4 |
|
#include <string> |
5 |
|
#include <vector> |
6 |
|
#include "Atom.hpp" |
7 |
+ |
#include "StuntDouble.hpp" |
8 |
|
#include "Molecule.hpp" |
9 |
|
#include "SRI.hpp" |
10 |
|
#include "AbstractClasses.hpp" |
13 |
|
#include "Thermo.hpp" |
14 |
|
#include "ReadWrite.hpp" |
15 |
|
#include "ZConsWriter.hpp" |
16 |
+ |
#include "Restraints.hpp" |
17 |
|
|
18 |
|
using namespace std; |
19 |
|
const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K |
22 |
|
const int maxIteration = 300; |
23 |
|
const double tol = 1.0e-6; |
24 |
|
|
23 |
– |
|
25 |
|
template<typename T = BaseIntegrator> class Integrator : public T { |
26 |
|
|
27 |
|
public: |
29 |
|
virtual ~Integrator(); |
30 |
|
void integrate( void ); |
31 |
|
virtual double getConservedQuantity(void); |
32 |
+ |
virtual string getAdditionalParameters(void); |
33 |
|
|
34 |
|
protected: |
35 |
< |
|
35 |
> |
|
36 |
|
virtual void integrateStep( int calcPot, int calcStress ); |
37 |
|
virtual void preMove( void ); |
38 |
|
virtual void moveA( void ); |
42 |
|
virtual int readyCheck( void ) { return 1; } |
43 |
|
|
44 |
|
virtual void resetIntegrator( void ) { } |
45 |
< |
|
46 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
45 |
> |
|
46 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
47 |
|
virtual void thermalize(); |
48 |
< |
|
48 |
> |
|
49 |
> |
virtual bool stopIntegrator() {return false;} |
50 |
> |
|
51 |
> |
virtual void rotationPropagation( StuntDouble* sd, double ji[3] ); |
52 |
> |
|
53 |
|
void checkConstraints( void ); |
54 |
< |
void rotate( int axes1, int axes2, double angle, double j[3], |
54 |
> |
void rotate( int axes1, int axes2, double angle, double j[3], |
55 |
|
double A[3][3] ); |
56 |
< |
|
56 |
> |
|
57 |
|
ForceFields* myFF; |
58 |
|
|
59 |
|
SimInfo *info; // all the info we'll ever need |
60 |
+ |
vector<StuntDouble*> integrableObjects; |
61 |
|
int nAtoms; /* the number of atoms */ |
62 |
|
int oldAtoms; |
63 |
|
Atom **atoms; /* array of atom pointers */ |
66 |
|
|
67 |
|
int isConstrained; // boolean to know whether the systems contains |
68 |
|
// constraints. |
69 |
< |
int nConstrained; // counter for number of constraints |
70 |
< |
int *constrainedA; // the i of a constraint pair |
71 |
< |
int *constrainedB; // the j of a constraint pair |
72 |
< |
double *constrainedDsqr; // the square of the constraint distance |
73 |
< |
|
69 |
> |
int nConstrained; // counter for number of constraints |
70 |
> |
int *constrainedA; // the i of a constraint pair |
71 |
> |
int *constrainedB; // the j of a constraint pair |
72 |
> |
double *constrainedDsqr; // the square of the constraint distance |
73 |
> |
|
74 |
|
int* moving; // tells whether we are moving atom i |
75 |
|
int* moved; // tells whether we have moved atom i |
76 |
< |
double* oldPos; // pre constrained positions |
76 |
> |
double* oldPos; // pre constrained positions |
77 |
|
|
78 |
|
short isFirst; /*boolean for the first time integrate is called */ |
79 |
< |
|
79 |
> |
|
80 |
|
double dt; |
81 |
|
double dt2; |
82 |
|
|
83 |
|
Thermo *tStats; |
84 |
|
StatWriter* statOut; |
85 |
|
DumpWriter* dumpOut; |
86 |
< |
|
86 |
> |
|
87 |
|
}; |
88 |
|
|
89 |
|
typedef Integrator<BaseIntegrator> RealIntegrator; |
90 |
|
|
91 |
+ |
// ansi instantiation |
92 |
+ |
template class Integrator<BaseIntegrator>; |
93 |
+ |
|
94 |
|
template<typename T> class NVE : public T { |
95 |
|
|
96 |
|
public: |
97 |
|
NVE ( SimInfo *theInfo, ForceFields* the_ff ): |
98 |
|
T( theInfo, the_ff ){} |
99 |
< |
virtual ~NVE(){} |
99 |
> |
virtual ~NVE(){} |
100 |
|
}; |
101 |
|
|
102 |
|
|
111 |
|
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
112 |
|
void setChiTolerance(double tol) {chiTolerance = tol;} |
113 |
|
virtual double getConservedQuantity(void); |
114 |
+ |
virtual string getAdditionalParameters(void); |
115 |
|
|
116 |
|
protected: |
117 |
|
|
133 |
|
|
134 |
|
double targetTemp; |
135 |
|
double tauThermostat; |
136 |
< |
|
136 |
> |
|
137 |
|
short int have_tau_thermostat, have_target_temp; |
138 |
|
|
139 |
|
double *oldVel; |
146 |
|
|
147 |
|
|
148 |
|
|
149 |
< |
template<typename T> class NPTi : public T{ |
149 |
> |
template<typename T> class NPT : public T{ |
150 |
|
|
151 |
|
public: |
152 |
|
|
153 |
< |
NPTi ( SimInfo *theInfo, ForceFields* the_ff); |
154 |
< |
virtual ~NPTi(); |
155 |
< |
|
153 |
> |
NPT ( SimInfo *theInfo, ForceFields* the_ff); |
154 |
> |
virtual ~NPT(); |
155 |
> |
|
156 |
|
virtual void integrateStep( int calcPot, int calcStress ){ |
157 |
|
calcStress = 1; |
158 |
|
T::integrateStep( calcPot, calcStress ); |
148 |
– |
/* accIntegralOfChidt(); */ |
159 |
|
} |
160 |
|
|
161 |
< |
virtual double getConservedQuantity(void); |
161 |
> |
virtual double getConservedQuantity(void) = 0; |
162 |
> |
virtual string getAdditionalParameters(void) = 0; |
163 |
> |
|
164 |
> |
double myTauThermo( void ) { return tauThermostat; } |
165 |
> |
double myTauBaro( void ) { return tauBarostat; } |
166 |
|
|
167 |
|
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
168 |
|
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
181 |
|
|
182 |
|
virtual void resetIntegrator( void ); |
183 |
|
|
184 |
+ |
virtual void getVelScaleA( double sc[3], double vel[3] ) = 0; |
185 |
+ |
virtual void getVelScaleB( double sc[3], int index ) = 0; |
186 |
+ |
virtual void getPosScale(double pos[3], double COM[3], |
187 |
+ |
int index, double sc[3]) = 0; |
188 |
+ |
|
189 |
+ |
virtual void calcVelScale( void ) = 0; |
190 |
+ |
|
191 |
+ |
virtual bool chiConverged( void ); |
192 |
+ |
virtual bool etaConverged( void ) = 0; |
193 |
+ |
|
194 |
+ |
virtual void evolveChiA( void ); |
195 |
+ |
virtual void evolveEtaA( void ) = 0; |
196 |
+ |
virtual void evolveChiB( void ); |
197 |
+ |
virtual void evolveEtaB( void ) = 0; |
198 |
+ |
|
199 |
+ |
virtual void scaleSimBox( void ) = 0; |
200 |
+ |
|
201 |
|
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
202 |
|
|
203 |
|
// chi and eta are the propagated degrees of freedom |
204 |
|
|
205 |
+ |
double oldChi; |
206 |
+ |
double prevChi; |
207 |
|
double chi; |
175 |
– |
double eta; |
208 |
|
double NkBT; |
209 |
|
double fkBT; |
210 |
|
|
211 |
+ |
double tt2, tb2; |
212 |
+ |
double instaTemp, instaPress, instaVol; |
213 |
+ |
double press[3][3]; |
214 |
+ |
|
215 |
|
int Nparticles; |
216 |
|
|
217 |
|
double integralOfChidt; |
218 |
|
|
219 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
219 |
> |
// targetTemp, targetPressure, and tauBarostat must be set. |
220 |
|
// One of qmass or tauThermostat must be set; |
221 |
|
|
222 |
|
double targetTemp; |
238 |
|
double etaTolerance; |
239 |
|
short int have_eta_tolerance; |
240 |
|
|
205 |
– |
double volume; |
206 |
– |
|
241 |
|
}; |
242 |
|
|
243 |
< |
template<typename T> class NPTim : public T{ |
243 |
> |
template<typename T> class NPTi : public T{ |
244 |
|
|
245 |
|
public: |
246 |
+ |
NPTi( SimInfo *theInfo, ForceFields* the_ff); |
247 |
+ |
~NPTi(); |
248 |
|
|
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 |
– |
|
249 |
|
virtual double getConservedQuantity(void); |
250 |
< |
|
251 |
< |
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 |
< |
|
250 |
> |
virtual void resetIntegrator(void); |
251 |
> |
virtual string getAdditionalParameters(void); |
252 |
|
protected: |
253 |
|
|
233 |
– |
virtual void moveA( void ); |
234 |
– |
virtual void moveB( void ); |
254 |
|
|
236 |
– |
virtual int readyCheck(); |
255 |
|
|
256 |
< |
virtual void resetIntegrator( void ); |
256 |
> |
virtual void evolveEtaA(void); |
257 |
> |
virtual void evolveEtaB(void); |
258 |
|
|
259 |
< |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
241 |
< |
|
242 |
< |
Molecule* myMolecules; |
243 |
< |
Atom** myAtoms; |
259 |
> |
virtual bool etaConverged( void ); |
260 |
|
|
261 |
< |
// chi and eta are the propagated degrees of freedom |
261 |
> |
virtual void scaleSimBox( void ); |
262 |
|
|
263 |
< |
double chi; |
264 |
< |
double eta; |
265 |
< |
double NkBT; |
266 |
< |
double integralOfChidt; |
263 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
264 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
265 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
266 |
> |
int index, double sc[3]); |
267 |
|
|
268 |
< |
// 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 |
< |
double chiTolerance; |
263 |
< |
short int have_chi_tolerance; |
264 |
< |
double posIterTolerance; |
265 |
< |
short int have_pos_iter_tolerance; |
266 |
< |
|
267 |
< |
}; |
268 |
< |
|
269 |
< |
template<typename T> class NPTzm : public T{ |
270 |
< |
|
271 |
< |
public: |
272 |
< |
|
273 |
< |
NPTzm ( SimInfo *theInfo, ForceFields* the_ff); |
274 |
< |
virtual ~NPTzm() {}; |
275 |
< |
|
276 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
277 |
< |
calcStress = 1; |
278 |
< |
T::integrateStep( calcPot, calcStress ); |
279 |
< |
} |
268 |
> |
virtual void calcVelScale( void ); |
269 |
|
|
270 |
< |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
271 |
< |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
283 |
< |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
284 |
< |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
285 |
< |
|
286 |
< |
protected: |
287 |
< |
|
288 |
< |
virtual void moveA( void ); |
289 |
< |
virtual void moveB( void ); |
290 |
< |
|
291 |
< |
virtual int readyCheck(); |
292 |
< |
|
293 |
< |
virtual void resetIntegrator( void ); |
294 |
< |
|
295 |
< |
Molecule* myMolecules; |
296 |
< |
Atom** myAtoms; |
297 |
< |
|
298 |
< |
// chi and eta are the propagated degrees of freedom |
299 |
< |
|
300 |
< |
double chi; |
301 |
< |
double eta; |
302 |
< |
double etaZ; |
303 |
< |
double NkBT; |
304 |
< |
|
305 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
306 |
< |
// One of qmass or tauThermostat must be set; |
307 |
< |
|
308 |
< |
double targetTemp; |
309 |
< |
double targetPressure; |
310 |
< |
double tauThermostat; |
311 |
< |
double tauBarostat; |
312 |
< |
|
313 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
314 |
< |
short int have_target_pressure; |
315 |
< |
|
270 |
> |
double eta, oldEta, prevEta; |
271 |
> |
double vScale; |
272 |
|
}; |
273 |
|
|
274 |
|
template<typename T> class NPTf : public T{ |
276 |
|
public: |
277 |
|
|
278 |
|
NPTf ( SimInfo *theInfo, ForceFields* the_ff); |
279 |
< |
virtual ~NPTf() {}; |
279 |
> |
virtual ~NPTf(); |
280 |
|
|
325 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
326 |
– |
calcStress = 1; |
327 |
– |
T::integrateStep( calcPot, calcStress ); |
328 |
– |
accIntegralOfChidt(); |
329 |
– |
} |
330 |
– |
|
281 |
|
virtual double getConservedQuantity(void); |
282 |
+ |
virtual string getAdditionalParameters(void); |
283 |
+ |
virtual void resetIntegrator(void); |
284 |
|
|
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 |
– |
|
285 |
|
protected: |
286 |
|
|
287 |
< |
virtual void moveA( void ); |
288 |
< |
virtual void moveB( void ); |
287 |
> |
virtual void evolveEtaA(void); |
288 |
> |
virtual void evolveEtaB(void); |
289 |
|
|
290 |
< |
virtual void resetIntegrator( void ); |
290 |
> |
virtual bool etaConverged( void ); |
291 |
|
|
292 |
< |
virtual int readyCheck(); |
292 |
> |
virtual void scaleSimBox( void ); |
293 |
|
|
294 |
< |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
294 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
295 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
296 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
297 |
> |
int index, double sc[3]); |
298 |
|
|
299 |
< |
// chi and eta are the propagated degrees of freedom |
299 |
> |
virtual void calcVelScale( void ); |
300 |
|
|
353 |
– |
double chi; |
301 |
|
double eta[3][3]; |
302 |
< |
double NkBT; |
303 |
< |
|
304 |
< |
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 |
< |
|
302 |
> |
double oldEta[3][3]; |
303 |
> |
double prevEta[3][3]; |
304 |
> |
double vScale[3][3]; |
305 |
|
}; |
306 |
|
|
307 |
< |
template<typename T> class NPTxym : public T{ |
307 |
> |
template<typename T> class NPTxyz : public T{ |
308 |
|
|
309 |
|
public: |
310 |
|
|
311 |
< |
NPTxym ( SimInfo *theInfo, ForceFields* the_ff); |
312 |
< |
virtual ~NPTxym() {}; |
311 |
> |
NPTxyz ( SimInfo *theInfo, ForceFields* the_ff); |
312 |
> |
virtual ~NPTxyz(); |
313 |
|
|
314 |
< |
virtual void integrateStep( int calcPot, int calcStress ){ |
315 |
< |
calcStress = 1; |
316 |
< |
T::integrateStep( calcPot, calcStress ); |
386 |
< |
} |
314 |
> |
virtual double getConservedQuantity(void); |
315 |
> |
virtual string getAdditionalParameters(void); |
316 |
> |
virtual void resetIntegrator(void); |
317 |
|
|
388 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
389 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
390 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
391 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
392 |
– |
|
318 |
|
protected: |
319 |
|
|
320 |
< |
virtual void moveA( void ); |
321 |
< |
virtual void moveB( void ); |
320 |
> |
virtual void evolveEtaA(void); |
321 |
> |
virtual void evolveEtaB(void); |
322 |
|
|
323 |
< |
virtual int readyCheck(); |
323 |
> |
virtual bool etaConverged( void ); |
324 |
|
|
325 |
< |
virtual void resetIntegrator( void ); |
325 |
> |
virtual void scaleSimBox( void ); |
326 |
|
|
327 |
< |
Molecule* myMolecules; |
328 |
< |
Atom** myAtoms; |
327 |
> |
virtual void getVelScaleA( double sc[3], double vel[3] ); |
328 |
> |
virtual void getVelScaleB( double sc[3], int index ); |
329 |
> |
virtual void getPosScale(double pos[3], double COM[3], |
330 |
> |
int index, double sc[3]); |
331 |
|
|
332 |
< |
// chi and eta are the propagated degrees of freedom |
332 |
> |
virtual void calcVelScale( void ); |
333 |
|
|
407 |
– |
double chi; |
408 |
– |
double eta; |
409 |
– |
double etaX; |
410 |
– |
double etaY; |
411 |
– |
double NkBT; |
412 |
– |
|
413 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
414 |
– |
// One of qmass or tauThermostat must be set; |
415 |
– |
|
416 |
– |
double targetTemp; |
417 |
– |
double targetPressure; |
418 |
– |
double tauThermostat; |
419 |
– |
double tauBarostat; |
420 |
– |
|
421 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
422 |
– |
short int have_target_pressure; |
423 |
– |
|
424 |
– |
}; |
425 |
– |
|
426 |
– |
|
427 |
– |
template<typename T> class NPTfm : public T{ |
428 |
– |
|
429 |
– |
public: |
430 |
– |
|
431 |
– |
NPTfm ( SimInfo *theInfo, ForceFields* the_ff); |
432 |
– |
virtual ~NPTfm() {}; |
433 |
– |
|
434 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
435 |
– |
calcStress = 1; |
436 |
– |
T::integrateStep( calcPot, calcStress ); |
437 |
– |
accIntegralOfChidt(); |
438 |
– |
} |
439 |
– |
|
440 |
– |
virtual double getConservedQuantity(void); |
441 |
– |
|
442 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
443 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
444 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
445 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
446 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
447 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
448 |
– |
|
449 |
– |
protected: |
450 |
– |
|
451 |
– |
virtual void moveA( void ); |
452 |
– |
virtual void moveB( void ); |
453 |
– |
|
454 |
– |
virtual void resetIntegrator( void ); |
455 |
– |
|
456 |
– |
virtual int readyCheck(); |
457 |
– |
|
458 |
– |
void accIntegralOfChidt(void) { integralOfChidt += dt * chi;} |
459 |
– |
|
460 |
– |
Molecule* myMolecules; |
461 |
– |
Atom** myAtoms; |
462 |
– |
|
463 |
– |
// chi and eta are the propagated degrees of freedom |
464 |
– |
|
465 |
– |
double chi; |
334 |
|
double eta[3][3]; |
335 |
< |
double NkBT; |
336 |
< |
double integralOfChidt; |
337 |
< |
|
470 |
< |
// targetTemp, targetPressure, and tauBarostat must be set. |
471 |
< |
// One of qmass or tauThermostat must be set; |
472 |
< |
|
473 |
< |
double targetTemp; |
474 |
< |
double targetPressure; |
475 |
< |
double tauThermostat; |
476 |
< |
double tauBarostat; |
477 |
< |
|
478 |
< |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
479 |
< |
short int have_target_pressure; |
480 |
< |
double chiTolerance; |
481 |
< |
short int have_chi_tolerance; |
482 |
< |
double posIterTolerance; |
483 |
< |
short int have_pos_iter_tolerance; |
484 |
< |
|
335 |
> |
double oldEta[3][3]; |
336 |
> |
double prevEta[3][3]; |
337 |
> |
double vScale[3][3]; |
338 |
|
}; |
339 |
|
|
340 |
|
|
488 |
– |
template<typename T> class NPTpr : public T{ |
489 |
– |
|
490 |
– |
public: |
491 |
– |
|
492 |
– |
NPTpr ( SimInfo *theInfo, ForceFields* the_ff); |
493 |
– |
virtual ~NPTpr() {}; |
494 |
– |
|
495 |
– |
virtual void integrateStep( int calcPot, int calcStress ){ |
496 |
– |
calcStress = 1; |
497 |
– |
T::integrateStep( calcPot, calcStress ); |
498 |
– |
} |
499 |
– |
|
500 |
– |
void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;} |
501 |
– |
void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;} |
502 |
– |
void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;} |
503 |
– |
void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;} |
504 |
– |
void setChiTolerance(double tol) {chiTolerance = tol;} |
505 |
– |
void setPosIterTolerance(double tol) {posIterTolerance = tol;} |
506 |
– |
|
507 |
– |
protected: |
508 |
– |
|
509 |
– |
virtual void moveA( void ); |
510 |
– |
virtual void moveB( void ); |
511 |
– |
|
512 |
– |
virtual int readyCheck(); |
513 |
– |
|
514 |
– |
virtual void resetIntegrator( void ); |
515 |
– |
|
516 |
– |
// chi and eta are the propagated degrees of freedom |
517 |
– |
|
518 |
– |
double chi; |
519 |
– |
double eta[3][3]; |
520 |
– |
double NkBT; |
521 |
– |
|
522 |
– |
// targetTemp, targetPressure, and tauBarostat must be set. |
523 |
– |
// One of qmass or tauThermostat must be set; |
524 |
– |
|
525 |
– |
double targetTemp; |
526 |
– |
double targetPressure; |
527 |
– |
double tauThermostat; |
528 |
– |
double tauBarostat; |
529 |
– |
|
530 |
– |
short int have_tau_thermostat, have_tau_barostat, have_target_temp; |
531 |
– |
short int have_target_pressure; |
532 |
– |
double chiTolerance; |
533 |
– |
short int have_chi_tolerance; |
534 |
– |
double posIterTolerance; |
535 |
– |
short int have_pos_iter_tolerance; |
536 |
– |
|
537 |
– |
}; |
538 |
– |
|
539 |
– |
|
341 |
|
template<typename T> class ZConstraint : public T { |
342 |
< |
|
343 |
< |
public: |
342 |
> |
|
343 |
> |
public: |
344 |
|
class ForceSubtractionPolicy{ |
345 |
|
public: |
346 |
|
ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;} |
347 |
|
|
348 |
< |
virtual void update() = 0; |
348 |
> |
virtual void update() = 0; |
349 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
350 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0; |
351 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0; |
352 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0; |
353 |
< |
|
353 |
> |
|
354 |
|
protected: |
355 |
< |
ZConstraint<T>* zconsIntegrator;; |
355 |
> |
ZConstraint<T>* zconsIntegrator; |
356 |
|
}; |
357 |
|
|
358 |
|
class PolicyByNumber : public ForceSubtractionPolicy{ |
359 |
|
|
360 |
|
public: |
361 |
< |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
362 |
< |
virtual void update(); |
361 |
> |
PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
362 |
> |
virtual void update(); |
363 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
364 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
365 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
366 |
|
virtual double getHFOfUnconsMols(Atom* atom, double totalForce); |
367 |
< |
|
367 |
> |
|
368 |
|
private: |
369 |
|
int totNumOfMovingAtoms; |
370 |
|
}; |
372 |
|
class PolicyByMass : public ForceSubtractionPolicy{ |
373 |
|
|
374 |
|
public: |
375 |
< |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
376 |
< |
|
377 |
< |
virtual void update(); |
375 |
> |
PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {} |
376 |
> |
|
377 |
> |
virtual void update(); |
378 |
|
virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ; |
379 |
|
virtual double getZFOfMovingMols(Atom* atom, double totalForce) ; |
380 |
|
virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce); |
388 |
|
|
389 |
|
ZConstraint( SimInfo *theInfo, ForceFields* the_ff); |
390 |
|
~ZConstraint(); |
391 |
< |
|
391 |
> |
|
392 |
|
void setZConsTime(double time) {this->zconsTime = time;} |
393 |
|
void getZConsTime() {return zconsTime;} |
394 |
< |
|
394 |
> |
|
395 |
|
void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;} |
396 |
|
void getIndexOfAllZConsMols() {return indexOfAllZConsMols;} |
397 |
< |
|
397 |
> |
|
398 |
|
void setZConsOutput(const char * fileName) {zconsOutput = fileName;} |
399 |
|
string getZConsOutput() {return zconsOutput;} |
400 |
< |
|
400 |
> |
|
401 |
|
virtual void integrate(); |
601 |
– |
|
402 |
|
|
403 |
+ |
|
404 |
|
#ifdef IS_MPI |
405 |
|
virtual void update(); //which is called to indicate the molecules' migration |
406 |
|
#endif |
407 |
|
|
408 |
+ |
enum ZConsState {zcsMoving, zcsFixed}; |
409 |
+ |
|
410 |
+ |
vector<Molecule*> zconsMols; //z-constraint molecules array |
411 |
+ |
vector<ZConsState> states; //state of z-constraint molecules |
412 |
+ |
|
413 |
+ |
|
414 |
+ |
|
415 |
+ |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
416 |
+ |
double totalMassOfUncons; //total mas of unconstraint molecules |
417 |
+ |
|
418 |
+ |
|
419 |
|
protected: |
420 |
|
|
421 |
< |
enum ZConsState {zcsMoving, zcsFixed}; |
422 |
< |
|
423 |
< |
virtual void calcForce( int calcPot, int calcStress ); |
421 |
> |
|
422 |
> |
|
423 |
> |
virtual void calcForce( int calcPot, int calcStress ); |
424 |
|
virtual void thermalize(void); |
425 |
< |
|
425 |
> |
|
426 |
|
void zeroOutVel(); |
427 |
|
void doZconstraintForce(); |
428 |
< |
void doHarmonic(); |
428 |
> |
void doHarmonic(vector<double>& resPos); |
429 |
|
bool checkZConsState(); |
430 |
|
|
431 |
|
bool haveFixedZMols(); |
440 |
|
double zconsTol; //tolerance of z-contratint |
441 |
|
double zForceConst; //base force constant term |
442 |
|
//which is estimate by OOPSE |
443 |
< |
|
444 |
< |
vector<Molecule*> zconsMols; //z-constraint molecules array |
445 |
< |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
443 |
> |
|
444 |
> |
|
445 |
> |
vector<double> massOfZConsMols; //mass of z-constraint molecule |
446 |
|
vector<double> kz; //force constant array |
447 |
< |
vector<ZConsState> states; //state of z-constraint molecules |
447 |
> |
|
448 |
|
vector<double> zPos; // |
449 |
< |
|
450 |
< |
|
449 |
> |
|
450 |
> |
|
451 |
|
vector<Molecule*> unconsMols; //unconstraint molecules array |
452 |
|
vector<double> massOfUnconsMols; //mass array of unconstraint molecules |
641 |
– |
double totalMassOfUncons; //total mas of unconstraint molecules |
453 |
|
|
454 |
+ |
|
455 |
|
vector<ZConsParaItem>* parameters; // |
456 |
< |
|
456 |
> |
|
457 |
|
vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
458 |
|
|
459 |
< |
int* indexOfZConsMols; //index of local Z-Constraint Molecules |
460 |
< |
double* fz; |
461 |
< |
double* curZPos; |
650 |
< |
|
651 |
< |
int totNumOfUnconsAtoms; //total number of uncontraint atoms |
459 |
> |
vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
460 |
> |
vector<double> fz; |
461 |
> |
vector<double> curZPos; |
462 |
|
|
463 |
< |
int whichDirection; //constraint direction |
463 |
> |
bool usingSMD; |
464 |
> |
vector<double> prevCantPos; |
465 |
> |
vector<double> cantPos; |
466 |
> |
vector<double> cantVel; |
467 |
> |
|
468 |
> |
double zconsFixTime; |
469 |
> |
double zconsGap; |
470 |
> |
bool hasZConsGap; |
471 |
> |
vector<double> endFixTime; |
472 |
|
|
473 |
+ |
int whichDirection; //constraint direction |
474 |
+ |
|
475 |
|
private: |
476 |
< |
|
476 |
> |
|
477 |
|
string zconsOutput; //filename of zconstraint output |
478 |
|
ZConsWriter* fzOut; //z-constraint writer |
479 |
|
|
480 |
< |
double curZconsTime; |
480 |
> |
double curZconsTime; |
481 |
|
|
482 |
|
double calcMovingMolsCOMVel(); |
483 |
|
double calcSysCOMVel(); |
484 |
|
double calcTotalForce(); |
485 |
+ |
void updateZPos(); |
486 |
+ |
void updateCantPos(); |
487 |
|
|
488 |
|
ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
489 |
|
friend class ForceSubtractionPolicy; |
490 |
|
|
491 |
|
}; |
492 |
|
|
493 |
+ |
/* |
494 |
+ |
template<typename T> class SingleZConstrain : public T{ |
495 |
+ |
|
496 |
+ |
|
497 |
+ |
}; |
498 |
+ |
*/ |
499 |
+ |
|
500 |
+ |
template<typename T> class NonEquMD : public T { |
501 |
+ |
public: |
502 |
+ |
|
503 |
+ |
|
504 |
+ |
|
505 |
+ |
}; |
506 |
+ |
|
507 |
+ |
|
508 |
+ |
// |
509 |
+ |
template<typename T> class SingleZConstraint : public T{ |
510 |
+ |
public: |
511 |
+ |
SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff); |
512 |
+ |
~SingleZConstraint(); |
513 |
+ |
|
514 |
+ |
bool stopIntegrator(); |
515 |
+ |
|
516 |
+ |
protected: |
517 |
+ |
|
518 |
+ |
}; |
519 |
+ |
|
520 |
+ |
//Steered Molecular Dynamics, curret implement only support one steered molecule |
521 |
+ |
template<typename T> class SMD : public T{ |
522 |
+ |
public: |
523 |
+ |
SMD( SimInfo *theInfo, ForceFields* the_ff); |
524 |
+ |
~SMD(); |
525 |
+ |
|
526 |
+ |
virtual void integrate(); |
527 |
+ |
virtual void calcForce( int calcPot, int calcStress ); |
528 |
+ |
bool stopIntegrator(); |
529 |
+ |
private: |
530 |
+ |
|
531 |
+ |
}; |
532 |
+ |
|
533 |
+ |
//By using state pattern, Coordinate Drive is responsible for switching back and forth between |
534 |
+ |
//Driven Molecular Dynamics and ZConstraint Method. |
535 |
+ |
template<typename T> class CoordinateDriver : public T { |
536 |
+ |
public: |
537 |
+ |
typedef T ParentIntegrator; |
538 |
+ |
|
539 |
+ |
CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*); |
540 |
+ |
~CoordinateDriver(); |
541 |
+ |
|
542 |
+ |
virtual void integrate(); |
543 |
+ |
|
544 |
+ |
private: |
545 |
+ |
BaseIntegrator* zconsIntegrator; |
546 |
+ |
BaseIntegrator* drivenIntegrator; |
547 |
+ |
|
548 |
+ |
}; |
549 |
+ |
|
550 |
|
#endif |