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);
}
}
MissionControlSpeedFilter::MissionControlSpeedFilter()
:
baseTwistInHeadingFrame_(),
maximumBaseTwistInHeadingFrame_(LinearVelocity(std::numeric_limits<LinearVelocity::Scalar>::max(),
std::numeric_limits<LinearVelocity::Scalar>::max(),
std::numeric_limits<LinearVelocity::Scalar>::max()),
LocalAngularVelocity(std::numeric_limits<LinearVelocity::Scalar>::max(),
std::numeric_limits<LinearVelocity::Scalar>::max(),
std::numeric_limits<LinearVelocity::Scalar>::max()) )
{
filteredVelocities_[0].setAlpha(0.005);
filteredVelocities_[1].setAlpha(0.05);
filteredVelocities_[2].setAlpha(0.05);
}
Float MolecularDynamics::get_kinetic_energy() const {
// Conversion factor to get energy in kcal/mol from velocities in A/fs and
// mass in g/mol
static const Float conversion = 1.0 / 4.1868e-4;
Float ekinetic = 0.;
ParticlesTemp ps = get_simulation_particles();
for (ParticlesTemp::iterator iter = ps.begin(); iter != ps.end();
++iter) {
Particle *p = *iter;
algebra::Vector3D v = LinearVelocity(p).get_velocity();
Float mass = Mass(p).get_mass();
ekinetic += mass * (v[0] * v[0] + v[1] * v[1] + v[2] * v[2]);
}
return 0.5 * ekinetic * conversion;
}
void ICreature::CastEigenToInduced()
{
SetLinearVelocity(LinearVelocity(ZERO, GetTotalLinVelocity()));
SetAngularSpeed(AngularSpeed(ZERO, GetTotalAngSpeed()));
}
