PetscErrorCode ComputeRHS(KSP ksp,Vec b,void *ctx)
{
PetscErrorCode ierr;
PetscInt mx;
PetscScalar h;
Vec x;
DM da;
PetscFunctionBeginUser;
ierr = KSPGetDM(ksp,&da);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&mx,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMGetApplicationContext(da,&x);CHKERRQ(ierr);
h = 2.0*PETSC_PI/((mx));
ierr = VecCopy(x,b);CHKERRQ(ierr);
ierr = VecScale(b,h);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
// assemble the right-hand side of the system for the Lagrangian forces
PetscErrorCode RigidKinematicsSolver::assembleRHSForces()
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscLogStagePush(stageRHSForces); CHKERRQ(ierr);
// rhsf = UB - E u^{**}
ierr = MatMult(E, solution->UGlobal, rhsf); CHKERRQ(ierr);
ierr = VecScale(rhsf, -1.0); CHKERRQ(ierr);
ierr = VecAYPX(rhsf, 1.0, UB); CHKERRQ(ierr);
ierr = PetscLogStagePop(); CHKERRQ(ierr);
PetscFunctionReturn(0);
} // assembleRHSForces
PetscErrorCode PCApply_Noise(PC pc,Vec xin,Vec xout)
{
PetscErrorCode ierr;
PCNoise_Ctx *ctx;
PetscReal nrmin, nrmnoise;
PetscFunctionBeginUser;
ierr = PCShellGetContext(pc,(void**)&ctx);CHKERRQ(ierr);
/* xout is ||xin|| * ctx->eta* f, where f is a pseudorandom unit vector
(Note that this should always be combined additively with another PC) */
ierr = VecSetRandom(xout,ctx->random);CHKERRQ(ierr);
ierr = VecNorm(xin,NORM_2,&nrmin);CHKERRQ(ierr);
ierr = VecNorm(xout,NORM_2,&nrmnoise);CHKERRQ(ierr);
ierr = VecScale(xout,ctx->eta*(nrmin/nrmnoise));CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatMult_SchurComplement(Mat N,Vec x,Vec y)
{
Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!Na->work1) {ierr = MatCreateVecs(Na->A,&Na->work1,NULL);CHKERRQ(ierr);}
if (!Na->work2) {ierr = MatCreateVecs(Na->A,&Na->work2,NULL);CHKERRQ(ierr);}
ierr = MatMult(Na->B,x,Na->work1);CHKERRQ(ierr);
ierr = KSPSolve(Na->ksp,Na->work1,Na->work2);CHKERRQ(ierr);
ierr = MatMult(Na->C,Na->work2,y);CHKERRQ(ierr);
ierr = VecScale(y,-1.0);CHKERRQ(ierr);
if (Na->D) {
ierr = MatMultAdd(Na->D,x,y,y);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode TronGradientProjections(Tao tao,TAO_TRON *tron)
{
PetscErrorCode ierr;
PetscInt i;
TaoLineSearchConvergedReason ls_reason;
PetscReal actred=-1.0,actred_max=0.0;
PetscReal f_new;
/*
The gradient and function value passed into and out of this
routine should be current and correct.
The free, active, and binding variables should be already identified
*/
PetscFunctionBegin;
if (tron->Free_Local) {
ierr = ISDestroy(&tron->Free_Local);CHKERRQ(ierr);
}
ierr = VecWhichBetween(tao->XL,tao->solution,tao->XU,&tron->Free_Local);CHKERRQ(ierr);
for (i=0;i<tron->maxgpits;i++){
if ( -actred <= (tron->pg_ftol)*actred_max) break;
tron->gp_iterates++; tron->total_gp_its++;
f_new=tron->f;
ierr = VecCopy(tao->gradient, tao->stepdirection);CHKERRQ(ierr);
ierr = VecScale(tao->stepdirection, -1.0);CHKERRQ(ierr);
ierr = TaoLineSearchSetInitialStepLength(tao->linesearch,tron->pgstepsize);CHKERRQ(ierr);
ierr = TaoLineSearchApply(tao->linesearch, tao->solution, &f_new, tao->gradient, tao->stepdirection,
&tron->pgstepsize, &ls_reason);CHKERRQ(ierr);
ierr = TaoAddLineSearchCounts(tao);CHKERRQ(ierr);
/* Update the iterate */
actred = f_new - tron->f;
actred_max = PetscMax(actred_max,-(f_new - tron->f));
tron->f = f_new;
if (tron->Free_Local) {
ierr = ISDestroy(&tron->Free_Local);CHKERRQ(ierr);
}
ierr = VecWhichBetween(tao->XL,tao->solution,tao->XU,&tron->Free_Local);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
void FractalProjector::
new_vertex(Vertex* vrt, Edge* parent)
{
// set the vertex to the center by calling the parents method
RefinementCallbackLinear<APosition>::new_vertex(vrt, parent);
// calculate the normal of the edge
vector3 n;
CalculateNormal(n, *m_pGrid, parent, m_aaPos);
// first scale it to the same length as the edge, then scale it with the
// given scaleFac
number len = VecDistance(m_aaPos[parent->vertex(0)], m_aaPos[parent->vertex(1)]);
VecScale (n, n, m_scaleFac * len);
// offset the vertex by the calculated normal
VecAdd(m_aaPos[vrt], m_aaPos[vrt], n);
}
PetscErrorCode MatGetDiagonal_Shell(Mat A,Vec v)
{
Mat_Shell *shell = (Mat_Shell*)A->data;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = (*shell->getdiagonal)(A,v);CHKERRQ(ierr);
ierr = VecScale(v,shell->vscale);CHKERRQ(ierr);
if (shell->dshift) {
ierr = VecPointwiseMult(v,v,shell->dshift);CHKERRQ(ierr);
} else {
ierr = VecShift(v,shell->vshift);CHKERRQ(ierr);
}
if (shell->left) {ierr = VecPointwiseMult(v,v,shell->left);CHKERRQ(ierr);}
if (shell->right) {ierr = VecPointwiseMult(v,v,shell->right);CHKERRQ(ierr);}
PetscFunctionReturn(0);
}
Mapping *
LinearMappingCreate(
Vector *center,
Vector *vaxis,
Vector *uaxis)
{
Mapping *res;
RSMatrix m;
Vector n;
res = (Mapping *)Malloc(sizeof(Mapping));
res->flags = OBJSPACE;
res->method= LinearMapping;
if (center)
res->center = *center;
else
res->center.x = res->center.y = res->center.z = 0.;
if (uaxis && vaxis) {
VecCross(uaxis, vaxis, &n);
/* this is wrong, since uaxis and vaxis
* give U and V in world space, and we
* need the inverse.
*/
ArbitraryMatrix(
uaxis->x, uaxis->y, uaxis->z,
vaxis->x, vaxis->y, vaxis->z,
n.x, n.y, n.z,
res->center.x, res->center.y, res->center.z,
&m);
MatrixInvert(&m, &res->m);
res->uaxis = *uaxis;
res->vaxis = *vaxis;
VecNormalize(&res->uaxis);
VecNormalize(&res->vaxis);
} else {
VecScale(-1., res->center, &n);
TranslationMatrix(n.x, n.y, n.z, &res->m);
res->uaxis.x = res->vaxis.y = 1.;
res->uaxis.y = res->uaxis.z = res->vaxis.x =
res->vaxis.z = 0.;
}
return res;
}
PetscErrorCode MatShift_Shell(Mat Y,PetscScalar a)
{
Mat_Shell *shell = (Mat_Shell*)Y->data;
PetscErrorCode ierr;
PetscFunctionBegin;
if (shell->left || shell->right || shell->dshift) {
if (!shell->dshift) {
if (!shell->dshift_owned) {ierr = VecDuplicate(shell->left ? shell->left : shell->right, &shell->dshift_owned);CHKERRQ(ierr);}
shell->dshift = shell->dshift_owned;
ierr = VecSet(shell->dshift,shell->vshift+a);CHKERRQ(ierr);
} else {ierr = VecScale(shell->dshift,a);CHKERRQ(ierr);}
if (shell->left) {ierr = VecPointwiseDivide(shell->dshift,shell->dshift,shell->left);CHKERRQ(ierr);}
if (shell->right) {ierr = VecPointwiseDivide(shell->dshift,shell->dshift,shell->right);CHKERRQ(ierr);}
} else shell->vshift += a;
ierr = MatShellUseScaledMethods(Y);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode MatMultTranspose_SubMatrix(Mat N,Vec x,Vec y)
{
Mat_SubMatrix *Na = (Mat_SubMatrix*)N->data;
Vec xx = 0;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PreScaleLeft(N,x,&xx);CHKERRQ(ierr);
ierr = VecZeroEntries(Na->lwork);CHKERRQ(ierr);
ierr = VecScatterBegin(Na->lrestrict,xx,Na->lwork,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd (Na->lrestrict,xx,Na->lwork,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = MatMultTranspose(Na->A,Na->lwork,Na->rwork);CHKERRQ(ierr);
ierr = VecScatterBegin(Na->rprolong,Na->rwork,y,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd (Na->rprolong,Na->rwork,y,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = PostScaleRight(N,y);CHKERRQ(ierr);
ierr = VecScale(y,Na->scale);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode GPCGGradProjections(Tao tao)
{
PetscErrorCode ierr;
TAO_GPCG *gpcg = (TAO_GPCG *)tao->data;
PetscInt i;
PetscReal actred=-1.0,actred_max=0.0, gAg,gtg=gpcg->gnorm,alpha;
PetscReal f_new,gdx,stepsize;
Vec DX=tao->stepdirection,XL=tao->XL,XU=tao->XU,Work=gpcg->Work;
Vec X=tao->solution,G=tao->gradient;
TaoLineSearchConvergedReason lsflag=TAOLINESEARCH_CONTINUE_ITERATING;
/*
The free, active, and binding variables should be already identified
*/
PetscFunctionBegin;
for (i=0;i<gpcg->maxgpits;i++){
if ( -actred <= (gpcg->pg_ftol)*actred_max) break;
ierr = VecBoundGradientProjection(G,X,XL,XU,DX);CHKERRQ(ierr);
ierr = VecScale(DX,-1.0);CHKERRQ(ierr);
ierr = VecDot(DX,G,&gdx);CHKERRQ(ierr);
ierr = MatMult(tao->hessian,DX,Work);CHKERRQ(ierr);
ierr = VecDot(DX,Work,&gAg);CHKERRQ(ierr);
gpcg->gp_iterates++;
gpcg->total_gp_its++;
gtg=-gdx;
alpha = PetscAbsReal(gtg/gAg);
ierr = TaoLineSearchSetInitialStepLength(tao->linesearch,alpha);CHKERRQ(ierr);
f_new=gpcg->f;
ierr = TaoLineSearchApply(tao->linesearch,X,&f_new,G,DX,&stepsize,&lsflag);CHKERRQ(ierr);
/* Update the iterate */
actred = f_new - gpcg->f;
actred_max = PetscMax(actred_max,-(f_new - gpcg->f));
gpcg->f = f_new;
ierr = ISDestroy(&gpcg->Free_Local);CHKERRQ(ierr);
ierr = VecWhichBetween(XL,X,XU,&gpcg->Free_Local);CHKERRQ(ierr);
}
gpcg->gnorm=gtg;
PetscFunctionReturn(0);
} /* End gradient projections */
PetscErrorCode Update_q(Vec q,Vec u,Mat M_0,AppCtx *user)
{
PetscErrorCode ierr;
PetscScalar *q_arr,*w_arr;
PetscInt i,n;
PetscFunctionBeginUser;
ierr = PetscLogEventBegin(event_update_q,0,0,0,0);CHKERRQ(ierr);
ierr = MatMult(M_0,u,user->work1);CHKERRQ(ierr);
ierr = VecScale(user->work1,-1.0);CHKERRQ(ierr);
ierr = VecGetLocalSize(u,&n);CHKERRQ(ierr);
ierr = VecGetArray(q,&q_arr);CHKERRQ(ierr);
ierr = VecGetArray(user->work1,&w_arr);CHKERRQ(ierr);
for (i=0; i<n; i++) q_arr[2*i]=q_arr[2*i+1] = w_arr[i];
ierr = VecRestoreArray(q,&q_arr);CHKERRQ(ierr);
ierr = VecRestoreArray(user->work1,&w_arr);CHKERRQ(ierr);
ierr = PetscLogEventEnd(event_update_q,0,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode VecScale_MultiVec(Vec x, PetscScalar alpha)
{
#if !defined(NDEBUG)
TBOX_ASSERT(x);
#endif
Vec_MultiVec* mx = static_cast<Vec_MultiVec*>(x->data);
#if !defined(NDEBUG)
TBOX_ASSERT(mx);
#endif
PetscErrorCode ierr;
for (PetscInt k = 0; k < mx->n; ++k)
{
ierr = VecScale(mx->array[k], alpha);
CHKERRQ(ierr);
}
ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(x));
CHKERRQ(ierr);
PetscFunctionReturn(0);
} // VecScale_MultiVec
static PetscErrorCode TaoBQNLSComputeStep(Tao tao, PetscBool shift, KSPConvergedReason *ksp_reason, PetscInt *step_type)
{
TAO_BNK *bnk = (TAO_BNK *)tao->data;
TAO_BQNK *bqnk = (TAO_BQNK*)bnk->ctx;
PetscErrorCode ierr;
PetscInt nupdates;
PetscFunctionBegin;
ierr = MatSolve(bqnk->B, tao->gradient, tao->stepdirection);CHKERRQ(ierr);
ierr = VecScale(tao->stepdirection, -1.0);CHKERRQ(ierr);
ierr = TaoBNKBoundStep(tao, bnk->as_type, tao->stepdirection);CHKERRQ(ierr);
*ksp_reason = KSP_CONVERGED_ATOL;
ierr = MatLMVMGetUpdateCount(bqnk->B, &nupdates);CHKERRQ(ierr);
if (nupdates == 0) {
*step_type = BNK_SCALED_GRADIENT;
} else {
*step_type = BNK_BFGS;
}
PetscFunctionReturn(0);
}
void ConvectionDiffusionFE<TDomain>::
lin_def_vector_source(const LocalVector& u,
std::vector<std::vector<MathVector<dim> > > vvvLinDef[],
const size_t nip)
{
// request geometry
const TFEGeom& geo = GeomProvider<TFEGeom>::get(m_lfeID, m_quadOrder);
// loop integration points
for(size_t ip = 0; ip < geo.num_ip(); ++ip)
{
// loop test spaces
for(size_t i = 0; i < geo.num_sh(); ++i)
{
// add to local defect
VecScale(vvvLinDef[ip][_C_][i], geo.global_grad(ip, i),
geo.weight(ip));
}
}
}
static PetscErrorCode PCBDDCApplyNullSpaceCorrectionPC(PC pc,Vec x,Vec y)
{
NullSpaceCorrection_ctx pc_ctx;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PCShellGetContext(pc,(void**)&pc_ctx);CHKERRQ(ierr);
/* E */
ierr = MatMultTranspose(pc_ctx->Lbasis_mat,x,pc_ctx->work_small_2);CHKERRQ(ierr);
ierr = MatMultAdd(pc_ctx->Kbasis_mat,pc_ctx->work_small_2,x,pc_ctx->work_full_1);CHKERRQ(ierr);
/* P^-1 */
ierr = PCApply(pc_ctx->local_pc,pc_ctx->work_full_1,pc_ctx->work_full_2);CHKERRQ(ierr);
/* E^T */
ierr = MatMultTranspose(pc_ctx->Kbasis_mat,pc_ctx->work_full_2,pc_ctx->work_small_1);CHKERRQ(ierr);
ierr = VecScale(pc_ctx->work_small_1,-1.0);CHKERRQ(ierr);
ierr = MatMultAdd(pc_ctx->Lbasis_mat,pc_ctx->work_small_1,pc_ctx->work_full_2,pc_ctx->work_full_1);CHKERRQ(ierr);
/* Sum contributions */
ierr = MatMultAdd(pc_ctx->basis_mat,pc_ctx->work_small_2,pc_ctx->work_full_1,y);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatGetDiagonal_Composite(Mat A,Vec v)
{
Mat_Composite *shell = (Mat_Composite*)A->data;
Mat_CompositeLink next = shell->head;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!next) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must provide at least one matrix with MatCompositeAddMat()");
if (shell->right || shell->left) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot get diagonal if left or right scaling");
ierr = MatGetDiagonal(next->mat,v);CHKERRQ(ierr);
if (next->next && !shell->work) {
ierr = VecDuplicate(v,&shell->work);CHKERRQ(ierr);
}
while ((next = next->next)) {
ierr = MatGetDiagonal(next->mat,shell->work);CHKERRQ(ierr);
ierr = VecAXPY(v,1.0,shell->work);CHKERRQ(ierr);
}
ierr = VecScale(v,shell->scale);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
typename ntree<tree_dim, world_dim, elem_t, common_data_t>::vector_t
ntree<tree_dim, world_dim, elem_t, common_data_t>::
calculate_center_of_mass(Node& node)
{
vector_t centerOfMass;
VecSet(centerOfMass, 0);
for(size_t entryInd = node.firstEntryInd; entryInd != s_invalidIndex;){
Entry& entry = m_entries[entryInd];
vector_t center;
traits::calculate_center(center, entry.elem, m_commonData);
VecAdd(centerOfMass, centerOfMass, center);
entryInd = entry.nextEntryInd;
}
if(node.numEntries > 0)
VecScale(centerOfMass, centerOfMass, (real_t)1 / (real_t)node.numEntries);
return centerOfMass;
}
PetscErrorCode DPsi(AppCtx *user)
{
PetscErrorCode ierr;
PetscScalar Evf=user->Evf,A=user->A,B=user->B,cv0=user->cv0;
PetscScalar *cv_p,*eta_p,*logcv_p,*logcv2_p,*DPsiv_p,*DPsieta_p;
PetscInt n,i;
PetscFunctionBeginUser;
ierr = VecGetLocalSize(user->cv,&n);
ierr = VecGetArray(user->cv,&cv_p);CHKERRQ(ierr);
ierr = VecGetArray(user->eta,&eta_p);CHKERRQ(ierr);
ierr = VecGetArray(user->logcv,&logcv_p);CHKERRQ(ierr);
ierr = VecGetArray(user->logcv2,&logcv2_p);CHKERRQ(ierr);
ierr = VecGetArray(user->DPsiv,&DPsiv_p);CHKERRQ(ierr);
ierr = VecGetArray(user->DPsieta,&DPsieta_p);CHKERRQ(ierr);
ierr = Llog(user->cv,user->logcv);CHKERRQ(ierr);
ierr = VecCopy(user->cv,user->work1);CHKERRQ(ierr);
ierr = VecScale(user->work1,-1.0);CHKERRQ(ierr);
ierr = VecShift(user->work1,1.0);CHKERRQ(ierr);
ierr = Llog(user->work1,user->logcv2);CHKERRQ(ierr);
for (i=0; i<n; i++)
{
DPsiv_p[i] = (eta_p[i]-1.0)*(eta_p[i]-1.0)*(eta_p[i]+1.0)*(eta_p[i]+1.0)*(Evf + logcv_p[i] - logcv2_p[i]) - 2.0*A*(cv_p[i] - cv0)*eta_p[i]*(eta_p[i]+2.0)*(eta_p[i]-1.0)*(eta_p[i]-1.0) + 2.0*B*(cv_p[i] - 1.0)*eta_p[i]*eta_p[i];
DPsieta_p[i] = 4.0*eta_p[i]*(eta_p[i]-1.0)*(eta_p[i]+1.0)*(Evf*cv_p[i] + cv_p[i]*logcv_p[i] + (1.0-cv_p[i])*logcv2_p[i]) - A*(cv_p[i] - cv0)*(cv_p[i] - cv0)*(4.0*eta_p[i]*eta_p[i]*eta_p[i] - 6.0*eta_p[i] + 2.0) + 2.0*B*(cv_p[i]-1.0)*(cv_p[i]-1.0)*eta_p[i];
}
ierr = VecRestoreArray(user->cv,&cv_p);CHKERRQ(ierr);
ierr = VecRestoreArray(user->eta,&eta_p);CHKERRQ(ierr);
ierr = VecGetArray(user->logcv,&logcv_p);CHKERRQ(ierr);
ierr = VecGetArray(user->logcv2,&logcv2_p);CHKERRQ(ierr);
ierr = VecRestoreArray(user->DPsiv,&DPsiv_p);CHKERRQ(ierr);
ierr = VecRestoreArray(user->DPsieta,&DPsieta_p);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode StokesCalcResidual(Stokes* s) {
PetscReal val;
Vec b0, b1;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* residual Ax-b (*warning* overwrites b) */
ierr = VecScale(s->b, -1.0);
CHKERRQ(ierr);
ierr = MatMultAdd(s->A, s->x, s->b, s->b);
CHKERRQ(ierr);
/* ierr = VecView(s->b, (PetscViewer)PETSC_VIEWER_DEFAULT);CHKERRQ(ierr); */
/* residual velocity */
ierr = VecGetSubVector(s->b, s->isg[0], &b0);
CHKERRQ(ierr);
ierr = VecNorm(b0, NORM_2, &val);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, " residual u = %g\n", (double)val);
CHKERRQ(ierr);
ierr = VecRestoreSubVector(s->b, s->isg[0], &b0);
CHKERRQ(ierr);
/* residual pressure */
ierr = VecGetSubVector(s->b, s->isg[1], &b1);
CHKERRQ(ierr);
ierr = VecNorm(b1, NORM_2, &val);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, " residual p = %g\n", (double)val);
CHKERRQ(ierr);
ierr = VecRestoreSubVector(s->b, s->isg[1], &b1);
CHKERRQ(ierr);
/* total residual */
ierr = VecNorm(s->b, NORM_2, &val);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, " residual [u,p] = %g\n", (double)val);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
// Matrix and Residual Fills
bool FiniteDifference::evaluate(FillType f,
const Vec* soln,
Vec* tmp_rhs,
Mat* tmp_matrix)
{
flag = f;
int ierr = 0;
// Set the incoming linear objects
if (flag == RHS_ONLY) {
rhs = tmp_rhs;
}
else if (flag == MATRIX_ONLY) {
A = tmp_matrix;
}
else if (flag == ALL) {
rhs = tmp_rhs;
A = tmp_matrix;
}
else {
std::cout << "ERROR: FiniteDifference::fillMatrix() - No such flag as "
<< flag << std::endl;
throw;
}
// Begin RHS fill
if((flag == RHS_ONLY) || (flag == ALL)) {
ierr = FormFunction(*snes, *soln, *rhs, ctx);CHKERRQ(ierr);
PetscScalar minusOne = 1.0;
ierr = VecScale( *rhs, minusOne );CHKERRQ(ierr);
}
// Begin Jacobian fill
if((flag == MATRIX_ONLY) || (flag == ALL)) {
ierr = FormJacobian(*snes, *soln, A, A, &matStruct, ctx);CHKERRQ(ierr);
}
return true;
}
PetscErrorCode MatMultAdd_SchurComplement(Mat N,Vec x,Vec y,Vec z)
{
Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!Na->work1) {ierr = MatGetVecs(Na->A,&Na->work1,PETSC_NULL);CHKERRQ(ierr);}
if (!Na->work2) {ierr = MatGetVecs(Na->A,&Na->work2,PETSC_NULL);CHKERRQ(ierr);}
ierr = MatMult(Na->B,x,Na->work1);CHKERRQ(ierr);
ierr = KSPSolve(Na->ksp,Na->work1,Na->work2);CHKERRQ(ierr);
if (y == z) {
ierr = VecScale(Na->work2,-1.0);CHKERRQ(ierr);
ierr = MatMultAdd(Na->C,Na->work2,z,z);CHKERRQ(ierr);
} else {
ierr = MatMult(Na->C,Na->work2,z);CHKERRQ(ierr);
ierr = VecAYPX(z,-1.0,y);CHKERRQ(ierr);
}
if (Na->D) {
ierr = MatMultAdd(Na->D,x,z,z);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode SNESTSFormFunction_Alpha(SNES snes,Vec x,Vec y,TS ts)
{
TS_Alpha *th = (TS_Alpha*)ts->data;
Vec X0 = th->X0, V0 = th->V0;
Vec X1 = x, V1 = th->V1, R = y;
PetscErrorCode ierr;
PetscFunctionBegin;
/* V1 = (1-1/Gamma)*V0 + 1/(Gamma*dT)*(X1-X0) */
ierr = VecWAXPY(V1,-1,X0,X1);CHKERRQ(ierr);
ierr = VecAXPBY(V1,1-1/th->Gamma,1/(th->Gamma*ts->time_step),V0);CHKERRQ(ierr);
/* Xa = X0 + Alpha_f*(X1-X0) */
ierr = VecWAXPY(th->Xa,-1,X0,X1);CHKERRQ(ierr);
ierr = VecAYPX(th->Xa,th->Alpha_f,X0);CHKERRQ(ierr);
/* Va = V0 + Alpha_m*(V1-V0) */
ierr = VecWAXPY(th->Va,-1,V0,V1);CHKERRQ(ierr);
ierr = VecAYPX(th->Va,th->Alpha_m,V0);CHKERRQ(ierr);
/* F = Function(ta,Xa,Va) */
ierr = TSComputeIFunction(ts,th->stage_time,th->Xa,th->Va,R,PETSC_FALSE);CHKERRQ(ierr);
ierr = VecScale(R,1/th->Alpha_f);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
// Monitor a sub-region of the full-domain PETSc Vec object.
PetscErrorCode ProbeVolume::monitorVec(const DM &da,
const Vec &fvec,
const PetscInt &n,
const PetscReal &t)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
// grab the part of the vector that corresponds to the sub-volume
Vec svec;
ierr = VecGetSubVector(fvec, is, &svec); CHKERRQ(ierr);
if (n_sum != 0) // we accumulate the data over the time-steps
{
if (dvec == PETSC_NULL)
{
ierr = VecDuplicate(svec, &dvec); CHKERRQ(ierr);
ierr = VecSet(dvec, 0.0); CHKERRQ(ierr);
}
ierr = VecAXPY(dvec, 1.0, svec); CHKERRQ(ierr);
count++;
if (count % n_sum == 0) // output the time-averaged data
{
ierr = VecScale(dvec, 1.0 / count); CHKERRQ(ierr);
ierr = writeVec(dvec, t); CHKERRQ(ierr);
// reset for the next accumulation cycle
ierr = VecSet(dvec, 0.0); CHKERRQ(ierr);
count = 0;
}
}
else // output the time-step sub-volume data to file
{
ierr = writeVec(svec, t); CHKERRQ(ierr);
}
ierr = VecRestoreSubVector(fvec, is, &svec); CHKERRQ(ierr);
PetscFunctionReturn(0);
} // ProbeVolume::monitorVec
PetscErrorCode MatMult_Advection(Mat A,Vec x,Vec y)
{
AppCtx *appctx;
PetscErrorCode ierr;
PetscReal **temp;
PetscInt j,xs,xn;
Vec xlocal,ylocal;
const PetscScalar *xl;
PetscScalar *yl;
PetscBLASInt _One = 1,n;
PetscScalar _DOne = 1;
ierr = MatShellGetContext(A,&appctx);CHKERRQ(ierr);
ierr = DMGetLocalVector(appctx->da,&xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(appctx->da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(appctx->da,x,INSERT_VALUES,xlocal);CHKERRQ(ierr);
ierr = DMGetLocalVector(appctx->da,&ylocal);CHKERRQ(ierr);
ierr = VecSet(ylocal,0.0);CHKERRQ(ierr);
ierr = PetscGLLElementAdvectionCreate(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(appctx->da,xlocal,(void*)&xl);CHKERRQ(ierr);
ierr = DMDAVecGetArray(appctx->da,ylocal,&yl);CHKERRQ(ierr);
ierr = DMDAGetCorners(appctx->da,&xs,NULL,NULL,&xn,NULL,NULL);CHKERRQ(ierr);
ierr = PetscBLASIntCast(appctx->param.N,&n);CHKERRQ(ierr);
for (j=xs; j<xs+xn; j += appctx->param.N-1) {
PetscStackCallBLAS("BLASgemv",BLASgemv_("N",&n,&n,&_DOne,&temp[0][0],&n,&xl[j],&_One,&_DOne,&yl[j],&_One));
}
ierr = DMDAVecRestoreArrayRead(appctx->da,xlocal,(void*)&xl);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(appctx->da,ylocal,&yl);CHKERRQ(ierr);
ierr = PetscGLLElementAdvectionDestroy(&appctx->SEMop.gll,&temp);CHKERRQ(ierr);
ierr = VecSet(y,0.0);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(appctx->da,ylocal,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(appctx->da,ylocal,ADD_VALUES,y);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(appctx->da,&xlocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(appctx->da,&ylocal);CHKERRQ(ierr);
ierr = VecPointwiseDivide(y,y,appctx->SEMop.mass);CHKERRQ(ierr);
ierr = VecScale(y,-1.0);CHKERRQ(ierr);
return 0;
}
/*@
EPSGetEigenvector - Gets the i-th right eigenvector as computed by EPSSolve().
Logically Collective on EPS
Input Parameters:
+ eps - eigensolver context
- i - index of the solution
Output Parameters:
+ Vr - real part of eigenvector
- Vi - imaginary part of eigenvector
Notes:
If the corresponding eigenvalue is real, then Vi is set to zero. If PETSc is
configured with complex scalars the eigenvector is stored
directly in Vr (Vi is set to zero).
The index i should be a value between 0 and nconv-1 (see EPSGetConverged()).
Eigenpairs are indexed according to the ordering criterion established
with EPSSetWhichEigenpairs().
The 2-norm of the eigenvector is one unless the problem is generalized
Hermitian. In this case the eigenvector is normalized with respect to the
norm defined by the B matrix.
Level: beginner
.seealso: EPSSolve(), EPSGetConverged(), EPSSetWhichEigenpairs(), EPSGetEigenpair()
@*/
PetscErrorCode EPSGetEigenvector(EPS eps,PetscInt i,Vec Vr,Vec Vi)
{
PetscErrorCode ierr;
PetscInt k;
PetscFunctionBegin;
PetscValidHeaderSpecific(eps,EPS_CLASSID,1);
PetscValidLogicalCollectiveInt(eps,i,2);
PetscValidHeaderSpecific(Vr,VEC_CLASSID,3);
PetscCheckSameComm(eps,1,Vr,3);
if (Vi) { PetscValidHeaderSpecific(Vi,VEC_CLASSID,4); PetscCheckSameComm(eps,1,Vi,4); }
EPSCheckSolved(eps,1);
if (i<0 || i>=eps->nconv) SETERRQ(PetscObjectComm((PetscObject)eps),PETSC_ERR_ARG_OUTOFRANGE,"Argument 2 out of range");
ierr = EPSComputeVectors(eps);CHKERRQ(ierr);
if (!eps->perm) k = i;
else k = eps->perm[i];
#if defined(PETSC_USE_COMPLEX)
ierr = BVCopyVec(eps->V,k,Vr);CHKERRQ(ierr);
if (Vi) { ierr = VecSet(Vi,0.0);CHKERRQ(ierr); }
#else
if (eps->eigi[k] > 0) { /* first value of conjugate pair */
ierr = BVCopyVec(eps->V,k,Vr);CHKERRQ(ierr);
if (Vi) {
ierr = BVCopyVec(eps->V,k+1,Vi);CHKERRQ(ierr);
}
} else if (eps->eigi[k] < 0) { /* second value of conjugate pair */
ierr = BVCopyVec(eps->V,k-1,Vr);CHKERRQ(ierr);
if (Vi) {
ierr = BVCopyVec(eps->V,k,Vi);CHKERRQ(ierr);
ierr = VecScale(Vi,-1.0);CHKERRQ(ierr);
}
} else { /* real eigenvalue */
ierr = BVCopyVec(eps->V,k,Vr);CHKERRQ(ierr);
if (Vi) { ierr = VecSet(Vi,0.0);CHKERRQ(ierr); }
}
#endif
PetscFunctionReturn(0);
}
PetscErrorCode H2PlusMatMultH(Mat H, Vec x, Vec y) {
PetscErrorCode ierr;
OceH2plus ctx;
ierr = MatShellGetContext(H, &ctx); CHKERRQ(ierr);
ierr = MatMatDecomposedMult(ctx->d2_r1, ctx->s_y1, x, y); CHKERRQ(ierr);
ierr = VecScale(y, -0.5); CHKERRQ(ierr);
Vec a; VecDuplicate(x, &a);
ierr = MatMatDecomposedMult(ctx->r2inv_r1, ctx->lambda_y1, x, a); CHKERRQ(ierr);
ierr = VecAXPY(y, 0.5, a); CHKERRQ(ierr);
ierr = VecDestroy(&a); CHKERRQ(ierr);
for(int i = 0; i < ctx->nq; i++) {
Vec b; VecDuplicate(x, &b);
ierr = MatMatDecomposedMult(ctx->ne_r1[i], ctx->pq_y1[i], x, b); CHKERRQ(ierr);
ierr = VecAXPY(y, -1.0, b);
ierr = VecDestroy(&a); CHKERRQ(ierr);
}
return 0;
}
virtual PetscErrorCode setup_RHS() override
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
ctx->compute_rhs = true;
ctx->compute_singularity = true;
ierr = MatMult(A, sol, rhs);CHKERRQ(ierr);
ierr = VecScale(rhs, -1.);CHKERRQ(ierr);
// dton_.ctx->compute_rhs = true;
// dton_.ctx->add_rigid_motion = false;
// dton_.ctx->compute_singularity = true;
// ierr = dton_.solve_last_problem();CHKERRQ(ierr);
// // save Stokes sol
// ierr = VecCopy(dton_.problem_.sol, stokes_sol_save);CHKERRQ(ierr);
// ierr = cafes::io::save_VTK("Resultats", "stokes_sol_rhs", dton_.problem_.sol, dton_.problem_.ctx->dm, dton_.problem_.ctx->h);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatMultHermitian_Normal(Mat N,Vec x,Vec y)
{
Mat_Normal *Na = (Mat_Normal*)N->data;
PetscErrorCode ierr;
Vec in;
PetscFunctionBegin;
in = x;
if (Na->right) {
if (!Na->rightwork) {
ierr = VecDuplicate(Na->right,&Na->rightwork);CHKERRQ(ierr);
}
ierr = VecPointwiseMult(Na->rightwork,Na->right,in);CHKERRQ(ierr);
in = Na->rightwork;
}
ierr = MatMult(Na->A,in,Na->w);CHKERRQ(ierr);
ierr = MatMultHermitianTranspose(Na->A,Na->w,y);CHKERRQ(ierr);
if (Na->left) {
ierr = VecPointwiseMult(y,Na->left,y);CHKERRQ(ierr);
}
ierr = VecScale(y,Na->scale);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode cHamiltonianMatrix::KernalPolynomialMethod(){
int cutoff0 = int(1.5*a_scaling*tmax);
if (rank==0) cout << "cutoff is chosen as " << cutoff0 << endl;
ierr = VecDuplicate(X1,&X3);CHKERRQ(ierr);
ierr = VecDuplicateVecs(X1,Nt,&WFt);CHKERRQ(ierr);
for(int i = 0; i<Nt; ++i) {ierr = VecZeroEntries(WFt[i]);CHKERRQ(ierr);}
/* //view matrix or vector
PetscViewer viewer;
PetscViewerASCIIOpen(PETSC_COMM_WORLD, NULL, &viewer);
PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_DENSE);
*/
ierr = VecCopy(X1,X3);CHKERRQ(ierr); // TODO: avoid the copy for efficiency.
WaveFunctionUpdate(0);
//if (rank==0) cout<< "iter_k="<< 1 <<": X3=" << endl;
//VecView(X3,viewer);
ierr = MatMult(Hpolaron,X1,X2);CHKERRQ(ierr);
ierr = VecCopy(X2,X3);CHKERRQ(ierr); // TODO: avoid the copy for efficiency.
WaveFunctionUpdate(1);
//if (rank==0) cout<< "iter_k="<< 2 <<": X3=" << endl;
//VecView(X3,viewer);
for (int iter_k = 2; iter_k <= cutoff0; ++iter_k) {
ierr = MatMult(Hpolaron,X2,X3);CHKERRQ(ierr);
ierr = VecScale(X3,2.0);CHKERRQ(ierr);
ierr = VecAXPY(X3,-1.0,X1);CHKERRQ(ierr);
WaveFunctionUpdate(iter_k);
/* if (iter_k==1000) {
if (rank==0) cout<< "iter_k="<< iter_k+1 <<": X3=" << endl;
VecView(X3,viewer);
}*/
ierr = VecCopy(X2,X1);CHKERRQ(ierr);
ierr = VecCopy(X3,X2);CHKERRQ(ierr);
if(iter_k%int(cutoff0*0.1)==0) if (rank==0) cout << iter_k << "th iteration within total of " << cutoff0 << " cutoff has finished." << endl;
}
/*PetscViewerDestroy(&viewer);*/
return ierr;
}
