| 38 |
|
virtual void constrainA( void ); |
| 39 |
|
virtual void constrainB( void ); |
| 40 |
|
virtual int readyCheck( void ) { return 1; } |
| 41 |
+ |
|
| 42 |
+ |
virtual void calcForce( int calcPot, int calcStress ); |
| 43 |
+ |
virtual void thermalize(); |
| 44 |
|
|
| 45 |
|
void checkConstraints( void ); |
| 46 |
|
void rotate( int axes1, int axes2, double angle, double j[3], |
| 47 |
|
double A[3][3] ); |
| 48 |
< |
|
| 46 |
< |
|
| 48 |
> |
|
| 49 |
|
ForceFields* myFF; |
| 50 |
|
|
| 51 |
|
SimInfo *info; // all the info we'll ever need |
| 304 |
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|
| 305 |
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ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
| 306 |
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~ZConstraint(); |
| 307 |
< |
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| 306 |
< |
virtual void integrateStep( int calcPot, int calcStress ); |
| 307 |
< |
|
| 308 |
< |
|
| 307 |
> |
|
| 308 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
| 309 |
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void getZConsTime() {return zconsTime;} |
| 310 |
|
|
| 313 |
|
|
| 314 |
|
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
| 315 |
|
string getZConsOutput() {return zconsOutput;} |
| 316 |
+ |
|
| 317 |
+ |
virtual void integrate(); |
| 318 |
+ |
|
| 319 |
|
|
| 320 |
|
#ifdef IS_MPI |
| 321 |
|
virtual void update(); //which is called to indicate the molecules' migration |
| 323 |
|
|
| 324 |
|
protected: |
| 325 |
|
|
| 326 |
< |
double zconsTime; |
| 326 |
> |
enum ZConsState {zcsMoving, zcsFixed}; |
| 327 |
> |
|
| 328 |
> |
|
| 329 |
> |
|
| 330 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
| 331 |
> |
virtual void thermalize(void); |
| 332 |
|
|
| 333 |
< |
void resetZ(void); |
| 333 |
> |
void zeroOutVel(); |
| 334 |
> |
void doZconstraintForce(); |
| 335 |
> |
void doHarmonic(); |
| 336 |
> |
bool checkZConsState(); |
| 337 |
> |
|
| 338 |
> |
bool haveFixedZMols(); |
| 339 |
> |
bool haveMovingZMols(); |
| 340 |
> |
|
| 341 |
> |
double calcZSys(); |
| 342 |
> |
|
| 343 |
> |
int isZConstraintMol(Molecule* mol); |
| 344 |
> |
|
| 345 |
> |
|
| 346 |
> |
double zconsTime; |
| 347 |
> |
double zconsTol; |
| 348 |
> |
double zForceConst; |
| 349 |
|
|
| 350 |
|
vector<Molecule*> zconsMols; |
| 351 |
|
vector<double> massOfZConsMols; |
| 352 |
+ |
vector<double> kz; |
| 353 |
+ |
vector<ZConsState> states; |
| 354 |
+ |
vector<double> zPos; |
| 355 |
|
|
| 356 |
+ |
|
| 357 |
|
vector<Molecule*> unconsMols; |
| 358 |
|
vector<double> massOfUnconsMols; |
| 359 |
|
double totalMassOfUncons; |
| 360 |
|
|
| 361 |
< |
vector<double> allRefZ; |
| 336 |
< |
vector<double> refZ; |
| 361 |
> |
vector<ZConsParaItem>* parameters; |
| 362 |
|
|
| 363 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
| 364 |
< |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
| 365 |
< |
|
| 364 |
> |
|
| 365 |
> |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
| 366 |
|
double* fz; |
| 367 |
|
|
| 368 |
< |
private: |
| 368 |
> |
int totNumOfUnconsAtoms; |
| 369 |
|
|
| 370 |
< |
int isZConstraintMol(Molecule* mol); |
| 370 |
> |
int whichDirection; //constraint direction |
| 371 |
> |
|
| 372 |
> |
private: |
| 373 |
> |
|
| 374 |
|
string zconsOutput; |
| 375 |
|
ZConsWriter* fzOut; |
| 376 |
+ |
|
| 377 |
+ |
double calcMovingMolsCOMVel(); |
| 378 |
+ |
double calcSysCOMVel(); |
| 379 |
+ |
double calcTotalForce(); |
| 380 |
+ |
|
| 381 |
|
}; |
| 382 |
|
|
| 383 |
|
#endif |
