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#include <math.h> |
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#include "Atom.hpp" |
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#include "SRI.hpp" |
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#include "AbstractClasses.hpp" |
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#include "SimInfo.hpp" |
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#include "ForceFields.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "Integrator.hpp" |
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#include "simError.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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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#include "brains/mpiSimulation.hpp" |
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#endif |
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// Basic isotropic thermostating and barostating via the Melchionna |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
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NPTi::NPTi ( 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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DoubleArrayData * etaValue; |
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DoubleVectorGenericData * etaValue; |
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vector<double> etaArray; |
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eta = 0.0; |
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if( theInfo->useInitXSstate ){ |
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// retrieve eta from simInfo if |
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data = info->getProperty(ETAVALUE_ID); |
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data = info->getPropertyByName(ETAVALUE_ID); |
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if(data){ |
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etaValue = dynamic_cast<DoubleArrayData*>(data); |
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etaValue = dynamic_cast<DoubleVectorGenericData*>(data); |
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if(etaValue){ |
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etaArray = etaValue->getData(); |
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eta = etaArray[0]; |
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eta = (*etaValue)[0]; |
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oldEta = eta; |
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} |
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} |
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} |
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} |
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template<typename T> NPTi<T>::~NPTi() { |
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NPTi::~NPTi() { |
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//nothing for now |
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} |
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template<typename T> void NPTi<T>::resetIntegrator() { |
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eta = 0.0; |
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T::resetIntegrator(); |
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} |
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template<typename T> void NPTi<T>::evolveEtaA() { |
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void NPTi::evolveEtaA() { |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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oldEta = eta; |
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} |
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template<typename T> void NPTi<T>::evolveEtaB() { |
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void NPTi::evolveEtaB() { |
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prevEta = eta; |
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eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) / |
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(p_convert*NkBT*tb2)); |
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} |
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template<typename T> void NPTi<T>::calcVelScale(void) { |
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void NPTi::calcVelScale() { |
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vScale = chi + eta; |
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} |
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template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) { |
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int i; |
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for(i=0; i<3; i++) sc[i] = vel[i] * vScale; |
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void NPTi::getVelScaleA(Vector3d& sc, const Vector3d& vel) { |
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sc = vel * vScale; |
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} |
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template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){ |
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int i; |
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for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * vScale; |
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void NPTi::getVelScaleB(Vector3d& sc, int index ){ |
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sc = oldVel[index] * vScale; |
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} |
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template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3], |
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int index, double sc[3]){ |
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int j; |
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for(j=0; j<3; j++) |
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sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j]; |
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for(j=0; j<3; j++) |
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sc[j] *= eta; |
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void NPTi::getPosScale(const Vector3d& pos, const Vector3d& COM, |
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int index, Vector3d& sc){ |
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/**@todo*/ |
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sc = oldPos[index] + pos/2.0 -COM; |
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sc *= eta; |
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} |
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template<typename T> void NPTi<T>::scaleSimBox( void ){ |
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void NPTi::scaleSimBox(){ |
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double scaleFactor; |
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} |
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template<typename T> bool NPTi<T>::etaConverged() { |
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bool NPTi::etaConverged() { |
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return ( fabs(prevEta - eta) <= etaTolerance ); |
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} |
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template<typename T> double NPTi<T>::getConservedQuantity(void){ |
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double NPTi::calcConservedQuantity(){ |
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double conservedQuantity; |
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double Energy; |
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
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barostat_kinetic + barostat_potential; |
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// cout.width(8); |
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// cout.precision(8); |
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// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
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// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
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// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
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return conservedQuantity; |
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} |
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template<typename T> string NPTi<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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sprintf(buffer,"\t%G\t0\t0;", eta); |
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parameters += buffer; |
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sprintf(buffer,"\t0\t%G\t0;", eta); |
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parameters += buffer; |
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sprintf(buffer,"\t0\t0\t%G;", eta); |
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parameters += buffer; |
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return parameters; |
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} |
