/*
* This function allocates data for the Newton basis GMRES implementation.
* Note that most data are allocated in KSPSetUp_DGMRES and KSPSetUp_GMRES, including the space for the basis vectors, the various Hessenberg matrices and the Givens rotations coefficients
*
*/
static PetscErrorCode KSPSetUp_AGMRES(KSP ksp)
{
PetscErrorCode ierr;
PetscInt hes;
PetscInt nloc;
KSP_AGMRES *agmres = (KSP_AGMRES*)ksp->data;
PetscInt neig = agmres->neig;
const PetscInt max_k = agmres->max_k;
PetscInt N = MAXKSPSIZE;
PetscInt lwork = PetscMax(8 * N + 16, 4 * neig * (N - neig));
PetscFunctionBegin;
if (ksp->pc_side == PC_SYMMETRIC) SETERRQ(PetscObjectComm((PetscObject)ksp),PETSC_ERR_SUP,"no symmetric preconditioning for KSPAGMRES");
N = MAXKSPSIZE;
/* Preallocate space during the call to KSPSetup_GMRES for the Krylov basis */
agmres->q_preallocate = PETSC_TRUE; /* No allocation on the fly */
/* Preallocate space to compute later the eigenvalues in GMRES */
ksp->calc_sings = PETSC_TRUE;
agmres->max_k = N; /* Set the augmented size to be allocated in KSPSetup_GMRES */
ierr = KSPSetUp_DGMRES(ksp);CHKERRQ(ierr);
agmres->max_k = max_k;
hes = (N + 1) * (N + 1);
/* Data for the Newton basis GMRES */
ierr = PetscCalloc4(max_k,&agmres->Rshift,max_k,&agmres->Ishift,hes,&agmres->Rloc,((N+1)*4),&agmres->wbufptr);CHKERRQ(ierr);
ierr = PetscMalloc7((N+1),&agmres->Scale,(N+1),&agmres->sgn,(N+1),&agmres->tloc,(N+1),&agmres->temp,(N+1),&agmres->tau,lwork,&agmres->work,(N+1),&agmres->nrs);CHKERRQ(ierr);
ierr = PetscMemzero(agmres->Scale, (N+1)*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = PetscMemzero(agmres->sgn, (N+1)*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = PetscMemzero(agmres->tloc, (N+1)*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = PetscMemzero(agmres->temp, (N+1)*sizeof(PetscScalar));CHKERRQ(ierr);
/* Allocate space for the vectors in the orthogonalized basis*/
ierr = VecGetLocalSize(agmres->vecs[0], &nloc);CHKERRQ(ierr);
ierr = PetscMalloc1(nloc*(N+1), &agmres->Qloc);CHKERRQ(ierr);
/* Init the ring of processors for the roddec orthogonalization */
ierr = KSPAGMRESRoddecInitNeighboor(ksp);CHKERRQ(ierr);
if (agmres->neig < 1) PetscFunctionReturn(0);
/* Allocate space for the deflation */
ierr = PetscMalloc1(N, &agmres->select);CHKERRQ(ierr);
ierr = VecDuplicateVecs(VEC_V(0), N, &agmres->TmpU);CHKERRQ(ierr);
ierr = PetscMalloc2(N*N, &agmres->MatEigL, N*N, &agmres->MatEigR);CHKERRQ(ierr);
/* ierr = PetscMalloc6(N*N, &agmres->Q, N*N, &agmres->Z, N, &agmres->wr, N, &agmres->wi, N, &agmres->beta, N, &agmres->modul);CHKERRQ(ierr); */
ierr = PetscMalloc3(N*N, &agmres->Q, N*N, &agmres->Z, N, &agmres->beta);CHKERRQ(ierr);
ierr = PetscMalloc2((N+1),&agmres->perm,(2*neig*N),&agmres->iwork);CHKERRQ(ierr);
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);
}
