bool MultiColvarBase::setupCurrentAtomList( const unsigned& taskCode, AtomValuePack& myatoms ) const {
if( usespecies ){
if( isDensity() ) return true;
unsigned natomsper=myatoms.setupAtomsFromLinkCells( taskCode, getPositionOfAtomForLinkCells(taskCode), linkcells );
return natomsper>1;
} else if( ablocks.size()<4 ){
std::vector<unsigned> atoms( ablocks.size() );
decodeIndexToAtoms( taskCode, atoms ); myatoms.setNumberOfAtoms( ablocks.size() );
for(unsigned i=0;i<ablocks.size();++i) myatoms.setAtom( i, atoms[i] );
} else {
myatoms.setNumberOfAtoms( ablocks.size() );
for(unsigned i=0;i<ablocks.size();++i) myatoms.setAtom( i, ablocks[i][taskCode] );
}
return true;
}
bool MultiColvarBase::setupCurrentAtomList( const unsigned& taskCode ){
if( usespecies ){
natomsper=1;
if( isDensity() ) return true;
current_atoms[0]=taskCode;
linkcells.retrieveNeighboringAtoms( getPositionOfAtomForLinkCells(current_atoms[0]), natomsper, current_atoms );
return natomsper>1;
} else if( current_atoms.size()<4 ){
natomsper=current_atoms.size();
unsigned scode = taskCode;
for(unsigned i=0;i<ablocks.size();++i){
unsigned ind=( scode / decoder[i] );
current_atoms[i]=ablocks[i][ind];
scode -= ind*decoder[i];
}
} else {
natomsper=current_atoms.size();
for(unsigned i=0;i<ablocks.size();++i) current_atoms[i]=ablocks[i][taskCode];
}
return true;
}
Vector MultiColvarBase::getCentralAtomPos( const unsigned& taskIndex ){
unsigned curr=getTaskCode( taskIndex );
if( usespecies || isDensity() ){
return getPositionOfAtomForLinkCells(curr);
} else if( ablocks.size()<4 ){
// double factor=1.0/static_cast<double>( ablocks.size() );
Vector mypos; mypos.zero();
std::vector<unsigned> atoms( ablocks.size() ); decodeIndexToAtoms( curr, atoms );
for(unsigned i=0;i<ablocks.size();++i){
if( use_for_central_atom[i] ) mypos+=numberForCentralAtom*getPositionOfAtomForLinkCells(atoms[i]);
}
return mypos;
} else {
Vector mypos; mypos.zero();
for(unsigned i=0;i<ablocks.size();++i){
if( use_for_central_atom[i] ) mypos+=numberForCentralAtom*getPositionOfAtomForLinkCells(ablocks[i][curr]);
}
return mypos;
}
}
