void MultiColvarBase::mergeDerivatives( const unsigned& ider, const double& df ){
unsigned vstart=getNumberOfDerivatives()*ider;
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned iatom=3*atoms_with_derivatives[i];
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) ); iatom++;
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) ); iatom++;
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) );
}
unsigned nvir=3*getNumberOfAtoms();
for(unsigned j=0;j<9;++j){
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
}
}
void ParticleManager::derivativeEvaluate( Eigen::Matrix< double, Eigen::Dynamic, 1 >& derivative )
{
clearForceAccumulators();
for (std::vector<IForce*>::iterator iter = m_pForces.begin(); iter != m_pForces.end(); iter++)
{
(*iter)->calculate();
}
if ( m_pConstraintManager != NULL )
{
m_pConstraintManager->computeConstraintForces();
m_pConstraintManager->applyConstraintForces();
}
derivative.resize( m_particles.size() * 6 );
accumulateDerivative( derivative );
}
void BridgedMultiColvarFunction::mergeDerivatives( const unsigned& ider, const double& df ){
unsigned vstart=getNumberOfDerivatives()*ider;
// Merge atom derivatives
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned iatom=3*atoms_with_derivatives[i];
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) ); iatom++;
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) ); iatom++;
accumulateDerivative( iatom, df*getElementDerivative(vstart+iatom) );
}
// Merge virial derivatives
unsigned nvir=3*mycolv->getNumberOfAtoms();
for(unsigned j=0;j<9;++j){
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
}
// Merge local atom derivatives
for(unsigned j=0;j<getNumberOfAtoms();++j){
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
accumulateDerivative( nvir, df*getElementDerivative(vstart+nvir) ); nvir++;
}
plumed_dbg_assert( nvir==getNumberOfDerivatives() );
}
void Mapping::mergeDerivatives( const unsigned& ider, const double& df ){
unsigned cur = getCurrentTask(), frameno=ider*getNumberOfReferencePoints() + cur;
for(unsigned i=0;i<getNumberOfArguments();++i){
accumulateDerivative( i, df*dfframes[frameno]*mymap->getArgumentDerivative(cur,i) );
}
if( getNumberOfAtoms()>0 ){
Vector ader; Tensor tmpvir; tmpvir.zero();
unsigned n=getNumberOfArguments();
for(unsigned i=0;i<getNumberOfAtoms();++i){
ader=mymap->getAtomDerivatives( cur, i );
accumulateDerivative( n, df*dfframes[frameno]*ader[0] ); n++;
accumulateDerivative( n, df*dfframes[frameno]*ader[1] ); n++;
accumulateDerivative( n, df*dfframes[frameno]*ader[2] ); n++;
tmpvir += -1.0*Tensor( getPosition(i), ader );
}
Tensor vir;
if( !mymap->getVirial( cur, vir ) ) vir=tmpvir;
accumulateDerivative( n, df*dfframes[frameno]*vir(0,0) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(0,1) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(0,2) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(1,0) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(1,1) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(1,2) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(2,0) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(2,1) ); n++;
accumulateDerivative( n, df*dfframes[frameno]*vir(2,2) );
}
}
void ActionWithVessel::mergeDerivatives( const unsigned& ider, const double& df ){
unsigned nder=getNumberOfDerivatives(), vstart=nder*ider;
for(unsigned i=0;i<getNumberOfDerivatives();++i){
accumulateDerivative( i, df*derivatives[vstart+i] );
}
}