IMPISD_BEGIN_NAMESPACE
Nuisance Nuisance::setup_particle(Particle *p, double nuisance) {
if (!Nuisance::particle_is_instance(p))
{
p->add_attribute(get_nuisance_key(), nuisance);
} else {
Nuisance(p).set_nuisance(nuisance);
}
return Nuisance(p);
}
IMPISD_BEGIN_NAMESPACE
void Scale::do_setup_particle(Model *m, ParticleIndex pi,
double scale) {
if (!Nuisance::get_is_setup(m, pi)) Nuisance::setup_particle(m, pi, scale);
Nuisance(m, pi).set_lower(0.);
}
void MolecularDynamicsMover::do_reject() {
IMP_OBJECT_LOG;
ParticlesTemp ps = md_->get_simulation_particles();
unsigned nparts = ps.size();
IMP_USAGE_CHECK(coordinates_.size() == ps.size(),
"The list of particles that move has been changed!");
IMP_USAGE_CHECK(velocities_.size() == ps.size(),
"The list of particles that move has been changed!");
for (unsigned i = 0; i < nparts; i++) {
bool isnuisance = Nuisance::get_is_setup(ps[i]);
bool isxyz = core::XYZ::get_is_setup(ps[i]);
IMP_USAGE_CHECK(isnuisance || isxyz,
"Particle " << ps[i] << " is neither nuisance nor xyz!");
if (isnuisance) {
IMP_USAGE_CHECK(coordinates_[i].size() == 1,
"wrong size for coordinates_[" << i << "] !");
IMP_USAGE_CHECK(velocities_[i].size() == 1, "wrong size for velocities_["
<< i << "] !");
Nuisance(ps[i]).set_nuisance(coordinates_[i][0]);
ps[i]->set_value(FloatKey("vel"), velocities_[i][0]);
}
if (isxyz) {
IMP_USAGE_CHECK(coordinates_[i].size() == 3,
"wrong size for coordinates_[" << i << "] !");
IMP_USAGE_CHECK(velocities_[i].size() == 3, "wrong size for velocities_["
<< i << "] !");
core::XYZ(ps[i]).set_coordinate(0, coordinates_[i][0]);
core::XYZ(ps[i]).set_coordinate(1, coordinates_[i][1]);
core::XYZ(ps[i]).set_coordinate(2, coordinates_[i][2]);
ps[i]->set_value(FloatKey("vx"), velocities_[i][0]);
ps[i]->set_value(FloatKey("vy"), velocities_[i][1]);
ps[i]->set_value(FloatKey("vz"), velocities_[i][2]);
}
}
}
void MolecularDynamicsMover::save_coordinates() {
IMP_OBJECT_LOG;
ParticlesTemp ps = md_->get_simulation_particles();
unsigned nparts = ps.size();
coordinates_.clear();
coordinates_.reserve(nparts);
velocities_.clear();
velocities_.reserve(nparts);
for (unsigned i = 0; i < nparts; i++) {
bool isnuisance = Nuisance::get_is_setup(ps[i]);
bool isxyz = core::XYZ::get_is_setup(ps[i]);
IMP_USAGE_CHECK(isnuisance || isxyz,
"Particle " << ps[i] << " is neither nuisance nor xyz!");
if (isnuisance) {
std::vector<double> x(1, Nuisance(ps[i]).get_nuisance());
coordinates_.push_back(x);
std::vector<double> v(1, ps[i]->get_value(FloatKey("vel")));
velocities_.push_back(v);
}
if (isxyz) {
std::vector<double> coords;
core::XYZ d(ps[i]);
coords.push_back(d.get_coordinate(0));
coords.push_back(d.get_coordinate(1));
coords.push_back(d.get_coordinate(2));
coordinates_.push_back(coords);
std::vector<double> v;
v.push_back(ps[i]->get_value(FloatKey("vx")));
v.push_back(ps[i]->get_value(FloatKey("vy")));
v.push_back(ps[i]->get_value(FloatKey("vz")));
velocities_.push_back(v);
}
}
}
IMPISD_BEGIN_NAMESPACE
Scale Scale::setup_particle(Particle *p, double scale)
{
if (!Nuisance::particle_is_instance(p))
Nuisance::setup_particle(p,scale);
Nuisance(p).set_lower(0.);
return Scale(p);
}
