44 |
|
|
45 |
|
void checkConstraints( void ); |
46 |
|
void rotate( int axes1, int axes2, double angle, double j[3], |
47 |
< |
double A[3][3] ); |
48 |
< |
|
47 |
> |
double A[3][3] ); |
48 |
> |
|
49 |
|
ForceFields* myFF; |
50 |
|
|
51 |
|
SimInfo *info; // all the info we'll ever need |
56 |
|
int nMols; |
57 |
|
|
58 |
|
int isConstrained; // boolean to know whether the systems contains |
59 |
< |
// constraints. |
59 |
> |
// constraints. |
60 |
|
int nConstrained; // counter for number of constraints |
61 |
|
int *constrainedA; // the i of a constraint pair |
62 |
|
int *constrainedB; // the j of a constraint pair |
297 |
|
short int have_target_pressure; |
298 |
|
|
299 |
|
}; |
300 |
+ |
|
301 |
+ |
|
302 |
+ |
template<typename T> class NPTpr : public T{ |
303 |
+ |
|
304 |
+ |
public: |
305 |
+ |
|
306 |
+ |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
307 |
+ |
virtual ~NPTpr() {}; |
308 |
+ |
|
309 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
310 |
+ |
calcStress = 1; |
311 |
+ |
T::integrateStep( calcPot, calcStress ); |
312 |
+ |
} |
313 |
+ |
|
314 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
315 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
316 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
317 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
318 |
|
|
319 |
+ |
protected: |
320 |
+ |
|
321 |
+ |
virtual void moveA( void ); |
322 |
+ |
virtual void moveB( void ); |
323 |
+ |
|
324 |
+ |
virtual int readyCheck(); |
325 |
+ |
|
326 |
+ |
// chi and eta are the propagated degrees of freedom |
327 |
+ |
|
328 |
+ |
double chi; |
329 |
+ |
double eta[3][3]; |
330 |
+ |
double NkBT; |
331 |
+ |
|
332 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
333 |
+ |
// One of qmass or tauThermostat must be set; |
334 |
+ |
|
335 |
+ |
double targetTemp; |
336 |
+ |
double targetPressure; |
337 |
+ |
double tauThermostat; |
338 |
+ |
double tauBarostat; |
339 |
+ |
|
340 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
341 |
+ |
short int have_target_pressure; |
342 |
+ |
|
343 |
+ |
}; |
344 |
+ |
|
345 |
+ |
|
346 |
|
template<typename T> class ZConstraint : public T { |
347 |
+ |
|
348 |
+ |
public: |
349 |
+ |
class ForceSubtractionPolicy{ |
350 |
+ |
public: |
351 |
+ |
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
352 |
|
|
353 |
+ |
virtual void update() = 0; |
354 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
355 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
356 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
357 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
358 |
+ |
|
359 |
+ |
protected: |
360 |
+ |
ZConstraint<T>* zconsIntegrator;; |
361 |
+ |
}; |
362 |
+ |
|
363 |
+ |
class PolicyByNumber : public ForceSubtractionPolicy{ |
364 |
+ |
public: |
365 |
+ |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
366 |
+ |
virtual void update(); |
367 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
368 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
369 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
370 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
371 |
+ |
|
372 |
+ |
private: |
373 |
+ |
int totNumOfMovingAtoms; |
374 |
+ |
}; |
375 |
+ |
|
376 |
+ |
class PolicyByMass : public ForceSubtractionPolicy{ |
377 |
+ |
public: |
378 |
+ |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
379 |
+ |
|
380 |
+ |
virtual void update(); |
381 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
382 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
383 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
384 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
385 |
+ |
|
386 |
+ |
private: |
387 |
+ |
double totMassOfMovingAtoms; |
388 |
+ |
}; |
389 |
+ |
|
390 |
|
public: |
391 |
|
|
392 |
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
395 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
396 |
|
void getZConsTime() {return zconsTime;} |
397 |
|
|
398 |
< |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
399 |
< |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
398 |
> |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
399 |
> |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
400 |
|
|
401 |
< |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
401 |
> |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
402 |
|
string getZConsOutput() {return zconsOutput;} |
403 |
|
|
404 |
|
virtual void integrate(); |
405 |
|
|
406 |
|
|
407 |
|
#ifdef IS_MPI |
408 |
< |
virtual void update(); //which is called to indicate the molecules' migration |
408 |
> |
virtual void update(); //which is called to indicate the molecules' migration |
409 |
|
#endif |
410 |
|
|
411 |
|
protected: |
412 |
|
|
413 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
327 |
< |
|
328 |
< |
|
413 |
> |
enum ZConsState {zcsMoving, zcsFixed}; |
414 |
|
|
415 |
|
virtual void calcForce( int calcPot, int calcStress ); |
416 |
|
virtual void thermalize(void); |
428 |
|
int isZConstraintMol(Molecule* mol); |
429 |
|
|
430 |
|
|
431 |
< |
double zconsTime; |
432 |
< |
double zconsTol; |
433 |
< |
double zForceConst; |
431 |
> |
double zconsTime; //sample time |
432 |
> |
double zconsTol; //tolerance of z-contratint |
433 |
> |
double zForceConst; //base force constant term |
434 |
> |
//which is estimate by OOPSE |
435 |
|
|
436 |
< |
vector<Molecule*> zconsMols; |
437 |
< |
vector<double> massOfZConsMols; |
438 |
< |
vector<double> kz; |
439 |
< |
vector<ZConsState> states; |
440 |
< |
vector<double> zPos; |
436 |
> |
vector<Molecule*> zconsMols; //z-constraint molecules array |
437 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
438 |
> |
vector<double> kz; //force constant array |
439 |
> |
vector<ZConsState> states; //state of z-constraint molecules |
440 |
> |
vector<double> zPos; // |
441 |
|
|
442 |
|
|
443 |
< |
vector<Molecule*> unconsMols; |
444 |
< |
vector<double> massOfUnconsMols; |
445 |
< |
double totalMassOfUncons; |
443 |
> |
vector<Molecule*> unconsMols; //unconstraint molecules array |
444 |
> |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
445 |
> |
double totalMassOfUncons; //total mas of unconstraint molecules |
446 |
|
|
447 |
< |
vector<ZConsParaItem>* parameters; |
447 |
> |
vector<ZConsParaItem>* parameters; // |
448 |
|
|
449 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
450 |
|
|
451 |
|
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
452 |
|
double* fz; |
453 |
+ |
double* curZPos; |
454 |
|
|
455 |
< |
int totNumOfUnconsAtoms; |
455 |
> |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
456 |
|
|
457 |
|
int whichDirection; //constraint direction |
458 |
|
|
459 |
|
private: |
460 |
|
|
461 |
< |
string zconsOutput; |
462 |
< |
ZConsWriter* fzOut; |
461 |
> |
string zconsOutput; //filename of zconstraint output |
462 |
> |
ZConsWriter* fzOut; //z-constraint writer |
463 |
|
|
464 |
< |
double calcCOMVel(); |
378 |
< |
double calcCOMVel2(); |
464 |
> |
double curZconsTime; |
465 |
|
|
466 |
+ |
double calcMovingMolsCOMVel(); |
467 |
+ |
double calcSysCOMVel(); |
468 |
+ |
double calcTotalForce(); |
469 |
+ |
|
470 |
+ |
ForceSubtractionPolicy* forcePolicy; //force substration policy |
471 |
+ |
friend class ForceSubtractionPolicy; |
472 |
+ |
|
473 |
|
}; |
474 |
|
|
475 |
|
#endif |