double MultiDomainRMSD::calculate( const std::vector<Vector>& pos, const Pbc& pbc, const bool& squared ){
clearDerivatives(); double totd=0.; Tensor tvirial; std::vector<Vector> mypos;
for(unsigned i=0;i<domains.size();++i){
// Must extract appropriate positions here
mypos.resize( blocks[i+1] - blocks[i] + 1 );
unsigned n=0;
for(unsigned j=blocks[i];j<blocks[i+1];++j){ mypos[n]=pos[j]; n++; }
// This actually does the calculation
totd += weights[i]*domains[i]->calculate( mypos, pbc, true );
// Must extract derivatives here
n=0;
for(unsigned j=blocks[i];j<blocks[i+1];++j){
addAtomicDerivatives( j, weights[i]*domains[i]->getAtomDerivative(n) ); n++;
}
if( domains[i]->getVirial( tvirial ) ){
addBoxDerivatives( weights[i]*tvirial );
}
}
if( !squared ){
totd=sqrt(totd); double xx=0.5/totd;
for(unsigned iat=0;iat<atom_ders.size();iat++) atom_ders[iat]*=xx;
if( virialWasSet ) virial*=xx;
}
return totd;
}
double SingleDomainRMSD::calculate( const std::vector<Vector>& pos, const Pbc& pbc, const bool& squared ){
clearDerivatives();
return calc( pos, pbc, squared );
}
double ArgumentOnlyDistance::calculate( const std::vector<Value*>& vals, const bool& squared ){
clearDerivatives();
if( tmparg.size()!=vals.size() ) tmparg.resize( vals.size() );
for(unsigned i=0;i<vals.size();++i) tmparg[i]=vals[i]->get();
return calc( vals, tmparg, squared );
}
double RMSDBase::calculate( const std::vector<Vector>& pos, const bool& squared ){
clearDerivatives();
return calc( pos, squared );
}
