source: src/Thermostats/GaussianThermostat.cpp@ 7d1b6a

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

/*
 * GaussianThermostat.cpp
 *
 *  Created on: Aug 18, 2010
 *      Author: crueger
 */

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

#include "CodePatterns/MemDebug.hpp"

#include "GaussianThermostat.hpp"

#include "Atom/AtomSet.hpp"
#include "CodePatterns/Log.hpp"
#include "config.hpp"
#include "Element/element.hpp"
#include "Helpers/defs.hpp"
#include "LinearAlgebra/Vector.hpp"
#include "Parser/PcpParser_helper.hpp"
#include "World.hpp"

#include <set>

GaussianThermostat::GaussianThermostat(int _ScaleTempStep) :
  E(0),G(0),
  ScaleTempStep(_ScaleTempStep)
{}

GaussianThermostat::GaussianThermostat() :
  E(0),G(0),
  ScaleTempStep(25)
{}

GaussianThermostat::~GaussianThermostat()
{}

const char *ThermostatTraits<GaussianThermostat>::name = "Gaussian";

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

Thermostat *ThermostatTraits<GaussianThermostat>::make(class ConfigFileBuffer * const fb){
  int ScaleTempStep;
  const int verbose = 0;
  ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
  return new class GaussianThermostat(ScaleTempStep);
}

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

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

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

template <class ForwardIterator>
double GaussianThermostat::doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end){
  LOG(2,  "Applying Gaussian thermostat...");
  init(step,begin,end);
  double G_over_E = G/E;
  LOG(1, "Gaussian Least Constraint constant is " << G_over_E << ".");
  double ekin =0;
  for(ForwardIterator iter=begin;iter!=end;++iter){
    Vector U = (*iter)->getAtomicVelocityAtStep(step);
    if ((*iter)->getFixedIon() == 0) {// even FixedIon moves, only not by other's forces
      U += World::getInstance().getConfig()->Deltat * G_over_E * U;
      ekin += (*iter)->getType()->getMass() * U.NormSquared();
    }
    (*iter)->setAtomicVelocityAtStep(step, U);
  }
  return ekin;
}

template <class ForwardIterator>
void GaussianThermostat::init(unsigned int step,ForwardIterator begin, ForwardIterator end){
  E=0;
  G=0;
  for(ForwardIterator iter=begin;iter!=end;++iter){
    const Vector &U = (*iter)->getAtomicVelocityAtStep(step);
    const Vector &F = (*iter)->getAtomicForceAtStep(step);
    if ((*iter)->getFixedIon() == 0){ // even FixedIon moves, only not by other's forces
      G += U.ScalarProduct(F);
      E += U.NormSquared()*(*iter)->getType()->getMass();
    }
  }
}

double GaussianThermostat::getE() const{
  return E;
}

double GaussianThermostat::getG() const{
  return G;
}

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

std::string GaussianThermostat::writeParams(){
  std::stringstream sstr;
  sstr << ScaleTempStep;
  return sstr.str();
}