| 195 |
|
|
| 196 |
|
double tt2, tb2; |
| 197 |
|
double instaTemp, instaPress, instaVol; |
| 198 |
+ |
double press[3][3]; |
| 199 |
|
|
| 200 |
|
int Nparticles; |
| 201 |
|
|
| 252 |
|
|
| 253 |
|
double eta, oldEta, prevEta; |
| 254 |
|
}; |
| 254 |
– |
|
| 255 |
– |
|
| 256 |
– |
template<typename T> class NPTim : public T{ |
| 257 |
– |
|
| 258 |
– |
public: |
| 259 |
– |
|
| 260 |
– |
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
| 261 |
– |
virtual ~NPTim() {} |
| 262 |
– |
|
| 263 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
| 264 |
– |
calcStress = 1; |
| 265 |
– |
T::integrateStep( calcPot, calcStress ); |
| 266 |
– |
accIntegralOfChidt(); |
| 267 |
– |
} |
| 268 |
– |
|
| 269 |
– |
virtual double getConservedQuantity(void); |
| 255 |
|
|
| 271 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
| 272 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
| 273 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
| 274 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
| 275 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
| 276 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
| 277 |
– |
|
| 278 |
– |
protected: |
| 279 |
– |
|
| 280 |
– |
virtual void moveA( void ); |
| 281 |
– |
virtual void moveB( void ); |
| 282 |
– |
|
| 283 |
– |
virtual int readyCheck(); |
| 284 |
– |
|
| 285 |
– |
virtual void resetIntegrator( void ); |
| 286 |
– |
|
| 287 |
– |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
| 288 |
– |
|
| 289 |
– |
Molecule* myMolecules; |
| 290 |
– |
Atom** myAtoms; |
| 291 |
– |
|
| 292 |
– |
// chi and eta are the propagated degrees of freedom |
| 293 |
– |
|
| 294 |
– |
double chi; |
| 295 |
– |
double eta; |
| 296 |
– |
double NkBT; |
| 297 |
– |
double integralOfChidt; |
| 298 |
– |
|
| 299 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
| 300 |
– |
// One of qmass or tauThermostat must be set; |
| 301 |
– |
|
| 302 |
– |
double targetTemp; |
| 303 |
– |
double targetPressure; |
| 304 |
– |
double tauThermostat; |
| 305 |
– |
double tauBarostat; |
| 306 |
– |
|
| 307 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
| 308 |
– |
short int have_target_pressure; |
| 309 |
– |
double chiTolerance; |
| 310 |
– |
short int have_chi_tolerance; |
| 311 |
– |
double posIterTolerance; |
| 312 |
– |
short int have_pos_iter_tolerance; |
| 313 |
– |
|
| 314 |
– |
}; |
| 315 |
– |
|
| 256 |
|
template<typename T> class NPTzm : public T{ |
| 257 |
|
|
| 258 |
|
public: |
| 309 |
|
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
| 310 |
|
virtual ~NPTf(); |
| 311 |
|
|
| 372 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
| 373 |
– |
calcStress = 1; |
| 374 |
– |
T::integrateStep( calcPot, calcStress ); |
| 375 |
– |
} |
| 376 |
– |
|
| 312 |
|
virtual double getConservedQuantity(void); |
| 313 |
+ |
virtual void resetIntegrator(void); |
| 314 |
|
|
| 379 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
| 380 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
| 381 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
| 382 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
| 383 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
| 384 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
| 385 |
– |
|
| 315 |
|
protected: |
| 316 |
|
|
| 317 |
< |
virtual void moveA( void ); |
| 318 |
< |
virtual void moveB( void ); |
| 317 |
> |
virtual void evolveEtaA(void); |
| 318 |
> |
virtual void evolveEtaB(void); |
| 319 |
|
|
| 320 |
< |
virtual void resetIntegrator( void ); |
| 320 |
> |
virtual bool etaConverged( void ); |
| 321 |
|
|
| 322 |
< |
virtual int readyCheck(); |
| 322 |
> |
virtual void scaleSimBox( void ); |
| 323 |
|
|
| 324 |
+ |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
| 325 |
+ |
virtual void getVelScaleB( double sc[3], int index ); |
| 326 |
+ |
virtual void getPosScale(double pos[3], double COM[3], |
| 327 |
+ |
int index, double sc[3]); |
| 328 |
|
|
| 396 |
– |
// chi and eta are the propagated degrees of freedom |
| 397 |
– |
|
| 398 |
– |
double chi; |
| 329 |
|
double eta[3][3]; |
| 330 |
< |
double NkBT; |
| 331 |
< |
double fkBT; |
| 402 |
< |
|
| 403 |
< |
int Nparticles; |
| 404 |
< |
|
| 405 |
< |
double *oldPos; |
| 406 |
< |
double *oldVel; |
| 407 |
< |
double *oldJi; |
| 408 |
< |
|
| 409 |
< |
double integralOfChidt; |
| 410 |
< |
|
| 411 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
| 412 |
< |
// One of qmass or tauThermostat must be set; |
| 413 |
< |
|
| 414 |
< |
double targetTemp; |
| 415 |
< |
double targetPressure; |
| 416 |
< |
double tauThermostat; |
| 417 |
< |
double tauBarostat; |
| 418 |
< |
|
| 419 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
| 420 |
< |
short int have_target_pressure; |
| 421 |
< |
double chiTolerance; |
| 422 |
< |
short int have_chi_tolerance; |
| 423 |
< |
double posIterTolerance; |
| 424 |
< |
short int have_pos_iter_tolerance; |
| 425 |
< |
double etaTolerance; |
| 426 |
< |
short int have_eta_tolerance; |
| 330 |
> |
double oldEta[3][3]; |
| 331 |
> |
double prevEta[3][3]; |
| 332 |
|
}; |
| 333 |
|
|
| 334 |
|
template<typename T> class NPTxym : public T{ |
