#include <petsc/private/dmpleximpl.h>   /*I      "petscdmplex.h"   I*/
#ifdef PETSC_HAVE_PRAGMATIC
#include <pragmatic/cpragmatic.h>
#endif



#undef __FUNCT__
#define __FUNCT__ "DMPlexAdapt"
/*@
  DMPlexAdapt - Generates a mesh adapted to the specified metric field using the pragmatic library.

  Input Parameters:
+ dm - The DM object
. metric - The metric to which the mesh is adapted, defined vertex-wise.
- bdyLabelName - Label name for boundary tags. These will be preserved in the output mesh. bdyLabelName should be different from "boundary".

  Output Parameter:
. dmAdapted  - Pointer to the DM object containing the adapted mesh

  Level: advanced

.seealso: DMCoarsen(), DMRefine()
@*/
PetscErrorCode DMPlexAdapt(DM dm, Vec metric, const char bdyLabelName[], DM *dmAdapted)
{
#ifdef PETSC_HAVE_PRAGMATIC
  DM                   udm, coordDM;
  DMLabel              bd, bdTags, bdTagsAdp;
  Vec                  coordinates;
  PetscSection         coordSection;
  IS                   bdIS;
  double              *coordsAdp;  
  const PetscScalar   *coords;
  PetscReal           *x, *y, *z, *xAdp, *yAdp, *zAdp;
  const PetscScalar   *metricArray;
  PetscReal           *met;
  const PetscInt      *faces;
  PetscInt            *cells, *cellsAdp, *bdFaces, *bdFaceIds;
  PetscInt            *boundaryTags;
  PetscInt             dim, numCornersAdp, cStart, cEnd, numCells, numCellsAdp, c; 
  PetscInt             vStart, vEnd, numVertices, numVerticesAdp, v;
  PetscInt             numBdFaces, f, maxConeSize, bdSize, coff;
  PetscInt            *cell, iVer, cellOff, i, j, idx, facet; 
  PetscInt             perm[4], isInFacetClosure[4]; // 4 = max number of facets for an element in 2D & 3D. Only for simplicial meshes
  PetscBool            flag, hasBdyFacet;
#endif
  PetscErrorCode       ierr;
  MPI_Comm             comm;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr);
#ifdef PETSC_HAVE_PRAGMATIC
  ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
  ierr = DMGetCoordinateDM(dm, &coordDM);CHKERRQ(ierr);
  ierr = DMGetDefaultSection(coordDM, &coordSection);CHKERRQ(ierr);
  ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
  ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
  ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr);
  ierr = DMPlexGetMaxSizes(udm, &maxConeSize, NULL);CHKERRQ(ierr);
  numCells    = cEnd - cStart;
  numVertices = vEnd - vStart;
  ierr = PetscCalloc5(numVertices, &x, numVertices, &y, numVertices, &z, numCells*maxConeSize, &cells, dim*dim*numVertices, &met);CHKERRQ(ierr);
  ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr);
  ierr = VecGetArrayRead(metric, &metricArray);CHKERRQ(ierr);
  for (v = vStart; v < vEnd; ++v) {
    PetscInt off;
  
    ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
    x[v-vStart] = coords[off+0];
    y[v-vStart] = coords[off+1];
    if (dim > 2) z[v-vStart] = coords[off+2];
    ierr = PetscMemcpy(&met[dim*dim*(v-vStart)], &metricArray[dim*off], dim*dim*sizeof(PetscScalar));CHKERRQ(ierr);
  }
  ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr);
  ierr = VecRestoreArrayRead(metric, &metricArray);CHKERRQ(ierr);
  for (c = 0, coff = 0; c < numCells; ++c) {
    const PetscInt *cone;
    PetscInt        coneSize, cl;
  
    ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr);
    ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr);
    for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart;
  }
  switch (dim) {
  case 2:
    pragmatic_2d_init(&numVertices, &numCells, cells, x, y);
    break;
  case 3:
    pragmatic_3d_init(&numVertices, &numCells, cells, x, y, z);
    break;
  default:
    SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic adaptation defined for dimension %d", dim);
  }
  /* Create boundary mesh */
  if (bdyLabelName) {
    ierr = PetscStrcmp(bdyLabelName, "boundary", &flag);CHKERRQ(ierr);
    if (flag) {
      SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "\"%s\" cannot be used as label for boundary facets", bdyLabelName);
    }
    ierr = DMGetLabel(dm, bdyLabelName, &bdTags);CHKERRQ(ierr);
  }
  /* TODO To avoid marking bdy facets again if bdyLabelName exists, could/should we loop over bdyLabelName stratas ? */
  ierr = DMLabelCreate("boundary", &bd);CHKERRQ(ierr);
  ierr = DMPlexMarkBoundaryFaces(dm, bd);CHKERRQ(ierr);        
  ierr = DMLabelGetStratumIS(bd, 1, &bdIS);CHKERRQ(ierr);
  ierr = DMLabelGetStratumSize(bd, 1, &numBdFaces);CHKERRQ(ierr);
  ierr = ISGetIndices(bdIS, &faces);CHKERRQ(ierr);
  /* TODO why not assume that we are considering simplicial meshes, in which case bdSize = dim*numBdFaces ? */
  for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
    PetscInt *closure = NULL;
    PetscInt  closureSize, cl;
  
    ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
    for (cl = 0; cl < closureSize*2; cl += 2) {
      if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
    }
    ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
  }
  ierr = PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);CHKERRQ(ierr);
  for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
    PetscInt *closure = NULL;
    PetscInt  closureSize, cl;
  
    ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
    for (cl = 0; cl < closureSize*2; cl += 2) {
      if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart;
    }
    if (bdyLabelName) {
      ierr = DMLabelGetValue(bdTags, faces[f], &bdFaceIds[f]);CHKERRQ(ierr);
    } else {
      bdFaceIds[f] = 1;
    }
    ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
  }
  ierr = ISDestroy(&bdIS);CHKERRQ(ierr);
  ierr = DMLabelDestroy(&bd);CHKERRQ(ierr);
  pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds);
  pragmatic_set_metric(met);
  pragmatic_adapt();
  ierr = PetscFree5(x, y, z, cells, met);CHKERRQ(ierr);
  ierr = PetscFree2(bdFaces, bdFaceIds);CHKERRQ(ierr);
  ierr = PetscFree(coords);CHKERRQ(ierr);
  /* Read out mesh */
  pragmatic_get_info(&numVerticesAdp, &numCellsAdp);
  ierr = PetscMalloc1(numVerticesAdp*dim, &coordsAdp);CHKERRQ(ierr);
  switch (dim) {
  case 2:
    ierr = PetscMalloc2(numVerticesAdp, &xAdp, numVerticesAdp, &yAdp);CHKERRQ(ierr);
    zAdp = NULL;
    pragmatic_get_coords_2d(xAdp, yAdp);
    numCornersAdp = 3;
    for (v = 0; v < numVerticesAdp; ++v) {coordsAdp[v*2+0] = xAdp[v]; coordsAdp[v*2+1] = yAdp[v];}
    break;
  case 3:
    ierr = PetscMalloc3(numVerticesAdp, &xAdp, numVerticesAdp, &yAdp, numVerticesAdp, &zAdp);CHKERRQ(ierr);
    pragmatic_get_coords_3d(xAdp, yAdp, zAdp);
    numCornersAdp = 4;
    for (v = 0; v < numVerticesAdp; ++v) {coordsAdp[v*3+0] = xAdp[v]; coordsAdp[v*3+1] = yAdp[v]; coordsAdp[v*3+2] = zAdp[v];}
    break;
  default:
    SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic adaptation defined for dimension %d", dim);
  }
  ierr = PetscMalloc1(numCellsAdp*(dim+1), &cellsAdp);CHKERRQ(ierr); // only for simplicial meshes
  pragmatic_get_elements(cellsAdp);
  ierr = DMPlexCreate(comm, dmAdapted);CHKERRQ(ierr);
  ierr = DMPlexCreateFromCellList(PetscObjectComm((PetscObject) dm), dim, numCellsAdp, numVerticesAdp, numCornersAdp, PETSC_TRUE, cellsAdp, dim, coordsAdp, dmAdapted);CHKERRQ(ierr);
  /* Read out boundary tags */
  pragmatic_get_boundaryTags(&boundaryTags);
  if (!bdyLabelName) bdyLabelName = "boundary";
  ierr = DMCreateLabel(*dmAdapted, bdyLabelName);CHKERRQ(ierr);
  ierr = DMGetLabel(*dmAdapted, bdyLabelName, &bdTagsAdp);CHKERRQ(ierr);
  ierr = DMPlexGetHeightStratum(*dmAdapted, 0, &cStart, &cEnd);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(*dmAdapted, 0, &vStart, &vEnd);CHKERRQ(ierr);
  for (c = cStart; c < cEnd; ++c) {
    PetscInt       *cellClosure = NULL;
    PetscInt        cellClosureSize, cl;
    PetscInt       *facetClosure = NULL;
    PetscInt        facetClosureSize, cl2;   
    const PetscInt *facetList;
    PetscInt        facetListSize, f;
    
    cellOff = (c-cStart)*(dim+1);  // gives the offset corresponding to the cell in pragmatic boundary arrays. Only for simplicial meshes
    hasBdyFacet = 0;
    for (i = 0; i < dim+1; ++i) {   // only for simplicial meshes
      if (boundaryTags[cellOff+i]) {
        hasBdyFacet = 1;
        break;
      }
    }
    if (!hasBdyFacet) continue; // The cell has no boundary edge/facet => no boundary tagging
    
    cell = &cellsAdp[cellOff]; // pointing to the current cell in the cellsAdp table
    ierr = DMPlexGetTransitiveClosure(*dmAdapted, c, PETSC_TRUE, &cellClosureSize, &cellClosure);CHKERRQ(ierr);
    /* first, encode the permutation of the vertices indices betwenn the cell closure and pragmatic ordering */
    j = 0;
    for (cl = 0; cl < cellClosureSize*2; cl += 2) {
      if ((cellClosure[cl] < vStart) || (cellClosure[cl] >= vEnd)) continue;
      iVer = cellClosure[cl] - vStart;
      for (i = 0; i < dim+1; ++i) {  // only for simplicial meshes
        if (iVer == cell[i]) {
          perm[j] = i;    // the cl-th element of the closure is the i-th vertex of the cell
          break;
        }
      }
      j++;
    }
    ierr = DMPlexGetCone(*dmAdapted, c, &facetList);CHKERRQ(ierr);     // list of edges/facets of the cell
    ierr = DMPlexGetConeSize(*dmAdapted, c, &facetListSize);CHKERRQ(ierr);
    /* then, for each edge/facet of the cell, find the opposite vertex (ie the one in the closure of the cell and not in the closure of the facet/edge) */
    for (f = 0; f < facetListSize; ++f){
      facet = facetList[f];
      ierr = DMPlexGetTransitiveClosure(*dmAdapted, facet, PETSC_TRUE, &facetClosureSize, &facetClosure);CHKERRQ(ierr);
      /* loop over the vertices of the cell closure, and check if each vertex belongs to the edge/facet closure */
      /* TODO should we use bitmaps to mark vertices instead of a static array ? */
      PetscMemzero(isInFacetClosure, sizeof(isInFacetClosure));
      j = 0;
      for (cl = 0; cl < cellClosureSize*2; cl += 2) {
        if ((cellClosure[cl] < vStart) || (cellClosure[cl] >= vEnd)) continue;
        for (cl2 = 0; cl2 < facetClosureSize*2; cl2 += 2){
          if ((facetClosure[cl2] < vStart) || (facetClosure[cl2] >= vEnd)) continue;
          if (cellClosure[cl] == facetClosure[cl2]) {
            isInFacetClosure[j] = 1;
          }
        }
        j++;
      }
      /* the vertex that was not marked is the vertex opposite to the edge/facet, ie the one giving the edge/facet boundary tag in pragmatic */
      j = 0;
      for (cl = 0; cl < cellClosureSize*2; cl += 2) {
        if ((cellClosure[cl] < vStart) || (cellClosure[cl] >= vEnd)) continue;
        if (!isInFacetClosure[j]) {
          idx = cellOff + perm[j];
          if (boundaryTags[idx]) {
            ierr = DMLabelSetValue(bdTagsAdp, facet, boundaryTags[idx]);CHKERRQ(ierr);
          }
          break;
        }
        j++;
      }
      ierr = DMPlexRestoreTransitiveClosure(*dmAdapted, facet, PETSC_TRUE, &facetClosureSize, &facetClosure);CHKERRQ(ierr);
    }
    ierr = DMPlexRestoreTransitiveClosure(*dmAdapted, c, PETSC_TRUE, &cellClosureSize, &cellClosure);CHKERRQ(ierr);
  }
  pragmatic_finalize();
  ierr = PetscFree5(xAdp, yAdp, zAdp, cellsAdp, coordsAdp);CHKERRQ(ierr);
#endif
  PetscFunctionReturn(0);
}