double SimpleRMSD::calc( const std::vector<Vector>& pos, ReferenceValuePack& myder, const bool& squared ) const {
if( myder.getAtomsDisplacementVector().size()!=pos.size() ) myder.getAtomsDisplacementVector().resize( pos.size() );
double d=myrmsd.simpleAlignment( getAlign(), getDisplace(), pos, getReferencePositions(), myder.getAtomVector(), myder.getAtomsDisplacementVector(), squared );
myder.clear(); for(unsigned i=0;i<pos.size();++i) myder.setAtomDerivatives( i, myder.getAtomVector()[i] );
if( !myder.updateComplete() ) myder.updateDynamicLists();
return d;
}
double OptimalRMSD::calc( const std::vector<Vector>& pos, ReferenceValuePack& myder, const bool& squared ) const {
double d;
if( myder.calcUsingPCAOption() ) {
std::vector<Vector> centeredreference( getNumberOfAtoms () );
d=myrmsd.calc_PCAelements(pos,myder.getAtomVector(),myder.rot[0],myder.DRotDPos,myder.getAtomsDisplacementVector(),myder.centeredpos,centeredreference,squared);
unsigned nat = pos.size();
for(unsigned i=0; i<nat; ++i) { myder.getAtomsDisplacementVector()[i] -= getReferencePosition(i); myder.getAtomsDisplacementVector()[i] *= getDisplace()[i]; }
} else if( fast ) {
if( getAlign()==getDisplace() ) d=myrmsd.optimalAlignment<false,true>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
else d=myrmsd.optimalAlignment<false,false>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
} else {
if( getAlign()==getDisplace() ) d=myrmsd.optimalAlignment<true,true>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
else d=myrmsd.optimalAlignment<true,false>(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);
}
myder.clear(); for(unsigned i=0; i<pos.size(); ++i) myder.setAtomDerivatives( i, myder.getAtomVector()[i] );
if( !myder.updateComplete() ) myder.updateDynamicLists();
return d;
}