153 |
|
|
154 |
|
virtual double getConservedQuantity(void) = 0; |
155 |
|
virtual string getAdditionalParameters(void) = 0; |
156 |
+ |
|
157 |
+ |
double myTauThermo( void ) { return tauThermostat; } |
158 |
+ |
double myTauBaro( void ) { return tauBarostat; } |
159 |
+ |
|
160 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
161 |
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
162 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
178 |
|
virtual void getVelScaleB( double sc[3], int index ) = 0; |
179 |
|
virtual void getPosScale(double pos[3], double COM[3], |
180 |
|
int index, double sc[3]) = 0; |
181 |
+ |
|
182 |
+ |
virtual void calcVelScale( void ) = 0; |
183 |
|
|
184 |
|
virtual bool chiConverged( void ); |
185 |
|
virtual bool etaConverged( void ) = 0; |
258 |
|
virtual void getPosScale(double pos[3], double COM[3], |
259 |
|
int index, double sc[3]); |
260 |
|
|
261 |
+ |
virtual void calcVelScale( void ); |
262 |
+ |
|
263 |
|
double eta, oldEta, prevEta; |
264 |
+ |
double vScale; |
265 |
|
}; |
266 |
|
|
267 |
|
template<typename T> class NPTf : public T{ |
289 |
|
virtual void getPosScale(double pos[3], double COM[3], |
290 |
|
int index, double sc[3]); |
291 |
|
|
292 |
+ |
virtual void calcVelScale( void ); |
293 |
+ |
|
294 |
|
double eta[3][3]; |
295 |
|
double oldEta[3][3]; |
296 |
|
double prevEta[3][3]; |
297 |
+ |
double vScale[3][3]; |
298 |
|
}; |
299 |
|
|
300 |
|
template<typename T> class NPTxyz : public T{ |
322 |
|
virtual void getPosScale(double pos[3], double COM[3], |
323 |
|
int index, double sc[3]); |
324 |
|
|
325 |
+ |
virtual void calcVelScale( void ); |
326 |
+ |
|
327 |
|
double eta[3][3]; |
328 |
|
double oldEta[3][3]; |
329 |
|
double prevEta[3][3]; |
330 |
+ |
double vScale[3][3]; |
331 |
|
}; |
332 |
|
|
333 |
|
|
418 |
|
|
419 |
|
void zeroOutVel(); |
420 |
|
void doZconstraintForce(); |
421 |
< |
void doHarmonic(); |
421 |
> |
void doHarmonic(vector<double>& resPos); |
422 |
|
bool checkZConsState(); |
423 |
|
|
424 |
|
bool haveFixedZMols(); |
449 |
|
|
450 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
451 |
|
|
452 |
< |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
453 |
< |
double* fz; |
454 |
< |
double* curZPos; |
452 |
> |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
453 |
> |
vector<double> fz; |
454 |
> |
vector<double> curZPos; |
455 |
|
|
456 |
< |
|
456 |
> |
bool usingSMD; |
457 |
> |
vector<double> cantPos; |
458 |
> |
vector<double> cantVel; |
459 |
|
|
460 |
+ |
double zconsFixTime; |
461 |
+ |
double zconsGap; |
462 |
+ |
bool hasZConsGap; |
463 |
+ |
vector<double> endFixTime; |
464 |
+ |
|
465 |
|
int whichDirection; //constraint direction |
466 |
|
|
467 |
|
private: |
474 |
|
double calcMovingMolsCOMVel(); |
475 |
|
double calcSysCOMVel(); |
476 |
|
double calcTotalForce(); |
477 |
< |
|
477 |
> |
void updateZPos(); |
478 |
> |
void updateCantPos(); |
479 |
> |
|
480 |
|
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
481 |
|
friend class ForceSubtractionPolicy; |
482 |
|
|
483 |
|
}; |
484 |
|
|
485 |
+ |
/* |
486 |
+ |
//Steered Molecular Dynamics |
487 |
+ |
template<typename T> class SMD : public T{ |
488 |
+ |
public: |
489 |
+ |
SMD( SimInfo *theInfo, ForceFields* the_ff); |
490 |
+ |
~SMD(); |
491 |
+ |
|
492 |
+ |
virtual void integrate(); |
493 |
+ |
virtual void calcForce( int calcPot, int calcStress ); |
494 |
+ |
}; |
495 |
+ |
*/ |
496 |
|
#endif |