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#include <math.h>
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#include "primitives/Atom.hpp"
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#include "primitives/SRI.hpp"
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#include "primitives/AbstractClasses.hpp"
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#include "brains/SimInfo.hpp"
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#include "UseTheForce/ForceFields.hpp"
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#include "brains/Thermo.hpp"
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#include "io/ReadWrite.hpp"
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#include "integrators/Integrator.hpp"
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#include "utils/simError.h"
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// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
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template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
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T( theInfo, the_ff )
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{
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GenericData* data;
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DoubleGenericData * chiValue;
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DoubleGenericData * integralOfChidtValue;
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chiValue = NULL;
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integralOfChidtValue = NULL;
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chi = 0.0;
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have_tau_thermostat = 0;
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have_target_temp = 0;
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have_chi_tolerance = 0;
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integralOfChidt = 0.0;
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if( theInfo->useInitXSstate ){
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// retrieve chi and integralOfChidt from simInfo
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data = info->getProperty(CHIVALUE_ID);
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if(data){
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chiValue = dynamic_cast<DoubleGenericData*>(data);
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}
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data = info->getProperty(INTEGRALOFCHIDT_ID);
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if(data){
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integralOfChidtValue = dynamic_cast<DoubleGenericData*>(data);
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}
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// chi and integralOfChidt should appear by pair
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if(chiValue && integralOfChidtValue){
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chi = chiValue->getData();
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integralOfChidt = integralOfChidtValue->getData();
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}
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}
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oldVel = new double[3*integrableObjects.size()];
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oldJi = new double[3*integrableObjects.size()];
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}
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template<typename T> NVT<T>::~NVT() {
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delete[] oldVel;
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delete[] oldJi;
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}
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template<typename T> void NVT<T>::moveA() {
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int i, j;
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DirectionalAtom* dAtom;
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Vector3d Tb;
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Vector3d ji;
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double mass;
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Vector3d vel;
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Vector3d pos;
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Vector3d frc;
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double instTemp;
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// We need the temperature at time = t for the chi update below:
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instTemp = tStats->getTemperature();
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for( i=0; i < integrableObjects.size(); i++ ){
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vel = integrableObjects[i]->getVel();
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pos = integrableObjects[i]->getPos();
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integrableObjects[i]->getFrc( frc );
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mass = integrableObjects[i]->getMass();
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for (j=0; j < 3; j++) {
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// velocity half step (use chi from previous step here):
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vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
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// position whole step
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pos[j] += dt * vel[j];
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}
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integrableObjects[i]->setVel( vel );
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integrableObjects[i]->setPos( pos );
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if( integrableObjects[i]->isDirectional() ){
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// get and convert the torque to body frame
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Tb = integrableObjects[i]->getTrq();
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integrableObjects[i]->lab2Body( Tb );
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// get the angular momentum, and propagate a half step
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ji = integrableObjects[i]->getJ();
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for (j=0; j < 3; j++)
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ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
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this->rotationPropagation( integrableObjects[i], ji );
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integrableObjects[i]->setJ( ji );
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}
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}
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if(nConstrained)
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constrainA();
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// Finally, evolve chi a half step (just like a velocity) using
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// temperature at time t, not time t+dt/2
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//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
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chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
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integralOfChidt += chi*dt2;
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}
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template<typename T> void NVT<T>::moveB( void ){
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int i, j, k;
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double Tb[3], ji[3];
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double vel[3], frc[3];
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double mass;
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double instTemp;
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double oldChi, prevChi;
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// Set things up for the iteration:
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oldChi = chi;
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for( i=0; i < integrableObjects.size(); i++ ){
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vel = integrableObjects[i]->getVel();
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for (j=0; j < 3; j++)
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oldVel[3*i + j] = vel[j];
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if( integrableObjects[i]->isDirectional() ){
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ji = integrableObjects[i]->getJ();
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for (j=0; j < 3; j++)
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oldJi[3*i + j] = ji[j];
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}
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}
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// do the iteration:
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for (k=0; k < 4; k++) {
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instTemp = tStats->getTemperature();
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// evolve chi another half step using the temperature at t + dt/2
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prevChi = chi;
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chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
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(tauThermostat*tauThermostat);
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for( i=0; i < integrableObjects.size(); i++ ){
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integrableObjects[i]->getFrc( frc );
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vel = integrableObjects[i]->getVel();
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mass = integrableObjects[i]->getMass();
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// velocity half step
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for (j=0; j < 3; j++)
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vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
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integrableObjects[i]->setVel( vel );
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if( integrableObjects[i]->isDirectional() ){
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// get and convert the torque to body frame
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Tb = integrableObjects[i]->getTrq();
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integrableObjects[i]->lab2Body( Tb );
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for (j=0; j < 3; j++)
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ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
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integrableObjects[i]->setJ( ji );
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}
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}
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if(nConstrained)
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constrainB();
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if (fabs(prevChi - chi) <= chiTolerance) break;
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}
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integralOfChidt += dt2*chi;
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}
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template<typename T> void NVT<T>::resetIntegrator( void ){
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chi = 0.0;
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integralOfChidt = 0.0;
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}
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template<typename T> int NVT<T>::readyCheck() {
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//check parent's readyCheck() first
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if (T::readyCheck() == -1)
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return -1;
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// First check to see if we have a target temperature.
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// Not having one is fatal.
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if (!have_target_temp) {
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sprintf( painCave.errMsg,
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"You can't use the NVT integrator without a targetTemp!\n"
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);
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painCave.isFatal = 1;
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painCave.severity = OOPSE_ERROR;
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simError();
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return -1;
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}
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// We must set tauThermostat.
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if (!have_tau_thermostat) {
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sprintf( painCave.errMsg,
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"If you use the constant temperature\n"
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"\tintegrator, you must set tauThermostat.\n");
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painCave.severity = OOPSE_ERROR;
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painCave.isFatal = 1;
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simError();
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return -1;
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}
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if (!have_chi_tolerance) {
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sprintf( painCave.errMsg,
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"In NVT integrator: setting chi tolerance to 1e-6\n");
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chiTolerance = 1e-6;
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have_chi_tolerance = 1;
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painCave.severity = OOPSE_INFO;
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painCave.isFatal = 0;
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simError();
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}
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return 1;
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}
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template<typename T> double NVT<T>::getConservedQuantity(void){
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double conservedQuantity;
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double fkBT;
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double Energy;
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double thermostat_kinetic;
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double thermostat_potential;
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fkBT = (double)(info->ndf) * kB * targetTemp;
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Energy = tStats->getTotalE();
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thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
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(2.0 * eConvert);
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thermostat_potential = fkBT * integralOfChidt / eConvert;
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
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return conservedQuantity;
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}
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template<typename T> string NVT<T>::getAdditionalParameters(void){
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string parameters;
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const int BUFFERSIZE = 2000; // size of the read buffer
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char buffer[BUFFERSIZE];
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sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
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parameters += buffer;
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return parameters;
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}
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