void BerendsenThermostatOptimizerState::rescale_velocities() const
{
MolecularDynamics *md = dynamic_cast<MolecularDynamics *>(get_optimizer());
IMP_INTERNAL_CHECK(md, "Can only use velocity scaling with "
"the molecular dynamics optimizer.");
double kinetic_temp = md->get_kinetic_temperature(md->get_kinetic_energy());
double rescale = std::sqrt(1.0 + (md->get_last_time_step() / tau_)
* (temperature_ / kinetic_temp - 1.0));
for (unsigned int i=0; i< pis_.size(); ++i) {
Particle *p = pis_[i];
for (int i = 0; i < 3; ++i) {
double velocity = p->get_value(vs_[i]);
velocity *= rescale;
p->set_value(vs_[i], velocity);
}
}
}
void LangevinThermostatOptimizerState::rescale_velocities() const {
static const double gas_constant = 8.31441e-7;
MolecularDynamics *md = dynamic_cast<MolecularDynamics *>(get_optimizer());
double c1 = exp(-gamma_ * md->get_last_time_step());
double c2 = sqrt((1.0 - c1) * gas_constant * temperature_);
IMP_INTERNAL_CHECK(md,
"Can only use velocity scaling with "
"the molecular dynamics optimizer.");
boost::normal_distribution<Float> mrng(0., 1.);
boost::variate_generator<RandomNumberGenerator &,
boost::normal_distribution<Float> >
sampler(random_number_generator, mrng);
for (unsigned int i = 0; i < pis_.size(); ++i) {
Particle *p = pis_[i];
double mass = Mass(p).get_mass();
LinearVelocity lv(p);
lv.set_velocity(c1 * lv.get_velocity()
+ c2 * sqrt((c1 + 1.0) / mass)
* algebra::Vector3D(sampler(), sampler(), sampler()));
}
}