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#include <BALL/MOLMEC/COMMON/stretchComponent.h>
#include <BALL/MOLMEC/COMMON/forceField.h>
namespace BALL
{
StretchComponent::StretchComponent()
{
}
StretchComponent::StretchComponent(ForceField& ff)
: ForceFieldComponent(ff)
{
}
StretchComponent::~StretchComponent()
{
}
double StretchComponent::updateEnergy()
{
// initial energy is zero
energy_ = 0;
bool use_selection = getForceField()->getUseSelection();
// iterate over all bonds, sum up the energies
for (Size i = 0; i < stretch_.size(); i++)
{
const Atom* atom1 = stretch_[i].atom1;
const Atom* atom2 = stretch_[i].atom2;
if (!use_selection || atom1->isSelected() || atom2->isSelected())
{
double distance = atom1->getDistance(*atom2);
energy_ += stretch_[i].values.k * (distance - stretch_[i].values.r0) * (distance - stretch_[i].values.r0);
}
}
return energy_;
}
// calculates and adds its forces to the current forces of the force field
void StretchComponent::updateForces()
{
if (getForceField() == 0)
{
return;
}
bool use_selection = getForceField()->getUseSelection();
// iterate over all bonds, update the forces
for (Size i = 0 ; i < stretch_.size(); i++)
{
Atom* atom1 = stretch_[i].atom1;
Atom* atom2 = stretch_[i].atom2;
Vector3 direction(atom1->getPosition() - atom2->getPosition());
double distance = direction.getLength();
if (distance != 0.0)
{
// unit conversion: from kJ/(mol A) -> N
// kJ -> J: 1e3
// A -> m: 1e10
// J/mol -> J: Avogadro
direction *= 1e13 / Constants::AVOGADRO * 2 * stretch_[i].values.k * (distance - stretch_[i].values.r0) / distance;
if (!use_selection || atom1->isSelected())
{
atom1->getForce() -= direction;
}
if (!use_selection || atom2->isSelected())
{
atom2->getForce() += direction;
}
}
}
}
}
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