void ClusterDist_DME::PairwiseDist(ClusterMatrix& frameDistances,
ClusterSieve::SievedFrames const& frames)
{
int f1, f2;
Frame frm2 = frm1_;
int f2end = (int)frames.size();
int f1end = f2end - 1;
#ifdef _OPENMP
Frame frm1 = frm1_;
# define frm1_ frm1
#pragma omp parallel private(f1, f2) firstprivate(frm1, frm2)
{
#pragma omp for schedule(dynamic)
#endif
for (f1 = 0; f1 < f1end; f1++) {
coords_->GetFrame( frames[f1], frm1_, mask_ );
for (f2 = f1 + 1; f2 < f2end; f2++) {
coords_->GetFrame( frames[f2], frm2, mask_ );
frameDistances.SetElement( f1, f2, frm1_.DISTRMSD( frm2 ) );
}
}
#ifdef _OPENMP
# undef frm1_
} // END pragma omp parallel
#endif
}
void ClusterDist_SRMSD::PairwiseDist(ClusterMatrix& frameDistances,
ClusterSieve::SievedFrames const& frames)
{
double rmsd;
int f1, f2;
Frame frm2 = frm1_;
int f2end = (int)frames.size();
int f1end = f2end - 1;
ParallelProgress progress(f1end);
#ifdef _OPENMP
Frame frm1 = frm1_;
# define frm1_ frm1
SymmetricRmsdCalc SRMSD_OMP = SRMSD_;
# define SRMSD_ SRMSD_OMP
#pragma omp parallel private(f1, f2, rmsd) firstprivate(SRMSD_OMP, frm1, frm2, progress)
{
progress.SetThread(omp_get_thread_num());
#pragma omp for schedule(dynamic)
#endif
for (f1 = 0; f1 < f1end; f1++) {
progress.Update(f1);
coords_->GetFrame( frames[f1], frm1_, mask_ );
for (f2 = f1 + 1; f2 < f2end; f2++) {
coords_->GetFrame( frames[f2], frm2, mask_ );
rmsd = SRMSD_.SymmRMSD(frm1_, frm2);
frameDistances.SetElement( f1, f2, rmsd );
}
}
#ifdef _OPENMP
# undef frm1_
# undef SRMSD_
} // END pragma omp parallel
#endif
progress.Finish();
}
void ClusterDist_Euclid::PairwiseDist(ClusterMatrix& frameDistances,
ClusterSieve::SievedFrames const& frames)
{
int f1, f2;
double dist, diff;
DcArray::iterator dcalc;
D1Array::iterator ds;
int f2end = (int)frames.size();
int f1end = f2end - 1;
#ifdef _OPENMP
#pragma omp parallel private(f1, f2, dist, diff, dcalc, ds)
{
#pragma omp for schedule(dynamic)
#endif
for (f1 = 0; f1 < f1end; f1++) {
for (f2 = f1 + 1; f2 < f2end; f2++) {
dist = 0.0;
dcalc = dcalcs_.begin();
for (ds = dsets_.begin(); ds != dsets_.end(); ++ds, ++dcalc) {
diff = (*dcalc)((*ds)->Dval(frames[f1]), (*ds)->Dval(frames[f2]));
dist += (diff * diff);
}
frameDistances.SetElement( f1, f2, sqrt(dist) );
}
}
#ifdef _OPENMP
}
#endif
}
void ClusterDist_Num::PairwiseDist(ClusterMatrix& frameDistances,
ClusterSieve::SievedFrames const& frames)
{
int f1, f2;
int f2end = (int)frames.size();
int f1end = f2end - 1;
#ifdef _OPENMP
#pragma omp parallel private(f1, f2)
{
#pragma omp for schedule(dynamic)
#endif
for (f1 = 0; f1 < f1end; f1++) {
for (f2 = f1 + 1; f2 < f2end; f2++)
frameDistances.SetElement( f1, f2, dcalc_(data_->Dval(frames[f1]),
data_->Dval(frames[f2])) );
}
#ifdef _OPENMP
}
#endif
}
