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;
}
double NumberOfLinks::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
if( getBaseMultiColvar(0)->getNumberOfQuantities()<3 ) return 1.0;
unsigned ncomp=getBaseMultiColvar(0)->getNumberOfQuantities();
std::vector<double> orient0( ncomp ), orient1( ncomp );
getVectorForTask( myatoms.getIndex(0), true, orient0 );
getVectorForTask( myatoms.getIndex(1), true, orient1 );
double dot=0;
for(unsigned k=2;k<orient0.size();++k){
dot+=orient0[k]*orient1[k];
}
if( !doNotCalculateDerivatives() ){
unsigned nder=myatoms.getNumberOfDerivatives(); //getNumberOfDerivatives();
MultiValue myder0(ncomp,nder), myder1(ncomp,nder);
getVectorDerivatives( myatoms.getIndex(0), true, myder0 );
mergeVectorDerivatives( 1, 2, orient1.size(), myatoms.getIndex(0), orient1, myder0, myatoms );
getVectorDerivatives( myatoms.getIndex(1), true, myder1 );
mergeVectorDerivatives( 1, 2, orient0.size(), myatoms.getIndex(1), orient0, myder1, myatoms );
}
return dot;
}
double DistanceFromContour::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
Vector distance = getSeparation( getPosition(getNumberOfAtoms()-1), myatoms.getPosition(0) );
std::vector<double> pp(3), der(3,0); for(unsigned j=0;j<3;++j) pp[j] = distance[j];
// Now create the kernel and evaluate
KernelFunctions kernel( pp, bw, kerneltype, false, 1.0, true );
double newval = kernel.evaluate( pval, der, true );
if( mybasemulticolvars[0]->isDensity() ){
if( !doNotCalculateDerivatives() && derivTime ){
MultiValue& myvals=myatoms.getUnderlyingMultiValue();
Vector vder; unsigned basen=myvals.getNumberOfDerivatives() - 12;
for(unsigned i=0;i<3;++i){
vder[i]=der[i]; myvals.addDerivative( 1, basen+i, vder[i] );
}
myatoms.setValue( 2, der[dir] );
addAtomDerivatives( 1, 0, -vder, myatoms );
myatoms.addBoxDerivatives( 1, Tensor(vder,distance) );
}
myatoms.setValue( 0, 1.0 ); return newval;
}
// This does the stuff for averaging
myatoms.setValue( 0, newval );
// This gets the average if we are using a phase field
std::vector<double> cvals( mybasemulticolvars[0]->getNumberOfQuantities() );
mybasedata[0]->retrieveValueWithIndex( tindex, false, cvals );
return newval*cvals[0]*cvals[1];
}
void MultiColvarBase::calculateWeight( AtomValuePack& myatoms ) const {
myatoms.setValue( 0, 1.0 );
}
