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#include "Integrator.hpp" |
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#include "simError.h" |
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|
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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// Basic isotropic thermostating and barostating via the Melchionna |
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// modification of the Hoover algorithm: |
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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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|
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< |
NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
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< |
Integrator( theInfo, the_ff ) |
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> |
template<typename T> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
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> |
T( theInfo, the_ff ) |
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{ |
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chi = 0.0; |
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eta = 0.0; |
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have_tau_thermostat = 0; |
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have_tau_barostat = 0; |
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have_target_temp = 0; |
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have_target_pressure = 0; |
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oldEta = 0.0; |
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} |
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|
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void NPTi::moveA() { |
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|
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int i,j,k; |
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int atomIndex, aMatIndex; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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double rj[3]; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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double angle; |
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template<typename T> NPTi<T>::~NPTi() { |
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//nothing for now |
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} |
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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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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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template<typename T> void NPTi<T>::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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|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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instaVol = tStats->getVolume(); |
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|
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// first evolve chi a half step |
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> |
template<typename T> void NPTi<T>::evolveEtaB() { |
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|
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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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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|
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for( i=0; i<nAtoms; i++ ){ |
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atomIndex = i * 3; |
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aMatIndex = i * 9; |
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|
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
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- vel[j]*(chi+eta)); |
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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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|
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// position whole step |
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for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta ); |
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> |
} |
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|
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rj[0] = pos[atomIndex]; |
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rj[1] = pos[atomIndex+1]; |
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rj[2] = pos[atomIndex+2]; |
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|
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info->wrapVector(rj); |
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> |
template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){ |
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> |
int i; |
| 63 |
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|
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< |
pos[atomIndex] += dt * (vel[atomIndex] + eta*rj[0]); |
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pos[atomIndex+1] += dt * (vel[atomIndex+1] + eta*rj[1]); |
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pos[atomIndex+2] += dt * (vel[atomIndex+2] + eta*rj[2]); |
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|
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if( atoms[i]->isDirectional() ){ |
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for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * ( chi + eta ); |
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} |
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
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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[0] = dAtom->getTx(); |
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Tb[1] = dAtom->getTy(); |
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Tb[2] = dAtom->getTz(); |
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|
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dAtom->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[0] = dAtom->getJx(); |
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ji[1] = dAtom->getJy(); |
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ji[2] = dAtom->getJz(); |
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|
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ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
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ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
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ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
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|
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// use the angular velocities to propagate the rotation matrix a |
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// full time step |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the z-axis |
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angle = dt * ji[2] / dAtom->getIzz(); |
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this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the y-axis |
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angle = dt2 * ji[1] / dAtom->getIyy(); |
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this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
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|
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// rotate about the x-axis |
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angle = dt2 * ji[0] / dAtom->getIxx(); |
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this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
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|
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dAtom->setJx( ji[0] ); |
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dAtom->setJy( ji[1] ); |
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dAtom->setJz( ji[2] ); |
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} |
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|
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} |
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// Scale the box after all the positions have been moved: |
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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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|
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cerr << "eta = " << eta |
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<< "; exp(dt*eta) = " << exp(eta*dt) << "\n"; |
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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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|
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< |
info->scaleBox(exp(dt*eta)); |
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|
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> |
for(j=0; j<3; j++) |
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sc[j] *= eta; |
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} |
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|
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< |
void NPTi::moveB( void ){ |
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< |
int i,j,k; |
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int atomIndex; |
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DirectionalAtom* dAtom; |
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double Tb[3]; |
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double ji[3]; |
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double instaTemp, instaPress, instaVol; |
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double tt2, tb2; |
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|
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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> |
template<typename T> void NPTi<T>::scaleSimBox( void ){ |
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|
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instaTemp = tStats->getTemperature(); |
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instaPress = tStats->getPressure(); |
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instaVol = tStats->getVolume(); |
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double scaleFactor; |
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|
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< |
chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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< |
eta += dt2 * ( instaVol * (instaPress - targetPressure) / |
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< |
(p_convert*NkBT*tb2)); |
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|
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< |
for( i=0; i<nAtoms; i++ ){ |
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< |
atomIndex = i * 3; |
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|
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// velocity half step |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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for( j=atomIndex; j<(atomIndex+3); j++ ) |
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vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert |
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< |
- vel[j]*(chi+eta)); |
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< |
|
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< |
if( atoms[i]->isDirectional() ){ |
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< |
|
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dAtom = (DirectionalAtom *)atoms[i]; |
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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[0] = dAtom->getTx(); |
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< |
Tb[1] = dAtom->getTy(); |
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< |
Tb[2] = dAtom->getTz(); |
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< |
|
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< |
dAtom->lab2Body( Tb ); |
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|
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// get the angular momentum, and complete the angular momentum |
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// half step |
| 184 |
< |
|
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< |
ji[0] = dAtom->getJx(); |
| 186 |
< |
ji[1] = dAtom->getJy(); |
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< |
ji[2] = dAtom->getJz(); |
| 188 |
< |
|
| 189 |
< |
ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi); |
| 190 |
< |
ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi); |
| 191 |
< |
ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi); |
| 192 |
< |
|
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< |
dAtom->setJx( ji[0] ); |
| 194 |
< |
dAtom->setJy( ji[1] ); |
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< |
dAtom->setJz( ji[2] ); |
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< |
} |
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< |
} |
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< |
} |
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> |
scaleFactor = exp(dt*eta); |
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|
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< |
int NPTi::readyCheck() { |
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< |
|
| 202 |
< |
// 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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> |
if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) { |
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|
sprintf( painCave.errMsg, |
| 87 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
| 88 |
< |
" without a targetTemp!\n" |
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> |
"NPTi error: Attempting a Box scaling of more than 10 percent" |
| 88 |
> |
" check your tauBarostat, as it is probably too small!\n" |
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> |
" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor |
| 90 |
|
); |
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painCave.isFatal = 1; |
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|
simError(); |
| 93 |
< |
return -1; |
| 94 |
< |
} |
| 93 |
> |
} else { |
| 94 |
> |
info->scaleBox(scaleFactor); |
| 95 |
> |
} |
| 96 |
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|
| 97 |
< |
if (!have_target_pressure) { |
| 216 |
< |
sprintf( painCave.errMsg, |
| 217 |
< |
"NPTi error: You can't use the NPTi integrator\n" |
| 218 |
< |
" without a targetPressure!\n" |
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< |
); |
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< |
painCave.isFatal = 1; |
| 221 |
< |
simError(); |
| 222 |
< |
return -1; |
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< |
} |
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< |
|
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< |
// We must set tauThermostat. |
| 226 |
< |
|
| 227 |
< |
if (!have_tau_thermostat) { |
| 228 |
< |
sprintf( painCave.errMsg, |
| 229 |
< |
"NPTi error: If you use the NPTi\n" |
| 230 |
< |
" integrator, you must set tauThermostat.\n"); |
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< |
painCave.isFatal = 1; |
| 232 |
< |
simError(); |
| 233 |
< |
return -1; |
| 234 |
< |
} |
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> |
} |
| 98 |
|
|
| 99 |
< |
// We must set tauBarostat. |
| 237 |
< |
|
| 238 |
< |
if (!have_tau_barostat) { |
| 239 |
< |
sprintf( painCave.errMsg, |
| 240 |
< |
"NPTi error: If you use the NPTi\n" |
| 241 |
< |
" integrator, you must set tauBarostat.\n"); |
| 242 |
< |
painCave.isFatal = 1; |
| 243 |
< |
simError(); |
| 244 |
< |
return -1; |
| 245 |
< |
} |
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> |
template<typename T> bool NPTi<T>::etaConverged() { |
| 100 |
|
|
| 101 |
< |
// We need NkBT a lot, so just set it here: |
| 101 |
> |
return ( fabs(prevEta - eta) <= etaTolerance ); |
| 102 |
> |
} |
| 103 |
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|
| 104 |
< |
NkBT = (double)info->ndf * kB * targetTemp; |
| 104 |
> |
template<typename T> double NPTi<T>::getConservedQuantity(void){ |
| 105 |
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|
| 106 |
< |
return 1; |
| 106 |
> |
double conservedQuantity; |
| 107 |
> |
double Three_NkBT; |
| 108 |
> |
double Energy; |
| 109 |
> |
double thermostat_kinetic; |
| 110 |
> |
double thermostat_potential; |
| 111 |
> |
double barostat_kinetic; |
| 112 |
> |
double barostat_potential; |
| 113 |
> |
double tb2; |
| 114 |
> |
double eta2; |
| 115 |
> |
|
| 116 |
> |
Energy = tStats->getTotalE(); |
| 117 |
> |
|
| 118 |
> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 119 |
> |
(2.0 * eConvert); |
| 120 |
> |
|
| 121 |
> |
thermostat_potential = fkBT* integralOfChidt / eConvert; |
| 122 |
> |
|
| 123 |
> |
|
| 124 |
> |
barostat_kinetic = 3.0 * NkBT * tauBarostat * tauBarostat * eta * eta / |
| 125 |
> |
(2.0 * eConvert); |
| 126 |
> |
|
| 127 |
> |
barostat_potential = (targetPressure * tStats->getVolume() / p_convert) / |
| 128 |
> |
eConvert; |
| 129 |
> |
|
| 130 |
> |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential + |
| 131 |
> |
barostat_kinetic + barostat_potential; |
| 132 |
> |
|
| 133 |
> |
// cout.width(8); |
| 134 |
> |
// cout.precision(8); |
| 135 |
> |
|
| 136 |
> |
// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 137 |
> |
// "\t" << thermostat_potential << "\t" << barostat_kinetic << |
| 138 |
> |
// "\t" << barostat_potential << "\t" << conservedQuantity << endl; |
| 139 |
> |
return conservedQuantity; |
| 140 |
|
} |
