IMPATOM_BEGIN_NAMESPACE
Simulator::Simulator(Model *m, std::string name, double wave_factor)
: Optimizer(m, name), wave_factor_(wave_factor) {
temperature_ = strip_units(IMP::internal::DEFAULT_TEMPERATURE);
max_time_step_ = 2;
current_time_ = 0;
last_time_step_ = -1;
}
/** Return the scale for diffusion under the specified force,
the diffusion coefficient D and the time step t.
@param D diffusion coefficient
@param force force coefficient
@param dtfs time step in femtoseconds
@param temp temperature in Kelvin
\*/
double get_diffusion_length(double D, double force, double dtfs, double temp) {
unit::Divide<unit::Femtosecond, unit::Femtojoule>::type dtikt =
unit::Femtosecond(dtfs) /
unit::Femtojoule(IMP::internal::KB * unit::Kelvin(temp));
unit::Femtonewton nforce(get_force_in_femto_newtons(force));
// unit::Angstrom R(sampler_());
unit::Angstrom force_term(nforce * unit::SquareAngstromPerFemtosecond(D) *
dtikt);
return strip_units(force_term);
}
double get_diffusion_length(double D, double dtfs) {
unit::Angstrom d = sqrt(6.0 * unit::SquareAngstromPerFemtosecond(D) *
unit::Femtosecond(dtfs));
return strip_units(d);
}
