void MolecularDynamics::propagate_coordinates(const ParticleIndexes &ps,
double ts) {
for (unsigned int i = 0; i < ps.size(); ++i) {
Float invmass = 1.0 / Mass(get_model(), ps[i]).get_mass();
core::XYZ d(get_model(), ps[i]);
LinearVelocity v(get_model(), ps[i]);
algebra::Vector3D coord = d.get_coordinates();
algebra::Vector3D dcoord = d.get_derivatives();
// calculate velocity at t+(delta t/2) from that at t
algebra::Vector3D velocity = v.get_velocity();
velocity += 0.5 * dcoord * deriv_to_acceleration * invmass * ts;
for (unsigned int j = 0; j < 3; ++j) {
cap_velocity_component(velocity[j]);
}
v.set_velocity(velocity);
// calculate position at t+(delta t) from that at t
coord += velocity * ts;
d.set_coordinates(coord);
}
}
void MolecularDynamics::propagate_coordinates(const ParticleIndexes &ps,
double ts)
{
for (unsigned int i=0; i< ps.size(); ++i) {
Float invmass = 1.0 / Mass(get_model(), ps[i]).get_mass();
for (unsigned j = 0; j < 3; ++j) {
core::XYZ d(get_model(), ps[i]);
Float coord = d.get_coordinate(j);
Float dcoord = d.get_derivative(j);
// calculate velocity at t+(delta t/2) from that at t
Float velocity = get_model()->get_attribute(vs_[j], ps[i]);
velocity += 0.5 * dcoord * deriv_to_acceleration * invmass * ts;
cap_velocity_component(velocity);
get_model()->set_attribute(vs_[j], ps[i], velocity);
// calculate position at t+(delta t) from that at t
coord += velocity * ts;
d.set_coordinate(j, coord);
}
}
}