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

#include <ctetgen.h>

/* This is to fix the tetrahedron orientation from TetGen */
static PetscErrorCode DMPlexInvertCells_CTetgen(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(0);
}

PETSC_EXTERN PetscErrorCode DMPlexGenerate_CTetgen(DM boundary, PetscBool interpolate, DM *dm)
{
  MPI_Comm       comm;
  const PetscInt dim       = 3;
  const char    *labelName = "marker";
  PLC           *in, *out;
  DMLabel        label;
  PetscInt       verbose = 0, vStart, vEnd, v, fStart, fEnd, f;
  PetscMPIInt    rank;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)boundary,&comm);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,((PetscObject) boundary)->prefix, "-ctetgen_verbose", &verbose, NULL);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(boundary, 0, &vStart, &vEnd);CHKERRQ(ierr);
  ierr = DMGetLabel(boundary, labelName, &label);CHKERRQ(ierr);
  ierr = PLCCreate(&in);CHKERRQ(ierr);
  ierr = PLCCreate(&out);CHKERRQ(ierr);

  in->numberofpoints = vEnd - vStart;
  if (in->numberofpoints > 0) {
    PetscSection coordSection;
    Vec          coordinates;
    PetscScalar *array;

    ierr = PetscMalloc1(in->numberofpoints*dim, &in->pointlist);CHKERRQ(ierr);
    ierr = PetscMalloc1(in->numberofpoints,       &in->pointmarkerlist);CHKERRQ(ierr);
    ierr = DMGetCoordinatesLocal(boundary, &coordinates);CHKERRQ(ierr);
    ierr = DMGetCoordinateSection(boundary, &coordSection);CHKERRQ(ierr);
    ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
    for (v = vStart; v < vEnd; ++v) {
      const PetscInt idx = v - vStart;
      PetscInt       off, d, m = -1;

      ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
      for (d = 0; d < dim; ++d) {
        in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
      }
      if (label) {ierr = DMLabelGetValue(label, v, &m);CHKERRQ(ierr);}

      in->pointmarkerlist[idx] = (int) m;
    }
    ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
  }
  ierr  = DMPlexGetHeightStratum(boundary, 0, &fStart, &fEnd);CHKERRQ(ierr);

  in->numberoffacets = fEnd - fStart;
  if (in->numberoffacets > 0) {
    ierr = PetscMalloc1(in->numberoffacets, &in->facetlist);CHKERRQ(ierr);
    ierr = PetscMalloc1(in->numberoffacets,   &in->facetmarkerlist);CHKERRQ(ierr);
    for (f = fStart; f < fEnd; ++f) {
      const PetscInt idx     = f - fStart;
      PetscInt      *points = NULL, numPoints, p, numVertices = 0, v, m = -1;
      polygon       *poly;

      in->facetlist[idx].numberofpolygons = 1;

      ierr = PetscMalloc1(in->facetlist[idx].numberofpolygons, &in->facetlist[idx].polygonlist);CHKERRQ(ierr);

      in->facetlist[idx].numberofholes    = 0;
      in->facetlist[idx].holelist         = NULL;

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

      poly                   = in->facetlist[idx].polygonlist;
      poly->numberofvertices = numVertices;
      ierr                   = PetscMalloc1(poly->numberofvertices, &poly->vertexlist);CHKERRQ(ierr);
      for (v = 0; v < numVertices; ++v) {
        const PetscInt vIdx = points[v] - vStart;
        poly->vertexlist[v] = vIdx;
      }
      if (label) {ierr = DMLabelGetValue(label, f, &m);CHKERRQ(ierr);}
      in->facetmarkerlist[idx] = (int) m;
      ierr = DMPlexRestoreTransitiveClosure(boundary, f, PETSC_TRUE, &numPoints, &points);CHKERRQ(ierr);
    }
  }
  if (!rank) {
    TetGenOpts t;

    ierr        = TetGenOptsInitialize(&t);CHKERRQ(ierr);
    t.in        = boundary; /* Should go away */
    t.plc       = 1;
    t.quality   = 1;
    t.edgesout  = 1;
    t.zeroindex = 1;
    t.quiet     = 1;
    t.verbose   = verbose;
    ierr        = TetGenCheckOpts(&t);CHKERRQ(ierr);
    ierr        = TetGenTetrahedralize(&t, in, out);CHKERRQ(ierr);
  }
  {
    DMLabel        glabel      = NULL;
    const PetscInt numCorners  = 4;
    const PetscInt numCells    = out->numberoftetrahedra;
    const PetscInt numVertices = out->numberofpoints;
    PetscReal      *meshCoords;
    PetscInt       *cells;

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

      ierr = PetscMalloc1(dim * numVertices,&meshCoords);CHKERRQ(ierr);
      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;

      ierr = PetscMalloc1(numCells * numCorners, &cells);CHKERRQ(ierr);
      for (i = 0; i < numCells * numCorners; i++) {
        cells[i] = (PetscInt) out->tetrahedronlist[i];
      }
    }

    ierr = DMPlexInvertCells_CTetgen(numCells, numCorners, cells);CHKERRQ(ierr);
    ierr = DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dm);CHKERRQ(ierr);
    if (sizeof (PetscReal) != sizeof (out->pointlist[0])) {
      ierr = PetscFree(meshCoords);CHKERRQ(ierr);
    }
    if (sizeof (PetscInt) != sizeof (out->tetrahedronlist[0])) {
      ierr = PetscFree(cells);CHKERRQ(ierr);
    }
    if (label) {
      ierr = DMCreateLabel(*dm, labelName);CHKERRQ(ierr);
      ierr = DMGetLabel(*dm, labelName, &glabel);CHKERRQ(ierr);
    }
    /* Set labels */
    for (v = 0; v < numVertices; ++v) {
      if (out->pointmarkerlist[v]) {
        if (glabel) {ierr = DMLabelSetValue(glabel, v+numCells, out->pointmarkerlist[v]);CHKERRQ(ierr);}
      }
    }
    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;

          ierr = DMPlexGetJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
          if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
          if (glabel) {ierr = DMLabelSetValue(glabel, edges[0], out->edgemarkerlist[e]);CHKERRQ(ierr);}
          ierr = DMPlexRestoreJoin(*dm, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
        }
      }
      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;

          ierr = DMPlexGetFullJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
          if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
          if (glabel) {ierr = DMLabelSetValue(glabel, faces[0], out->trifacemarkerlist[f]);CHKERRQ(ierr);}
          ierr = DMPlexRestoreJoin(*dm, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
        }
      }
    }
    ierr = DMPlexSetRefinementUniform(*dm, PETSC_FALSE);CHKERRQ(ierr);
  }

  ierr = PLCDestroy(&in);CHKERRQ(ierr);
  ierr = PLCDestroy(&out);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

PETSC_EXTERN PetscErrorCode DMPlexRefine_CTetgen(DM dm, PetscReal *maxVolumes, DM *dmRefined)
{
  MPI_Comm       comm;
  const PetscInt dim       = 3;
  const char    *labelName = "marker";
  PLC           *in, *out;
  DMLabel        label;
  PetscInt       verbose = 0, vStart, vEnd, v, cStart, cEnd, c, depth, depthGlobal;
  PetscMPIInt    rank;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,((PetscObject) dm)->prefix, "-ctetgen_verbose", &verbose, NULL);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
  ierr = MPIU_Allreduce(&depth, &depthGlobal, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
  ierr = DMGetLabel(dm, labelName, &label);CHKERRQ(ierr);
  ierr = PLCCreate(&in);CHKERRQ(ierr);
  ierr = PLCCreate(&out);CHKERRQ(ierr);

  in->numberofpoints = vEnd - vStart;
  if (in->numberofpoints > 0) {
    PetscSection coordSection;
    Vec          coordinates;
    PetscScalar *array;

    ierr = PetscMalloc1(in->numberofpoints*dim, &in->pointlist);CHKERRQ(ierr);
    ierr = PetscMalloc1(in->numberofpoints, &in->pointmarkerlist);CHKERRQ(ierr);
    ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
    ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
    ierr = VecGetArray(coordinates, &array);CHKERRQ(ierr);
    for (v = vStart; v < vEnd; ++v) {
      const PetscInt idx = v - vStart;
      PetscInt       off, d, m = -1;

      ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
      for (d = 0; d < dim; ++d) {
        in->pointlist[idx*dim + d] = PetscRealPart(array[off+d]);
      }
      if (label) {ierr = DMLabelGetValue(label, v, &m);CHKERRQ(ierr);}

      in->pointmarkerlist[idx] = (int) m;
    }
    ierr = VecRestoreArray(coordinates, &array);CHKERRQ(ierr);
  }
  ierr  = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);

  in->numberofcorners       = 4;
  in->numberoftetrahedra    = cEnd - cStart;
  in->tetrahedronvolumelist = maxVolumes;
  if (in->numberoftetrahedra > 0) {
    ierr = PetscMalloc1(in->numberoftetrahedra*in->numberofcorners, &in->tetrahedronlist);CHKERRQ(ierr);
    for (c = cStart; c < cEnd; ++c) {
      const PetscInt idx      = c - cStart;
      PetscInt      *closure = NULL;
      PetscInt       closureSize;

      ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
      if ((closureSize != 5) && (closureSize != 15)) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Mesh has cell which is not a tetrahedron, %D vertices in closure", closureSize);
      for (v = 0; v < 4; ++v) {
        in->tetrahedronlist[idx*in->numberofcorners + v] = closure[(v+closureSize-4)*2] - vStart;
      }
      ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
    }
  }
  if (!rank) {
    TetGenOpts t;

    ierr = TetGenOptsInitialize(&t);CHKERRQ(ierr);

    t.in        = dm; /* Should go away */
    t.refine    = 1;
    t.varvolume = 1;
    t.quality   = 1;
    t.edgesout  = 1;
    t.zeroindex = 1;
    t.quiet     = 1;
    t.verbose   = verbose; /* Change this */

    ierr = TetGenCheckOpts(&t);CHKERRQ(ierr);
    ierr = TetGenTetrahedralize(&t, in, out);CHKERRQ(ierr);
  }
  in->tetrahedronvolumelist = NULL;
  {
    DMLabel        rlabel      = NULL;
    const PetscInt numCorners  = 4;
    const PetscInt numCells    = out->numberoftetrahedra;
    const PetscInt numVertices = out->numberofpoints;
    PetscReal      *meshCoords;
    PetscInt       *cells;
    PetscBool      interpolate = depthGlobal > 1 ? PETSC_TRUE : PETSC_FALSE;

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

      ierr = PetscMalloc1(dim * numVertices,&meshCoords);CHKERRQ(ierr);
      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;

      ierr = PetscMalloc1(numCells * numCorners, &cells);CHKERRQ(ierr);
      for (i = 0; i < numCells * numCorners; i++) {
        cells[i] = (PetscInt) out->tetrahedronlist[i];
      }
    }

    ierr = DMPlexInvertCells_CTetgen(numCells, numCorners, cells);CHKERRQ(ierr);
    ierr = DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, cells, dim, meshCoords, dmRefined);CHKERRQ(ierr);
    if (sizeof (PetscReal) != sizeof (out->pointlist[0])) {
      ierr = PetscFree(meshCoords);CHKERRQ(ierr);
    }
    if (sizeof (PetscInt) != sizeof (out->tetrahedronlist[0])) {
      ierr = PetscFree(cells);CHKERRQ(ierr);
    }
    if (label) {
      ierr = DMCreateLabel(*dmRefined, labelName);CHKERRQ(ierr);
      ierr = DMGetLabel(*dmRefined, labelName, &rlabel);CHKERRQ(ierr);
    }
    /* Set labels */
    for (v = 0; v < numVertices; ++v) {
      if (out->pointmarkerlist[v]) {
        if (rlabel) {ierr = DMLabelSetValue(rlabel, v+numCells, out->pointmarkerlist[v]);CHKERRQ(ierr);}
      }
    }
    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;

          ierr = DMPlexGetJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
          if (numEdges != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Two vertices must cover only one edge, not %D", numEdges);
          if (rlabel) {ierr = DMLabelSetValue(rlabel, edges[0], out->edgemarkerlist[e]);CHKERRQ(ierr);}
          ierr = DMPlexRestoreJoin(*dmRefined, 2, vertices, &numEdges, &edges);CHKERRQ(ierr);
        }
      }
      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;

          ierr = DMPlexGetFullJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
          if (numFaces != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Three vertices must cover only one face, not %D", numFaces);
          if (rlabel) {ierr = DMLabelSetValue(rlabel, faces[0], out->trifacemarkerlist[f]);CHKERRQ(ierr);}
          ierr = DMPlexRestoreJoin(*dmRefined, 3, vertices, &numFaces, &faces);CHKERRQ(ierr);
        }
      }
    }
    ierr = DMPlexSetRefinementUniform(*dmRefined, PETSC_FALSE);CHKERRQ(ierr);
  }
  ierr = PLCDestroy(&in);CHKERRQ(ierr);
  ierr = PLCDestroy(&out);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}