source: src/Thermostats/Langevin.cpp@ 4464ef

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
 * 
 *
 *   This file is part of MoleCuilder.
 *
 *    MoleCuilder is free software: you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation, either version 2 of the License, or
 *    (at your option) any later version.
 *
 *    MoleCuilder is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
 */

/*
 * Langevin.cpp
 *
 *  Created on: Aug 20, 2010
 *      Author: crueger
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "CodePatterns/MemDebug.hpp"

#include "Langevin.hpp"

#include "CodePatterns/Log.hpp"
#include "Parser/PcpParser_helper.hpp"
#include "Element/element.hpp"
#include "Helpers/defs.hpp"
#include "Thermostats/ThermoStatContainer.hpp"

#include <boost/random/mersenne_twister.hpp>
#include <boost/random/normal_distribution.hpp>
#include <boost/random/variate_generator.hpp>

#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
#include "RandomNumbers/RandomNumberGenerator.hpp"

Langevin::Langevin(double _TempFrequency,double _alpha) :
  TempFrequency(_TempFrequency),
  alpha(_alpha),
  rng_engine(new boost::mt19937),
  rng_distribution(NULL)
{}

Langevin::Langevin() :
  TempFrequency(2.5),
  alpha(0.),
  rng_engine(new boost::mt19937),
  rng_distribution(NULL)
{}

Langevin::~Langevin()
{
  delete rng_engine;
  delete rng_distribution;
}

const char *ThermostatTraits<Langevin>::name = "Langevin";

std::string ThermostatTraits<Langevin>::getName(){
  return ThermostatTraits<Langevin>::name;
}

Thermostat *ThermostatTraits<Langevin>::make(class ConfigFileBuffer * const fb){
  double TempFrequency;
  double alpha;
  const int verbose = 0;
  ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read gamma
  if (ParseForParameter(verbose,fb,"Thermostat", 0, 3, 1, double_type, &alpha, 1, optional)) {
    LOG(2, "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << ".");
  } else {
    alpha = 1.;
  }
  return new Langevin(TempFrequency,alpha);
}

double Langevin::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::list) atoms){
  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
}

double Langevin::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::vector) atoms){
  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
}

double Langevin::scaleAtoms(unsigned int step,double ActualTemp,ATOMSET(std::set) atoms){
  return doScaleAtoms(step,ActualTemp,atoms.begin(),atoms.end());
}

template <class ForwardIterator>
double Langevin::doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end){
  LOG(2,  "Applying Langevin thermostat...");
  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator("mt19937", "normal_distribution");
  const double rng_min = random.min();
  const double rng_max = random.max();
  double ekin=0;
  for(ForwardIterator iter=begin;iter!=end;++iter){
    double sigma  = sqrt(getContainer().TargetTemp/(*iter)->getType()->getMass()); // sigma = (k_b T)/m (Hartree/atomicmass = atomiclength/atomictime)
    rng_distribution = new boost::normal_distribution<>(0,sigma);
    boost::variate_generator<boost::mt19937&, boost::normal_distribution<> > rng(*rng_engine, *rng_distribution);
    Vector U = (*iter)->getAtomicVelocityAtStep(step);
    if ((*iter)->getFixedIon() == 0) { // even FixedIon moves, only not by other's forces
      // throw a dice to determine whether it gets hit by a heat bath particle
      if (((((random()/(rng_max-rng_min)))*TempFrequency) < 1.)) {
        // pick three random numbers from a Boltzmann distribution around the desired temperature T for each momenta axis
        const double oldNorm = U.Norm();
        for (int d=0; d<NDIM; d++)
          U[d] = rng();
        LOG(3, "Particle " << (**iter) << " was hit (sigma " << sigma << "): " << oldNorm << " -> " << U.Norm());
      }
      ekin += 0.5*(*iter)->getType()->getMass() * U.NormSquared();
    }
    (*iter)->setAtomicVelocityAtStep(step, U);
    delete rng_distribution;
    rng_distribution = NULL;
  }
  return ekin;
}

std::string Langevin::name(){
  return ThermostatTraits<Langevin>::name;
}

std::string Langevin::writeParams(){
  stringstream sstr;
  sstr << TempFrequency << "\t" << alpha;
  return sstr.str();
}