/*@C
DMPlexGetStratumSize - Get the number of points in a label stratum
Not Collective
Input Parameters:
+ dm - The DMPlex object
. name - The label name
- value - The stratum value
Output Parameter:
. size - The stratum size
Level: beginner
.keywords: mesh
.seealso: DMLabelGetStratumSize(), DMPlexGetLabelSize(), DMPlexGetLabelIds()
@*/
PetscErrorCode DMPlexGetStratumSize(DM dm, const char name[], PetscInt value, PetscInt *size)
{
DMLabel label;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
PetscValidCharPointer(name, 2);
PetscValidPointer(size, 4);
ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr);
*size = 0;
if (!label) PetscFunctionReturn(0);
ierr = DMLabelGetStratumSize(label, value, size);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMLabelConvertToSection(DMLabel label, PetscSection *section, IS *is)
{
IS vIS;
const PetscInt *values;
PetscInt *points;
PetscInt nV, vS = 0, vE = 0, v, N;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMLabelGetNumValues(label, &nV);CHKERRQ(ierr);
ierr = DMLabelGetValueIS(label, &vIS);CHKERRQ(ierr);
ierr = ISGetIndices(vIS, &values);CHKERRQ(ierr);
if (nV) {vS = values[0]; vE = values[0]+1;}
for (v = 1; v < nV; ++v) {
vS = PetscMin(vS, values[v]);
vE = PetscMax(vE, values[v]+1);
}
ierr = PetscSectionCreate(PETSC_COMM_SELF, section);CHKERRQ(ierr);
ierr = PetscSectionSetChart(*section, vS, vE);CHKERRQ(ierr);
for (v = 0; v < nV; ++v) {
PetscInt n;
ierr = DMLabelGetStratumSize(label, values[v], &n);CHKERRQ(ierr);
ierr = PetscSectionSetDof(*section, values[v], n);CHKERRQ(ierr);
}
ierr = PetscSectionSetUp(*section);CHKERRQ(ierr);
ierr = PetscSectionGetStorageSize(*section, &N);CHKERRQ(ierr);
ierr = PetscMalloc1(N, &points);CHKERRQ(ierr);
for (v = 0; v < nV; ++v) {
IS is;
const PetscInt *spoints;
PetscInt dof, off, p;
ierr = PetscSectionGetDof(*section, values[v], &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(*section, values[v], &off);CHKERRQ(ierr);
ierr = DMLabelGetStratumIS(label, values[v], &is);CHKERRQ(ierr);
ierr = ISGetIndices(is, &spoints);CHKERRQ(ierr);
for (p = 0; p < dof; ++p) points[off+p] = spoints[p];
ierr = ISRestoreIndices(is, &spoints);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(vIS, &values);CHKERRQ(ierr);
ierr = ISDestroy(&vIS);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF, N, points, PETSC_OWN_POINTER, is);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexGetOrdering - Calculate a reordering of the mesh
Collective on DM
Input Parameter:
+ dm - The DMPlex object
. otype - type of reordering, one of the following:
$ MATORDERINGNATURAL - Natural
$ MATORDERINGND - Nested Dissection
$ MATORDERING1WD - One-way Dissection
$ MATORDERINGRCM - Reverse Cuthill-McKee
$ MATORDERINGQMD - Quotient Minimum Degree
- label - [Optional] Label used to segregate ordering into sets, or NULL
Output Parameter:
. perm - The point permutation as an IS, perm[old point number] = new point number
Note: The label is used to group sets of points together by label value. This makes it easy to reorder a mesh which
has different types of cells, and then loop over each set of reordered cells for assembly.
Level: intermediate
.keywords: mesh
.seealso: MatGetOrdering()
@*/
PetscErrorCode DMPlexGetOrdering(DM dm, MatOrderingType otype, DMLabel label, IS *perm)
{
PetscInt numCells = 0;
PetscInt *start = NULL, *adjacency = NULL, *cperm, *clperm, *invclperm, *mask, *xls, pStart, pEnd, c, i;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
PetscValidPointer(perm, 3);
ierr = DMPlexCreateNeighborCSR(dm, 0, &numCells, &start, &adjacency);CHKERRQ(ierr);
ierr = PetscMalloc3(numCells,&cperm,numCells,&mask,numCells*2,&xls);CHKERRQ(ierr);
if (numCells) {
/* Shift for Fortran numbering */
for (i = 0; i < start[numCells]; ++i) ++adjacency[i];
for (i = 0; i <= numCells; ++i) ++start[i];
ierr = SPARSEPACKgenrcm(&numCells, start, adjacency, cperm, mask, xls);CHKERRQ(ierr);
}
ierr = PetscFree(start);CHKERRQ(ierr);
ierr = PetscFree(adjacency);CHKERRQ(ierr);
/* Shift for Fortran numbering */
for (c = 0; c < numCells; ++c) --cperm[c];
/* Segregate */
if (label) {
IS valueIS;
const PetscInt *values;
PetscInt numValues, numPoints = 0;
PetscInt *sperm, *vsize, *voff, v;
ierr = DMLabelGetValueIS(label, &valueIS);CHKERRQ(ierr);
ierr = ISSort(valueIS);CHKERRQ(ierr);
ierr = ISGetLocalSize(valueIS, &numValues);CHKERRQ(ierr);
ierr = ISGetIndices(valueIS, &values);CHKERRQ(ierr);
ierr = PetscCalloc3(numCells,&sperm,numValues,&vsize,numValues+1,&voff);CHKERRQ(ierr);
for (v = 0; v < numValues; ++v) {
ierr = DMLabelGetStratumSize(label, values[v], &vsize[v]);CHKERRQ(ierr);
if (v < numValues-1) voff[v+2] += vsize[v] + voff[v+1];
numPoints += vsize[v];
}
if (numPoints != numCells) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Label only covers %D cells < %D total", numPoints, numCells);
for (c = 0; c < numCells; ++c) {
const PetscInt oldc = cperm[c];
PetscInt val, vloc;
ierr = DMLabelGetValue(label, oldc, &val);CHKERRQ(ierr);
if (val == -1) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cell %D not present in label", oldc);
ierr = PetscFindInt(val, numValues, values, &vloc);CHKERRQ(ierr);
if (vloc < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Value %D not present label", val);
sperm[voff[vloc+1]++] = oldc;
}
for (v = 0; v < numValues; ++v) {
if (voff[v+1] - voff[v] != vsize[v]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Number of %D values found is %D != %D", values[v], voff[v+1] - voff[v], vsize[v]);
}
ierr = ISRestoreIndices(valueIS, &values);CHKERRQ(ierr);
ierr = ISDestroy(&valueIS);CHKERRQ(ierr);
ierr = PetscMemcpy(cperm, sperm, numCells * sizeof(PetscInt));CHKERRQ(ierr);
ierr = PetscFree3(sperm, vsize, voff);CHKERRQ(ierr);
}
/* Construct closure */
ierr = DMPlexCreateOrderingClosure_Static(dm, numCells, cperm, &clperm, &invclperm);CHKERRQ(ierr);
ierr = PetscFree3(cperm,mask,xls);CHKERRQ(ierr);
ierr = PetscFree(clperm);CHKERRQ(ierr);
/* Invert permutation */
ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
ierr = ISCreateGeneral(PetscObjectComm((PetscObject) dm), pEnd-pStart, invclperm, PETSC_OWN_POINTER, perm);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened)
{
DM_Plex *mesh = (DM_Plex*) dm->data;
#ifdef PETSC_HAVE_PRAGMATIC
DM udm, coordDM;
DMLabel bd;
Mat A;
Vec coordinates, mb, mx;
PetscSection coordSection;
const PetscScalar *coords;
double *coarseCoords;
IS bdIS;
PetscReal *x, *y, *z, *eqns, *metric;
PetscReal coarseRatio = PetscSqr(0.5);
const PetscInt *faces;
PetscInt *cells, *bdFaces, *bdFaceIds;
PetscInt dim, numCorners, cStart, cEnd, numCells, numCoarseCells, c, vStart, vEnd, numVertices, numCoarseVertices, v, numBdFaces, f, maxConeSize, size, bdSize, coff;
#endif
PetscErrorCode ierr;
PetscFunctionBegin;
#ifdef PETSC_HAVE_PRAGMATIC
if (!mesh->coarseMesh) {
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &coordDM);CHKERRQ(ierr);
ierr = DMGetDefaultSection(coordDM, &coordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexUninterpolate(dm, &udm);CHKERRQ(ierr);
ierr = DMPlexGetMaxSizes(udm, &maxConeSize, NULL);CHKERRQ(ierr);
numCells = cEnd - cStart;
numVertices = vEnd - vStart;
ierr = PetscCalloc5(numVertices, &x, numVertices, &y, numVertices, &z, numVertices*PetscSqr(dim), &metric, numCells*maxConeSize, &cells);CHKERRQ(ierr);
ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
x[v-vStart] = coords[off+0];
y[v-vStart] = coords[off+1];
if (dim > 2) z[v-vStart] = coords[off+2];
}
ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (c = 0, coff = 0; c < numCells; ++c) {
const PetscInt *cone;
PetscInt coneSize, cl;
ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr);
ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr);
for (cl = 0; cl < coneSize; ++cl) cells[coff++] = cone[cl] - vStart;
}
switch (dim) {
case 2:
pragmatic_2d_init(&numVertices, &numCells, cells, x, y);
break;
case 3:
pragmatic_3d_init(&numVertices, &numCells, cells, x, y, z);
break;
default:
SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim);
}
/* Create boundary mesh */
ierr = DMLabelCreate("boundary", &bd);CHKERRQ(ierr);
ierr = DMPlexMarkBoundaryFaces(dm, bd);CHKERRQ(ierr);
ierr = DMLabelGetStratumIS(bd, 1, &bdIS);CHKERRQ(ierr);
ierr = DMLabelGetStratumSize(bd, 1, &numBdFaces);CHKERRQ(ierr);
ierr = ISGetIndices(bdIS, &faces);CHKERRQ(ierr);
for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
PetscInt *closure = NULL;
PetscInt closureSize, cl;
ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) ++bdSize;
}
ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
ierr = PetscMalloc2(bdSize, &bdFaces, numBdFaces, &bdFaceIds);CHKERRQ(ierr);
for (f = 0, bdSize = 0; f < numBdFaces; ++f) {
PetscInt *closure = NULL;
PetscInt closureSize, cl;
ierr = DMPlexGetTransitiveClosure(dm, faces[f], PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (cl = 0; cl < closureSize*2; cl += 2) {
if ((closure[cl] >= vStart) && (closure[cl] < vEnd)) bdFaces[bdSize++] = closure[cl] - vStart;
}
/* TODO Fix */
bdFaceIds[f] = 1;
ierr = DMPlexRestoreTransitiveClosure(dm, f, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
ierr = ISDestroy(&bdIS);CHKERRQ(ierr);
ierr = DMLabelDestroy(&bd);CHKERRQ(ierr);
pragmatic_set_boundary(&numBdFaces, bdFaces, bdFaceIds);
/* Create metric */
size = (dim*(dim+1))/2;
ierr = PetscMalloc1(PetscSqr(size), &eqns);CHKERRQ(ierr);
ierr = MatCreateSeqDense(PETSC_COMM_SELF, size, size, eqns, &A);CHKERRQ(ierr);
ierr = MatCreateVecs(A, &mx, &mb);CHKERRQ(ierr);
ierr = VecSet(mb, 1.0);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
const PetscScalar *sol;
PetscScalar *cellCoords = NULL;
PetscReal e[3], vol;
const PetscInt *cone;
PetscInt coneSize, cl, i, j, d, r;
ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr);
/* Only works for simplices */
for (i = 0, r = 0; i < dim+1; ++i) {
for (j = 0; j < i; ++j, ++r) {
for (d = 0; d < dim; ++d) e[d] = cellCoords[i*dim+d] - cellCoords[j*dim+d];
/* FORTRAN ORDERING */
if (dim == 2) {
eqns[0*size+r] = PetscSqr(e[0]);
eqns[1*size+r] = 2.0*e[0]*e[1];
eqns[2*size+r] = PetscSqr(e[1]);
} else {
eqns[0*size+r] = PetscSqr(e[0]);
eqns[1*size+r] = 2.0*e[0]*e[1];
eqns[2*size+r] = 2.0*e[0]*e[2];
eqns[3*size+r] = PetscSqr(e[1]);
eqns[4*size+r] = 2.0*e[1]*e[2];
eqns[5*size+r] = PetscSqr(e[2]);
}
}
}
ierr = MatSetUnfactored(A);CHKERRQ(ierr);
ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, c, NULL, &cellCoords);CHKERRQ(ierr);
ierr = MatLUFactor(A, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = MatSolve(A, mb, mx);CHKERRQ(ierr);
ierr = VecGetArrayRead(mx, &sol);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, c, &vol, NULL, NULL);CHKERRQ(ierr);
ierr = DMPlexGetCone(udm, c, &cone);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(udm, c, &coneSize);CHKERRQ(ierr);
for (cl = 0; cl < coneSize; ++cl) {
const PetscInt v = cone[cl] - vStart;
if (dim == 2) {
metric[v*4+0] += vol*coarseRatio*sol[0];
metric[v*4+1] += vol*coarseRatio*sol[1];
metric[v*4+2] += vol*coarseRatio*sol[1];
metric[v*4+3] += vol*coarseRatio*sol[2];
} else {
metric[v*9+0] += vol*coarseRatio*sol[0];
metric[v*9+1] += vol*coarseRatio*sol[1];
metric[v*9+3] += vol*coarseRatio*sol[1];
metric[v*9+2] += vol*coarseRatio*sol[2];
metric[v*9+6] += vol*coarseRatio*sol[2];
metric[v*9+4] += vol*coarseRatio*sol[3];
metric[v*9+5] += vol*coarseRatio*sol[4];
metric[v*9+7] += vol*coarseRatio*sol[4];
metric[v*9+8] += vol*coarseRatio*sol[5];
}
}
ierr = VecRestoreArrayRead(mx, &sol);CHKERRQ(ierr);
}
for (v = 0; v < numVertices; ++v) {
const PetscInt *support;
PetscInt supportSize, s;
PetscReal vol, totVol = 0.0;
ierr = DMPlexGetSupport(udm, v+vStart, &support);CHKERRQ(ierr);
ierr = DMPlexGetSupportSize(udm, v+vStart, &supportSize);CHKERRQ(ierr);
for (s = 0; s < supportSize; ++s) {ierr = DMPlexComputeCellGeometryFVM(dm, support[s], &vol, NULL, NULL);CHKERRQ(ierr); totVol += vol;}
for (s = 0; s < PetscSqr(dim); ++s) metric[v*PetscSqr(dim)+s] /= totVol;
}
ierr = VecDestroy(&mx);CHKERRQ(ierr);
ierr = VecDestroy(&mb);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = DMDestroy(&udm);CHKERRQ(ierr);
ierr = PetscFree(eqns);CHKERRQ(ierr);
pragmatic_set_metric(metric);
pragmatic_adapt();
/* Read out mesh */
pragmatic_get_info(&numCoarseVertices, &numCoarseCells);
ierr = PetscMalloc1(numCoarseVertices*dim, &coarseCoords);CHKERRQ(ierr);
switch (dim) {
case 2:
pragmatic_get_coords_2d(x, y);
numCorners = 3;
for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*2+0] = x[v]; coarseCoords[v*2+1] = y[v];}
break;
case 3:
pragmatic_get_coords_3d(x, y, z);
numCorners = 4;
for (v = 0; v < numCoarseVertices; ++v) {coarseCoords[v*3+0] = x[v]; coarseCoords[v*3+1] = y[v]; coarseCoords[v*3+2] = z[v];}
break;
default:
SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "No Pragmatic coarsening defined for dimension %d", dim);
}
pragmatic_get_elements(cells);
/* TODO Read out markers for boundary */
ierr = DMPlexCreateFromCellList(PetscObjectComm((PetscObject) dm), dim, numCoarseCells, numCoarseVertices, numCorners, PETSC_TRUE, cells, dim, coarseCoords, &mesh->coarseMesh);CHKERRQ(ierr);
pragmatic_finalize();
ierr = PetscFree5(x, y, z, metric, cells);CHKERRQ(ierr);
ierr = PetscFree2(bdFaces, bdFaceIds);CHKERRQ(ierr);
ierr = PetscFree(coarseCoords);CHKERRQ(ierr);
}
#endif
ierr = PetscObjectReference((PetscObject) mesh->coarseMesh);CHKERRQ(ierr);
*dmCoarsened = mesh->coarseMesh;
PetscFunctionReturn(0);
}
