#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/ScdInterface.hpp>
#include <moab/CN.hpp>


#undef __FUNCT__
#define __FUNCT__ "DMMoabComputeDomainBounds_Private"
static PetscErrorCode DMMoabComputeDomainBounds_Private(moab::ParallelComm* pcomm, PetscInt dim, PetscInt neleglob, PetscInt *ise)
{
  PetscInt size,rank;
  PetscInt fraction,remainder;
  PetscInt starts[3],sizes[3];

  PetscFunctionBegin;
  if(dim<1 && dim>3) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"The problem dimension is invalid: %D",dim);
  
  size=pcomm->size();
  rank=pcomm->rank();
  fraction=neleglob/size;    /* partition only by the largest dimension */
  remainder=neleglob%size;   /* remainder after partition which gets evenly distributed by round-robin */

  if(fraction==0) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"The leading dimension size should be greater than number of processors: %D < %D",neleglob,size);

  starts[0]=starts[1]=starts[2]=0;       /* default dimensional element = 1 */
  sizes[0]=sizes[1]=sizes[2]=neleglob;   /* default dimensional element = 1 */

  if(rank < remainder) { /* This process gets "fraction+1" elements */
    sizes[dim-1] = (fraction + 1);
    starts[dim-1] = rank * (fraction+1);
  } else { /* This process gets "fraction" elements */
    sizes[dim-1] = fraction;
    starts[dim-1] = (remainder*(fraction+1) + fraction*(rank-remainder));
  }

  for(int i=dim-1; i>=0; --i) {
    ise[2*i]=starts[i];ise[2*i+1]=starts[i]+sizes[i];
  }
  PetscFunctionReturn(0);
}

#undef __FUNCT__
#define __FUNCT__ "DMMoab_SetStructuredCoords_Private"
static void DMMoab_SetStructuredCoords_Private(PetscInt i, PetscInt j, PetscInt k, PetscReal hx, PetscReal hy, PetscReal hz, PetscInt vcount, std::vector<double*>& vcoords)
{
  vcoords[0][vcount] = i*hx;
  vcoords[1][vcount] = j*hy;
  vcoords[2][vcount] = k*hz;
}

#undef __FUNCT__
#define __FUNCT__ "DMMoab_SetTensorElementConnectivity_Private"
static void DMMoab_SetTensorElementConnectivity_Private(PetscInt dim, moab::EntityType etype, PetscInt offset, PetscInt nele, PetscInt i, PetscInt j, PetscInt k, PetscInt vfirst, moab::EntityHandle *connectivity)
{
  std::vector<int>    subent_conn(pow(2,dim));  /* only linear edge, quad, hex supported now */

  moab::CN::SubEntityVertexIndices(etype, dim, 0, subent_conn.data());

  switch(dim) {
    case 1:
      connectivity[offset+subent_conn[0]] = vfirst+i;
      connectivity[offset+subent_conn[1]] = vfirst+(i+1);
      break;
    case 2:
      connectivity[offset+subent_conn[0]] = vfirst+i+j*(nele+1);
      connectivity[offset+subent_conn[1]] = vfirst+(i+1)+j*(nele+1);
      connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(j+1)*(nele+1);
      connectivity[offset+subent_conn[3]] = vfirst+i+(j+1)*(nele+1);
      break;
    case 3:
    default:
      connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
      connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*k);
      connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
      connectivity[offset+subent_conn[3]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*k);
      connectivity[offset+subent_conn[4]] = vfirst+i+(nele+1)*(j+(nele+1)*(k+1));
      connectivity[offset+subent_conn[5]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
      connectivity[offset+subent_conn[6]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*(k+1));
      connectivity[offset+subent_conn[7]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
      break;
  }
}

#undef __FUNCT__
#define __FUNCT__ "DMMoab_SetSimplexElementConnectivity_Private"
static void DMMoab_SetSimplexElementConnectivity_Private(PetscInt dim, PetscInt subelem, moab::EntityType etype, PetscInt offset, PetscInt nele, PetscInt i, PetscInt j, PetscInt k, PetscInt vfirst, moab::EntityHandle *connectivity)
{
  std::vector<int>    subent_conn(pow(2,dim));  /* only linear edge, quad, hex supported now */

  moab::CN::SubEntityVertexIndices(etype, dim, 0, subent_conn.data());

  switch(dim) {
    case 1:
      connectivity[offset+subent_conn[0]] = vfirst+i;
      connectivity[offset+subent_conn[1]] = vfirst+(i+1);
      break;
    case 2:
      if (subelem) { /* 1 2 3 of a QUAD */
        connectivity[offset+subent_conn[0]] = vfirst+i+j*(nele+1);
        connectivity[offset+subent_conn[1]] = vfirst+(i+1)+j*(nele+1);
        connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(j+1)*(nele+1);
      }
      else {        /* 3 4 1 of a QUAD */
        connectivity[offset+subent_conn[0]] = vfirst+(i+1)+(j+1)*(nele+1);
        connectivity[offset+subent_conn[1]] = vfirst+i+(j+1)*(nele+1);
        connectivity[offset+subent_conn[2]] = vfirst+i+j*(nele+1);
      }
      break;
    case 3:
    default:
      switch(subelem) {
        case 0: /* 0 1 2 5 of a HEX */
          connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
          connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*k);
          connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
          connectivity[offset+subent_conn[3]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
          break;
        case 1: /* 0 2 7 5 of a HEX */
          connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
          connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
          connectivity[offset+subent_conn[2]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
          connectivity[offset+subent_conn[3]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
          break;
        case 2: /* 0 2 3 7 of a HEX */
          connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
          connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
          connectivity[offset+subent_conn[2]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*k);
          connectivity[offset+subent_conn[3]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
          break;
        case 3: /* 0 5 7 4 of a HEX */
          connectivity[offset+subent_conn[0]] = vfirst+i+(nele+1)*(j+(nele+1)*k);
          connectivity[offset+subent_conn[1]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
          connectivity[offset+subent_conn[2]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
          connectivity[offset+subent_conn[3]] = vfirst+i+(nele+1)*(j+(nele+1)*(k+1));
          break;
        case 4: /* 2 7 5 6 of a HEX */
          connectivity[offset+subent_conn[0]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*k);
          connectivity[offset+subent_conn[1]] = vfirst+i+(nele+1)*((j+1)+(nele+1)*(k+1));
          connectivity[offset+subent_conn[2]] = vfirst+(i+1)+(nele+1)*(j+(nele+1)*(k+1));
          connectivity[offset+subent_conn[3]] = vfirst+(i+1)+(nele+1)*((j+1)+(nele+1)*(k+1));
          break;
      }
      break;
  }
}

#undef __FUNCT__
#define __FUNCT__ "DMMoab_SetElementConnectivity_Private"
static void DMMoab_SetElementConnectivity_Private(PetscBool useSimplex, PetscInt dim, moab::EntityType etype, PetscInt *ecount, PetscInt vpere, PetscInt nele, PetscInt i, PetscInt j, PetscInt k, PetscInt vfirst, moab::EntityHandle *connectivity)
{
  PetscInt m,subelem;
  if (useSimplex) {
    subelem=(dim==1 ? 1 : (dim==2 ? 2 : 5));
    for (m=0; m<subelem; m++)
      DMMoab_SetSimplexElementConnectivity_Private(dim, m, etype, (*ecount+m)*vpere, nele, i, j, k, vfirst, connectivity);

  }
  else {
    subelem=1;
    DMMoab_SetTensorElementConnectivity_Private(dim, etype, (*ecount)*vpere, nele, i, j, k, vfirst, connectivity);
  }
  *ecount+=subelem;
}


#undef __FUNCT__
#define __FUNCT__ "DMMoabCreateBoxMesh"
/*@
  DMMoabCreateBoxMesh - Creates a mesh on the tensor product (box) of intervals with user 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 user_nghost, DM *dm)
{
  PetscErrorCode  ierr;
  moab::ErrorCode merr;
  PetscInt        i,j,k,n,nprocs;
  DM_Moab        *dmmoab;
  moab::Interface *mbiface;
  moab::ParallelComm *pcomm;
  moab::ReadUtilIface* readMeshIface;

  moab::Tag  id_tag=PETSC_NULL;
  moab::Range         ownedvtx,ownedelms;
  moab::EntityHandle  vfirst,efirst,regionset,faceset,edgeset,vtxset;
  std::vector<double*> vcoords;
  moab::EntityHandle  *connectivity = 0;
  moab::EntityType etype=moab::MBHEX;
  PetscInt    ise[6];
  PetscReal   xse[6],defbounds[6];
  /* TODO: Fix nghost > 0 - now relying on exchange_ghost_cells */
  const PetscInt nghost=0;

  moab::Tag geom_tag;

  moab::Range adj,dim3,dim2;
  bool build_adjacencies=false;

  const PetscInt npts=nele+1;        /* Number of points in every dimension */
  PetscInt vpere=0,locnele=0,locnpts=0,ghnele,ghnpts;    /* Number of verts/element, vertices, elements owned by this process */

  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, &nprocs);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(nprocs > 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, PETSC_NULL, PETSC_NULL, PETSC_NULL, PETSC_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;
  id_tag = dmmoab->ltog_tag;
  nprocs = pcomm->size();
  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);

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

  ierr = PetscMemzero(ise,sizeof(PetscInt)*6);CHKERRQ(ierr);  

  /* call the collective routine that computes the domain bounds for a structured mesh using MOAB */
  ierr = DMMoabComputeDomainBounds_Private(pcomm, dim, nele, ise);CHKERRQ(ierr);

  /* set some variables based on dimension */
  switch(dim) {
   case 1:
    vpere = 2;
    locnele = (ise[1]-ise[0]);
    locnpts = (ise[1]-ise[0]+1);
    ghnele = (nghost > 0 ? (ise[0] > nghost ? 1 : 0) + (ise[1] < nele - nghost ? 1 : 0) : 0 );
    ghnpts = (nghost > 0 ? (ise[0] > 0 ? 1 : 0) + (ise[1] < nele ? 1 : 0) : 0);
    etype = moab::MBEDGE;
    break;
   case 2:
    locnpts = (ise[1]-ise[0]+1)*(ise[3]-ise[2]+1);
    ghnpts = (nghost > 0 ? (ise[2] > 0 ? npts : 0) + (ise[3] < nele ? npts : 0) : 0);
    if (useSimplex) {
      vpere = 3;
      locnele = 2*(ise[1]-ise[0])*(ise[3]-ise[2]);
      ghnele = 2*(nghost > 0 ? (ise[2] > 0 ? nele : 0) + (ise[3] < nele ? nele : 0) : 0);
      etype = moab::MBTRI;
    }
    else {
      vpere = 4;
      locnele = (ise[1]-ise[0])*(ise[3]-ise[2]);
      ghnele = (nghost > 0 ? (ise[2] > 0 ? nele : 0) + (ise[3] < nele ? nele : 0) : 0);
      etype = moab::MBQUAD;
    }
    break;
   case 3:
   default:
    locnpts = (ise[1]-ise[0]+1)*(ise[3]-ise[2]+1)*(ise[5]-ise[4]+1);
    ghnpts = (nghost > 0 ? (ise[4] > 0 ? npts*npts : 0) + (ise[5] < nele ? npts*npts : 0) : 0);
    if (useSimplex) {
      vpere = 4;
      locnele = 5*(ise[1]-ise[0])*(ise[3]-ise[2])*(ise[5]-ise[4]);
      ghnele = 5*(nghost > 0 ? (ise[4] > 0 ? nele*nele : 0) + (ise[5] < nele ? nele*nele : 0) : 0);
      etype = moab::MBTET;
    }
    else {
      vpere = 8;
      locnele = (ise[1]-ise[0])*(ise[3]-ise[2])*(ise[5]-ise[4]);
      ghnele = (nghost > 0 ? (ise[4] > 0 ? nele*nele : 0) + (ise[5] < nele ? nele*nele : 0) : 0);
      etype = moab::MBHEX;
    }
    break;
  }

  /* we have a domain of size [1,1,1] - now compute local co-ordinate box */
  ierr = PetscMemzero(xse,sizeof(PetscReal)*6);CHKERRQ(ierr);  
  for(i=0; i<6; ++i) {
    xse[i]=(PetscReal)ise[i]/nele;
  }

  /* Create vertexes and set the coodinate of each vertex */
  merr = readMeshIface->get_node_coords(3,locnpts+ghnpts,0,vfirst,vcoords,n);MBERRNM(merr);

  /* Compute the co-ordinates of vertices and global IDs */
  std::vector<int>    vgid(locnpts+ghnpts);
  int vcount=0;

  if (!bounds) { /* default box mesh is defined on a unit-cube */
    defbounds[0]=0.0; defbounds[1]=1.0;
    defbounds[2]=0.0; defbounds[3]=1.0;
    defbounds[4]=0.0; defbounds[5]=1.0;
    bounds=defbounds;
  }
  else {
    /* validate the bounds data */
    if(bounds[0] >= bounds[1]) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"X-dim: Left boundary cannot be greater than right. [%G >= %G]\n",bounds[0],bounds[1]);
    if(dim > 1 && (bounds[2] >= bounds[3])) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Y-dim: Left boundary cannot be greater than right. [%G >= %G]\n",bounds[2],bounds[3]);
    if(dim > 2 && (bounds[4] >= bounds[5])) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Z-dim: Left boundary cannot be greater than right. [%G >= %G]\n",bounds[4],bounds[5]);
  }

  const double hx=(bounds[1]-bounds[0])/nele;
  const double hy=(dim > 1 ? (bounds[3]-bounds[2])/nele : 0.0);
  const double hz=(dim > 2 ? (bounds[5]-bounds[4])/nele : 0.0);

  /* create all the owned vertices */
  for (k = ise[4]; k <= ise[5]; k++) {
    for (j = ise[2]; j <= ise[3]; j++) {
      for (i = ise[0]; i <= ise[1]; i++, vcount++) {
        DMMoab_SetStructuredCoords_Private(i,j,k,hx,hy,hz,vcount,vcoords);
        vgid[vcount] = (k*npts+j)*npts+i+1;
      }
    }
  }

  /* create ghosted vertices requested by user - below the current plane */
  if (ise[2*dim-2] > 0) {
    for (k = (dim==3?ise[4]-nghost:ise[4]); k <= (dim==3?ise[4]-1:ise[5]); k++) {
      for (j = (dim==2?ise[2]-nghost:ise[2]); j <= (dim==2?ise[2]-1:ise[3]); j++) {
        for (i = (dim>1?ise[0]:ise[0]-nghost); i <= (dim>1?ise[1]:ise[0]-1); i++, vcount++) {
          DMMoab_SetStructuredCoords_Private(i,j,k,hx,hy,hz,vcount,vcoords);
          vgid[vcount] = (k*npts+j)*npts+i+1;
        }
      }
    }
  }

  /* create ghosted vertices requested by user - above the current plane */
  if (ise[2*dim-1] < nele) {
    for (k = (dim==3?ise[5]+1:ise[4]); k <= (dim==3?ise[5]+nghost:ise[5]); k++) {
      for (j = (dim==2?ise[3]+1:ise[2]); j <= (dim==2?ise[3]+nghost:ise[3]); j++) {
        for (i = (dim>1?ise[0]:ise[1]+1); i <= (dim>1?ise[1]:ise[1]+nghost); i++, vcount++) {
          DMMoab_SetStructuredCoords_Private(i,j,k,hx,hy,hz,vcount,vcoords);
          vgid[vcount] = (k*npts+j)*npts+i+1;
        }
      }
    }
  }

  if (locnpts+ghnpts != vcount) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Created the wrong number of vertices! (%D!=%D)",locnpts+ghnpts,vcount);

  merr = mbiface->get_entities_by_type(0,moab::MBVERTEX,ownedvtx,true);MBERRNM(merr);

  /* The global ID tag is applied to each owned
     vertex. It acts as an global identifier which MOAB uses to
     assemble the individual pieces of the mesh:
     Set the global ID indices */
  merr = mbiface->tag_set_data(id_tag,ownedvtx,vgid.data());MBERRNM(merr);
  
  /* Create elements between mesh points using the ReadUtilInterface 
     get the reference to element connectivities for all local elements from the ReadUtilInterface */
  merr = readMeshIface->get_element_connect (locnele+ghnele,vpere,etype,1,efirst,connectivity);MBERRNM(merr);

  /* offset appropriately so that only local ID and not global ID numbers are set for connectivity array */
  vfirst-=vgid[0]-1;

   /* 3. Loop over elements in 3 nested loops over i, j, k; for each (i,j,k):
         and then set the connectivity for each element appropriately */
  int ecount=0;

  /* create ghosted elements requested by user - below the current plane */
  if (ise[2*dim-2] >= nghost) {
    for (k = (dim==3?ise[4]-nghost:ise[4]); k < (dim==3?ise[4]:std::max(ise[5],1)); k++) {
      for (j = (dim==2?ise[2]-nghost:ise[2]); j < (dim==2?ise[2]:std::max(ise[3],1)); j++) {
        for (i = (dim>1?ise[0]:ise[0]-nghost); i < (dim>1?std::max(ise[1],1):ise[0]); i++) {
          DMMoab_SetElementConnectivity_Private(useSimplex, dim, etype, &ecount, vpere, nele, i, j, k, vfirst, connectivity);
        }
      }
    }
  }

  /* create owned elements requested by user */
  for (k = ise[4]; k < std::max(ise[5],1); k++) {
    for (j = ise[2]; j < std::max(ise[3],1); j++) {
      for (i = ise[0]; i < std::max(ise[1],1); i++) {
        DMMoab_SetElementConnectivity_Private(useSimplex, dim, etype, &ecount, vpere, nele, i, j, k, vfirst, connectivity);
      }
    }
  }

  /* create ghosted elements requested by user - above the current plane */
  if (ise[2*dim-1] <= nele-nghost) {
    for (k = (dim==3?ise[5]:ise[4]); k < (dim==3?ise[5]+nghost:std::max(ise[5],1)); k++) {
      for (j = (dim==2?ise[3]:ise[2]); j < (dim==2?ise[3]+nghost:std::max(ise[3],1)); j++) {
        for (i = (dim>1?ise[0]:ise[1]); i < (dim>1?std::max(ise[1],1):ise[1]+nghost); i++) {
          DMMoab_SetElementConnectivity_Private(useSimplex, dim, etype, &ecount, vpere, nele, i, j, k, vfirst, connectivity);
        }
      }
    }
  }

  merr = readMeshIface->update_adjacencies(efirst,locnele+ghnele,vpere,connectivity);MBERRNM(merr);
  
  /* 2. Get the vertices and hexes from moab and check their numbers against I*J*K and (I-1)*(J-1)*(K-1), resp.
        first '0' specifies "root set", or entire MOAB instance, second the entity dimension being requested */
  merr = mbiface->get_entities_by_dimension(0, dim, ownedelms);MBERRNM(merr);

  if (locnele+ghnele != (int) ownedelms.size()) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Created the wrong number of elements! (%D!=%D)",locnele+ghnele,ownedelms.size());
  else if(locnpts+ghnpts != (int) ownedvtx.size()) SETERRQ2(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Created the wrong number of vertices! (%D!=%D)",locnpts+ghnpts,ownedvtx.size());    
  else {
    ierr = PetscInfo2(NULL, "Created %D elements and %D vertices.\n", ownedelms.size(), ownedvtx.size());CHKERRQ(ierr);
  }
  
  /* lets create some sets */
  merr = mbiface->tag_get_handle(GEOM_DIMENSION_TAG_NAME, 1, moab::MB_TYPE_INTEGER, geom_tag, moab::MB_TAG_SPARSE|moab::MB_TAG_CREAT);MBERRNM(merr);

  merr = mbiface->create_meshset(moab::MESHSET_SET, regionset);MBERRNM(merr);
  merr = mbiface->add_entities(regionset, ownedelms);MBERRNM(merr);
  merr = mbiface->tag_set_data(geom_tag, &regionset, 1, &dmmoab->dim);MBERRNM(merr);
  merr = mbiface->add_parent_child(dmmoab->fileset,regionset);MBERRNM(merr);
  merr = mbiface->unite_meshset(dmmoab->fileset, regionset);MBERRNM(merr);

  merr = mbiface->create_meshset(moab::MESHSET_SET, vtxset);MBERRNM(merr);
  merr = mbiface->add_entities(vtxset, ownedvtx);MBERRNM(merr);
  merr = mbiface->add_parent_child(dmmoab->fileset,vtxset);MBERRNM(merr);
  merr = mbiface->unite_meshset(dmmoab->fileset, vtxset);MBERRNM(merr);

  if (build_adjacencies) {
    // generate all lower dimensional adjacencies
    merr = mbiface->get_adjacencies( ownedelms, dim-1, true, adj, moab::Interface::UNION );MBERRNM(merr);
    merr = dmmoab->pcomm->get_part_entities(dim2, dim-1);MBERRNM(merr);
    adj.merge(dim2);

    /* create face sets */
    merr = mbiface->create_meshset(moab::MESHSET_SET, faceset);MBERRNM(merr);
    merr = mbiface->add_entities(faceset, adj);MBERRNM(merr);
    merr = mbiface->add_parent_child(dmmoab->fileset,faceset);MBERRNM(merr);
    i=dim-1;
    merr = mbiface->tag_set_data(geom_tag, &faceset, 1, &i);MBERRNM(merr);
    merr = mbiface->unite_meshset(dmmoab->fileset, faceset);MBERRNM(merr);
    PetscInfo2(NULL, "Found %d %d-Dim quantities.\n", adj.size(), dim-1);

    if (dim > 2) {
      dim2.clear();
      /* create edge sets, if appropriate i.e., if dim=3 */
      merr = mbiface->create_meshset(moab::MESHSET_SET, edgeset);MBERRNM(merr);
      merr = mbiface->get_adjacencies(adj, dim-1, true, dim2, moab::Interface::UNION );MBERRNM(merr);
      merr = mbiface->add_entities(edgeset, dim2);MBERRNM(merr);
      merr = mbiface->add_parent_child(dmmoab->fileset,edgeset);MBERRNM(merr);
      i=dim-2;
      merr = mbiface->tag_set_data(geom_tag, &edgeset, 1, &i);MBERRNM(merr);
      merr = mbiface->unite_meshset(dmmoab->fileset, edgeset);MBERRNM(merr);
      PetscInfo2(NULL, "Found %d %d-Dim quantities.\n", adj.size(), dim-2);
    }
  }

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

  /* resolve the shared entities by exchanging information to adjacent processors */
  merr = mbiface->get_entities_by_type(dmmoab->fileset,etype,ownedelms,true);MBERRNM(merr);
  merr = pcomm->resolve_shared_ents(dmmoab->fileset,ownedelms,dim,dim-1,NULL,&id_tag);MBERRV(mbiface,merr);

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

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

  /* Everything is set up, now just do a tag exchange to update tags
     on all of the ghost vertexes */
  merr = mbiface->get_entities_by_type(dmmoab->fileset,moab::MBVERTEX,ownedvtx,true);MBERRNM(merr);
  merr = mbiface->get_entities_by_dimension(dmmoab->fileset, dim, ownedelms);MBERRNM(merr);
  
  merr = pcomm->exchange_tags(id_tag,ownedvtx);MBERRV(mbiface,merr);
  merr = pcomm->exchange_tags(id_tag,ownedelms);MBERRV(mbiface,merr);
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "DMMoab_GetReadOptions_Private"
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 = PetscMalloc(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);
}


#undef __FUNCT__
#define __FUNCT__ "DMMoabLoadFromFile"
/*@
  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, PETSC_NULL, PETSC_NULL, PETSC_NULL, PETSC_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);
}