27 |
|
Integrator( SimInfo *theInfo, ForceFields* the_ff ); |
28 |
|
virtual ~Integrator(); |
29 |
|
void integrate( void ); |
30 |
+ |
virtual double getConservedQuantity(void); |
31 |
+ |
virtual string getAdditionalParameters(void); |
32 |
|
|
31 |
– |
|
33 |
|
protected: |
34 |
< |
|
34 |
> |
|
35 |
|
virtual void integrateStep( int calcPot, int calcStress ); |
36 |
|
virtual void preMove( void ); |
37 |
|
virtual void moveA( void ); |
42 |
|
|
43 |
|
virtual void resetIntegrator( void ) { } |
44 |
|
|
45 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
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 |
|
|
98 |
|
public: |
99 |
|
|
100 |
|
NVT ( SimInfo *theInfo, ForceFields* the_ff); |
101 |
< |
virtual ~NVT() {} |
101 |
> |
virtual ~NVT(); |
102 |
|
|
103 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
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 |
|
|
119 |
|
|
120 |
|
double chi; |
121 |
|
|
122 |
+ |
//integral of chi(t)dt |
123 |
+ |
double integralOfChidt; |
124 |
+ |
|
125 |
|
// targetTemp must be set. tauThermostat must also be set; |
126 |
|
|
127 |
|
double targetTemp; |
128 |
|
double tauThermostat; |
129 |
< |
|
129 |
> |
|
130 |
|
short int have_tau_thermostat, have_target_temp; |
131 |
|
|
132 |
+ |
double *oldVel; |
133 |
+ |
double *oldJi; |
134 |
+ |
|
135 |
+ |
double chiTolerance; |
136 |
+ |
short int have_chi_tolerance; |
137 |
+ |
|
138 |
|
}; |
139 |
|
|
140 |
|
|
141 |
|
|
142 |
< |
template<typename T> class NPTi : public T{ |
142 |
> |
template<typename T> class NPT : public T{ |
143 |
|
|
144 |
|
public: |
145 |
|
|
146 |
< |
NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
147 |
< |
virtual ~NPTi() {}; |
146 |
> |
NPT ( SimInfo *theInfo, ForceFields* the_ff); |
147 |
> |
virtual ~NPT(); |
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;} |
162 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
163 |
|
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
164 |
+ |
void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;} |
165 |
+ |
void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;} |
166 |
+ |
void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;} |
167 |
|
|
168 |
|
protected: |
169 |
|
|
174 |
|
|
175 |
|
virtual void resetIntegrator( void ); |
176 |
|
|
177 |
< |
// chi and eta are the propagated degrees of freedom |
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], |
180 |
> |
int index, double sc[3]) = 0; |
181 |
|
|
182 |
< |
double chi; |
156 |
< |
double eta; |
157 |
< |
double NkBT; |
182 |
> |
virtual void calcVelScale( void ) = 0; |
183 |
|
|
184 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
185 |
< |
// One of qmass or tauThermostat must be set; |
184 |
> |
virtual bool chiConverged( void ); |
185 |
> |
virtual bool etaConverged( void ) = 0; |
186 |
|
|
187 |
< |
double targetTemp; |
188 |
< |
double targetPressure; |
189 |
< |
double tauThermostat; |
190 |
< |
double tauBarostat; |
187 |
> |
virtual void evolveChiA( void ); |
188 |
> |
virtual void evolveEtaA( void ) = 0; |
189 |
> |
virtual void evolveChiB( void ); |
190 |
> |
virtual void evolveEtaB( void ) = 0; |
191 |
|
|
192 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
168 |
< |
short int have_target_pressure; |
192 |
> |
virtual void scaleSimBox( void ) = 0; |
193 |
|
|
194 |
< |
}; |
194 |
> |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
195 |
|
|
172 |
– |
template<typename T> class NPTim : public T{ |
173 |
– |
|
174 |
– |
public: |
175 |
– |
|
176 |
– |
NPTim ( SimInfo *theInfo, ForceFields* the_ff); |
177 |
– |
virtual ~NPTim() {}; |
178 |
– |
|
179 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
180 |
– |
calcStress = 1; |
181 |
– |
T::integrateStep( calcPot, calcStress ); |
182 |
– |
} |
183 |
– |
|
184 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
185 |
– |
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;} |
188 |
– |
|
189 |
– |
protected: |
190 |
– |
|
191 |
– |
virtual void moveA( void ); |
192 |
– |
virtual void moveB( void ); |
193 |
– |
|
194 |
– |
virtual int readyCheck(); |
195 |
– |
|
196 |
– |
virtual void resetIntegrator( void ); |
197 |
– |
|
198 |
– |
Molecule* myMolecules; |
199 |
– |
Atom** myAtoms; |
200 |
– |
|
196 |
|
// chi and eta are the propagated degrees of freedom |
197 |
|
|
198 |
+ |
double oldChi; |
199 |
+ |
double prevChi; |
200 |
|
double chi; |
204 |
– |
double eta; |
201 |
|
double NkBT; |
202 |
+ |
double fkBT; |
203 |
|
|
204 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
204 |
> |
double tt2, tb2; |
205 |
> |
double instaTemp, instaPress, instaVol; |
206 |
> |
double press[3][3]; |
207 |
> |
|
208 |
> |
int Nparticles; |
209 |
> |
|
210 |
> |
double integralOfChidt; |
211 |
> |
|
212 |
> |
// targetTemp, targetPressure, and tauBarostat must be set. |
213 |
|
// One of qmass or tauThermostat must be set; |
214 |
|
|
215 |
|
double targetTemp; |
220 |
|
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
221 |
|
short int have_target_pressure; |
222 |
|
|
223 |
+ |
double *oldPos; |
224 |
+ |
double *oldVel; |
225 |
+ |
double *oldJi; |
226 |
+ |
|
227 |
+ |
double chiTolerance; |
228 |
+ |
short int have_chi_tolerance; |
229 |
+ |
double posIterTolerance; |
230 |
+ |
short int have_pos_iter_tolerance; |
231 |
+ |
double etaTolerance; |
232 |
+ |
short int have_eta_tolerance; |
233 |
+ |
|
234 |
|
}; |
235 |
|
|
236 |
< |
template<typename T> class NPTf : public T{ |
236 |
> |
template<typename T> class NPTi : public T{ |
237 |
|
|
238 |
|
public: |
239 |
+ |
NPTi( SimInfo *theInfo, ForceFields* the_ff); |
240 |
+ |
~NPTi(); |
241 |
|
|
242 |
< |
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
243 |
< |
virtual ~NPTf() {}; |
244 |
< |
|
227 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
228 |
< |
calcStress = 1; |
229 |
< |
T::integrateStep( calcPot, calcStress ); |
230 |
< |
} |
231 |
< |
|
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 |
< |
|
242 |
> |
virtual double getConservedQuantity(void); |
243 |
> |
virtual void resetIntegrator(void); |
244 |
> |
virtual string getAdditionalParameters(void); |
245 |
|
protected: |
246 |
|
|
239 |
– |
virtual void moveA( void ); |
240 |
– |
virtual void moveB( void ); |
247 |
|
|
242 |
– |
virtual void resetIntegrator( void ); |
248 |
|
|
249 |
< |
virtual int readyCheck(); |
249 |
> |
virtual void evolveEtaA(void); |
250 |
> |
virtual void evolveEtaB(void); |
251 |
|
|
252 |
< |
// chi and eta are the propagated degrees of freedom |
252 |
> |
virtual bool etaConverged( void ); |
253 |
|
|
254 |
< |
double chi; |
249 |
< |
double eta[3][3]; |
250 |
< |
double NkBT; |
254 |
> |
virtual void scaleSimBox( void ); |
255 |
|
|
256 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
257 |
< |
// One of qmass or tauThermostat must be set; |
256 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
257 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
258 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
259 |
> |
int index, double sc[3]); |
260 |
|
|
261 |
< |
double targetTemp; |
256 |
< |
double targetPressure; |
257 |
< |
double tauThermostat; |
258 |
< |
double tauBarostat; |
261 |
> |
virtual void calcVelScale( void ); |
262 |
|
|
263 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
264 |
< |
short int have_target_pressure; |
262 |
< |
|
263 |
> |
double eta, oldEta, prevEta; |
264 |
> |
double vScale; |
265 |
|
}; |
266 |
|
|
267 |
< |
template<typename T> class NPTfm : public T{ |
267 |
> |
template<typename T> class NPTf : public T{ |
268 |
|
|
269 |
|
public: |
270 |
|
|
271 |
< |
NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
272 |
< |
virtual ~NPTfm() {}; |
271 |
> |
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
272 |
> |
virtual ~NPTf(); |
273 |
|
|
274 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
275 |
< |
calcStress = 1; |
276 |
< |
T::integrateStep( calcPot, calcStress ); |
275 |
< |
} |
274 |
> |
virtual double getConservedQuantity(void); |
275 |
> |
virtual string getAdditionalParameters(void); |
276 |
> |
virtual void resetIntegrator(void); |
277 |
|
|
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 |
– |
|
278 |
|
protected: |
279 |
|
|
280 |
< |
virtual void moveA( void ); |
281 |
< |
virtual void moveB( void ); |
280 |
> |
virtual void evolveEtaA(void); |
281 |
> |
virtual void evolveEtaB(void); |
282 |
|
|
283 |
< |
virtual void resetIntegrator( void ); |
283 |
> |
virtual bool etaConverged( void ); |
284 |
|
|
285 |
< |
virtual int readyCheck(); |
285 |
> |
virtual void scaleSimBox( void ); |
286 |
|
|
287 |
< |
Molecule* myMolecules; |
288 |
< |
Atom** myAtoms; |
287 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
288 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
289 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
290 |
> |
int index, double sc[3]); |
291 |
|
|
292 |
< |
// chi and eta are the propagated degrees of freedom |
292 |
> |
virtual void calcVelScale( void ); |
293 |
|
|
296 |
– |
double chi; |
294 |
|
double eta[3][3]; |
295 |
< |
double NkBT; |
296 |
< |
|
297 |
< |
// 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 |
< |
|
295 |
> |
double oldEta[3][3]; |
296 |
> |
double prevEta[3][3]; |
297 |
> |
double vScale[3][3]; |
298 |
|
}; |
299 |
|
|
300 |
+ |
template<typename T> class NPTxyz : public T{ |
301 |
|
|
314 |
– |
template<typename T> class NPTpr : public T{ |
315 |
– |
|
302 |
|
public: |
303 |
|
|
304 |
< |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
305 |
< |
virtual ~NPTpr() {}; |
304 |
> |
NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
305 |
> |
virtual ~NPTxyz(); |
306 |
|
|
307 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
308 |
< |
calcStress = 1; |
309 |
< |
T::integrateStep( calcPot, calcStress ); |
324 |
< |
} |
307 |
> |
virtual double getConservedQuantity(void); |
308 |
> |
virtual string getAdditionalParameters(void); |
309 |
> |
virtual void resetIntegrator(void); |
310 |
|
|
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 |
– |
|
311 |
|
protected: |
312 |
|
|
313 |
< |
virtual void moveA( void ); |
314 |
< |
virtual void moveB( void ); |
313 |
> |
virtual void evolveEtaA(void); |
314 |
> |
virtual void evolveEtaB(void); |
315 |
|
|
316 |
< |
virtual int readyCheck(); |
316 |
> |
virtual bool etaConverged( void ); |
317 |
|
|
318 |
< |
virtual void resetIntegrator( void ); |
318 |
> |
virtual void scaleSimBox( void ); |
319 |
|
|
320 |
< |
// chi and eta are the propagated degrees of freedom |
320 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
321 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
322 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
323 |
> |
int index, double sc[3]); |
324 |
|
|
325 |
< |
double chi; |
343 |
< |
double eta[3][3]; |
344 |
< |
double NkBT; |
325 |
> |
virtual void calcVelScale( void ); |
326 |
|
|
327 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
328 |
< |
// One of qmass or tauThermostat must be set; |
329 |
< |
|
330 |
< |
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 |
< |
|
327 |
> |
double eta[3][3]; |
328 |
> |
double oldEta[3][3]; |
329 |
> |
double prevEta[3][3]; |
330 |
> |
double vScale[3][3]; |
331 |
|
}; |
332 |
|
|
333 |
|
|
334 |
|
template<typename T> class ZConstraint : public T { |
335 |
< |
|
336 |
< |
public: |
335 |
> |
|
336 |
> |
public: |
337 |
|
class ForceSubtractionPolicy{ |
338 |
|
public: |
339 |
|
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
340 |
|
|
341 |
< |
virtual void update() = 0; |
341 |
> |
virtual void update() = 0; |
342 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
343 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
344 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
345 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
346 |
< |
|
346 |
> |
|
347 |
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protected: |
348 |
< |
ZConstraint<T>* zconsIntegrator;; |
348 |
> |
ZConstraint<T>* zconsIntegrator; |
349 |
|
}; |
350 |
|
|
351 |
|
class PolicyByNumber : public ForceSubtractionPolicy{ |
352 |
+ |
|
353 |
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public: |
354 |
< |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
355 |
< |
virtual void update(); |
354 |
> |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
355 |
> |
virtual void update(); |
356 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
357 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
358 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
359 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
360 |
< |
|
360 |
> |
|
361 |
|
private: |
362 |
< |
int totNumOfMovingAtoms; |
362 |
> |
int totNumOfMovingAtoms; |
363 |
|
}; |
364 |
|
|
365 |
|
class PolicyByMass : public ForceSubtractionPolicy{ |
366 |
+ |
|
367 |
|
public: |
368 |
< |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
369 |
< |
|
370 |
< |
virtual void update(); |
368 |
> |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
369 |
> |
|
370 |
> |
virtual void update(); |
371 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
372 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
373 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
381 |
|
|
382 |
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
383 |
|
~ZConstraint(); |
384 |
< |
|
384 |
> |
|
385 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
386 |
|
void getZConsTime() {return zconsTime;} |
387 |
< |
|
387 |
> |
|
388 |
|
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
389 |
|
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
390 |
< |
|
390 |
> |
|
391 |
|
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
392 |
|
string getZConsOutput() {return zconsOutput;} |
393 |
< |
|
393 |
> |
|
394 |
|
virtual void integrate(); |
419 |
– |
|
395 |
|
|
396 |
+ |
|
397 |
|
#ifdef IS_MPI |
398 |
|
virtual void update(); //which is called to indicate the molecules' migration |
399 |
|
#endif |
400 |
|
|
401 |
+ |
enum ZConsState {zcsMoving, zcsFixed}; |
402 |
+ |
|
403 |
+ |
vector<Molecule*> zconsMols; //z-constraint molecules array |
404 |
+ |
vector<ZConsState> states; //state of z-constraint molecules |
405 |
+ |
|
406 |
+ |
|
407 |
+ |
|
408 |
+ |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
409 |
+ |
double totalMassOfUncons; //total mas of unconstraint molecules |
410 |
+ |
|
411 |
+ |
|
412 |
|
protected: |
413 |
|
|
414 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
415 |
< |
|
416 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
414 |
> |
|
415 |
> |
|
416 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
417 |
|
virtual void thermalize(void); |
418 |
< |
|
418 |
> |
|
419 |
|
void zeroOutVel(); |
420 |
|
void doZconstraintForce(); |
421 |
|
void doHarmonic(); |
433 |
|
double zconsTol; //tolerance of z-contratint |
434 |
|
double zForceConst; //base force constant term |
435 |
|
//which is estimate by OOPSE |
436 |
< |
|
437 |
< |
vector<Molecule*> zconsMols; //z-constraint molecules array |
438 |
< |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
436 |
> |
|
437 |
> |
|
438 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
439 |
|
vector<double> kz; //force constant array |
440 |
< |
vector<ZConsState> states; //state of z-constraint molecules |
440 |
> |
|
441 |
|
vector<double> zPos; // |
442 |
< |
|
443 |
< |
|
442 |
> |
|
443 |
> |
|
444 |
|
vector<Molecule*> unconsMols; //unconstraint molecules array |
445 |
|
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
459 |
– |
double totalMassOfUncons; //total mas of unconstraint molecules |
446 |
|
|
447 |
+ |
|
448 |
|
vector<ZConsParaItem>* parameters; // |
449 |
< |
|
449 |
> |
|
450 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
451 |
|
|
452 |
< |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
452 |
> |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
453 |
|
double* fz; |
454 |
|
double* curZPos; |
468 |
– |
|
469 |
– |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
455 |
|
|
456 |
< |
int whichDirection; //constraint direction |
457 |
< |
|
456 |
> |
|
457 |
> |
|
458 |
> |
int whichDirection; //constraint direction |
459 |
> |
|
460 |
|
private: |
461 |
< |
|
461 |
> |
|
462 |
|
string zconsOutput; //filename of zconstraint output |
463 |
|
ZConsWriter* fzOut; //z-constraint writer |
464 |
|
|
465 |
< |
double curZconsTime; |
465 |
> |
double curZconsTime; |
466 |
|
|
467 |
|
double calcMovingMolsCOMVel(); |
468 |
|
double calcSysCOMVel(); |
469 |
|
double calcTotalForce(); |
470 |
< |
|
471 |
< |
ForceSubtractionPolicy* forcePolicy; //force substration policy |
470 |
> |
|
471 |
> |
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
472 |
|
friend class ForceSubtractionPolicy; |
473 |
|
|
474 |
|
}; |
475 |
|
|
476 |
+ |
class OOPSEMinimizerBase : public RealIntegrator { |
477 |
+ |
public: |
478 |
+ |
|
479 |
+ |
OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff ); |
480 |
+ |
virtual ~OOPSEMinimizerBase(); |
481 |
+ |
|
482 |
+ |
double calcGradient(vector<double>& x, vector<double>& grad); |
483 |
+ |
void setCoor(vector<double>& x); |
484 |
+ |
vector<double> getCoor(); |
485 |
+ |
void output(vector<double>& x, int iteration); |
486 |
+ |
int getDim() {return dim;} |
487 |
+ |
void constraintMove(); |
488 |
+ |
void shakeF(); |
489 |
+ |
void shakeR(); |
490 |
+ |
protected: |
491 |
+ |
|
492 |
+ |
int dim; |
493 |
+ |
void calcDim(); |
494 |
+ |
}; |
495 |
+ |
|
496 |
+ |
//template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{ |
497 |
+ |
// public: |
498 |
+ |
// void writeOutput(); |
499 |
+ |
//}; |
500 |
+ |
|
501 |
|
#endif |