double MultiDomainRMSD::calculate( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const {
double totd=0.; Tensor tvirial; std::vector<Vector> mypos; MultiValue tvals( 1, 3*pos.size()+9 );
ReferenceValuePack tder( 0, getNumberOfAtoms(), tvals ); myder.clear();
for(unsigned i=0; i<domains.size(); ++i) {
// Must extract appropriate positions here
mypos.resize( blocks[i+1] - blocks[i] );
if( myder.calcUsingPCAOption() ) domains[i]->setupPCAStorage( tder );
unsigned n=0; for(unsigned j=blocks[i]; j<blocks[i+1]; ++j) { tder.setAtomIndex(n,j); mypos[n]=pos[j]; n++; }
for(unsigned k=n; k<getNumberOfAtoms(); ++k) tder.setAtomIndex(k,3*pos.size()+10);
// This actually does the calculation
totd += weights[i]*domains[i]->calculate( mypos, pbc, tder, true );
// Now merge the derivative
myder.copyScaledDerivatives( 0, weights[i], tvals );
// If PCA copy PCA stuff
if( myder.calcUsingPCAOption() ) {
unsigned n=0;
if( tder.centeredpos.size()>0 ) myder.rot[i]=tder.rot[0];
for(unsigned j=blocks[i]; j<blocks[i+1]; ++j) {
myder.displacement[j]=weights[i]*tder.displacement[n]; // Multiplication by weights here ensures that normalisation is done correctly
if( tder.centeredpos.size()>0 ) {
myder.centeredpos[j]=tder.centeredpos[n];
for(unsigned p=0; p<3; ++p) for(unsigned q=0; q<3; ++q) myder.DRotDPos(p,q)[j]=tder.DRotDPos(p,q)[n];
}
n++;
}
}
// Make sure virial status is set correctly in output derivative pack
// This is only done here so I do this by using class friendship
if( tder.virialWasSet() ) myder.boxWasSet=true;
}
if( !myder.updateComplete() ) myder.updateDynamicLists();
if( !squared ) {
totd=sqrt(totd); double xx=0.5/totd;
myder.scaleAllDerivatives( xx );
}
return totd;
}
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;
}