double TopologyMatrix::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( kerneltype );
// Initialise to zero density on all bins
for(unsigned bin=0; bin<maxbins; ++bin) myatoms.setValue(bin+1,0);
// Calculate whether or not atoms 1 and 2 are within cutoff (can use delta here as pbc are done in atom setup)
Vector d1 = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) ); double d1_len = d1.modulo();
d1 = d1 / d1_len; // Convert vector into director
AtomNumber a1 = myatoms.getAbsoluteIndex( 0 );
AtomNumber a2 = myatoms.getAbsoluteIndex( 1 );
for(unsigned i=2; i<myatoms.getNumberOfAtoms(); ++i) {
AtomNumber a3 = myatoms.getAbsoluteIndex( i );
if( a3!=a1 && a3!=a2 ) calculateForThreeAtoms( i, d1, d1_len, bead, myatoms );
}
// std::vector<double> binvals( 1+maxbins ); for(unsigned i=1;i<maxbins;++i) binvals[i]=myatoms.getValue(i);
// unsigned ii; double fdf;
//std::cout<<"HELLO DENSITY "<<myatoms.getIndex(0)<<" "<<myatoms.getIndex(1)<<" "<<transformStoredValues( binvals, ii, fdf )<<std::endl;
// Now find the element for which the density is maximal
unsigned vout=2; double max=myatoms.getValue( 2 );
for(unsigned i=3; i<myatoms.getUnderlyingMultiValue().getNumberOfValues()-1; ++i) {
if( myatoms.getValue(i)>max ) { max=myatoms.getValue(i); vout=i; }
}
// Calculate value and derivative of switching function between atoms 1 and 2
double dfuncl, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ),
getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( d1_len, dfuncl );
// Transform the density
double df, tsw = threshold_switch.calculate( max, df );
if( !doNotCalculateDerivatives() ) {
// Factor of d1_len is required here because d1 is normalized
d1 *= d1_len;
addAtomDerivatives( 2+maxbins, 0, -dfuncl*d1, myatoms );
addAtomDerivatives( 2+maxbins, 1, dfuncl*d1, myatoms );
myatoms.addBoxDerivatives( 2+maxbins, (-dfuncl)*Tensor(d1,d1) );
// Update active atoms so that next bit works
updateActiveAtoms( myatoms );
// Now finish caclulation of derivatives
MultiValue& myvals=myatoms.getUnderlyingMultiValue();
for(unsigned jd=0; jd<myvals.getNumberActive(); ++jd) {
unsigned ider=myvals.getActiveIndex(jd);
myvals.addDerivative( 1, ider, sw*df*max*myvals.getDerivative( vout, ider ) + tsw*myvals.getDerivative( 2+maxbins, ider ) );
}
}
return sw*tsw;
}
