/*@C
DMPlexGetLabelIdIS - Get the integer ids in a label
Not Collective
Input Parameters:
+ mesh - The DMPlex object
- name - The label name
Output Parameter:
. ids - The integer ids, or NULL if the label does not exist
Level: beginner
.keywords: mesh
.seealso: DMLabelGetValueIS(), DMPlexGetLabelSize()
@*/
PetscErrorCode DMPlexGetLabelIdIS(DM dm, const char name[], IS *ids)
{
DMLabel label;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
PetscValidCharPointer(name, 2);
PetscValidPointer(ids, 3);
ierr = DMPlexGetLabel(dm, name, &label);CHKERRQ(ierr);
*ids = NULL;
if (!label) PetscFunctionReturn(0);
ierr = DMLabelGetValueIS(label, ids);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);
}
