void
PenaltyIBMethod::postprocessIntegrateData(double current_time, double new_time, int num_cycles)
{
IBMethod::postprocessIntegrateData(current_time, new_time, num_cycles);
const int coarsest_ln = 0;
const int finest_ln = d_hierarchy->getFinestLevelNumber();
// Reset time-dependent Lagrangian data.
for (int ln = coarsest_ln; ln <= finest_ln; ++ln)
{
if (!d_l_data_manager->levelContainsLagrangianData(ln)) continue;
int ierr;
ierr = VecSwap(d_Y_current_data[ln]->getVec(), d_Y_new_data[ln]->getVec());
IBTK_CHKERRQ(ierr);
ierr = VecSwap(d_V_current_data[ln]->getVec(), d_V_new_data[ln]->getVec());
IBTK_CHKERRQ(ierr);
}
// Deallocate Lagrangian scratch data.
d_K_data.clear();
d_M_data.clear();
d_Y_current_data.clear();
d_Y_new_data.clear();
d_V_current_data.clear();
d_V_new_data.clear();
return;
} // postprocessIntegrateData
PetscErrorCode VecSwap_MultiVec(Vec x, Vec y)
{
#if !defined(NDEBUG)
TBOX_ASSERT(x);
TBOX_ASSERT(y);
#endif
Vec_MultiVec* mx = static_cast<Vec_MultiVec*>(x->data);
Vec_MultiVec* my = static_cast<Vec_MultiVec*>(y->data);
#if !defined(NDEBUG)
TBOX_ASSERT(mx);
TBOX_ASSERT(my);
TBOX_ASSERT(mx->n == my->n);
#endif
PetscErrorCode ierr;
for (PetscInt k = 0; k < mx->n; ++k)
{
ierr = VecSwap(mx->array[k], my->array[k]);
CHKERRQ(ierr);
}
ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(x));
CHKERRQ(ierr);
ierr = PetscObjectStateIncrease(reinterpret_cast<PetscObject>(y));
CHKERRQ(ierr);
PetscFunctionReturn(0);
} // VecSwap_MultiVec
static PetscErrorCode VecSwap_Nest(Vec x,Vec y)
{
Vec_Nest *bx = (Vec_Nest*)x->data;
Vec_Nest *by = (Vec_Nest*)y->data;
PetscInt i,nr;
PetscErrorCode ierr;
PetscFunctionBegin;
VecNestCheckCompatible2(x,1,y,2);
nr = bx->nb;
for (i=0; i<nr; i++) {
ierr = VecSwap(bx->v[i],by->v[i]);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
void
IBSimpleHierarchyIntegrator::postprocessIntegrateHierarchy(const double current_time,
const double new_time,
const bool skip_synchronize_new_state_data,
const int num_cycles)
{
IBHierarchyIntegrator::postprocessIntegrateHierarchy(
current_time, new_time, skip_synchronize_new_state_data, num_cycles);
const int coarsest_level_num = 0;
const int finest_level_num = d_hierarchy->getFinestLevelNumber();
PetscErrorCode ierr;
// Deallocate Eulerian scratch data.
for (int level_num = coarsest_level_num; level_num <= finest_level_num; ++level_num)
{
Pointer<PatchLevel<NDIM> > level = d_hierarchy->getPatchLevel(level_num);
level->deallocatePatchData(d_u_idx);
level->deallocatePatchData(d_f_idx);
level->deallocatePatchData(d_scratch_data);
level->deallocatePatchData(d_new_data);
}
// Deallocate the fluid solver.
const int ins_num_cycles = d_ins_hier_integrator->getNumberOfCycles();
d_ins_hier_integrator->postprocessIntegrateHierarchy(
current_time, new_time, skip_synchronize_new_state_data, ins_num_cycles);
// Reset and deallocate IB data.
//
// NOTE: We assume here that all IB data are assigned to the finest level of
// the AMR patch hierarchy.
ierr = VecSwap(d_X_current_data->getVec(), d_X_new_data->getVec());
IBTK_CHKERRQ(ierr);
d_X_current_data = NULL;
d_X_new_data = NULL;
d_U_data = NULL;
d_F_data = NULL;
return;
} // postprocessIntegrateHierarchy
/*
* depth: the current depth of how much is sorted.
* bound: how far to sort.
*/
void MediankeyBoundedQuicksort(unsigned char text[], UInt index[], UInt length,
UInt low, UInt high, int depth, int bound, UInt maxChar, UInt *freq) {
if (high - low <= 1)
return;
if (depth > bound)
return;
bool deleteFreq = false;
if (freq == NULL) {
UInt ci;
maxChar = 0;
for (ci = low; ci < high; ci++) {
UInt c = text[index[ci]+depth];
if ( c > maxChar) {
maxChar = c;
}
}
freq = ProtectedNew<UInt>(maxChar+1);
deleteFreq = true;
}
Nucleotide medianChar = ComputeMedianValue(text, index, length, low, high, depth, maxChar, freq );
UInt medianCharPos = FindFirstOf(text, index, low, high, depth, medianChar);
UInt medLeft, lastLeft;
UInt medRight, lastRight;
//
// Pack the median characters into the sides of the array.
//
SwapIndices(index[low], index[medianCharPos]);
medLeft = lastLeft = low+1;
medRight = lastRight = high-1;
for(;;) {
Nucleotide nuc;
while(lastLeft <= lastRight and (nuc = text[index[lastLeft]+depth]) <= medianChar) {
if (nuc == medianChar) {
SwapIndices(index[medLeft], index[lastLeft]);
medLeft++;
}
lastLeft++;
}
while(lastLeft <= lastRight and (nuc = text[index[lastRight]+depth]) >= medianChar) {
if (nuc == medianChar) {
SwapIndices(index[medRight], index[lastRight]);
medRight--;
}
lastRight--;
}
if (lastLeft > lastRight) {
// done with median sort.
break;
}
//
// Otherwise, this ends with an index at the left out of order
// from the right
assert(text[index[lastLeft]+depth] > text[index[lastRight]+depth]);
SwapIndices(index[lastLeft], index[lastRight]);
}
//
// Now join the indices of the median charactes in the middle of the
// array.
//
// move left outside to middle
UInt swapLeftLength = std::min(medLeft - low, lastLeft - medLeft);
VecSwap(low, lastLeft - swapLeftLength, swapLeftLength, index);
// move right outside to middle
UInt swapRightLength = std::min(high - medRight - 1, medRight - lastRight);
VecSwap(lastRight+1, high-swapRightLength, swapRightLength, index);
UInt medianStartIndex = low + lastLeft - medLeft;
UInt medianEndIndex = lastRight + (high - medRight);
// Sort the suffices with keys lower than the median.
// Since these may contain multiple keys that are less than the
// median, the same depth is used.
MediankeyBoundedQuicksort(text, index, length,
low,
medianStartIndex,
depth, bound, maxChar,freq);
if (medianEndIndex - medianStartIndex > 1) {
MediankeyBoundedQuicksort(text, index, length,
medianStartIndex, medianEndIndex, depth+1, bound, maxChar, freq);
}
MediankeyBoundedQuicksort(text, index, length,
medianEndIndex,
high,
depth, bound, maxChar, freq);
if (deleteFreq) {delete [] freq; freq = NULL;}
}
int main(int argc,char **argv)
{
Vec V,W;
MPI_Comm comm;
PetscScalar one=1,e=2.7181;
PetscReal nrm1,nrm2,nrm3,nrm4;
PetscInt ione=1;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
comm = MPI_COMM_SELF;
ierr = VecCreateSeq(comm,10,&V);CHKERRQ(ierr);
ierr = VecSetRandom(V,NULL);CHKERRQ(ierr);
ierr = VecAssemblyBegin(V);CHKERRQ(ierr);
ierr = VecAssemblyEnd(V);CHKERRQ(ierr);
/*
* Initial
*/
/* display norm 1 & 2 */
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Original: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/* display cached norm 1 & 2 */
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"cached: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/*
* Alter an element
*/
ierr = VecSetValues(V,1,&ione,&one,INSERT_VALUES);CHKERRQ(ierr);
/* display norm 1 & 2 */
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Altered: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/* display cached norm 1 & 2 */
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"recomputed: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/*
* Scale the vector a little
*/
ierr = VecScale(V,e);CHKERRQ(ierr);
/* display updated cached norm 1 & 2 */
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Scale: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/* display forced norm 1 & 2 */
ierr = PetscObjectStateIncrease((PetscObject)V);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"recompute: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/*
* Normalize the vector a little
*/
ierr = VecNormalize(V,&nrm1);CHKERRQ(ierr);
/* display updated cached norm 1 & 2 */
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Normalize: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/* display forced norm 1 & 2 */
ierr = PetscObjectStateIncrease((PetscObject)V);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"recompute: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/*
* Copy to another vector
*/
ierr = VecDuplicate(V,&W);CHKERRQ(ierr);
ierr = VecCopy(V,W);CHKERRQ(ierr);
/* display norm 1 & 2 */
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Original: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/* display cached norm 1 & 2 */
ierr = VecNorm(W,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(W,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"copied: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/*
* Copy while data is invalid
*/
ierr = VecSetValues(V,1,&ione,&one,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecCopy(V,W);CHKERRQ(ierr);
/* display norm 1 & 2 */
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Invalidated: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/* display norm 1 & 2 */
ierr = VecNorm(W,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(W,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"copied: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/*
* Constant vector
*/
ierr = VecSet(V,e);CHKERRQ(ierr);
/* display updated cached norm 1 & 2 */
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Constant: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/* display forced norm 1 & 2 */
ierr = PetscObjectStateIncrease((PetscObject)V);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_2,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"recomputed: norm1=%e,norm2=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/*
* Swap vectors
*/
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(W,NORM_1,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Orig: norm_V=%e,norm_W=%e\n",(double)nrm1,(double)nrm2);CHKERRQ(ierr);
/* store inf norm */
ierr = VecNorm(V,NORM_INFINITY,&nrm3);CHKERRQ(ierr);
ierr = VecNorm(W,NORM_INFINITY,&nrm4);CHKERRQ(ierr);
ierr = VecSwap(V,W);CHKERRQ(ierr);
ierr = PetscObjectStateIncrease((PetscObject)V);CHKERRQ(ierr);
ierr = PetscObjectStateIncrease((PetscObject)W);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_1,&nrm1);CHKERRQ(ierr);
ierr = VecNorm(W,NORM_1,&nrm2);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"swapped: norm_V=%e,norm_W=%e\n",(double)nrm2,(double)nrm1);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"orig: F-norm_V=%e,F-norm_W=%e\n",(double)nrm3,(double)nrm4);CHKERRQ(ierr);
ierr = VecNorm(V,NORM_INFINITY,&nrm3);CHKERRQ(ierr);
ierr = VecNorm(W,NORM_INFINITY,&nrm4);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"swapped: F-norm_V=%e,F-norm_W=%e\n",(double)nrm4,(double)nrm3);CHKERRQ(ierr);
ierr = VecDestroy(&V);CHKERRQ(ierr);
ierr = VecDestroy(&W);CHKERRQ(ierr);
PetscFinalize();
PetscFunctionReturn(0);
}
void PETSC_STDCALL vecswap_(Vec x,Vec y, int *__ierr ){
*__ierr = VecSwap(
(Vec)PetscToPointer((x) ),
(Vec)PetscToPointer((y) ));
}
PetscErrorCode EPSSolve_Lanczos(EPS eps)
{
EPS_LANCZOS *lanczos = (EPS_LANCZOS*)eps->data;
PetscErrorCode ierr;
PetscInt nconv,i,j,k,l,x,n,*perm,restart,ncv=eps->ncv,r,ld;
Vec vi,vj,w;
Mat U;
PetscScalar *Y,*ritz,stmp;
PetscReal *d,*e,*bnd,anorm,beta,norm,rtmp,resnorm;
PetscBool breakdown;
char *conv,ctmp;
PetscFunctionBegin;
ierr = DSGetLeadingDimension(eps->ds,&ld);CHKERRQ(ierr);
ierr = PetscMalloc4(ncv,&ritz,ncv,&bnd,ncv,&perm,ncv,&conv);CHKERRQ(ierr);
/* The first Lanczos vector is the normalized initial vector */
ierr = EPSGetStartVector(eps,0,NULL);CHKERRQ(ierr);
anorm = -1.0;
nconv = 0;
/* Restart loop */
while (eps->reason == EPS_CONVERGED_ITERATING) {
eps->its++;
/* Compute an ncv-step Lanczos factorization */
n = PetscMin(nconv+eps->mpd,ncv);
ierr = DSGetArrayReal(eps->ds,DS_MAT_T,&d);CHKERRQ(ierr);
e = d + ld;
ierr = EPSBasicLanczos(eps,d,e,nconv,&n,&breakdown,anorm);CHKERRQ(ierr);
beta = e[n-1];
ierr = DSRestoreArrayReal(eps->ds,DS_MAT_T,&d);CHKERRQ(ierr);
ierr = DSSetDimensions(eps->ds,n,0,nconv,0);CHKERRQ(ierr);
ierr = DSSetState(eps->ds,DS_STATE_INTERMEDIATE);CHKERRQ(ierr);
ierr = BVSetActiveColumns(eps->V,nconv,n);CHKERRQ(ierr);
/* Solve projected problem */
ierr = DSSolve(eps->ds,ritz,NULL);CHKERRQ(ierr);
ierr = DSSort(eps->ds,ritz,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
/* Estimate ||A|| */
for (i=nconv;i<n;i++)
anorm = PetscMax(anorm,PetscAbsReal(PetscRealPart(ritz[i])));
/* Compute residual norm estimates as beta*abs(Y(m,:)) + eps*||A|| */
ierr = DSGetArray(eps->ds,DS_MAT_Q,&Y);CHKERRQ(ierr);
for (i=nconv;i<n;i++) {
resnorm = beta*PetscAbsScalar(Y[n-1+i*ld]) + PETSC_MACHINE_EPSILON*anorm;
ierr = (*eps->converged)(eps,ritz[i],eps->eigi[i],resnorm,&bnd[i],eps->convergedctx);CHKERRQ(ierr);
if (bnd[i]<eps->tol) conv[i] = 'C';
else conv[i] = 'N';
}
ierr = DSRestoreArray(eps->ds,DS_MAT_Q,&Y);CHKERRQ(ierr);
/* purge repeated ritz values */
if (lanczos->reorthog == EPS_LANCZOS_REORTHOG_LOCAL) {
for (i=nconv+1;i<n;i++) {
if (conv[i] == 'C' && PetscAbsScalar((ritz[i]-ritz[i-1])/ritz[i]) < eps->tol) conv[i] = 'R';
}
}
/* Compute restart vector */
if (breakdown) {
ierr = PetscInfo2(eps,"Breakdown in Lanczos method (it=%D norm=%g)\n",eps->its,(double)beta);CHKERRQ(ierr);
} else {
restart = nconv;
while (restart<n && conv[restart] != 'N') restart++;
if (restart >= n) {
breakdown = PETSC_TRUE;
} else {
for (i=restart+1;i<n;i++) {
if (conv[i] == 'N') {
ierr = SlepcSCCompare(eps->sc,ritz[restart],0.0,ritz[i],0.0,&r);CHKERRQ(ierr);
if (r>0) restart = i;
}
}
ierr = DSGetArray(eps->ds,DS_MAT_Q,&Y);CHKERRQ(ierr);
ierr = BVMultColumn(eps->V,1.0,0.0,n,Y+restart*ld+nconv);CHKERRQ(ierr);
ierr = DSRestoreArray(eps->ds,DS_MAT_Q,&Y);CHKERRQ(ierr);
}
}
/* Count and put converged eigenvalues first */
for (i=nconv;i<n;i++) perm[i] = i;
for (k=nconv;k<n;k++) {
if (conv[perm[k]] != 'C') {
j = k + 1;
while (j<n && conv[perm[j]] != 'C') j++;
if (j>=n) break;
l = perm[k]; perm[k] = perm[j]; perm[j] = l;
}
}
/* Sort eigenvectors according to permutation */
ierr = DSGetArray(eps->ds,DS_MAT_Q,&Y);CHKERRQ(ierr);
for (i=nconv;i<k;i++) {
x = perm[i];
if (x != i) {
j = i + 1;
while (perm[j] != i) j++;
/* swap eigenvalues i and j */
stmp = ritz[x]; ritz[x] = ritz[i]; ritz[i] = stmp;
rtmp = bnd[x]; bnd[x] = bnd[i]; bnd[i] = rtmp;
ctmp = conv[x]; conv[x] = conv[i]; conv[i] = ctmp;
perm[j] = x; perm[i] = i;
/* swap eigenvectors i and j */
for (l=0;l<n;l++) {
stmp = Y[l+x*ld]; Y[l+x*ld] = Y[l+i*ld]; Y[l+i*ld] = stmp;
}
}
}
ierr = DSRestoreArray(eps->ds,DS_MAT_Q,&Y);CHKERRQ(ierr);
/* compute converged eigenvectors */
ierr = DSGetMat(eps->ds,DS_MAT_Q,&U);CHKERRQ(ierr);
ierr = BVMultInPlace(eps->V,U,nconv,k);CHKERRQ(ierr);
ierr = MatDestroy(&U);CHKERRQ(ierr);
/* purge spurious ritz values */
if (lanczos->reorthog == EPS_LANCZOS_REORTHOG_LOCAL) {
for (i=nconv;i<k;i++) {
ierr = BVGetColumn(eps->V,i,&vi);CHKERRQ(ierr);
ierr = VecNorm(vi,NORM_2,&norm);CHKERRQ(ierr);
ierr = VecScale(vi,1.0/norm);CHKERRQ(ierr);
w = eps->work[0];
ierr = STApply(eps->st,vi,w);CHKERRQ(ierr);
ierr = VecAXPY(w,-ritz[i],vi);CHKERRQ(ierr);
ierr = BVRestoreColumn(eps->V,i,&vi);CHKERRQ(ierr);
ierr = VecNorm(w,NORM_2,&norm);CHKERRQ(ierr);
ierr = (*eps->converged)(eps,ritz[i],eps->eigi[i],norm,&bnd[i],eps->convergedctx);CHKERRQ(ierr);
if (bnd[i]>=eps->tol) conv[i] = 'S';
}
for (i=nconv;i<k;i++) {
if (conv[i] != 'C') {
j = i + 1;
while (j<k && conv[j] != 'C') j++;
if (j>=k) break;
/* swap eigenvalues i and j */
stmp = ritz[j]; ritz[j] = ritz[i]; ritz[i] = stmp;
rtmp = bnd[j]; bnd[j] = bnd[i]; bnd[i] = rtmp;
ctmp = conv[j]; conv[j] = conv[i]; conv[i] = ctmp;
/* swap eigenvectors i and j */
ierr = BVGetColumn(eps->V,i,&vi);CHKERRQ(ierr);
ierr = BVGetColumn(eps->V,j,&vj);CHKERRQ(ierr);
ierr = VecSwap(vi,vj);CHKERRQ(ierr);
ierr = BVRestoreColumn(eps->V,i,&vi);CHKERRQ(ierr);
ierr = BVRestoreColumn(eps->V,j,&vj);CHKERRQ(ierr);
}
}
k = i;
}
/* store ritz values and estimated errors */
for (i=nconv;i<n;i++) {
eps->eigr[i] = ritz[i];
eps->errest[i] = bnd[i];
}
ierr = EPSMonitor(eps,eps->its,nconv,eps->eigr,eps->eigi,eps->errest,n);CHKERRQ(ierr);
nconv = k;
if (eps->its >= eps->max_it) eps->reason = EPS_DIVERGED_ITS;
if (nconv >= eps->nev) eps->reason = EPS_CONVERGED_TOL;
if (eps->reason == EPS_CONVERGED_ITERATING) { /* copy restart vector */
ierr = BVCopyColumn(eps->V,n,nconv);CHKERRQ(ierr);
if (lanczos->reorthog == EPS_LANCZOS_REORTHOG_LOCAL && !breakdown) {
/* Reorthonormalize restart vector */
ierr = BVOrthogonalizeColumn(eps->V,nconv,NULL,&norm,&breakdown);CHKERRQ(ierr);
ierr = BVScaleColumn(eps->V,nconv,1.0/norm);CHKERRQ(ierr);
}
if (breakdown) {
/* Use random vector for restarting */
ierr = PetscInfo(eps,"Using random vector for restart\n");CHKERRQ(ierr);
ierr = EPSGetStartVector(eps,nconv,&breakdown);CHKERRQ(ierr);
}
if (breakdown) { /* give up */
eps->reason = EPS_DIVERGED_BREAKDOWN;
ierr = PetscInfo(eps,"Unable to generate more start vectors\n");CHKERRQ(ierr);
}
}
}
eps->nconv = nconv;
ierr = PetscFree4(ritz,bnd,perm,conv);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
Vec x,y,w; /* vectors */
Vec *z; /* array of vectors */
PetscReal norm,v,v1,v2,maxval;
PetscInt n = 20,maxind;
PetscErrorCode ierr;
PetscScalar one = 1.0,two = 2.0,three = 3.0,dots[3],dot;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
/*
Create a vector, specifying only its global dimension.
When using VecCreate(), VecSetSizes() and VecSetFromOptions(), the vector format
(currently parallel, shared, or sequential) is determined at runtime. Also, the
parallel partitioning of the vector is determined by PETSc at runtime.
Routines for creating particular vector types directly are:
VecCreateSeq() - uniprocessor vector
VecCreateMPI() - distributed vector, where the user can
determine the parallel partitioning
VecCreateShared() - parallel vector that uses shared memory
(available only on the SGI); otherwise,
is the same as VecCreateMPI()
With VecCreate(), VecSetSizes() and VecSetFromOptions() the option -vec_type mpi or
-vec_type shared causes the particular type of vector to be formed.
*/
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
/*
Duplicate some work vectors (of the same format and
partitioning as the initial vector).
*/
ierr = VecDuplicate(x,&y);CHKERRQ(ierr);
ierr = VecDuplicate(x,&w);CHKERRQ(ierr);
/*
Duplicate more work vectors (of the same format and
partitioning as the initial vector). Here we duplicate
an array of vectors, which is often more convenient than
duplicating individual ones.
*/
ierr = VecDuplicateVecs(x,3,&z);CHKERRQ(ierr);
/*
Set the vectors to entries to a constant value.
*/
ierr = VecSet(x,one);CHKERRQ(ierr);
ierr = VecSet(y,two);CHKERRQ(ierr);
ierr = VecSet(z[0],one);CHKERRQ(ierr);
ierr = VecSet(z[1],two);CHKERRQ(ierr);
ierr = VecSet(z[2],three);CHKERRQ(ierr);
/*
Demonstrate various basic vector routines.
*/
ierr = VecDot(x,y,&dot);CHKERRQ(ierr);
ierr = VecMDot(x,3,z,dots);CHKERRQ(ierr);
/*
Note: If using a complex numbers version of PETSc, then
PETSC_USE_COMPLEX is defined in the makefiles; otherwise,
(when using real numbers) it is undefined.
*/
ierr = PetscPrintf(PETSC_COMM_WORLD,"Vector length %D\n",n);CHKERRQ(ierr);
ierr = VecMax(x,&maxind,&maxval);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecMax %g, VecInd %D\n",(double)maxval,maxind);CHKERRQ(ierr);
ierr = VecMin(x,&maxind,&maxval);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecMin %g, VecInd %D\n",(double)maxval,maxind);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"All other values should be near zero\n");CHKERRQ(ierr);
ierr = VecScale(x,two);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
v = norm-2.0*PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecScale %g\n",(double)v);CHKERRQ(ierr);
ierr = VecCopy(x,w);CHKERRQ(ierr);
ierr = VecNorm(w,NORM_2,&norm);CHKERRQ(ierr);
v = norm-2.0*PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecCopy %g\n",(double)v);CHKERRQ(ierr);
ierr = VecAXPY(y,three,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr);
v = norm-8.0*PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecAXPY %g\n",(double)v);CHKERRQ(ierr);
ierr = VecAYPX(y,two,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr);
v = norm-18.0*PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecAYPX %g\n",(double)v);CHKERRQ(ierr);
ierr = VecSwap(x,y);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm);CHKERRQ(ierr);
v = norm-2.0*PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecSwap %g\n",(double)v);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
v = norm-18.0*PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecSwap %g\n",(double)v);CHKERRQ(ierr);
ierr = VecWAXPY(w,two,x,y);CHKERRQ(ierr);
ierr = VecNorm(w,NORM_2,&norm);CHKERRQ(ierr);
v = norm-38.0*PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecWAXPY %g\n",(double)v);CHKERRQ(ierr);
ierr = VecPointwiseMult(w,y,x);CHKERRQ(ierr);
ierr = VecNorm(w,NORM_2,&norm);CHKERRQ(ierr);
v = norm-36.0*PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecPointwiseMult %g\n",(double)v);CHKERRQ(ierr);
ierr = VecPointwiseDivide(w,x,y);CHKERRQ(ierr);
ierr = VecNorm(w,NORM_2,&norm);CHKERRQ(ierr);
v = norm-9.0*PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecPointwiseDivide %g\n",(double)v);CHKERRQ(ierr);
dots[0] = one;
dots[1] = three;
dots[2] = two;
ierr = VecSet(x,one);CHKERRQ(ierr);
ierr = VecMAXPY(x,3,dots,z);CHKERRQ(ierr);
ierr = VecNorm(z[0],NORM_2,&norm);CHKERRQ(ierr);
v = norm-PetscSqrtReal((PetscReal)n); if (v > -PETSC_SMALL && v < PETSC_SMALL) v = 0.0;
ierr = VecNorm(z[1],NORM_2,&norm);CHKERRQ(ierr);
v1 = norm-2.0*PetscSqrtReal((PetscReal)n); if (v1 > -PETSC_SMALL && v1 < PETSC_SMALL) v1 = 0.0;
ierr = VecNorm(z[2],NORM_2,&norm);CHKERRQ(ierr);
v2 = norm-3.0*PetscSqrtReal((PetscReal)n); if (v2 > -PETSC_SMALL && v2 < PETSC_SMALL) v2 = 0.0;
ierr = PetscPrintf(PETSC_COMM_WORLD,"VecMAXPY %g %g %g \n",(double)v,(double)v1,(double)v2);CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&w);CHKERRQ(ierr);
ierr = VecDestroyVecs(3,&z);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PETSC_EXTERN PetscErrorCode SNESComputeNGSDefaultSecant(SNES snes,Vec X,Vec B,void *ctx)
{
PetscErrorCode ierr;
SNES_NGS *gs = (SNES_NGS*)snes->data;
PetscInt i,j,k,ncolors;
DM dm;
PetscBool flg;
ISColoring coloring = gs->coloring;
MatColoring mc;
Vec W,G,F;
PetscScalar h=gs->h;
IS *coloris;
PetscScalar f,g,x,w,d;
PetscReal dxt,xt,ft,ft1=0;
const PetscInt *idx;
PetscInt size,s;
PetscReal atol,rtol,stol;
PetscInt its;
PetscErrorCode (*func)(SNES,Vec,Vec,void*);
void *fctx;
PetscBool mat = gs->secant_mat,equal,isdone,alldone;
PetscScalar *xa,*fa,*wa,*ga;
PetscFunctionBegin;
if (snes->nwork < 3) {
ierr = SNESSetWorkVecs(snes,3);CHKERRQ(ierr);
}
W = snes->work[0];
G = snes->work[1];
F = snes->work[2];
ierr = VecGetOwnershipRange(X,&s,NULL);CHKERRQ(ierr);
ierr = SNESNGSGetTolerances(snes,&atol,&rtol,&stol,&its);CHKERRQ(ierr);
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = SNESGetFunction(snes,NULL,&func,&fctx);CHKERRQ(ierr);
if (!coloring) {
/* create the coloring */
ierr = DMHasColoring(dm,&flg);CHKERRQ(ierr);
if (flg && !mat) {
ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&coloring);CHKERRQ(ierr);
} else {
if (!snes->jacobian) {ierr = SNESSetUpMatrices(snes);CHKERRQ(ierr);}
ierr = MatColoringCreate(snes->jacobian,&mc);CHKERRQ(ierr);
ierr = MatColoringSetDistance(mc,1);CHKERRQ(ierr);
ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr);
ierr = MatColoringApply(mc,&coloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&mc);CHKERRQ(ierr);
}
gs->coloring = coloring;
}
ierr = ISColoringGetIS(coloring,&ncolors,&coloris);CHKERRQ(ierr);
ierr = VecEqual(X,snes->vec_sol,&equal);CHKERRQ(ierr);
if (equal && snes->normschedule == SNES_NORM_ALWAYS) {
/* assume that the function is already computed */
ierr = VecCopy(snes->vec_func,F);CHKERRQ(ierr);
} else {
ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
ierr = (*func)(snes,X,F,fctx);CHKERRQ(ierr);
ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
if (B) {ierr = VecAXPY(F,-1.0,B);CHKERRQ(ierr);}
}
ierr = VecGetArray(X,&xa);CHKERRQ(ierr);
ierr = VecGetArray(F,&fa);CHKERRQ(ierr);
ierr = VecGetArray(G,&ga);CHKERRQ(ierr);
ierr = VecGetArray(W,&wa);CHKERRQ(ierr);
for (i=0;i<ncolors;i++) {
ierr = ISGetIndices(coloris[i],&idx);CHKERRQ(ierr);
ierr = ISGetLocalSize(coloris[i],&size);CHKERRQ(ierr);
ierr = VecCopy(X,W);CHKERRQ(ierr);
for (j=0;j<size;j++) {
wa[idx[j]-s] += h;
}
ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
ierr = (*func)(snes,W,G,fctx);CHKERRQ(ierr);
ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
if (B) {ierr = VecAXPY(G,-1.0,B);CHKERRQ(ierr);}
for (k=0;k<its;k++) {
dxt = 0.;
xt = 0.;
ft = 0.;
for (j=0;j<size;j++) {
f = fa[idx[j]-s];
x = xa[idx[j]-s];
g = ga[idx[j]-s];
w = wa[idx[j]-s];
if (PetscAbsScalar(g-f) > atol) {
/* This is equivalent to d = x - (h*f) / PetscRealPart(g-f) */
d = (x*g-w*f) / PetscRealPart(g-f);
} else {
d = x;
}
dxt += PetscRealPart(PetscSqr(d-x));
xt += PetscRealPart(PetscSqr(x));
ft += PetscRealPart(PetscSqr(f));
xa[idx[j]-s] = d;
}
if (k == 0) ft1 = PetscSqrtReal(ft);
if (k<its-1) {
isdone = PETSC_FALSE;
if (stol*PetscSqrtReal(xt) > PetscSqrtReal(dxt)) isdone = PETSC_TRUE;
if (PetscSqrtReal(ft) < atol) isdone = PETSC_TRUE;
if (rtol*ft1 > PetscSqrtReal(ft)) isdone = PETSC_TRUE;
ierr = MPIU_Allreduce(&isdone,&alldone,1,MPIU_BOOL,MPI_BAND,PetscObjectComm((PetscObject)snes));CHKERRQ(ierr);
if (alldone) break;
}
if (i < ncolors-1 || k < its-1) {
ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
ierr = (*func)(snes,X,F,fctx);CHKERRQ(ierr);
ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
if (B) {ierr = VecAXPY(F,-1.0,B);CHKERRQ(ierr);}
}
if (k<its-1) {
ierr = VecSwap(X,W);CHKERRQ(ierr);
ierr = VecSwap(F,G);CHKERRQ(ierr);
}
}
}
ierr = VecRestoreArray(X,&xa);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&fa);CHKERRQ(ierr);
ierr = VecRestoreArray(G,&ga);CHKERRQ(ierr);
ierr = VecRestoreArray(W,&wa);CHKERRQ(ierr);
ierr = ISColoringRestoreIS(coloring,&coloris);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
