/*
There is a problem here with uninterpolated meshes. The index in numDof[] is not dimension in this case,
but sieve depth.
*/
PetscErrorCode SetupSection(DM dm, AppCtx *user)
{
PetscSection section;
const PetscInt numFields = NUM_FIELDS;
PetscInt dim = user->dim;
PetscInt numBC = 0;
PetscInt bcFields[1] = {0};
IS bcPoints[1] = {NULL};
PetscInt numComp[NUM_FIELDS];
const PetscInt *numFieldDof[NUM_FIELDS];
PetscInt *numDof;
PetscInt f, d;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscFEGetNumComponents(user->fe[0], &numComp[0]);CHKERRQ(ierr);
ierr = PetscFEGetNumComponents(user->fe[1], &numComp[1]);CHKERRQ(ierr);
ierr = PetscFEGetNumDof(user->fe[0], &numFieldDof[0]);CHKERRQ(ierr);
ierr = PetscFEGetNumDof(user->fe[1], &numFieldDof[1]);CHKERRQ(ierr);
ierr = PetscMalloc(NUM_FIELDS*(dim+1) * sizeof(PetscInt), &numDof);CHKERRQ(ierr);
for (f = 0; f < NUM_FIELDS; ++f) {
for (d = 0; d <= dim; ++d) {
numDof[f*(dim+1)+d] = numFieldDof[f][d];
}
}
for (f = 0; f < numFields; ++f) {
for (d = 1; d < dim; ++d) {
if ((numDof[f*(dim+1)+d] > 0) && !user->interpolate) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Mesh must be interpolated when unknowns are specified on edges or faces.");
}
}
if (user->bcType == DIRICHLET) {
numBC = 1;
ierr = DMPlexGetStratumIS(dm, "marker", 1, &bcPoints[0]);CHKERRQ(ierr);
}
ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcFields, bcPoints, §ion);CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 0, "velocity");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 1, "pressure");CHKERRQ(ierr);
ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr);
if (user->bcType == DIRICHLET) {
ierr = ISDestroy(&bcPoints[0]);CHKERRQ(ierr);
}
ierr = PetscFree(numDof);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
There is a problem here with uninterpolated meshes. The index in numDof[] is not dimension in this case,
but sieve depth.
*/
PetscErrorCode SetupSection(DM dm, AppCtx *user)
{
PetscSection section;
const PetscInt numFields = NUM_FIELDS;
PetscInt dim = user->dim;
PetscInt numBC = 0;
PetscInt numComp[NUM_FIELDS] = {NUM_BASIS_COMPONENTS_0, NUM_BASIS_COMPONENTS_1};
PetscInt bcFields[1] = {0};
IS bcPoints[1] = {NULL};
PetscInt numDof[NUM_FIELDS*(SPATIAL_DIM_0+1)];
PetscInt f, d;
PetscErrorCode ierr;
PetscFunctionBeginUser;
if (dim != SPATIAL_DIM_0) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_SIZ, "Spatial dimension %d should be %d", dim, SPATIAL_DIM_0);
if (dim != SPATIAL_DIM_1) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_SIZ, "Spatial dimension %d should be %d", dim, SPATIAL_DIM_1);
for (d = 0; d <= dim; ++d) {
numDof[0*(dim+1)+d] = numDof_0[d];
numDof[1*(dim+1)+d] = numDof_1[d];
}
for (f = 0; f < numFields; ++f) {
for (d = 1; d < dim; ++d) {
if ((numDof[f*(dim+1)+d] > 0) && !user->interpolate) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Mesh must be interpolated when unknowns are specified on edges or faces.");
}
}
if (user->bcType == DIRICHLET) {
numBC = 1;
ierr = DMPlexGetStratumIS(dm, "marker", 1, &bcPoints[0]);CHKERRQ(ierr);
}
ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcFields, bcPoints, §ion);CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 0, "velocity");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 1, "pressure");CHKERRQ(ierr);
ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr);
if (user->bcType == DIRICHLET) {
ierr = ISDestroy(&bcPoints[0]);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode ApplyBC(DM dm, PetscReal time, Vec locX, User user)
{
const char *name = "Face Sets"; /*Set up in the function DMPlexCreateExodus. is the side set*/
DM dmFace;
IS idIS;
const PetscInt *ids;
PetscScalar *x;
const PetscScalar *facegeom;
PetscInt numFS, fs;
PetscErrorCode ierr;
PetscMPIInt rank;
PetscFunctionBeginUser;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = VecGetDM(user->facegeom,&dmFace);CHKERRQ(ierr);
ierr = DMPlexGetLabelIdIS(dm, name, &idIS);CHKERRQ(ierr);
// ISView(idIS, PETSC_VIEWER_STDOUT_SELF);
if (!idIS) PetscFunctionReturn(0);
ierr = ISGetLocalSize(idIS, &numFS);CHKERRQ(ierr);
ierr = ISGetIndices(idIS, &ids);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->facegeom, &facegeom);CHKERRQ(ierr);
ierr = VecGetArray(locX, &x);CHKERRQ(ierr);
for (fs = 0; fs < numFS; ++fs) {
IS faceIS;
const PetscInt *faces;
PetscInt numFaces, f;
ierr = DMPlexGetStratumIS(dm, name, ids[fs], &faceIS);CHKERRQ(ierr);
ierr = ISGetLocalSize(faceIS, &numFaces);CHKERRQ(ierr);
ierr = ISGetIndices(faceIS, &faces);CHKERRQ(ierr);
for (f = 0; f < numFaces; ++f) {
// PetscPrintf(PETSC_COMM_SELF, "rank[%d]: ids[%d] = %d, faceIS[%d] = %d, numFaces = %d\n", rank, fs, ids[fs], f, faces[f], numFaces);
const PetscInt face = faces[f], *cells;
const PetscScalar *xI; /*Inner point*/
PetscScalar *xG; /*Ghost point*/
const FaceGeom *fg;
ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm, cells[0], x, &xI);CHKERRQ(ierr);
ierr = DMPlexPointLocalRef(dm, cells[1], x, &xG);CHKERRQ(ierr);
if (ids[fs]==1){
//PetscPrintf(PETSC_COMM_SELF, "Set Inlfow Boundary Condition! \n");
ierr = BoundaryInflow(time, fg->centroid, fg->normal, xI, xG, user);CHKERRQ(ierr);
// DM dmCell;
// const PetscScalar *cellgeom;
// const CellGeom *cgL, *cgR;
// ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
// ierr = VecGetArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
// ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr);
// ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr);
// ierr = PetscPrintf(PETSC_COMM_WORLD,"cells[0] = (%f, %f, %f), cells[1] = (%f, %f, %f)\n",cgL->centroid[0], cgL->centroid[1], cgL->centroid[2],cgR->centroid[0], cgR->centroid[1], cgR->centroid[2]);CHKERRQ(ierr);
}else if (ids[fs]==2){
//PetscPrintf(PETSC_COMM_SELF, "Set Outlfow Boundary Condition! \n");
ierr = BoundaryOutflow(time, fg->centroid, fg->normal, xI, xG, user);CHKERRQ(ierr);
}else if (ids[fs]==3){
//PetscPrintf(PETSC_COMM_SELF, "Set Wall Boundary Condition! \n");
ierr = BoundaryWallflow(time, fg->centroid, fg->normal, xI, xG, user);CHKERRQ(ierr);
}else {
SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Wrong type of boundary condition setup!!! \n The set up of the boundary should be: 1 for the inflow, 2 for the outflow, and 3 for the wallflow");
}
}
// PetscPrintf(PETSC_COMM_SELF, " \n");
ierr = ISRestoreIndices(faceIS, &faces);CHKERRQ(ierr);
ierr = ISDestroy(&faceIS);CHKERRQ(ierr);
}
ierr = VecRestoreArray(locX, &x);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = ISRestoreIndices(idIS, &ids);CHKERRQ(ierr);
ierr = ISDestroy(&idIS);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);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL, "-dim", &dim, NULL);CHKERRQ(ierr);
/* Create a mesh */
ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD, dim, 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 = DMPlexGetStratumIS(dm, "marker", 1, &bcPointIS[0]);CHKERRQ(ierr);
/* Create a PetscSection with this data layout */
ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcField, 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 = DMSetDefaultSection(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 = PetscViewerSetFormat(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 0;
}
