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#include <BALL/MOLMEC/COMMON/bendComponent.h>
#include <BALL/MOLMEC/COMMON/forceField.h>
namespace BALL
{
BendComponent::BendComponent()
{
}
BendComponent::BendComponent(ForceField& ff)
: ForceFieldComponent(ff)
{
}
BendComponent::~BendComponent()
{
}
// calculates the current energy of this component
double BendComponent::updateEnergy()
{
energy_ = 0;
// abort for an empty vector
if (bend_.empty())
{
return 0.0;
}
Vector3 v1, v2;
bool use_selection = getForceField()->getUseSelection();
QuadraticAngleBend::Data* bend_it = &(bend_[0]);
QuadraticAngleBend::Data* bend_end = &(bend_[bend_.size() - 1]);
for (; bend_it <= bend_end ; ++bend_it)
{
const Atom* atom1 = bend_it->atom1;
const Atom* atom2 = bend_it->atom2;
const Atom* atom3 = bend_it->atom3;
if (!use_selection ||
( atom1->isSelected()
|| atom2->isSelected()
|| atom3->isSelected()))
{
v1 = atom1->getPosition() - atom2->getPosition();
v2 = atom3->getPosition() - atom2->getPosition();
double square_length = v1.getSquareLength() * v2.getSquareLength();
if (square_length == 0.0)
{
continue;
}
double costheta = v1 * v2 / sqrt(square_length);
double theta;
if (costheta > 1.0)
{
theta = 0.0;
}
else if (costheta < -1.0)
{
theta = Constants::PI;
}
else
{
theta = acos(costheta);
}
theta -= bend_it->values.theta0;
energy_ += bend_it->values.k * theta * theta;
}
}
return energy_;
}
// calculates and adds its forces to the current forces of the force field
void BendComponent::updateForces()
{
if ((getForceField() == 0) || (getForceField()->getSystem() == 0))
{
return;
}
bool use_selection = getForceField()->getUseSelection();
for (Size i = 0; i < bend_.size(); i++)
{
Atom* atom1 = bend_[i].atom1;
Atom* atom2 = bend_[i].atom2;
Atom* atom3 = bend_[i].atom3;
if (!use_selection
|| atom1->isSelected()
|| atom2->isSelected()
|| atom3->isSelected())
{
// Calculate the vector between atom1 and atom2,
// test if the vector has length larger than 0 and normalize it
Vector3 v1 = atom1->getPosition() - atom2->getPosition();
Vector3 v2 = atom3->getPosition() - atom2->getPosition();
double length = v1.getLength();
if (length == 0.0) continue;
double inverse_length_v1 = 1.0 / length;
v1 *= inverse_length_v1 ;
// Calculate the vector between atom3 and atom2,
// test if the vector has length larger than 0 and normalize it
length = v2.getLength();
if (length == 0.0) continue;
double inverse_length_v2 = 1/length;
v2 *= inverse_length_v2;
// Calculate the cos of theta and then theta
double costheta = v1 * v2;
double theta;
if (costheta > 1.0)
{
theta = 0.0;
}
else if (costheta < -1.0)
{
theta = Constants::PI;
}
else
{
theta = acos(costheta);
}
// unit conversion: kJ/(mol A) -> N
// kJ -> J: 1e3
// A -> m : 1e10
// J/mol -> mol: Avogadro
double factor = 1e13 / Constants::AVOGADRO * 2 * bend_[i].values.k * (theta - bend_[i].values.theta0);
// Calculate the cross product of v1 and v2, test if it has length unequal 0,
// and normalize it.
Vector3 cross = v1 % v2;
if ((length = cross.getLength()) != 0)
{
cross *= (1.0 / length);
}
else
{
continue;
}
Vector3 n1 = v1 % cross;
Vector3 n2 = v2 % cross;
n1 *= factor * inverse_length_v1;
n2 *= factor * inverse_length_v2;
if (!use_selection)
{
atom1->getForce() -= n1;
atom2->getForce() += n1;
atom2->getForce() -= n2;
atom3->getForce() += n2;
}
else
{
if (atom1->isSelected())
{
atom1->getForce() -= n1;
}
if (atom2->isSelected())
{
atom2->getForce() += n1;
atom2->getForce() -= n2;
}
if (atom3->isSelected())
{
atom3->getForce() += n2;
}
}
}
}
}
}
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