C++ (Cpp) setup_degrees_of_freedom Examples

Example #1

File: MolecularDynamics.cpp Project: drussel/imp

void MolecularDynamics::setup(const ParticleIndexes &ps)
{
  // Get starting score and derivatives, for first dynamics step velocities
  get_scoring_function()->evaluate(true);

  setup_degrees_of_freedom(ps);
}

Example #2

File: MolecularDynamics.cpp Project: j-ma-bu-l-l-ock/imp

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);
  }
}

Example #3

File: MolecularDynamics.cpp Project: drussel/imp

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);
    }

  }
}