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// |
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// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499. |
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< |
NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff): |
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> |
NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff): |
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Integrator( theInfo, the_ff ) |
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{ |
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int i; |
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have_target_pressure = 0; |
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} |
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< |
void NPTi::moveA() { |
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> |
void NPTf::moveA() { |
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int i,j,k; |
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int atomIndex, aMatIndex; |
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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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+ |
double press[9]; |
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+ |
const double p_convert = 1.63882576e8; |
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tt2 = tauThermostat * tauThermostat; |
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tb2 = tauBarostat * tauBarostat; |
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instaTemp = tStats->getTemperature(); |
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< |
instaPress = tStats->getPressure(); |
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> |
tStats->getPressureTensor(press); |
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> |
|
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> |
for (i=0; i < 9; i++) press[i] *= p_convert; |
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> |
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instaVol = tStats->getVolume(); |
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// first evolve chi a half step |
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chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2; |
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< |
for (i = 0; i < 9; i++) { |
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< |
eta[i] += dt2 * ( instaVol * (sigma[i] - targetPressure*identMat[i])) |
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< |
/ (NkBT*tb2)); |
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< |
} |
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< |
|
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> |
eta[0] += dt2 * instaVol * (press[0] - targetPressure) / (NkBT*tb2); |
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> |
eta[1] += dt2 * instaVol * press[1] / (NkBT*tb2); |
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> |
eta[2] += dt2 * instaVol * press[2] / (NkBT*tb2); |
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> |
eta[3] += dt2 * instaVol * press[3] / (NkBT*tb2); |
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> |
eta[4] += dt2 * instaVol * (press[4] - targetPressure) / (NkBT*tb2); |
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> |
eta[5] += dt2 * instaVol * press[5] / (NkBT*tb2); |
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> |
eta[6] += dt2 * instaVol * press[6] / (NkBT*tb2); |
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> |
eta[7] += dt2 * instaVol * press[7] / (NkBT*tb2); |
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> |
eta[8] += dt2 * instaVol * (press[8] - targetPressure) / (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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aMatIndex = i * 9; |
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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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> |
|
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> |
vx = vel[atomIndex]; |
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> |
vy = vel[atomIndex+1]; |
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> |
vz = vel[atomIndex+2]; |
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> |
|
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> |
scx = (chi + eta[0])*vx + eta[1]*vy + eta[2]*vz; |
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> |
scy = eta[3]*vx + (chi + eta[4])*vy + eta[5]*vz; |
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> |
scz = eta[6]*vx + eta[7]*vy + (chi + eta[8])*vz; |
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> |
|
| 86 |
> |
vx += dt2 * ((frc[atomIndex] /atoms[i]->getMass())*eConvert - scx); |
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> |
vy += dt2 * ((frc[atomIndex+1]/atoms[i]->getMass())*eConvert - scy); |
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> |
vz += dt2 * ((frc[atomIndex+2]/atoms[i]->getMass())*eConvert - scz); |
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> |
|
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> |
vel[atomIndex] = vx; |
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> |
vel[atomIndex+1] = vy; |
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> |
vel[atomIndex+2] = vz; |
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// position whole step |
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< |
for( j=atomIndex; j<(atomIndex+3); j=j+3 ) { |
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< |
rj[0] = pos[j]; |
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< |
rj[1] = pos[j+1]; |
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< |
rj[2] = pos[j+2]; |
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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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< |
info->wrapVector(rj); |
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> |
info->wrapVector(rj); |
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| 102 |
< |
pos[j] += dt * (vel[j] + eta*rj[0]); |
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< |
pos[j+1] += dt * (vel[j+1] + eta*rj[1]); |
| 104 |
< |
pos[j+2] += dt * (vel[j+2] + eta*rj[2]); |
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< |
} |
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> |
scx = eta[0]*rj[0] + eta[1]*rj[1] + eta[2]*rj[2]; |
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> |
scy = eta[3]*rj[0] + eta[4]*rj[1] + eta[5]*rj[2]; |
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> |
scz = eta[6]*rj[0] + eta[7]*rj[1] + eta[8]*rj[2]; |
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< |
// Scale the box after all the positions have been moved: |
| 107 |
< |
|
| 108 |
< |
info->scaleBox(exp(dt*eta)); |
| 106 |
> |
pos[atomIndex] += dt * (vel[atomIndex] + scx); |
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> |
pos[atomIndex+1] += dt * (vel[atomIndex+1] + scy); |
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> |
pos[atomIndex+2] += dt * (vel[atomIndex+2] + scz); |
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|
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if( atoms[i]->isDirectional() ){ |
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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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+ |
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+ |
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| 165 |
+ |
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+ |
// Use a taylor expansion for eta products |
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+ |
|
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+ |
info->getBoxM(hm); |
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+ |
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+ |
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| 171 |
+ |
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| 172 |
+ |
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| 173 |
+ |
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| 174 |
+ |
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| 175 |
+ |
info->scaleBox(exp(dt*eta)); |
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+ |
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+ |
|
| 178 |
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} |
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|
| 180 |
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void NPTi::moveB( void ){ |
