| 10 |
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class ExtendedSystem{ |
| 11 |
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public: |
| 12 |
|
|
| 13 |
< |
ExtendedSystem(SimInfo &info); |
| 13 |
> |
ExtendedSystem(SimInfo* the_entry_plug); |
| 14 |
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virtual ~ExtendedSystem() {} |
| 15 |
|
|
| 16 |
< |
void setQmass(double q) {qmass = q;} |
| 17 |
< |
void setTargetTemp(double tt) {targetTemp = tt;} |
| 18 |
< |
void setTargetPressure(double tp) {targetPressure = tp;} |
| 16 |
> |
void setQmass(double q) {qmass = q; have_qmass = 1;} |
| 17 |
> |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
| 18 |
> |
void setTauBarostat(double tt) {tauBarostat = tt; have_tau_barostat = 1;} |
| 19 |
> |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
| 20 |
> |
void setTargetPressure(double tp) {targetPressure=tp;have_target_pressure=1;} |
| 21 |
|
|
| 22 |
< |
void NoseHooverNVT(double dt); |
| 23 |
< |
void NoseHooverAndersonNPT(double dt); |
| 24 |
< |
void AffineTransform(double scale); |
| 22 |
> |
void NoseHooverNVT(double dt, double ke); |
| 23 |
> |
void NoseHooverAndersonNPT(double dt, double ke, double p_mol); |
| 24 |
> |
void AffineTransform(double oldBox[3], double newBox[3]); |
| 25 |
|
|
| 26 |
|
protected: |
| 27 |
|
|
| 28 |
+ |
SimInfo* entry_plug; |
| 29 |
+ |
|
| 30 |
+ |
short int NVTready(); |
| 31 |
+ |
short int NPTready(); |
| 32 |
+ |
|
| 33 |
+ |
// |
| 34 |
+ |
int nAtoms; |
| 35 |
+ |
int nMols; |
| 36 |
+ |
int nOriented; |
| 37 |
+ |
int ndf; |
| 38 |
+ |
|
| 39 |
+ |
Molecule* molecules; |
| 40 |
+ |
Atom** atoms; |
| 41 |
+ |
|
| 42 |
+ |
// zeta and epsilonDot are propagated |
| 43 |
|
double zeta; |
| 44 |
+ |
double epsilonDot; |
| 45 |
+ |
|
| 46 |
+ |
// qmass, tauRelax, targetTemp, and targetPressure are parameters that |
| 47 |
+ |
// must be set |
| 48 |
|
double qmass; |
| 49 |
|
double targetTemp; |
| 50 |
|
double targetPressure; |
| 51 |
< |
double epsilonScale; |
| 52 |
< |
double epsilonDot; |
| 51 |
> |
double tauThermostat; |
| 52 |
> |
double tauBarostat; |
| 53 |
|
|
| 54 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
| 55 |
+ |
short int have_target_pressure, have_qmass; |
| 56 |
+ |
|
| 57 |
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}; |
| 58 |
+ |
#endif |
