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);
}
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);
}
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);
}
PetscErrorCode ComputeJacobian_LS(DM dm, Vec locX, PetscInt cell, PetscScalar CellValues[], void *ctx)
{
User user = (User) ctx;
Physics phys = user->model->physics;
PetscInt dof = phys->dof;
const PetscScalar *facegeom, *cellgeom,*x;
PetscErrorCode ierr;
DM dmFace, dmCell;
DM dmGrad = user->dmGrad;
PetscInt fStart, fEnd, face, cStart;
Vec locGrad, locGradLimiter, Grad;
/*here the localGradLimiter refers to the gradient that has been multiplied by the limiter function.
The locGradLimiter is used to construct the uL and uR, and the locGrad is used to caculate the diffusion term*/
Vec TempVec; /*a temperal vec for the vector restore*/
PetscFunctionBeginUser;
ierr = VecGetDM(user->facegeom,&dmFace);CHKERRQ(ierr);
ierr = VecGetDM(user->cellgeom,&dmCell);CHKERRQ(ierr);
ierr = DMGetGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecDuplicate(Grad, &TempVec);CHKERRQ(ierr);
ierr = VecCopy(Grad, TempVec);CHKERRQ(ierr);
/*Backup the original vector and use it to restore the value of dmGrad,
because I do not want to change the values of the cell gradient*/
ierr = VecGetArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX,&x);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, NULL);CHKERRQ(ierr);
{
PetscScalar *grad;
ierr = VecGetArray(Grad,&grad);CHKERRQ(ierr);
/* Limit interior gradients. Using cell-based loop because it generalizes better to vector limiters. */
const PetscInt *faces;
PetscInt numFaces,f;
PetscReal *cellPhi; /* Scalar limiter applied to each component separately */
const PetscScalar *cx;
const CellGeom *cg;
PetscScalar *cgrad;
PetscInt i;
ierr = PetscMalloc(phys->dof*sizeof(PetscScalar),&cellPhi);CHKERRQ(ierr);
ierr = DMPlexGetConeSize(dm,cell,&numFaces);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(dmGrad,cell,grad,&cgrad);CHKERRQ(ierr);
/* Limiter will be minimum value over all neighbors */
for (i=0; i<dof; i++) {
cellPhi[i] = PETSC_MAX_REAL;
}
for (f=0; f<numFaces; f++) {
const PetscScalar *ncx;
const CellGeom *ncg;
const PetscInt *fcells;
PetscInt face = faces[f],ncell;
PetscScalar v[DIM];
PetscBool ghost;
ierr = IsExteriorGhostFace(dm,face,&ghost);CHKERRQ(ierr);
if (ghost) continue;
ierr = DMPlexGetSupport(dm,face,&fcells);CHKERRQ(ierr);
ncell = cell == fcells[0] ? fcells[1] : fcells[0]; /*The expression (x ? y : z) has the value of y if x is nonzero, z otherwise */
ierr = DMPlexPointLocalRead(dm,ncell,x,&ncx);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell,ncell,cellgeom,&ncg);CHKERRQ(ierr);
Waxpy2(-1, cg->centroid, ncg->centroid, v);
for (i=0; i<dof; i++) {
/* We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005 */
PetscScalar phi,flim = 0.5 * (ncx[i] - cx[i]) / Dot2(&cgrad[i*DIM],v);
phi = (*user->LimitGrad)(flim);
cellPhi[i] = PetscMin(cellPhi[i],phi);
}
}
/* Apply limiter to gradient */
for (i=0; i<dof; i++) Scale2(cellPhi[i],&cgrad[i*DIM],&cgrad[i*DIM]);
ierr = PetscFree(cellPhi);CHKERRQ(ierr);
ierr = VecRestoreArray(Grad,&grad);CHKERRQ(ierr);
}
ierr = DMGetLocalVector(dmGrad,&locGradLimiter);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmGrad,Grad,INSERT_VALUES,locGradLimiter);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmGrad,Grad,INSERT_VALUES,locGradLimiter);CHKERRQ(ierr);
ierr = VecCopy(TempVec, Grad);CHKERRQ(ierr);/*Restore the vector*/
ierr = DMGetLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecDestroy(&TempVec);CHKERRQ(ierr);
{
const PetscScalar *grad, *gradlimiter;
ierr = VecGetArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = VecGetArrayRead(locGradLimiter,&gradlimiter);CHKERRQ(ierr);
for (face=fStart; face<fEnd; face++) {
const PetscInt *cells;
PetscInt ghost,i,j;
PetscScalar *fluxcon, *fluxdiff, *fx[2];
const FaceGeom *fg;
const CellGeom *cg[2];
const PetscScalar *cx[2],*cgrad[2], *cgradlimiter[2];
PetscScalar *uL, *uR;
PetscReal FaceArea;
ierr = PetscMalloc(phys->dof * phys->dof * sizeof(PetscScalar), &fluxcon);CHKERRQ(ierr); /*For the convection terms*/
ierr = PetscMalloc(phys->dof * phys->dof * sizeof(PetscScalar), &fluxdiff);CHKERRQ(ierr); /*For the diffusion terms*/
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &uL);CHKERRQ(ierr);
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &uR);CHKERRQ(ierr);
fx[0] = uL; fx[1] = uR;
ierr = DMPlexGetLabelValue(dm, "ghost", face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmFace,face,facegeom,&fg);CHKERRQ(ierr);
for (i=0; i<2; i++) {
PetscScalar dx[DIM];
ierr = DMPlexPointLocalRead(dmCell,cells[i],cellgeom,&cg[i]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm,cells[i],x,&cx[i]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad,cells[i],gradlimiter,&cgradlimiter[i]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad,cells[i],grad,&cgrad[i]);CHKERRQ(ierr);
Waxpy2(-1,cg[i]->centroid,fg->centroid,dx);
for (j=0; j<dof; j++) {
fx[i][j] = cx[i][j] + Dot2(cgradlimiter[i],dx);
}
/*fx[0] and fx[1] are the value of the variables on the left and right
side of the face, respectively, that is u_L and u_R.*/
}
ierr = RiemannSolver_Rusanov_Jacobian(user, cgrad[0], cgrad[1], fg->centroid, cg[0]->centroid, cg[1]->centroid, fg->normal,
fx[0], fx[1], fluxcon, fluxdiff);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, face, &FaceArea, NULL, NULL);CHKERRQ(ierr);
/*Compute the face area*/
for (i=0; i<phys->dof; i++) {
for (j=0; j<phys->dof; j++) {
if(cells[0]<user->cEndInterior) CellValues[cells[0]*dof*dof + i*dof + j] -= cells[0]*1.0;
if(cells[1]<user->cEndInterior) CellValues[cells[1]*dof*dof + i*dof + j] += cells[1]*1.2;
}
}
// ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
ierr = PetscFree(fluxcon);CHKERRQ(ierr);
ierr = PetscFree(fluxdiff);CHKERRQ(ierr);
ierr = PetscFree(uL);CHKERRQ(ierr);
ierr = PetscFree(uR);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locGradLimiter,&gradlimiter);CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGradLimiter);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/**
Caculate the flux using the Monotonic Upstream-Centered Scheme for Conservation Laws (van Leer, 1979)
*/
PetscErrorCode CaculateLocalFunction_LS(DM dm,DM dmFace,DM dmCell,PetscReal time,Vec locX,Vec F,User user)
{
DM dmGrad = user->dmGrad;
Model mod = user->model;
Physics phys = mod->physics;
const PetscInt dof = phys->dof;
PetscErrorCode ierr;
const PetscScalar *facegeom, *cellgeom, *x;
PetscScalar *f;
PetscInt fStart, fEnd, face, cStart, cell;
Vec locGrad, locGradLimiter, Grad;
/*
Here the localGradLimiter refers to the gradient that
has been multiplied by the limiter function.
The locGradLimiter is used to construct the uL and uR,
and the locGrad is used to caculate the diffusion term
*/
Vec TempVec; /*a temperal vec for the vector restore*/
PetscFunctionBeginUser;
ierr = DMGetGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecDuplicate(Grad, &TempVec);CHKERRQ(ierr);
ierr = VecCopy(Grad, TempVec);CHKERRQ(ierr);
/*
Backup the original vector and use it to restore the value of dmGrad,
because I do not want to change the values of the cell gradient.
*/
ierr = VecGetArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX,&x);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 0, &cStart, NULL);CHKERRQ(ierr);
{
PetscScalar *grad;
ierr = VecGetArray(Grad,&grad);CHKERRQ(ierr);
const PetscInt *faces;
PetscInt numFaces,f;
PetscReal *cellPhi; // Scalar limiter applied to each component separately
const PetscScalar *cx;
const CellGeom *cg;
PetscScalar *cgrad;
PetscInt i;
ierr = PetscMalloc(phys->dof*sizeof(PetscScalar),&cellPhi);CHKERRQ(ierr);
// Limit interior gradients. Using cell-based loop because it generalizes better to vector limiters.
for (cell=cStart; cell<user->cEndInterior; cell++) {
ierr = DMPlexGetConeSize(dm,cell,&numFaces);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(dmGrad,cell,grad,&cgrad);CHKERRQ(ierr);
if (!cgrad) continue; // ghost cell, we don't compute
// Limiter will be minimum value over all neighbors
for (i=0; i<dof; i++) cellPhi[i] = PETSC_MAX_REAL;
for (f=0; f<numFaces; f++) {
const PetscScalar *ncx;
const CellGeom *ncg;
const PetscInt *fcells;
PetscInt face = faces[f],ncell;
PetscScalar v[DIM];
PetscBool ghost;
ierr = IsExteriorGhostFace(dm,face,&ghost);CHKERRQ(ierr);
if (ghost) continue;
ierr = DMPlexGetSupport(dm,face,&fcells);CHKERRQ(ierr);
ncell = cell == fcells[0] ? fcells[1] : fcells[0];
// The expression (x ? y : z) has the value of y if x is nonzero, z otherwise
ierr = DMPlexPointLocalRead(dm,ncell,x,&ncx);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell,ncell,cellgeom,&ncg);CHKERRQ(ierr);
Waxpy2(-1, cg->centroid, ncg->centroid, v);
for (i=0; i<dof; i++) {
// We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005
PetscScalar phi,flim = 0.5 * (ncx[i] - cx[i]) / Dot2(&cgrad[i*DIM],v);
phi = (*user->Limit)(flim);
cellPhi[i] = PetscMin(cellPhi[i],phi);
}
}
// Apply limiter to gradient
for (i=0; i<dof; i++) Scale2(cellPhi[i],&cgrad[i*DIM],&cgrad[i*DIM]);
}
ierr = PetscFree(cellPhi);CHKERRQ(ierr);
ierr = VecRestoreArray(Grad,&grad);CHKERRQ(ierr);
}
ierr = DMGetLocalVector(dmGrad,&locGradLimiter);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmGrad,Grad,INSERT_VALUES,locGradLimiter);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmGrad,Grad,INSERT_VALUES,locGradLimiter);CHKERRQ(ierr);
ierr = VecCopy(TempVec, Grad);CHKERRQ(ierr);//Restore the vector
ierr = DMGetLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmGrad,Grad,INSERT_VALUES,locGrad);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dmGrad,&Grad);CHKERRQ(ierr);
ierr = VecDestroy(&TempVec);CHKERRQ(ierr);
{
const PetscScalar *grad, *gradlimiter;
const PetscInt *cells;
PetscInt ghost,i,j;
PetscScalar *fluxcon, *fluxdiff, *fx[2],*cf[2];
const FaceGeom *fg;
const CellGeom *cg[2];
const PetscScalar *cx[2],*cgrad[2], *cgradlimiter[2];
PetscScalar *uL, *uR;
PetscReal FaceArea;
ierr = VecGetArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = VecGetArrayRead(locGradLimiter,&gradlimiter);CHKERRQ(ierr);
ierr = VecGetArray(F,&f);CHKERRQ(ierr);
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &fluxcon);CHKERRQ(ierr); // For the convection terms
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &fluxdiff);CHKERRQ(ierr); // For the diffusion terms
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &uL);CHKERRQ(ierr);
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &uR);CHKERRQ(ierr);// Please do not put the Malloc function into a for loop!!!!
for (face=fStart; face<fEnd; face++) {
fx[0] = uL; fx[1] = uR;
ierr = DMPlexGetLabelValue(dm, "ghost", face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmFace,face,facegeom,&fg);CHKERRQ(ierr);
for (i=0; i<2; i++) {
PetscScalar dx[DIM];
ierr = DMPlexPointLocalRead(dmCell,cells[i],cellgeom,&cg[i]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dm,cells[i],x,&cx[i]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad,cells[i],gradlimiter,&cgradlimiter[i]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad,cells[i],grad,&cgrad[i]);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dm,cells[i],f,&cf[i]);CHKERRQ(ierr);
Waxpy2(-1,cg[i]->centroid,fg->centroid,dx);
for (j=0; j<dof; j++) {
fx[i][j] = cx[i][j] + Dot2(cgradlimiter[i],dx);
}
// fx[0] and fx[1] are the value of the variables on the left and right
// side of the face, respectively, that is u_L and u_R.
}
ierr = RiemannSolver_Rusanov(user, cgrad[0], cgrad[1], fg->centroid, cg[0]->centroid, cg[1]->centroid, fg->normal, fx[0], fx[1], fluxcon, fluxdiff);CHKERRQ(ierr);
ierr = DMPlexComputeCellGeometryFVM(dm, face, &FaceArea, NULL, NULL);CHKERRQ(ierr);
// Compute the face area
for (i=0; i<phys->dof; i++) {
if (cf[0]) cf[0][i] -= FaceArea*(fluxcon[i] + fluxdiff[i])/cg[0]->volume;
if (cf[1]) cf[1][i] += FaceArea*(fluxcon[i] + fluxdiff[i])/cg[1]->volume;
// The flux on the interface, for the cell[0], it is an outcome flux and for the cell[1], it is
// an income flux.
}
// ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
}
ierr = VecRestoreArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locGradLimiter,&gradlimiter);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);CHKERRQ(ierr);
ierr = PetscFree(fluxcon);CHKERRQ(ierr);
ierr = PetscFree(fluxdiff);CHKERRQ(ierr);
ierr = PetscFree(uL);CHKERRQ(ierr);
ierr = PetscFree(uR);CHKERRQ(ierr);
// VecView(F,PETSC_VIEWER_STDOUT_WORLD);
}
ierr = VecRestoreArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGradLimiter);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Use the first order upwind scheme to compute the flux
*/
PetscErrorCode CaculateLocalFunction_Upwind(DM dm,DM dmFace,DM dmCell,PetscReal time,Vec locX,Vec F,User user)
{
Physics phys = user->model->physics;
DM dmGrad = user->dmGrad;
PetscErrorCode ierr;
const PetscScalar *facegeom, *cellgeom, *x;
PetscScalar *f;
PetscInt fStart, fEnd, face;
Vec locGrad, Grad;
PetscFunctionBeginUser;
ierr = VecGetArrayRead(user->facegeom, &facegeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(user->cellgeom, &cellgeom);CHKERRQ(ierr);
ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr);
ierr = VecGetArray(F, &f);CHKERRQ(ierr);
ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr);
ierr = DMGetGlobalVector(dmGrad, &Grad);CHKERRQ(ierr);
ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dmGrad, Grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dmGrad, Grad, INSERT_VALUES, locGrad);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dmGrad, &Grad);CHKERRQ(ierr);
const PetscScalar *grad;
ierr = VecGetArrayRead(locGrad, &grad);CHKERRQ(ierr);
{
const PetscInt *cells;
PetscInt i,ghost;
PetscScalar *fluxcon, *fluxdiff, *fL,*fR;
const FaceGeom *fg;
const CellGeom *cgL,*cgR;
const PetscScalar *xL,*xR;
const PetscScalar *cgrad[2];
PetscReal FaceArea;
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &fluxcon);CHKERRQ(ierr); /*For the convection terms*/
ierr = PetscMalloc(phys->dof * sizeof(PetscScalar), &fluxdiff);CHKERRQ(ierr); /*For the diffusion terms*/
for (face = fStart; face < fEnd; ++face) {
ierr = DMPlexGetLabelValue(dm, "ghost", face, &ghost);CHKERRQ(ierr);
if (ghost >= 0) continue;
ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr);/*The support of a face is the cells (two cells)*/
ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr);/*Read the data from "facegeom" for the point "face"*/
ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr);
/*
PetscPrintf(PETSC_COMM_SELF, "face[%d]:(%f, %f, %f), cgL:(%f, %f, %f), cgR:(%f, %f, %f), fnorm:(%f, %f, %f)\n",
face, fg->centroid[0], fg->centroid[1], fg->centroid[2],
cgL->centroid[0], cgL->centroid[1], cgL->centroid[2], cgR->centroid[0], cgR->centroid[1], cgR->centroid[2],
fg->normal[0], fg->normal[1], fg->normal[2]);
*/
ierr = DMPlexPointLocalRead(dm, cells[0], x, &xL);CHKERRQ(ierr); /*For the unkown variables*/
ierr = DMPlexPointLocalRead(dm, cells[1], x, &xR);CHKERRQ(ierr);
ierr = DMPlexPointGlobalRef(dm, cells[0], f, &fL);CHKERRQ(ierr); /*For the functions*/
ierr = DMPlexPointGlobalRef(dm, cells[1], f, &fR);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad, cells[0], grad, &cgrad[0]);CHKERRQ(ierr);
ierr = DMPlexPointLocalRead(dmGrad, cells[1], grad, &cgrad[1]);CHKERRQ(ierr);
ierr = RiemannSolver_Rusanov(user, cgrad[0], cgrad[1], fg->centroid, cgL->centroid, cgR->centroid, fg->normal, xL, xR, fluxcon, fluxdiff);CHKERRQ(ierr);
/*Caculate the flux*/
ierr = DMPlexComputeCellGeometryFVM(dm, face, &FaceArea, NULL, NULL);CHKERRQ(ierr);
//PetscPrintf(PETSC_COMM_SELF, "FaceArea=%f, Volume=%f\n",FaceArea,cgL->volume);
/*Compute the face area*/
// FaceArea = 0.0;
for (i=0; i<phys->dof; i++) {
/*
PetscPrintf(PETSC_COMM_SELF, "face[%d]:(%f, %f, %f), GradL[%d] = (%f, %f, %f), GradR[%d] = (%f, %f, %f), fluxcon[%d] = %f\n",
face, fg->centroid[0], fg->centroid[1], fg->centroid[2],
i, cgrad[0][DIM*i], cgrad[0][DIM*i + 1], cgrad[0][DIM*i + 2],
i, cgrad[1][DIM*i], cgrad[1][DIM*i + 1], cgrad[1][DIM*i + 2], i, fluxcon[i]);
*/
if (fL) {
fL[i] -= FaceArea*(fluxcon[i] + fluxdiff[i])/cgL->volume;
// if (fL) PetscPrintf(PETSC_COMM_SELF, "x=%g, y=%g, z=%g,fluxcon[i]=%g, FaceArea=%g, volume=%g, fLc=%g, fL=%g\n",fg->centroid[0], fg->centroid[1], fg->centroid[2],fluxcon[i],FaceArea,cgL->volume,FaceArea*(fluxcon[i] + fluxdiff[i])/cgL->volume,fL[i]);
}
if (fR) fR[i] += FaceArea*(fluxcon[i] + fluxdiff[i])/cgR->volume;
}
}
ierr = PetscFree(fluxcon);CHKERRQ(ierr);
ierr = PetscFree(fluxdiff);CHKERRQ(ierr);
}
// VecView(F,PETSC_VIEWER_STDOUT_WORLD);
ierr = VecRestoreArrayRead(locGrad,&grad);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dmGrad,&locGrad);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->facegeom,&facegeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(user->cellgeom,&cellgeom);CHKERRQ(ierr);
ierr = VecRestoreArrayRead(locX,&x);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);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);
}