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 ); |
40 |
|
virtual int readyCheck( void ) { return 1; } |
41 |
|
|
42 |
|
virtual void resetIntegrator( void ) { } |
43 |
< |
|
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] ); |
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 |
|
|
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 |
|
|
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; |
156 |
– |
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; |
206 |
|
|
212 |
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
213 |
|
short int have_target_pressure; |
214 |
|
|
215 |
< |
}; |
215 |
> |
double *oldPos; |
216 |
> |
double *oldVel; |
217 |
> |
double *oldJi; |
218 |
|
|
219 |
< |
template<typename T> class NPTim : public T{ |
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 |
< |
public: |
226 |
> |
}; |
227 |
|
|
228 |
< |
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
229 |
< |
virtual ~NPTim() {}; |
230 |
< |
|
231 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
232 |
< |
calcStress = 1; |
181 |
< |
T::integrateStep( calcPot, calcStress ); |
182 |
< |
} |
228 |
> |
template<typename T> class NPTi : public T{ |
229 |
> |
|
230 |
> |
public: |
231 |
> |
NPTi( SimInfo *theInfo, ForceFields* the_ff); |
232 |
> |
~NPTi(); |
233 |
|
|
234 |
< |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
235 |
< |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
186 |
< |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
187 |
< |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
234 |
> |
virtual double getConservedQuantity(void); |
235 |
> |
virtual void resetIntegrator(void); |
236 |
|
|
237 |
|
protected: |
238 |
|
|
239 |
< |
virtual void moveA( void ); |
192 |
< |
virtual void moveB( void ); |
239 |
> |
|
240 |
|
|
241 |
< |
virtual int readyCheck(); |
241 |
> |
virtual void evolveEtaA(void); |
242 |
> |
virtual void evolveEtaB(void); |
243 |
|
|
244 |
< |
virtual void resetIntegrator( void ); |
244 |
> |
virtual bool etaConverged( void ); |
245 |
|
|
246 |
< |
Molecule* myMolecules; |
199 |
< |
Atom** myAtoms; |
246 |
> |
virtual void scaleSimBox( void ); |
247 |
|
|
248 |
< |
// chi and eta are the propagated degrees of freedom |
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 chi; |
204 |
< |
double eta; |
205 |
< |
double NkBT; |
206 |
< |
|
207 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
208 |
< |
// One of qmass or tauThermostat must be set; |
209 |
< |
|
210 |
< |
double targetTemp; |
211 |
< |
double targetPressure; |
212 |
< |
double tauThermostat; |
213 |
< |
double tauBarostat; |
214 |
< |
|
215 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
216 |
< |
short int have_target_pressure; |
217 |
< |
|
253 |
> |
double eta, oldEta, prevEta; |
254 |
|
}; |
255 |
|
|
256 |
|
template<typename T> class NPTf : public T{ |
258 |
|
public: |
259 |
|
|
260 |
|
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
261 |
< |
virtual ~NPTf() {}; |
261 |
> |
virtual ~NPTf(); |
262 |
|
|
263 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
264 |
< |
calcStress = 1; |
229 |
< |
T::integrateStep( calcPot, calcStress ); |
230 |
< |
} |
263 |
> |
virtual double getConservedQuantity(void); |
264 |
> |
virtual void resetIntegrator(void); |
265 |
|
|
232 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
233 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
234 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
235 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
236 |
– |
|
266 |
|
protected: |
267 |
|
|
268 |
< |
virtual void moveA( void ); |
269 |
< |
virtual void moveB( void ); |
268 |
> |
virtual void evolveEtaA(void); |
269 |
> |
virtual void evolveEtaB(void); |
270 |
|
|
271 |
< |
virtual void resetIntegrator( void ); |
271 |
> |
virtual bool etaConverged( void ); |
272 |
|
|
273 |
< |
virtual int readyCheck(); |
273 |
> |
virtual void scaleSimBox( void ); |
274 |
|
|
275 |
< |
// chi and eta are the propagated degrees of freedom |
276 |
< |
|
277 |
< |
double chi; |
278 |
< |
double eta[3][3]; |
250 |
< |
double NkBT; |
275 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
276 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
277 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
278 |
> |
int index, double sc[3]); |
279 |
|
|
252 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
253 |
– |
// One of qmass or tauThermostat must be set; |
254 |
– |
|
255 |
– |
double targetTemp; |
256 |
– |
double targetPressure; |
257 |
– |
double tauThermostat; |
258 |
– |
double tauBarostat; |
259 |
– |
|
260 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
261 |
– |
short int have_target_pressure; |
262 |
– |
|
263 |
– |
}; |
264 |
– |
|
265 |
– |
template<typename T> class NPTfm : public T{ |
266 |
– |
|
267 |
– |
public: |
268 |
– |
|
269 |
– |
NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
270 |
– |
virtual ~NPTfm() {}; |
271 |
– |
|
272 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
273 |
– |
calcStress = 1; |
274 |
– |
T::integrateStep( calcPot, calcStress ); |
275 |
– |
} |
276 |
– |
|
277 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
278 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
279 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
280 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
281 |
– |
|
282 |
– |
protected: |
283 |
– |
|
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; |
280 |
|
double eta[3][3]; |
281 |
< |
double NkBT; |
282 |
< |
|
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 |
< |
|
281 |
> |
double oldEta[3][3]; |
282 |
> |
double prevEta[3][3]; |
283 |
|
}; |
284 |
|
|
285 |
+ |
template<typename T> class NPTxyz : public T{ |
286 |
|
|
314 |
– |
template<typename T> class NPTpr : public T{ |
315 |
– |
|
287 |
|
public: |
288 |
|
|
289 |
< |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
290 |
< |
virtual ~NPTpr() {}; |
289 |
> |
NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
290 |
> |
virtual ~NPTxyz(); |
291 |
|
|
292 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
293 |
< |
calcStress = 1; |
323 |
< |
T::integrateStep( calcPot, calcStress ); |
324 |
< |
} |
292 |
> |
virtual double getConservedQuantity(void); |
293 |
> |
virtual void resetIntegrator(void); |
294 |
|
|
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 |
– |
|
295 |
|
protected: |
296 |
|
|
297 |
< |
virtual void moveA( void ); |
298 |
< |
virtual void moveB( void ); |
297 |
> |
virtual void evolveEtaA(void); |
298 |
> |
virtual void evolveEtaB(void); |
299 |
|
|
300 |
< |
virtual int readyCheck(); |
300 |
> |
virtual bool etaConverged( void ); |
301 |
|
|
302 |
< |
virtual void resetIntegrator( void ); |
302 |
> |
virtual void scaleSimBox( void ); |
303 |
|
|
304 |
< |
// chi and eta are the propagated degrees of freedom |
304 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
305 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
306 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
307 |
> |
int index, double sc[3]); |
308 |
|
|
342 |
– |
double chi; |
309 |
|
double eta[3][3]; |
310 |
< |
double NkBT; |
311 |
< |
|
346 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
347 |
< |
// One of qmass or tauThermostat must be set; |
348 |
< |
|
349 |
< |
double targetTemp; |
350 |
< |
double targetPressure; |
351 |
< |
double tauThermostat; |
352 |
< |
double tauBarostat; |
353 |
< |
|
354 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
355 |
< |
short int have_target_pressure; |
356 |
< |
|
310 |
> |
double oldEta[3][3]; |
311 |
> |
double prevEta[3][3]; |
312 |
|
}; |
313 |
|
|
314 |
|
|
326 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
327 |
|
|
328 |
|
protected: |
329 |
< |
ZConstraint<T>* zconsIntegrator;; |
329 |
> |
ZConstraint<T>* zconsIntegrator; |
330 |
|
}; |
331 |
|
|
332 |
|
class PolicyByNumber : public ForceSubtractionPolicy{ |
340 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
341 |
|
|
342 |
|
private: |
343 |
< |
int totNumOfMovingAtoms; |
343 |
> |
int totNumOfMovingAtoms; |
344 |
|
}; |
345 |
|
|
346 |
|
class PolicyByMass : public ForceSubtractionPolicy{ |
379 |
|
virtual void update(); //which is called to indicate the molecules' migration |
380 |
|
#endif |
381 |
|
|
382 |
+ |
enum ZConsState {zcsMoving, zcsFixed}; |
383 |
+ |
|
384 |
+ |
vector<Molecule*> zconsMols; //z-constraint molecules array |
385 |
+ |
vector<ZConsState> states; //state of z-constraint molecules |
386 |
+ |
|
387 |
+ |
|
388 |
+ |
|
389 |
+ |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
390 |
+ |
double totalMassOfUncons; //total mas of unconstraint molecules |
391 |
+ |
|
392 |
+ |
|
393 |
|
protected: |
394 |
|
|
395 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
395 |
> |
|
396 |
|
|
397 |
|
virtual void calcForce( int calcPot, int calcStress ); |
398 |
|
virtual void thermalize(void); |
415 |
|
double zForceConst; //base force constant term |
416 |
|
//which is estimate by OOPSE |
417 |
|
|
418 |
< |
vector<Molecule*> zconsMols; //z-constraint molecules array |
418 |
> |
|
419 |
|
vector<double> massOfZConsMols; //mass of z-constraint molecule |
420 |
|
vector<double> kz; //force constant array |
421 |
< |
vector<ZConsState> states; //state of z-constraint molecules |
421 |
> |
|
422 |
|
vector<double> zPos; // |
423 |
|
|
424 |
|
|
425 |
|
vector<Molecule*> unconsMols; //unconstraint molecules array |
426 |
|
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
461 |
– |
double totalMassOfUncons; //total mas of unconstraint molecules |
427 |
|
|
428 |
+ |
|
429 |
|
vector<ZConsParaItem>* parameters; // |
430 |
|
|
431 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
434 |
|
double* fz; |
435 |
|
double* curZPos; |
436 |
|
|
471 |
– |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
437 |
|
|
438 |
+ |
|
439 |
|
int whichDirection; //constraint direction |
440 |
|
|
441 |
|
private: |