f, defVal;
  DMPlexInterpolatedFlag isInterpolated;
  PetscMPIInt            rank;

  PetscFunctionBegin;
  PetscCall(PetscObjectGetComm((PetscObject)boundary, &comm));
  PetscCallMPI(MPI_Comm_rank(comm, &rank));
  PetscCall(DMPlexIsInterpolatedCollective(boundary, &isInterpolated));
  PetscCall(DMUniversalLabelCreate(boundary, &universal));
  PetscCall(DMLabelGetDefaultValue(universal->label, &defVal));

  PetscCall(DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd));
  in.numberofpoints = vEnd - vStart;
  if (in.numberofpoints > 0) {
    PetscSection       coordSection;
    Vec                coordinates;
    const PetscScalar *array;

    in.pointlist       = new double[in.numberofpoints * dim];
    in.pointmarkerlist = new int[in.numberofpoints];

    PetscCall(PetscArrayzero(in.pointmarkerlist, (size_t)in.numberofpoints));
    PetscCall(DMGetCoordinatesLocal(boundary, &coordinates));
    PetscCall(DMGetCoordinateSection(boundary, &coordSection));
    PetscCall(VecGetArrayRead(coordinates, &array));
    for (v = vStart; v < vEnd; ++v) {
      const PetscInt idx = v - vStart;
      PetscInt       off, d, val;

      PetscCall(PetscSectionGetOffset(coordSection, v, &off));
      for (d = 0; d < dim; ++d) in.pointlist[idx * dim + d] = PetscRealPart(array[off + d]);
      PetscCall(DMLabelGetValue(universal->label, v, &val));
      if (val != defVal) in.pointmarkerlist[idx] = (int)val;
    }
    PetscCall(VecRestoreArrayRead(coordinates, &array));
  }

  PetscCall(DMPlexGetHeightStratum(boundary, 1, &eStart, &eEnd));
  in.numberofedges = eEnd - eStart;
  if (isInterpolated == DMPLEX_INTERPOLATED_FULL && in.numberofedges > 0) {
    in.edgelist       = new int[in.numberofedges * 2];
    in.edgemarkerlist = new int[in.numberofedges];
    for (e = eStart; e < eEnd; ++e) {
      const PetscInt  idx = e - eStart;
      const PetscInt *cone;
      PetscInt        coneSize, val;

      PetscCall(DMPlexGetConeSize(boundary, e, &coneSize));
      PetscCall(DMPlexGetCone(boundary, e, &cone));
      in.edgelist[idx * 2]     = cone[0] - vStart;
      in.edgelist[idx * 2 + 1] = cone[1] - vStart;

      PetscCall(DMLabelGetValue(universal->label, e, &val));
      if (val != defVal) in.edgemarkerlist[idx] = (int)val;
    }
  }

  PetscCall(DMPlexGetHeightStratum(boundary, 0, &fStart, &fEnd));
  in.numberoffacets = fEnd - fStart;
  if (in.numberoffacets > 0) {
    in.facetlist       = new tetgenio::facet[in.numberoffacets];
    in.facetmarkerlist = new int[in.numberoffacets];
    for (f = fStart; f < fEnd; ++f) {
      const PetscInt idx    = f - fStart;
      PetscInt      *points = nullptr, numPoints, p, numVertices = 0, v, val = -1;

      in.facetlist[idx].numberofpolygons = 1;
      in.facetlist[idx].polygonlist      = new tetgenio::polygon[in.facetlist[idx].numberofpolygons];
      in.facetlist[idx].numberofholes    = 0;
      in.facetlist[idx].holelist         = nullptr;

      PetscCall(DMPlexGetTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points));
      for (p = 0; p < numPoints * 2; p += 2) {
        const PetscInt point = points[p];
        if ((point >= vStart) && (point < vEnd)) points[numVertices++] = point;
      }

      tetgenio::polygon *poly = in.facetlist[idx].polygonlist;
      poly->numberofvertices  = numVertices;
      poly->vertexlist        = new int[poly->numberofvertices];
      for (v = 0; v < numVertices; ++v) {
        const PetscInt vIdx = points[v] - vStart;
        poly->vertexlist[v] = vIdx;
      }
      PetscCall(DMLabelGetValue(universal->label, f, &val));
      if (val != defVal) in.facetmarkerlist[idx] = (int)val;
      PetscCall(DMPlexRestoreTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points));
    }
  }
  if (rank == 0) {
    DM_Plex *mesh = (DM_Plex *)boundary->data;
    char     args[32];

    /* Take away 'Q' for verbose output */
#ifdef PETSC_HAVE_EGADS
    PetscCall(PetscStrncpy(args, "pqezQY", sizeof(args)));
#else
    PetscCall(PetscStrncpy(args, "pqezQ", sizeof(args)));
#endif
    if (mesh->tetgenOpts) {
      ::tetrahedralize(mesh->tetgenOpts, &in, &out);
    } else {
      ::tetrahedralize(args, &in, &out);
    }
  }
  {
    const PetscInt numCorners  = 4;
    const PetscInt numCells    = out.numberoftetrahedra;
    const PetscInt numVertices = out.numberofpoints;
    PetscReal     *meshCoords  = nullptr;
    PetscInt      *cells       = nullptr;

    if (sizeof(PetscReal) == sizeof(out.pointlist[0])) {
      meshCoords = (PetscReal *)out.pointlist;
    } else {
      PetscInt i;

      meshCoords = new PetscReal[dim * numVertices];
      for (i = 0; i < dim * numVertices; ++i) meshCoords[i] = (PetscReal)out.pointlist[i];
    }
    if (sizeof(PetscInt) == sizeof(out.tetrahedronlist[0])) {
      cells = (PetscInt *)out.tetrahedronlist;
    } else {
      PetscInt i;

      cells = new PetscInt[numCells * numCorners];
      for (i = 0; i < numCells * numCorners; i++) cells[i] = (PetscInt)out.tetrahedronlist[i];
    }

    PetscCall(DMPlexInvertCells_Tetgen(numCells, numCorners, cells));
    PetscCall(DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dm));

    /* Set labels */
    PetscCall(DMUniversalLabelCreateLabels(universal, PETSC_TRUE, *dm));
    for (v = 0; v < numVertices; ++v) {
      if (out.pointmarkerlist[v]) PetscCall(DMUniversalLabelSetLabelValue(universal, *dm, PETSC_TRUE, v + numCells, out.pointmarkerlist[v]));
    }
    if (interpolate) {
      PetscInt e;

      for (e = 0; e < out.numberofedges; e++) {
        if (out.edgemarkerlist[e]) {
          const PetscInt  vertices[2] = {out.edgelist[e * 2 + 0] + numCells, out.edgelist[e * 2 + 1] + numCells};
          const PetscInt *edges;
          PetscInt        numEdges;

          PetscCall(DMPlexGetJoin(*dm, 2, vertices, &numEdges, &edges));
          PetscCheck(numEdges == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %" PetscInt_FMT, numEdges);
          PetscCall(DMUniversalLabelSetLabelValue(universal, *dm, PETSC_TRUE, edges[0], out.edgemarkerlist[e]));
          PetscCall(DMPlexRestoreJoin(*dm, 2, vertices, &numEdges, &edges));
        }
      }
      for (f = 0; f < out.numberoftrifaces; f++) {
        if (out.trifacemarkerlist[f]) {
          const PetscInt  vertices[3] = {out.trifacelist[f * 3 + 0] + numCells, out.trifacelist[f * 3 + 1] + numCells, out.trifacelist[f * 3 + 2] + numCells};
          const PetscInt *faces;
          PetscInt        numFaces;

          PetscCall(DMPlexGetFullJoin(*dm, 3, vertices, &numFaces, &faces));
          PetscCheck(numFaces == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %" PetscInt_FMT, numFaces);
          PetscCall(DMUniversalLabelSetLabelValue(universal, *dm, PETSC_TRUE, faces[0], out.trifacemarkerlist[f]));
          PetscCall(DMPlexRestoreJoin(*dm, 3, vertices, &numFaces, &faces));
        }
      }
    }

    PetscCall(PetscObjectQuery((PetscObject)boundary, "EGADS Model", (PetscObject *)&modelObj));
    if (modelObj) {
#ifdef PETSC_HAVE_EGADS
      DMLabel   bodyLabel;
      PetscInt  cStart, cEnd, c, eStart, eEnd, fStart, fEnd;
      PetscBool islite = PETSC_FALSE;
      ego      *bodies;
      ego       model, geom;
      int       Nb, oclass, mtype, *senses;

      /* Get Attached EGADS Model from Original DMPlex */
      PetscCall(PetscObjectQuery((PetscObject)boundary, "EGADS Model", (PetscObject *)&modelObj));
      if (modelObj) {
        PetscCall(PetscContainerGetPointer(modelObj, (void **)&model));
        PetscCall(EG_getTopology(model, &geom, &oclass, &mtype, nullptr, &Nb, &bodies, &senses));
        /* Transfer EGADS Model to Volumetric Mesh */
        PetscCall(PetscObjectCompose((PetscObject)*dm, "EGADS Model", (PetscObject)modelObj));
      } else {
        PetscCall(PetscObjectQuery((PetscObject)boundary, "EGADSLite Model", (PetscObject *)&modelObj));
        if (modelObj) {
          PetscCall(PetscContainerGetPointer(modelObj, (void **)&model));
          PetscCall(EGlite_getTopology(model, &geom, &oclass, &mtype, nullptr, &Nb, &bodies, &senses));
          /* Transfer EGADS Model to Volumetric Mesh */
          PetscCall(PetscObjectCompose((PetscObject)*dm, "EGADSLite Model", (PetscObject)modelObj));
          islite = PETSC_TRUE;
        }
      }
      if (!modelObj) goto skip_egads;

      /* Set Cell Labels */
      PetscCall(DMGetLabel(*dm, "EGADS Body ID", &bodyLabel));
      PetscCall(DMPlexGetHeightStratum(*dm, 0, &cStart, &cEnd));
      PetscCall(DMPlexGetHeightStratum(*dm, 1, &fStart, &fEnd));
      PetscCall(DMPlexGetDepthStratum(*dm, 1, &eStart, &eEnd));

      for (c = cStart; c < cEnd; ++c) {
        PetscReal centroid[3] = {0., 0., 0.};
        PetscInt  b;

        /* Determine what body the cell's centroid is located in */
        if (!interpolate) {
          PetscSection coordSection;
          Vec          coordinates;
          PetscScalar *coords = nullptr;
          PetscInt     coordSize, s, d;

          PetscCall(DMGetCoordinatesLocal(*dm, &coordinates));
          PetscCall(DMGetCoordinateSection(*dm, &coordSection));
          PetscCall(DMPlexVecGetClosure(*dm, coordSection, coordinates, c, &coordSize, &coords));
          for (s = 0; s < coordSize; ++s)
            for (d = 0; d < dim; ++d) centroid[d] += coords[s * dim + d];
          PetscCall(DMPlexVecRestoreClosure(*dm, coordSection, coordinates, c, &coordSize, &coords));
        } else PetscCall(DMPlexComputeCellGeometryFVM(*dm, c, nullptr, centroid, nullptr));
        for (b = 0; b < Nb; ++b) {
          if (islite) {
            if (EGlite_inTopology(bodies[b], centroid) == EGADS_SUCCESS) break;
          } else {
            if (EG_inTopology(bodies[b], centroid) == EGADS_SUCCESS) break;
          }
        }
        if (b < Nb) {
          PetscInt  cval    = b, eVal, fVal;
          PetscInt *closure = nullptr, Ncl, cl;

          PetscCall(DMLabelSetValue(bodyLabel, c, cval));
          PetscCall(DMPlexGetTransitiveClosure(*dm, c, PETSC_TRUE, &Ncl, &closure));
          for (cl = 0; cl < Ncl; cl += 2) {
            const PetscInt p = closure[cl];

            if (p >= eStart && p < eEnd) {
              PetscCall(DMLabelGetValue(bodyLabel, p, &eVal));
              if (eVal < 0) PetscCall(DMLabelSetValue(bodyLabel, p, cval));
            }
            if (p >= fStart && p < fEnd) {
              PetscCall(DMLabelGetValue(bodyLabel, p, &fVal));
              if (fVal < 0) PetscCall(DMLabelSetValue(bodyLabel, p, cval));
            }
          }
          PetscCall(DMPlexRestoreTransitiveClosure(*dm, c, PETSC_TRUE, &Ncl, &closure));
        }
      }
    skip_egads:;
#endif
    }
    PetscCall(DMPlexSetRefinementUniform(*dm, PETSC_FALSE));
  }
  PetscCall(DMUniversalLabelDestroy(&universal));
  PetscFunctionReturn(PETSC_SUCCESS);
}

PETSC_EXTERN PetscErrorCode DMPlexRefine_Tetgen(DM dm, double *maxVolumes, DM *dmRefined)
{
  MPI_Comm               comm;
  const PetscInt         dim = 3;
  ::tetgenio             in;
  ::tetgenio             out;
  PetscContainer         modelObj;
  DMUniversalLabel       universal;
  PetscInt               vStart, vEnd, v, eStart, eEnd, e, fStart, fEnd, f, cStart, cEnd, c, defVal;
  DMPlexInterpolatedFlag isInterpolated;
  PetscMPIInt            rank;

  PetscFunctionBegin;
  PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
  PetscCallMPI(MPI_Comm_rank(comm, &rank));
  PetscCall(DMPlexIsInterpolatedCollective(dm, &isInterpolated));
  PetscCall(DMUniversalLabelCreate(dm, &universal));
  PetscCall(DMLabelGetDefaultValue(universal->label, &defVal));

  PetscCall(DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd));
  in.numberofpoints = vEnd - vStart;
  if (in.numberofpoints > 0) {
    PetscSection coordSection;
    Vec          coordinates;
    PetscScalar *array;

    in.pointlist       = new double[in.numberofpoints * dim];
    in.pointmarkerlist = new int[in.numberofpoints];

    PetscCall(PetscArrayzero(in.pointmarkerlist, (size_t)in.numberofpoints));
    PetscCall(DMGetCoordinatesLocal(dm, &coordinates));
    PetscCall(DMGetCoordinateSection(dm, &coordSection));
    PetscCall(VecGetArray(coordinates, &array));
    for (v = vStart; v < vEnd; ++v) {
      const PetscInt idx = v - vStart;
      PetscInt       off, d, val;

      PetscCall(PetscSectionGetOffset(coordSection, v, &off));
      for (d = 0; d < dim; ++d) in.pointlist[idx * dim + d] = PetscRealPart(array[off + d]);
      PetscCall(DMLabelGetValue(universal->label, v, &val));
      if (val != defVal) in.pointmarkerlist[idx] = (int)val;
    }
    PetscCall(VecRestoreArray(coordinates, &array));
  }

  PetscCall(DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd));
  in.numberofedges = eEnd - eStart;
  if (isInterpolated == DMPLEX_INTERPOLATED_FULL && in.numberofedges > 0) {
    in.edgelist       = new int[in.numberofedges * 2];
    in.edgemarkerlist = new int[in.numberofedges];
    for (e = eStart; e < eEnd; ++e) {
      const PetscInt  idx = e - eStart;
      const PetscInt *cone;
      PetscInt        coneSize, val;

      PetscCall(DMPlexGetConeSize(dm, e, &coneSize));
      PetscCall(DMPlexGetCone(dm, e, &cone));
      in.edgelist[idx * 2]     = cone[0] - vStart;
      in.edgelist[idx * 2 + 1] = cone[1] - vStart;

      PetscCall(DMLabelGetValue(universal->label, e, &val));
      if (val != defVal) in.edgemarkerlist[idx] = (int)val;
    }
  }

  PetscCall(DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd));
  in.numberoffacets = fEnd - fStart;
  if (isInterpolated == DMPLEX_INTERPOLATED_FULL && in.numberoffacets > 0) {
    in.facetlist       = new tetgenio::facet[in.numberoffacets];
    in.facetmarkerlist = new int[in.numberoffacets];
    for (f = fStart; f < fEnd; ++f) {
      const PetscInt idx    = f - fStart;
      PetscInt      *points = nullptr, numPoints, p, numVertices = 0, v, val;

      in.facetlist[idx].numberofpolygons = 1;
      in.facetlist[idx].polygonlist      = new tetgenio::polygon[in.facetlist[idx].numberofpolygons];
      in.facetlist[idx].numberofholes    = 0;
      in.facetlist[idx].holelist         = nullptr;

      PetscCall(DMPlexGetTransitiveClosure(dm, f, PETSC_TRUE, &numPoints, &points));
      for (p = 0; p < numPoints * 2; p += 2) {
        const PetscInt point = points[p];
        if ((point >= vStart) && (point < vEnd)) points[numVertices++] = point;
      }

      tetgenio::polygon *poly = in.facetlist[idx].polygonlist;
      poly->numberofvertices  = numVertices;
      poly->vertexlist        = new int[poly->numberofvertices];
      for (v = 0; v < numVertices; ++v) {
        const PetscInt vIdx = points[v] - vStart;
        poly->vertexlist[v] = vIdx;
      }

      PetscCall(DMLabelGetValue(universal->label, f, &val));
      if (val != defVal) in.facetmarkerlist[idx] = (int)val;

      PetscCall(DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &numPoints, &points));
    }
  }

  PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
  in.numberofcorners       = 4;
  in.numberoftetrahedra    = cEnd - cStart;
  in.tetrahedronvolumelist = (double *)maxVolumes;
  if (in.numberoftetrahedra > 0) {
    in.tetrahedronlist = new int[in.numberoftetrahedra * in.numberofcorners];
    for (c = cStart; c < cEnd; ++c) {
      const PetscInt idx     = c - cStart;
      PetscInt      *closure = nullptr;
      PetscInt       closureSize;

      PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure));
      PetscCheck(!(closureSize != 5) || !(closureSize != 15), comm, PETSC_ERR_ARG_WRONG, "Mesh has cell which is not a tetrahedron, %" PetscInt_FMT " vertices in closure", closureSize);
      for (v = 0; v < 4; ++v) in.tetrahedronlist[idx * in.numberofcorners + v] = closure[(v + closureSize - 4) * 2] - vStart;
      PetscCall(DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure));
    }
  }

  if (rank == 0) {
    char args[32];

    /* Take away 'Q' for verbose output */
    PetscCall(PetscStrncpy(args, "qezQra", sizeof(args)));
    ::tetrahedralize(args, &in, &out);
  }

  in.tetrahedronvolumelist = nullptr;
  {
    const PetscInt numCorners  = 4;
    const PetscInt numCells    = out.numberoftetrahedra;
    const PetscInt numVertices = out.numberofpoints;
    PetscReal     *meshCoords  = nullptr;
    PetscInt      *cells       = nullptr;
    PetscBool      interpolate = isInterpolated == DMPLEX_INTERPOLATED_FULL ? PETSC_TRUE : PETSC_FALSE;

    if (sizeof(PetscReal) == sizeof(out.pointlist[0])) {
      meshCoords = (PetscReal *)out.pointlist;
    } else {
      PetscInt i;

      meshCoords = new PetscReal[dim * numVertices];
      for (i = 0; i < dim * numVertices; ++i) meshCoords[i] = (PetscReal)out.pointlist[i];
    }
    if (sizeof(PetscInt) == sizeof(out.tetrahedronlist[0])) {
      cells = (PetscInt *)out.tetrahedronlist;
    } else {
      PetscInt i;

      cells = new PetscInt[numCells * numCorners];
      for (i = 0; i < numCells * numCorners; ++i) cells[i] = (PetscInt)out.tetrahedronlist[i];
    }

    PetscCall(DMPlexInvertCells_Tetgen(numCells, numCorners, cells));
    PetscCall(DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dmRefined));
    if (sizeof(PetscReal) != sizeof(out.pointlist[0])) delete[] meshCoords;
    if (sizeof(PetscInt) != sizeof(out.tetrahedronlist[0])) delete[] cells;

    /* Set labels */
    PetscCall(DMUniversalLabelCreateLabels(universal, PETSC_TRUE, *dmRefined));
    for (v = 0; v < numVertices; ++v) {
      if (out.pointmarkerlist[v]) PetscCall(DMUniversalLabelSetLabelValue(universal, *dmRefined, PETSC_TRUE, v + numCells, out.pointmarkerlist[v]));
    }
    if (interpolate) {
      PetscInt e, f;

      for (e = 0; e < out.numberofedges; ++e) {
        if (out.edgemarkerlist[e]) {
          const PetscInt  vertices[2] = {out.edgelist[e * 2 + 0] + numCells, out.edgelist[e * 2 + 1] + numCells};
          const PetscInt *edges;
          PetscInt        numEdges;

          PetscCall(DMPlexGetJoin(*dmRefined, 2, vertices, &numEdges, &edges));
          PetscCheck(numEdges == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %" PetscInt_FMT, numEdges);
          PetscCall(DMUniversalLabelSetLabelValue(universal, *dmRefined, PETSC_TRUE, edges[0], out.edgemarkerlist[e]));
          PetscCall(DMPlexRestoreJoin(*dmRefined, 2, vertices, &numEdges, &edges));
        }
      }
      for (f = 0; f < out.numberoftrifaces; ++f) {
        if (out.trifacemarkerlist[f]) {
          const PetscInt  vertices[3] = {out.trifacelist[f * 3 + 0] + numCells, out.trifacelist[f * 3 + 1] + numCells, out.trifacelist[f * 3 + 2] + numCells};
          const PetscInt *faces;
          PetscInt        numFaces;

          PetscCall(DMPlexGetFullJoin(*dmRefined, 3, vertices, &numFaces, &faces));
          PetscCheck(numFaces == 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %" PetscInt_FMT, numFaces);
          PetscCall(DMUniversalLabelSetLabelValue(universal, *dmRefined, PETSC_TRUE, faces[0], out.trifacemarkerlist[f]));
          PetscCall(DMPlexRestoreJoin(*dmRefined, 3, vertices, &numFaces, &faces));
        }
      }
    }

    PetscCall(PetscObjectQuery((PetscObject)dm, "EGADS Model", (PetscObject *)&modelObj));
    if (modelObj) {
#ifdef PETSC_HAVE_EGADS
      DMLabel   bodyLabel;
      PetscInt  cStart, cEnd, c, eStart, eEnd, fStart, fEnd;
      PetscBool islite = PETSC_FALSE;
      ego      *bodies;
      ego       model, geom;
      int       Nb, oclass, mtype, *senses;

      /* Get Attached EGADS Model from Original DMPlex */
      PetscCall(PetscObjectQuery((PetscObject)dm, "EGADS Model", (PetscObject *)&modelObj));
      if (modelObj) {
        PetscCall(PetscContainerGetPointer(modelObj, (void **)&model));
        PetscCall(EG_getTopology(model, &geom, &oclass, &mtype, nullptr, &Nb, &bodies, &senses));
        /* Transfer EGADS Model to Volumetric Mesh */
        PetscCall(PetscObjectCompose((PetscObject)*dmRefined, "EGADS Model", (PetscObject)modelObj));
      } else {
        PetscCall(PetscObjectQuery((PetscObject)dm, "EGADSLite Model", (PetscObject *)&modelObj));
        if (modelObj) {
          PetscCall(PetscContainerGetPointer(modelObj, (void **)&model));
          PetscCall(EGlite_getTopology(model, &geom, &oclass, &mtype, nullptr, &Nb, &bodies, &senses));
          /* Transfer EGADS Model to Volumetric Mesh */
          PetscCall(PetscObjectCompose((PetscObject)*dmRefined, "EGADSLite Model", (PetscObject)modelObj));
          islite = PETSC_TRUE;
        }
      }
      if (!modelObj) goto skip_egads;

      /* Set Cell Labels */
      PetscCall(DMGetLabel(*dmRefined, "EGADS Body ID", &bodyLabel));
      PetscCall(DMPlexGetHeightStratum(*dmRefined, 0, &cStart, &cEnd));
      PetscCall(DMPlexGetHeightStratum(*dmRefined, 1, &fStart, &fEnd));
      PetscCall(DMPlexGetDepthStratum(*dmRefined, 1, &eStart, &eEnd));

      for (c = cStart; c < cEnd; ++c) {
        PetscReal centroid[3] = {0., 0., 0.};
        PetscInt  b;

        /* Determine what body the cell's centroid is located in */
        if (!interpolate) {
          PetscSection coordSection;
          Vec          coordinates;
          PetscScalar *coords = nullptr;
          PetscInt     coordSize, s, d;

          PetscCall(DMGetCoordinatesLocal(*dmRefined, &coordinates));
          PetscCall(DMGetCoordinateSection(*dmRefined, &coordSection));
          PetscCall(DMPlexVecGetClosure(*dmRefined, coordSection, coordinates, c, &coordSize, &coords));
          for (s = 0; s < coordSize; ++s)
            for (d = 0; d < dim; ++d) centroid[d] += coords[s * dim + d];
          PetscCall(DMPlexVecRestoreClosure(*dmRefined, coordSection, coordinates, c, &coordSize, &coords));
        } else PetscCall(DMPlexComputeCellGeometryFVM(*dmRefined, c, nullptr, centroid, nullptr));
        for (b = 0; b < Nb; ++b) {
          if (islite) {
            if (EGlite_inTopology(bodies[b], centroid) == EGADS_SUCCESS) break;
          } else {
            if (EG_inTopology(bodies[b], centroid) == EGADS_SUCCESS) break;
          }
        }
        if (b < Nb) {
          PetscInt  cval    = b, eVal, fVal;
          PetscInt *closure = nullptr, Ncl, cl;

          PetscCall(DMLabelSetValue(bodyLabel, c, cval));
          PetscCall(DMPlexGetTransitiveClosure(*dmRefined, c, PETSC_TRUE, &Ncl, &closure));
          for (cl = 0; cl < Ncl; cl += 2) {
            const PetscInt p = closure[cl];

            if (p >= eStart && p < eEnd) {
              PetscCall(DMLabelGetValue(bodyLabel, p, &eVal));
              if (eVal < 0) PetscCall(DMLabelSetValue(bodyLabel, p, cval));
            }
            if (p >= fStart && p < fEnd) {
              PetscCall(DMLabelGetValue(bodyLabel, p, &fVal));
              if (fVal < 0) PetscCall(DMLabelSetValue(bodyLabel, p, cval));
            }
          }
          PetscCall(DMPlexRestoreTransitiveClosure(*dmRefined, c, PETSC_TRUE, &Ncl, &closure));
        }
      }
    skip_egads:;
#endif
    }
    PetscCall(DMPlexSetRefinementUniform(*dmRefined, PETSC_FALSE));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}
