void MolecularDynamics::assign_velocities(Float temperature) {
ParticleIndexes ips = get_simulation_particle_indexes();
setup_degrees_of_freedom(ips);
ParticlesTemp ps = IMP::internal::get_particle(get_model(), ips);
boost::normal_distribution<Float> mrng(0., 1.);
boost::variate_generator<RandomNumberGenerator &,
boost::normal_distribution<Float> >
sampler(random_number_generator, mrng);
for (ParticlesTemp::iterator iter = ps.begin(); iter != ps.end();
++iter) {
Particle *p = *iter;
LinearVelocity(p).set_velocity(algebra::Vector3D(sampler(), sampler(),
sampler()));
}
Float rescale =
sqrt(temperature / get_kinetic_temperature(get_kinetic_energy()));
for (ParticlesTemp::iterator iter = ps.begin(); iter != ps.end();
++iter) {
Particle *p = *iter;
LinearVelocity v(p);
algebra::Vector3D velocity = v.get_velocity();
velocity *= rescale;
v.set_velocity(velocity);
}
}
void MolecularDynamics::assign_velocities(Float temperature)
{
ParticleIndexes ips=get_simulation_particle_indexes();
setup_degrees_of_freedom(ips);
ParticlesTemp ps= IMP::internal::get_particle(get_model(), ips);
boost::normal_distribution<Float> mrng(0., 1.);
boost::variate_generator<RandomNumberGenerator&,
boost::normal_distribution<Float> >
sampler(random_number_generator, mrng);
for (ParticlesTemp::iterator iter = ps.begin();
iter != ps.end(); ++iter) {
Particle *p = *iter;
for (int i = 0; i < 3; ++i) {
p->set_value(vs_[i], sampler());
}
}
Float rescale = sqrt(temperature/
get_kinetic_temperature(get_kinetic_energy()));
for (ParticlesTemp::iterator iter = ps.begin();
iter != ps.end(); ++iter) {
Particle *p = *iter;
for (int i = 0; i < 3; ++i) {
Float 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()));
}
}
core::MonteCarloMoverResult RevoluteJointMover::do_propose() {
IMP_OBJECT_LOG;
boost::normal_distribution<double> mrng(0, stddev_);
boost::variate_generator<RandomNumberGenerator &,
boost::normal_distribution<double> >
sampler(random_number_generator, mrng);
for (unsigned int i = 0; i < joints_.size(); ++i) {
originals_[i] = joints_[i]->get_angle();
joints_[i]->set_angle(originals_[i] + sampler());
}
//get changed particles' coordinates
ParticleIndexes idx;
core::RigidMembers tmp(joints_[0]->get_parent_node().get_rigid_members());
for (unsigned int i = 0; i < tmp.size(); ++i)
idx.push_back(tmp[i]->get_index());
for (unsigned int j = 0; j < joints_.size(); ++j) {
tmp = joints_[j]->get_child_node().get_rigid_members();
for (unsigned int i = 0; i < tmp.size(); ++i)
idx.push_back(tmp[i]->get_index());
}
return core::MonteCarloMoverResult(idx, 1.0);
}
MonteCarloMoverResult NormalMover::do_propose() {
IMP_OBJECT_LOG;
boost::normal_distribution<double> mrng(0, stddev_);
boost::variate_generator<RandomNumberGenerator &,
boost::normal_distribution<double> >
sampler(random_number_generator, mrng);
for (unsigned int i = 0; i < pis_.size(); ++i) {
for (unsigned int j = 0; j < keys_.size(); ++j) {
originals_[i][j] = get_model()->get_attribute(keys_[j], pis_[i]);
}
for (unsigned int j = 0; j < keys_.size(); ++j) {
IMP_USAGE_CHECK(
get_model()->get_is_optimized(keys_[j], pis_[i]),
"NormalMover can't move non-optimized attribute. "
<< "particle: " << get_model()->get_particle_name(pis_[i])
<< "attribute: " << keys_[j]);
get_model()->set_attribute(keys_[j], pis_[i],
originals_[i][j] + sampler());
}
}
return MonteCarloMoverResult(pis_, 1.0);
}
