Dynamics.h

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/*
** This file is part of eOn.
**
** SPDX-License-Identifier: BSD-3-Clause
**
** Copyright (c) 2010--present, eOn Development Team
** All rights reserved.
**
** Repo:
** https://github.com/TheochemUI/eOn
*/
#pragma once
 
#include "HelperFunctions.h"
#include "Matter.h"
#include "Parameters.h"
 
#include <cstdint>
 
#include "Eigen.h"
#include "EonLogger.h"
 
namespace eonc {

struct DynamicsConfig {
  double time_step{0.0};
  long steps{0};
  std::string thermostat_kind{"none"};
  double andersen_alpha{1.0};
  double andersen_tcol{0.0};
  double nose_mass{1.0};
  double langevin_friction{0.0};
  double kB{8.6173324e-5};
  double timeUnit{10.1805055};
  double temperature{300.0};
  bool write_movies{false};
  long write_movies_interval{1};
  long path_beads{8};
  std::string path_springs{"trotter"};
  double path_eco_omega_max{0.0};
  std::string path_gle_file;
  double path_pile_tau{0.0};
  double path_pile_scale{1.0};
  std::uint64_t path_seed{1};
 
  static DynamicsConfig fromParams(const Parameters &p) {
    return {p.dynamics_options().time_step,
            p.dynamics_options().steps,
            p.thermostat_options().kind,
            p.thermostat_options().andersen_alpha,
            p.thermostat_options().andersen_tcol,
            p.thermostat_options().nose_mass,
            p.thermostat_options().langevin_friction,
            p.constants().kB,
            p.constants().timeUnit,
            p.main_options().temperature,
            p.debug_options().write_movies,
            p.debug_options().write_movies_interval,
            p.thermostat_options().path_beads,
            p.thermostat_options().path_springs,
            p.thermostat_options().path_eco_omega_max,
            p.thermostat_options().path_gle_file,
            p.thermostat_options().path_pile_tau,
            p.thermostat_options().path_pile_scale,
            p.thermostat_options().path_seed};
  }
};
 
class Dynamics {
 
public:
  static const char ANDERSEN[];
  static const char NOSE_HOOVER[];
  static const char LANGEVIN[];
  static const char NONE[];
  static const char PILE[];
  static const char PIGLET[];
 
  Dynamics(Matter *matter, const DynamicsConfig &config);
 
  [[deprecated("Pass DynamicsConfig directly")]]
  Dynamics(Matter *matter, const Parameters &parameters)
      : Dynamics(matter, DynamicsConfig::fromParams(parameters)) {}
 
  ~Dynamics();
 
  void setTemperature(double temperature);
  void oneStep(int stepNumber = -1);
  void velocityVerlet();
  void run();
  void andersenCollision();
  void setThermalVelocity();
  void rescaleVelocity();
  void noseHooverVerlet();
  void langevinVerlet();
 
private:
  void nhcChainHalfStep(AtomMatrix &vel, double &kinE);
  void runPathIntegral();
 
  long nAtoms{0}, nFreeCoords{0};
 
  Matter *matter;
  DynamicsConfig m_config;
 
  double dt{0.0};
  double kB{0.0};
  double temperature{0.0};
  double vxi1{0.0}, vxi2{0.0}, xi1{0.0}, xi2{0.0};
  eonc::log::Scoped log;
};
 
} // namespace eonc