PetscErrorCode SetupSection(DM dm, AppCtx *user)
{
DM cdm = dm;
const PetscInt id = 1;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscObjectSetName((PetscObject) user->fe[0], "potential");CHKERRQ(ierr);
while (cdm) {
ierr = DMSetNumFields(cdm, 1);CHKERRQ(ierr);
ierr = DMSetField(cdm, 0, (PetscObject) user->fe[0]);CHKERRQ(ierr);
ierr = DMPlexAddBoundary(cdm, user->bcType == DIRICHLET, user->bcType == NEUMANN ? "boundary" : "marker", 0, user->exactFuncs[0], 1, &id, user);CHKERRQ(ierr);
ierr = DMPlexGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm, dmDist = NULL;
Vec u;
PetscSection section;
PetscViewer viewer;
PetscInt dim = 2, numFields, numBC, i;
PetscInt numComp[3];
PetscInt numDof[12];
PetscInt bcField[1];
IS bcPointIS[1];
PetscBool interpolate = PETSC_TRUE;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL, "-dim", &dim, NULL);CHKERRQ(ierr);
/* Create a mesh */
ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD, dim, PETSC_TRUE, NULL, NULL, NULL, NULL, interpolate, &dm);CHKERRQ(ierr);
/* Distribute mesh over processes */
ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = dmDist;}
/* Create a scalar field u, a vector field v, and a surface vector field w */
numFields = 3;
numComp[0] = 1;
numComp[1] = dim;
numComp[2] = dim-1;
for (i = 0; i < numFields*(dim+1); ++i) numDof[i] = 0;
/* Let u be defined on vertices */
numDof[0*(dim+1)+0] = 1;
/* Let v be defined on cells */
numDof[1*(dim+1)+dim] = dim;
/* Let v be defined on faces */
numDof[2*(dim+1)+dim-1] = dim-1;
/* Setup boundary conditions */
numBC = 1;
/* Prescribe a Dirichlet condition on u on the boundary
Label "marker" is made by the mesh creation routine */
bcField[0] = 0;
ierr = DMGetStratumIS(dm, "marker", 1, &bcPointIS[0]);CHKERRQ(ierr);
/* Create a PetscSection with this data layout */
ierr = DMSetNumFields(dm, numFields);CHKERRQ(ierr);
ierr = DMPlexCreateSection(dm, NULL, numComp, numDof, numBC, bcField, NULL, bcPointIS, NULL, §ion);CHKERRQ(ierr);
ierr = ISDestroy(&bcPointIS[0]);CHKERRQ(ierr);
/* Name the Field variables */
ierr = PetscSectionSetFieldName(section, 0, "u");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 1, "v");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 2, "w");CHKERRQ(ierr);
ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Tell the DM to use this data layout */
ierr = DMSetSection(dm, section);CHKERRQ(ierr);
/* Create a Vec with this layout and view it */
ierr = DMGetGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "sol.vtk");CHKERRQ(ierr);
ierr = VecView(u, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm, &u);CHKERRQ(ierr);
/* Cleanup */
ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/* This assumes that the DM has been cloned prior to the call */
PetscErrorCode DMCreateSubDM_Section_Private(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm)
{
PetscSection section, sectionGlobal;
PetscInt *subIndices;
PetscInt subSize = 0, subOff = 0, nF, f, pStart, pEnd, p;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!numFields) PetscFunctionReturn(0);
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = DMGetDefaultGlobalSection(dm, §ionGlobal);CHKERRQ(ierr);
if (!section) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting fields");
if (!sectionGlobal) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default global section for DM before splitting fields");
ierr = PetscSectionGetNumFields(section, &nF);CHKERRQ(ierr);
if (numFields > nF) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Number of requested fields %d greater than number of DM fields %d", numFields, nF);
if (is) {
ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt gdof;
ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
if (gdof > 0) {
for (f = 0; f < numFields; ++f) {
PetscInt fdof, fcdof;
ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
subSize += fdof-fcdof;
}
}
}
ierr = PetscMalloc1(subSize, &subIndices);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt gdof, goff;
ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
if (gdof > 0) {
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
PetscInt fdof, fcdof, fc, f2, poff = 0;
/* Can get rid of this loop by storing field information in the global section */
for (f2 = 0; f2 < fields[f]; ++f2) {
ierr = PetscSectionGetFieldDof(section, p, f2, &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);CHKERRQ(ierr);
poff += fdof-fcdof;
}
ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) {
subIndices[subOff] = goff+poff+fc;
}
}
}
}
ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is);CHKERRQ(ierr);
}
if (subdm) {
PetscSection subsection;
PetscBool haveNull = PETSC_FALSE;
PetscInt f, nf = 0;
ierr = PetscSectionCreateSubsection(section, numFields, fields, &subsection);CHKERRQ(ierr);
ierr = DMSetDefaultSection(*subdm, subsection);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&subsection);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
(*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[fields[f]];
if ((*subdm)->nullspaceConstructors[f]) {
haveNull = PETSC_TRUE;
nf = f;
}
}
if (haveNull && is) {
MatNullSpace nullSpace;
ierr = (*(*subdm)->nullspaceConstructors[nf])(*subdm, nf, &nullSpace);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
}
if (dm->prob) {
PetscInt Nf;
ierr = PetscDSGetNumFields(dm->prob, &Nf);CHKERRQ(ierr);
if (nF != Nf) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "The number of DM fields %d does not match the number of Section fields %d", Nf, nF);
ierr = DMSetNumFields(*subdm, numFields);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
PetscObject disc;
ierr = DMGetField(dm, fields[f], &disc);CHKERRQ(ierr);
ierr = DMSetField(*subdm, f, disc);CHKERRQ(ierr);
}
if (numFields == 1 && is) {
PetscObject disc, space, pmat;
ierr = DMGetField(*subdm, 0, &disc);CHKERRQ(ierr);
ierr = PetscObjectQuery(disc, "nullspace", &space);CHKERRQ(ierr);
if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nullspace", space);CHKERRQ(ierr);}
ierr = PetscObjectQuery(disc, "nearnullspace", &space);CHKERRQ(ierr);
if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nearnullspace", space);CHKERRQ(ierr);}
ierr = PetscObjectQuery(disc, "pmat", &pmat);CHKERRQ(ierr);
if (pmat) {ierr = PetscObjectCompose((PetscObject) *is, "pmat", pmat);CHKERRQ(ierr);}
}
}
}
#if 0
/* We need a way to filter the original SF for given fields:
- Keeping the original section around it too much I think
- We could keep the distributed section, and subset it
*/
if (dm->sfNatural) {
PetscSF sfNatural;
ierr = PetscSectionCreateSubsection(dm->originalSection, numFields, fields, &(*subdm)->originalSection);CHKERRQ(ierr);
ierr = DMPlexCreateGlobalToNaturalPetscSF(*subdm, &sfNatural);CHKERRQ(ierr);
ierr = DMPlexSetGlobalToNaturalPetscSF(*subdm, sfNatural);CHKERRQ(ierr);
}
#endif
PetscFunctionReturn(0);
}
/* This assumes that the DM has been cloned prior to the call */
PetscErrorCode DMCreateSubDM_Section_Private(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm)
{
PetscSection section, sectionGlobal;
PetscInt *subIndices;
PetscInt subSize = 0, subOff = 0, nF, f, pStart, pEnd, p;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!numFields) PetscFunctionReturn(0);
ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr);
ierr = DMGetDefaultGlobalSection(dm, §ionGlobal);CHKERRQ(ierr);
if (!section) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default section for DM before splitting fields");
if (!sectionGlobal) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Must set default global section for DM before splitting fields");
ierr = PetscSectionGetNumFields(section, &nF);CHKERRQ(ierr);
if (numFields > nF) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Number of requested fields %d greater than number of DM fields %d", numFields, nF);
if (is) {
ierr = PetscSectionGetChart(sectionGlobal, &pStart, &pEnd);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt gdof;
ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
if (gdof > 0) {
for (f = 0; f < numFields; ++f) {
PetscInt fdof, fcdof;
ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
subSize += fdof-fcdof;
}
}
}
ierr = PetscMalloc1(subSize, &subIndices);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt gdof, goff;
ierr = PetscSectionGetDof(sectionGlobal, p, &gdof);CHKERRQ(ierr);
if (gdof > 0) {
ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
PetscInt fdof, fcdof, fc, f2, poff = 0;
/* Can get rid of this loop by storing field information in the global section */
for (f2 = 0; f2 < fields[f]; ++f2) {
ierr = PetscSectionGetFieldDof(section, p, f2, &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, f2, &fcdof);CHKERRQ(ierr);
poff += fdof-fcdof;
}
ierr = PetscSectionGetFieldDof(section, p, fields[f], &fdof);CHKERRQ(ierr);
ierr = PetscSectionGetFieldConstraintDof(section, p, fields[f], &fcdof);CHKERRQ(ierr);
for (fc = 0; fc < fdof-fcdof; ++fc, ++subOff) {
subIndices[subOff] = goff+poff+fc;
}
}
}
}
ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), subSize, subIndices, PETSC_OWN_POINTER, is);CHKERRQ(ierr);
}
if (subdm) {
PetscSection subsection;
PetscBool haveNull = PETSC_FALSE;
PetscInt f, nf = 0;
ierr = PetscSectionCreateSubsection(section, numFields, fields, &subsection);CHKERRQ(ierr);
ierr = DMSetDefaultSection(*subdm, subsection);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&subsection);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
(*subdm)->nullspaceConstructors[f] = dm->nullspaceConstructors[fields[f]];
if ((*subdm)->nullspaceConstructors[f]) {
haveNull = PETSC_TRUE;
nf = f;
}
}
if (haveNull) {
MatNullSpace nullSpace;
ierr = (*(*subdm)->nullspaceConstructors[nf])(*subdm, nf, &nullSpace);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) nullSpace);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
}
if (dm->fields) {
if (nF != dm->numFields) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "The number of DM fields %d does not match the number of Section fields %d", dm->numFields, nF);
ierr = DMSetNumFields(*subdm, numFields);CHKERRQ(ierr);
for (f = 0; f < numFields; ++f) {
ierr = PetscObjectListDuplicate(dm->fields[fields[f]]->olist, &(*subdm)->fields[f]->olist);CHKERRQ(ierr);
}
if (numFields == 1) {
MatNullSpace space;
Mat pmat;
ierr = PetscObjectQuery((*subdm)->fields[0], "nullspace", (PetscObject*) &space);CHKERRQ(ierr);
if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nullspace", (PetscObject) space);CHKERRQ(ierr);}
ierr = PetscObjectQuery((*subdm)->fields[0], "nearnullspace", (PetscObject*) &space);CHKERRQ(ierr);
if (space) {ierr = PetscObjectCompose((PetscObject) *is, "nearnullspace", (PetscObject) space);CHKERRQ(ierr);}
ierr = PetscObjectQuery((*subdm)->fields[0], "pmat", (PetscObject*) &pmat);CHKERRQ(ierr);
if (pmat) {ierr = PetscObjectCompose((PetscObject) *is, "pmat", (PetscObject) pmat);CHKERRQ(ierr);}
}
}
}
PetscFunctionReturn(0);
}
