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 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 InterMolecularTorsions::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
Vector v1, v2, dv1, dv2, dconn, conn = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
// Retrieve vectors
std::vector<double> orient0( 5 ), orient1( 5 );
getInputData( 0, true, myatoms, orient0 );
getInputData( 1, true, myatoms, orient1 );
for(unsigned i=0; i<3; ++i) { v1[i]=orient0[2+i]; v2[i]=orient1[2+i]; }
if( getBaseMultiColvar(0)->getNumberOfQuantities()<3 ) return 1.0;
// Evaluate angle
Torsion t; double angle = t.compute( v1, conn, v2, dv1, dconn, dv2 );
for(unsigned i=0; i<3; ++i) { orient0[i+2]=dv1[i]; orient1[i+2]=dv2[i]; }
// And accumulate derivatives
if( !doNotCalculateDerivatives() ) {
MultiValue& myder0=getInputDerivatives( 0, true, myatoms );
mergeInputDerivatives( 1, 2, orient1.size(), 0, orient0, myder0, myatoms );
MultiValue& myder1=getInputDerivatives( 1, true, myatoms );
mergeInputDerivatives( 1, 2, orient0.size(), 1, orient1, myder1, myatoms );
addAtomDerivatives( 1, 0, -dconn, myatoms ); addAtomDerivatives( 1, 1, dconn, myatoms );
myatoms.addBoxDerivatives( 1, -extProduct( conn, dconn ) );
}
return angle;
}
