#include <petsc/private/dmmbimpl.h> /*I  "petscdmmoab.h"   I*/
#include <petsc/private/vecimpl.h>

#include <petscdmmoab.h>
#include <MBTagConventions.hpp>
#include <moab/ReadUtilIface.hpp>
#include <moab/MergeMesh.hpp>
#include <moab/CN.hpp>

typedef struct {
  // options
  PetscInt  A,B,C,M,N,K,dim;
  PetscInt  blockSizeVertexXYZ[3];              // Number of element blocks per partition
  PetscInt  blockSizeElementXYZ[3];
  PetscReal xyzbounds[6]; // the physical size of the domain
  bool      newMergeMethod,keep_skins,simplex,adjEnts;

  // compute params
  PetscReal dx,dy,dz;
  PetscInt  NX,NY,NZ,nex,ney,nez;
  PetscInt  q,xstride,ystride,zstride;
  PetscBool usrxyzgrid,usrprocgrid,usrrefgrid;
} DMMoabMeshGeneratorCtx;


#undef __FUNCT__
#define __FUNCT__ "DMMoab_SetTensorElementConnectivity_Private"
int DMMoab_SetTensorElementConnectivity_Private(DMMoabMeshGeneratorCtx& genCtx, int offset, int corner, std::vector<int>& subent_conn, moab::EntityHandle *connectivity)
{
  switch(genCtx.dim) {
    case 1:
      subent_conn.resize(2);
      moab::CN::SubEntityVertexIndices(moab::MBEDGE, 1, 0, subent_conn.data());
      connectivity[offset+subent_conn[0]] = corner;
      connectivity[offset+subent_conn[1]] = corner + 1;
      break;
    case 2:
      subent_conn.resize(4);
      moab::CN::SubEntityVertexIndices(moab::MBQUAD, 2, 0, subent_conn.data());
      connectivity[offset+subent_conn[0]] = corner;
      connectivity[offset+subent_conn[1]] = corner + 1;
      connectivity[offset+subent_conn[2]] = corner + 1 + genCtx.ystride;
      connectivity[offset+subent_conn[3]] = corner + genCtx.ystride;
      break;
    case 3:
    default:
      subent_conn.resize(8);
      moab::CN::SubEntityVertexIndices(moab::MBHEX, 3, 0, subent_conn.data());
      connectivity[offset+subent_conn[0]] = corner;
      connectivity[offset+subent_conn[1]] = corner + 1;
      connectivity[offset+subent_conn[2]] = corner + 1 + genCtx.ystride;
      connectivity[offset+subent_conn[3]] = corner + genCtx.ystride;
      connectivity[offset+subent_conn[4]] = corner + genCtx.zstride;
      connectivity[offset+subent_conn[5]] = corner + 1 + genCtx.zstride;
      connectivity[offset+subent_conn[6]] = corner + 1 + genCtx.ystride + genCtx.zstride;
      connectivity[offset+subent_conn[7]] = corner + genCtx.ystride + genCtx.zstride;
      break;
  }
  return subent_conn.size();  
}


#undef __FUNCT__
#define __FUNCT__ "DMMoab_SetSimplexElementConnectivity_Private"
int DMMoab_SetSimplexElementConnectivity_Private(DMMoabMeshGeneratorCtx& genCtx, int subelem, int offset, int corner, std::vector<int>& subent_conn, moab::EntityHandle *connectivity)
{
  switch(genCtx.dim) {
    case 1:
      subent_conn.resize(2);  /* only linear EDGE supported now */
      moab::CN::SubEntityVertexIndices(moab::MBEDGE, 1, 0, subent_conn.data());
      connectivity[offset+subent_conn[0]] = corner;
      connectivity[offset+subent_conn[1]] = corner+1;
      break;
    case 2:
      subent_conn.resize(3);  /* only linear TRI supported */
      moab::CN::SubEntityVertexIndices(moab::MBTRI, 2, 0, subent_conn.data());
      if (subelem) { /* 0 1 2 of a QUAD */
        connectivity[offset+subent_conn[0]] = corner;
        connectivity[offset+subent_conn[1]] = corner + 1;
        connectivity[offset+subent_conn[2]] = corner + 1 + genCtx.ystride;
      }
      else {        /* 2 3 0 of a QUAD */
        connectivity[offset+subent_conn[0]] = corner + 1 + genCtx.ystride;
        connectivity[offset+subent_conn[1]] = corner + genCtx.ystride;
        connectivity[offset+subent_conn[2]] = corner;
      }
      break;
    case 3:
    default:
      subent_conn.resize(4);  /* only linear TET supported */
      moab::CN::SubEntityVertexIndices(moab::MBTET, 3, 0, subent_conn.data());
      switch(subelem) {
        case 0: /* 0 1 2 5 of a HEX */
          connectivity[offset+subent_conn[0]] = corner;
          connectivity[offset+subent_conn[1]] = corner + 1;
          connectivity[offset+subent_conn[2]] = corner + 1 + genCtx.ystride;
          connectivity[offset+subent_conn[3]] = corner + 1 + genCtx.zstride;
          break;
        case 1: /* 0 2 7 5 of a HEX */
          connectivity[offset+subent_conn[0]] = corner;
          connectivity[offset+subent_conn[1]] = corner + 1 + genCtx.ystride;
          connectivity[offset+subent_conn[2]] = corner + genCtx.ystride + genCtx.zstride;
          connectivity[offset+subent_conn[3]] = corner + 1 + genCtx.zstride;
          break;
        case 2: /* 0 2 3 7 of a HEX */
          connectivity[offset+subent_conn[0]] = corner;
          connectivity[offset+subent_conn[1]] = corner + 1 + genCtx.ystride;
          connectivity[offset+subent_conn[2]] = corner + genCtx.ystride;
          connectivity[offset+subent_conn[3]] = corner + genCtx.ystride + genCtx.zstride;
          break;
        case 3: /* 0 5 7 4 of a HEX */
          connectivity[offset+subent_conn[0]] = corner;
          connectivity[offset+subent_conn[1]] = corner + 1 + genCtx.zstride;
          connectivity[offset+subent_conn[2]] = corner + genCtx.ystride + genCtx.zstride;
          connectivity[offset+subent_conn[3]] = corner + genCtx.zstride;
          break;
        case 4: /* 2 7 5 6 of a HEX */
          connectivity[offset+subent_conn[0]] = corner + 1 + genCtx.ystride;
          connectivity[offset+subent_conn[1]] = corner + genCtx.ystride + genCtx.zstride;
          connectivity[offset+subent_conn[2]] = corner + 1 + genCtx.zstride;
          connectivity[offset+subent_conn[3]] = corner + 1 + genCtx.ystride + genCtx.zstride;
          break;
      }
      break;
  }
  return subent_conn.size();
}


#undef __FUNCT__
#define __FUNCT__ "DMMoab_SetElementConnectivity_Private"
std::pair<int,int> DMMoab_SetElementConnectivity_Private(DMMoabMeshGeneratorCtx& genCtx, int offset, int corner, moab::EntityHandle *connectivity)
{
  int vcount=0;
  std::vector<int> subent_conn;  /* only linear edge, tri, tet supported now */
  subent_conn.reserve(27);
  int m,subelem;
  if (genCtx.simplex) {
    subelem=(genCtx.dim==1 ? 1 : (genCtx.dim==2 ? 2 : 5));
    for (m=0; m<subelem; m++) {
      vcount=DMMoab_SetSimplexElementConnectivity_Private(genCtx, m, offset, corner, subent_conn, connectivity);
      offset+=vcount;
    }
  }
  else {
    subelem=1;
    vcount=DMMoab_SetTensorElementConnectivity_Private(genCtx, offset, corner, subent_conn, connectivity);
  }
  return std::pair<int,int>(vcount*subelem,subelem);
}


#undef __FUNCT__
#define __FUNCT__ "DMMoab_GenerateVertices_Private"
PetscErrorCode DMMoab_GenerateVertices_Private(moab::Interface *mbImpl, moab::ReadUtilIface *iface, DMMoabMeshGeneratorCtx& genCtx, int m, int n, int k,
    int a, int b, int c, moab::Tag& global_id_tag, moab::EntityHandle& startv, moab::Range& uverts)
{
  int x,y,z,ix,nnodes;
  int ii,jj,kk;
  std::vector<double*> arrays;
  std::vector<int> gids;
  moab::ErrorCode merr;

  PetscFunctionBegin;
  /* we will generate (q*block+1)^3 vertices, and block^3 hexas; q is 1 for linear, 2 for quadratic
   * the global id of the vertices will come from m, n, k, a, b, c
   * x will vary from  m*A*q*block + a*q*block to m*A*q*block+(a+1)*q*block etc.
   */
  nnodes = genCtx.blockSizeVertexXYZ[0]*(genCtx.dim>1? genCtx.blockSizeVertexXYZ[1]*(genCtx.dim>2 ? genCtx.blockSizeVertexXYZ[2]:1) :1);

  merr = iface->get_node_coords(3, nnodes, 0, startv, arrays);MBERR("Can't get node coords.", merr);

  /* will start with the lower corner: */
  x = m * genCtx.A * genCtx.q * genCtx.blockSizeElementXYZ[0] + a * genCtx.q * genCtx.blockSizeElementXYZ[0];
  y = n * genCtx.B * genCtx.q * genCtx.blockSizeElementXYZ[1] + b * genCtx.q * genCtx.blockSizeElementXYZ[1];
  z = k * genCtx.C * genCtx.q * genCtx.blockSizeElementXYZ[2] + c * genCtx.q * genCtx.blockSizeElementXYZ[2];
  ix = 0;
  gids.resize(nnodes);
  moab::Range verts(startv, startv + nnodes - 1);
  for (kk = 0; kk < (genCtx.dim>2?genCtx.blockSizeVertexXYZ[2]:1); kk++) {
    for (jj = 0; jj < (genCtx.dim>1?genCtx.blockSizeVertexXYZ[1]:1); jj++) {
      for (ii = 0; ii < genCtx.blockSizeVertexXYZ[0]; ii++,ix++) {
        /* set coordinates for the vertices */
        arrays[0][ix] = (x + ii)*genCtx.dx + genCtx.xyzbounds[0];
        arrays[1][ix] = (y + jj)*genCtx.dy + genCtx.xyzbounds[2];
        arrays[2][ix] = (z + kk)*genCtx.dz + genCtx.xyzbounds[4];

        /* If we want to set some tags on the vertices -> use the following entity handle definition:
           moab::EntityHandle v = startv + ix;
        */
        /* compute the global ID for vertex */
        gids[ix] = 1 + (x + ii) + (y + jj) * genCtx.NX + (z + kk) * (genCtx.NX * genCtx.NY);
      }
    }
  }
  /* set global ID data on vertices */
  mbImpl->tag_set_data(global_id_tag, verts, &gids[0]);
  verts.swap(uverts);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMMoab_GenerateElements_Private"
PetscErrorCode DMMoab_GenerateElements_Private(moab::Interface* mbImpl, moab::ReadUtilIface* iface, DMMoabMeshGeneratorCtx& genCtx, int m, int n, int k,
    int a, int b, int c, moab::Tag& global_id_tag, moab::EntityHandle startv, moab::Range& cells)
{
  moab::ErrorCode merr;
  PetscInt ix,ie,xe,ye,ze;
  PetscInt ii,jj,kk,nvperelem;
  PetscInt ntensorelems = genCtx.blockSizeElementXYZ[0]*(genCtx.dim>1? genCtx.blockSizeElementXYZ[1]*(genCtx.dim>2 ? genCtx.blockSizeElementXYZ[2]:1) :1); /*pow(genCtx.blockSizeElement,genCtx.dim);*/
  PetscInt nelems = ntensorelems;
  moab::EntityHandle starte; // connectivity
  moab::EntityHandle* conn;

  PetscFunctionBegin;
  switch(genCtx.dim) {
    case 1:
      nvperelem = 2;
      merr = iface->get_element_connect(nelems, 2, moab::MBEDGE, 0, starte, conn);MBERR("Can't get EDGE2 element connectivity.", merr);
      break;
    case 2:
      if (genCtx.simplex) {
        nvperelem = 3;
        nelems = ntensorelems*2;
        merr = iface->get_element_connect(nelems, 3, moab::MBTRI, 0, starte, conn);MBERR("Can't get TRI3 element connectivity.", merr);
      }
      else {
        nvperelem = 4;
        merr = iface->get_element_connect(nelems, 4, moab::MBQUAD, 0, starte, conn);MBERR("Can't get QUAD4 element connectivity.", merr);
      }
      break;
    case 3:
    default:
      if (genCtx.simplex) {
        nvperelem = 4;
        nelems = ntensorelems*5;
        merr = iface->get_element_connect(nelems, 4, moab::MBTET, 0, starte, conn);MBERR("Can't get TET4 element connectivity.", merr);
      }
      else {
        nvperelem = 8;
        merr = iface->get_element_connect(nelems, 8, moab::MBHEX, 0, starte, conn);MBERR("Can't get HEX8 element connectivity.", merr);
      }
      break;
  }

  ix = ie = 0; // index now in the elements, for global ids

  /* create a temporary range to store local element handles */
  moab::Range tmp(starte, starte + nelems - 1);
  std::vector<int> gids(nelems);

  /* identify the elements at the lower corner, for their global ids */
  xe = m * genCtx.A * genCtx.blockSizeElementXYZ[0] + a * genCtx.blockSizeElementXYZ[0];
  ye = (genCtx.dim > 1 ? n * genCtx.B * genCtx.blockSizeElementXYZ[1] + b * genCtx.blockSizeElementXYZ[1] : 0);
  ze = (genCtx.dim > 2 ? k * genCtx.C * genCtx.blockSizeElementXYZ[2] + c * genCtx.blockSizeElementXYZ[2] : 0);

  /* create owned elements requested by genCtx */
  for (kk = 0; kk < (genCtx.dim>2?genCtx.blockSizeElementXYZ[2]:1); kk++) {
    for (jj = 0; jj < (genCtx.dim>1?genCtx.blockSizeElementXYZ[1]:1); jj++) {
      for (ii = 0; ii < genCtx.blockSizeElementXYZ[0]; ii++) {

        moab::EntityHandle corner = startv + genCtx.q * ii + genCtx.q * jj * genCtx.ystride + genCtx.q * kk * genCtx.zstride;

        std::pair<int,int> entoffset = DMMoab_SetElementConnectivity_Private(genCtx, ix, corner, conn);

        for (int j = 0; j < entoffset.second; j++) {
          /* The entity handle for the particular element -> if we want to set some tags is
             moab::EntityHandle eh = starte + ie + j;
          */
          gids[ie+j] = 1 + ((xe + ii) + (ye + jj) * genCtx.nex + (ze + kk) * (genCtx.nex * genCtx.ney));
          //gids[ie+j] = ie + j + ((xe + ii) + (ye + jj) * genCtx.nex + (ze + kk) * (genCtx.nex * genCtx.ney)) ;
          //gids[ie+j] = 1 + ie;
          ie++;
        }

        ix += entoffset.first;
        //ie += entoffset.second;
      }
    }
  }
  if (genCtx.adjEnts) { /* we need to update adjacencies now, because some elements are new */
    merr = iface->update_adjacencies(starte, nelems, nvperelem, conn);MBERR("Can't update adjacencies", merr);
  }
  tmp.swap(cells);
  merr = mbImpl->tag_set_data(global_id_tag, cells, &gids[0]);MBERR("Can't set global ids to elements.", merr);
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMMBUtil_InitializeOptions"
PetscErrorCode DMMBUtil_InitializeOptions(DMMoabMeshGeneratorCtx& genCtx, PetscInt dim, PetscBool simplex, PetscInt rank, PetscInt nprocs, const PetscReal* bounds, PetscInt nele)
{
  PetscFunctionBegin;
  if(nele<nprocs) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"The dimensional discretization size should be greater or equal to number of processors: %D < %D",nele,nprocs);
  /* Initialize all genCtx data */
  genCtx.dim=dim;
  genCtx.simplex=simplex;
  genCtx.newMergeMethod=genCtx.keep_skins=genCtx.adjEnts=true;
  /* determine other global quantities for the mesh used for nodes increments */
  genCtx.q = 1;

  if (!genCtx.usrxyzgrid) { /* not overridden by genCtx - assume nele equally and that genCtx wants a uniform cube mesh */
    //genCtx.blockSizeElementXYZ[0]=genCtx.blockSizeElementXYZ[1]=genCtx.blockSizeElementXYZ[2]=std::pow(nlocalele,1.0/dim);
    genCtx.blockSizeElementXYZ[0]=nele;
    genCtx.blockSizeElementXYZ[1]=(dim>2?nele:nele/nprocs);
    genCtx.blockSizeElementXYZ[2]=(dim>2?nele/nprocs:1);
  }

  /* partition only by the largest dimension */
  /* Total number of local elements := genCtx.blockSizeElementXYZ[0]*(genCtx.dim>1? genCtx.blockSizeElementXYZ[1]*(genCtx.dim>2 ? genCtx.blockSizeElementXYZ[2]:1) :1); */
  if (bounds) {
    for (int i=0; i<6; i++)
      genCtx.xyzbounds[i]=bounds[i];
  }
  else {
    genCtx.xyzbounds[0]=genCtx.xyzbounds[2]=genCtx.xyzbounds[4]=0.0;
    genCtx.xyzbounds[1]=genCtx.xyzbounds[3]=genCtx.xyzbounds[5]=1.0;
  }

  if (!genCtx.usrprocgrid) {
    genCtx.M=genCtx.N=genCtx.K=std::pow(nprocs,1.0/dim);
    switch(genCtx.dim) {
     case 1:
       genCtx.M=nprocs;
       genCtx.N=genCtx.K=1;
       break;
     case 2:
       genCtx.K=1;
       genCtx.N=nprocs/(genCtx.M);
       break;
     default:
       genCtx.K=nprocs/(genCtx.M*genCtx.N);
       break;
    }
  }

  if (!genCtx.usrrefgrid) {
    genCtx.A=genCtx.B=genCtx.C=1;
  }

  /* more default values */
  genCtx.nex=genCtx.ney=genCtx.nez=0;
  genCtx.xstride=genCtx.ystride=genCtx.zstride=0;
  genCtx.NX=genCtx.NY=genCtx.NZ=0;
  genCtx.nex=genCtx.ney=genCtx.nez=0;
  genCtx.blockSizeVertexXYZ[0]=genCtx.blockSizeVertexXYZ[1]=genCtx.blockSizeVertexXYZ[2]=1;

  //genCtx.blockSizeElementXYZ[0]=genCtx.blockSizeElementXYZ[1]=genCtx.blockSizeElementXYZ[2]=nele;
  //genCtx.blockSizeVertexXYZ[0]=genCtx.blockSizeVertexXYZ[1]=genCtx.blockSizeVertexXYZ[2]=nele+1;

  switch(genCtx.dim) {
   case 3:
     //genCtx.blockSizeElementXYZ[2]=std::max(1,genCtx.blockSizeElementXYZ[2]/nprocs);
     //genCtx.blockSizeElementXYZ[2]=std::max(1,nele/nprocs);
     genCtx.blockSizeVertexXYZ[0] = genCtx.q*genCtx.blockSizeElementXYZ[0] + 1;
     genCtx.blockSizeVertexXYZ[1] = genCtx.q*genCtx.blockSizeElementXYZ[1] + 1;
     //genCtx.blockSizeElementXYZ[2]=fraction/(genCtx.blockSizeElementXYZ[0]*genCtx.blockSizeElementXYZ[1]);
     genCtx.blockSizeVertexXYZ[2] = genCtx.q*genCtx.blockSizeElementXYZ[2] + 1;

     genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0];   /* number of elements in x direction, used for global id on element */
     genCtx.dx = (genCtx.xyzbounds[1]-genCtx.xyzbounds[0])/(genCtx.nex*genCtx.q);  /* distance between 2 nodes in x direction */
     genCtx.NX = (genCtx.q * genCtx.nex + 1);
     genCtx.xstride = 1;
     genCtx.ney = genCtx.N * genCtx.B * genCtx.blockSizeElementXYZ[1];  /* number of elements in y direction  .... */
     genCtx.dy = (genCtx.xyzbounds[3]-genCtx.xyzbounds[2])/(genCtx.ney*genCtx.q);   /* distance between 2 nodes in y direction */
     genCtx.NY = (genCtx.q * genCtx.ney + 1);
     genCtx.ystride = genCtx.blockSizeVertexXYZ[0];
     genCtx.nez = genCtx.K * genCtx.C * genCtx.blockSizeElementXYZ[2];  /* number of elements in z direction  .... */
     genCtx.dz = (genCtx.xyzbounds[5]-genCtx.xyzbounds[4])/(genCtx.nez*genCtx.q);   /* distance between 2 nodes in z direction */
     genCtx.NZ = (genCtx.q * genCtx.nez + 1);
     genCtx.zstride = genCtx.blockSizeVertexXYZ[0] * genCtx.blockSizeVertexXYZ[1];
     break;
   case 2:
     //genCtx.blockSizeElementXYZ[1]=genCtx.blockSizeElementXYZ[2]=std::max(1,nele/nprocs);
     //genCtx.blockSizeElementXYZ[1]=fraction/genCtx.blockSizeElementXYZ[0];
     genCtx.blockSizeVertexXYZ[0] = genCtx.q*genCtx.blockSizeElementXYZ[0] + 1;
     genCtx.blockSizeVertexXYZ[1] = genCtx.q*genCtx.blockSizeElementXYZ[1] + 1;
     genCtx.blockSizeElementXYZ[2]=0;

     genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0];   /* number of elements in x direction, used for global id on element */
     genCtx.dx = (genCtx.xyzbounds[1]-genCtx.xyzbounds[0])/(genCtx.nex*genCtx.q);  /* distance between 2 nodes in x direction */
     genCtx.NX = (genCtx.q * genCtx.nex + 1);
     genCtx.xstride = 1;
     genCtx.ney = genCtx.N * genCtx.B * genCtx.blockSizeElementXYZ[1];  /* number of elements in y direction  .... */
     genCtx.dy = (genCtx.xyzbounds[3]-genCtx.xyzbounds[2])/(genCtx.ney*genCtx.q);   /* distance between 2 nodes in y direction */
     genCtx.NY = (genCtx.q * genCtx.ney + 1);
     genCtx.ystride = genCtx.blockSizeVertexXYZ[0];
     break;
   case 1:
     genCtx.blockSizeElementXYZ[1]=genCtx.blockSizeElementXYZ[2]=0;
     genCtx.blockSizeElementXYZ[0]=nele;
     genCtx.blockSizeVertexXYZ[0] = genCtx.q*genCtx.blockSizeElementXYZ[0] + 1;

     genCtx.nex = genCtx.M * genCtx.A * genCtx.blockSizeElementXYZ[0];   /* number of elements in x direction, used for global id on element */
     genCtx.dx = (genCtx.xyzbounds[1]-genCtx.xyzbounds[0])/(genCtx.nex*genCtx.q);  /* distance between 2 nodes in x direction */
     genCtx.NX = (genCtx.q * genCtx.nex + 1);
     genCtx.xstride = 1;
     break;
  }

  /*
  PetscInfo3(NULL, "Local elements:= %d, %d, %d\n",genCtx.blockSizeElementXYZ[0],genCtx.blockSizeElementXYZ[1],genCtx.blockSizeElementXYZ[2]);
  PetscInfo3(NULL, "Local vertices:= %d, %d, %d\n",genCtx.blockSizeVertexXYZ[0],genCtx.blockSizeVertexXYZ[1],genCtx.blockSizeVertexXYZ[2]);
  PetscInfo3(NULL, "Local nexyz:= %d, %d, %d\n",genCtx.nex,genCtx.ney,genCtx.nez);
  PetscInfo3(NULL, "Local delxyz:= %g, %g, %g\n",genCtx.dx,genCtx.dy,genCtx.dz);
  PetscInfo3(NULL, "Local strides:= %d, %d, %d\n",genCtx.xstride,genCtx.ystride,genCtx.zstride);
  */
  PetscFunctionReturn(0);
}

/*@
  DMMoabCreateBoxMesh - Creates a mesh on the tensor product (box) of intervals with genCtx specified bounds.

  Collective on MPI_Comm

  Input Parameters:
+ comm - The communicator for the DM object
. dim - The spatial dimension
. bounds - The bounds of the box specified with [x-left, x-right, y-bottom, y-top, z-bottom, z-top] depending on the spatial dimension
. nele - The number of discrete elements in each direction
. user_nghost - The number of ghosted layers needed in the partitioned mesh

  Output Parameter:
. dm  - The DM object

  Level: beginner

.keywords: DM, create
.seealso: DMSetType(), DMCreate(), DMMoabLoadFromFile()
@*/
PetscErrorCode DMMoabCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool useSimplex, const PetscReal* bounds, PetscInt nele, PetscInt nghost, DM *dm)
{
  PetscErrorCode       ierr;
  moab::ErrorCode      merr;
  PetscInt             a,b,c,n,global_size,global_rank=-1;
  DM_Moab             *dmmoab;
  moab::Interface     *mbImpl;
  moab::ParallelComm  *pcomm;
  moab::ReadUtilIface *readMeshIface;
  moab::Range          verts,cells,edges,faces,adj,dim3,dim2;
  DMMoabMeshGeneratorCtx          genCtx;
  const PetscInt       npts=nele+1;        /* Number of points in every dimension */

  moab::Tag            global_id_tag,part_tag,geom_tag;
  moab::Range          ownedvtx,ownedelms,localvtxs,localelms;
  moab::EntityHandle   regionset;
  PetscInt             ml=0,nl=0,kl=0,leftover;

  PetscFunctionBegin;
  if(dim < 1 || dim > 3) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Invalid dimension argument for mesh: dim=[1,3].\n");

  ierr = MPI_Comm_size(comm, &global_size);CHKERRQ(ierr);
  /* total number of vertices in all dimensions */
  n=pow(npts,dim);

  /* do some error checking */
  if(n < 2) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Number of points must be >= 2.\n");
  if(global_size > n) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Number of processors must be less than or equal to number of elements.\n");
  if(nghost < 0) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Number of ghost layers cannot be negative.\n");

  /* Create the basic DMMoab object and keep the default parameters created by DM impls */
  ierr = DMMoabCreateMoab(comm, NULL, NULL, NULL, NULL, dm);CHKERRQ(ierr);

  /* get all the necessary handles from the private DM object */
  dmmoab = (DM_Moab*)(*dm)->data;
  mbImpl = dmmoab->mbiface;
  pcomm = dmmoab->pcomm;
  global_id_tag = dmmoab->ltog_tag;
  global_rank = pcomm->rank();
  dmmoab->dim = dim;

  /* create a file set to associate all entities in current mesh */
  merr = mbImpl->create_meshset(moab::MESHSET_SET, dmmoab->fileset);MBERR("Creating file set failed", merr);

  /* No errors yet; proceed with building the mesh */
  merr = mbImpl->query_interface(readMeshIface);MBERRNM(merr);

  //PetscObjectOptionsBegin(dm);
  PetscOptionsBegin(comm,"","DMMoab Creation Options","DMMOAB");
  /* Handle DMMoab spatial resolution */
  PetscOptionsInt("-dmb_grid_x","Number of grid points in x direction","DMMoabSetSizes",genCtx.blockSizeElementXYZ[0],&genCtx.blockSizeElementXYZ[0],&genCtx.usrxyzgrid);
  if (dim > 1) {PetscOptionsInt("-dmb_grid_y","Number of grid points in y direction","DMMoabSetSizes",genCtx.blockSizeElementXYZ[1],&genCtx.blockSizeElementXYZ[1],&genCtx.usrxyzgrid);}
  if (dim > 2) {PetscOptionsInt("-dmb_grid_z","Number of grid points in z direction","DMMoabSetSizes",genCtx.blockSizeElementXYZ[2],&genCtx.blockSizeElementXYZ[2],&genCtx.usrxyzgrid);}

  /* Handle DMMoab parallel distibution */
  PetscOptionsInt("-dmb_processors_x","Number of processors in x direction","DMMoabSetNumProcs",genCtx.M,&genCtx.M,&genCtx.usrprocgrid);
  if (dim > 1) {PetscOptionsInt("-dmb_processors_y","Number of processors in y direction","DMMoabSetNumProcs",genCtx.N,&genCtx.N,&genCtx.usrprocgrid);}
  if (dim > 2) {PetscOptionsInt("-dmb_processors_z","Number of processors in z direction","DMMoabSetNumProcs",genCtx.K,&genCtx.K,&genCtx.usrprocgrid);}

  /* Handle DMMoab block refinement */
  PetscOptionsInt("-dmb_refine_x","Number of refinement blocks in x direction","DMMoabSetRefinement",genCtx.A,&genCtx.A,&genCtx.usrrefgrid);
  if (dim > 1) {PetscOptionsInt("-dmb_refine_y","Number of refinement blocks in y direction","DMMoabSetRefinement",genCtx.B,&genCtx.B,&genCtx.usrrefgrid);}
  if (dim > 2) {PetscOptionsInt("-dmb_refine_z","Number of refinement blocks in z direction","DMMoabSetRefinement",genCtx.C,&genCtx.C,&genCtx.usrrefgrid);}
  PetscOptionsEnd();

  ierr = DMMBUtil_InitializeOptions(genCtx, dim, useSimplex, global_rank, global_size, bounds, nele);CHKERRQ(ierr);

  /* Lets check for some valid input */
  if (genCtx.dim < 1 || genCtx.dim > 3) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Invalid topological dimension specified: %d.\n",genCtx.dim);
  if (genCtx.M * genCtx.N * genCtx.K != global_size) SETERRQ4(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Invalid [m, n, k] data: %d, %d, %d. Product must be equal to global size = %d.\n",genCtx.M,genCtx.N,genCtx.K,global_size);
  if (genCtx.xyzbounds) {
    /* validate the bounds data */
    if(genCtx.xyzbounds[0] >= genCtx.xyzbounds[1]) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"X-dim: Left boundary cannot be greater than right. [%G >= %G]\n",genCtx.xyzbounds[0],genCtx.xyzbounds[1]);
    if(genCtx.dim > 1 && (genCtx.xyzbounds[2] >= genCtx.xyzbounds[3])) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Y-dim: Left boundary cannot be greater than right. [%G >= %G]\n",genCtx.xyzbounds[2],genCtx.xyzbounds[3]);
    if(genCtx.dim > 2 && (genCtx.xyzbounds[4] >= genCtx.xyzbounds[5])) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Z-dim: Left boundary cannot be greater than right. [%G >= %G]\n",genCtx.xyzbounds[4],genCtx.xyzbounds[5]);
  }
  if (genCtx.adjEnts) genCtx.keep_skins = true; /* do not delete anything - consumes more memory */

  /* determine m, n, k for processor rank */
  kl = (genCtx.dim>2?global_rank/(genCtx.M*genCtx.N):0);
  leftover = global_rank%(genCtx.M*genCtx.N);
  nl = leftover/genCtx.M;
  ml = leftover%genCtx.M;
  //if (global_rank==global_size-1) cout << "m, n, k for last rank:" << m << " " << n << " " << k << "\n";

  /*
   * so there are a total of M * A * blockSizeElement elements in x direction (so M * A * blockSizeElement + 1 verts in x direction)
   * so there are a total of N * B * blockSizeElement elements in y direction (so N * B * blockSizeElement + 1 verts in y direction)
   * so there are a total of K * C * blockSizeElement elements in z direction (so K * C * blockSizeElement + 1 verts in z direction)

   * there are ( M * A blockSizeElement )      *  ( N * B * blockSizeElement)      * (K * C * blockSizeElement )    hexas
   * there are ( M * A * blockSizeElement + 1) *  ( N * B * blockSizeElement + 1 ) * (K * C * blockSizeElement + 1) vertices
   * x is the first dimension that varies
   */

  /* generate the block at (a, b, c); it will represent a partition , it will get a partition tag */
  int dum_id=-1;
  merr = mbImpl->tag_get_handle("GLOBAL_ID", 1, moab::MB_TYPE_INTEGER, global_id_tag);MBERR("Getting Tag handle failed", merr);

  merr = mbImpl->tag_get_handle("PARALLEL_PARTITION", 1, moab::MB_TYPE_INTEGER, part_tag, moab::MB_TAG_CREAT|moab::MB_TAG_SPARSE, &dum_id);MBERR("Getting Tag handle failed", merr);

  /* lets create some sets */
  merr = mbImpl->tag_get_handle(GEOM_DIMENSION_TAG_NAME, 1, moab::MB_TYPE_INTEGER, geom_tag, moab::MB_TAG_CREAT|moab::MB_TAG_SPARSE, &dum_id);MBERRNM(merr);

  for (a=0; a<(genCtx.dim>0?genCtx.A:genCtx.A); a++) {
    for (b=0; b<(genCtx.dim>1?genCtx.B:1); b++) {
      for (c=0; c<(genCtx.dim>2?genCtx.C:1); c++) {
        moab::EntityHandle startv,part_set;
        ierr = DMMoab_GenerateVertices_Private(mbImpl, readMeshIface, genCtx, ml, nl, kl, a, b, c, global_id_tag, startv, verts);CHKERRQ(ierr);

        ierr = DMMoab_GenerateElements_Private(mbImpl, readMeshIface, genCtx, ml, nl, kl, a, b, c, global_id_tag, startv, cells);CHKERRQ(ierr);

        merr = mbImpl->create_meshset(moab::MESHSET_SET, part_set);MBERR("Can't create mesh set.", merr);

        merr = mbImpl->add_entities(part_set, verts);MBERR("Can't add vertices to set.", merr);
        //merr = mbImpl->add_entities(part_set, cells);MBERR("Can't add entities to set.", merr);

        merr = mbImpl->create_meshset(moab::MESHSET_SET, regionset);MBERRNM(merr);
        merr = mbImpl->add_entities(regionset, cells);MBERR("Can't add entities to set.", merr);
        merr = mbImpl->tag_set_data(geom_tag, &regionset, 1, &dmmoab->dim);MBERRNM(merr);
        merr = mbImpl->add_parent_child(part_set,regionset);MBERRNM(merr);
        merr = mbImpl->unite_meshset(part_set, regionset);MBERRNM(merr);

        /* if needed, add all edges and faces */
        if (genCtx.adjEnts)
        {
          if (genCtx.dim > 1) {
            merr = mbImpl->get_adjacencies(cells, 1, true, edges, moab::Interface::UNION);MBERR("Can't get edges", merr);
            merr = mbImpl->add_entities(part_set, edges);MBERR("Can't add edges to partition set.", merr);
          }
          if (genCtx.dim > 2) {
            merr = mbImpl->get_adjacencies(cells, 2, true, faces, moab::Interface::UNION);MBERR("Can't get faces", merr);
            merr = mbImpl->add_entities(part_set, faces);MBERR("Can't add faces to partition set.", merr);
          }
          edges.clear();
          faces.clear();
        }

        int part_num=0;
        switch(genCtx.dim) {
          case 3:
            part_num += (c+kl*genCtx.C)*(genCtx.M*genCtx.A * genCtx.N*genCtx.B);
          case 2:
            part_num += (b+nl*genCtx.B)*(genCtx.M*genCtx.A);
          case 1:
            part_num += (a+ml*genCtx.A);
           break;
        }

        merr = mbImpl->tag_set_data(part_tag, &part_set, 1, &part_num);MBERR("Can't set part tag on set", merr);
        merr = mbImpl->add_parent_child(dmmoab->fileset, part_set);MBERR("Can't add part set to file set.", merr);
        merr = mbImpl->unite_meshset(dmmoab->fileset, part_set);MBERRNM(merr);

        cells.clear();
        verts.clear();
      }
    }
  }

  PetscInfo2(NULL, "Generated local mesh: %D vertices and %D elements.\n", verts.size(), cells.size());

  /* resolving shared entities between processors */
  if (global_size>1) {

    moab::MergeMesh mm(mbImpl);

    merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, genCtx.dim, cells);MBERR("Can't get all d-dimensional elements.", merr);
    merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 0, verts);MBERR("Can't get all vertices.", merr);

    if (genCtx.A*genCtx.B*genCtx.C!=1) { //  merge needed
      if (genCtx.newMergeMethod) {
        merr = mm.merge_using_integer_tag(verts, global_id_tag);MBERR("Can't merge with GLOBAL_ID tag", merr);
      }
      else {
        merr = mm.merge_entities(cells, 0.0001);MBERR("Can't merge with coordinates", merr);
      }
    }

    /* check the handles */
    merr = pcomm->check_all_shared_handles();MBERRV(mbImpl,merr);

    /* resolve the shared entities by exchanging information to adjacent processors */
    merr = pcomm->resolve_shared_ents(dmmoab->fileset,cells,dim,dim-1,NULL,&global_id_tag);MBERRV(mbImpl,merr);
    merr = pcomm->exchange_ghost_cells(dim,0,nghost,dim,true,false,&dmmoab->fileset);MBERRV(mbImpl,merr);

    /* Reassign global IDs on all entities. */
    merr = pcomm->assign_global_ids(dmmoab->fileset,dim,1,false,true,false);MBERRNM(merr);
    merr = pcomm->exchange_tags(global_id_tag,verts);MBERRV(mbImpl,merr);
    merr = pcomm->exchange_tags(global_id_tag,cells);MBERRV(mbImpl,merr);

    /* now resolve the shared entities */
    //merr = dmmoab->pcomm->resolve_shared_ents( dmmoab->fileset, cells, genCtx.dim, 0 );MBERR("Can't resolve shared entities", merr);
    //PetscInfo(NULL, "Resolving shared entities.\n");

    if (!genCtx.keep_skins) { // default is to delete the 1- and 2-dimensional entities
      // delete all quads and edges
      moab::Range toDelete;
      if (genCtx.dim > 1) {
        merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 1, toDelete);MBERR("Can't get edges", merr);
      }

      if (genCtx.dim > 2) {
        merr = mbImpl->get_entities_by_dimension(dmmoab->fileset, 2, toDelete);MBERR("Can't get faces", merr);
      }

      merr = dmmoab->pcomm->delete_entities(toDelete) ;MBERR("Can't delete entities", merr);
      PetscInfo(NULL, "Deleted edges and faces, and correct sharedEnts.\n");
    }

  }
  PetscFunctionReturn(0);
}


PetscErrorCode DMMoab_GetReadOptions_Private(PetscBool by_rank, PetscInt numproc, PetscInt dim, MoabReadMode mode, PetscInt dbglevel, const char* dm_opts, const char* extra_opts, const char** read_opts)
{
  char           *ropts;
  char           ropts_par[PETSC_MAX_PATH_LEN];
  char           ropts_dbg[PETSC_MAX_PATH_LEN];
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscMalloc1(PETSC_MAX_PATH_LEN,&ropts);CHKERRQ(ierr);
  ierr = PetscMemzero(&ropts_par,PETSC_MAX_PATH_LEN);CHKERRQ(ierr);
  ierr = PetscMemzero(&ropts_dbg,PETSC_MAX_PATH_LEN);CHKERRQ(ierr);

  /* do parallel read unless using only one processor */
  if (numproc > 1) {
    ierr = PetscSNPrintf(ropts_par, PETSC_MAX_PATH_LEN, "PARALLEL=%s;PARTITION=PARALLEL_PARTITION;PARTITION_DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=%d.0.1%s;",MoabReadModes[mode],dim,(by_rank ? ";PARTITION_BY_RANK":""));CHKERRQ(ierr);
  }

  if (dbglevel) {
    if (numproc>1) {
      ierr = PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "%sCPUTIME;DEBUG_IO=%d;DEBUG_PIO=%d;",dbglevel,dbglevel);CHKERRQ(ierr);
    }
    else {
      ierr = PetscSNPrintf(ropts_dbg, PETSC_MAX_PATH_LEN, "%sCPUTIME;DEBUG_IO=%d;",dbglevel);CHKERRQ(ierr);
    }
  }

  ierr = PetscSNPrintf(ropts, PETSC_MAX_PATH_LEN, "%s%s%s%s",ropts_par,ropts_dbg,(extra_opts?extra_opts:""),(dm_opts?dm_opts:""));CHKERRQ(ierr);
  *read_opts = ropts;
  PetscFunctionReturn(0);
}


/*@
  DMMoabLoadFromFile - Creates a DM object by loading the mesh from a user specified file.

  Collective on MPI_Comm

  Input Parameters:
+ comm - The communicator for the DM object
. dim - The spatial dimension
. filename - The name of the mesh file to be loaded
. usrreadopts - The options string to read a MOAB mesh. 
  Reference (Parallel Mesh Initialization: http://www.mcs.anl.gov/~fathom/moab-docs/html/contents.html#fivetwo)

  Output Parameter:
. dm  - The DM object

  Level: beginner

.keywords: DM, create

.seealso: DMSetType(), DMCreate(), DMMoabCreateBoxMesh()
@*/
PetscErrorCode DMMoabLoadFromFile(MPI_Comm comm,PetscInt dim,const char* filename, const char* usrreadopts, DM *dm)
{
  moab::ErrorCode merr;
  PetscInt        nprocs;
  DM_Moab        *dmmoab;
  moab::Interface *mbiface;
  moab::ParallelComm *pcomm;
  moab::Range verts,elems;
  const char *readopts;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidPointer(dm,5);

  /* Create the basic DMMoab object and keep the default parameters created by DM impls */
  ierr = DMMoabCreateMoab(comm, NULL, NULL, NULL, NULL, dm);CHKERRQ(ierr);

  /* get all the necessary handles from the private DM object */
  dmmoab = (DM_Moab*)(*dm)->data;
  mbiface = dmmoab->mbiface;
  pcomm = dmmoab->pcomm;
  nprocs = pcomm->size();
  /* TODO: Decipher dimension based on the loaded mesh instead of getting from user */
  dmmoab->dim = dim;

  /* create a file set to associate all entities in current mesh */
  merr = dmmoab->mbiface->create_meshset(moab::MESHSET_SET, dmmoab->fileset);MBERR("Creating file set failed", merr);

  /* add mesh loading options specific to the DM */
  ierr = DMMoab_GetReadOptions_Private(dmmoab->partition_by_rank, nprocs, dim, dmmoab->read_mode,
                                        dmmoab->rw_dbglevel, dmmoab->extra_read_options, usrreadopts, &readopts);CHKERRQ(ierr);

  PetscInfo2(*dm, "Reading file %s with options: %s\n",filename,readopts);

  /* Load the mesh from a file. */
  merr = mbiface->load_file(filename, &dmmoab->fileset, readopts);MBERRVM(mbiface,"Reading MOAB file failed.", merr);

  /* Reassign global IDs on all entities. */
  merr = pcomm->assign_global_ids(dmmoab->fileset,dim,1,true,true,true);MBERRNM(merr);

  /* load the local vertices */
  merr = mbiface->get_entities_by_type(dmmoab->fileset, moab::MBVERTEX, verts, true);MBERRNM(merr);
  /* load the local elements */
  merr = mbiface->get_entities_by_dimension(dmmoab->fileset, dim, elems, true);MBERRNM(merr);

  /* Everything is set up, now just do a tag exchange to update tags
     on all of the ghost vertexes */
  merr = pcomm->exchange_tags(dmmoab->ltog_tag,verts);MBERRV(mbiface,merr);
  merr = pcomm->exchange_tags(dmmoab->ltog_tag,elems);MBERRV(mbiface,merr);

  merr = pcomm->exchange_ghost_cells(dim,0,1,0,true,true,&dmmoab->fileset);MBERRV(mbiface,merr);

  merr = pcomm->collective_sync_partition();MBERR("Collective sync failed", merr);

  PetscInfo3(*dm, "MOAB file '%s' was successfully loaded. Found %D vertices and %D elements.\n", filename, verts.size(), elems.size());
  ierr = PetscFree(readopts);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}