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);
}
static PetscErrorCode TestCellShape(DM dm)
{
PetscMPIInt rank;
PetscInt dim, c, cStart, cEnd, count = 0;
ex1_stats_t stats, globalStats;
PetscReal *J, *invJ, min = 0, max = 0, mean = 0, stdev = 0;
MPI_Comm comm = PetscObjectComm((PetscObject)dm);
DM dmCoarse;
PetscErrorCode ierr;
PetscFunctionBegin;
stats.min = PETSC_MAX_REAL;
stats.max = PETSC_MIN_REAL;
stats.sum = stats.squaresum = 0.;
stats.count = 0;
ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr);
ierr = PetscMalloc2(dim * dim, &J, dim * dim, &invJ);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; c++) {
PetscInt i;
PetscReal frobJ = 0., frobInvJ = 0., cond2, cond, detJ;
ierr = DMPlexComputeCellGeometryAffineFEM(dm,c,NULL,J,invJ,&detJ);CHKERRQ(ierr);
for (i = 0; i < dim * dim; i++) {
frobJ += J[i] * J[i];
frobInvJ += invJ[i] * invJ[i];
}
cond2 = frobJ * frobInvJ;
cond = PetscSqrtReal(cond2);
stats.min = PetscMin(stats.min,cond);
stats.max = PetscMax(stats.max,cond);
stats.sum += cond;
stats.squaresum += cond2;
stats.count++;
}
{
PetscMPIInt blockLengths[2] = {4,1};
MPI_Aint blockOffsets[2] = {offsetof(ex1_stats_t,min),offsetof(ex1_stats_t,count)};
MPI_Datatype blockTypes[2] = {MPIU_REAL,MPIU_INT}, statType;
MPI_Op statReduce;
ierr = MPI_Type_create_struct(2,blockLengths,blockOffsets,blockTypes,&statType);CHKERRQ(ierr);
ierr = MPI_Type_commit(&statType);CHKERRQ(ierr);
ierr = MPI_Op_create(ex1_stats_reduce, PETSC_TRUE, &statReduce);CHKERRQ(ierr);
ierr = MPI_Reduce(&stats,&globalStats,1,statType,statReduce,0,comm);CHKERRQ(ierr);
ierr = MPI_Op_free(&statReduce);CHKERRQ(ierr);
ierr = MPI_Type_free(&statType);CHKERRQ(ierr);
}
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
if (!rank) {
count = globalStats.count;
min = globalStats.min;
max = globalStats.max;
mean = globalStats.sum / globalStats.count;
stdev = PetscSqrtReal(globalStats.squaresum / globalStats.count - mean * mean);
}
ierr = PetscPrintf(comm,"Mesh with %d cells, shape condition numbers: min = %g, max = %g, mean = %g, stddev = %g\n", count, (double) min, (double) max, (double) mean, (double) stdev);
ierr = PetscFree2(J,invJ);CHKERRQ(ierr);
ierr = DMPlexGetCoarseDM(dm,&dmCoarse);CHKERRQ(ierr);
if (dmCoarse) {
ierr = TestCellShape(dmCoarse);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode SetupDiscretization(DM dm, AppCtx *user)
{
DM cdm = dm;
const PetscInt dim = user->dim;
const PetscInt id = 1;
PetscFE feAux = NULL;
PetscFE feBd = NULL;
PetscFE feCh = NULL;
PetscFE fe;
PetscDS prob;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* Create finite element */
ierr = PetscFECreateDefault(dm, dim, 1, PETSC_TRUE, NULL, -1, &fe);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe, "potential");CHKERRQ(ierr);
if (user->bcType == NEUMANN) {
ierr = PetscFECreateDefault(dm, dim-1, 1, PETSC_TRUE, "bd_", -1, &feBd);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) feBd, "potential");CHKERRQ(ierr);
}
if (user->variableCoefficient == COEFF_FIELD) {
PetscQuadrature q;
ierr = PetscFECreateDefault(dm, dim, 1, PETSC_TRUE, "mat_", -1, &feAux);CHKERRQ(ierr);
ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr);
ierr = PetscFESetQuadrature(feAux, q);CHKERRQ(ierr);
}
if (user->check) {ierr = PetscFECreateDefault(dm, dim, 1, PETSC_TRUE, "ch_", -1, &feCh);CHKERRQ(ierr);}
/* Set discretization and boundary conditions for each mesh */
while (cdm) {
ierr = DMGetDS(cdm, &prob);CHKERRQ(ierr);
ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr);
ierr = PetscDSSetBdDiscretization(prob, 0, (PetscObject) feBd);CHKERRQ(ierr);
if (feAux) {
DM dmAux;
PetscDS probAux;
ierr = DMClone(cdm, &dmAux);CHKERRQ(ierr);
ierr = DMPlexCopyCoordinates(cdm, dmAux);CHKERRQ(ierr);
ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr);
ierr = PetscDSSetDiscretization(probAux, 0, (PetscObject) feAux);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) dmAux);CHKERRQ(ierr);
ierr = SetupMaterial(cdm, dmAux, user);CHKERRQ(ierr);
ierr = DMDestroy(&dmAux);CHKERRQ(ierr);
}
if (feCh) {
DM dmCh;
PetscDS probCh;
ierr = DMClone(cdm, &dmCh);CHKERRQ(ierr);
ierr = DMPlexCopyCoordinates(cdm, dmCh);CHKERRQ(ierr);
ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr);
ierr = PetscDSSetDiscretization(probCh, 0, (PetscObject) feCh);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject) dm, "dmCh", (PetscObject) dmCh);CHKERRQ(ierr);
ierr = DMDestroy(&dmCh);CHKERRQ(ierr);
}
ierr = SetupProblem(cdm, user);CHKERRQ(ierr);
ierr = DMPlexAddBoundary(cdm, user->bcType == DIRICHLET, "wall", user->bcType == NEUMANN ? "boundary" : "marker", 0, user->exactFuncs[0], 1, &id, user);CHKERRQ(ierr);
ierr = DMPlexGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
ierr = PetscFEDestroy(&feBd);CHKERRQ(ierr);
ierr = PetscFEDestroy(&feAux);CHKERRQ(ierr);
ierr = PetscFEDestroy(&feCh);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
