39 |
|
virtual void constrainB( void ); |
40 |
|
virtual int readyCheck( void ) { return 1; } |
41 |
|
|
42 |
+ |
virtual void resetIntegrator( void ) { } |
43 |
+ |
|
44 |
|
virtual void calcForce( int calcPot, int calcStress ); |
45 |
|
virtual void thermalize(); |
46 |
|
|
47 |
|
void checkConstraints( void ); |
48 |
|
void rotate( int axes1, int axes2, double angle, double j[3], |
49 |
< |
double A[3][3] ); |
50 |
< |
|
49 |
> |
double A[3][3] ); |
50 |
> |
|
51 |
|
ForceFields* myFF; |
52 |
|
|
53 |
|
SimInfo *info; // all the info we'll ever need |
58 |
|
int nMols; |
59 |
|
|
60 |
|
int isConstrained; // boolean to know whether the systems contains |
61 |
< |
// constraints. |
61 |
> |
// constraints. |
62 |
|
int nConstrained; // counter for number of constraints |
63 |
|
int *constrainedA; // the i of a constraint pair |
64 |
|
int *constrainedB; // the j of a constraint pair |
107 |
|
|
108 |
|
virtual int readyCheck(); |
109 |
|
|
110 |
+ |
virtual void resetIntegrator( void ); |
111 |
+ |
|
112 |
|
// chi is a propagated degree of freedom. |
113 |
|
|
114 |
|
double chi; |
148 |
|
|
149 |
|
virtual int readyCheck(); |
150 |
|
|
151 |
+ |
virtual void resetIntegrator( void ); |
152 |
+ |
|
153 |
|
// chi and eta are the propagated degrees of freedom |
154 |
|
|
155 |
|
double chi; |
193 |
|
|
194 |
|
virtual int readyCheck(); |
195 |
|
|
196 |
+ |
virtual void resetIntegrator( void ); |
197 |
+ |
|
198 |
|
Molecule* myMolecules; |
199 |
|
Atom** myAtoms; |
200 |
|
|
239 |
|
virtual void moveA( void ); |
240 |
|
virtual void moveB( void ); |
241 |
|
|
242 |
+ |
virtual void resetIntegrator( void ); |
243 |
+ |
|
244 |
|
virtual int readyCheck(); |
245 |
|
|
246 |
|
// chi and eta are the propagated degrees of freedom |
284 |
|
virtual void moveA( void ); |
285 |
|
virtual void moveB( void ); |
286 |
|
|
287 |
+ |
virtual void resetIntegrator( void ); |
288 |
+ |
|
289 |
|
virtual int readyCheck(); |
290 |
|
|
291 |
|
Molecule* myMolecules; |
292 |
|
Atom** myAtoms; |
293 |
+ |
|
294 |
+ |
// chi and eta are the propagated degrees of freedom |
295 |
+ |
|
296 |
+ |
double chi; |
297 |
+ |
double eta[3][3]; |
298 |
+ |
double NkBT; |
299 |
+ |
|
300 |
+ |
// targetTemp, targetPressure, and tauBarostat must be set. |
301 |
+ |
// One of qmass or tauThermostat must be set; |
302 |
+ |
|
303 |
+ |
double targetTemp; |
304 |
+ |
double targetPressure; |
305 |
+ |
double tauThermostat; |
306 |
+ |
double tauBarostat; |
307 |
+ |
|
308 |
+ |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
309 |
+ |
short int have_target_pressure; |
310 |
+ |
|
311 |
+ |
}; |
312 |
+ |
|
313 |
+ |
|
314 |
+ |
template<typename T> class NPTpr : public T{ |
315 |
+ |
|
316 |
+ |
public: |
317 |
+ |
|
318 |
+ |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
319 |
+ |
virtual ~NPTpr() {}; |
320 |
|
|
321 |
+ |
virtual void integrateStep( int calcPot, int calcStress ){ |
322 |
+ |
calcStress = 1; |
323 |
+ |
T::integrateStep( calcPot, calcStress ); |
324 |
+ |
} |
325 |
+ |
|
326 |
+ |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
327 |
+ |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
328 |
+ |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
329 |
+ |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
330 |
+ |
|
331 |
+ |
protected: |
332 |
+ |
|
333 |
+ |
virtual void moveA( void ); |
334 |
+ |
virtual void moveB( void ); |
335 |
+ |
|
336 |
+ |
virtual int readyCheck(); |
337 |
+ |
|
338 |
+ |
virtual void resetIntegrator( void ); |
339 |
+ |
|
340 |
|
// chi and eta are the propagated degrees of freedom |
341 |
|
|
342 |
|
double chi; |
356 |
|
|
357 |
|
}; |
358 |
|
|
359 |
+ |
|
360 |
|
template<typename T> class ZConstraint : public T { |
361 |
+ |
|
362 |
+ |
public: |
363 |
+ |
class ForceSubtractionPolicy{ |
364 |
+ |
public: |
365 |
+ |
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
366 |
|
|
367 |
+ |
virtual void update() = 0; |
368 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
369 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
370 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
371 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
372 |
+ |
|
373 |
+ |
protected: |
374 |
+ |
ZConstraint<T>* zconsIntegrator;; |
375 |
+ |
}; |
376 |
+ |
|
377 |
+ |
class PolicyByNumber : public ForceSubtractionPolicy{ |
378 |
+ |
public: |
379 |
+ |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
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 |
+ |
int totNumOfMovingAtoms; |
388 |
+ |
}; |
389 |
+ |
|
390 |
+ |
class PolicyByMass : public ForceSubtractionPolicy{ |
391 |
+ |
public: |
392 |
+ |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
393 |
+ |
|
394 |
+ |
virtual void update(); |
395 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
396 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
397 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
398 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
399 |
+ |
|
400 |
+ |
private: |
401 |
+ |
double totMassOfMovingAtoms; |
402 |
+ |
}; |
403 |
+ |
|
404 |
|
public: |
405 |
|
|
406 |
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
409 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
410 |
|
void getZConsTime() {return zconsTime;} |
411 |
|
|
412 |
< |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
413 |
< |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
412 |
> |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
413 |
> |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
414 |
|
|
415 |
< |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
415 |
> |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
416 |
|
string getZConsOutput() {return zconsOutput;} |
417 |
|
|
418 |
|
virtual void integrate(); |
419 |
|
|
420 |
|
|
421 |
|
#ifdef IS_MPI |
422 |
< |
virtual void update(); //which is called to indicate the molecules' migration |
422 |
> |
virtual void update(); //which is called to indicate the molecules' migration |
423 |
|
#endif |
424 |
|
|
425 |
|
protected: |
426 |
|
|
427 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
327 |
< |
|
328 |
< |
|
427 |
> |
enum ZConsState {zcsMoving, zcsFixed}; |
428 |
|
|
429 |
|
virtual void calcForce( int calcPot, int calcStress ); |
430 |
|
virtual void thermalize(void); |
442 |
|
int isZConstraintMol(Molecule* mol); |
443 |
|
|
444 |
|
|
445 |
< |
double zconsTime; |
446 |
< |
double zconsTol; |
447 |
< |
double zForceConst; |
445 |
> |
double zconsTime; //sample time |
446 |
> |
double zconsTol; //tolerance of z-contratint |
447 |
> |
double zForceConst; //base force constant term |
448 |
> |
//which is estimate by OOPSE |
449 |
|
|
450 |
< |
vector<Molecule*> zconsMols; |
451 |
< |
vector<double> massOfZConsMols; |
452 |
< |
vector<double> kz; |
453 |
< |
vector<ZConsState> states; |
454 |
< |
vector<double> zPos; |
450 |
> |
vector<Molecule*> zconsMols; //z-constraint molecules array |
451 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
452 |
> |
vector<double> kz; //force constant array |
453 |
> |
vector<ZConsState> states; //state of z-constraint molecules |
454 |
> |
vector<double> zPos; // |
455 |
|
|
456 |
|
|
457 |
< |
vector<Molecule*> unconsMols; |
458 |
< |
vector<double> massOfUnconsMols; |
459 |
< |
double totalMassOfUncons; |
457 |
> |
vector<Molecule*> unconsMols; //unconstraint molecules array |
458 |
> |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
459 |
> |
double totalMassOfUncons; //total mas of unconstraint molecules |
460 |
|
|
461 |
< |
vector<ZConsParaItem>* parameters; |
461 |
> |
vector<ZConsParaItem>* parameters; // |
462 |
|
|
463 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
464 |
|
|
465 |
|
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
466 |
|
double* fz; |
467 |
+ |
double* curZPos; |
468 |
|
|
469 |
< |
int totNumOfUnconsAtoms; |
469 |
> |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
470 |
|
|
471 |
|
int whichDirection; //constraint direction |
472 |
|
|
473 |
|
private: |
474 |
|
|
475 |
< |
string zconsOutput; |
476 |
< |
ZConsWriter* fzOut; |
475 |
> |
string zconsOutput; //filename of zconstraint output |
476 |
> |
ZConsWriter* fzOut; //z-constraint writer |
477 |
|
|
478 |
< |
double calcCOMVel(); |
378 |
< |
double calcCOMVel2(); |
478 |
> |
double curZconsTime; |
479 |
|
|
480 |
+ |
double calcMovingMolsCOMVel(); |
481 |
+ |
double calcSysCOMVel(); |
482 |
+ |
double calcTotalForce(); |
483 |
+ |
|
484 |
+ |
ForceSubtractionPolicy* forcePolicy; //force substration policy |
485 |
+ |
friend class ForceSubtractionPolicy; |
486 |
+ |
|
487 |
|
}; |
488 |
|
|
489 |
|
#endif |