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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 755 by mmeineke, Tue Sep 9 20:35:25 2003 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 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  
23 –
25   template<typename T = BaseIntegrator> class Integrator : public T {
26  
27   public:
28    Integrator( SimInfo *theInfo, ForceFields* the_ff );
29    virtual ~Integrator();
30    void integrate( void );
31 +  virtual double  getConservedQuantity(void);
32 +  virtual string getAdditionalParameters(void);
33  
31 –
34   protected:
35 <  
35 >
36    virtual void integrateStep( int calcPot, int calcStress );
37    virtual void preMove( void );
38    virtual void moveA( void );
# Line 41 | Line 43 | template<typename T = BaseIntegrator> class Integrator
43  
44    virtual void resetIntegrator( void ) { }
45  
46 <  virtual void calcForce( int calcPot, int calcStress );  
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 */
# Line 59 | Line 66 | template<typename T = BaseIntegrator> class Integrator
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  
# Line 95 | Line 105 | template<typename T> class NVT : public T { (public)
105   public:
106  
107    NVT ( SimInfo *theInfo, ForceFields* the_ff);
108 <  virtual ~NVT() {}
108 >  virtual ~NVT();
109  
110    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
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  
# Line 113 | Line 126 | template<typename T> class NVT : public T { (public)
126  
127    double chi;
128  
129 +  //integral of chi(t)dt
130 +  double integralOfChidt;
131 +
132    // targetTemp must be set.  tauThermostat must also be set;
133  
134    double targetTemp;
135    double tauThermostat;
136 <  
136 >
137    short int have_tau_thermostat, have_target_temp;
138  
139 +  double *oldVel;
140 +  double *oldJi;
141 +
142 +  double chiTolerance;
143 +  short int have_chi_tolerance;
144 +
145   };
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() {};
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 );
159    }
160  
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;}
169    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
170    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
171 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
172 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
173 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
174  
175   protected:
176  
# Line 150 | Line 181 | template<typename T> class NPTi : public T{ (protected
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;
156 –  double eta;
208    double NkBT;
209 +  double fkBT;
210  
211 <  // targetTemp, targetPressure, and tauBarostat must be set.  
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.
220    // One of qmass or tauThermostat must be set;
221  
222    double targetTemp;
# Line 167 | Line 227 | template<typename T> class NPTi : public T{ (protected
227    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
228    short int have_target_pressure;
229  
230 +  double *oldPos;
231 +  double *oldVel;
232 +  double *oldJi;
233 +
234 +  double chiTolerance;
235 +  short int have_chi_tolerance;
236 +  double posIterTolerance;
237 +  short int have_pos_iter_tolerance;
238 +  double etaTolerance;
239 +  short int have_eta_tolerance;
240 +
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  
249 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
250 <  virtual ~NPTim() {};
249 >  virtual double getConservedQuantity(void);
250 >  virtual void resetIntegrator(void);
251 >  virtual string getAdditionalParameters(void);
252 > protected:
253  
179 –  virtual void integrateStep( int calcPot, int calcStress ){
180 –    calcStress = 1;
181 –    T::integrateStep( calcPot, calcStress );
182 –  }
254  
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;}
255  
256 < protected:
256 >  virtual void evolveEtaA(void);
257 >  virtual void evolveEtaB(void);
258  
259 <  virtual void moveA( void );
192 <  virtual void moveB( void );
259 >  virtual bool etaConverged( void );
260  
261 <  virtual int readyCheck();
261 >  virtual void scaleSimBox( void );
262  
263 <  virtual void resetIntegrator( void );
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 <  Molecule* myMolecules;
199 <  Atom** myAtoms;
268 >  virtual void calcVelScale( void );
269  
270 <  // chi and eta are the propagated degrees of freedom
271 <
203 <  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 <
270 >  double eta, oldEta, prevEta;
271 >  double vScale;
272   };
273  
220 – template<typename T> class NPTzm : public T{
221 –
222 – public:
223 –
224 –  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
225 –  virtual ~NPTzm() {};
226 –
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 –
237 – protected:
238 –
239 –  virtual void moveA( void );
240 –  virtual void moveB( void );
241 –
242 –  virtual int readyCheck();
243 –
244 –  virtual void resetIntegrator( void );
245 –
246 –  Molecule* myMolecules;
247 –  Atom** myAtoms;
248 –
249 –  // chi and eta are the propagated degrees of freedom
250 –
251 –  double chi;
252 –  double eta;
253 –  double etaZ;
254 –  double NkBT;
255 –
256 –  // targetTemp, targetPressure, and tauBarostat must be set.  
257 –  // One of qmass or tauThermostat must be set;
258 –
259 –  double targetTemp;
260 –  double targetPressure;
261 –  double tauThermostat;
262 –  double tauBarostat;
263 –
264 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
265 –  short int have_target_pressure;
266 –
267 – };
268 –
274   template<typename T> class NPTf : public T{
275  
276   public:
277  
278    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
279 <  virtual ~NPTf() {};
279 >  virtual ~NPTf();
280  
281 <  virtual void integrateStep( int calcPot, int calcStress ){
282 <    calcStress = 1;
283 <    T::integrateStep( calcPot, calcStress );
279 <  }
281 >  virtual double getConservedQuantity(void);
282 >  virtual string getAdditionalParameters(void);
283 >  virtual void resetIntegrator(void);
284  
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 –
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 <  // chi and eta are the propagated degrees of freedom
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 <  double chi;
298 <  double eta[3][3];
299 <  double NkBT;
299 >  virtual void calcVelScale( void );
300  
301 <  // targetTemp, targetPressure, and tauBarostat must be set.  
302 <  // One of qmass or tauThermostat must be set;
303 <
304 <  double targetTemp;
305 <  double targetPressure;
306 <  double tauThermostat;
307 <  double tauBarostat;
308 <
309 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
310 <  short int have_target_pressure;
311 <
301 >  double eta[3][3];
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() {};
320 <
321 <  virtual void integrateStep( int calcPot, int calcStress ){
322 <    calcStress = 1;
323 <    T::integrateStep( calcPot, calcStress );
324 <  }
311 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
312 >  virtual ~NPTxyz();
313  
314 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
315 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
316 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
329 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
314 >  virtual double getConservedQuantity(void);
315 >  virtual string getAdditionalParameters(void);
316 >  virtual void resetIntegrator(void);
317  
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  
345 –  double chi;
346 –  double eta;
347 –  double etaX;
348 –  double etaY;
349 –  double NkBT;
350 –
351 –  // targetTemp, targetPressure, and tauBarostat must be set.  
352 –  // One of qmass or tauThermostat must be set;
353 –
354 –  double targetTemp;
355 –  double targetPressure;
356 –  double tauThermostat;
357 –  double tauBarostat;
358 –
359 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
360 –  short int have_target_pressure;
361 –
362 – };
363 –
364 –
365 – template<typename T> class NPTfm : public T{
366 –
367 – public:
368 –
369 –  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
370 –  virtual ~NPTfm() {};
371 –
372 –  virtual void integrateStep( int calcPot, int calcStress ){
373 –    calcStress = 1;
374 –    T::integrateStep( calcPot, calcStress );
375 –  }
376 –
377 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
378 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
379 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
380 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
381 –
382 – protected:
383 –
384 –  virtual void  moveA( void );
385 –  virtual void moveB( void );
386 –
387 –  virtual void resetIntegrator( void );
388 –
389 –  virtual int readyCheck();
390 –
391 –  Molecule* myMolecules;
392 –  Atom** myAtoms;
393 –
394 –  // chi and eta are the propagated degrees of freedom
395 –
396 –  double chi;
334    double eta[3][3];
335 <  double NkBT;
336 <
337 <  // targetTemp, targetPressure, and tauBarostat must be set.  
401 <  // One of qmass or tauThermostat must be set;
402 <
403 <  double targetTemp;
404 <  double targetPressure;
405 <  double tauThermostat;
406 <  double tauBarostat;
407 <
408 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
409 <  short int have_target_pressure;
410 <
335 >  double oldEta[3][3];
336 >  double prevEta[3][3];
337 >  double vScale[3][3];
338   };
339  
340  
414 – template<typename T> class NPTpr : public T{
415 –
416 – public:
417 –
418 –  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
419 –  virtual ~NPTpr() {};
420 –
421 –  virtual void integrateStep( int calcPot, int calcStress ){
422 –    calcStress = 1;
423 –    T::integrateStep( calcPot, calcStress );
424 –  }
425 –
426 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
427 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
428 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
429 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
430 –
431 – protected:
432 –
433 –  virtual void  moveA( void );
434 –  virtual void moveB( void );
435 –
436 –  virtual int readyCheck();
437 –
438 –  virtual void resetIntegrator( void );
439 –
440 –  // chi and eta are the propagated degrees of freedom
441 –
442 –  double chi;
443 –  double eta[3][3];
444 –  double NkBT;
445 –
446 –  // targetTemp, targetPressure, and tauBarostat must be set.  
447 –  // One of qmass or tauThermostat must be set;
448 –
449 –  double targetTemp;
450 –  double targetPressure;
451 –  double tauThermostat;
452 –  double tauBarostat;
453 –
454 –  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
455 –  short int have_target_pressure;
456 –
457 – };
458 –
459 –
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;
369 >      int totNumOfMovingAtoms;
370    };
371  
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);
# Line 507 | Line 388 | template<typename T> class ZConstraint : public T { (p
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();
521 –  
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();
# Line 548 | Line 440 | template<typename T> class ZConstraint : public T { (p
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
561 –  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;
570 <  
571 <  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;

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