double ContactAlignedMatrix::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
double f_dot, dot_df;
std::vector<double> orient0(ncomp), orient1(ncomp);
getOrientationVector( myatoms.getIndex(0), true, orient0 );
getOrientationVector( myatoms.getIndex(1), true, orient1 );
double dot=0; for(unsigned k=2;k<orient0.size();++k) dot+=orient0[k]*orient1[k];
f_dot=0.5*( 1 + dot ); dot_df=0.5;
// Retrieve the weight of the connection
double weight = myatoms.getValue(0); myatoms.setValue(0,1.0);
if( !doNotCalculateDerivatives() ){
Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
double dfunc, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( distance.modulo(), dfunc );
addAtomDerivatives( 1, 0, (-dfunc)*f_dot*distance, myatoms );
addAtomDerivatives( 1, 1, (+dfunc)*f_dot*distance, myatoms );
myatoms.addBoxDerivatives( 1, (-dfunc)*f_dot*Tensor(distance,distance) );
// Add derivatives of orientation
for(unsigned k=2;k<orient0.size();++k){ orient0[k]*=sw*dot_df; orient1[k]*=sw*dot_df; }
addOrientationDerivatives( 1, 0, orient1, myatoms );
addOrientationDerivatives( 1, 1, orient0, myatoms );
}
return weight*f_dot;
}
double NumberOfLinks::compute(){
getValueForBaseTask( 0, orient0 );
getValueForBaseTask( 1, orient1 );
double dot=0;
for(unsigned k=0;k<orient0.size();++k){
dot+=orient0[k]*orient1[k];
}
// for(unsigned k=0;k<orient0.size();++k){
// orient0[k]*=dot_df; orient1[k]*=dot_df;
// }
addOrientationDerivatives( 0, orient1 );
addOrientationDerivatives( 1, orient0 );
return dot;
}
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;
}
