void VectorMultiColvar::addWeightedValueDerivatives( const unsigned& iatom, const unsigned& base_cv_no, const double& weight, multicolvar::MultiColvarFunction* func ){
if( usingLowMem() ){
vecs->recompute( iatom, 1 );
for(unsigned j=0;j<getNumberOfQuantities()-5;++j) vecs->chainRuleForComponent( 1, j, 5+j, base_cv_no, weight, func );
} else {
for(unsigned j=0;j<getNumberOfQuantities()-5;++j) vecs->chainRuleForComponent( iatom, j, 5+j, base_cv_no, weight, func );
}
}
void MultiColvarBase::addWeightedValueDerivatives( const unsigned& iatom, const unsigned& base_cv_no, const double& weight, MultiColvarFunction* func ){
plumed_dbg_assert( myvalues );
if( usingLowMem() ){
myvalues->recompute( iatom, 0 );
myvalues->chainRuleForComponent( 0, 0, base_cv_no, weight, func );
} else {
myvalues->chainRuleForComponent( iatom, 0, base_cv_no, weight, func );
}
}
void MultiColvarBase::addCentralAtomDerivativeToFunction( const unsigned& iatom, const unsigned& jout, const unsigned& base_cv_no, const Vector& der, MultiColvarFunction* func ){
plumed_dbg_assert( mycatoms );
if( usingLowMem() ){
mycatoms->recompute( iatom, 0 ); ;
mycatoms->addAtomsDerivatives( 0, jout, base_cv_no, der, func );
} else{
mycatoms->addAtomsDerivatives( iatom, jout, base_cv_no, der, func );
}
}
void VectorMultiColvar::addOrientationDerivativesToBase( const unsigned& iatom, const unsigned& jstore, const unsigned& base_cv_no,
const std::vector<double>& der, multicolvar::MultiColvarFunction* func ){
if( usingLowMem() ){
if(jstore==1){
if(firstcall){ vecs->recompute( iatom, jstore ); firstcall=false; }
vecs->chainRuleForVector( jstore, 0, base_cv_no, der, func );
} else {
vecs->recompute( iatom, jstore );
vecs->chainRuleForVector( jstore, 0, base_cv_no, der, func );
}
} else {
vecs->chainRuleForVector( iatom, 0, base_cv_no, der, func );
}
}
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;
}