27 |
|
Integrator( SimInfo *theInfo, ForceFields* the_ff ); |
28 |
|
virtual ~Integrator(); |
29 |
|
void integrate( void ); |
30 |
+ |
virtual double getConservedQuantity(void); |
31 |
|
|
31 |
– |
|
32 |
|
protected: |
33 |
< |
|
33 |
> |
|
34 |
|
virtual void integrateStep( int calcPot, int calcStress ); |
35 |
|
virtual void preMove( void ); |
36 |
|
virtual void moveA( void ); |
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 |
+ |
virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] ); |
48 |
+ |
|
49 |
|
void checkConstraints( void ); |
50 |
|
void rotate( int axes1, int axes2, double angle, double j[3], |
51 |
< |
double A[3][3] ); |
52 |
< |
|
51 |
> |
double A[3][3] ); |
52 |
> |
|
53 |
|
ForceFields* myFF; |
54 |
|
|
55 |
|
SimInfo *info; // all the info we'll ever need |
60 |
|
int nMols; |
61 |
|
|
62 |
|
int isConstrained; // boolean to know whether the systems contains |
63 |
< |
// constraints. |
63 |
> |
// constraints. |
64 |
|
int nConstrained; // counter for number of constraints |
65 |
|
int *constrainedA; // the i of a constraint pair |
66 |
|
int *constrainedB; // the j of a constraint pair |
97 |
|
public: |
98 |
|
|
99 |
|
NVT ( SimInfo *theInfo, ForceFields* the_ff); |
100 |
< |
virtual ~NVT() {} |
100 |
> |
virtual ~NVT(); |
101 |
|
|
102 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
103 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
104 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol;} |
105 |
+ |
virtual double getConservedQuantity(void); |
106 |
|
|
107 |
|
protected: |
108 |
|
|
111 |
|
|
112 |
|
virtual int readyCheck(); |
113 |
|
|
114 |
+ |
virtual void resetIntegrator( void ); |
115 |
+ |
|
116 |
|
// chi is a propagated degree of freedom. |
117 |
|
|
118 |
|
double chi; |
119 |
|
|
120 |
+ |
//integral of chi(t)dt |
121 |
+ |
double integralOfChidt; |
122 |
+ |
|
123 |
|
// targetTemp must be set. tauThermostat must also be set; |
124 |
|
|
125 |
|
double targetTemp; |
127 |
|
|
128 |
|
short int have_tau_thermostat, have_target_temp; |
129 |
|
|
130 |
+ |
double *oldVel; |
131 |
+ |
double *oldJi; |
132 |
+ |
|
133 |
+ |
double chiTolerance; |
134 |
+ |
short int have_chi_tolerance; |
135 |
+ |
|
136 |
|
}; |
137 |
|
|
138 |
|
|
139 |
|
|
140 |
< |
template<typename T> class NPTi : public T{ |
140 |
> |
template<typename T> class NPT : public T{ |
141 |
|
|
142 |
|
public: |
143 |
|
|
144 |
< |
NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
145 |
< |
virtual ~NPTi() {}; |
146 |
< |
|
144 |
> |
NPT ( SimInfo *theInfo, ForceFields* the_ff); |
145 |
> |
virtual ~NPT(); |
146 |
> |
|
147 |
|
virtual void integrateStep( int calcPot, int calcStress ){ |
148 |
|
calcStress = 1; |
149 |
|
T::integrateStep( calcPot, calcStress ); |
150 |
|
} |
151 |
|
|
152 |
+ |
virtual double getConservedQuantity(void) = 0; |
153 |
+ |
|
154 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
155 |
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
156 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
157 |
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
158 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;} |
159 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;} |
160 |
+ |
void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;} |
161 |
|
|
162 |
|
protected: |
163 |
|
|
166 |
|
|
167 |
|
virtual int readyCheck(); |
168 |
|
|
169 |
+ |
virtual void resetIntegrator( void ); |
170 |
+ |
|
171 |
+ |
virtual void getVelScaleA( double sc[3], double vel[3] ) = 0; |
172 |
+ |
virtual void getVelScaleB( double sc[3], int index ) = 0; |
173 |
+ |
virtual void getPosScale(double pos[3], double COM[3], |
174 |
+ |
int index, double sc[3]) = 0; |
175 |
+ |
|
176 |
+ |
virtual bool chiConverged( void ); |
177 |
+ |
virtual bool etaConverged( void ) = 0; |
178 |
+ |
|
179 |
+ |
virtual void evolveChiA( void ); |
180 |
+ |
virtual void evolveEtaA( void ) = 0; |
181 |
+ |
virtual void evolveChiB( void ); |
182 |
+ |
virtual void evolveEtaB( void ) = 0; |
183 |
+ |
|
184 |
+ |
virtual void scaleSimBox( void ) = 0; |
185 |
+ |
|
186 |
+ |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
187 |
+ |
|
188 |
|
// chi and eta are the propagated degrees of freedom |
189 |
|
|
190 |
+ |
double oldChi; |
191 |
+ |
double prevChi; |
192 |
|
double chi; |
150 |
– |
double eta; |
193 |
|
double NkBT; |
194 |
+ |
double fkBT; |
195 |
+ |
|
196 |
+ |
double tt2, tb2; |
197 |
+ |
double instaTemp, instaPress, instaVol; |
198 |
+ |
double press[3][3]; |
199 |
+ |
|
200 |
+ |
int Nparticles; |
201 |
+ |
|
202 |
+ |
double integralOfChidt; |
203 |
|
|
204 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
205 |
|
// One of qmass or tauThermostat must be set; |
212 |
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
213 |
|
short int have_target_pressure; |
214 |
|
|
215 |
+ |
double *oldPos; |
216 |
+ |
double *oldVel; |
217 |
+ |
double *oldJi; |
218 |
+ |
|
219 |
+ |
double chiTolerance; |
220 |
+ |
short int have_chi_tolerance; |
221 |
+ |
double posIterTolerance; |
222 |
+ |
short int have_pos_iter_tolerance; |
223 |
+ |
double etaTolerance; |
224 |
+ |
short int have_eta_tolerance; |
225 |
+ |
|
226 |
|
}; |
227 |
|
|
228 |
< |
template<typename T> class NPTim : public T{ |
228 |
> |
template<typename T> class NPTi : public T{ |
229 |
> |
|
230 |
> |
public: |
231 |
> |
NPTi( SimInfo *theInfo, ForceFields* the_ff); |
232 |
> |
~NPTi(); |
233 |
|
|
234 |
+ |
virtual double getConservedQuantity(void); |
235 |
+ |
virtual void resetIntegrator(void); |
236 |
+ |
|
237 |
+ |
protected: |
238 |
+ |
|
239 |
+ |
|
240 |
+ |
|
241 |
+ |
virtual void evolveEtaA(void); |
242 |
+ |
virtual void evolveEtaB(void); |
243 |
+ |
|
244 |
+ |
virtual bool etaConverged( void ); |
245 |
+ |
|
246 |
+ |
virtual void scaleSimBox( void ); |
247 |
+ |
|
248 |
+ |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
249 |
+ |
virtual void getVelScaleB( double sc[3], int index ); |
250 |
+ |
virtual void getPosScale(double pos[3], double COM[3], |
251 |
+ |
int index, double sc[3]); |
252 |
+ |
|
253 |
+ |
double eta, oldEta, prevEta; |
254 |
+ |
}; |
255 |
+ |
|
256 |
+ |
template<typename T> class NPTzm : public T{ |
257 |
+ |
|
258 |
|
public: |
259 |
|
|
260 |
< |
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
261 |
< |
virtual ~NPTim() {}; |
260 |
> |
NPTzm ( SimInfo *theInfo, ForceFields* the_ff); |
261 |
> |
virtual ~NPTzm() {}; |
262 |
|
|
263 |
|
virtual void integrateStep( int calcPot, int calcStress ){ |
264 |
|
calcStress = 1; |
277 |
|
|
278 |
|
virtual int readyCheck(); |
279 |
|
|
280 |
+ |
virtual void resetIntegrator( void ); |
281 |
+ |
|
282 |
|
Molecule* myMolecules; |
283 |
|
Atom** myAtoms; |
284 |
|
|
286 |
|
|
287 |
|
double chi; |
288 |
|
double eta; |
289 |
+ |
double etaZ; |
290 |
|
double NkBT; |
291 |
|
|
292 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
307 |
|
public: |
308 |
|
|
309 |
|
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
310 |
< |
virtual ~NPTf() {}; |
310 |
> |
virtual ~NPTf(); |
311 |
|
|
312 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
313 |
< |
calcStress = 1; |
221 |
< |
T::integrateStep( calcPot, calcStress ); |
222 |
< |
} |
312 |
> |
virtual double getConservedQuantity(void); |
313 |
> |
virtual void resetIntegrator(void); |
314 |
|
|
224 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
225 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
226 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
227 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
228 |
– |
|
315 |
|
protected: |
316 |
|
|
317 |
< |
virtual void moveA( void ); |
318 |
< |
virtual void moveB( void ); |
317 |
> |
virtual void evolveEtaA(void); |
318 |
> |
virtual void evolveEtaB(void); |
319 |
|
|
320 |
< |
virtual int readyCheck(); |
320 |
> |
virtual bool etaConverged( void ); |
321 |
|
|
322 |
< |
// chi and eta are the propagated degrees of freedom |
237 |
< |
|
238 |
< |
double chi; |
239 |
< |
double eta[3][3]; |
240 |
< |
double NkBT; |
322 |
> |
virtual void scaleSimBox( void ); |
323 |
|
|
324 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
325 |
< |
// One of qmass or tauThermostat must be set; |
324 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
325 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
326 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
327 |
> |
int index, double sc[3]); |
328 |
|
|
329 |
< |
double targetTemp; |
330 |
< |
double targetPressure; |
331 |
< |
double tauThermostat; |
248 |
< |
double tauBarostat; |
249 |
< |
|
250 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
251 |
< |
short int have_target_pressure; |
252 |
< |
|
329 |
> |
double eta[3][3]; |
330 |
> |
double oldEta[3][3]; |
331 |
> |
double prevEta[3][3]; |
332 |
|
}; |
333 |
|
|
334 |
< |
template<typename T> class NPTfm : public T{ |
334 |
> |
template<typename T> class NPTxym : public T{ |
335 |
|
|
336 |
|
public: |
337 |
|
|
338 |
< |
NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
339 |
< |
virtual ~NPTfm() {}; |
338 |
> |
NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
339 |
> |
virtual ~NPTxym() {}; |
340 |
|
|
341 |
|
virtual void integrateStep( int calcPot, int calcStress ){ |
342 |
|
calcStress = 1; |
350 |
|
|
351 |
|
protected: |
352 |
|
|
353 |
< |
virtual void moveA( void ); |
353 |
> |
virtual void moveA( void ); |
354 |
|
virtual void moveB( void ); |
355 |
|
|
356 |
|
virtual int readyCheck(); |
357 |
|
|
358 |
+ |
virtual void resetIntegrator( void ); |
359 |
+ |
|
360 |
|
Molecule* myMolecules; |
361 |
|
Atom** myAtoms; |
362 |
|
|
363 |
|
// chi and eta are the propagated degrees of freedom |
364 |
|
|
365 |
|
double chi; |
366 |
< |
double eta[3][3]; |
366 |
> |
double eta; |
367 |
> |
double etaX; |
368 |
> |
double etaY; |
369 |
|
double NkBT; |
370 |
|
|
371 |
|
// targetTemp, targetPressure, and tauBarostat must be set. |
382 |
|
}; |
383 |
|
|
384 |
|
template<typename T> class ZConstraint : public T { |
385 |
+ |
|
386 |
+ |
public: |
387 |
+ |
class ForceSubtractionPolicy{ |
388 |
+ |
public: |
389 |
+ |
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
390 |
|
|
391 |
+ |
virtual void update() = 0; |
392 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
393 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
394 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
395 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
396 |
+ |
|
397 |
+ |
protected: |
398 |
+ |
ZConstraint<T>* zconsIntegrator;; |
399 |
+ |
}; |
400 |
+ |
|
401 |
+ |
class PolicyByNumber : public ForceSubtractionPolicy{ |
402 |
+ |
|
403 |
+ |
public: |
404 |
+ |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
405 |
+ |
virtual void update(); |
406 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
407 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
408 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
409 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
410 |
+ |
|
411 |
+ |
private: |
412 |
+ |
int totNumOfMovingAtoms; |
413 |
+ |
}; |
414 |
+ |
|
415 |
+ |
class PolicyByMass : public ForceSubtractionPolicy{ |
416 |
+ |
|
417 |
+ |
public: |
418 |
+ |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
419 |
+ |
|
420 |
+ |
virtual void update(); |
421 |
+ |
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
422 |
+ |
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
423 |
+ |
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
424 |
+ |
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
425 |
+ |
|
426 |
+ |
private: |
427 |
+ |
double totMassOfMovingAtoms; |
428 |
+ |
}; |
429 |
+ |
|
430 |
|
public: |
431 |
|
|
432 |
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
435 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
436 |
|
void getZConsTime() {return zconsTime;} |
437 |
|
|
438 |
< |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
439 |
< |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
438 |
> |
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
439 |
> |
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
440 |
|
|
441 |
< |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
441 |
> |
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
442 |
|
string getZConsOutput() {return zconsOutput;} |
443 |
|
|
444 |
|
virtual void integrate(); |
445 |
|
|
446 |
|
|
447 |
|
#ifdef IS_MPI |
448 |
< |
virtual void update(); //which is called to indicate the molecules' migration |
448 |
> |
virtual void update(); //which is called to indicate the molecules' migration |
449 |
|
#endif |
450 |
|
|
451 |
|
protected: |
452 |
|
|
453 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
327 |
< |
|
328 |
< |
|
453 |
> |
enum ZConsState {zcsMoving, zcsFixed}; |
454 |
|
|
455 |
|
virtual void calcForce( int calcPot, int calcStress ); |
456 |
|
virtual void thermalize(void); |
468 |
|
int isZConstraintMol(Molecule* mol); |
469 |
|
|
470 |
|
|
471 |
< |
double zconsTime; |
472 |
< |
double zconsTol; |
473 |
< |
double zForceConst; |
471 |
> |
double zconsTime; //sample time |
472 |
> |
double zconsTol; //tolerance of z-contratint |
473 |
> |
double zForceConst; //base force constant term |
474 |
> |
//which is estimate by OOPSE |
475 |
|
|
476 |
< |
vector<Molecule*> zconsMols; |
477 |
< |
vector<double> massOfZConsMols; |
478 |
< |
vector<double> kz; |
479 |
< |
vector<ZConsState> states; |
480 |
< |
vector<double> zPos; |
476 |
> |
vector<Molecule*> zconsMols; //z-constraint molecules array |
477 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
478 |
> |
vector<double> kz; //force constant array |
479 |
> |
vector<ZConsState> states; //state of z-constraint molecules |
480 |
> |
vector<double> zPos; // |
481 |
|
|
482 |
|
|
483 |
< |
vector<Molecule*> unconsMols; |
484 |
< |
vector<double> massOfUnconsMols; |
485 |
< |
double totalMassOfUncons; |
483 |
> |
vector<Molecule*> unconsMols; //unconstraint molecules array |
484 |
> |
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
485 |
> |
double totalMassOfUncons; //total mas of unconstraint molecules |
486 |
|
|
487 |
< |
vector<ZConsParaItem>* parameters; |
487 |
> |
vector<ZConsParaItem>* parameters; // |
488 |
|
|
489 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
490 |
|
|
491 |
|
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
492 |
|
double* fz; |
493 |
+ |
double* curZPos; |
494 |
|
|
495 |
< |
int totNumOfUnconsAtoms; |
495 |
> |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
496 |
|
|
497 |
|
int whichDirection; //constraint direction |
498 |
|
|
499 |
|
private: |
500 |
|
|
501 |
< |
string zconsOutput; |
502 |
< |
ZConsWriter* fzOut; |
501 |
> |
string zconsOutput; //filename of zconstraint output |
502 |
> |
ZConsWriter* fzOut; //z-constraint writer |
503 |
|
|
504 |
< |
double calcCOMVel(); |
378 |
< |
double calcCOMVel2(); |
504 |
> |
double curZconsTime; |
505 |
|
|
506 |
+ |
double calcMovingMolsCOMVel(); |
507 |
+ |
double calcSysCOMVel(); |
508 |
+ |
double calcTotalForce(); |
509 |
+ |
|
510 |
+ |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
511 |
+ |
friend class ForceSubtractionPolicy; |
512 |
+ |
|
513 |
|
}; |
514 |
|
|
515 |
|
#endif |