28 |
|
virtual ~Integrator(); |
29 |
|
void integrate( void ); |
30 |
|
virtual double getConservedQuantity(void); |
31 |
+ |
virtual string getAdditionalParameters(void); |
32 |
|
|
33 |
|
protected: |
34 |
|
|
41 |
|
virtual int readyCheck( void ) { return 1; } |
42 |
|
|
43 |
|
virtual void resetIntegrator( void ) { } |
44 |
< |
|
45 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
44 |
> |
|
45 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
46 |
|
virtual void thermalize(); |
47 |
< |
|
47 |
> |
|
48 |
|
virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] ); |
49 |
|
|
50 |
|
void checkConstraints( void ); |
51 |
< |
void rotate( int axes1, int axes2, double angle, double j[3], |
51 |
> |
void rotate( int axes1, int axes2, double angle, double j[3], |
52 |
|
double A[3][3] ); |
53 |
< |
|
53 |
> |
|
54 |
|
ForceFields* myFF; |
55 |
|
|
56 |
|
SimInfo *info; // all the info we'll ever need |
62 |
|
|
63 |
|
int isConstrained; // boolean to know whether the systems contains |
64 |
|
// constraints. |
65 |
< |
int nConstrained; // counter for number of constraints |
66 |
< |
int *constrainedA; // the i of a constraint pair |
67 |
< |
int *constrainedB; // the j of a constraint pair |
68 |
< |
double *constrainedDsqr; // the square of the constraint distance |
69 |
< |
|
65 |
> |
int nConstrained; // counter for number of constraints |
66 |
> |
int *constrainedA; // the i of a constraint pair |
67 |
> |
int *constrainedB; // the j of a constraint pair |
68 |
> |
double *constrainedDsqr; // the square of the constraint distance |
69 |
> |
|
70 |
|
int* moving; // tells whether we are moving atom i |
71 |
|
int* moved; // tells whether we have moved atom i |
72 |
< |
double* oldPos; // pre constrained positions |
72 |
> |
double* oldPos; // pre constrained positions |
73 |
|
|
74 |
|
short isFirst; /*boolean for the first time integrate is called */ |
75 |
< |
|
75 |
> |
|
76 |
|
double dt; |
77 |
|
double dt2; |
78 |
|
|
79 |
|
Thermo *tStats; |
80 |
|
StatWriter* statOut; |
81 |
|
DumpWriter* dumpOut; |
82 |
< |
|
82 |
> |
|
83 |
|
}; |
84 |
|
|
85 |
|
typedef Integrator<BaseIntegrator> RealIntegrator; |
89 |
|
public: |
90 |
|
NVE ( SimInfo *theInfo, ForceFields* the_ff ): |
91 |
|
T( theInfo, the_ff ){} |
92 |
< |
virtual ~NVE(){} |
92 |
> |
virtual ~NVE(){} |
93 |
|
}; |
94 |
|
|
95 |
|
|
104 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
105 |
|
void setChiTolerance(double tol) {chiTolerance = tol;} |
106 |
|
virtual double getConservedQuantity(void); |
107 |
+ |
virtual string getAdditionalParameters(void); |
108 |
|
|
109 |
|
protected: |
110 |
|
|
126 |
|
|
127 |
|
double targetTemp; |
128 |
|
double tauThermostat; |
129 |
< |
|
129 |
> |
|
130 |
|
short int have_tau_thermostat, have_target_temp; |
131 |
|
|
132 |
|
double *oldVel; |
145 |
|
|
146 |
|
NPT ( SimInfo *theInfo, ForceFields* the_ff); |
147 |
|
virtual ~NPT(); |
148 |
< |
|
148 |
> |
|
149 |
|
virtual void integrateStep( int calcPot, int calcStress ){ |
150 |
|
calcStress = 1; |
151 |
|
T::integrateStep( calcPot, calcStress ); |
152 |
|
} |
153 |
|
|
154 |
|
virtual double getConservedQuantity(void) = 0; |
155 |
+ |
virtual string getAdditionalParameters(void) = 0; |
156 |
+ |
|
157 |
+ |
double myTauThermo( void ) { return tauThermostat; } |
158 |
+ |
double myTauBaro( void ) { return tauBarostat; } |
159 |
|
|
160 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
161 |
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
176 |
|
|
177 |
|
virtual void getVelScaleA( double sc[3], double vel[3] ) = 0; |
178 |
|
virtual void getVelScaleB( double sc[3], int index ) = 0; |
179 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
179 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
180 |
|
int index, double sc[3]) = 0; |
181 |
|
|
182 |
|
virtual bool chiConverged( void ); |
183 |
|
virtual bool etaConverged( void ) = 0; |
184 |
< |
|
184 |
> |
|
185 |
|
virtual void evolveChiA( void ); |
186 |
|
virtual void evolveEtaA( void ) = 0; |
187 |
|
virtual void evolveChiB( void ); |
207 |
|
|
208 |
|
double integralOfChidt; |
209 |
|
|
210 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
210 |
> |
// targetTemp, targetPressure, and tauBarostat must be set. |
211 |
|
// One of qmass or tauThermostat must be set; |
212 |
|
|
213 |
|
double targetTemp; |
232 |
|
}; |
233 |
|
|
234 |
|
template<typename T> class NPTi : public T{ |
235 |
< |
|
235 |
> |
|
236 |
|
public: |
237 |
|
NPTi( SimInfo *theInfo, ForceFields* the_ff); |
238 |
|
~NPTi(); |
239 |
|
|
240 |
|
virtual double getConservedQuantity(void); |
241 |
|
virtual void resetIntegrator(void); |
242 |
< |
|
242 |
> |
virtual string getAdditionalParameters(void); |
243 |
|
protected: |
244 |
|
|
239 |
– |
|
245 |
|
|
246 |
+ |
|
247 |
|
virtual void evolveEtaA(void); |
248 |
|
virtual void evolveEtaB(void); |
249 |
|
|
253 |
|
|
254 |
|
virtual void getVelScaleA( double sc[3], double vel[3] ); |
255 |
|
virtual void getVelScaleB( double sc[3], int index ); |
256 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
256 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
257 |
|
int index, double sc[3]); |
258 |
|
|
259 |
|
double eta, oldEta, prevEta; |
260 |
|
}; |
261 |
|
|
256 |
– |
template<typename T> class NPTzm : public T{ |
257 |
– |
|
258 |
– |
public: |
259 |
– |
|
260 |
– |
NPTzm ( SimInfo *theInfo, ForceFields* the_ff); |
261 |
– |
virtual ~NPTzm() {}; |
262 |
– |
|
263 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
264 |
– |
calcStress = 1; |
265 |
– |
T::integrateStep( calcPot, calcStress ); |
266 |
– |
} |
267 |
– |
|
268 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
269 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
270 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
271 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
272 |
– |
|
273 |
– |
protected: |
274 |
– |
|
275 |
– |
virtual void moveA( void ); |
276 |
– |
virtual void moveB( void ); |
277 |
– |
|
278 |
– |
virtual int readyCheck(); |
279 |
– |
|
280 |
– |
virtual void resetIntegrator( void ); |
281 |
– |
|
282 |
– |
Molecule* myMolecules; |
283 |
– |
Atom** myAtoms; |
284 |
– |
|
285 |
– |
// chi and eta are the propagated degrees of freedom |
286 |
– |
|
287 |
– |
double chi; |
288 |
– |
double eta; |
289 |
– |
double etaZ; |
290 |
– |
double NkBT; |
291 |
– |
|
292 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
293 |
– |
// One of qmass or tauThermostat must be set; |
294 |
– |
|
295 |
– |
double targetTemp; |
296 |
– |
double targetPressure; |
297 |
– |
double tauThermostat; |
298 |
– |
double tauBarostat; |
299 |
– |
|
300 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
301 |
– |
short int have_target_pressure; |
302 |
– |
|
303 |
– |
}; |
304 |
– |
|
262 |
|
template<typename T> class NPTf : public T{ |
263 |
|
|
264 |
|
public: |
267 |
|
virtual ~NPTf(); |
268 |
|
|
269 |
|
virtual double getConservedQuantity(void); |
270 |
+ |
virtual string getAdditionalParameters(void); |
271 |
|
virtual void resetIntegrator(void); |
272 |
|
|
273 |
|
protected: |
281 |
|
|
282 |
|
virtual void getVelScaleA( double sc[3], double vel[3] ); |
283 |
|
virtual void getVelScaleB( double sc[3], int index ); |
284 |
< |
virtual void getPosScale(double pos[3], double COM[3], |
284 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
285 |
|
int index, double sc[3]); |
286 |
|
|
287 |
|
double eta[3][3]; |
289 |
|
double prevEta[3][3]; |
290 |
|
}; |
291 |
|
|
292 |
< |
template<typename T> class NPTxym : public T{ |
292 |
> |
template<typename T> class NPTxyz : public T{ |
293 |
|
|
294 |
|
public: |
295 |
|
|
296 |
< |
NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
297 |
< |
virtual ~NPTxym() {}; |
296 |
> |
NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
297 |
> |
virtual ~NPTxyz(); |
298 |
|
|
299 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
300 |
< |
calcStress = 1; |
301 |
< |
T::integrateStep( calcPot, calcStress ); |
344 |
< |
} |
299 |
> |
virtual double getConservedQuantity(void); |
300 |
> |
virtual string getAdditionalParameters(void); |
301 |
> |
virtual void resetIntegrator(void); |
302 |
|
|
346 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
347 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
348 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
349 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
350 |
– |
|
303 |
|
protected: |
304 |
|
|
305 |
< |
virtual void moveA( void ); |
306 |
< |
virtual void moveB( void ); |
305 |
> |
virtual void evolveEtaA(void); |
306 |
> |
virtual void evolveEtaB(void); |
307 |
|
|
308 |
< |
virtual int readyCheck(); |
308 |
> |
virtual bool etaConverged( void ); |
309 |
|
|
310 |
< |
virtual void resetIntegrator( void ); |
310 |
> |
virtual void scaleSimBox( void ); |
311 |
|
|
312 |
< |
Molecule* myMolecules; |
313 |
< |
Atom** myAtoms; |
312 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
313 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
314 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
315 |
> |
int index, double sc[3]); |
316 |
|
|
317 |
< |
// chi and eta are the propagated degrees of freedom |
318 |
< |
|
319 |
< |
double chi; |
366 |
< |
double eta; |
367 |
< |
double etaX; |
368 |
< |
double etaY; |
369 |
< |
double NkBT; |
370 |
< |
|
371 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
372 |
< |
// One of qmass or tauThermostat must be set; |
373 |
< |
|
374 |
< |
double targetTemp; |
375 |
< |
double targetPressure; |
376 |
< |
double tauThermostat; |
377 |
< |
double tauBarostat; |
378 |
< |
|
379 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
380 |
< |
short int have_target_pressure; |
381 |
< |
|
317 |
> |
double eta[3][3]; |
318 |
> |
double oldEta[3][3]; |
319 |
> |
double prevEta[3][3]; |
320 |
|
}; |
321 |
|
|
322 |
+ |
|
323 |
|
template<typename T> class ZConstraint : public T { |
324 |
< |
|
325 |
< |
public: |
324 |
> |
|
325 |
> |
public: |
326 |
|
class ForceSubtractionPolicy{ |
327 |
|
public: |
328 |
|
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
329 |
|
|
330 |
< |
virtual void update() = 0; |
330 |
> |
virtual void update() = 0; |
331 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
332 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
333 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
334 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
335 |
< |
|
335 |
> |
|
336 |
|
protected: |
337 |
< |
ZConstraint<T>* zconsIntegrator;; |
337 |
> |
ZConstraint<T>* zconsIntegrator; |
338 |
|
}; |
339 |
|
|
340 |
|
class PolicyByNumber : public ForceSubtractionPolicy{ |
341 |
|
|
342 |
|
public: |
343 |
< |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
344 |
< |
virtual void update(); |
343 |
> |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
344 |
> |
virtual void update(); |
345 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
346 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
347 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
348 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
349 |
< |
|
349 |
> |
|
350 |
|
private: |
351 |
|
int totNumOfMovingAtoms; |
352 |
|
}; |
354 |
|
class PolicyByMass : public ForceSubtractionPolicy{ |
355 |
|
|
356 |
|
public: |
357 |
< |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
358 |
< |
|
359 |
< |
virtual void update(); |
357 |
> |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
358 |
> |
|
359 |
> |
virtual void update(); |
360 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
361 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
362 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
370 |
|
|
371 |
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
372 |
|
~ZConstraint(); |
373 |
< |
|
373 |
> |
|
374 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
375 |
|
void getZConsTime() {return zconsTime;} |
376 |
< |
|
376 |
> |
|
377 |
|
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
378 |
|
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
379 |
< |
|
379 |
> |
|
380 |
|
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
381 |
|
string getZConsOutput() {return zconsOutput;} |
382 |
< |
|
382 |
> |
|
383 |
|
virtual void integrate(); |
445 |
– |
|
384 |
|
|
385 |
+ |
|
386 |
|
#ifdef IS_MPI |
387 |
|
virtual void update(); //which is called to indicate the molecules' migration |
388 |
|
#endif |
389 |
|
|
390 |
+ |
enum ZConsState {zcsMoving, zcsFixed}; |
391 |
+ |
|
392 |
+ |
vector<Molecule*> zconsMols; //z-constraint molecules array |
393 |
+ |
vector<ZConsState> states; //state of z-constraint molecules |
394 |
+ |
|
395 |
+ |
|
396 |
+ |
|
397 |
+ |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
398 |
+ |
double totalMassOfUncons; //total mas of unconstraint molecules |
399 |
+ |
|
400 |
+ |
|
401 |
|
protected: |
402 |
|
|
403 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
404 |
< |
|
405 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
403 |
> |
|
404 |
> |
|
405 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
406 |
|
virtual void thermalize(void); |
407 |
< |
|
407 |
> |
|
408 |
|
void zeroOutVel(); |
409 |
|
void doZconstraintForce(); |
410 |
|
void doHarmonic(); |
422 |
|
double zconsTol; //tolerance of z-contratint |
423 |
|
double zForceConst; //base force constant term |
424 |
|
//which is estimate by OOPSE |
425 |
< |
|
426 |
< |
vector<Molecule*> zconsMols; //z-constraint molecules array |
427 |
< |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
425 |
> |
|
426 |
> |
|
427 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
428 |
|
vector<double> kz; //force constant array |
429 |
< |
vector<ZConsState> states; //state of z-constraint molecules |
429 |
> |
|
430 |
|
vector<double> zPos; // |
431 |
< |
|
432 |
< |
|
431 |
> |
|
432 |
> |
|
433 |
|
vector<Molecule*> unconsMols; //unconstraint molecules array |
434 |
|
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
485 |
– |
double totalMassOfUncons; //total mas of unconstraint molecules |
435 |
|
|
436 |
+ |
|
437 |
|
vector<ZConsParaItem>* parameters; // |
438 |
< |
|
438 |
> |
|
439 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
440 |
|
|
441 |
< |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
441 |
> |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
442 |
|
double* fz; |
443 |
|
double* curZPos; |
494 |
– |
|
495 |
– |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
444 |
|
|
445 |
< |
int whichDirection; //constraint direction |
446 |
< |
|
445 |
> |
|
446 |
> |
|
447 |
> |
int whichDirection; //constraint direction |
448 |
> |
|
449 |
|
private: |
450 |
< |
|
450 |
> |
|
451 |
|
string zconsOutput; //filename of zconstraint output |
452 |
|
ZConsWriter* fzOut; //z-constraint writer |
453 |
|
|
454 |
< |
double curZconsTime; |
454 |
> |
double curZconsTime; |
455 |
|
|
456 |
|
double calcMovingMolsCOMVel(); |
457 |
|
double calcSysCOMVel(); |
458 |
|
double calcTotalForce(); |
459 |
< |
|
459 |
> |
|
460 |
|
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
461 |
|
friend class ForceSubtractionPolicy; |
462 |
|
|