static PetscErrorCode DMPlexTSSetupGradient(DM dm, PetscFV fvm, DMTS_Plex *dmplexts)
{
DM dmFace, dmCell;
PetscScalar *fgeom, *cgeom;
PetscSection sectionGrad;
PetscInt dim, pdim, cStart, cEnd, cEndInterior, c;
PetscErrorCode ierr;
PetscFunctionBegin;
if (dmplexts->setupGrad) PetscFunctionReturn(0);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
/* Construct the interpolant corresponding to each face from the leat-square solution over the cell neighborhood */
ierr = VecGetDM(dmplexts->facegeom, &dmFace);CHKERRQ(ierr);
ierr = VecGetDM(dmplexts->cellgeom, &dmCell);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
ierr = BuildGradientReconstruction(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
/* Create storage for gradients */
ierr = DMClone(dm, &dmplexts->dmGrad);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionGrad);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionGrad, cStart, cEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionGrad, c, pdim*dim);CHKERRQ(ierr);}
ierr = PetscSectionSetUp(sectionGrad);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dmplexts->dmGrad, sectionGrad);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionGrad);CHKERRQ(ierr);
dmplexts->setupGrad = PETSC_TRUE;
PetscFunctionReturn(0);
}
static PetscErrorCode DMPlexGetVTKConnectivity(DM dm,PieceInfo *piece,PetscVTKInt **oconn,PetscVTKInt **ooffsets,PetscVTKType **otypes)
{
PetscErrorCode ierr;
PetscVTKInt *conn,*offsets;
PetscVTKType *types;
PetscInt dim,vStart,vEnd,cStart,cEnd,pStart,pEnd,cellHeight,cMax,numLabelCells,hasLabel,c,v,countcell,countconn;
PetscFunctionBegin;
ierr = PetscMalloc3(piece->nconn,PetscVTKInt,&conn,piece->ncells,PetscVTKInt,&offsets,piece->ncells,PetscVTKType,&types);CHKERRQ(ierr);
ierr = DMPlexGetDimension(dm,&dim);CHKERRQ(ierr);
ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr);
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
hasLabel = numLabelCells > 0 ? PETSC_TRUE : PETSC_FALSE;
countcell = 0;
countconn = 0;
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize,nverts,celltype,startoffset,nC=0;
if (hasLabel) {
PetscInt value;
ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
startoffset = countconn;
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
conn[countconn++] = closure[v] - vStart;
++nC;
}
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
ierr = DMPlexInvertCell(dim, nC, &conn[countconn-nC]);CHKERRQ(ierr);
offsets[countcell] = countconn;
nverts = countconn - startoffset;
ierr = DMPlexVTKGetCellType(dm,dim,nverts,&celltype);CHKERRQ(ierr);
types[countcell] = celltype;
countcell++;
}
if (countcell != piece->ncells) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Inconsistent cell count");
if (countconn != piece->nconn) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Inconsistent connectivity count");
*oconn = conn;
*ooffsets = offsets;
*otypes = types;
PetscFunctionReturn(0);
}
static PetscErrorCode BuildGradientReconstruction(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom)
{
DMLabel ghostLabel;
PetscScalar *dx, *grad, **gref;
PetscInt dim, cStart, cEnd, c, cEndInterior, maxNumFaces;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = DMPlexGetMaxSizes(dm, &maxNumFaces, NULL);CHKERRQ(ierr);
ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr);
ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr);
for (c = cStart; c < cEndInterior; c++) {
const PetscInt *faces;
PetscInt numFaces, usedFaces, f, d;
const CellGeom *cg;
PetscBool boundary;
PetscInt ghost;
ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(dm, c, &numFaces);CHKERRQ(ierr);
ierr = DMPlexGetCone(dm, c, &faces);CHKERRQ(ierr);
if (numFaces < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cell %D has only %D faces, not enough for gradient reconstruction", c, numFaces);
for (f = 0, usedFaces = 0; f < numFaces; ++f) {
const CellGeom *cg1;
FaceGeom *fg;
const PetscInt *fcells;
PetscInt ncell, side;
ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr);
ierr = DMPlexIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr);
if ((ghost >= 0) || boundary) continue;
ierr = DMPlexGetSupport(dm, faces[f], &fcells);CHKERRQ(ierr);
side = (c != fcells[0]); /* c is on left=0 or right=1 of face */
ncell = fcells[!side]; /* the neighbor */
ierr = DMPlexPointLocalRef(dmFace, faces[f], fgeom, &fg);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) dx[usedFaces*dim+d] = cg1->centroid[d] - cg->centroid[d];
gref[usedFaces++] = fg->grad[side]; /* Gradient reconstruction term will go here */
}
if (!usedFaces) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_USER, "Mesh contains isolated cell (no neighbors). Is it intentional?");
ierr = PetscFVComputeGradient(fvm, usedFaces, dx, grad);CHKERRQ(ierr);
for (f = 0, usedFaces = 0; f < numFaces; ++f) {
ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr);
ierr = DMPlexIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr);
if ((ghost >= 0) || boundary) continue;
for (d = 0; d < dim; ++d) gref[usedFaces][d] = grad[usedFaces*dim+d];
++usedFaces;
}
}
ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeIFunctionFEM - Form the local residual F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
. locX_t - Local solution time derivative, or NULL
- user - The user context
Output Parameter:
. locF - Local output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeIFunctionFEM(DM dm, PetscReal time, Vec locX, Vec locX_t, Vec locF, void *user)
{
PetscInt cStart, cEnd, cEndInterior;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMPlexComputeResidual_Internal(dm, cStart, cEnd, time, locX, locX_t, locF, user);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeIJacobianFEM - Form the local Jacobian J from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
. locX_t - Local solution time derivative, or NULL
. X_tshift - The multiplicative parameter for dF/du_t
- user - The user context
Output Parameter:
. locF - Local output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeIJacobianFEM(DM dm, PetscReal time, Vec locX, Vec locX_t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user)
{
PetscInt cStart, cEnd, cEndInterior;
DM plex;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMTSConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMPlexComputeJacobian_Internal(plex, cStart, cEnd, time, X_tShift, locX, locX_t, Jac, JacP, user);CHKERRQ(ierr);
ierr = DMDestroy(&plex);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeRHSFunctionFVM - Form the local forcing F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
- user - The user context
Output Parameter:
. F - Global output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM dm, PetscReal time, Vec locX, Vec F, void *user)
{
Vec locF;
PetscInt cStart, cEnd, cEndInterior;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMGetLocalVector(dm, &locF);CHKERRQ(ierr);
ierr = VecZeroEntries(locF);CHKERRQ(ierr);
ierr = DMPlexComputeResidual_Internal(dm, cStart, cEnd, time, locX, NULL, locF, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(dm, locF, INSERT_VALUES, F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm, locF, INSERT_VALUES, F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locF);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMPlexVTKWritePartition_ASCII(DM dm, FILE *fp)
{
MPI_Comm comm;
PetscInt numCells = 0, cellHeight;
PetscInt numLabelCells, cMax, cStart, cEnd, c;
PetscMPIInt numProcs, rank, proc, tag;
PetscBool hasLabel;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscCommGetNewTag(comm, &tag);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
hasLabel = numLabelCells > 0 ? PETSC_TRUE : PETSC_FALSE;
for (c = cStart; c < cEnd; ++c) {
if (hasLabel) {
PetscInt value;
ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
++numCells;
}
if (!rank) {
for (c = 0; c < numCells; ++c) {ierr = PetscFPrintf(comm, fp, "%d\n", rank);CHKERRQ(ierr);}
for (proc = 1; proc < numProcs; ++proc) {
MPI_Status status;
ierr = MPI_Recv(&numCells, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {ierr = PetscFPrintf(comm, fp, "%d\n", proc);CHKERRQ(ierr);}
}
} else {
ierr = MPI_Send(&numCells, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
/*@
DMPlexTSComputeRHSFunctionFVM - Form the local forcing F from the local input X using pointwise functions specified by the user
Input Parameters:
+ dm - The mesh
. t - The time
. locX - Local solution
- user - The user context
Output Parameter:
. F - Global output vector
Level: developer
.seealso: DMPlexComputeJacobianActionFEM()
@*/
PetscErrorCode DMPlexTSComputeRHSFunctionFVM(DM dm, PetscReal time, Vec locX, Vec F, void *user)
{
Vec locF;
PetscInt cStart, cEnd, cEndInterior;
DM plex;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = DMTSConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
ierr = DMGetLocalVector(plex, &locF);CHKERRQ(ierr);
ierr = VecZeroEntries(locF);CHKERRQ(ierr);
ierr = DMPlexComputeResidual_Internal(plex, cStart, cEnd, time, locX, NULL, time, locF, user);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(plex, locF, ADD_VALUES, F);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(plex, locF, ADD_VALUES, F);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(plex, &locF);CHKERRQ(ierr);
ierr = DMDestroy(&plex);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMPlexVTKWriteCells_ASCII(DM dm, FILE *fp, PetscInt *totalCells)
{
MPI_Comm comm;
DMLabel label;
IS globalVertexNumbers = NULL;
const PetscInt *gvertex;
PetscInt dim;
PetscInt numCorners = 0, totCorners = 0, maxCorners, *corners;
PetscInt numCells = 0, totCells = 0, maxCells, cellHeight;
PetscInt numLabelCells, maxLabelCells, cMax, cStart, cEnd, c, vStart, vEnd, v;
PetscMPIInt numProcs, rank, proc, tag;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscCommGetNewTag(comm, &tag);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
ierr = DMPlexGetLabel(dm, "vtk", &label);CHKERRQ(ierr);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
ierr = MPI_Allreduce(&numLabelCells, &maxLabelCells, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
if (!maxLabelCells) label = NULL;
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize, value;
if (label) {
ierr = DMLabelGetValue(label, c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) ++numCorners;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
++numCells;
}
maxCells = numCells;
ierr = MPI_Reduce(&numCells, &totCells, 1, MPIU_INT, MPI_SUM, 0, comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&numCells, &maxCells, 1, MPIU_INT, MPI_MAX, 0, comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&numCorners, &totCorners, 1, MPIU_INT, MPI_SUM, 0, comm);CHKERRQ(ierr);
ierr = MPI_Reduce(&numCorners, &maxCorners, 1, MPIU_INT, MPI_MAX, 0, comm);CHKERRQ(ierr);
ierr = DMPlexGetVertexNumbering(dm, &globalVertexNumbers);CHKERRQ(ierr);
ierr = ISGetIndices(globalVertexNumbers, &gvertex);CHKERRQ(ierr);
ierr = PetscMalloc1(maxCells, &corners);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "CELLS %d %d\n", totCells, totCorners+totCells);CHKERRQ(ierr);
if (!rank) {
PetscInt *remoteVertices;
int *vertices;
ierr = PetscMalloc1(maxCorners, &vertices);CHKERRQ(ierr);
for (c = cStart, numCells = 0; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize, value, nC = 0;
if (label) {
ierr = DMLabelGetValue(label, c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
const PetscInt gv = gvertex[closure[v] - vStart];
vertices[nC++] = gv < 0 ? -(gv+1) : gv;
}
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
corners[numCells++] = nC;
ierr = PetscFPrintf(comm, fp, "%d ", nC);CHKERRQ(ierr);
ierr = DMPlexInvertCell(dim, nC, vertices);CHKERRQ(ierr);
for (v = 0; v < nC; ++v) {
ierr = PetscFPrintf(comm, fp, " %d", vertices[v]);CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr);
}
if (numProcs > 1) {ierr = PetscMalloc1(maxCorners+maxCells, &remoteVertices);CHKERRQ(ierr);}
for (proc = 1; proc < numProcs; ++proc) {
MPI_Status status;
ierr = MPI_Recv(&numCorners, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
ierr = MPI_Recv(remoteVertices, numCorners, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
for (c = 0; c < numCorners;) {
PetscInt nC = remoteVertices[c++];
for (v = 0; v < nC; ++v, ++c) {
vertices[v] = remoteVertices[c];
}
ierr = DMPlexInvertCell(dim, nC, vertices);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "%d ", nC);CHKERRQ(ierr);
for (v = 0; v < nC; ++v) {
ierr = PetscFPrintf(comm, fp, " %d", vertices[v]);CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr);
}
}
if (numProcs > 1) {ierr = PetscFree(remoteVertices);CHKERRQ(ierr);}
ierr = PetscFree(vertices);CHKERRQ(ierr);
} else {
PetscInt *localVertices, numSend = numCells+numCorners, k = 0;
ierr = PetscMalloc1(numSend, &localVertices);CHKERRQ(ierr);
for (c = cStart, numCells = 0; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize, value, nC = 0;
if (label) {
ierr = DMLabelGetValue(label, c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) {
const PetscInt gv = gvertex[closure[v] - vStart];
closure[nC++] = gv < 0 ? -(gv+1) : gv;
}
}
corners[numCells++] = nC;
localVertices[k++] = nC;
for (v = 0; v < nC; ++v, ++k) {
localVertices[k] = closure[v];
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
}
if (k != numSend) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid number of vertices to send %d should be %d", k, numSend);
ierr = MPI_Send(&numSend, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
ierr = MPI_Send(localVertices, numSend, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
ierr = PetscFree(localVertices);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(globalVertexNumbers, &gvertex);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "CELL_TYPES %d\n", totCells);CHKERRQ(ierr);
if (!rank) {
PetscInt cellType;
for (c = 0; c < numCells; ++c) {
ierr = DMPlexVTKGetCellType(dm, dim, corners[c], &cellType);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "%d\n", cellType);CHKERRQ(ierr);
}
for (proc = 1; proc < numProcs; ++proc) {
MPI_Status status;
ierr = MPI_Recv(&numCells, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
ierr = MPI_Recv(corners, numCells, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
for (c = 0; c < numCells; ++c) {
ierr = DMPlexVTKGetCellType(dm, dim, corners[c], &cellType);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "%d\n", cellType);CHKERRQ(ierr);
}
}
} else {
ierr = MPI_Send(&numCells, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
ierr = MPI_Send(corners, numCells, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
}
ierr = PetscFree(corners);CHKERRQ(ierr);
*totalCells = totCells;
PetscFunctionReturn(0);
}
static PetscErrorCode DMPlexVTKWriteAll_ASCII(DM dm, PetscViewer viewer)
{
MPI_Comm comm;
PetscViewer_VTK *vtk = (PetscViewer_VTK*) viewer->data;
FILE *fp;
PetscViewerVTKObjectLink link;
PetscSection coordSection, globalCoordSection;
PetscLayout vLayout;
Vec coordinates;
PetscReal lengthScale;
PetscInt vMax, totVertices, totCells;
PetscBool hasPoint = PETSC_FALSE, hasCell = PETSC_FALSE, writePartition = PETSC_FALSE;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
ierr = PetscFOpen(comm, vtk->filename, "wb", &fp);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "# vtk DataFile Version 2.0\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "Simplicial Mesh Example\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "ASCII\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "DATASET UNSTRUCTURED_GRID\n");CHKERRQ(ierr);
/* Vertices */
ierr = DMPlexGetScale(dm, PETSC_UNIT_LENGTH, &lengthScale);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = PetscSectionCreateGlobalSection(coordSection, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalCoordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, NULL, NULL, NULL, &vMax);CHKERRQ(ierr);
if (vMax >= 0) {
PetscInt pStart, pEnd, p, localSize = 0;
ierr = PetscSectionGetChart(globalCoordSection, &pStart, &pEnd);CHKERRQ(ierr);
pEnd = PetscMin(pEnd, vMax);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof;
ierr = PetscSectionGetDof(globalCoordSection, p, &dof);CHKERRQ(ierr);
if (dof > 0) ++localSize;
}
ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)dm), &vLayout);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(vLayout, localSize);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr);
} else {
ierr = PetscSectionGetPointLayout(PetscObjectComm((PetscObject)dm), globalCoordSection, &vLayout);CHKERRQ(ierr);
}
ierr = PetscLayoutGetSize(vLayout, &totVertices);CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "POINTS %d double\n", totVertices);CHKERRQ(ierr);
ierr = DMPlexVTKWriteSection_ASCII(dm, coordSection, globalCoordSection, coordinates, fp, 3, PETSC_DETERMINE, lengthScale);CHKERRQ(ierr);
/* Cells */
ierr = DMPlexVTKWriteCells_ASCII(dm, fp, &totCells);CHKERRQ(ierr);
/* Vertex fields */
for (link = vtk->link; link; link = link->next) {
if ((link->ft == PETSC_VTK_POINT_FIELD) || (link->ft == PETSC_VTK_POINT_VECTOR_FIELD)) hasPoint = PETSC_TRUE;
if ((link->ft == PETSC_VTK_CELL_FIELD) || (link->ft == PETSC_VTK_CELL_VECTOR_FIELD)) hasCell = PETSC_TRUE;
}
if (hasPoint) {
ierr = PetscFPrintf(comm, fp, "POINT_DATA %d\n", totVertices);CHKERRQ(ierr);
for (link = vtk->link; link; link = link->next) {
Vec X = (Vec) link->vec;
DM dmX;
PetscSection section, globalSection, newSection = NULL;
const char *name;
PetscInt enforceDof = PETSC_DETERMINE;
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
if (link->ft == PETSC_VTK_POINT_VECTOR_FIELD) enforceDof = 3;
ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
if (dmX) {
DMLabel subpointMap, subpointMapX;
PetscInt dim, dimX, pStart, pEnd, qStart, qEnd;
ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr);
/* Here is where we check whether dmX is a submesh of dm */
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetDimension(dmX, &dimX);CHKERRQ(ierr);
ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
ierr = DMPlexGetChart(dmX, &qStart, &qEnd);CHKERRQ(ierr);
ierr = DMPlexGetSubpointMap(dm, &subpointMap);CHKERRQ(ierr);
ierr = DMPlexGetSubpointMap(dmX, &subpointMapX);CHKERRQ(ierr);
if (((dim != dimX) || ((pEnd-pStart) < (qEnd-qStart))) && subpointMap && !subpointMapX) {
const PetscInt *ind = NULL;
IS subpointIS;
PetscInt n = 0, q;
ierr = PetscSectionGetChart(section, &qStart, &qEnd);CHKERRQ(ierr);
ierr = DMPlexCreateSubpointIS(dm, &subpointIS);CHKERRQ(ierr);
if (subpointIS) {
ierr = ISGetLocalSize(subpointIS, &n);CHKERRQ(ierr);
ierr = ISGetIndices(subpointIS, &ind);CHKERRQ(ierr);
}
ierr = PetscSectionCreate(comm, &newSection);CHKERRQ(ierr);
ierr = PetscSectionSetChart(newSection, pStart, pEnd);CHKERRQ(ierr);
for (q = qStart; q < qEnd; ++q) {
PetscInt dof, off, p;
ierr = PetscSectionGetDof(section, q, &dof);CHKERRQ(ierr);
if (dof) {
ierr = PetscFindInt(q, n, ind, &p);CHKERRQ(ierr);
if (p >= pStart) {
ierr = PetscSectionSetDof(newSection, p, dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, q, &off);CHKERRQ(ierr);
ierr = PetscSectionSetOffset(newSection, p, off);CHKERRQ(ierr);
}
}
}
if (subpointIS) {
ierr = ISRestoreIndices(subpointIS, &ind);CHKERRQ(ierr);
ierr = ISDestroy(&subpointIS);CHKERRQ(ierr);
}
/* No need to setup section */
section = newSection;
}
} else {
ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) §ion);CHKERRQ(ierr);
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
}
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
if (newSection) {ierr = PetscSectionDestroy(&newSection);CHKERRQ(ierr);}
}
}
/* Cell Fields */
ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_view_partition", &writePartition, NULL);CHKERRQ(ierr);
if (hasCell || writePartition) {
ierr = PetscFPrintf(comm, fp, "CELL_DATA %d\n", totCells);CHKERRQ(ierr);
for (link = vtk->link; link; link = link->next) {
Vec X = (Vec) link->vec;
DM dmX;
PetscSection section, globalSection;
const char *name;
PetscInt enforceDof = PETSC_DETERMINE;
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
if (link->ft == PETSC_VTK_CELL_VECTOR_FIELD) enforceDof = 3;
ierr = PetscObjectGetName(link->vec, &name);CHKERRQ(ierr);
ierr = VecGetDM(X, &dmX);CHKERRQ(ierr);
if (dmX) {
ierr = DMGetDefaultSection(dmX, §ion);CHKERRQ(ierr);
} else {
PetscContainer c;
ierr = PetscObjectQuery(link->vec, "section", (PetscObject*) &c);CHKERRQ(ierr);
if (!c) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscContainerGetPointer(c, (void**) §ion);CHKERRQ(ierr);
}
if (!section) SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Vector %s had no PetscSection composed with it", name);
ierr = PetscSectionCreateGlobalSection(section, dm->sf, PETSC_FALSE, PETSC_FALSE, &globalSection);CHKERRQ(ierr);
ierr = DMPlexVTKWriteField_ASCII(dm, section, globalSection, X, name, fp, enforceDof, PETSC_DETERMINE, 1.0);CHKERRQ(ierr);
ierr = PetscSectionDestroy(&globalSection);CHKERRQ(ierr);
}
if (writePartition) {
ierr = PetscFPrintf(comm, fp, "SCALARS partition int 1\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm, fp, "LOOKUP_TABLE default\n");CHKERRQ(ierr);
ierr = DMPlexVTKWritePartition_ASCII(dm, fp);CHKERRQ(ierr);
}
}
/* Cleanup */
ierr = PetscSectionDestroy(&globalCoordSection);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr);
ierr = PetscFClose(comm, fp);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMPlexVTKWriteSection_ASCII(DM dm, PetscSection section, PetscSection globalSection, Vec v, FILE *fp, PetscInt enforceDof, PetscInt precision, PetscReal scale)
{
MPI_Comm comm;
const MPI_Datatype mpiType = MPIU_SCALAR;
PetscScalar *array;
PetscInt numDof = 0, maxDof;
PetscInt numLabelCells, cellHeight, cMax, cStart, cEnd, numLabelVertices, vMax, vStart, vEnd, pStart, pEnd, p;
PetscMPIInt numProcs, rank, proc, tag;
PetscBool hasLabel;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
PetscValidHeaderSpecific(v,VEC_CLASSID,4);
if (precision < 0) precision = 6;
ierr = PetscCommGetNewTag(comm, &tag);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr);
/* VTK only wants the values at cells or vertices */
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, &vMax);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
if (vMax >= 0) vEnd = PetscMin(vEnd, vMax);
pStart = PetscMax(PetscMin(cStart, vStart), pStart);
pEnd = PetscMin(PetscMax(cEnd, vEnd), pEnd);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
ierr = DMPlexGetStratumSize(dm, "vtk", 2, &numLabelVertices);CHKERRQ(ierr);
hasLabel = numLabelCells > 0 || numLabelVertices > 0 ? PETSC_TRUE : PETSC_FALSE;
for (p = pStart; p < pEnd; ++p) {
/* Reject points not either cells or vertices */
if (((p < cStart) || (p >= cEnd)) && ((p < vStart) || (p >= vEnd))) continue;
if (hasLabel) {
PetscInt value;
if (((p >= cStart) && (p < cEnd) && numLabelCells) ||
((p >= vStart) && (p < vEnd) && numLabelVertices)) {
ierr = DMPlexGetLabelValue(dm, "vtk", p, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
}
ierr = PetscSectionGetDof(section, p, &numDof);CHKERRQ(ierr);
if (numDof) break;
}
ierr = MPI_Allreduce(&numDof, &maxDof, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr);
enforceDof = PetscMax(enforceDof, maxDof);
ierr = VecGetArray(v, &array);CHKERRQ(ierr);
if (!rank) {
char formatString[8];
ierr = PetscSNPrintf(formatString, 8, "%%.%de", precision);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
/* Here we lose a way to filter points by keeping them out of the Numbering */
PetscInt dof, off, goff, d;
/* Reject points not either cells or vertices */
if (((p < cStart) || (p >= cEnd)) && ((p < vStart) || (p >= vEnd))) continue;
if (hasLabel) {
PetscInt value;
if (((p >= cStart) && (p < cEnd) && numLabelCells) ||
((p >= vStart) && (p < vEnd) && numLabelVertices)) {
ierr = DMPlexGetLabelValue(dm, "vtk", p, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
}
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(globalSection, p, &goff);CHKERRQ(ierr);
if (dof && goff >= 0) {
for (d = 0; d < dof; d++) {
if (d > 0) {
ierr = PetscFPrintf(comm, fp, " ");CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm, fp, formatString, PetscRealPart(array[off+d])*scale);CHKERRQ(ierr);
}
for (d = dof; d < enforceDof; d++) {
ierr = PetscFPrintf(comm, fp, " 0.0");CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr);
}
}
for (proc = 1; proc < numProcs; ++proc) {
PetscScalar *remoteValues;
PetscInt size = 0, d;
MPI_Status status;
ierr = MPI_Recv(&size, 1, MPIU_INT, proc, tag, comm, &status);CHKERRQ(ierr);
ierr = PetscMalloc1(size, &remoteValues);CHKERRQ(ierr);
ierr = MPI_Recv(remoteValues, size, mpiType, proc, tag, comm, &status);CHKERRQ(ierr);
for (p = 0; p < size/maxDof; ++p) {
for (d = 0; d < maxDof; ++d) {
if (d > 0) {
ierr = PetscFPrintf(comm, fp, " ");CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm, fp, formatString, PetscRealPart(remoteValues[p*maxDof+d])*scale);CHKERRQ(ierr);
}
for (d = maxDof; d < enforceDof; ++d) {
ierr = PetscFPrintf(comm, fp, " 0.0");CHKERRQ(ierr);
}
ierr = PetscFPrintf(comm, fp, "\n");CHKERRQ(ierr);
}
ierr = PetscFree(remoteValues);CHKERRQ(ierr);
}
} else {
PetscScalar *localValues;
PetscInt size, k = 0;
ierr = PetscSectionGetStorageSize(section, &size);CHKERRQ(ierr);
ierr = PetscMalloc1(size, &localValues);CHKERRQ(ierr);
for (p = pStart; p < pEnd; ++p) {
PetscInt dof, off, goff, d;
/* Reject points not either cells or vertices */
if (((p < cStart) || (p >= cEnd)) && ((p < vStart) || (p >= vEnd))) continue;
if (hasLabel) {
PetscInt value;
if (((p >= cStart) && (p < cEnd) && numLabelCells) ||
((p >= vStart) && (p < vEnd) && numLabelVertices)) {
ierr = DMPlexGetLabelValue(dm, "vtk", p, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
}
ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
ierr = PetscSectionGetOffset(globalSection, p, &goff);CHKERRQ(ierr);
if (goff >= 0) {
for (d = 0; d < dof; ++d) {
localValues[k++] = array[off+d];
}
}
}
ierr = MPI_Send(&k, 1, MPIU_INT, 0, tag, comm);CHKERRQ(ierr);
ierr = MPI_Send(localValues, k, mpiType, 0, tag, comm);CHKERRQ(ierr);
ierr = PetscFree(localValues);CHKERRQ(ierr);
}
ierr = VecRestoreArray(v, &array);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode DMPlexTSSetupGeometry(DM dm, PetscFV fvm, DMTS_Plex *dmplexts)
{
DM dmFace, dmCell;
DMLabel ghostLabel;
PetscSection sectionFace, sectionCell;
PetscSection coordSection;
Vec coordinates;
PetscReal minradius;
PetscScalar *fgeom, *cgeom;
PetscInt dim, cStart, cEnd, cEndInterior, c, fStart, fEnd, f;
PetscErrorCode ierr;
PetscFunctionBegin;
if (dmplexts->setupGeom) PetscFunctionReturn(0);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
/* Make cell centroids and volumes */
ierr = DMClone(dm, &dmCell);CHKERRQ(ierr);
ierr = DMSetCoordinateSection(dmCell, coordSection);CHKERRQ(ierr);
ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr);
for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, sizeof(CellGeom)/sizeof(PetscScalar));CHKERRQ(ierr);}
ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr);
ierr = DMCreateLocalVector(dmCell, &dmplexts->cellgeom);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
for (c = cStart; c < cEndInterior; ++c) {
CellGeom *cg;
ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr);
ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dmCell, c, &cg->volume, cg->centroid, NULL);CHKERRQ(ierr);
}
/* Compute face normals and minimum cell radius */
ierr = DMClone(dm, &dmFace);CHKERRQ(ierr);
ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionFace);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = PetscSectionSetChart(sectionFace, fStart, fEnd);CHKERRQ(ierr);
for (f = fStart; f < fEnd; ++f) {ierr = PetscSectionSetDof(sectionFace, f, sizeof(FaceGeom)/sizeof(PetscScalar));CHKERRQ(ierr);}
ierr = PetscSectionSetUp(sectionFace);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dmFace, sectionFace);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ionFace);CHKERRQ(ierr);
ierr = DMCreateLocalVector(dmFace, &dmplexts->facegeom);CHKERRQ(ierr);
ierr = VecGetArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
minradius = PETSC_MAX_REAL;
for (f = fStart; f < fEnd; ++f) {
FaceGeom *fg;
PetscReal area;
PetscInt ghost, d;
ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexPointLocalRef(dmFace, f, fgeom, &fg);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, fg->centroid, fg->normal);CHKERRQ(ierr);
for (d = 0; d < dim; ++d) fg->normal[d] *= area;
/* Flip face orientation if necessary to match ordering in support, and Update minimum radius */
{
CellGeom *cL, *cR;
const PetscInt *cells;
PetscReal *lcentroid, *rcentroid;
PetscReal v[3];
ierr = DMPlexGetSupport(dm, f, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[1], cgeom, &cR);CHKERRQ(ierr);
lcentroid = cells[0] >= cEndInterior ? fg->centroid : cL->centroid;
rcentroid = cells[1] >= cEndInterior ? fg->centroid : cR->centroid;
WaxpyD(dim, -1, lcentroid, rcentroid, v);
if (DotRealD(dim, fg->normal, v) < 0) {
for (d = 0; d < dim; ++d) fg->normal[d] = -fg->normal[d];
}
if (DotRealD(dim, fg->normal, v) <= 0) {
if (dim == 2) SETERRQ5(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g) v (%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) v[0], (double) v[1]);
if (dim == 3) SETERRQ7(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g,%g) v (%g,%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) fg->normal[2], (double) v[0], (double) v[1], (double) v[2]);
SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed", f);
}
if (cells[0] < cEndInterior) {
WaxpyD(dim, -1, fg->centroid, cL->centroid, v);
minradius = PetscMin(minradius, NormD(dim, v));
}
if (cells[1] < cEndInterior) {
WaxpyD(dim, -1, fg->centroid, cR->centroid, v);
minradius = PetscMin(minradius, NormD(dim, v));
}
}
}
ierr = MPI_Allreduce(&minradius, &dmplexts->minradius, 1, MPIU_REAL, MPI_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr);
/* Compute centroids of ghost cells */
for (c = cEndInterior; c < cEnd; ++c) {
FaceGeom *fg;
const PetscInt *cone, *support;
PetscInt coneSize, supportSize, s;
ierr = DMPlexGetConeSize(dmCell, c, &coneSize);CHKERRQ(ierr);
if (coneSize != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Ghost cell %d has cone size %d != 1", c, coneSize);
ierr = DMPlexGetCone(dmCell, c, &cone);CHKERRQ(ierr);
ierr = DMPlexGetSupportSize(dmCell, cone[0], &supportSize);CHKERRQ(ierr);
if (supportSize != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %d has support size %d != 1", cone[0], supportSize);
ierr = DMPlexGetSupport(dmCell, cone[0], &support);CHKERRQ(ierr);
ierr = DMPlexPointLocalRef(dmFace, cone[0], fgeom, &fg);CHKERRQ(ierr);
for (s = 0; s < 2; ++s) {
/* Reflect ghost centroid across plane of face */
if (support[s] == c) {
const CellGeom *ci;
CellGeom *cg;
PetscReal c2f[3], a;
ierr = DMPlexPointLocalRead(dmCell, support[(s+1)%2], cgeom, &ci);CHKERRQ(ierr);
WaxpyD(dim, -1, ci->centroid, fg->centroid, c2f); /* cell to face centroid */
a = DotRealD(dim, c2f, fg->normal)/DotRealD(dim, fg->normal, fg->normal);
ierr = DMPlexPointLocalRef(dmCell, support[s], cgeom, &cg);CHKERRQ(ierr);
WaxpyD(dim, 2*a, fg->normal, ci->centroid, cg->centroid);
cg->volume = ci->volume;
}
}
}
ierr = VecRestoreArray(dmplexts->facegeom, &fgeom);CHKERRQ(ierr);
ierr = VecRestoreArray(dmplexts->cellgeom, &cgeom);CHKERRQ(ierr);
ierr = DMDestroy(&dmCell);CHKERRQ(ierr);
ierr = DMDestroy(&dmFace);CHKERRQ(ierr);
dmplexts->setupGeom = PETSC_TRUE;
PetscFunctionReturn(0);
}
static PetscErrorCode TSComputeRHSFunction_DMPlex(TS ts, PetscReal time, Vec X, Vec F, void *ctx)
{
DM dm;
DMTS_Plex *dmplexts = (DMTS_Plex *) ctx;
void (*riemann)(const PetscReal[], const PetscReal[], const PetscScalar[], const PetscScalar[], PetscScalar[], void *) = dmplexts->riemann;
PetscFV fvm;
PetscLimiter lim;
Vec faceGeometry = dmplexts->facegeom;
Vec cellGeometry = dmplexts->cellgeom;
Vec Grad = NULL, locGrad, locX;
DM dmFace, dmCell;
DMLabel ghostLabel;
PetscCellGeometry fgeom, cgeom;
const PetscScalar *facegeom, *cellgeom, *x, *lgrad;
PetscScalar *grad, *f, *uL, *uR, *fluxL, *fluxR;
PetscReal *centroid, *normal, *vol, *cellPhi;
PetscBool computeGradients;
PetscInt Nf, dim, pdim, fStart, fEnd, numFaces = 0, face, iface, cell, cStart, cEnd, cEndInterior;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(ts,TS_CLASSID,1);
PetscValidHeaderSpecific(X,VEC_CLASSID,3);
PetscValidHeaderSpecific(F,VEC_CLASSID,5);
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &locX);CHKERRQ(ierr);
ierr = VecZeroEntries(locX);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, X, INSERT_VALUES, locX);CHKERRQ(ierr);
ierr = VecZeroEntries(F);CHKERRQ(ierr);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
ierr = DMGetField(dm, 0, (PetscObject *) &fvm);CHKERRQ(ierr);
ierr = PetscFVGetLimiter(fvm, &lim);CHKERRQ(ierr);
ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr);
ierr = PetscFVGetComputeGradients(fvm, &computeGradients);CHKERRQ(ierr);
if (computeGradients) {
ierr = DMGetGlobalVector(dmplexts->dmGrad, &Grad);CHKERRQ(ierr);
ierr = VecZeroEntries(Grad);CHKERRQ(ierr);
ierr = VecGetArray(Grad, &grad);CHKERRQ(ierr);
}
ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr);
ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr);
ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr);
/* Count faces and reconstruct gradients */
for (face = fStart; face < fEnd; ++face) {
const PetscInt *cells;
const FaceGeom *fg;
const PetscScalar *cx[2];
PetscScalar *cgrad[2];
PetscBool boundary;
PetscInt ghost, c, pd, d;
ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
++numFaces;
if (!computeGradients) continue;
ierr = DMPlexIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr);
if (boundary) continue;
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);
for (c = 0; c < 2; ++c) {
ierr = DMPlexPointLocalRead(dm, cells[c], x, &cx[c]);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dmplexts->dmGrad, cells[c], grad, &cgrad[c]);CHKERRQ(ierr);
}
for (pd = 0; pd < pdim; ++pd) {
PetscScalar delta = cx[1][pd] - cx[0][pd];
for (d = 0; d < dim; ++d) {
if (cgrad[0]) cgrad[0][pd*dim+d] += fg->grad[0][d] * delta;
if (cgrad[1]) cgrad[1][pd*dim+d] -= fg->grad[1][d] * delta;
}
}
}
/* Limit interior gradients (using cell-based loop because it generalizes better to vector limiters) */
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr);
ierr = DMGetWorkArray(dm, pdim, PETSC_REAL, &cellPhi);CHKERRQ(ierr);
for (cell = computeGradients && lim ? cStart : cEnd; cell < cEndInterior; ++cell) {
const PetscInt *faces;
const PetscScalar *cx;
const CellGeom *cg;
PetscScalar *cgrad;
PetscInt coneSize, f, pd, d;
ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr);
ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm, cell, x, &cx);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cell, cellgeom, &cg);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dmplexts->dmGrad, cell, grad, &cgrad);CHKERRQ(ierr);
if (!cgrad) continue; /* Unowned overlap cell, we do not compute */
/* Limiter will be minimum value over all neighbors */
for (d = 0; d < pdim; ++d) cellPhi[d] = PETSC_MAX_REAL;
for (f = 0; f < coneSize; ++f) {
const PetscScalar *ncx;
const CellGeom *ncg;
const PetscInt *fcells;
PetscInt face = faces[f], ncell, ghost;
PetscReal v[3];
PetscBool boundary;
ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
ierr = DMPlexIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr);
if ((ghost >= 0) || boundary) continue;
ierr = DMPlexGetSupport(dm, face, &fcells);CHKERRQ(ierr);
ncell = cell == fcells[0] ? fcells[1] : fcells[0];
ierr = DMPlexPointLocalRead(dm, ncell, x, &ncx);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, ncell, cellgeom, &ncg);CHKERRQ(ierr);
WaxpyD(dim, -1, cg->centroid, ncg->centroid, v);
for (d = 0; d < pdim; ++d) {
/* We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005 */
PetscReal phi, flim = 0.5 * PetscRealPart(ncx[d] - cx[d]) / DotD(dim, &cgrad[d*dim], v);
ierr = PetscLimiterLimit(lim, flim, &phi);CHKERRQ(ierr);
cellPhi[d] = PetscMin(cellPhi[d], phi);
}
}
/* Apply limiter to gradient */
for (pd = 0; pd < pdim; ++pd)
/* Scalar limiter applied to each component separately */
for (d = 0; d < dim; ++d) cgrad[pd*dim+d] *= cellPhi[pd];
}
ierr = DMRestoreWorkArray(dm, pdim, PETSC_REAL, &cellPhi);CHKERRQ(ierr);
ierr = DMPlexInsertBoundaryValuesFVM_Static(dm, fvm, time, locX, Grad, dmplexts);CHKERRQ(ierr);
if (computeGradients) {
ierr = VecRestoreArray(Grad, &grad);CHKERRQ(ierr);
ierr = DMGetLocalVector(dmplexts->dmGrad, &locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmplexts->dmGrad, Grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmplexts->dmGrad, Grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dmplexts->dmGrad, &Grad);CHKERRQ(ierr);
ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr);
}
ierr = PetscMalloc7(numFaces*dim,¢roid,numFaces*dim,&normal,numFaces*2,&vol,numFaces*pdim,&uL,numFaces*pdim,&uR,numFaces*pdim,&fluxL,numFaces*pdim,&fluxR);CHKERRQ(ierr);
/* Read out values */
for (face = fStart, iface = 0; face < fEnd; ++face) {
const PetscInt *cells;
const FaceGeom *fg;
const CellGeom *cgL, *cgR;
const PetscScalar *xL, *xR, *gL, *gR;
PetscInt ghost, d;
ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm, cells[0], x, &xL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm, cells[1], x, &xR);CHKERRQ(ierr);
if (computeGradients) {
PetscReal dxL[3], dxR[3];
ierr = DMPlexPointLocalRead(dmplexts->dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmplexts->dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr);
WaxpyD(dim, -1, cgL->centroid, fg->centroid, dxL);
WaxpyD(dim, -1, cgR->centroid, fg->centroid, dxR);
for (d = 0; d < pdim; ++d) {
uL[iface*pdim+d] = xL[d] + DotD(dim, &gL[d*dim], dxL);
uR[iface*pdim+d] = xR[d] + DotD(dim, &gR[d*dim], dxR);
}
} else {
for (d = 0; d < pdim; ++d) {
uL[iface*pdim+d] = xL[d];
uR[iface*pdim+d] = xR[d];
}
}
for (d = 0; d < dim; ++d) {
centroid[iface*dim+d] = fg->centroid[d];
normal[iface*dim+d] = fg->normal[d];
}
vol[iface*2+0] = cgL->volume;
vol[iface*2+1] = cgR->volume;
++iface;
}
if (computeGradients) {
ierr = VecRestoreArrayRead(locGrad,&lgrad);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmplexts->dmGrad, &locGrad);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr);
fgeom.v0 = centroid;
fgeom.n = normal;
cgeom.vol = vol;
/* Riemann solve */
ierr = PetscFVIntegrateRHSFunction(fvm, numFaces, Nf, &fvm, 0, fgeom, cgeom, uL, uR, riemann, fluxL, fluxR, dmplexts->rhsfunctionlocalctx);CHKERRQ(ierr);
/* Insert fluxes */
ierr = VecGetArray(F, &f);CHKERRQ(ierr);
for (face = fStart, iface = 0; face < fEnd; ++face) {
const PetscInt *cells;
PetscScalar *fL, *fR;
PetscInt ghost, d;
ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dm, cells[0], f, &fL);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dm, cells[1], f, &fR);CHKERRQ(ierr);
for (d = 0; d < pdim; ++d) {
if (fL) fL[d] -= fluxL[iface*pdim+d];
if (fR) fR[d] += fluxR[iface*pdim+d];
}
++iface;
}
ierr = VecRestoreArray(F, &f);CHKERRQ(ierr);
ierr = PetscFree7(centroid,normal,vol,uL,uR,fluxL,fluxR);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &locX);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Write all fields that have been provided to the viewer
Multi-block XML format with binary appended data.
*/
PetscErrorCode DMPlexVTKWriteAll_VTU(DM dm,PetscViewer viewer)
{
MPI_Comm comm;
PetscViewer_VTK *vtk = (PetscViewer_VTK*)viewer->data;
PetscViewerVTKObjectLink link;
FILE *fp;
PetscMPIInt rank,size,tag;
PetscErrorCode ierr;
PetscInt dim,cellHeight,cStart,cEnd,vStart,vEnd,cMax,numLabelCells,hasLabel,c,v,r,i;
PieceInfo piece,*gpiece = NULL;
void *buffer = NULL;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
#if defined(PETSC_USE_COMPLEX)
SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Complex values not supported");
#endif
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
tag = ((PetscObject)viewer)->tag;
ierr = PetscFOpen(comm,vtk->filename,"wb",&fp);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"<?xml version=\"1.0\"?>\n");CHKERRQ(ierr);
#if defined(PETSC_WORDS_BIGENDIAN)
ierr = PetscFPrintf(comm,fp,"<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"BigEndian\">\n");CHKERRQ(ierr);
#else
ierr = PetscFPrintf(comm,fp,"<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n");CHKERRQ(ierr);
#endif
ierr = PetscFPrintf(comm,fp," <UnstructuredGrid>\n");CHKERRQ(ierr);
ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetVTKCellHeight(dm, &cellHeight);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr);
if (cMax >= 0) cEnd = PetscMin(cEnd, cMax);
ierr = DMPlexGetStratumSize(dm, "vtk", 1, &numLabelCells);CHKERRQ(ierr);
hasLabel = numLabelCells > 0 ? PETSC_TRUE : PETSC_FALSE;
piece.nvertices = vEnd - vStart;
piece.ncells = 0;
piece.nconn = 0;
for (c = cStart; c < cEnd; ++c) {
PetscInt *closure = NULL;
PetscInt closureSize;
if (hasLabel) {
PetscInt value;
ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
for (v = 0; v < closureSize*2; v += 2) {
if ((closure[v] >= vStart) && (closure[v] < vEnd)) piece.nconn++;
}
ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr);
piece.ncells++;
}
if (!rank) {ierr = PetscMalloc(size*sizeof(piece),&gpiece);CHKERRQ(ierr);}
ierr = MPI_Gather((PetscInt*)&piece,sizeof(piece)/sizeof(PetscInt),MPIU_INT,(PetscInt*)gpiece,sizeof(piece)/sizeof(PetscInt),MPIU_INT,0,comm);CHKERRQ(ierr);
/*
* Write file header
*/
if (!rank) {
PetscInt boffset = 0;
for (r=0; r<size; r++) {
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <Piece NumberOfPoints=\"%D\" NumberOfCells=\"%D\">\n",gpiece[r].nvertices,gpiece[r].ncells);CHKERRQ(ierr);
/* Coordinate positions */
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <Points>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"%s\" Name=\"Position\" NumberOfComponents=\"3\" format=\"appended\" offset=\"%D\" />\n",precision,boffset);CHKERRQ(ierr);
boffset += gpiece[r].nvertices*3*sizeof(PetscScalar) + sizeof(int);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </Points>\n");CHKERRQ(ierr);
/* Cell connectivity */
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <Cells>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"Int32\" Name=\"connectivity\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",boffset);CHKERRQ(ierr);
boffset += gpiece[r].nconn*sizeof(PetscInt) + sizeof(int);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"Int32\" Name=\"offsets\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",boffset);CHKERRQ(ierr);
boffset += gpiece[r].ncells*sizeof(PetscInt) + sizeof(int);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"UInt8\" Name=\"types\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",boffset);CHKERRQ(ierr);
boffset += gpiece[r].ncells*sizeof(unsigned char) + sizeof(int);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </Cells>\n");CHKERRQ(ierr);
/*
* Cell Data headers
*/
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <CellData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <DataArray type=\"Int32\" Name=\"Rank\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",boffset);CHKERRQ(ierr);
boffset += gpiece[r].ncells*sizeof(int) + sizeof(int);
/* all the vectors */
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
PetscInt bs,nfields,field;
const char *vecname = "";
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
if (((PetscObject)X)->name || link != vtk->link) { /* If the object is already named, use it. If it is past the first link, name it to disambiguate. */
ierr = PetscObjectGetName((PetscObject)X,&vecname);CHKERRQ(ierr);
}
ierr = PetscSectionGetDof(dm->defaultSection,cStart,&bs);CHKERRQ(ierr);
ierr = PetscSectionGetNumFields(dm->defaultSection,&nfields);CHKERRQ(ierr);
for (field=0,i=0; field<(nfields?nfields:1); field++) {
PetscInt fbs,j;
const char *fieldname = NULL;
char buf[256];
if (nfields) { /* We have user-defined fields/components */
ierr = PetscSectionGetFieldDof(dm->defaultSection,cStart,field,&fbs);CHKERRQ(ierr);
ierr = PetscSectionGetFieldName(dm->defaultSection,field,&fieldname);CHKERRQ(ierr);
} else fbs = bs; /* Say we have one field with 'bs' components */
if (!fieldname) {
ierr = PetscSNPrintf(buf,sizeof(buf),"CellField%D",field);CHKERRQ(ierr);
fieldname = buf;
}
for (j=0; j<fbs; j++) {
ierr = PetscFPrintf(comm,fp," <DataArray type=\"%s\" Name=\"%s%s.%D\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",precision,vecname,fieldname,j,boffset);CHKERRQ(ierr);
boffset += gpiece[r].ncells*sizeof(PetscScalar) + sizeof(int);
i++;
}
}
if (i != bs) SETERRQ2(comm,PETSC_ERR_PLIB,"Total number of field components %D != block size %D",i,bs);
}
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </CellData>\n");CHKERRQ(ierr);
/*
* Point Data headers
*/
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," <PointData>\n");CHKERRQ(ierr);
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
PetscInt bs,nfields,field;
const char *vecname = "";
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
if (((PetscObject)X)->name || link != vtk->link) { /* If the object is already named, use it. If it is past the first link, name it to disambiguate. */
ierr = PetscObjectGetName((PetscObject)X,&vecname);CHKERRQ(ierr);
}
ierr = PetscSectionGetDof(dm->defaultSection,vStart,&bs);CHKERRQ(ierr);
ierr = PetscSectionGetNumFields(dm->defaultSection,&nfields);CHKERRQ(ierr);
for (field=0,i=0; field<(nfields?nfields:1); field++) {
PetscInt fbs,j;
const char *fieldname = NULL;
char buf[256];
if (nfields) { /* We have user-defined fields/components */
ierr = PetscSectionGetFieldDof(dm->defaultSection,vStart,field,&fbs);CHKERRQ(ierr);
ierr = PetscSectionGetFieldName(dm->defaultSection,field,&fieldname);CHKERRQ(ierr);
} else fbs = bs; /* Say we have one field with 'bs' components */
if (!fieldname) {
ierr = PetscSNPrintf(buf,sizeof(buf),"PointField%D",field);CHKERRQ(ierr);
fieldname = buf;
}
for (j=0; j<fbs; j++) {
ierr = PetscFPrintf(comm,fp," <DataArray type=\"%s\" Name=\"%s%s.%D\" NumberOfComponents=\"1\" format=\"appended\" offset=\"%D\" />\n",precision,vecname,fieldname,j,boffset);CHKERRQ(ierr);
boffset += gpiece[r].nvertices*sizeof(PetscScalar) + sizeof(int);
}
}
}
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </PointData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(PETSC_COMM_SELF,fp," </Piece>\n");CHKERRQ(ierr);
}
}
ierr = PetscFPrintf(comm,fp," </UnstructuredGrid>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp," <AppendedData encoding=\"raw\">\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"_");CHKERRQ(ierr);
if (!rank) {
PetscInt maxsize = 0;
for (r=0; r<size; r++) {
maxsize = PetscMax(maxsize, (PetscInt) (gpiece[r].nvertices*3*sizeof(PetscScalar)));
maxsize = PetscMax(maxsize, (PetscInt) (gpiece[r].ncells*sizeof(PetscScalar)));
maxsize = PetscMax(maxsize, (PetscInt) (gpiece[r].nconn*sizeof(PetscVTKInt)));
}
ierr = PetscMalloc(maxsize,&buffer);CHKERRQ(ierr);
}
for (r=0; r<size; r++) {
if (r == rank) {
PetscInt nsend;
{ /* Position */
const PetscScalar *x;
PetscScalar *y = NULL;
Vec coords;
nsend = piece.nvertices*3;
ierr = DMGetCoordinatesLocal(dm,&coords);CHKERRQ(ierr);
ierr = VecGetArrayRead(coords,&x);CHKERRQ(ierr);
if (dim != 3) {
ierr = PetscMalloc(piece.nvertices*3*sizeof(PetscScalar),&y);CHKERRQ(ierr);
for (i=0; i<piece.nvertices; i++) {
y[i*3+0] = x[i*dim+0];
y[i*3+1] = (dim > 1) ? x[i*dim+1] : 0;
y[i*3+2] = 0;
}
}
ierr = TransferWrite(viewer,fp,r,0,y ? y : x,buffer,nsend,PETSC_SCALAR,tag);CHKERRQ(ierr);
ierr = PetscFree(y);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(coords,&x);CHKERRQ(ierr);
}
{ /* Connectivity, offsets, types */
PetscVTKInt *connectivity = NULL,*offsets;
PetscVTKType *types;
ierr = DMPlexGetVTKConnectivity(dm,&piece,&connectivity,&offsets,&types);CHKERRQ(ierr);
ierr = TransferWrite(viewer,fp,r,0,connectivity,buffer,piece.nconn,PETSC_INT32,tag);CHKERRQ(ierr);
ierr = TransferWrite(viewer,fp,r,0,offsets,buffer,piece.ncells,PETSC_INT32,tag);CHKERRQ(ierr);
ierr = TransferWrite(viewer,fp,r,0,types,buffer,piece.ncells,PETSC_UINT8,tag);CHKERRQ(ierr);
ierr = PetscFree3(connectivity,offsets,types);CHKERRQ(ierr);
}
{ /* Owners (cell data) */
PetscVTKInt *owners;
ierr = PetscMalloc(piece.ncells*sizeof(PetscVTKInt),&owners);CHKERRQ(ierr);
for (i=0; i<piece.ncells; i++) owners[i] = rank;
ierr = TransferWrite(viewer,fp,r,0,owners,buffer,piece.ncells,PETSC_INT32,tag);CHKERRQ(ierr);
ierr = PetscFree(owners);CHKERRQ(ierr);
}
/* Cell data */
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
const PetscScalar *x;
PetscScalar *y;
PetscInt bs;
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
ierr = PetscSectionGetDof(dm->defaultSection,cStart,&bs);CHKERRQ(ierr);
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
ierr = PetscMalloc(piece.ncells*sizeof(PetscScalar),&y);CHKERRQ(ierr);
for (i=0; i<bs; i++) {
PetscInt cnt;
for (c=cStart,cnt=0; c<cEnd; c++) {
const PetscScalar *xpoint;
if (hasLabel) { /* Ignore some cells */
PetscInt value;
ierr = DMPlexGetLabelValue(dm, "vtk", c, &value);CHKERRQ(ierr);
if (value != 1) continue;
}
ierr = DMPlexPointLocalRead(dm,c,x,&xpoint);CHKERRQ(ierr);
y[cnt++] = xpoint[i];
}
if (cnt != piece.ncells) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Count does not match");
ierr = TransferWrite(viewer,fp,r,0,y,buffer,piece.ncells,PETSC_SCALAR,tag);CHKERRQ(ierr);
}
ierr = PetscFree(y);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
}
for (link=vtk->link; link; link=link->next) {
Vec X = (Vec)link->vec;
const PetscScalar *x;
PetscScalar *y;
PetscInt bs;
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
ierr = PetscSectionGetDof(dm->defaultSection,vStart,&bs);CHKERRQ(ierr);
ierr = VecGetArrayRead(X,&x);CHKERRQ(ierr);
ierr = PetscMalloc(piece.nvertices*sizeof(PetscScalar),&y);CHKERRQ(ierr);
for (i=0; i<bs; i++) {
PetscInt cnt;
for (v=vStart,cnt=0; v<vEnd; v++) {
const PetscScalar *xpoint;
ierr = DMPlexPointLocalRead(dm,v,x,&xpoint);CHKERRQ(ierr);
y[cnt++] = xpoint[i];
}
if (cnt != piece.nvertices) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Count does not match");
ierr = TransferWrite(viewer,fp,r,0,y,buffer,piece.nvertices,PETSC_SCALAR,tag);CHKERRQ(ierr);
}
ierr = PetscFree(y);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(X,&x);CHKERRQ(ierr);
}
} else if (!rank) {
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].nvertices*3,PETSC_SCALAR,tag);CHKERRQ(ierr); /* positions */
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].nconn,PETSC_INT32,tag);CHKERRQ(ierr); /* connectivity */
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,PETSC_INT32,tag);CHKERRQ(ierr); /* offsets */
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,PETSC_UINT8,tag);CHKERRQ(ierr); /* types */
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,PETSC_INT32,tag);CHKERRQ(ierr); /* owner rank (cells) */
/* all cell data */
for (link=vtk->link; link; link=link->next) {
PetscInt bs;
if ((link->ft != PETSC_VTK_CELL_FIELD) && (link->ft != PETSC_VTK_CELL_VECTOR_FIELD)) continue;
ierr = PetscSectionGetDof(dm->defaultSection,cStart,&bs);CHKERRQ(ierr);
for (i=0; i<bs; i++) {
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].ncells,PETSC_SCALAR,tag);CHKERRQ(ierr);
}
}
/* all point data */
for (link=vtk->link; link; link=link->next) {
PetscInt bs;
if ((link->ft != PETSC_VTK_POINT_FIELD) && (link->ft != PETSC_VTK_POINT_VECTOR_FIELD)) continue;
ierr = PetscSectionGetDof(dm->defaultSection,vStart,&bs);CHKERRQ(ierr);
for (i=0; i<bs; i++) {
ierr = TransferWrite(viewer,fp,r,0,NULL,buffer,gpiece[r].nvertices,PETSC_SCALAR,tag);CHKERRQ(ierr);
}
}
}
}
ierr = PetscFree(gpiece);CHKERRQ(ierr);
ierr = PetscFree(buffer);CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"\n </AppendedData>\n");CHKERRQ(ierr);
ierr = PetscFPrintf(comm,fp,"</VTKFile>\n");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
DMGlobalToLocalSolve - Solve for the global vector that is mapped to a given local vector by DMGlobalToLocalBegin()/DMGlobalToLocalEnd() with mode
= INSERT_VALUES. It is assumed that the sum of all the local vector sizes is greater than or equal to the global vector size, so the solution is
a least-squares solution. It is also assumed that DMLocalToGlobalBegin()/DMLocalToGlobalEnd() with mode = ADD_VALUES is the adjoint of the
global-to-local map, so that the least-squares solution may be found by the normal equations.
collective
Input Parameters:
+ dm - The DM object
. x - The local vector
- y - The global vector: the input value of globalVec is used as an initial guess
Output Parameters:
. y - The least-squares solution
Level: advanced
Note: If the DM is of type DMPLEX, then y is the solution of L' * D * L * y = L' * D * x, where D is a diagonal mask that is 1 for every point in
the union of the closures of the local cells and 0 otherwise. This difference is only relevant if there are anchor points that are not in the
closure of any local cell (see DMPlexGetAnchors()/DMPlexSetAnchors()).
.seealso: DMGlobalToLocalBegin(), DMGlobalToLocalEnd(), DMLocalToGlobalBegin(), DMLocalToGlobalEnd(), DMPlexGetAnchors(), DMPlexSetAnchors()
@*/
PetscErrorCode DMGlobalToLocalSolve(DM dm, Vec x, Vec y)
{
Mat CtC;
PetscInt n, N, cStart, cEnd, cEndInterior, c;
PetscBool isPlex;
KSP ksp;
PC pc;
Vec global, mask=NULL;
projectConstraintsCtx ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectTypeCompare((PetscObject)dm,DMPLEX,&isPlex);CHKERRQ(ierr);
if (isPlex) {
/* mark points in the closure */
ierr = DMCreateLocalVector(dm,&mask);CHKERRQ(ierr);
ierr = VecSet(mask,0.0);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm,0,&cStart,&cEnd);CHKERRQ(ierr);
ierr = DMPlexGetHybridBounds(dm,&cEndInterior,NULL,NULL,NULL);CHKERRQ(ierr);
cEnd = cEndInterior < 0 ? cEnd : cEndInterior;
if (cEnd > cStart) {
PetscScalar *ones;
PetscInt numValues, i;
ierr = DMPlexVecGetClosure(dm,NULL,mask,cStart,&numValues,NULL);CHKERRQ(ierr);
ierr = PetscMalloc1(numValues,&ones);CHKERRQ(ierr);
for (i = 0; i < numValues; i++) {
ones[i] = 1.;
}
for (c = cStart; c < cEnd; c++) {
ierr = DMPlexVecSetClosure(dm,NULL,mask,c,ones,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = PetscFree(ones);CHKERRQ(ierr);
}
}
else {
PetscBool hasMask;
ierr = DMHasNamedLocalVector(dm, "_DMGlobalToLocalSolve_mask", &hasMask);CHKERRQ(ierr);
if (!hasMask) {
PetscErrorCode (**func) (PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx);
void **ctx;
PetscInt Nf, f;
ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr);
ierr = PetscMalloc2(Nf, &func, Nf, &ctx);CHKERRQ(ierr);
for (f = 0; f < Nf; ++f) {
func[f] = DMGlobalToLocalSolve_project1;
ctx[f] = NULL;
}
ierr = DMGetNamedLocalVector(dm, "_DMGlobalToLocalSolve_mask", &mask);CHKERRQ(ierr);
ierr = DMProjectFunctionLocal(dm,0.0,func,ctx,INSERT_ALL_VALUES,mask);CHKERRQ(ierr);
ierr = DMRestoreNamedLocalVector(dm, "_DMGlobalToLocalSolve_mask", &mask);CHKERRQ(ierr);
ierr = PetscFree2(func, ctx);CHKERRQ(ierr);
}
ierr = DMGetNamedLocalVector(dm, "_DMGlobalToLocalSolve_mask", &mask);CHKERRQ(ierr);
}
ctx.dm = dm;
ctx.mask = mask;
ierr = VecGetSize(y,&N);CHKERRQ(ierr);
ierr = VecGetLocalSize(y,&n);CHKERRQ(ierr);
ierr = MatCreate(PetscObjectComm((PetscObject)dm),&CtC);CHKERRQ(ierr);
ierr = MatSetSizes(CtC,n,n,N,N);CHKERRQ(ierr);
ierr = MatSetType(CtC,MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(CtC);CHKERRQ(ierr);
ierr = MatShellSetContext(CtC,&ctx);CHKERRQ(ierr);
ierr = MatShellSetOperation(CtC,MATOP_MULT,(void(*)(void))MatMult_GlobalToLocalNormal);CHKERRQ(ierr);
ierr = KSPCreate(PetscObjectComm((PetscObject)dm),&ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,CtC,CtC);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPCG);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp,PETSC_TRUE);CHKERRQ(ierr);
ierr = KSPSetUp(ksp);CHKERRQ(ierr);
ierr = DMGetGlobalVector(dm,&global);CHKERRQ(ierr);
ierr = VecSet(global,0.);CHKERRQ(ierr);
if (mask) {ierr = VecPointwiseMult(x,mask,x);CHKERRQ(ierr);}
ierr = DMLocalToGlobalBegin(dm,x,ADD_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(dm,x,ADD_VALUES,global);CHKERRQ(ierr);
ierr = KSPSolve(ksp,global,y);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm,&global);CHKERRQ(ierr);
/* clean up */
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = MatDestroy(&CtC);CHKERRQ(ierr);
if (isPlex) {
ierr = VecDestroy(&mask);CHKERRQ(ierr);
}
else {
ierr = DMRestoreNamedLocalVector(dm, "_DMGlobalToLocalSolve_mask", &mask);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
