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#include <math.h> |
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|
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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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|
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|
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// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
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|
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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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|
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chiValue = NULL; |
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integralOfChidtValue = NULL; |
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|
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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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|
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|
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if( theInfo->useInitXSstate ){ |
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|
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// retrieve chi and integralOfChidt from simInfo |
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data = info->getPropertyByName(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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|
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data = info->getPropertyByName(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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|
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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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|
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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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|
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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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|
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template<typename T> void NVT<T>::moveA() { |
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|
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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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|
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double instTemp; |
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|
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// We need the temperature at time = t for the chi update below: |
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|
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instTemp = tStats->getTemperature(); |
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|
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for( i=0; i < integrableObjects.size(); i++ ){ |
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|
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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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|
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mass = integrableObjects[i]->getMass(); |
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|
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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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|
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integrableObjects[i]->setVel( vel ); |
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integrableObjects[i]->setPos( pos ); |
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|
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if( integrableObjects[i]->isDirectional() ){ |
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|
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// get and convert the torque to body frame |
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|
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Tb = integrableObjects[i]->getTrq(); |
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integrableObjects[i]->lab2Body( Tb ); |
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|
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// get the angular momentum, and propagate a half step |
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|
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ji = integrableObjects[i]->getJ(); |
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|
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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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|
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this->rotationPropagation( integrableObjects[i], ji ); |
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|
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integrableObjects[i]->setJ( ji ); |
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} |
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} |
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|
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if(nConstrained) |
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constrainA(); |
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|
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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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|
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//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n"; |
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|
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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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} |
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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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|
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// Set things up for the iteration: |
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|
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oldChi = chi; |
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|
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for( i=0; i < integrableObjects.size(); i++ ){ |
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|
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vel = integrableObjects[i]->getVel(); |
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|
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for (j=0; j < 3; j++) |
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oldVel[3*i + j] = vel[j]; |
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|
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if( integrableObjects[i]->isDirectional() ){ |
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|
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ji = integrableObjects[i]->getJ(); |
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|
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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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} |
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|
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// do the iteration: |
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|
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for (k=0; k < 4; k++) { |
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|
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instTemp = tStats->getTemperature(); |
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|
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// evolve chi another half step using the temperature at t + dt/2 |
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|
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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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|
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for( i=0; i < integrableObjects.size(); i++ ){ |
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|
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integrableObjects[i]->getFrc( frc ); |
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vel = integrableObjects[i]->getVel(); |
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|
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mass = integrableObjects[i]->getMass(); |
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|
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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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|
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integrableObjects[i]->setVel( vel ); |
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|
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if( integrableObjects[i]->isDirectional() ){ |
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|
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// get and convert the torque to body frame |
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|
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Tb = integrableObjects[i]->getTrq(); |
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integrableObjects[i]->lab2Body( Tb ); |
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|
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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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|
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integrableObjects[i]->setJ( ji ); |
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} |
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} |
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|
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if(nConstrained) |
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constrainB(); |
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|
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if (fabs(prevChi - chi) <= chiTolerance) break; |
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} |
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|
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integralOfChidt += dt2*chi; |
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} |
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|
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template<typename T> void NVT<T>::resetIntegrator( void ){ |
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|
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chi = 0.0; |
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integralOfChidt = 0.0; |
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} |
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|
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template<typename T> int NVT<T>::readyCheck() { |
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|
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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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|
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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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|
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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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|
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// We must set tauThermostat. |
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|
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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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|
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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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|
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return 1; |
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|
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} |
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|
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template<typename T> double NVT<T>::getConservedQuantity(void){ |
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|
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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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|
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fkBT = (double)(info->ndf) * kB * targetTemp; |
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|
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Energy = tStats->getTotalE(); |
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|
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thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
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(2.0 * eConvert); |
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|
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thermostat_potential = fkBT * integralOfChidt / eConvert; |
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|
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conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
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|
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return conservedQuantity; |
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} |
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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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|
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sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt); |
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parameters += buffer; |
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|
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return parameters; |
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} |
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#inlcude "integrators/NVT.hpp" |
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|
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namespace oopse { |
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|
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NVT::NVT(SimInfo* Info) : VelocityVerletIntegrator(info){ |
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GenericData *data; |
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DoubleGenericData *chiValue; |
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DoubleGenericData *integralOfChidtValue; |
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|
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chiValue = NULL; |
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integralOfChidtValue = NULL; |
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|
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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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|
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if (theInfo->useInitXSstate) { |
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|
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// retrieve chi and integralOfChidt from simInfo |
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data = info->getPropertyByName(CHIVALUE_ID); |
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|
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if (data) { |
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chiValue = dynamic_cast<DoubleGenericData *>(data); |
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} |
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|
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data = info->getPropertyByName(INTEGRALOFCHIDT_ID); |
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|
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if (data) { |
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integralOfChidtValue = dynamic_cast<DoubleGenericData *>(data); |
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} |
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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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|
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oldVel_.resize(info_->getNIntegrableObjects()); |
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oldJi_.resize(info_->getNIntegrableObjects()); |
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} |
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|
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NVT::~NVT() { |
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} |
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|
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void NVT::moveA() { |
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typename SimInfo::MoleculeIterator i; |
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typename Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* integrableObject; |
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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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|
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double instTemp; |
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|
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// We need the temperature at time = t for the chi update below: |
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|
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instTemp = tStats->getTemperature(); |
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|
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for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
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for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(j)) { |
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|
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vel = integrableObject->getVel(); |
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pos = integrableObject->getPos(); |
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frc = integrableObject->getFrc(); |
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|
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mass = integrableObject->getMass(); |
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|
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// velocity half step (use chi from previous step here): |
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//vel[j] += halfStep * ((frc[j] / mass ) * eConvert - vel[j]*chi); |
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vel = halfStep *eConvert/mass*frc - halfStep*chi*vel; |
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|
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// position whole step |
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//pos[j] += dt * vel[j]; |
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pos += fullStep * vel; |
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|
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integrableObject->setVel(vel); |
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integrableObject->setPos(pos); |
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|
| 87 |
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if (integrableObject->isDirectional()) { |
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|
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// get and convert the torque to body frame |
| 90 |
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|
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Tb = integrableObject->getTrq(); |
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integrableObject->lab2Body(Tb); |
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|
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// get the angular momentum, and propagate a half step |
| 95 |
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|
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ji = integrableObject->getJ(); |
| 97 |
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|
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//ji[j] += halfStep * (Tb[j] * eConvert - ji[j]*chi); |
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ji += halfStep*eConvert*Tb - halfStep*ch *ji; |
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this->rotationPropagation(integrableObject, ji); |
| 101 |
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|
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integrableObject->setJ(ji); |
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} |
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} |
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|
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} |
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|
| 108 |
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if (nConstrained) |
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constrainA(); |
| 110 |
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|
| 111 |
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// Finally, evolve chi a half step (just like a velocity) using |
| 112 |
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// temperature at time t, not time t+dt/2 |
| 113 |
> |
|
| 114 |
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Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 115 |
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double chi = currSnapshot->getChi(); |
| 116 |
> |
double integralOfChidt = currSnapshot->getIntegralOfChiDt(); |
| 117 |
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|
| 118 |
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chi += halfStep * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
| 119 |
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integralOfChidt += chi * halfStep; |
| 120 |
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|
| 121 |
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currSnapshot->setChi(chi); |
| 122 |
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currSnapshot->setIntegralOfChiDt(integralOfChidt); |
| 123 |
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} |
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|
| 125 |
> |
void NVT::moveB() { |
| 126 |
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typename SimInfo::MoleculeIterator i; |
| 127 |
> |
typename Molecule::IntegrableObjectIterator j; |
| 128 |
> |
Molecule* mol; |
| 129 |
> |
StuntDouble* integrableObject; |
| 130 |
> |
|
| 131 |
> |
Vector3d Tb; |
| 132 |
> |
Vector3d ji; |
| 133 |
> |
Vector3d vel; |
| 134 |
> |
Vector3d frc; |
| 135 |
> |
double mass; |
| 136 |
> |
double instTemp; |
| 137 |
> |
double oldChi, prevChi; |
| 138 |
> |
int index; |
| 139 |
> |
// Set things up for the iteration: |
| 140 |
> |
|
| 141 |
> |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 142 |
> |
double chi = currSnapshot->getChi(); |
| 143 |
> |
double integralOfChidt = currSnapshot->getIntegralOfChiDt(); |
| 144 |
> |
oldChi = chi; |
| 145 |
> |
|
| 146 |
> |
index = 0; |
| 147 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 148 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 149 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 150 |
> |
oldVel_[index] = integrableObject->getVel(); |
| 151 |
> |
oldJi_[index] = integrableObject->getJ(); |
| 152 |
> |
} |
| 153 |
> |
++index; |
| 154 |
> |
} |
| 155 |
> |
|
| 156 |
> |
// do the iteration: |
| 157 |
> |
|
| 158 |
> |
for(int k = 0; k < maxIterNum_; k++) { |
| 159 |
> |
index = 0; |
| 160 |
> |
instTemp = tStats->getTemperature(); |
| 161 |
> |
|
| 162 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
| 163 |
> |
|
| 164 |
> |
prevChi = chi; |
| 165 |
> |
chi = oldChi + halfStep * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
| 166 |
> |
|
| 167 |
> |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 168 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 169 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 170 |
> |
|
| 171 |
> |
frc = integrableObject->getFrc(); |
| 172 |
> |
vel = integrableObject->getVel(); |
| 173 |
> |
|
| 174 |
> |
mass = integrableObject->getMass(); |
| 175 |
> |
|
| 176 |
> |
// velocity half step |
| 177 |
> |
//for(j = 0; j < 3; j++) |
| 178 |
> |
// vel[j] = oldVel_[3*i+j] + halfStep * ((frc[j] / mass ) * eConvert - oldVel_[3*i + j]*chi); |
| 179 |
> |
vel = oldVel_ + halfStep/mass*eConvert * frc - halfStep*chi*oldVel_[index]; |
| 180 |
> |
|
| 181 |
> |
integrableObject->setVel(vel); |
| 182 |
> |
|
| 183 |
> |
if (integrableObject->isDirectional()) { |
| 184 |
> |
|
| 185 |
> |
// get and convert the torque to body frame |
| 186 |
> |
|
| 187 |
> |
Tb = integrableObject->getTrq(); |
| 188 |
> |
integrableObject->lab2Body(Tb); |
| 189 |
> |
|
| 190 |
> |
//for(j = 0; j < 3; j++) |
| 191 |
> |
// ji[j] = oldJi_[3*i + j] + halfStep * (Tb[j] * eConvert - oldJi_[3*i+j]*chi); |
| 192 |
> |
ji += halfStep*eConvert*Tb - halfStep*ch *oldJi_[index]; |
| 193 |
> |
|
| 194 |
> |
integrableObject->setJ(ji); |
| 195 |
> |
} |
| 196 |
> |
} |
| 197 |
> |
} |
| 198 |
> |
|
| 199 |
> |
|
| 200 |
> |
if (nConstrained) |
| 201 |
> |
constrainB(); |
| 202 |
> |
|
| 203 |
> |
if (fabs(prevChi - chi) <= chiTolerance) |
| 204 |
> |
break; |
| 205 |
> |
|
| 206 |
> |
++index; |
| 207 |
> |
} |
| 208 |
> |
|
| 209 |
> |
integralOfChidt += halfStep * chi; |
| 210 |
> |
|
| 211 |
> |
currSnapshot->setChi(chi); |
| 212 |
> |
currSnapshot->setIntegralOfChiDt(integralOfChidt); |
| 213 |
> |
} |
| 214 |
> |
|
| 215 |
> |
template <typename T> |
| 216 |
> |
int NVT<T>::readyCheck() { |
| 217 |
> |
|
| 218 |
> |
//check parent's readyCheck() first |
| 219 |
> |
if (T::readyCheck() == -1) |
| 220 |
> |
return -1; |
| 221 |
> |
|
| 222 |
> |
// First check to see if we have a target temperature. |
| 223 |
> |
// Not having one is fatal. |
| 224 |
> |
|
| 225 |
> |
if (!have_target_temp) { |
| 226 |
> |
sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp_!\n"); |
| 227 |
> |
painCave.isFatal = 1; |
| 228 |
> |
painCave.severity = OOPSE_ERROR; |
| 229 |
> |
simError(); |
| 230 |
> |
return -1; |
| 231 |
> |
} |
| 232 |
> |
|
| 233 |
> |
// We must set tauThermostat_. |
| 234 |
> |
|
| 235 |
> |
if (!have_tau_thermostat) { |
| 236 |
> |
sprintf(painCave.errMsg, "If you use the constant temperature\n" |
| 237 |
> |
"\tintegrator, you must set tauThermostat_.\n"); |
| 238 |
> |
|
| 239 |
> |
painCave.severity = OOPSE_ERROR; |
| 240 |
> |
painCave.isFatal = 1; |
| 241 |
> |
simError(); |
| 242 |
> |
return -1; |
| 243 |
> |
} |
| 244 |
> |
|
| 245 |
> |
if (!have_chi_tolerance) { |
| 246 |
> |
sprintf(painCave.errMsg, "In NVT integrator: setting chi tolerance to 1e-6\n"); |
| 247 |
> |
chiTolerance = 1e - 6; |
| 248 |
> |
have_chi_tolerance = 1; |
| 249 |
> |
painCave.severity = OOPSE_INFO; |
| 250 |
> |
painCave.isFatal = 0; |
| 251 |
> |
simError(); |
| 252 |
> |
} |
| 253 |
> |
|
| 254 |
> |
return 1; |
| 255 |
> |
} |
| 256 |
> |
|
| 257 |
> |
template <typename T> |
| 258 |
> |
double NVT<T>::getConservedQuantity(void) { |
| 259 |
> |
double conservedQuantity; |
| 260 |
> |
double fkBT; |
| 261 |
> |
double Energy; |
| 262 |
> |
double thermostat_kinetic; |
| 263 |
> |
double thermostat_potential; |
| 264 |
> |
|
| 265 |
> |
fkBT = info_->getNdf() *kB *targetTemp_; |
| 266 |
> |
|
| 267 |
> |
Energy = tStats->getTotalE(); |
| 268 |
> |
|
| 269 |
> |
thermostat_kinetic = fkBT * tauThermostat_ * tauThermostat_ * chi * chi / (2.0 * eConvert); |
| 270 |
> |
|
| 271 |
> |
thermostat_potential = fkBT * integralOfChidt / eConvert; |
| 272 |
> |
|
| 273 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 274 |
> |
|
| 275 |
> |
return conservedQuantity; |
| 276 |
> |
} |
| 277 |
> |
|
| 278 |
> |
|
| 279 |
> |
}//end namespace oopse |
