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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC vs.
Revision 1330 by gezelter, Fri Jul 16 16:29:44 2004 UTC

# Line 4 | Line 4
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"
# Line 12 | Line 13
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
# Line 20 | Line 22 | const double tol = 1.0e-6;
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
25 <
25 > class VelVerletConsFramework;
26   template<typename T = BaseIntegrator> class Integrator : public T {
27  
28   public:
# Line 28 | Line 30 | template<typename T = BaseIntegrator> class Integrator
30    virtual ~Integrator();
31    void integrate( void );
32    virtual double  getConservedQuantity(void);
33 +  virtual string getAdditionalParameters(void);
34  
35   protected:
36 <  
36 >
37    virtual void integrateStep( int calcPot, int calcStress );
38 <  virtual void preMove( void );
38 >  //virtual void preMove( void );
39    virtual void moveA( void );
40    virtual void moveB( void );
41 <  virtual void constrainA( void );
42 <  virtual void constrainB( void );
41 >  //virtual void constrainA( void );
42 >  //virtual void constrainB( void );
43    virtual int  readyCheck( void ) { return 1; }
44  
45    virtual void resetIntegrator( void ) { }
46 <
47 <  virtual void calcForce( int calcPot, int calcStress );  
46 >
47 >  virtual void calcForce( int calcPot, int calcStress );
48    virtual void thermalize();
49 <  
50 <  void checkConstraints( void );
51 <  void rotate( int axes1, int axes2, double angle, double j[3],
49 >
50 >  virtual bool stopIntegrator() {return false;}
51 >
52 >  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
53 >
54 >  //void checkConstraints( void );
55 >  void rotate( int axes1, int axes2, double angle, double j[3],
56           double A[3][3] );
57 <        
57 >
58    ForceFields* myFF;
59  
60    SimInfo *info; // all the info we'll ever need
61 +  vector<StuntDouble*> integrableObjects;
62    int nAtoms;  /* the number of atoms */
63    int oldAtoms;
64    Atom **atoms; /* array of atom pointers */
65    Molecule* molecules;
66    int nMols;
67  
68 <  int isConstrained; // boolean to know whether the systems contains
61 <         // constraints.
62 <  int nConstrained;  // counter for number of constraints
63 <  int *constrainedA; // the i of a constraint pair
64 <  int *constrainedB; // the j of a constraint pair
65 <  double *constrainedDsqr; // the square of the constraint distance
66 <  
67 <  int* moving; // tells whether we are moving atom i
68 <  int* moved;  // tells whether we have moved atom i
69 <  double* oldPos; // pre constrained positions
68 >  VelVerletConsFramework* consFramework;
69  
70 +  //int isConstrained; // boolean to know whether the systems contains constraints.
71 +  //int nConstrained;  // counter for number of constraints
72 +  //int *constrainedA; // the i of a constraint pair
73 +  //int *constrainedB; // the j of a constraint pair
74 +  //double *constrainedDsqr; // the square of the constraint distance
75 +
76 +  //int* moving; // tells whether we are moving atom i
77 +  //int* moved;  // tells whether we have moved atom i
78 +  //double* oldPos; // pre constrained positions
79 +
80    short isFirst; /*boolean for the first time integrate is called */
81 <  
81 >
82    double dt;
83    double dt2;
84  
85    Thermo *tStats;
86    StatWriter*  statOut;
87    DumpWriter*  dumpOut;
88 <  
88 >
89   };
90  
91   typedef Integrator<BaseIntegrator> RealIntegrator;
92  
93 + // ansi instantiation
94 + // template class Integrator<BaseIntegrator>;
95 +
96 +
97   template<typename T> class NVE : public T {
98  
99   public:
100    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
101      T( theInfo, the_ff ){}
102 <  virtual ~NVE(){}  
102 >  virtual ~NVE(){}
103   };
104  
105  
# Line 101 | Line 114 | template<typename T> class NVT : public T { (public)
114    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
115    void setChiTolerance(double tol) {chiTolerance = tol;}
116    virtual double  getConservedQuantity(void);
117 +  virtual string getAdditionalParameters(void);
118  
119   protected:
120  
# Line 122 | Line 136 | template<typename T> class NVT : public T { (public)
136  
137    double targetTemp;
138    double tauThermostat;
139 <  
139 >
140    short int have_tau_thermostat, have_target_temp;
141  
142    double *oldVel;
# Line 135 | Line 149 | template<typename T> class NVT : public T { (public)
149  
150  
151  
152 < template<typename T> class NPTi : public T{
152 > template<typename T> class NPT : public T{
153  
154   public:
155  
156 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
157 <  virtual ~NPTi();
158 <  
156 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
157 >  virtual ~NPT();
158 >
159    virtual void integrateStep( int calcPot, int calcStress ){
160      calcStress = 1;
161      T::integrateStep( calcPot, calcStress );
148 –    /* accIntegralOfChidt(); */
162    }
163  
164 <  virtual double getConservedQuantity(void);
164 >  virtual double getConservedQuantity(void) = 0;
165 >  virtual string getAdditionalParameters(void) = 0;
166 >  
167 >  double myTauThermo( void ) { return tauThermostat; }
168 >  double myTauBaro( void ) { return tauBarostat; }
169  
170    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
171    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
# Line 166 | Line 183 | template<typename T> class NPTi : public T{ (protected
183    virtual int readyCheck();
184  
185    virtual void resetIntegrator( void );
186 +
187 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
188 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
189 +  virtual void getPosScale(double pos[3], double COM[3],
190 +                           int index, double sc[3]) = 0;
191 +
192 +  virtual void calcVelScale( void ) = 0;
193  
194 +  virtual bool chiConverged( void );
195 +  virtual bool etaConverged( void ) = 0;
196 +
197 +  virtual void evolveChiA( void );
198 +  virtual void evolveEtaA( void ) = 0;
199 +  virtual void evolveChiB( void );
200 +  virtual void evolveEtaB( void ) = 0;
201 +
202 +  virtual void scaleSimBox( void ) = 0;
203 +
204    void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
205  
206    // chi and eta are the propagated degrees of freedom
207  
208 +  double oldChi;
209 +  double prevChi;
210    double chi;
175 –  double eta;
211    double NkBT;
212    double fkBT;
213  
214 +  double tt2, tb2;
215 +  double instaTemp, instaPress, instaVol;
216 +  double press[3][3];
217 +
218    int Nparticles;
219  
220    double integralOfChidt;
221  
222 <  // targetTemp, targetPressure, and tauBarostat must be set.  
222 >  // targetTemp, targetPressure, and tauBarostat must be set.
223    // One of qmass or tauThermostat must be set;
224  
225    double targetTemp;
# Line 202 | Line 241 | template<typename T> class NPTi : public T{ (protected
241    double etaTolerance;
242    short int have_eta_tolerance;
243  
205 –  double volume;
206 –
244   };
245  
246 < template<typename T> class NPTim : public T{
246 > template<typename T> class NPTi : public T{
247  
248   public:
249 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
250 +  ~NPTi();
251  
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 –
252    virtual double getConservedQuantity(void);
253 <
254 <  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 <
253 >  virtual void resetIntegrator(void);
254 >  virtual string getAdditionalParameters(void);
255   protected:
256  
233 –  virtual void moveA( void );
234 –  virtual void moveB( void );
257  
236 –  virtual int readyCheck();
258  
259 <  virtual void resetIntegrator( void );
259 >  virtual void evolveEtaA(void);
260 >  virtual void evolveEtaB(void);
261  
262 <  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
241 <  
242 <  Molecule* myMolecules;
243 <  Atom** myAtoms;
262 >  virtual bool etaConverged( void );
263  
264 <  // chi and eta are the propagated degrees of freedom
264 >  virtual void scaleSimBox( void );
265  
266 <  double chi;
267 <  double eta;
268 <  double NkBT;
269 <  double integralOfChidt;
266 >  virtual void getVelScaleA( double sc[3], double vel[3] );
267 >  virtual void getVelScaleB( double sc[3], int index );
268 >  virtual void getPosScale(double pos[3], double COM[3],
269 >                           int index, double sc[3]);
270  
271 <  // targetTemp, targetPressure, and tauBarostat must be set.  
253 <  // One of qmass or tauThermostat must be set;
271 >  virtual void calcVelScale( void );
272  
273 <  double targetTemp;
274 <  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 <
273 >  double eta, oldEta, prevEta;
274 >  double vScale;
275   };
276  
277 < template<typename T> class NPTzm : public T{
277 > template<typename T> class NPTf : public T{
278  
279   public:
280  
281 <  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
282 <  virtual ~NPTzm() {};
281 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
282 >  virtual ~NPTf();
283  
284 <  virtual void integrateStep( int calcPot, int calcStress ){
285 <    calcStress = 1;
286 <    T::integrateStep( calcPot, calcStress );
279 <  }
284 >  virtual double getConservedQuantity(void);
285 >  virtual string getAdditionalParameters(void);
286 >  virtual void resetIntegrator(void);
287  
281 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
282 –  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 –
288   protected:
289  
290 <  virtual void moveA( void );
291 <  virtual void moveB( void );
290 >  virtual void evolveEtaA(void);
291 >  virtual void evolveEtaB(void);
292  
293 <  virtual int readyCheck();
293 >  virtual bool etaConverged( void );
294  
295 <  virtual void resetIntegrator( void );
295 >  virtual void scaleSimBox( void );
296  
297 <  Molecule* myMolecules;
298 <  Atom** myAtoms;
297 >  virtual void getVelScaleA( double sc[3], double vel[3] );
298 >  virtual void getVelScaleB( double sc[3], int index );
299 >  virtual void getPosScale(double pos[3], double COM[3],
300 >                           int index, double sc[3]);
301  
302 <  // chi and eta are the propagated degrees of freedom
302 >  virtual void calcVelScale( void );
303  
304 <  double chi;
305 <  double eta;
306 <  double etaZ;
307 <  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 <
304 >  double eta[3][3];
305 >  double oldEta[3][3];
306 >  double prevEta[3][3];
307 >  double vScale[3][3];
308   };
309  
310 < template<typename T> class NPTf : public T{
310 > template<typename T> class NPTxyz : public T{
311  
312   public:
313  
314 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
315 <  virtual ~NPTf() {};
314 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
315 >  virtual ~NPTxyz();
316  
325 –  virtual void integrateStep( int calcPot, int calcStress ){
326 –    calcStress = 1;
327 –    T::integrateStep( calcPot, calcStress );
328 –    accIntegralOfChidt();
329 –  }
330 –  
317    virtual double getConservedQuantity(void);
318 +  virtual string getAdditionalParameters(void);
319 +  virtual void resetIntegrator(void);
320  
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 –
321   protected:
322  
323 <  virtual void  moveA( void );
324 <  virtual void moveB( void );
323 >  virtual void evolveEtaA(void);
324 >  virtual void evolveEtaB(void);
325  
326 <  virtual void resetIntegrator( void );
326 >  virtual bool etaConverged( void );
327  
328 <  virtual int readyCheck();
328 >  virtual void scaleSimBox( void );
329  
330 <  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
330 >  virtual void getVelScaleA( double sc[3], double vel[3] );
331 >  virtual void getVelScaleB( double sc[3], int index );
332 >  virtual void getPosScale(double pos[3], double COM[3],
333 >                           int index, double sc[3]);
334  
335 <  // chi and eta are the propagated degrees of freedom
335 >  virtual void calcVelScale( void );
336  
353 –  double chi;
337    double eta[3][3];
338 <  double NkBT;
339 <
340 <  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 <
374 < };
375 <
376 < template<typename T> class NPTxym : public T{
377 <
378 < public:
379 <
380 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
381 <  virtual ~NPTxym() {};
382 <
383 <  virtual void integrateStep( int calcPot, int calcStress ){
384 <    calcStress = 1;
385 <    T::integrateStep( calcPot, calcStress );
386 <  }
387 <
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 <
393 < protected:
394 <
395 <  virtual void moveA( void );
396 <  virtual void moveB( void );
397 <
398 <  virtual int readyCheck();
399 <
400 <  virtual void resetIntegrator( void );
401 <
402 <  Molecule* myMolecules;
403 <  Atom** myAtoms;
404 <
405 <  // chi and eta are the propagated degrees of freedom
406 <
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 <
338 >  double oldEta[3][3];
339 >  double prevEta[3][3];
340 >  double vScale[3][3];
341   };
342  
343  
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;
466 –  double eta[3][3];
467 –  double NkBT;
468 –  double integralOfChidt;
469 –
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 –
485 – };
486 –
487 –
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 –
344   template<typename T> class ZConstraint : public T {
345 <  
346 <  public:
345 >
346 >  public:
347    class ForceSubtractionPolicy{
348      public:
349        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
350  
351 <      virtual void update() = 0;    
351 >      virtual void update() = 0;
352        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
353        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
354        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
355        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
356 <    
356 >
357     protected:
358 <     ZConstraint<T>* zconsIntegrator;;
358 >     ZConstraint<T>* zconsIntegrator;
359    };
360  
361    class PolicyByNumber : public ForceSubtractionPolicy{
362  
363      public:
364 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
365 <      virtual void update();    
364 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
365 >      virtual void update();
366        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
367        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
368        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
369        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
370 <    
370 >
371      private:
372        int totNumOfMovingAtoms;
373    };
# Line 571 | Line 375 | template<typename T> class ZConstraint : public T {
375    class PolicyByMass : public ForceSubtractionPolicy{
376  
377      public:
378 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
379 <      
380 <      virtual void update();    
378 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
379 >
380 >      virtual void update();
381        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
382        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
383        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 587 | Line 391 | template<typename T> class ZConstraint : public T {
391  
392    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
393    ~ZConstraint();
394 <    
394 >
395    void setZConsTime(double time)                  {this->zconsTime = time;}
396    void getZConsTime()                             {return zconsTime;}
397 <  
397 >
398    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
399    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
400 <  
400 >
401    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
402    string getZConsOutput()                         {return zconsOutput;}
403 <  
403 >
404    virtual void integrate();
601 –  
405  
406 +
407   #ifdef IS_MPI
408    virtual void update();                      //which is called to indicate the molecules' migration
409   #endif
410  
411 +  enum ZConsState {zcsMoving, zcsFixed};
412 +
413 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
414 +  vector<ZConsState> states;                 //state of z-constraint molecules
415 +
416 +
417 +
418 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
419 +  double totalMassOfUncons;                //total mas of unconstraint molecules
420 +
421 +
422   protected:
423  
424 <  enum ZConsState {zcsMoving, zcsFixed};  
425 <
426 <  virtual void calcForce( int calcPot, int calcStress );
424 >
425 >
426 >  virtual void calcForce( int calcPot, int calcStress );
427    virtual void thermalize(void);
428 <  
428 >
429    void zeroOutVel();
430    void doZconstraintForce();
431 <  void doHarmonic();
431 >  void doHarmonic(vector<double>& resPos);
432    bool checkZConsState();
433  
434    bool haveFixedZMols();
# Line 628 | Line 443 | template<typename T> class ZConstraint : public T {
443    double zconsTol;                                 //tolerance of z-contratint
444    double zForceConst;                           //base force constant term
445                                                            //which is estimate by OOPSE
446 <  
447 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
448 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
446 >
447 >
448 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
449    vector<double> kz;                              //force constant array
450 <  vector<ZConsState> states;                 //state of z-constraint molecules
450 >
451    vector<double> zPos;                          //
452 <  
453 <  
452 >
453 >
454    vector<Molecule*> unconsMols;           //unconstraint molecules array
455    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
641 –  double totalMassOfUncons;                //total mas of unconstraint molecules
456  
457 +
458    vector<ZConsParaItem>* parameters; //
459 <  
459 >
460    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
461  
462 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
463 <  double* fz;
464 <  double* curZPos;
650 <  
651 <  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
462 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
463 >  vector<double> fz;
464 >  vector<double> curZPos;
465  
466 <  int whichDirection;                           //constraint direction
466 >  bool usingSMD;
467 >  vector<double> prevCantPos;
468 >  vector<double> cantPos;
469 >  vector<double> cantVel;
470 >
471 >  double zconsFixTime;  
472 >  double zconsGap;
473 >  bool hasZConsGap;
474 >  vector<double> endFixTime;
475    
476 +  int whichDirection;                           //constraint direction
477 +
478   private:
479 <  
479 >
480    string zconsOutput;                         //filename of zconstraint output
481    ZConsWriter* fzOut;                         //z-constraint writer
482  
483 <  double curZconsTime;                      
483 >  double curZconsTime;
484  
485    double calcMovingMolsCOMVel();
486    double calcSysCOMVel();
487    double calcTotalForce();
488 +  void updateZPos();
489 +  void updateCantPos();
490    
491    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
492    friend class ForceSubtractionPolicy;
493  
494   };
495  
496 +
497 + //Sympletic quaternion Scheme Integrator
498 + //Reference:
499 + // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
500 + //Symplectic quaternion Scheme for biophysical molecular dynamics
501 + //116(20), 8649, J. Chem. Phys. (2002)
502 + template<typename T> class SQSIntegrator : public T{
503 +  public:
504 +    virtual void moveA();
505 +    virtual void moveB();
506 +  protected:
507 +    void freeRotor();
508 +    void rotate(int k, double dt);
509 +    
510 + };
511   #endif

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