30 |
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virtual double getConservedQuantity(void); |
31 |
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32 |
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protected: |
33 |
< |
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33 |
> |
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34 |
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virtual void integrateStep( int calcPot, int calcStress ); |
35 |
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virtual void preMove( void ); |
36 |
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virtual void moveA( void ); |
44 |
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virtual void calcForce( int calcPot, int calcStress ); |
45 |
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virtual void thermalize(); |
46 |
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47 |
+ |
virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] ); |
48 |
+ |
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49 |
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void checkConstraints( void ); |
50 |
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void rotate( int axes1, int axes2, double angle, double j[3], |
51 |
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double A[3][3] ); |
137 |
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138 |
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139 |
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140 |
< |
template<typename T> class NPTi : public T{ |
140 |
> |
template<typename T> class NPT : public T{ |
141 |
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142 |
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public: |
143 |
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144 |
< |
NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
145 |
< |
virtual ~NPTi(); |
144 |
> |
NPT ( SimInfo *theInfo, ForceFields* the_ff); |
145 |
> |
virtual ~NPT(); |
146 |
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147 |
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virtual void integrateStep( int calcPot, int calcStress ){ |
148 |
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calcStress = 1; |
149 |
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T::integrateStep( calcPot, calcStress ); |
148 |
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/* accIntegralOfChidt(); */ |
150 |
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} |
151 |
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152 |
< |
virtual double getConservedQuantity(void); |
152 |
> |
virtual double getConservedQuantity(void) = 0; |
153 |
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154 |
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void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
155 |
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void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
168 |
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169 |
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virtual void resetIntegrator( void ); |
170 |
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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 |
+ |
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176 |
+ |
virtual bool chiConverged( void ); |
177 |
+ |
virtual bool etaConverged( void ) = 0; |
178 |
+ |
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179 |
+ |
virtual void evolveChiA( void ); |
180 |
+ |
virtual void evolveEtaA( void ) = 0; |
181 |
+ |
virtual void evolveChiB( void ); |
182 |
+ |
virtual void evolveEtaB( void ) = 0; |
183 |
+ |
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184 |
+ |
virtual void scaleSimBox( void ) = 0; |
185 |
+ |
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186 |
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void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
187 |
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188 |
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// chi and eta are the propagated degrees of freedom |
189 |
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190 |
+ |
double oldChi; |
191 |
+ |
double prevChi; |
192 |
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double chi; |
175 |
– |
double eta; |
193 |
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double NkBT; |
194 |
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double fkBT; |
195 |
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196 |
+ |
double tt2, tb2; |
197 |
+ |
double instaTemp, instaPress, instaVol; |
198 |
+ |
double press[3][3]; |
199 |
+ |
|
200 |
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int Nparticles; |
201 |
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202 |
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double integralOfChidt; |
223 |
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double etaTolerance; |
224 |
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short int have_eta_tolerance; |
225 |
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205 |
– |
double volume; |
206 |
– |
|
226 |
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}; |
227 |
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228 |
< |
template<typename T> class NPTim : public T{ |
229 |
< |
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228 |
> |
template<typename T> class NPTi : public T{ |
229 |
> |
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230 |
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public: |
231 |
+ |
NPTi( SimInfo *theInfo, ForceFields* the_ff); |
232 |
+ |
~NPTi(); |
233 |
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213 |
– |
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
214 |
– |
virtual ~NPTim() {} |
215 |
– |
|
216 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
217 |
– |
calcStress = 1; |
218 |
– |
T::integrateStep( calcPot, calcStress ); |
219 |
– |
accIntegralOfChidt(); |
220 |
– |
} |
221 |
– |
|
234 |
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virtual double getConservedQuantity(void); |
235 |
+ |
virtual void resetIntegrator(void); |
236 |
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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 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
229 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
230 |
– |
|
237 |
|
protected: |
238 |
|
|
239 |
< |
virtual void moveA( void ); |
234 |
< |
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 |
< |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
241 |
< |
|
242 |
< |
Molecule* myMolecules; |
243 |
< |
Atom** myAtoms; |
246 |
> |
virtual void scaleSimBox( void ); |
247 |
|
|
248 |
< |
// chi and eta are the propagated degrees of freedom |
249 |
< |
|
250 |
< |
double chi; |
251 |
< |
double eta; |
249 |
< |
double NkBT; |
250 |
< |
double integralOfChidt; |
251 |
< |
|
252 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
253 |
< |
// One of qmass or tauThermostat must be set; |
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 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 |
< |
double chiTolerance; |
263 |
< |
short int have_chi_tolerance; |
264 |
< |
double posIterTolerance; |
265 |
< |
short int have_pos_iter_tolerance; |
266 |
< |
|
253 |
> |
double eta, oldEta, prevEta; |
254 |
|
}; |
255 |
|
|
256 |
|
template<typename T> class NPTzm : public T{ |
307 |
|
public: |
308 |
|
|
309 |
|
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
310 |
< |
virtual ~NPTf() {}; |
310 |
> |
virtual ~NPTf(); |
311 |
|
|
325 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
326 |
– |
calcStress = 1; |
327 |
– |
T::integrateStep( calcPot, calcStress ); |
328 |
– |
accIntegralOfChidt(); |
329 |
– |
} |
330 |
– |
|
312 |
|
virtual double getConservedQuantity(void); |
313 |
+ |
virtual void resetIntegrator(void); |
314 |
|
|
333 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
334 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
335 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
336 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
337 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
338 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
339 |
– |
|
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 void resetIntegrator( void ); |
320 |
> |
virtual bool etaConverged( void ); |
321 |
> |
|
322 |
> |
virtual void scaleSimBox( void ); |
323 |
|
|
324 |
< |
virtual int readyCheck(); |
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 |
|
|
349 |
– |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
350 |
– |
|
351 |
– |
// chi and eta are the propagated degrees of freedom |
352 |
– |
|
353 |
– |
double chi; |
329 |
|
double eta[3][3]; |
330 |
< |
double NkBT; |
331 |
< |
|
357 |
< |
double integralOfChidt; |
358 |
< |
|
359 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
360 |
< |
// One of qmass or tauThermostat must be set; |
361 |
< |
|
362 |
< |
double targetTemp; |
363 |
< |
double targetPressure; |
364 |
< |
double tauThermostat; |
365 |
< |
double tauBarostat; |
366 |
< |
|
367 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
368 |
< |
short int have_target_pressure; |
369 |
< |
double chiTolerance; |
370 |
< |
short int have_chi_tolerance; |
371 |
< |
double posIterTolerance; |
372 |
< |
short int have_pos_iter_tolerance; |
373 |
< |
|
330 |
> |
double oldEta[3][3]; |
331 |
> |
double prevEta[3][3]; |
332 |
|
}; |
333 |
|
|
334 |
|
template<typename T> class NPTxym : public T{ |