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); }