double VectorMultiColvar::doCalculation(){
// Now calculate the vector
calculateVector();
// Sort out the active derivatives
updateActiveAtoms();
// Now calculate the norm of the vector (this is what we return here)
double norm=0, inorm;
if(complexvec){
for(unsigned i=0;i<ncomponents;++i) norm += getComponent(i)*getComponent(i) + getImaginaryComponent(i)*getImaginaryComponent(i);
norm=sqrt(norm); inorm = 1.0 / norm;
for(unsigned i=0;i<ncomponents;++i){ dervec[i] = inorm*getComponent(i); dervec[ncomponents+i] = inorm*getImaginaryComponent(i); }
} else {
for(unsigned i=0;i<ncomponents;++i) norm += getComponent(i)*getComponent(i);
norm=sqrt(norm); inorm = 1.0 / norm;
for(unsigned i=0;i<ncomponents;++i) dervec[i] = inorm*getComponent(i);
}
if( usingLowMem() ){
vecs->storeDerivativesLowMem( 0 );
vecs->chainRule( 0, dervec );
} else {
vecs->storeDerivativesHighMem( getCurrentPositionInTaskList() );
vecs->chainRule( getCurrentPositionInTaskList(), dervec );
}
// Add derivatives to base multicolvars
Vector tmpd;
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned k=atoms_with_derivatives[i];
tmpd[0]=vecs->getFinalDerivative(3*i+0);
tmpd[1]=vecs->getFinalDerivative(3*i+1);
tmpd[2]=vecs->getFinalDerivative(3*i+2);
MultiColvarBase::addAtomsDerivatives( 0, k, tmpd );
}
unsigned vvbase=3*atoms_with_derivatives.getNumberActive(); Tensor tmpv;
for(unsigned i=0;i<3;++i){
for(unsigned j=0;j<3;++j){
tmpv(i,j) = vecs->getFinalDerivative( vvbase+3*i+j );
}
}
MultiColvarBase::addBoxDerivatives( 0, tmpv );
return norm;
}
void BridgedMultiColvarFunction::performTask(){
atoms_with_derivatives.deactivateAll();
if( !myBridgeVessel->prerequisitsCalculated() ){
mycolv->setTaskIndexToCompute( getCurrentPositionInTaskList() );
mycolv->performTask();
} else {
}
completeTask();
atoms_with_derivatives.updateActiveMembers();
}
void BridgedMultiColvarFunction::performTask(){
atoms_with_derivatives.deactivateAll();
if( !myBridgeVessel->prerequisitsCalculated() ){
mycolv->setTaskIndexToCompute( getCurrentPositionInTaskList() );
mycolv->performTask();
} else {
}
completeTask();
atoms_with_derivatives.emptyActiveMembers();
if( mycolv->isDensity() ){
for(unsigned j=0;j<mycolv->atomsWithCatomDer.getNumberActive();++j) atoms_with_derivatives.updateIndex( mycolv->atomsWithCatomDer[j] );
} else {
for(unsigned j=0;j<mycolv->atoms_with_derivatives.getNumberActive();++j) atoms_with_derivatives.updateIndex( mycolv->atoms_with_derivatives[j] );
}
atoms_with_derivatives.sortActiveList();
}
