/*@
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, §ion);CHKERRQ(ierr);
if (section) {
ierr = PetscSectionPermute(section, perm, §ionNew);CHKERRQ(ierr);
ierr = DMSetDefaultSection(*pdm, sectionNew);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionNew);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);
}
/*@
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);
}