| 418 |
|
|
| 419 |
|
void zeroOutVel(); |
| 420 |
|
void doZconstraintForce(); |
| 421 |
< |
void doHarmonic(); |
| 421 |
> |
void doHarmonic(vector<double>& resPos); |
| 422 |
|
bool checkZConsState(); |
| 423 |
|
|
| 424 |
|
bool haveFixedZMols(); |
| 448 |
|
vector<ZConsParaItem>* parameters; // |
| 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; |
| 451 |
|
|
| 452 |
+ |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
| 453 |
+ |
vector<double> fz; |
| 454 |
+ |
vector<double> curZPos; |
| 455 |
|
|
| 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 |
< |
class OOPSEMinimizerBase : public RealIntegrator { |
| 486 |
> |
//Steered Molecular Dynamics |
| 487 |
> |
template<typename T> class SMD : public T{ |
| 488 |
|
public: |
| 489 |
< |
|
| 490 |
< |
OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff ); |
| 491 |
< |
virtual ~OOPSEMinimizerBase(); |
| 492 |
< |
|
| 493 |
< |
double calcGradient(vector<double>& x, vector<double>& grad); |
| 484 |
< |
void setCoor(vector<double>& x); |
| 485 |
< |
vector<double> getCoor(); |
| 486 |
< |
void output(vector<double>& x, int iteration); |
| 487 |
< |
int getDim() {return dim;} |
| 488 |
< |
void constraintMove(); |
| 489 |
< |
void shakeF(); |
| 490 |
< |
void shakeR(); |
| 491 |
< |
protected: |
| 492 |
< |
|
| 493 |
< |
int dim; |
| 494 |
< |
void calcDim(); |
| 489 |
> |
SMD( SimInfo *theInfo, ForceFields* the_ff); |
| 490 |
> |
~SMD(); |
| 491 |
> |
|
| 492 |
> |
virtual void integrate(); |
| 493 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
| 494 |
|
}; |
| 495 |
< |
|
| 497 |
< |
//template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{ |
| 498 |
< |
// public: |
| 499 |
< |
// void writeOutput(); |
| 500 |
< |
//}; |
| 501 |
< |
*/ |
| 495 |
> |
*/ |
| 496 |
|
#endif |
