예제 #1
0
/*@
  DMPlexPermute - Reorder the mesh according to the input permutation

  Collective on DM

  Input Parameter:
+ dm - The DMPlex object
- perm - The point permutation, perm[old point number] = new point number

  Output Parameter:
. pdm - The permuted DM

  Level: intermediate

.keywords: mesh
.seealso: MatPermute()
@*/
PetscErrorCode DMPlexPermute(DM dm, IS perm, DM *pdm)
{
  DM_Plex       *plex = (DM_Plex *) dm->data, *plexNew;
  PetscSection   section, sectionNew;
  PetscInt       dim;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidHeaderSpecific(perm, IS_CLASSID, 2);
  PetscValidPointer(pdm, 3);
  ierr = DMCreate(PetscObjectComm((PetscObject) dm), pdm);CHKERRQ(ierr);
  ierr = DMSetType(*pdm, DMPLEX);CHKERRQ(ierr);
  ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
  ierr = DMSetDimension(*pdm, dim);CHKERRQ(ierr);
  ierr = DMGetDefaultSection(dm, &section);CHKERRQ(ierr);
  if (section) {
    ierr = PetscSectionPermute(section, perm, &sectionNew);CHKERRQ(ierr);
    ierr = DMSetDefaultSection(*pdm, sectionNew);CHKERRQ(ierr);
    ierr = PetscSectionDestroy(&sectionNew);CHKERRQ(ierr);
  }
  plexNew = (DM_Plex *) (*pdm)->data;
  /* Ignore ltogmap, ltogmapb */
  /* Ignore sf, defaultSF */
  /* Ignore globalVertexNumbers, globalCellNumbers */
  /* Remap coordinates */
  {
    DM              cdm, cdmNew;
    PetscSection    csection, csectionNew;
    Vec             coordinates, coordinatesNew;
    PetscScalar    *coords, *coordsNew;
    const PetscInt *pperm;
    PetscInt        pStart, pEnd, p;
    const char     *name;

    ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
    ierr = DMGetDefaultSection(cdm, &csection);CHKERRQ(ierr);
    ierr = PetscSectionPermute(csection, perm, &csectionNew);CHKERRQ(ierr);
    ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
    ierr = VecDuplicate(coordinates, &coordinatesNew);CHKERRQ(ierr);
    ierr = PetscObjectGetName((PetscObject)coordinates,&name);CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject)coordinatesNew,name);CHKERRQ(ierr);
    ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
    ierr = VecGetArray(coordinatesNew, &coordsNew);CHKERRQ(ierr);
    ierr = PetscSectionGetChart(csectionNew, &pStart, &pEnd);CHKERRQ(ierr);
    ierr = ISGetIndices(perm, &pperm);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt dof, off, offNew, d;

      ierr = PetscSectionGetDof(csectionNew, p, &dof);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(csection, p, &off);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(csectionNew, pperm[p], &offNew);CHKERRQ(ierr);
      for (d = 0; d < dof; ++d) coordsNew[offNew+d] = coords[off+d];
    }
    ierr = ISRestoreIndices(perm, &pperm);CHKERRQ(ierr);
    ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
    ierr = VecRestoreArray(coordinatesNew, &coordsNew);CHKERRQ(ierr);
    ierr = DMGetCoordinateDM(*pdm, &cdmNew);CHKERRQ(ierr);
    ierr = DMSetDefaultSection(cdmNew, csectionNew);CHKERRQ(ierr);
    ierr = DMSetCoordinatesLocal(*pdm, coordinatesNew);CHKERRQ(ierr);
    ierr = PetscSectionDestroy(&csectionNew);CHKERRQ(ierr);
    ierr = VecDestroy(&coordinatesNew);CHKERRQ(ierr);
  }
  /* Reorder labels */
  {
    PetscInt numLabels, l;
    DMLabel  label, labelNew;

    ierr = DMGetNumLabels(dm, &numLabels);CHKERRQ(ierr);
    for (l = numLabels-1; l >= 0; --l) {
      ierr = DMGetLabelByNum(dm, l, &label);CHKERRQ(ierr);
      ierr = DMLabelPermute(label, perm, &labelNew);CHKERRQ(ierr);
      ierr = DMAddLabel(*pdm, labelNew);CHKERRQ(ierr);
    }
    if (plex->subpointMap) {ierr = DMLabelPermute(plex->subpointMap, perm, &plexNew->subpointMap);CHKERRQ(ierr);}
  }
  /* Reorder topology */
  {
    const PetscInt *pperm;
    PetscInt        maxConeSize, maxSupportSize, n, pStart, pEnd, p;

    ierr = DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);CHKERRQ(ierr);
    plexNew->maxConeSize    = maxConeSize;
    plexNew->maxSupportSize = maxSupportSize;
    ierr = PetscSectionDestroy(&plexNew->coneSection);CHKERRQ(ierr);
    ierr = PetscSectionPermute(plex->coneSection, perm, &plexNew->coneSection);CHKERRQ(ierr);
    ierr = PetscSectionGetStorageSize(plexNew->coneSection, &n);CHKERRQ(ierr);
    ierr = PetscMalloc1(n, &plexNew->cones);CHKERRQ(ierr);
    ierr = PetscMalloc1(n, &plexNew->coneOrientations);CHKERRQ(ierr);
    ierr = ISGetIndices(perm, &pperm);CHKERRQ(ierr);
    ierr = PetscSectionGetChart(plex->coneSection, &pStart, &pEnd);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt dof, off, offNew, d;

      ierr = PetscSectionGetDof(plexNew->coneSection, pperm[p], &dof);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(plex->coneSection, p, &off);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(plexNew->coneSection, pperm[p], &offNew);CHKERRQ(ierr);
      for (d = 0; d < dof; ++d) {
        plexNew->cones[offNew+d]            = pperm[plex->cones[off+d]];
        plexNew->coneOrientations[offNew+d] = plex->coneOrientations[off+d];
      }
    }
    ierr = PetscSectionDestroy(&plexNew->supportSection);CHKERRQ(ierr);
    ierr = PetscSectionPermute(plex->supportSection, perm, &plexNew->supportSection);CHKERRQ(ierr);
    ierr = PetscSectionGetStorageSize(plexNew->supportSection, &n);CHKERRQ(ierr);
    ierr = PetscMalloc1(n, &plexNew->supports);CHKERRQ(ierr);
    ierr = PetscSectionGetChart(plex->supportSection, &pStart, &pEnd);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt dof, off, offNew, d;

      ierr = PetscSectionGetDof(plexNew->supportSection, pperm[p], &dof);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(plex->supportSection, p, &off);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(plexNew->supportSection, pperm[p], &offNew);CHKERRQ(ierr);
      for (d = 0; d < dof; ++d) {
        plexNew->supports[offNew+d] = pperm[plex->supports[off+d]];
      }
    }
    ierr = ISRestoreIndices(perm, &pperm);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}
예제 #2
0
파일: plexexodusii.c 프로젝트: 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);
}