43 |
|
update(); |
44 |
|
} |
45 |
|
|
46 |
< |
void NVT::update() { |
46 |
> |
void NVT::doUpdate() { |
47 |
|
oldVel_.resize(info_->getNIntegrableObjects()); |
48 |
|
oldJi_.resize(info_->getNIntegrableObjects()); |
49 |
|
} |
59 |
|
Vector3d pos; |
60 |
|
Vector3d frc; |
61 |
|
|
62 |
< |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
63 |
< |
double chi = currSnapshot->getChi(); |
64 |
< |
double integralOfChidt = currSnapshot->getIntegralOfChiDt(); |
62 |
> |
double chi = currentSnapshot_->getChi(); |
63 |
> |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
64 |
|
|
65 |
|
// We need the temperature at time = t for the chi update below: |
66 |
|
|
78 |
|
|
79 |
|
// velocity half step (use chi from previous step here): |
80 |
|
//vel[j] += dt2 * ((frc[j] / mass ) * OOPSEConstant::energyConvert - vel[j]*chi); |
81 |
< |
vel = dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel; |
81 |
> |
vel += dt2 *OOPSEConstant::energyConvert/mass*frc - dt2*chi*vel; |
82 |
|
|
83 |
|
// position whole step |
84 |
|
//pos[j] += dt * vel[j]; |
89 |
|
|
90 |
|
if (integrableObject->isDirectional()) { |
91 |
|
|
92 |
< |
// get and convert the torque to body frame |
92 |
> |
//convert the torque to body frame |
93 |
> |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
94 |
|
|
95 |
– |
Tb = integrableObject->getTrq(); |
96 |
– |
integrableObject->lab2Body(Tb); |
97 |
– |
|
95 |
|
// get the angular momentum, and propagate a half step |
96 |
|
|
97 |
|
ji = integrableObject->getJ(); |
115 |
|
chi += dt2 * (instTemp / targetTemp_ - 1.0) / (tauThermostat_ * tauThermostat_); |
116 |
|
integralOfChidt += chi * dt2; |
117 |
|
|
118 |
< |
currSnapshot->setChi(chi); |
119 |
< |
currSnapshot->setIntegralOfChiDt(integralOfChidt); |
118 |
> |
currentSnapshot_->setChi(chi); |
119 |
> |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
120 |
|
} |
121 |
|
|
122 |
|
void NVT::moveB() { |
134 |
|
int index; |
135 |
|
// Set things up for the iteration: |
136 |
|
|
137 |
< |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
141 |
< |
double chi = currSnapshot->getChi(); |
137 |
> |
double chi = currentSnapshot_->getChi(); |
138 |
|
double oldChi = chi; |
139 |
|
double prevChi; |
140 |
< |
double integralOfChidt = currSnapshot->getIntegralOfChiDt(); |
140 |
> |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
141 |
|
|
142 |
|
index = 0; |
143 |
|
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
145 |
|
integrableObject = mol->nextIntegrableObject(j)) { |
146 |
|
oldVel_[index] = integrableObject->getVel(); |
147 |
|
oldJi_[index] = integrableObject->getJ(); |
148 |
+ |
|
149 |
+ |
++index; |
150 |
|
} |
151 |
< |
++index; |
151 |
> |
|
152 |
|
} |
153 |
|
|
154 |
|
// do the iteration: |
182 |
|
|
183 |
|
// get and convert the torque to body frame |
184 |
|
|
185 |
< |
Tb = integrableObject->getTrq(); |
188 |
< |
integrableObject->lab2Body(Tb); |
185 |
> |
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
186 |
|
|
187 |
|
//for(j = 0; j < 3; j++) |
188 |
|
// ji[j] = oldJi_[3*i + j] + dt2 * (Tb[j] * OOPSEConstant::energyConvert - oldJi_[3*i+j]*chi); |
189 |
< |
ji += dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index]; |
189 |
> |
ji = oldJi_[index] + dt2*OOPSEConstant::energyConvert*Tb - dt2*chi *oldJi_[index]; |
190 |
|
|
191 |
|
integrableObject->setJ(ji); |
192 |
|
} |
193 |
+ |
|
194 |
+ |
|
195 |
+ |
++index; |
196 |
|
} |
197 |
|
} |
198 |
|
|
202 |
|
if (fabs(prevChi - chi) <= chiTolerance_) |
203 |
|
break; |
204 |
|
|
205 |
– |
++index; |
205 |
|
} |
206 |
|
|
207 |
|
integralOfChidt += dt2 * chi; |
208 |
|
|
209 |
< |
currSnapshot->setChi(chi); |
210 |
< |
currSnapshot->setIntegralOfChiDt(integralOfChidt); |
209 |
> |
currentSnapshot_->setChi(chi); |
210 |
> |
currentSnapshot_->setIntegralOfChiDt(integralOfChidt); |
211 |
|
} |
212 |
|
|
213 |
|
|
214 |
|
double NVT::calcConservedQuantity() { |
215 |
< |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
216 |
< |
double chi = currSnapshot->getChi(); |
217 |
< |
double integralOfChidt = currSnapshot->getIntegralOfChiDt(); |
215 |
> |
|
216 |
> |
double chi = currentSnapshot_->getChi(); |
217 |
> |
double integralOfChidt = currentSnapshot_->getIntegralOfChiDt(); |
218 |
|
double conservedQuantity; |
219 |
|
double fkBT; |
220 |
|
double Energy; |