コード例 #1
0
ファイル: plexcreate.c プロジェクト: feelpp/debian-petsc
/*
  This takes as input the coordinates for each vertex
*/
PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
{
  PetscSection   coordSection;
  Vec            coordinates;
  PetscScalar   *coords;
  PetscInt       coordSize, v, d;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
  ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
  ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
  for (v = numCells; v < numCells+numVertices; ++v) {
    ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr);
    ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
  ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
  ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  for (v = 0; v < numVertices; ++v) {
    for (d = 0; d < spaceDim; ++d) {
      coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
    }
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
コード例 #2
0
ファイル: plexcreate.c プロジェクト: feelpp/debian-petsc
/*
  This takes as input the raw Hasse Diagram data
*/
PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[])
{
  Vec            coordinates;
  PetscSection   coordSection;
  PetscScalar    *coords;
  PetscInt       coordSize, firstVertex = numPoints[depth], pStart = 0, pEnd = 0, p, v, dim, d, off;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
  for (d = 0; d <= depth; ++d) pEnd += numPoints[d];
  ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr);
  for (p = pStart; p < pEnd; ++p) {
    ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr);
  }
  ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */
  for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) {
    ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr);
    ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr);
  }
  ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr);
  ierr = DMPlexStratify(dm);CHKERRQ(ierr);
  /* Build coordinates */
  ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
  ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
  ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr);
  for (v = firstVertex; v < firstVertex+numPoints[0]; ++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(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
  ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  for (v = 0; v < numPoints[0]; ++v) {
    PetscInt off;

    ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr);
    for (d = 0; d < dim; ++d) {
      coords[off+d] = vertexCoords[v*dim+d];
    }
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
コード例 #3
0
ファイル: plexinterpolate.c プロジェクト: tom-klotz/petsc
/*@
  DMPlexCopyCoordinates - Copy coordinates from one mesh to another with the same vertices

  Collective on DM

  Input Parameter:
. dmA - The DMPlex object with initial coordinates

  Output Parameter:
. dmB - The DMPlex object with copied coordinates

  Level: intermediate

  Note: This is typically used when adding pieces other than vertices to a mesh

.keywords: mesh
.seealso: DMCopyLabels(), DMGetCoordinates(), DMGetCoordinatesLocal(), DMGetCoordinateDM(), DMGetCoordinateSection()
@*/
PetscErrorCode DMPlexCopyCoordinates(DM dmA, DM dmB)
{
  Vec            coordinatesA, coordinatesB;
  PetscSection   coordSectionA, coordSectionB;
  PetscScalar   *coordsA, *coordsB;
  PetscInt       spaceDim, vStartA, vStartB, vEndA, vEndB, coordSizeB, v, d;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (dmA == dmB) PetscFunctionReturn(0);
  ierr = DMPlexGetDepthStratum(dmA, 0, &vStartA, &vEndA);CHKERRQ(ierr);
  ierr = DMPlexGetDepthStratum(dmB, 0, &vStartB, &vEndB);CHKERRQ(ierr);
  if ((vEndA-vStartA) != (vEndB-vStartB)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "The number of vertices in first DM %d != %d in the second DM", vEndA-vStartA, vEndB-vStartB);
  ierr = DMGetCoordinateSection(dmA, &coordSectionA);CHKERRQ(ierr);
  ierr = DMGetCoordinateSection(dmB, &coordSectionB);CHKERRQ(ierr);
  if (!coordSectionB) {
    PetscInt dim;

    ierr = PetscSectionCreate(PetscObjectComm((PetscObject) coordSectionA), &coordSectionB);CHKERRQ(ierr);
    ierr = DMGetCoordinateDim(dmA, &dim);CHKERRQ(ierr);
    ierr = DMSetCoordinateSection(dmB, dim, coordSectionB);CHKERRQ(ierr);
    ierr = PetscObjectDereference((PetscObject) coordSectionB);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetNumFields(coordSectionB, 1);CHKERRQ(ierr);
  ierr = PetscSectionGetFieldComponents(coordSectionA, 0, &spaceDim);CHKERRQ(ierr);
  ierr = PetscSectionSetFieldComponents(coordSectionB, 0, spaceDim);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(coordSectionB, vStartB, vEndB);CHKERRQ(ierr);
  for (v = vStartB; v < vEndB; ++v) {
    ierr = PetscSectionSetDof(coordSectionB, v, spaceDim);CHKERRQ(ierr);
    ierr = PetscSectionSetFieldDof(coordSectionB, v, 0, spaceDim);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetUp(coordSectionB);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(coordSectionB, &coordSizeB);CHKERRQ(ierr);
  ierr = DMGetCoordinatesLocal(dmA, &coordinatesA);CHKERRQ(ierr);
  ierr = VecCreate(PetscObjectComm((PetscObject) dmB), &coordinatesB);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) coordinatesB, "coordinates");CHKERRQ(ierr);
  ierr = VecSetSizes(coordinatesB, coordSizeB, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetType(coordinatesB,VECSTANDARD);CHKERRQ(ierr);
  ierr = VecGetArray(coordinatesA, &coordsA);CHKERRQ(ierr);
  ierr = VecGetArray(coordinatesB, &coordsB);CHKERRQ(ierr);
  for (v = 0; v < vEndB-vStartB; ++v) {
    for (d = 0; d < spaceDim; ++d) {
      coordsB[v*spaceDim+d] = coordsA[v*spaceDim+d];
    }
  }
  ierr = VecRestoreArray(coordinatesA, &coordsA);CHKERRQ(ierr);
  ierr = VecRestoreArray(coordinatesB, &coordsB);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(dmB, coordinatesB);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinatesB);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
コード例 #4
0
ファイル: ex7.c プロジェクト: petsc/petsc
static PetscErrorCode SetupSection(DM dm)
{
  PetscSection   s;
  PetscInt       vStart, vEnd, v;
  PetscErrorCode ierr;

  PetscFunctionBeginUser;
  ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
  ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &s);CHKERRQ(ierr);
  ierr = PetscSectionSetNumFields(s, 1);CHKERRQ(ierr);
  ierr = PetscSectionSetFieldComponents(s, 0, 1);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(s, vStart, vEnd);CHKERRQ(ierr);
  for (v = vStart; v < vEnd; ++v) {
    ierr = PetscSectionSetDof(s, v, 1);CHKERRQ(ierr);
    ierr = PetscSectionSetFieldDof(s, v, 0, 1);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetUp(s);CHKERRQ(ierr);
  ierr = DMSetSection(dm, s);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&s);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
コード例 #5
0
ファイル: ex8.c プロジェクト: feelpp/debian-petsc
PetscErrorCode ChangeCoordinates(DM dm, PetscInt spaceDim, PetscScalar vertexCoords[])
{
  PetscSection   coordSection;
  Vec            coordinates;
  PetscScalar   *coords;
  PetscInt       vStart, vEnd, v, d, coordSize;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
  ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
  ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
  ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr);
  for (v = vStart; v < vEnd; ++v) {
    ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr);
    ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
  ierr = VecCreate(PetscObjectComm((PetscObject) dm), &coordinates);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
  ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  for (v = vStart; v < vEnd; ++v) {
    PetscInt off;

    ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
    for (d = 0; d < spaceDim; ++d) {
      coords[off+d] = vertexCoords[(v-vStart)*spaceDim+d];
    }
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
  ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
コード例 #6
0
ファイル: plexgmsh.c プロジェクト: ZJLi2013/petsc
/*@
  DMPlexCreateGmsh - Create a DMPlex mesh from a Gmsh file.

  Collective on comm

  Input Parameters:
+ comm  - The MPI communicator
. viewer - The Viewer associated with a Gmsh file
- interpolate - Create faces and edges in the mesh

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

  Note: http://www.geuz.org/gmsh/doc/texinfo/#MSH-ASCII-file-format

  Level: beginner

.keywords: mesh,Gmsh
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateGmsh(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm)
{
  FILE          *fd;
  PetscSection   coordSection;
  Vec            coordinates;
  PetscScalar   *coords, *coordsIn = NULL;
  PetscInt       dim = 0, coordSize, c, v, d;
  int            numVertices = 0, numCells = 0, snum;
  long           fpos = 0;
  PetscMPIInt    num_proc, rank;
  char           line[PETSC_MAX_PATH_LEN];
  PetscBool      match;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  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);
  if (!rank) {
    PetscBool match;
    int       fileType, dataSize;

    ierr = PetscViewerASCIIGetPointer(viewer, &fd);CHKERRQ(ierr);
    /* Read header */
    fgets(line, PETSC_MAX_PATH_LEN, fd);
    ierr = PetscStrncmp(line, "$MeshFormat\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    snum = fscanf(fd, "2.2 %d %d\n", &fileType, &dataSize);CHKERRQ(snum != 2);
    if (fileType) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh ASCII file", fileType);
    if (dataSize != sizeof(double)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Data size %d is not valid for a Gmsh file", dataSize);
    fgets(line, PETSC_MAX_PATH_LEN, fd);
    ierr = PetscStrncmp(line, "$EndMeshFormat\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    /* Read vertices */
    fgets(line, PETSC_MAX_PATH_LEN, fd);
    ierr = PetscStrncmp(line, "$Nodes\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    snum = fscanf(fd, "%d\n", &numVertices);CHKERRQ(snum != 1);
    ierr = PetscMalloc(numVertices*3 * sizeof(PetscScalar), &coordsIn);CHKERRQ(ierr);
    for (v = 0; v < numVertices; ++v) {
      double x, y, z;
      int    i;

      snum = fscanf(fd, "%d %lg %lg %lg\n", &i, &x, &y, &z);CHKERRQ(snum != 4);
      coordsIn[v*3+0] = x; coordsIn[v*3+1] = y; coordsIn[v*3+2] = z;
      if (i != v+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid node number %d should be %d", i, v+1);
    }
    fgets(line, PETSC_MAX_PATH_LEN, fd);
    ierr = PetscStrncmp(line, "$EndNodes\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    /* Read cells */
    fgets(line, PETSC_MAX_PATH_LEN, fd);
    ierr = PetscStrncmp(line, "$Elements\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    snum = fscanf(fd, "%d\n", &numCells);CHKERRQ(snum != 1);
  }
  ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr);
  if (!rank) {
    fpos = ftell(fd);
    for (c = 0; c < numCells; ++c) {
      PetscInt numCorners, t;
      int      cone[8], i, cellType, numTags, tag;

      snum = fscanf(fd, "%d %d %d", &i, &cellType, &numTags);CHKERRQ(snum != 3);
      if (numTags) for (t = 0; t < numTags; ++t) {snum = fscanf(fd, "%d", &tag);CHKERRQ(snum != 1);}
      switch (cellType) {
      case 1: /* 2-node line */
        dim = 1;
        numCorners = 2;
        snum = fscanf(fd, "%d %d\n", &cone[0], &cone[1]);CHKERRQ(snum != numCorners);
        break;
      case 2: /* 3-node triangle */
        dim = 2;
        numCorners = 3;
        snum = fscanf(fd, "%d %d %d\n", &cone[0], &cone[1], &cone[2]);CHKERRQ(snum != numCorners);
        break;
      case 3: /* 4-node quadrangle */
        dim = 2;
        numCorners = 4;
        snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners);
        break;
      case 4: /* 4-node tetrahedron */
        dim  = 3;
        numCorners = 4;
        snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners);
        break;
      case 5: /* 8-node hexahedron */
        dim = 3;
        numCorners = 8;
        snum = fscanf(fd, "%d %d %d %d %d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3], &cone[4], &cone[5], &cone[6], &cone[7]);CHKERRQ(snum != numCorners);
        break;
      default:
        SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unsupported Gmsh element type %d", cellType);
      }
      ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr);
      if (i != c+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell number %d should be %d", i, c+1);
    }
  }
  ierr = DMSetUp(*dm);CHKERRQ(ierr);
  if (!rank) {
    ierr = fseek(fd, fpos, SEEK_SET);CHKERRQ(ierr);
    for (c = 0; c < numCells; ++c) {
      PetscInt pcone[8], numCorners, corner, t;
      int      cone[8], i, cellType, numTags, tag;

      snum = fscanf(fd, "%d %d %d", &i, &cellType, &numTags);CHKERRQ(snum != 3);
      if (numTags) for (t = 0; t < numTags; ++t) {snum = fscanf(fd, "%d", &tag);CHKERRQ(snum != 1);}
      switch (cellType) {
      case 1: /* 2-node line */
        dim = 1;
        numCorners = 2;
        snum = fscanf(fd, "%d %d\n", &cone[0], &cone[1]);CHKERRQ(snum != numCorners);
        break;
      case 2: /* 3-node triangle */
        dim = 2;
        numCorners = 3;
        snum = fscanf(fd, "%d %d %d\n", &cone[0], &cone[1], &cone[2]);CHKERRQ(snum != numCorners);
        break;
      case 3: /* 4-node quadrangle */
        dim = 2;
        numCorners = 4;
        snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners);
        break;
      case 4: /* 4-node tetrahedron */
        dim  = 3;
        numCorners = 4;
        snum = fscanf(fd, "%d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3]);CHKERRQ(snum != numCorners);
        ierr = DMPlexInvertCell(dim, numCorners, cone);CHKERRQ(ierr);
        break;
      case 5: /* 8-node hexahedron */
        dim = 3;
        numCorners = 8;
        snum = fscanf(fd, "%d %d %d %d %d %d %d %d\n", &cone[0], &cone[1], &cone[2], &cone[3], &cone[4], &cone[5], &cone[6], &cone[7]);CHKERRQ(snum != numCorners);
        ierr = DMPlexInvertCell(dim, numCorners, cone);CHKERRQ(ierr);
        break;
      default:
        SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unsupported Gmsh element type %d", cellType);
      }
      for (corner = 0; corner < numCorners; ++corner) pcone[corner] = cone[corner] + numCells-1;
      ierr = DMPlexSetCone(*dm, c, pcone);CHKERRQ(ierr);
      if (i != c+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell number %d should be %d", i, c+1);
    }
    fgets(line, PETSC_MAX_PATH_LEN, fd);
    ierr = PetscStrncmp(line, "$EndElements\n", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
  }
  ierr = MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
  ierr = DMPlexSetDimension(*dm, dim);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;
  }
  /* 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(comm, &coordinates);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
  ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  if (!rank) {
    for (v = 0; v < numVertices; ++v) {
      for (d = 0; d < dim; ++d) {
        coords[v*dim+d] = coordsIn[v*3+d];
      }
    }
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = PetscFree(coordsIn);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
コード例 #7
0
ファイル: plexexodusii.c プロジェクト: ziolai/petsc
/*@
  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_elem_blk_ids(exoid, 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_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &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_elem_block(exoid, cs_id[cs], buffer, &num_cell_in_set, &num_vertex_per_cell, &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_elem_conn(exoid, cs_id[cs], cs_connect);CHKERRQ(ierr);
      /* EXO uses Fortran-based indexing, sieve 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 = NULL;

    ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
    /* Maintain Cell Sets label */
    {
      DMLabel label;

      ierr = DMRemoveLabel(*dm, "Cell Sets", &label);CHKERRQ(ierr);
      if (label) {ierr = DMAddLabel(idm, label);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, num_attr;
    /* 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_node_set_ids(exoid, vs_id);CHKERRQ(ierr);
    for (vs = 0; vs < num_vs; ++vs) {
      ierr = ex_get_node_set_param(exoid, vs_id[vs], &num_vertex_in_set, &num_attr);CHKERRQ(ierr);
      ierr = PetscMalloc1(num_vertex_in_set, &vs_vertex_list);CHKERRQ(ierr);
      ierr = ex_get_node_set(exoid, vs_id[vs], vs_vertex_list);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) {
    float *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, num_dist_fact_in_set;
    /* Read from ex_get_side_set_node_list() */
    int *fs_vertex_count_list, *fs_vertex_list;

    /* Get side set ids */
    ierr = PetscMalloc1(num_fs, &fs_id);CHKERRQ(ierr);
    ierr = ex_get_side_set_ids(exoid, fs_id);CHKERRQ(ierr);
    for (fs = 0; fs < num_fs; ++fs) {
      ierr = ex_get_side_set_param(exoid, fs_id[fs], &num_side_in_set, &num_dist_fact_in_set);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);
      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);
        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);
}
コード例 #8
0
ファイル: plexcgns.c プロジェクト: pombredanne/petsc
/*@
  DMPlexCreateCGNS - Create a DMPlex mesh from a CGNS file ID.

  Collective on comm

  Input Parameters:
+ comm  - The MPI communicator
. cgid - The CG id associated with a file and obtained using cg_open
- interpolate - Create faces and edges in the mesh

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

  Note: http://www.grc.nasa.gov/WWW/cgns/CGNS_docs_current/index.html

  Level: beginner

.keywords: mesh,CGNS
.seealso: DMPlexCreate(), DMPlexCreateExodus()
@*/
PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpolate, DM *dm)
{
#if defined(PETSC_HAVE_CGNS)
  PetscMPIInt    num_proc, rank;
  PetscSection   coordSection;
  Vec            coordinates;
  PetscScalar   *coords;
  PetscInt      *cellStart, *vertStart;
  PetscInt       coordSize, v;
  PetscErrorCode ierr;
  /* Read from file */
  char basename[CGIO_MAX_NAME_LENGTH+1];
  char buffer[CGIO_MAX_NAME_LENGTH+1];
  int  dim    = 0, physDim = 0, numVertices = 0, numCells = 0;
  int  nzones = 0;
#endif

  PetscFunctionBegin;
#if defined(PETSC_HAVE_CGNS)
  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 CGNS II file and read basic informations on rank 0, then broadcast to all processors */
  if (!rank) {
    int nbases, z;

    ierr = cg_nbases(cgid, &nbases);CHKERRQ(ierr);
    if (nbases > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single base, not %d\n",nbases);
    ierr = cg_base_read(cgid, 1, basename, &dim, &physDim);CHKERRQ(ierr);
    ierr = cg_nzones(cgid, 1, &nzones);CHKERRQ(ierr);
    ierr = PetscCalloc2(nzones+1, &cellStart, nzones+1, &vertStart);CHKERRQ(ierr);
    for (z = 1; z <= nzones; ++z) {
      cgsize_t sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */

      ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr);
      numVertices += sizes[0];
      numCells    += sizes[1];
      cellStart[z] += sizes[1] + cellStart[z-1];
      vertStart[z] += sizes[0] + vertStart[z-1];
    }
    for (z = 1; z <= nzones; ++z) {
      vertStart[z] += numCells;
    }
  }
  ierr = MPI_Bcast(basename, CGIO_MAX_NAME_LENGTH+1, MPI_CHAR, 0, comm);CHKERRQ(ierr);
  ierr = MPI_Bcast(&dim, 1, MPI_INT, 0, comm);CHKERRQ(ierr);
  ierr = MPI_Bcast(&nzones, 1, MPI_INT, 0, comm);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) *dm, basename);CHKERRQ(ierr);
  ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
  ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr);

  /* Read zone information */
  if (!rank) {
    int z, c, c_loc, v, v_loc;

    /* Read the cell set connectivity table and build mesh topology
       CGNS standard requires that cells in a zone be numbered sequentially and be pairwise disjoint. */
    /* First set sizes */
    for (z = 1, c = 0; z <= nzones; ++z) {
      ZoneType_t    zonetype;
      int           nsections;
      ElementType_t cellType;
      cgsize_t      start, end;
      int           nbndry, parentFlag;
      PetscInt      numCorners;

      ierr = cg_zone_type(cgid, 1, z, &zonetype);CHKERRQ(ierr);
      if (zonetype == Structured) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"Can only handle Unstructured zones for CGNS");
      ierr = cg_nsections(cgid, 1, z, &nsections);CHKERRQ(ierr);
      if (nsections > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single section, not %d\n",nsections);
      ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr);
      /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
      if (cellType == MIXED) {
        cgsize_t elementDataSize, *elements;
        PetscInt off;

        ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr);
        ierr = PetscMalloc1(elementDataSize, &elements);CHKERRQ(ierr);
        ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr);
        for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) {
          switch (elements[off]) {
          case TRI_3:   numCorners = 3;break;
          case QUAD_4:  numCorners = 4;break;
          case TETRA_4: numCorners = 4;break;
          case HEXA_8:  numCorners = 8;break;
          default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[off]);
          }
          ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr);
          off += numCorners+1;
        }
        ierr = PetscFree(elements);CHKERRQ(ierr);
      } else {
        switch (cellType) {
        case TRI_3:   numCorners = 3;break;
        case QUAD_4:  numCorners = 4;break;
        case TETRA_4: numCorners = 4;break;
        case HEXA_8:  numCorners = 8;break;
        default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
        }
        for (c_loc = start; c_loc <= end; ++c_loc, ++c) {
          ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr);
        }
      }
    }
    ierr = DMSetUp(*dm);CHKERRQ(ierr);
    for (z = 1, c = 0; z <= nzones; ++z) {
      ElementType_t cellType;
      cgsize_t     *elements, elementDataSize, start, end;
      int           nbndry, parentFlag;
      PetscInt     *cone, numc, numCorners, maxCorners = 27;

      ierr = cg_section_read(cgid, 1, z, 1, buffer, &cellType, &start, &end, &nbndry, &parentFlag);CHKERRQ(ierr);
      numc = end - start;
      /* This alone is reason enough to bludgeon every single CGNDS developer, this must be what they describe as the "idiocy of crowds" */
      ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr);
      ierr = PetscMalloc2(elementDataSize,&elements,maxCorners,&cone);CHKERRQ(ierr);
      ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr);
      if (cellType == MIXED) {
        /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
        for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
          switch (elements[v]) {
          case TRI_3:   numCorners = 3;break;
          case QUAD_4:  numCorners = 4;break;
          case TETRA_4: numCorners = 4;break;
          case HEXA_8:  numCorners = 8;break;
          default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) elements[v]);
          }
          ++v;
          for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
            cone[v_loc] = elements[v]+numCells-1;
          }
          /* Tetrahedra are inverted */
          if (elements[v] == TETRA_4) {
            PetscInt tmp = cone[0];
            cone[0] = cone[1];
            cone[1] = tmp;
          }
          /* Hexahedra are inverted */
          if (elements[v] == HEXA_8) {
            PetscInt tmp = cone[5];
            cone[5] = cone[7];
            cone[7] = tmp;
          }
          ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
          ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr);
        }
      } else {
        switch (cellType) {
        case TRI_3:   numCorners = 3;break;
        case QUAD_4:  numCorners = 4;break;
        case TETRA_4: numCorners = 4;break;
        case HEXA_8:  numCorners = 8;break;
        default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
        }

        /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
        for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
          for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
            cone[v_loc] = elements[v]+numCells-1;
          }
          /* Tetrahedra are inverted */
          if (cellType == TETRA_4) {
            PetscInt tmp = cone[0];
            cone[0] = cone[1];
            cone[1] = tmp;
          }
          /* Hexahedra are inverted, and they give the top first */
          if (cellType == HEXA_8) {
            PetscInt tmp = cone[5];
            cone[5] = cone[7];
            cone[7] = tmp;
          }
          ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
          ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr);
        }
      }
      ierr = PetscFree2(elements,cone);CHKERRQ(ierr);
    }
  }
  ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
  ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
  if (interpolate) {
    DM idm = NULL;

    ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr);
    /* Maintain zone label */
    {
      DMLabel label;

      ierr = DMPlexRemoveLabel(*dm, "zone", &label);CHKERRQ(ierr);
      if (label) {ierr = DMPlexAddLabel(idm, label);CHKERRQ(ierr);}
    }
    ierr = DMDestroy(dm);CHKERRQ(ierr);
    *dm  = idm;
  }

  /* 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(comm, &coordinates);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
  ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  if (!rank) {
    PetscInt off = 0;
    float   *x[3];
    int      z, d;

    ierr = PetscMalloc3(numVertices,&x[0],numVertices,&x[1],numVertices,&x[2]);CHKERRQ(ierr);
    for (z = 1; z <= nzones; ++z) {
      DataType_t datatype;
      cgsize_t   sizes[3]; /* Number of vertices, number of cells, number of boundary vertices */
      cgsize_t   range_min[3] = {1, 1, 1};
      cgsize_t   range_max[3] = {1, 1, 1};
      int        ngrids, ncoords;


      ierr = cg_zone_read(cgid, 1, z, buffer, sizes);CHKERRQ(ierr);
      range_max[0] = sizes[0];
      ierr = cg_ngrids(cgid, 1, z, &ngrids);CHKERRQ(ierr);
      if (ngrids > 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a single grid, not %d\n",ngrids);
      ierr = cg_ncoords(cgid, 1, z, &ncoords);CHKERRQ(ierr);
      if (ncoords != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a coordinate array for each dimension, not %d\n",ncoords);
      for (d = 0; d < dim; ++d) {
        ierr = cg_coord_info(cgid, 1, z, 1+d, &datatype, buffer);CHKERRQ(ierr);
        ierr = cg_coord_read(cgid, 1, z, buffer, RealSingle, range_min, range_max, x[d]);CHKERRQ(ierr);
      }
      if (dim > 0) {
        for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+0] = x[0][v];
      }
      if (dim > 1) {
        for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+1] = x[1][v];
      }
      if (dim > 2) {
        for (v = 0; v < sizes[0]; ++v) coords[(v+off)*dim+2] = x[2][v];
      }
      off += sizes[0];
    }
    ierr = PetscFree3(x[0],x[1],x[2]);CHKERRQ(ierr);
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
  /* Read boundary conditions */
  if (!rank) {
    DMLabel        label;
    BCType_t       bctype;
    DataType_t     datatype;
    PointSetType_t pointtype;
    cgsize_t      *points;
    PetscReal     *normals;
    int            normal[3];
    char          *bcname = buffer;
    cgsize_t       npoints, nnormals;
    int            z, nbc, bc, c, ndatasets;

    for (z = 1; z <= nzones; ++z) {
      ierr = cg_nbocos(cgid, 1, z, &nbc);CHKERRQ(ierr);
      for (bc = 1; bc <= nbc; ++bc) {
        ierr = cg_boco_info(cgid, 1, z, bc, bcname, &bctype, &pointtype, &npoints, normal, &nnormals, &datatype, &ndatasets);CHKERRQ(ierr);
        ierr = DMPlexCreateLabel(*dm, bcname);CHKERRQ(ierr);
        ierr = DMPlexGetLabel(*dm, bcname, &label);CHKERRQ(ierr);
        ierr = PetscMalloc2(npoints, &points, nnormals, &normals);CHKERRQ(ierr);
        ierr = cg_boco_read(cgid, 1, z, bc, points, (void *) normals);CHKERRQ(ierr);
        if (pointtype == ElementRange) {
          /* Range of cells: assuming half-open interval since the documentation sucks */
          for (c = points[0]; c < points[1]; ++c) {
            ierr = DMLabelSetValue(label, c - cellStart[z-1], 1);CHKERRQ(ierr);
          }
        } else if (pointtype == ElementList) {
          /* List of cells */
          for (c = 0; c < npoints; ++c) {
            ierr = DMLabelSetValue(label, points[c] - cellStart[z-1], 1);CHKERRQ(ierr);
          }
        } else if (pointtype == PointRange) {
          GridLocation_t gridloc;

          /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
          ierr = cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");CHKERRQ(ierr);
          ierr = cg_gridlocation_read(&gridloc);CHKERRQ(ierr);
          /* Range of points: assuming half-open interval since the documentation sucks */
          for (c = points[0]; c < points[1]; ++c) {
            if (gridloc == Vertex) {ierr = DMLabelSetValue(label, c - vertStart[z-1], 1);CHKERRQ(ierr);}
            else                   {ierr = DMLabelSetValue(label, c - cellStart[z-1], 1);CHKERRQ(ierr);}
          }
        } else if (pointtype == PointList) {
          GridLocation_t gridloc;

          /* List of points: Oh please, someone get the CGNS developers away from a computer. This is unconscionable. */
          ierr = cg_goto(cgid, 1, "Zone_t", z, "BC_t", bc, "end");
          ierr = cg_gridlocation_read(&gridloc);
          for (c = 0; c < npoints; ++c) {
            if (gridloc == Vertex) {ierr = DMLabelSetValue(label, points[c] - vertStart[z-1], 1);CHKERRQ(ierr);}
            else                   {ierr = DMLabelSetValue(label, points[c] - cellStart[z-1], 1);CHKERRQ(ierr);}
          }
        } else SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported point set type %d", (int) pointtype);
        ierr = PetscFree2(points, normals);CHKERRQ(ierr);
      }
    }
    ierr = PetscFree2(cellStart, vertStart);CHKERRQ(ierr);
  }
#else
  SETERRQ(comm, PETSC_ERR_SUP, "This method requires CGNS support. Reconfigure using --with-cgns-dir");
#endif
  PetscFunctionReturn(0);
}
コード例 #9
0
ファイル: plexfluent.c プロジェクト: pombredanne/petsc
/*@C
  DMPlexCreateFluent - Create a DMPlex mesh from a Fluent mesh file.

  Collective on comm

  Input Parameters:
+ comm  - The MPI communicator
. viewer - The Viewer associated with a Fluent mesh file
- interpolate - Create faces and edges in the mesh

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

  Note: http://aerojet.engr.ucdavis.edu/fluenthelp/html/ug/node1490.htm

  Level: beginner

.keywords: mesh, fluent, case
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateFluent(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm)
{
  PetscMPIInt    rank;
  PetscInt       c, f, v, dim = PETSC_DETERMINE, numCells = 0, numVertices = 0, numCellVertices = PETSC_DETERMINE;
  PetscInt       numFaces = PETSC_DETERMINE, numFaceEntries = PETSC_DETERMINE, numFaceVertices = PETSC_DETERMINE;
  PetscInt      *faces = NULL, *cellVertices, *faceZoneIDs = NULL;
  PetscInt       d, coordSize;
  PetscScalar   *coords, *coordsIn = NULL;
  PetscSection   coordSection;
  Vec            coordinates;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);

  if (!rank) {
    FluentSection s;
    do {
      ierr = DMPlexCreateFluent_ReadSection(viewer, &s);CHKERRQ(ierr);
      if (s.index == 2) {                 /* Dimension */
        dim = s.nd;

      } else if (s.index == 10 || s.index == 2010) { /* Vertices */
        if (s.zoneID == 0) numVertices = s.last;
        else {
          if (coordsIn) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Currently no support for multiple coordinate sets in Fluent files");
          coordsIn = (PetscScalar *) s.data;
        }

      } else if (s.index == 12 || s.index == 2012) { /* Cells */
        if (s.zoneID == 0) numCells = s.last;
        else {
          switch (s.nd) {
          case 0: numCellVertices = PETSC_DETERMINE; break;
          case 1: numCellVertices = 3; break;  /* triangular */
          case 2: numCellVertices = 4; break;  /* tetrahedral */
          case 3: numCellVertices = 4; break;  /* quadrilateral */
          case 4: numCellVertices = 8; break;  /* hexahedral */
          case 5: numCellVertices = 5; break;  /* pyramid */
          case 6: numCellVertices = 6; break;  /* wedge */
          default: numCellVertices = PETSC_DETERMINE;
          }
        }

      } else if (s.index == 13 || s.index == 2013) { /* Facets */
        if (s.zoneID == 0) {  /* Header section */
          numFaces = s.last - s.first + 1;
          if (s.nd == 0 || s.nd == 5) numFaceVertices = PETSC_DETERMINE;
          else numFaceVertices = s.nd;
        } else {              /* Data section */
          if (numFaceVertices != PETSC_DETERMINE && s.nd != numFaceVertices) {
            SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mixed facets in Fluent files are not supported");
          }
          if (numFaces < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "No header section for facets in Fluent file");
          if (numFaceVertices == PETSC_DETERMINE) numFaceVertices = s.nd;
          numFaceEntries = numFaceVertices + 2;
          if (!faces) {ierr = PetscMalloc1(numFaces*numFaceEntries, &faces);CHKERRQ(ierr);}
          if (!faceZoneIDs) {ierr = PetscMalloc1(numFaces, &faceZoneIDs);CHKERRQ(ierr);}
          ierr = PetscMemcpy(&(faces[(s.first-1)*numFaceEntries]), s.data, (s.last-s.first+1)*numFaceEntries*sizeof(PetscInt));CHKERRQ(ierr);
          /* Record the zoneID for each face set */
          for (f = s.first -1; f < s.last; f++) faceZoneIDs[f] = s.zoneID;
          ierr = PetscFree(s.data);CHKERRQ(ierr);
        }
      }
    } while (s.index >= 0);
  }
  ierr = MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
  if (dim < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Fluent file does not include dimension");

  /* Allocate cell-vertex mesh */
  ierr = DMCreate(comm, dm);CHKERRQ(ierr);
  ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);
  ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
  ierr = DMPlexSetChart(*dm, 0, numCells + numVertices);CHKERRQ(ierr);
  if (!rank) {
    if (numCells < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unknown number of cells in Fluent file");
    /* If no cell type was given we assume simplices */
    if (numCellVertices == PETSC_DETERMINE) numCellVertices = numFaceVertices + 1;
    for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(*dm, c, numCellVertices);CHKERRQ(ierr);}
  }
  ierr = DMSetUp(*dm);CHKERRQ(ierr);

  if (!rank) {
    /* Derive cell-vertex list from face-vertex and face-cell maps */
    ierr = PetscMalloc1(numCells*numCellVertices, &cellVertices);CHKERRQ(ierr);
    for (c = 0; c < numCells*numCellVertices; c++) cellVertices[c] = -1;
    for (f = 0; f < numFaces; f++) {
      PetscInt *cell;
      const PetscInt cl = faces[f*numFaceEntries + numFaceVertices];
      const PetscInt cr = faces[f*numFaceEntries + numFaceVertices + 1];
      const PetscInt *face = &(faces[f*numFaceEntries]);

      if (cl > 0) {
        cell = &(cellVertices[(cl-1) * numCellVertices]);
        for (v = 0; v < numFaceVertices; v++) {
          PetscBool found = PETSC_FALSE;
          for (c = 0; c < numCellVertices; c++) {
            if (cell[c] < 0) break;
            if (cell[c] == face[v]-1 + numCells) {found = PETSC_TRUE; break;}
          }
          if (!found) cell[c] = face[v]-1 + numCells;
        }
      }
      if (cr > 0) {
        cell = &(cellVertices[(cr-1) * numCellVertices]);
        for (v = 0; v < numFaceVertices; v++) {
          PetscBool found = PETSC_FALSE;
          for (c = 0; c < numCellVertices; c++) {
            if (cell[c] < 0) break;
            if (cell[c] == face[v]-1 + numCells) {found = PETSC_TRUE; break;}
          }
          if (!found) cell[c] = face[v]-1 + numCells;
        }
      }
    }
    for (c = 0; c < numCells; c++) {
      ierr = DMPlexSetCone(*dm, c, &(cellVertices[c*numCellVertices]));CHKERRQ(ierr);
    }
  }
  ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
  ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
  if (interpolate) {
    DM idm = NULL;

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

  if (!rank) {
    PetscInt fi, joinSize, meetSize, *fverts, cells[2];
    const PetscInt *join, *meet;
    ierr = PetscMalloc1(numFaceVertices, &fverts);CHKERRQ(ierr);
    /* Mark facets by finding the full join of all adjacent vertices */
    for (f = 0; f < numFaces; f++) {
      const PetscInt cl = faces[f*numFaceEntries + numFaceVertices] - 1;
      const PetscInt cr = faces[f*numFaceEntries + numFaceVertices + 1] - 1;
      if (cl > 0 && cr > 0) {
        /* If we know both adjoining cells we can use a single-level meet */
        cells[0] = cl; cells[1] = cr;
        ierr = DMPlexGetMeet(*dm, 2, cells, &meetSize, &meet);CHKERRQ(ierr);
        if (meetSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for Fluent face %d", f);
        ierr = DMPlexSetLabelValue(*dm, "Face Sets", meet[0], faceZoneIDs[f]);CHKERRQ(ierr);
        ierr = DMPlexRestoreMeet(*dm, numFaceVertices, fverts, &meetSize, &meet);CHKERRQ(ierr);
      } else {
        for (fi = 0; fi < numFaceVertices; fi++) fverts[fi] = faces[f*numFaceEntries + fi] + numCells - 1;
        ierr = DMPlexGetFullJoin(*dm, numFaceVertices, fverts, &joinSize, &join);CHKERRQ(ierr);
        if (joinSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for Fluent face %d", f);
        ierr = DMPlexSetLabelValue(*dm, "Face Sets", join[0], faceZoneIDs[f]);CHKERRQ(ierr);
        ierr = DMPlexRestoreJoin(*dm, numFaceVertices, fverts, &joinSize, &join);CHKERRQ(ierr);
      }
    }
    ierr = PetscFree(fverts);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(comm, &coordinates);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
  ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  if (!rank) {
    for (v = 0; v < numVertices; ++v) {
      for (d = 0; d < dim; ++d) {
        coords[v*dim+d] = coordsIn[v*dim+d];
      }
    }
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
  if (!rank) {
    ierr = PetscFree(cellVertices);CHKERRQ(ierr);
    ierr = PetscFree(faces);CHKERRQ(ierr);
    ierr = PetscFree(faceZoneIDs);CHKERRQ(ierr);
    ierr = PetscFree(coordsIn);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}
コード例 #10
0
ファイル: plexgmsh.c プロジェクト: ziolai/petsc
/*@
  DMPlexCreateGmsh - Create a DMPlex mesh from a Gmsh file viewer

  Collective on comm

  Input Parameters:
+ comm  - The MPI communicator
. viewer - The Viewer associated with a Gmsh file
- interpolate - Create faces and edges in the mesh

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

  Note: http://www.geuz.org/gmsh/doc/texinfo/#MSH-ASCII-file-format
  and http://www.geuz.org/gmsh/doc/texinfo/#MSH-binary-file-format

  Level: beginner

.keywords: mesh,Gmsh
.seealso: DMPLEX, DMCreate()
@*/
PetscErrorCode DMPlexCreateGmsh(MPI_Comm comm, PetscViewer viewer, PetscBool interpolate, DM *dm)
{
  PetscViewerType vtype;
  GmshElement   *gmsh_elem;
  PetscSection   coordSection;
  Vec            coordinates;
  PetscScalar   *coords, *coordsIn = NULL;
  PetscInt       dim = 0, coordSize, c, v, d, r, cell;
  int            i, numVertices = 0, numCells = 0, trueNumCells = 0, numRegions = 0, snum;
  PetscMPIInt    num_proc, rank;
  char           line[PETSC_MAX_PATH_LEN];
  PetscBool      match, binary, bswap = PETSC_FALSE;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  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);
  ierr = PetscLogEventBegin(DMPLEX_CreateGmsh,*dm,0,0,0);CHKERRQ(ierr);
  ierr = PetscViewerGetType(viewer, &vtype);CHKERRQ(ierr);
  ierr = PetscStrcmp(vtype, PETSCVIEWERBINARY, &binary);CHKERRQ(ierr);
  if (!rank || binary) {
    PetscBool match;
    int       fileType, dataSize;
    float     version;

    /* Read header */
    ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
    ierr = PetscStrncmp(line, "$MeshFormat", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    ierr = PetscViewerRead(viewer, line, 3, NULL, PETSC_STRING);CHKERRQ(ierr);
    snum = sscanf(line, "%f %d %d", &version, &fileType, &dataSize);
    if (snum != 3) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Gmsh file header: %s", line);
    if (version < 2.0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Gmsh file must be at least version 2.0");
    if (dataSize != sizeof(double)) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Data size %d is not valid for a Gmsh file", dataSize);
    if (binary) {
      int checkInt;
      ierr = PetscViewerRead(viewer, &checkInt, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
      if (checkInt != 1) {
        ierr = PetscByteSwap(&checkInt, PETSC_ENUM, 1);CHKERRQ(ierr);
        if (checkInt == 1) bswap = PETSC_TRUE;
        else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh binary file", fileType);
      }
    } else if (fileType) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File type %d is not a valid Gmsh ASCII file", fileType);
    ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
    ierr = PetscStrncmp(line, "$EndMeshFormat", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    /* OPTIONAL Read physical names */
    ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
    ierr = PetscStrncmp(line, "$PhysicalNames", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (match) {
      ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
      snum = sscanf(line, "%d", &numRegions);
      if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
      for (r = 0; r < numRegions; ++r) {
        PetscInt rdim, tag;

        ierr = PetscViewerRead(viewer, &rdim, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
        ierr = PetscViewerRead(viewer, &tag,  1, NULL, PETSC_ENUM);CHKERRQ(ierr);
        ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
      }
      ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
      ierr = PetscStrncmp(line, "$EndPhysicalNames", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
      if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
      /* Initial read for vertex section */
      ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
    }
    /* Read vertices */
    ierr = PetscStrncmp(line, "$Nodes", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);
    snum = sscanf(line, "%d", &numVertices);
    if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    ierr = PetscMalloc1(numVertices*3, &coordsIn);CHKERRQ(ierr);
    if (binary) {
      size_t doubleSize, intSize;
      PetscInt elementSize;
      char *buffer;
      PetscScalar *baseptr;
      ierr = PetscDataTypeGetSize(PETSC_ENUM, &intSize);CHKERRQ(ierr);
      ierr = PetscDataTypeGetSize(PETSC_DOUBLE, &doubleSize);CHKERRQ(ierr);
      elementSize = (intSize + 3*doubleSize);
      ierr = PetscMalloc1(elementSize*numVertices, &buffer);CHKERRQ(ierr);
      ierr = PetscViewerRead(viewer, buffer, elementSize*numVertices, NULL, PETSC_CHAR);CHKERRQ(ierr);
      if (bswap) ierr = PetscByteSwap(buffer, PETSC_CHAR, elementSize*numVertices);CHKERRQ(ierr);
      for (v = 0; v < numVertices; ++v) {
        baseptr = ((PetscScalar*)(buffer+v*elementSize+intSize));
        coordsIn[v*3+0] = baseptr[0];
        coordsIn[v*3+1] = baseptr[1];
        coordsIn[v*3+2] = baseptr[2];
      }
      ierr = PetscFree(buffer);CHKERRQ(ierr);
    } else {
      for (v = 0; v < numVertices; ++v) {
        ierr = PetscViewerRead(viewer, &i, 1, NULL, PETSC_ENUM);CHKERRQ(ierr);
        ierr = PetscViewerRead(viewer, &(coordsIn[v*3]), 3, NULL, PETSC_DOUBLE);CHKERRQ(ierr);
        if (i != (int)v+1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid node number %d should be %d", i, v+1);
      }
    }
    ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
    ierr = PetscStrncmp(line, "$EndNodes", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    /* Read cells */
    ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
    ierr = PetscStrncmp(line, "$Elements", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
    ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
    snum = sscanf(line, "%d", &numCells);
    if (snum != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
  }

  if (!rank || binary) {
    /* Gmsh elements can be of any dimension/co-dimension, so we need to traverse the
       file contents multiple times to figure out the true number of cells and facets
       in the given mesh. To make this more efficient we read the file contents only
       once and store them in memory, while determining the true number of cells. */
    ierr = DMPlexCreateGmsh_ReadElement(viewer, numCells, binary, bswap, &gmsh_elem);CHKERRQ(ierr);
    for (trueNumCells=0, c = 0; c < numCells; ++c) {
      if (gmsh_elem[c].dim > dim) {dim = gmsh_elem[c].dim; trueNumCells = 0;}
      if (gmsh_elem[c].dim == dim) trueNumCells++;
    }
    ierr = PetscViewerRead(viewer, line, 1, NULL, PETSC_STRING);CHKERRQ(ierr);;
    ierr = PetscStrncmp(line, "$EndElements", PETSC_MAX_PATH_LEN, &match);CHKERRQ(ierr);
    if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
  }
  /* For binary we read on all ranks, but only build the plex on rank 0 */
  if (binary && rank) {trueNumCells = 0; numVertices = 0;};
  /* Allocate the cell-vertex mesh */
  ierr = DMPlexSetChart(*dm, 0, trueNumCells+numVertices);CHKERRQ(ierr);
  if (!rank) {
    for (cell = 0, c = 0; c < numCells; ++c) {
      if (gmsh_elem[c].dim == dim) {
        ierr = DMPlexSetConeSize(*dm, cell, gmsh_elem[c].numNodes);CHKERRQ(ierr);
        cell++;
      }
    }
  }
  ierr = DMSetUp(*dm);CHKERRQ(ierr);
  /* Add cell-vertex connections */
  if (!rank) {
    PetscInt pcone[8], corner;
    for (cell = 0, c = 0; c < numCells; ++c) {
      if (gmsh_elem[c].dim == dim) {
        for (corner = 0; corner < gmsh_elem[c].numNodes; ++corner) {
          pcone[corner] = gmsh_elem[c].nodes[corner] + trueNumCells-1;
        }
        if (dim == 3) {
          /* Tetrahedra are inverted */
          if (gmsh_elem[c].numNodes == 4) {
            PetscInt tmp = pcone[0];
            pcone[0] = pcone[1];
            pcone[1] = tmp;
          }
          /* Hexahedra are inverted */
          if (gmsh_elem[c].numNodes == 8) {
            PetscInt tmp = pcone[1];
            pcone[1] = pcone[3];
            pcone[3] = tmp;
          }
        }   
        ierr = DMPlexSetCone(*dm, cell, pcone);CHKERRQ(ierr);
        cell++;
      }
    }
  }
  ierr = MPI_Bcast(&dim, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
  ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr);
  ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr);
  ierr = DMPlexStratify(*dm);CHKERRQ(ierr);
  if (interpolate) {
    DM idm = NULL;

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

  if (!rank) {
    /* Apply boundary IDs by finding the relevant facets with vertex joins */
    PetscInt pcone[8], corner, vStart, vEnd;

    ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
    for (c = 0; c < numCells; ++c) {
      if (gmsh_elem[c].dim == dim-1) {
        PetscInt joinSize;
        const PetscInt *join;
        for (corner = 0; corner < gmsh_elem[c].numNodes; ++corner) {
          pcone[corner] = gmsh_elem[c].nodes[corner] + vStart - 1;
        }
        ierr = DMPlexGetFullJoin(*dm, gmsh_elem[c].numNodes, (const PetscInt *) pcone, &joinSize, &join);CHKERRQ(ierr);
        if (joinSize != 1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Could not determine Plex facet for element %d", gmsh_elem[c].id);
        ierr = DMSetLabelValue(*dm, "Face Sets", join[0], gmsh_elem[c].tags[0]);CHKERRQ(ierr);
        ierr = DMPlexRestoreJoin(*dm, gmsh_elem[c].numNodes, (const PetscInt *) pcone, &joinSize, &join);CHKERRQ(ierr);
      }
    }

    /* Create cell sets */
    for (cell = 0, c = 0; c < numCells; ++c) {
      if (gmsh_elem[c].dim == dim) {
        if (gmsh_elem[c].numTags > 0) {
          ierr = DMSetLabelValue(*dm, "Cell Sets", cell, gmsh_elem[c].tags[0]);CHKERRQ(ierr);
          cell++;
        }
      }
    }
  }

  /* Read coordinates */
  ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr);
  ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
  ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(coordSection, trueNumCells, trueNumCells + numVertices);CHKERRQ(ierr);
  for (v = trueNumCells; v < trueNumCells+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) {
    for (v = 0; v < numVertices; ++v) {
      for (d = 0; d < dim; ++d) {
        coords[v*dim+d] = coordsIn[v*3+d];
      }
    }
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = PetscFree(coordsIn);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
  /* Clean up intermediate storage */
  if (!rank || binary) ierr = PetscFree(gmsh_elem);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(DMPLEX_CreateGmsh,*dm,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}