double OrientationSphere::compute(){
// Make sure derivatives for central atom are only calculated once
VectorMultiColvar* vv = dynamic_cast<VectorMultiColvar*>( getBaseMultiColvar(0) );
vv->firstcall=true;
weightHasDerivatives=true; // The weight has no derivatives really
double sw, value=0, denom=0, dot, f_dot, dot_df, dfunc; Vector distance;
getVectorForBaseTask(0, catom_orient );
for(unsigned i=1;i<getNAtoms();++i){
distance=getSeparation( getPositionOfCentralAtom(0), getPositionOfCentralAtom(i) );
sw = switchingFunction.calculateSqr( distance.modulo2(), dfunc );
if( sw>=getTolerance() ){
getVectorForBaseTask( i, this_orient );
// Calculate the dot product wrt to this position
dot=0; for(unsigned k=0;k<catom_orient.size();++k) dot+=catom_orient[k]*this_orient[k];
f_dot = transformDotProduct( dot, dot_df );
// N.B. We are assuming here that the imaginary part of the dot product is zero
for(unsigned k=0;k<catom_orient.size();++k){
this_orient[k]*=sw*dot_df; catom_der[k]=sw*dot_df*catom_orient[k];
}
// Set the derivatives wrt of the numerator
addOrientationDerivatives( 0, this_orient );
addOrientationDerivatives( i, catom_der );
addCentralAtomsDerivatives( 0, 0, f_dot*(-dfunc)*distance );
addCentralAtomsDerivatives( i, 0, f_dot*(dfunc)*distance );
addBoxDerivatives( f_dot*(-dfunc)*Tensor(distance,distance) );
value += sw*f_dot;
// Set the derivatives wrt to the numerator
addCentralAtomsDerivatives( 0, 1, (-dfunc)*distance );
addCentralAtomsDerivatives( i, 1, (dfunc)*distance );
addBoxDerivativesOfWeight( (-dfunc)*Tensor(distance,distance) );
denom += sw;
}
}
// Now divide everything
unsigned nder = getNumberOfDerivatives();
for(unsigned i=0;i<nder;++i){
setElementDerivative( i, getElementDerivative(i)/denom - (value*getElementDerivative(nder+i))/(denom*denom) );
setElementDerivative( nder + i, 0.0 );
}
weightHasDerivatives=false; // Weight has no derivatives we just use the holder for weight to store some stuff
return value / denom;
}
Vector NumberOfLinks::getCentralAtom(){
addDerivativeOfCentralAtomPos( 0, 0.5*Tensor::identity() );
addDerivativeOfCentralAtomPos( 1, 0.5*Tensor::identity() );
return 0.5*( getPositionOfCentralAtom(0) + getPositionOfCentralAtom(1) );
}
Vector LocalAverage::getCentralAtom(){
addDerivativeOfCentralAtomPos( 0, Tensor::identity() );
return getPositionOfCentralAtom(0);
}
Vector OrientationSphere::getCentralAtom(){
addDerivativeOfCentralAtomPos( 0, Tensor::identity() );
return getPositionOfCentralAtom(0);
}
