| 34 |
|
int i, j; |
| 35 |
|
DirectionalAtom* dAtom; |
| 36 |
|
double Tb[3], ji[3]; |
| 37 |
< |
double A[3][3], I[3][3]; |
| 38 |
< |
double angle, mass; |
| 37 |
> |
double mass; |
| 38 |
|
double vel[3], pos[3], frc[3]; |
| 39 |
|
|
| 40 |
|
double instTemp; |
| 77 |
|
for (j=0; j < 3; j++) |
| 78 |
|
ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi); |
| 79 |
|
|
| 80 |
< |
// use the angular velocities to propagate the rotation matrix a |
| 82 |
< |
// full time step |
| 83 |
< |
|
| 84 |
< |
dAtom->getA(A); |
| 85 |
< |
dAtom->getI(I); |
| 86 |
< |
|
| 87 |
< |
// rotate about the x-axis |
| 88 |
< |
angle = dt2 * ji[0] / I[0][0]; |
| 89 |
< |
this->rotate( 1, 2, angle, ji, A ); |
| 90 |
< |
|
| 91 |
< |
// rotate about the y-axis |
| 92 |
< |
angle = dt2 * ji[1] / I[1][1]; |
| 93 |
< |
this->rotate( 2, 0, angle, ji, A ); |
| 80 |
> |
this->rotationPropagation( dAtom, ji ); |
| 81 |
|
|
| 95 |
– |
// rotate about the z-axis |
| 96 |
– |
angle = dt * ji[2] / I[2][2]; |
| 97 |
– |
this->rotate( 0, 1, angle, ji, A); |
| 98 |
– |
|
| 99 |
– |
// rotate about the y-axis |
| 100 |
– |
angle = dt2 * ji[1] / I[1][1]; |
| 101 |
– |
this->rotate( 2, 0, angle, ji, A ); |
| 102 |
– |
|
| 103 |
– |
// rotate about the x-axis |
| 104 |
– |
angle = dt2 * ji[0] / I[0][0]; |
| 105 |
– |
this->rotate( 1, 2, angle, ji, A ); |
| 106 |
– |
|
| 82 |
|
dAtom->setJ( ji ); |
| 108 |
– |
dAtom->setA( A ); |
| 83 |
|
} |
| 84 |
+ |
} |
| 85 |
+ |
|
| 86 |
+ |
if (nConstrained){ |
| 87 |
+ |
constrainA(); |
| 88 |
|
} |
| 89 |
|
|
| 90 |
|
// Finally, evolve chi a half step (just like a velocity) using |
| 168 |
|
} |
| 169 |
|
} |
| 170 |
|
|
| 171 |
+ |
if (nConstrained){ |
| 172 |
+ |
constrainB(); |
| 173 |
+ |
} |
| 174 |
+ |
|
| 175 |
|
if (fabs(prevChi - chi) <= chiTolerance) break; |
| 176 |
|
} |
| 177 |
|
|
| 229 |
|
template<typename T> double NVT<T>::getConservedQuantity(void){ |
| 230 |
|
|
| 231 |
|
double conservedQuantity; |
| 232 |
< |
double E_NVT; |
| 232 |
> |
double fkBT; |
| 233 |
> |
double Energy; |
| 234 |
> |
double thermostat_kinetic; |
| 235 |
> |
double thermostat_potential; |
| 236 |
|
|
| 237 |
< |
//HNVE |
| 238 |
< |
conservedQuantity = tStats->getTotalE(); |
| 239 |
< |
//HNVE |
| 255 |
< |
|
| 256 |
< |
E_NVT = (info->getNDF() * kB * targetTemp * |
| 257 |
< |
(integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0 )) / eConvert; |
| 237 |
> |
fkBT = (double)(info->getNDF() ) * kB * targetTemp; |
| 238 |
> |
|
| 239 |
> |
Energy = tStats->getTotalE(); |
| 240 |
|
|
| 241 |
< |
conservedQuantity += E_NVT; |
| 241 |
> |
thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi / |
| 242 |
> |
(2.0 * eConvert); |
| 243 |
|
|
| 244 |
< |
//cerr << info->getTime() << "\t" << chi << "\t" << integralOfChidt << "\t" << E_NVT << endl; |
| 244 |
> |
thermostat_potential = fkBT * integralOfChidt / eConvert; |
| 245 |
|
|
| 246 |
+ |
conservedQuantity = Energy + thermostat_kinetic + thermostat_potential; |
| 247 |
+ |
|
| 248 |
+ |
cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << |
| 249 |
+ |
"\t" << thermostat_potential << "\t" << conservedQuantity << endl; |
| 250 |
+ |
|
| 251 |
|
return conservedQuantity; |
| 252 |
|
} |
