impls/plex/plexexodusii.c

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

#if defined(PETSC_HAVE_EXODUSII)
#include <netcdf.h>
#include <exodusII.h>
#endif

#if defined(PETSC_HAVE_EXODUSII)
/*
  EXOGetVarIndex - Locate a result in an exodus file based on its name

  Not collective

  Input Parameters:
+ exoid    - the exodus id of a file (obtained from ex_open or ex_create for instance)
. obj_type - the type of entity for instance EX_NODAL, EX_ELEM_BLOCK
- name     - the name of the result

  Output Parameters:
. varIndex - the location in the exodus file of the result

  Notes:
  The exodus variable index is obtained by comparing name and the
  names of zonal variables declared in the exodus file. For instance if name is "V"
  the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
  amongst all variables of type obj_type.

  Level: beginner

.keywords: mesh,ExodusII
.seealso: EXOGetVarIndex(),DMView_Exodus(),VecViewPlex_ExodusII_Nodal_Internal(),VecLoadNodal_PlexEXO(),VecLoadZonal_PlexEXO()
*/
static PetscErrorCode EXOGetVarIndex_Private(int exoid, ex_entity_type obj_type, const char name[], int *varIndex)
{
  int            exoerr, num_vars, i, j;
  char           ext_name[MAX_STR_LENGTH+1], var_name[MAX_STR_LENGTH+1];
  const int      num_suffix = 5;
  char          *suffix[5];
  PetscBool      flg;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  suffix[0] = (char *) "";
  suffix[1] = (char *) "_X";
  suffix[2] = (char *) "_XX";
  suffix[3] = (char *) "_1";
  suffix[4] = (char *) "_11";

  *varIndex = 0;
  exoerr = ex_get_variable_param(exoid, obj_type, &num_vars);
  for (i = 0; i < num_vars; ++i) {
    exoerr = ex_get_variable_name(exoid, obj_type, i+1, var_name);
    for (j = 0; j < num_suffix; ++j){
      ierr = PetscStrncpy(ext_name, name, MAX_STR_LENGTH);CHKERRQ(ierr);
      ierr = PetscStrncat(ext_name, suffix[j], MAX_STR_LENGTH);CHKERRQ(ierr);
      ierr = PetscStrcasecmp(ext_name, var_name, &flg);
      if (flg) {
        *varIndex = i+1;
        PetscFunctionReturn(0);
      }
    }
  }
  SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to locate variable %s in ExodusII file.", name);
 PetscFunctionReturn(-1);
}
#endif

/*
  DMPlexView_ExodusII_Internal - Write a DM to disk in exodus format

  Collective on dm

  Input Parameters:
+ dm  - The dm to be written
. exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
- degree - the degree of the interpolation space

  Notes:
  Not all DM can be written to disk this way. For instance, exodus assume that element blocks (mapped to "Cell sets" labels)
  consists of sequentially numbered cells. If this is not the case, the exodus file will be corrupted.

  If the dm has been distributed and exoid points to different files on each MPI rank, only the "local" part of the DM
  (including "ghost" cells and vertices) will be written. If all exoid points to the same file, the resulting file will
  probably be corrupted.

  DMPlex only represents geometry while most post-processing software expect that a mesh also provides information
  on the discretization space. This function assumes that the file represents Lagrange finite elements of order 1 or 2.
  It should be extended to use PetscFE objects.

  This function will only handle TRI, TET, QUAD and HEX cells.
  Level: beginner

.keywords: mesh, ExodusII
.seealso: EXOGetVarIndex_Private(), VecViewPlex_ExodusII_Nodal_Internal(), VecLoadNodal_PlexEXO(), VecViewZonal_PlexEXO(), VecLoadZonal_PlexEXO()
*/
PetscErrorCode DMPlexView_ExodusII_Internal(DM dm, int exoid, PetscInt degree)
{
  enum ElemType {TRI, QUAD, TET, HEX};
  MPI_Comm        comm;
  /* Connectivity Variables */
  PetscInt        cellsNotInConnectivity;
  /* Cell Sets */
  DMLabel         csLabel;
  IS              csIS;
  const PetscInt *csIdx;
  PetscInt        num_cs, cs;
  enum ElemType  *type;
  /* Coordinate Variables */
  DM              cdm;
  PetscSection    section;
  Vec             coord;
  PetscInt      **nodes;
  PetscInt        depth, d, dim, skipCells = 0;
  PetscInt        pStart, pEnd, p, cStart, cEnd, numCells, vStart, vEnd, numVertices, eStart, eEnd, numEdges, fStart, fEnd, numFaces, numNodes;
  PetscInt        num_vs, num_fs;
  PetscMPIInt     rank, size;
  const char     *dmName;
  PetscErrorCode  ierr;

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
  /* --- Get DM info --- */
  ierr = PetscObjectGetName((PetscObject) dm, &dmName);CHKERRQ(ierr);
  ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
  ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
  ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
  ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
  ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(dm, 1, &eStart, &eEnd);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
  numCells    = cEnd - cStart;
  numEdges    = eEnd - eStart;
  numVertices = vEnd - vStart;
  if (depth == 3) {numFaces = fEnd - fStart;}
  else            {numFaces = 0;}
  ierr = DMGetLabelSize(dm, "Cell Sets", &num_cs);CHKERRQ(ierr);
  ierr = DMGetLabelSize(dm, "Vertex Sets", &num_vs);CHKERRQ(ierr);
  ierr = DMGetLabelSize(dm, "Face Sets", &num_fs);CHKERRQ(ierr);
  ierr = DMGetCoordinatesLocal(dm, &coord);CHKERRQ(ierr);
  ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
  if (num_cs > 0) {
    ierr = DMGetLabel(dm, "Cell Sets", &csLabel);CHKERRQ(ierr);
    ierr = DMLabelGetValueIS(csLabel, &csIS);CHKERRQ(ierr);
    ierr = ISGetIndices(csIS, &csIdx);CHKERRQ(ierr);
  }
  ierr = PetscMalloc1(num_cs, &nodes);CHKERRQ(ierr);
  /* Set element type for each block and compute total number of nodes */
  ierr = PetscMalloc1(num_cs, &type);CHKERRQ(ierr);
  numNodes = numVertices;
  if (degree == 2) {numNodes += numEdges;}
  cellsNotInConnectivity = numCells;
  for (cs = 0; cs < num_cs; ++cs) {
    IS              stratumIS;
    const PetscInt *cells;
    PetscScalar    *xyz = NULL;
    PetscInt        csSize, closureSize;
    PetscInt        nodesTriP1[4]  = {3,0,0,0};
    PetscInt        nodesTriP2[4]  = {3,3,0,0};
    PetscInt        nodesQuadP1[4] = {4,0,0,0};
    PetscInt        nodesQuadP2[4] = {4,4,0,1};
    PetscInt        nodesTetP1[4]  = {4,0,0,0};
    PetscInt        nodesTetP2[4]  = {4,6,0,0};
    PetscInt        nodesHexP1[4]  = {8,0,0,0};
    PetscInt        nodesHexP2[4]  = {8,12,6,1};

    ierr = DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS);CHKERRQ(ierr);
    ierr = ISGetIndices(stratumIS, &cells);CHKERRQ(ierr);
    ierr = ISGetSize(stratumIS, &csSize);CHKERRQ(ierr);
    ierr = DMPlexVecGetClosure(cdm, NULL, coord, cells[0], &closureSize, &xyz);CHKERRQ(ierr);
    switch (dim) {
    case 2:
      if      (closureSize == 3*dim) {type[cs] = TRI;}
      else if (closureSize == 4*dim) {type[cs] = QUAD;}
      else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices %D in dimension %D has no ExodusII type", closureSize/dim, dim);
      break;
    case 3:
      if      (closureSize == 4*dim) {type[cs] = TET;}
      else if (closureSize == 8*dim) {type[cs] = HEX;}
      else SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of vertices %D in dimension %D has no ExodusII type", closureSize/dim, dim);
      break;
    default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D not handled by ExodusII viewer", dim);
    }
    if ((degree == 2) && (type[cs] == QUAD)) {numNodes += csSize;}
    if ((degree == 2) && (type[cs] == HEX))  {numNodes += csSize; numNodes += numFaces;}
    ierr = DMPlexVecRestoreClosure(cdm, NULL, coord, cells[0], &closureSize, &xyz);CHKERRQ(ierr);
    /* Set nodes and Element type */
    if (type[cs] == TRI) {
      if      (degree == 1) nodes[cs] = nodesTriP1;
      else if (degree == 2) nodes[cs] = nodesTriP2;
    } else if (type[cs] == QUAD) {
      if      (degree == 1) nodes[cs] = nodesQuadP1;
      else if (degree == 2) nodes[cs] = nodesQuadP2;
    } else if (type[cs] == TET) {
      if      (degree == 1) nodes[cs] = nodesTetP1;
      else if (degree == 2) nodes[cs] = nodesTetP2;
    } else if (type[cs] == HEX) {
      if      (degree == 1) nodes[cs] = nodesHexP1;
      else if (degree == 2) nodes[cs] = nodesHexP2;
    }
    /* Compute the number of cells not in the connectivity table */
    cellsNotInConnectivity -= nodes[cs][3]*csSize;

    ierr = ISRestoreIndices(stratumIS, &cells);CHKERRQ(ierr);
    ierr = ISDestroy(&stratumIS);CHKERRQ(ierr);
  }
  if (num_cs > 0) {ierr = ex_put_init(exoid, dmName, dim, numNodes, numCells, num_cs, num_vs, num_fs);CHKERRQ(ierr);}
  /* --- Connectivity --- */
  for (cs = 0; cs < num_cs; ++cs) {
    IS              stratumIS;
    const PetscInt *cells;
    PetscInt       *connect;
    PetscInt        edgesInClosure = 0, facesInClosure = 0, verticesInClosure = 0;
    PetscInt        csSize, c, connectSize, closureSize;
    char           *elem_type = NULL;
    char            elem_type_tri3[]  = "TRI3",  elem_type_quad4[] = "QUAD4";
    char            elem_type_tri6[]  = "TRI6",  elem_type_quad9[] = "QUAD9";
    char            elem_type_tet4[]  = "TET4",  elem_type_hex8[]  = "HEX8";
    char            elem_type_tet10[] = "TET10", elem_type_hex27[] = "HEX27";

    ierr = DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS);CHKERRQ(ierr);
    ierr = ISGetIndices(stratumIS, &cells);CHKERRQ(ierr);
    ierr = ISGetSize(stratumIS, &csSize);CHKERRQ(ierr);
    /* Set Element type */
    if (type[cs] == TRI) {
      if      (degree == 1) elem_type = elem_type_tri3;
      else if (degree == 2) elem_type = elem_type_tri6;
    } else if (type[cs] == QUAD) {
      if      (degree == 1) elem_type = elem_type_quad4;
      else if (degree == 2) elem_type = elem_type_quad9;
    } else if (type[cs] == TET) {
      if      (degree == 1) elem_type = elem_type_tet4;
      else if (degree == 2) elem_type = elem_type_tet10;
    } else if (type[cs] == HEX) {
      if      (degree == 1) elem_type = elem_type_hex8;
      else if (degree == 2) elem_type = elem_type_hex27;
    }
    connectSize = nodes[cs][0] + nodes[cs][1] + nodes[cs][2] + nodes[cs][3];
    ierr = PetscMalloc1(connectSize, &connect);CHKERRQ(ierr);
    ierr = ex_put_block(exoid, EX_ELEM_BLOCK, cs, elem_type, csSize, connectSize, 0, 0, 1);
    /* Find number of vertices, edges, and faces in the closure */
    verticesInClosure = nodes[cs][0];
    if (depth > 1) {
      if (dim == 2) {
        ierr = DMPlexGetConeSize(dm, cells[0], &edgesInClosure);CHKERRQ(ierr);
      } else if (dim == 3) {
        PetscInt *closure = NULL;

        ierr = DMPlexGetConeSize(dm, cells[0], &facesInClosure);CHKERRQ(ierr);
        ierr = DMPlexGetTransitiveClosure(dm, cells[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
        edgesInClosure = closureSize - facesInClosure - 1 - verticesInClosure;
        ierr = DMPlexRestoreTransitiveClosure(dm, cells[0], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
      }
    }
    /* Get connectivity for each cell */
    for (c = 0; c < csSize; ++c) {
      PetscInt *closure = NULL;
      PetscInt  temp, i;

      ierr = DMPlexGetTransitiveClosure(dm, cells[c], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
      for (i = 0; i < connectSize; ++i) {
        if (i < nodes[cs][0]) {/* Vertices */
          connect[i] = closure[(i+edgesInClosure+facesInClosure+1)*2] + 1;
          connect[i] -= cellsNotInConnectivity;
        } else if (i < nodes[cs][0]+nodes[cs][1]) { /* Edges */
          connect[i] = closure[(i-verticesInClosure+facesInClosure+1)*2] + 1;
          if (nodes[cs][2] == 0) connect[i] -= numFaces;
          connect[i] -= cellsNotInConnectivity;
        } else if (i < nodes[cs][0]+nodes[cs][1]+nodes[cs][3]){ /* Cells */
          connect[i] = closure[0] + 1;
          connect[i] -= skipCells;
        } else if (i < nodes[cs][0]+nodes[cs][1]+nodes[cs][3]+nodes[cs][2]){ /* Faces */
          connect[i] = closure[(i-edgesInClosure-verticesInClosure)*2] + 1;
          connect[i] -= cellsNotInConnectivity;
        } else {
          connect[i] = -1;
        }
      }
      /* Tetrahedra are inverted */
      if (type[cs] == TET) {
        temp = connect[0]; connect[0] = connect[1]; connect[1] = temp;
        if (degree == 2) {
          temp = connect[5]; connect[5] = connect[6]; connect[6] = temp;
          temp = connect[7]; connect[7] = connect[8]; connect[8] = temp;
        }
      }
      /* Hexahedra are inverted */
      if (type[cs] == HEX) {
        temp = connect[1]; connect[1] = connect[3]; connect[3] = temp;
        if (degree == 2) {
          temp = connect[8];  connect[8]  = connect[11]; connect[11] = temp;
          temp = connect[9];  connect[9]  = connect[10]; connect[10] = temp;
          temp = connect[16]; connect[16] = connect[17]; connect[17] = temp;
          temp = connect[18]; connect[18] = connect[19]; connect[19] = temp;

          temp = connect[12]; connect[12] = connect[16]; connect[16] = temp;
          temp = connect[13]; connect[13] = connect[17]; connect[17] = temp;
          temp = connect[14]; connect[14] = connect[18]; connect[18] = temp;
          temp = connect[15]; connect[15] = connect[19]; connect[19] = temp;

          temp = connect[23]; connect[23] = connect[26]; connect[26] = temp;
          temp = connect[24]; connect[24] = connect[25]; connect[25] = temp;
          temp = connect[25]; connect[25] = connect[26]; connect[26] = temp;
        }
      }
      ierr = ex_put_partial_conn(exoid, EX_ELEM_BLOCK, cs, c+1, 1, connect, NULL, NULL);
      ierr = DMPlexRestoreTransitiveClosure(dm, cells[c], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
    }
    skipCells += (nodes[cs][3] == 0)*csSize;
    ierr = PetscFree(connect);CHKERRQ(ierr);
    ierr = ISRestoreIndices(stratumIS, &cells);CHKERRQ(ierr);
    ierr = ISDestroy(&stratumIS);CHKERRQ(ierr);
  }
  ierr = PetscFree(type);CHKERRQ(ierr);
  /* --- Coordinates --- */
  ierr = PetscSectionCreate(comm, &section);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(section, pStart, pEnd);CHKERRQ(ierr);
  for (d = 0; d < depth; ++d) {
    ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      ierr = PetscSectionSetDof(section, p, nodes[0][d] > 0);CHKERRQ(ierr);
    }
  }
  for (cs = 0; cs < num_cs; ++cs) {
    IS              stratumIS;
    const PetscInt *cells;
    PetscInt        csSize, c;

    ierr = DMLabelGetStratumIS(csLabel, csIdx[cs], &stratumIS);CHKERRQ(ierr);
    ierr = ISGetIndices(stratumIS, &cells);CHKERRQ(ierr);
    ierr = ISGetSize(stratumIS, &csSize);CHKERRQ(ierr);
    for (c = 0; c < csSize; ++c) {
      ierr = PetscSectionSetDof(section, cells[c], nodes[cs][3] > 0);CHKERRQ(ierr);
    }
    ierr = ISRestoreIndices(stratumIS, &cells);CHKERRQ(ierr);
    ierr = ISDestroy(&stratumIS);CHKERRQ(ierr);
  }
  if (num_cs > 0) {
    ierr = ISRestoreIndices(csIS, &csIdx);CHKERRQ(ierr);
    ierr = ISDestroy(&csIS);CHKERRQ(ierr);
  }
  ierr = PetscFree(nodes);CHKERRQ(ierr);
  ierr = PetscSectionSetUp(section);CHKERRQ(ierr);
  if (numNodes > 0) {
    const char  *coordNames[3] = {"x", "y", "z"};
    PetscScalar *coords, *closure;
    PetscReal   *cval;
    PetscInt     hasDof, n = 0;

    /* There can't be more than 24 values in the closure of a point for the coord section */
    ierr = PetscMalloc3(numNodes*3, &coords, dim, &cval, 24, &closure);CHKERRQ(ierr);
    ierr = DMGetCoordinatesLocal(dm, &coord);CHKERRQ(ierr);
    ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      ierr = PetscSectionGetDof(section, p, &hasDof);
      if (hasDof) {
        PetscInt closureSize = 24, j;

        ierr = DMPlexVecGetClosure(cdm, NULL, coord, p, &closureSize, &closure);CHKERRQ(ierr);
        for (d = 0; d < dim; ++d) {
          cval[d] = 0.0;
          for (j = 0; j < closureSize/dim; j++) cval[d] += closure[j*dim+d];
          coords[d*numNodes+n] = cval[d] * dim / closureSize;
        }
        ++n;
      }
    }
    ierr = ex_put_coord(exoid, &coords[0*numNodes], &coords[1*numNodes], &coords[2*numNodes]);CHKERRQ(ierr);
    ierr = PetscFree3(coords, cval, closure);CHKERRQ(ierr);
    ierr = ex_put_coord_names(exoid, (char **) coordNames);CHKERRQ(ierr);
  }
  ierr = PetscSectionDestroy(&section);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

/*
  VecViewPlex_ExodusII_Nodal_Internal - Write a Vec corresponding to a nodal field to an exodus file

  Collective on v

  Input Parameters:
+ v  - The vector to be written
. exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
- step - the time step to write at (exodus steps are numbered starting from 1)

  Notes:
  The exodus result nodal variable index is obtained by comparing the Vec name and the
  names of nodal variables declared in the exodus file. For instance for a Vec named "V"
  the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
  amongst all nodal variables.

  Level: beginner

.keywords: mesh,ExodusII
.seealso: EXOGetVarIndex_Private(),DMPlexView_ExodusII_Internal(),VecLoadNodal_PlexEXO(),VecViewZonal_PlexEXO(),VecLoadZonal_PlexEXO()
@*/
PetscErrorCode VecViewPlex_ExodusII_Nodal_Internal(Vec v, int exoid, int step)
{
  MPI_Comm         comm;
  PetscMPIInt      size;
#if defined(PETSC_HAVE_EXODUSII)
  DM               dm;
  Vec              vNatural, vComp;
  const PetscReal *varray;
  const char      *vecname;
  PetscInt         xs, xe, bs;
  PetscBool        useNatural;
  int              offset;
  PetscErrorCode   ierr;
#endif

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject) v, &comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
#if defined(PETSC_HAVE_EXODUSII)
  ierr = VecGetDM(v, &dm);CHKERRQ(ierr);
  ierr = DMGetUseNatural(dm, &useNatural);CHKERRQ(ierr);
  useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
  if (useNatural) {
    ierr = DMGetGlobalVector(dm, &vNatural);CHKERRQ(ierr);
    ierr = DMPlexGlobalToNaturalBegin(dm, v, vNatural);CHKERRQ(ierr);
    ierr = DMPlexGlobalToNaturalEnd(dm, v, vNatural);CHKERRQ(ierr);
  } else {
    vNatural = v;
  }
  /* Get the location of the variable in the exodus file */
  ierr = PetscObjectGetName((PetscObject) v, &vecname);CHKERRQ(ierr);
  ierr = EXOGetVarIndex_Private(exoid, EX_NODAL, vecname, &offset);CHKERRQ(ierr);
  if (!offset) SETERRQ1(comm, PETSC_ERR_FILE_UNEXPECTED, "Cannot locate nodal variable %s in exodus file\n", vecname);
  /* Write local chunk of the result in the exodus file
     exodus stores each component of a vector-valued field as a separate variable.
     We assume that they are stored sequentially */
  ierr = VecGetOwnershipRange(vNatural, &xs, &xe);CHKERRQ(ierr);
  ierr = VecGetBlockSize(vNatural, &bs);CHKERRQ(ierr);
  if (bs == 1) {
    ierr = VecGetArrayRead(vNatural, &varray);CHKERRQ(ierr);
    ierr = ex_put_partial_var(exoid, step, EX_NODAL, offset, 1, xs+1, xe-xs, varray);CHKERRQ(ierr);
    ierr = VecRestoreArrayRead(vNatural, &varray);CHKERRQ(ierr);
  } else {
    IS       compIS;
    PetscInt c;

    ierr = ISCreateStride(PETSC_COMM_SELF, (xe-xs)/bs, xs, bs, &compIS);CHKERRQ(ierr);
    for (c = 0; c < bs; ++c) {
      ierr = ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);CHKERRQ(ierr);
      ierr = VecGetSubVector(vNatural, compIS, &vComp);CHKERRQ(ierr);
      ierr = VecGetArrayRead(vComp, &varray);CHKERRQ(ierr);
      ierr = ex_put_partial_var(exoid, step, EX_NODAL, offset+c, 1, xs/bs+1, (xe-xs)/bs, varray);CHKERRQ(ierr);
      ierr = VecRestoreArrayRead(vComp, &varray);CHKERRQ(ierr);
      ierr = VecRestoreSubVector(vNatural, compIS, &vComp);CHKERRQ(ierr);
    }
    ierr = ISDestroy(&compIS);CHKERRQ(ierr);
  }
  if (useNatural) {ierr = DMRestoreGlobalVector(dm, &vNatural);CHKERRQ(ierr);}
#else
  SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
#endif
  PetscFunctionReturn(0);
}

/*
  VecLoadPlex_ExodusII_Nodal_Internal - Read a Vec corresponding to a nodal field from an exodus file

  Collective on v

  Input Parameters:
+ v  - The vector to be written
. exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
- step - the time step to read at (exodus steps are numbered starting from 1)

  Notes:
  The exodus result nodal variable index is obtained by comparing the Vec name and the
  names of nodal variables declared in the exodus file. For instance for a Vec named "V"
  the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
  amongst all nodal variables.

  Level: beginner

.keywords: mesh, ExodusII
.seealso: EXOGetVarIndex_Private(), DMPlexView_ExodusII_Internal(), VecViewPlex_ExodusII_Nodal_Internal(), VecViewZonal_PlexEXO(), VecLoadZonal_PlexEXO()
*/
PetscErrorCode VecLoadPlex_ExodusII_Nodal_Internal(Vec v, int exoid, int step)
{
  MPI_Comm       comm;
  PetscMPIInt    size;
#if defined(PETSC_HAVE_EXODUSII)
  DM             dm;
  Vec            vNatural, vComp;
  PetscReal     *varray;
  const char    *vecname;
  PetscInt       xs, xe, bs;
  PetscBool      useNatural;
  int            offset;
  PetscErrorCode ierr;
#endif

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject) v, &comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
#if defined(PETSC_HAVE_EXODUSII)
  ierr = VecGetDM(v,&dm);CHKERRQ(ierr);
  ierr = DMGetUseNatural(dm, &useNatural);CHKERRQ(ierr);
  useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
  if (useNatural) {ierr = DMGetGlobalVector(dm,&vNatural);CHKERRQ(ierr);}
  else            {vNatural = v;}
  /* Get the location of the variable in the exodus file */
  ierr = PetscObjectGetName((PetscObject) v, &vecname);CHKERRQ(ierr);
  ierr = EXOGetVarIndex_Private(exoid, EX_NODAL, vecname, &offset);CHKERRQ(ierr);
  if (!offset) SETERRQ1(comm, PETSC_ERR_FILE_UNEXPECTED, "Cannot locate nodal variable %s in exodus file", vecname);
  /* Read local chunk from the file */
  ierr = VecGetOwnershipRange(vNatural, &xs, &xe);CHKERRQ(ierr);
  ierr = VecGetBlockSize(vNatural, &bs);CHKERRQ(ierr);
  if (bs == 1) {
    ierr = VecGetArray(vNatural, &varray);CHKERRQ(ierr);
    ierr = ex_get_partial_var(exoid, step, EX_NODAL, offset, 1, xs+1, xe-xs, varray);CHKERRQ(ierr);
    ierr = VecRestoreArray(vNatural, &varray);CHKERRQ(ierr);
  } else {
    IS       compIS;
    PetscInt c;

    ierr = ISCreateStride(PETSC_COMM_SELF, (xe-xs)/bs, xs, bs, &compIS);CHKERRQ(ierr);
    for (c = 0; c < bs; ++c) {
      ierr = ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);CHKERRQ(ierr);
      ierr = VecGetSubVector(vNatural, compIS, &vComp);CHKERRQ(ierr);
      ierr = VecGetArray(vComp, &varray);CHKERRQ(ierr);
      ierr = ex_get_partial_var(exoid, step, EX_NODAL, offset+c, 1, xs/bs+1, (xe-xs)/bs, varray);CHKERRQ(ierr);
      ierr = VecRestoreArray(vComp, &varray);CHKERRQ(ierr);
      ierr = VecRestoreSubVector(vNatural, compIS, &vComp);CHKERRQ(ierr);
    }
    ierr = ISDestroy(&compIS);CHKERRQ(ierr);
  }
  if (useNatural) {
    ierr = DMPlexNaturalToGlobalBegin(dm, vNatural, v);CHKERRQ(ierr);
    ierr = DMPlexNaturalToGlobalEnd(dm, vNatural, v);CHKERRQ(ierr);
    ierr = DMRestoreGlobalVector(dm, &vNatural);CHKERRQ(ierr);
  }
#else
  SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
#endif
  PetscFunctionReturn(0);
}

/*
  VecViewPlex_ExodusII_Zonal_Internal - Write a Vec corresponding to a zonal (cell based) field to an exodus file

  Collective on v

  Input Parameters:
+ v  - The vector to be written
. exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
- step - the time step to write at (exodus steps are numbered starting from 1)

  Notes:
  The exodus result zonal variable index is obtained by comparing the Vec name and the
  names of zonal variables declared in the exodus file. For instance for a Vec named "V"
  the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
  amongst all zonal variables.

  Level: beginner

.keywords: mesh,ExodusII
.seealso: EXOGetVarIndex_Private(),DMPlexView_ExodusII_Internal(),VecViewPlex_ExodusII_Nodal_Internal(),VecLoadPlex_ExodusII_Nodal_Internal(),VecLoadPlex_ExodusII_Zonal_Internal()
*/
PetscErrorCode VecViewPlex_ExodusII_Zonal_Internal(Vec v, int exoid, int step)
{
  MPI_Comm          comm;
  PetscMPIInt       size;
#if defined(PETSC_HAVE_EXODUSII)
  DM                dm;
  Vec               vNatural, vComp;
  const PetscReal  *varray;
  const char       *vecname;
  PetscInt          xs, xe, bs;
  PetscBool         useNatural;
  int               offset;
  IS                compIS;
  PetscInt         *csSize, *csID;
  PetscInt          numCS, set, csxs = 0;
  PetscErrorCode    ierr;
#endif

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)v, &comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
#if defined(PETSC_HAVE_EXODUSII)
  ierr = VecGetDM(v, &dm);CHKERRQ(ierr);
  ierr = DMGetUseNatural(dm, &useNatural);CHKERRQ(ierr);
  useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
  if (useNatural) {
    ierr = DMGetGlobalVector(dm, &vNatural);CHKERRQ(ierr);
    ierr = DMPlexGlobalToNaturalBegin(dm, v, vNatural);CHKERRQ(ierr);
    ierr = DMPlexGlobalToNaturalEnd(dm, v, vNatural);CHKERRQ(ierr);
  } else {
    vNatural = v;
  }
  /* Get the location of the variable in the exodus file */
  ierr = PetscObjectGetName((PetscObject) v, &vecname);CHKERRQ(ierr);
  ierr = EXOGetVarIndex_Private(exoid, EX_ELEM_BLOCK, vecname, &offset);CHKERRQ(ierr);
  if (!offset) SETERRQ1(comm, PETSC_ERR_FILE_UNEXPECTED, "Cannot locate zonal variable %s in exodus file\n", vecname);
  /* Write local chunk of the result in the exodus file
     exodus stores each component of a vector-valued field as a separate variable.
     We assume that they are stored sequentially
     Zonal variables are accessed one element block at a time, so we loop through the cell sets,
     but once the vector has been reordered to natural size, we cannot use the label informations
     to figure out what to save where. */
  numCS = ex_inquire_int(exoid, EX_INQ_ELEM_BLK);
  ierr = PetscMalloc2(numCS, &csID, numCS, &csSize);CHKERRQ(ierr);
  ierr = ex_get_ids(exoid, EX_ELEM_BLOCK, csID);CHKERRQ(ierr);
  for (set = 0; set < numCS; ++set) {
    ex_block block;

    block.id   = csID[set];
    block.type = EX_ELEM_BLOCK;
    ierr = ex_get_block_param(exoid, &block);CHKERRQ(ierr);
    csSize[set] = block.num_entry;
  }
  ierr = VecGetOwnershipRange(vNatural, &xs, &xe);CHKERRQ(ierr);
  ierr = VecGetBlockSize(vNatural, &bs);CHKERRQ(ierr);
  if (bs > 1) {ierr = ISCreateStride(comm, (xe-xs)/bs, xs, bs, &compIS);CHKERRQ(ierr);}
  for (set = 0; set < numCS; set++) {
    PetscInt csLocalSize, c;

    /* range of indices for set setID[set]: csxs:csxs + csSize[set]-1
       local slice of zonal values:         xs/bs,xm/bs-1
       intersection:                        max(xs/bs,csxs),min(xm/bs-1,csxs + csSize[set]-1) */
    csLocalSize = PetscMax(0, PetscMin(xe/bs, csxs+csSize[set]) - PetscMax(xs/bs, csxs));
    if (bs == 1) {
      ierr = VecGetArrayRead(vNatural, &varray);CHKERRQ(ierr);
      ierr = ex_put_partial_var(exoid, step, EX_ELEM_BLOCK, offset, csID[set], PetscMax(xs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs)]);CHKERRQ(ierr);
      ierr = VecRestoreArrayRead(vNatural, &varray);CHKERRQ(ierr);
    } else {
      for (c = 0; c < bs; ++c) {
        ierr = ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);CHKERRQ(ierr);
        ierr = VecGetSubVector(vNatural, compIS, &vComp);CHKERRQ(ierr);
        ierr = VecGetArrayRead(vComp, &varray);CHKERRQ(ierr);
        ierr = ex_put_partial_var(exoid, step, EX_ELEM_BLOCK, offset+c, csID[set], PetscMax(xs/bs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs/bs)]);
        ierr = VecRestoreArrayRead(vComp, &varray);CHKERRQ(ierr);
        ierr = VecRestoreSubVector(vNatural, compIS, &vComp);CHKERRQ(ierr);
      }
    }
    csxs += csSize[set];
  }
  ierr = PetscFree2(csID, csSize);CHKERRQ(ierr);
  if (bs > 1) {ierr = ISDestroy(&compIS);CHKERRQ(ierr);}
  if (useNatural) {ierr = DMRestoreGlobalVector(dm,&vNatural);CHKERRQ(ierr);}
#else
  SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
#endif
  PetscFunctionReturn(0);
}

/*
  VecLoadPlex_ExodusII_Zonal_Internal - Read a Vec corresponding to a zonal (cell based) field from an exodus file

  Collective on v

  Input Parameters:
+ v  - The vector to be written
. exoid - the exodus id of a file (obtained from ex_open or ex_create for instance)
- step - the time step to read at (exodus steps are numbered starting from 1)

  Notes:
  The exodus result zonal variable index is obtained by comparing the Vec name and the
  names of zonal variables declared in the exodus file. For instance for a Vec named "V"
  the location in the exodus file will be the first match of "V", "V_X", "V_XX", "V_1", or "V_11"
  amongst all zonal variables.

  Level: beginner

.keywords: mesh,ExodusII
.seealso: EXOGetVarIndex_Private(), DMPlexView_ExodusII_Internal(), VecViewPlex_ExodusII_Nodal_Internal(), VecLoadPlex_ExodusII_Nodal_Internal(), VecLoadPlex_ExodusII_Zonal_Internal()
*/
PetscErrorCode VecLoadPlex_ExodusII_Zonal_Internal(Vec v, int exoid, int step)
{
  MPI_Comm          comm;
  PetscMPIInt       size;
#if defined(PETSC_HAVE_EXODUSII)
  DM                dm;
  Vec               vNatural, vComp;
  PetscReal        *varray;
  const char       *vecname;
  PetscInt          xs, xe, bs;
  PetscBool         useNatural;
  int               offset;
  IS                compIS;
  PetscInt         *csSize, *csID;
  PetscInt          numCS, set, csxs = 0;
  PetscErrorCode    ierr;
#endif

  PetscFunctionBegin;
  ierr = PetscObjectGetComm((PetscObject)v,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
#if defined(PETSC_HAVE_EXODUSII)
  ierr = VecGetDM(v, &dm);CHKERRQ(ierr);
  ierr = DMGetUseNatural(dm, &useNatural);CHKERRQ(ierr);
  useNatural = useNatural && size > 1 ? PETSC_TRUE : PETSC_FALSE;
  if (useNatural) {ierr = DMGetGlobalVector(dm,&vNatural);CHKERRQ(ierr);}
  else            {vNatural = v;}
  /* Get the location of the variable in the exodus file */
  ierr = PetscObjectGetName((PetscObject) v, &vecname);CHKERRQ(ierr);
  ierr = EXOGetVarIndex_Private(exoid, EX_ELEM_BLOCK, vecname, &offset);CHKERRQ(ierr);
  if (!offset) SETERRQ1(comm, PETSC_ERR_FILE_UNEXPECTED, "Cannot locate zonal variable %s in exodus file\n", vecname);
  /* Read local chunk of the result in the exodus file
     exodus stores each component of a vector-valued field as a separate variable.
     We assume that they are stored sequentially
     Zonal variables are accessed one element block at a time, so we loop through the cell sets,
     but once the vector has been reordered to natural size, we cannot use the label informations
     to figure out what to save where. */
  numCS = ex_inquire_int(exoid, EX_INQ_ELEM_BLK);
  ierr = PetscMalloc2(numCS, &csID, numCS, &csSize);CHKERRQ(ierr);
  ierr = ex_get_ids(exoid, EX_ELEM_BLOCK, csID);CHKERRQ(ierr);
  for (set = 0; set < numCS; ++set) {
    ex_block block;

    block.id   = csID[set];
    block.type = EX_ELEM_BLOCK;
    ierr = ex_get_block_param(exoid, &block);CHKERRQ(ierr);
    csSize[set] = block.num_entry;
  }
  ierr = VecGetOwnershipRange(vNatural, &xs, &xe);CHKERRQ(ierr);
  ierr = VecGetBlockSize(vNatural, &bs);CHKERRQ(ierr);
  if (bs > 1) {ierr = ISCreateStride(comm, (xe-xs)/bs, xs, bs, &compIS);CHKERRQ(ierr);}
  for (set = 0; set < numCS; ++set) {
    PetscInt csLocalSize, c;

    /* range of indices for set setID[set]: csxs:csxs + csSize[set]-1
       local slice of zonal values:         xs/bs,xm/bs-1
       intersection:                        max(xs/bs,csxs),min(xm/bs-1,csxs + csSize[set]-1) */
    csLocalSize = PetscMax(0, PetscMin(xe/bs, csxs+csSize[set]) - PetscMax(xs/bs, csxs));
    if (bs == 1) {
      ierr = VecGetArray(vNatural, &varray);CHKERRQ(ierr);
      ierr = ex_get_partial_var(exoid, step, EX_ELEM_BLOCK, offset, csID[set], PetscMax(xs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs)]);CHKERRQ(ierr);
      ierr = VecRestoreArray(vNatural, &varray);CHKERRQ(ierr);
    } else {
      for (c = 0; c < bs; ++c) {
        ierr = ISStrideSetStride(compIS, (xe-xs)/bs, xs+c, bs);CHKERRQ(ierr);
        ierr = VecGetSubVector(vNatural, compIS, &vComp);CHKERRQ(ierr);
        ierr = VecGetArray(vComp, &varray);CHKERRQ(ierr);
        ierr = ex_get_partial_var(exoid, step, EX_ELEM_BLOCK, offset+c, csID[set], PetscMax(xs/bs-csxs, 0)+1, csLocalSize, &varray[PetscMax(0, csxs-xs/bs)]);
        ierr = VecRestoreArray(vComp, &varray);CHKERRQ(ierr);
        ierr = VecRestoreSubVector(vNatural, compIS, &vComp);CHKERRQ(ierr);
      }
    }
    csxs += csSize[set];
  }
  ierr = PetscFree2(csID, csSize);CHKERRQ(ierr);
  if (bs > 1) {ierr = ISDestroy(&compIS);CHKERRQ(ierr);}
  if (useNatural) {
    ierr = DMPlexNaturalToGlobalBegin(dm, vNatural, v);CHKERRQ(ierr);
    ierr = DMPlexNaturalToGlobalEnd(dm, vNatural, v);CHKERRQ(ierr);
    ierr = DMRestoreGlobalVector(dm, &vNatural);CHKERRQ(ierr);
  }
#else
  SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
#endif
  PetscFunctionReturn(0);
}

/*@C
  DMPlexCreateExodusFromFile - Create a DMPlex mesh from an ExodusII file.

  Collective on comm

  Input Parameters:
+ comm  - The MPI communicator
. filename - The name of the ExodusII file
- interpolate - Create faces and edges in the mesh

  Output Parameter:
. dm  - The DM object representing the mesh

  Level: beginner

.keywords: mesh,ExodusII
.seealso: DMPLEX, DMCreate(), DMPlexCreateExodus()
@*/
PetscErrorCode DMPlexCreateExodusFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
{
  PetscMPIInt    rank;
  PetscErrorCode ierr;
#if defined(PETSC_HAVE_EXODUSII)
  int   CPU_word_size = sizeof(PetscReal), IO_word_size = 0, exoid = -1;
  float version;
#endif

  PetscFunctionBegin;
  PetscValidCharPointer(filename, 2);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
#if defined(PETSC_HAVE_EXODUSII)
  if (!rank) {
    exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size, &version);
    if (exoid <= 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_LIB, "ex_open(\"%s\",...) did not return a valid file ID", filename);
  }
  ierr = DMPlexCreateExodus(comm, exoid, interpolate, dm);CHKERRQ(ierr);
  if (!rank) {ierr = ex_close(exoid);CHKERRQ(ierr);}
#else
  SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
#endif
  PetscFunctionReturn(0);
}

/*@
  DMPlexCreateExodus - Create a DMPlex mesh from an ExodusII file ID.

  Collective on comm

  Input Parameters:
+ comm  - The MPI communicator
. exoid - The ExodusII id associated with a exodus file and obtained using ex_open
- interpolate - Create faces and edges in the mesh

  Output Parameter:
. dm  - The DM object representing the mesh

  Level: beginner

.keywords: mesh,ExodusII
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateExodus(MPI_Comm comm, PetscInt exoid, PetscBool interpolate, DM *dm)
{
#if defined(PETSC_HAVE_EXODUSII)
  PetscMPIInt    num_proc, rank;
  PetscSection   coordSection;
  Vec            coordinates;
  PetscScalar    *coords;
  PetscInt       coordSize, v;
  PetscErrorCode ierr;
  /* Read from ex_get_init() */
  char title[PETSC_MAX_PATH_LEN+1];
  int  dim    = 0, numVertices = 0, numCells = 0;
  int  num_cs = 0, num_vs = 0, num_fs = 0;
#endif

  PetscFunctionBegin;
#if defined(PETSC_HAVE_EXODUSII)
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &num_proc);CHKERRQ(ierr);
  ierr = DMCreate(comm, dm);CHKERRQ(ierr);
  ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
  /* Open EXODUS II file and read basic informations on rank 0, then broadcast to all processors */
  if (!rank) {
    ierr = PetscMemzero(title,(PETSC_MAX_PATH_LEN+1)*sizeof(char));CHKERRQ(ierr);
    ierr = ex_get_init(exoid, title, &dim, &numVertices, &numCells, &num_cs, &num_vs, &num_fs);
    if (ierr) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"ExodusII ex_get_init() failed with error code %D\n",ierr);
    if (!num_cs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Exodus file does not contain any cell set\n");
  }
  ierr = MPI_Bcast(title, PETSC_MAX_PATH_LEN+1, MPI_CHAR, 0, comm);CHKERRQ(ierr);
  ierr = MPI_Bcast(&dim, 1, MPI_INT, 0, comm);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) *dm, title);CHKERRQ(ierr);
  ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
  ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr);

  /* Read cell sets information */
  if (!rank) {
    PetscInt *cone;
    int      c, cs, c_loc, v, v_loc;
    /* Read from ex_get_elem_blk_ids() */
    int *cs_id;
    /* Read from ex_get_elem_block() */
    char buffer[PETSC_MAX_PATH_LEN+1];
    int  num_cell_in_set, num_vertex_per_cell, num_attr;
    /* Read from ex_get_elem_conn() */
    int *cs_connect;

    /* Get cell sets IDs */
    ierr = PetscMalloc1(num_cs, &cs_id);CHKERRQ(ierr);
    ierr = ex_get_ids (exoid, EX_ELEM_BLOCK, cs_id);CHKERRQ(ierr);
    /* Read the cell set connectivity table and build mesh topology
       EXO standard requires that cells in cell sets be numbered sequentially and be pairwise disjoint. */
    /* First set sizes */
    for (cs = 0, c = 0; cs < num_cs; cs++) {
      ierr = ex_get_block(exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set,&num_vertex_per_cell, 0, 0, &num_attr);CHKERRQ(ierr);
      for (c_loc = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
        ierr = DMPlexSetConeSize(*dm, c, num_vertex_per_cell);CHKERRQ(ierr);
      }
    }
    ierr = DMSetUp(*dm);CHKERRQ(ierr);
    for (cs = 0, c = 0; cs < num_cs; cs++) {
      ierr = ex_get_block(exoid, EX_ELEM_BLOCK, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, 0, 0, &num_attr);CHKERRQ(ierr);
      ierr = PetscMalloc2(num_vertex_per_cell*num_cell_in_set,&cs_connect,num_vertex_per_cell,&cone);CHKERRQ(ierr);
      ierr = ex_get_conn (exoid, EX_ELEM_BLOCK, cs_id[cs], cs_connect,NULL,NULL);CHKERRQ(ierr);
      /* EXO uses Fortran-based indexing, DMPlex uses C-style and numbers cell first then vertices. */
      for (c_loc = 0, v = 0; c_loc < num_cell_in_set; ++c_loc, ++c) {
        for (v_loc = 0; v_loc < num_vertex_per_cell; ++v_loc, ++v) {
          cone[v_loc] = cs_connect[v]+numCells-1;
        }
        if (dim == 3) {
          /* Tetrahedra are inverted */
          if (num_vertex_per_cell == 4) {
            PetscInt tmp = cone[0];
            cone[0] = cone[1];
            cone[1] = tmp;
          }
          /* Hexahedra are inverted */
          if (num_vertex_per_cell == 8) {
            PetscInt tmp = cone[1];
            cone[1] = cone[3];
            cone[3] = tmp;
          }
        }
        ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
        ierr = DMSetLabelValue(*dm, "Cell Sets", c, cs_id[cs]);CHKERRQ(ierr);
      }
      ierr = PetscFree2(cs_connect,cone);CHKERRQ(ierr);
    }
    ierr = PetscFree(cs_id);CHKERRQ(ierr);
  }
  ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
  ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
  if (interpolate) {
    DM idm;

    ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
    ierr = DMDestroy(dm);CHKERRQ(ierr);
    *dm  = idm;
  }

  /* Create vertex set label */
  if (!rank && (num_vs > 0)) {
    int vs, v;
    /* Read from ex_get_node_set_ids() */
    int *vs_id;
    /* Read from ex_get_node_set_param() */
    int num_vertex_in_set;
    /* Read from ex_get_node_set() */
    int *vs_vertex_list;

    /* Get vertex set ids */
    ierr = PetscMalloc1(num_vs, &vs_id);CHKERRQ(ierr);
    ierr = ex_get_ids(exoid, EX_NODE_SET, vs_id);CHKERRQ(ierr);
    for (vs = 0; vs < num_vs; ++vs) {
      ierr = ex_get_set_param(exoid, EX_NODE_SET, vs_id[vs], &num_vertex_in_set, NULL);
      ierr = PetscMalloc1(num_vertex_in_set, &vs_vertex_list);CHKERRQ(ierr);
      ierr = ex_get_set(exoid, EX_NODE_SET, vs_id[vs], vs_vertex_list, NULL);CHKERRQ(ierr);
      for (v = 0; v < num_vertex_in_set; ++v) {
        ierr = DMSetLabelValue(*dm, "Vertex Sets", vs_vertex_list[v]+numCells-1, vs_id[vs]);CHKERRQ(ierr);
      }
      ierr = PetscFree(vs_vertex_list);CHKERRQ(ierr);
    }
    ierr = PetscFree(vs_id);CHKERRQ(ierr);
  }
  /* Read coordinates */
  ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr);
  ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
  ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
  for (v = numCells; v < numCells+numVertices; ++v) {
    ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr);
    ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
  ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
  ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr);
  ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  if (!rank) {
    PetscReal *x, *y, *z;

    ierr = PetscMalloc3(numVertices,&x,numVertices,&y,numVertices,&z);CHKERRQ(ierr);
    ierr = ex_get_coord(exoid, x, y, z);CHKERRQ(ierr);
    if (dim > 0) {
      for (v = 0; v < numVertices; ++v) coords[v*dim+0] = x[v];
    }
    if (dim > 1) {
      for (v = 0; v < numVertices; ++v) coords[v*dim+1] = y[v];
    }
    if (dim > 2) {
      for (v = 0; v < numVertices; ++v) coords[v*dim+2] = z[v];
    }
    ierr = PetscFree3(x,y,z);CHKERRQ(ierr);
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);

  /* Create side set label */
  if (!rank && interpolate && (num_fs > 0)) {
    int fs, f, voff;
    /* Read from ex_get_side_set_ids() */
    int *fs_id;
    /* Read from ex_get_side_set_param() */
    int num_side_in_set;
    /* Read from ex_get_side_set_node_list() */
    int *fs_vertex_count_list, *fs_vertex_list;
    /* Read side set labels */
    char fs_name[MAX_STR_LENGTH+1];

    /* Get side set ids */
    ierr = PetscMalloc1(num_fs, &fs_id);CHKERRQ(ierr);
    ierr = ex_get_ids(exoid, EX_SIDE_SET, fs_id);CHKERRQ(ierr);
    for (fs = 0; fs < num_fs; ++fs) {
      ierr = ex_get_set_param(exoid, EX_SIDE_SET, fs_id[fs], &num_side_in_set, NULL);CHKERRQ(ierr);
      ierr = PetscMalloc2(num_side_in_set,&fs_vertex_count_list,num_side_in_set*4,&fs_vertex_list);CHKERRQ(ierr);
      ierr = ex_get_side_set_node_list(exoid, fs_id[fs], fs_vertex_count_list, fs_vertex_list);CHKERRQ(ierr);
      /* Get the specific name associated with this side set ID. */
      int fs_name_err = ex_get_name(exoid, EX_SIDE_SET, fs_id[fs], fs_name);
      for (f = 0, voff = 0; f < num_side_in_set; ++f) {
        const PetscInt *faces   = NULL;
        PetscInt       faceSize = fs_vertex_count_list[f], numFaces;
        PetscInt       faceVertices[4], v;

        if (faceSize > 4) SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "ExodusII side cannot have %d > 4 vertices", faceSize);
        for (v = 0; v < faceSize; ++v, ++voff) {
          faceVertices[v] = fs_vertex_list[voff]+numCells-1;
        }
        ierr = DMPlexGetFullJoin(*dm, faceSize, faceVertices, &numFaces, &faces);CHKERRQ(ierr);
        if (numFaces != 1) SETERRQ3(comm, PETSC_ERR_ARG_WRONG, "Invalid ExodusII side %d in set %d maps to %d faces", f, fs, numFaces);
        ierr = DMSetLabelValue(*dm, "Face Sets", faces[0], fs_id[fs]);CHKERRQ(ierr);
        /* Only add the label if one has been detected for this side set. */
        if (!fs_name_err) {
          ierr = DMSetLabelValue(*dm, fs_name, faces[0], fs_id[fs]);CHKERRQ(ierr);
        }
        ierr = DMPlexRestoreJoin(*dm, faceSize, faceVertices, &numFaces, &faces);CHKERRQ(ierr);
      }
      ierr = PetscFree2(fs_vertex_count_list,fs_vertex_list);CHKERRQ(ierr);
    }
    ierr = PetscFree(fs_id);CHKERRQ(ierr);
  }
#else
  SETERRQ(comm, PETSC_ERR_SUP, "This method requires ExodusII support. Reconfigure using --download-exodusii");
#endif
  PetscFunctionReturn(0);
}