double MultiDomainRMSD::projectAtomicDisplacementOnVector( const bool& normalized, const std::vector<Vector>& vecs, ReferenceValuePack& mypack ) const {
double totd=0.; std::vector<Vector> tvecs; mypack.clear();
MultiValue tvals( 1, mypack.getNumberOfDerivatives() ); ReferenceValuePack tder( 0, getNumberOfAtoms(), tvals );
for(unsigned i=0; i<domains.size(); ++i) {
// Must extract appropriate positions here
tvecs.resize( blocks[i+1] - blocks[i] ); domains[i]->setupPCAStorage( tder );
if( tder.centeredpos.size()>0 ) {
for(unsigned p=0; p<3; ++p) for(unsigned q=0; q<3; ++q) tder.DRotDPos(p,q).resize( tvecs.size() );
}
// Extract information from storage pack and put in local pack
if( tder.centeredpos.size()>0 ) tder.rot[0]=mypack.rot[i];
unsigned n=0;
for(unsigned j=blocks[i]; j<blocks[i+1]; ++j) {
tder.setAtomIndex(n,j); tvecs[n] = vecs[j]; tder.displacement[n]=mypack.displacement[j] / weights[i];
if( tder.centeredpos.size()>0 ) {
tder.centeredpos[n]=mypack.centeredpos[j];
for(unsigned p=0; p<3; ++p) for(unsigned q=0; q<3; ++q) tder.DRotDPos(p,q)[n]=mypack.DRotDPos(p,q)[j];
}
n++;
}
for(unsigned k=n; k<getNumberOfAtoms(); ++k) tder.setAtomIndex(k,3*vecs.size()+10);
// Do the calculations
totd += weights[i]*domains[i]->projectAtomicDisplacementOnVector( normalized, tvecs, tder );
// And derivatives
mypack.copyScaledDerivatives( 0, weights[i], tvals );
}
if( !mypack.updateComplete() ) mypack.updateDynamicLists();
return totd;
}
void ActionWithInputMatrix::getInputData( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms, std::vector<double>& orient0 ) const {
if( (mymatrix->function)->mybasemulticolvars.size()==0 ) {
std::vector<double> tvals( mymatrix->getNumberOfComponents() ); orient0.assign(orient0.size(),0);
for(unsigned i=0; i<mymatrix->getNumberOfColumns(); ++i) {
if( mymatrix->undirectedGraph() && ind==i ) continue;
orient0[1]+=retrieveConnectionValue( ind, i, tvals );
}
orient0[0]=1.0; return;
}
(mymatrix->function)->getInputData( ind, normed, myatoms, orient0 );
}
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;
}
