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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; |
| 267 |
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|
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Energy = tStats->getTotalE(); |
| 269 |
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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; |
| 276 |
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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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} |
| 1 |
> |
#include <math.h> |
| 2 |
> |
|
| 3 |
> |
#include "primitives/Atom.hpp" |
| 4 |
> |
#include "primitives/SRI.hpp" |
| 5 |
> |
#include "primitives/AbstractClasses.hpp" |
| 6 |
> |
#include "brains/SimInfo.hpp" |
| 7 |
> |
#include "UseTheForce/ForceFields.hpp" |
| 8 |
> |
#include "brains/Thermo.hpp" |
| 9 |
> |
#include "io/ReadWrite.hpp" |
| 10 |
> |
#include "integrators/Integrator.hpp" |
| 11 |
> |
#include "utils/simError.h" |
| 12 |
> |
|
| 13 |
> |
// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697 |
| 14 |
> |
|
| 15 |
> |
template <typename T>NVT<T>::NVT(SimInfo *theInfo, ForceFields *the_ff) : |
| 16 |
> |
T(theInfo, the_ff) { |
| 17 |
> |
GenericData *data; |
| 18 |
> |
DoubleGenericData *chiValue; |
| 19 |
> |
DoubleGenericData *integralOfChidtValue; |
| 20 |
> |
|
| 21 |
> |
chiValue = NULL; |
| 22 |
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integralOfChidtValue = NULL; |
| 23 |
> |
|
| 24 |
> |
chi = 0.0; |
| 25 |
> |
have_tau_thermostat = 0; |
| 26 |
> |
have_target_temp = 0; |
| 27 |
> |
have_chi_tolerance = 0; |
| 28 |
> |
integralOfChidt = 0.0; |
| 29 |
> |
|
| 30 |
> |
if (theInfo->useInitXSstate) { |
| 31 |
> |
|
| 32 |
> |
// retrieve chi and integralOfChidt from simInfo |
| 33 |
> |
data = info->getPropertyByName(CHIVALUE_ID); |
| 34 |
> |
|
| 35 |
> |
if (data) { |
| 36 |
> |
chiValue = dynamic_cast<DoubleGenericData *>(data); |
| 37 |
> |
} |
| 38 |
> |
|
| 39 |
> |
data = info->getPropertyByName(INTEGRALOFCHIDT_ID); |
| 40 |
> |
|
| 41 |
> |
if (data) { |
| 42 |
> |
integralOfChidtValue = dynamic_cast<DoubleGenericData *>(data); |
| 43 |
> |
} |
| 44 |
> |
|
| 45 |
> |
// chi and integralOfChidt should appear by pair |
| 46 |
> |
if (chiValue && integralOfChidtValue) { |
| 47 |
> |
chi = chiValue->getData(); |
| 48 |
> |
integralOfChidt = integralOfChidtValue->getData(); |
| 49 |
> |
} |
| 50 |
> |
} |
| 51 |
> |
|
| 52 |
> |
oldVel = new double[3 * integrableObjects.size()]; |
| 53 |
> |
oldJi = new double[3 * integrableObjects.size()]; |
| 54 |
> |
} |
| 55 |
> |
|
| 56 |
> |
template <typename T>NVT<T>::~NVT() { |
| 57 |
> |
delete [] oldVel; |
| 58 |
> |
delete [] oldJi; |
| 59 |
> |
} |
| 60 |
> |
|
| 61 |
> |
template <typename T> |
| 62 |
> |
void NVT<T>::moveA() { |
| 63 |
> |
int i, j; |
| 64 |
> |
DirectionalAtom *dAtom; |
| 65 |
> |
Vector3d Tb; |
| 66 |
> |
Vector3d ji; |
| 67 |
> |
double mass; |
| 68 |
> |
Vector3d vel; |
| 69 |
> |
Vector3d pos; |
| 70 |
> |
Vector3d frc; |
| 71 |
> |
|
| 72 |
> |
double instTemp; |
| 73 |
> |
|
| 74 |
> |
// We need the temperature at time = t for the chi update below: |
| 75 |
> |
|
| 76 |
> |
instTemp = tStats->getTemperature(); |
| 77 |
> |
|
| 78 |
> |
for(i = 0; i < integrableObjects.size(); i++) { |
| 79 |
> |
vel = integrableObjects[i]->getVel(); |
| 80 |
> |
pos = integrableObjects[i]->getPos(); |
| 81 |
> |
integrableObjects[i]->getFrc(frc); |
| 82 |
> |
|
| 83 |
> |
mass = integrableObjects[i]->getMass(); |
| 84 |
> |
|
| 85 |
> |
for(j = 0; j < 3; j++) { |
| 86 |
> |
// velocity half step (use chi from previous step here): |
| 87 |
> |
vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi); |
| 88 |
> |
|
| 89 |
> |
// position whole step |
| 90 |
> |
pos[j] += dt * vel[j]; |
| 91 |
> |
} |
| 92 |
> |
|
| 93 |
> |
integrableObjects[i]->setVel(vel); |
| 94 |
> |
integrableObjects[i]->setPos(pos); |
| 95 |
> |
|
| 96 |
> |
if (integrableObjects[i]->isDirectional()) { |
| 97 |
> |
|
| 98 |
> |
// get and convert the torque to body frame |
| 99 |
> |
|
| 100 |
> |
Tb = integrableObjects[i]->getTrq(); |
| 101 |
> |
integrableObjects[i]->lab2Body(Tb); |
| 102 |
> |
|
| 103 |
> |
// get the angular momentum, and propagate a half step |
| 104 |
> |
|
| 105 |
> |
ji = integrableObjects[i]->getJ(); |
| 106 |
> |
|
| 107 |
> |
for(j = 0; j < 3; j++) |
| 108 |
> |
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 109 |
> |
|
| 110 |
> |
this->rotationPropagation(integrableObjects[i], ji); |
| 111 |
> |
|
| 112 |
> |
integrableObjects[i]->setJ(ji); |
| 113 |
> |
} |
| 114 |
> |
} |
| 115 |
> |
|
| 116 |
> |
if (nConstrained) |
| 117 |
> |
constrainA(); |
| 118 |
> |
|
| 119 |
> |
// Finally, evolve chi a half step (just like a velocity) using |
| 120 |
> |
// temperature at time t, not time t+dt/2 |
| 121 |
> |
|
| 122 |
> |
//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n"; |
| 123 |
> |
|
| 124 |
> |
chi += dt2 * (instTemp / targetTemp - 1.0) / (tauThermostat * tauThermostat); |
| 125 |
> |
integralOfChidt += chi * dt2; |
| 126 |
> |
} |
| 127 |
> |
|
| 128 |
> |
template <typename T> |
| 129 |
> |
void NVT<T>::moveB(void) { |
| 130 |
> |
int i, j, k; |
| 131 |
> |
double Tb[3], ji[3]; |
| 132 |
> |
double vel[3], frc[3]; |
| 133 |
> |
double mass; |
| 134 |
> |
double instTemp; |
| 135 |
> |
double oldChi, prevChi; |
| 136 |
> |
|
| 137 |
> |
// Set things up for the iteration: |
| 138 |
> |
|
| 139 |
> |
oldChi = chi; |
| 140 |
> |
|
| 141 |
> |
for(i = 0; i < integrableObjects.size(); i++) { |
| 142 |
> |
vel = integrableObjects[i]->getVel(); |
| 143 |
> |
|
| 144 |
> |
for(j = 0; j < 3; j++) |
| 145 |
> |
oldVel[3 * i + j] = vel[j]; |
| 146 |
> |
|
| 147 |
> |
if (integrableObjects[i]->isDirectional()) { |
| 148 |
> |
ji = integrableObjects[i]->getJ(); |
| 149 |
> |
|
| 150 |
> |
for(j = 0; j < 3; j++) |
| 151 |
> |
oldJi[3 * i + j] = ji[j]; |
| 152 |
> |
} |
| 153 |
> |
} |
| 154 |
> |
|
| 155 |
> |
// do the iteration: |
| 156 |
> |
|
| 157 |
> |
for(k = 0; k < 4; k++) { |
| 158 |
> |
instTemp = tStats->getTemperature(); |
| 159 |
> |
|
| 160 |
> |
// evolve chi another half step using the temperature at t + dt/2 |
| 161 |
> |
|
| 162 |
> |
prevChi = chi; |
| 163 |
> |
chi = oldChi + dt2 * (instTemp / targetTemp - 1.0) / (tauThermostat * tauThermostat); |
| 164 |
> |
|
| 165 |
> |
for(i = 0; i < integrableObjects.size(); i++) { |
| 166 |
> |
integrableObjects[i]->getFrc(frc); |
| 167 |
> |
vel = integrableObjects[i]->getVel(); |
| 168 |
> |
|
| 169 |
> |
mass = integrableObjects[i]->getMass(); |
| 170 |
> |
|
| 171 |
> |
// velocity half step |
| 172 |
> |
for(j = 0; j < 3; j++) |
| 173 |
> |
vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi); |
| 174 |
> |
|
| 175 |
> |
integrableObjects[i]->setVel(vel); |
| 176 |
> |
|
| 177 |
> |
if (integrableObjects[i]->isDirectional()) { |
| 178 |
> |
|
| 179 |
> |
// get and convert the torque to body frame |
| 180 |
> |
|
| 181 |
> |
Tb = integrableObjects[i]->getTrq(); |
| 182 |
> |
integrableObjects[i]->lab2Body(Tb); |
| 183 |
> |
|
| 184 |
> |
for(j = 0; j < 3; j++) |
| 185 |
> |
ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi); |
| 186 |
> |
|
| 187 |
> |
integrableObjects[i]->setJ(ji); |
| 188 |
> |
} |
| 189 |
> |
} |
| 190 |
> |
|
| 191 |
> |
if (nConstrained) |
| 192 |
> |
constrainB(); |
| 193 |
> |
|
| 194 |
> |
if (fabs(prevChi - chi) <= chiTolerance) |
| 195 |
> |
break; |
| 196 |
> |
} |
| 197 |
> |
|
| 198 |
> |
integralOfChidt += dt2 * chi; |
| 199 |
> |
} |
| 200 |
> |
|
| 201 |
> |
template <typename T> |
| 202 |
> |
void NVT<T>::resetIntegrator(void) { |
| 203 |
> |
chi = 0.0; |
| 204 |
> |
integralOfChidt = 0.0; |
| 205 |
> |
} |
| 206 |
> |
|
| 207 |
> |
template <typename T> |
| 208 |
> |
int NVT<T>::readyCheck() { |
| 209 |
> |
|
| 210 |
> |
//check parent's readyCheck() first |
| 211 |
> |
if (T::readyCheck() == -1) |
| 212 |
> |
return -1; |
| 213 |
> |
|
| 214 |
> |
// First check to see if we have a target temperature. |
| 215 |
> |
// Not having one is fatal. |
| 216 |
> |
|
| 217 |
> |
if (!have_target_temp) { |
| 218 |
> |
sprintf(painCave.errMsg, "You can't use the NVT integrator without a targetTemp!\n"); |
| 219 |
> |
painCave.isFatal = 1; |
| 220 |
> |
painCave.severity = OOPSE_ERROR; |
| 221 |
> |
simError(); |
| 222 |
> |
return -1; |
| 223 |
> |
} |
| 224 |
> |
|
| 225 |
> |
// We must set tauThermostat. |
| 226 |
> |
|
| 227 |
> |
if (!have_tau_thermostat) { |
| 228 |
> |
sprintf(painCave.errMsg, "If you use the constant temperature\n" |
| 229 |
> |
"\tintegrator, you must set tauThermostat.\n"); |
| 230 |
> |
|
| 231 |
> |
painCave.severity = OOPSE_ERROR; |
| 232 |
> |
painCave.isFatal = 1; |
| 233 |
> |
simError(); |
| 234 |
> |
return -1; |
| 235 |
> |
} |
| 236 |
> |
|
| 237 |
> |
if (!have_chi_tolerance) { |
| 238 |
> |
sprintf(painCave.errMsg, "In NVT integrator: setting chi tolerance to 1e-6\n"); |
| 239 |
> |
chiTolerance = 1e - 6; |
| 240 |
> |
have_chi_tolerance = 1; |
| 241 |
> |
painCave.severity = OOPSE_INFO; |
| 242 |
> |
painCave.isFatal = 0; |
| 243 |
> |
simError(); |
| 244 |
> |
} |
| 245 |
> |
|
| 246 |
> |
return 1; |
| 247 |
> |
} |
| 248 |
> |
|
| 249 |
> |
template <typename T> |
| 250 |
> |
double NVT<T>::getConservedQuantity(void) { |
| 251 |
> |
double conservedQuantity; |
| 252 |
> |
double fkBT; |
| 253 |
> |
double Energy; |
| 254 |
> |
double thermostat_kinetic; |
| 255 |
> |
double thermostat_potential; |
| 256 |
> |
|
| 257 |
> |
fkBT = (double)(info->ndf) *kB *targetTemp; |
| 258 |
> |
|
| 259 |
> |
Energy = tStats->getTotalE(); |
| 260 |
> |
|
| 261 |
> |
thermostat_kinetic = fkBT * tauThermostat * tauThermostat * chi * chi / (2.0 * eConvert); |
| 262 |
> |
|
| 263 |
> |
thermostat_potential = fkBT * integralOfChidt / eConvert; |
| 264 |
> |
|
| 265 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 266 |
> |
|
| 267 |
> |
return conservedQuantity; |
| 268 |
> |
} |
| 269 |
> |
|
| 270 |
> |
template <typename T> |
| 271 |
> |
string NVT<T>::getAdditionalParameters(void) { |
| 272 |
> |
string parameters; |
| 273 |
> |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 274 |
> |
char buffer[BUFFERSIZE]; |
| 275 |
> |
|
| 276 |
> |
sprintf(buffer, "\t%G\t%G;", chi, integralOfChidt); |
| 277 |
> |
parameters += buffer; |
| 278 |
> |
|
| 279 |
> |
return parameters; |
| 280 |
> |
} |
