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 );
}
