double OptimalRMSD::projectAtomicDisplacementOnVector( const bool& normalized, const std::vector<Vector>& vecs, ReferenceValuePack& mypack ) const {
plumed_dbg_assert( mypack.calcUsingPCAOption() );
double proj=0.0; mypack.clear();
for(unsigned i=0; i<vecs.size(); ++i) {
proj += dotProduct( mypack.getAtomsDisplacementVector()[i], vecs[i] );
}
for(unsigned a=0; a<3; a++) {
for(unsigned b=0; b<3; b++) {
for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) {
double tmp1=0.;
for(unsigned n=0; n<getNumberOfAtoms(); n++) tmp1+=mypack.centeredpos[n][b]*vecs[n][a];
if( normalized ) mypack.addAtomDerivatives( iat, getDisplace()[iat]*mypack.DRotDPos[a][b][iat]*tmp1 );
else mypack.addAtomDerivatives( iat, mypack.DRotDPos[a][b][iat]*tmp1 );
}
}
}
Tensor trot=mypack.rot[0].transpose();
Vector v1; v1.zero(); double prefactor = 1. / static_cast<double>( getNumberOfAtoms() );
for(unsigned n=0; n<getNumberOfAtoms(); n++) v1+=prefactor*matmul(trot,vecs[n]);
if( normalized ) {
for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) mypack.addAtomDerivatives( iat, getDisplace()[iat]*(matmul(trot,vecs[iat]) - v1) );
} else {
for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) mypack.addAtomDerivatives( iat, (matmul(trot,vecs[iat]) - v1) );
}
if( !mypack.updateComplete() ) mypack.updateDynamicLists();
return proj;
}
double DRMSD::calc( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const {
plumed_dbg_assert(!targets.empty());
Vector distance;
myder.clear();
double drmsd=0.;
for(std::map< std::pair <unsigned,unsigned> , double>::const_iterator it=targets.begin();it!=targets.end();++it){
const unsigned i=getAtomIndex( it->first.first );
const unsigned j=getAtomIndex( it->first.second );
if(nopbc) distance=delta( pos[i] , pos[j] );
else distance=pbc.distance( pos[i] , pos[j] );
const double len = distance.modulo();
const double diff = len - it->second;
const double der = diff / len;
drmsd += diff * diff;
myder.addAtomDerivatives( i, -der * distance );
myder.addAtomDerivatives( j, der * distance );
myder.addBoxDerivatives( - der * Tensor(distance,distance) );
}
const double inpairs = 1./static_cast<double>(targets.size());
double idrmsd;
if(squared){
drmsd = drmsd * inpairs;
idrmsd = 2.0 * inpairs;
} else {
drmsd = sqrt( drmsd * inpairs );
idrmsd = inpairs / drmsd ;
}
myder.scaleAllDerivatives( idrmsd );
return drmsd;
}