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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 1141 by tim, Wed Apr 28 23:09:32 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 20 | Line 21 | const double tol = 1.0e-6;
21   const int maxIteration = 300;
22   const double tol = 1.0e-6;
23  
23 –
24   template<typename T = BaseIntegrator> class Integrator : public T {
25  
26   public:
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 );
# Line 41 | Line 42 | template<typename T = BaseIntegrator> class Integrator
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 bool stopIntegrator() {return false;}
49 >
50 >  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
51 >
52    void checkConstraints( void );
53 <  void rotate( int axes1, int axes2, double angle, double j[3],
53 >  void rotate( int axes1, int axes2, double angle, double j[3],
54           double A[3][3] );
55 <        
55 >
56    ForceFields* myFF;
57  
58    SimInfo *info; // all the info we'll ever need
59 +  vector<StuntDouble*> integrableObjects;
60    int nAtoms;  /* the number of atoms */
61    int oldAtoms;
62    Atom **atoms; /* array of atom pointers */
# Line 59 | Line 65 | template<typename T = BaseIntegrator> class Integrator
65  
66    int isConstrained; // boolean to know whether the systems contains
67           // constraints.
68 <  int nConstrained;  // counter for number of constraints
69 <  int *constrainedA; // the i of a constraint pair
70 <  int *constrainedB; // the j of a constraint pair
71 <  double *constrainedDsqr; // the square of the constraint distance
72 <  
68 >  int nConstrained;  // counter for number of constraints
69 >  int *constrainedA; // the i of a constraint pair
70 >  int *constrainedB; // the j of a constraint pair
71 >  double *constrainedDsqr; // the square of the constraint distance
72 >
73    int* moving; // tells whether we are moving atom i
74    int* moved;  // tells whether we have moved atom i
75 <  double* oldPos; // pre constrained positions
75 >  double* oldPos; // pre constrained positions
76  
77    short isFirst; /*boolean for the first time integrate is called */
78 <  
78 >
79    double dt;
80    double dt2;
81  
82    Thermo *tStats;
83    StatWriter*  statOut;
84    DumpWriter*  dumpOut;
85 <  
85 >
86   };
87  
88   typedef Integrator<BaseIntegrator> RealIntegrator;
# Line 86 | Line 92 | template<typename T> class NVE : public T { (public)
92   public:
93    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
94      T( theInfo, the_ff ){}
95 <  virtual ~NVE(){}  
95 >  virtual ~NVE(){}
96   };
97  
98  
# Line 95 | Line 101 | template<typename T> class NVT : public T { (public)
101   public:
102  
103    NVT ( SimInfo *theInfo, ForceFields* the_ff);
104 <  virtual ~NVT() {}
104 >  virtual ~NVT();
105  
106    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
107    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
108 +  void setChiTolerance(double tol) {chiTolerance = tol;}
109 +  virtual double  getConservedQuantity(void);
110 +  virtual string getAdditionalParameters(void);
111  
112   protected:
113  
# Line 113 | Line 122 | template<typename T> class NVT : public T { (public)
122  
123    double chi;
124  
125 +  //integral of chi(t)dt
126 +  double integralOfChidt;
127 +
128    // targetTemp must be set.  tauThermostat must also be set;
129  
130    double targetTemp;
131    double tauThermostat;
132 <  
132 >
133    short int have_tau_thermostat, have_target_temp;
134  
135 +  double *oldVel;
136 +  double *oldJi;
137 +
138 +  double chiTolerance;
139 +  short int have_chi_tolerance;
140 +
141   };
142  
143  
144  
145 < template<typename T> class NPTi : public T{
145 > template<typename T> class NPT : public T{
146  
147   public:
148  
149 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
150 <  virtual ~NPTi() {};
149 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
150 >  virtual ~NPT();
151  
152    virtual void integrateStep( int calcPot, int calcStress ){
153      calcStress = 1;
154      T::integrateStep( calcPot, calcStress );
155    }
156  
157 +  virtual double getConservedQuantity(void) = 0;
158 +  virtual string getAdditionalParameters(void) = 0;
159 +  
160 +  double myTauThermo( void ) { return tauThermostat; }
161 +  double myTauBaro( void ) { return tauBarostat; }
162 +
163    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
164    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
165    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
166    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
167 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
168 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
169 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
170  
171   protected:
172  
# Line 150 | Line 177 | template<typename T> class NPTi : public T{ (protected
177  
178    virtual void resetIntegrator( void );
179  
180 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
181 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
182 +  virtual void getPosScale(double pos[3], double COM[3],
183 +                           int index, double sc[3]) = 0;
184 +
185 +  virtual void calcVelScale( void ) = 0;
186 +
187 +  virtual bool chiConverged( void );
188 +  virtual bool etaConverged( void ) = 0;
189 +
190 +  virtual void evolveChiA( void );
191 +  virtual void evolveEtaA( void ) = 0;
192 +  virtual void evolveChiB( void );
193 +  virtual void evolveEtaB( void ) = 0;
194 +
195 +  virtual void scaleSimBox( void ) = 0;
196 +
197 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
198 +
199    // chi and eta are the propagated degrees of freedom
200  
201 +  double oldChi;
202 +  double prevChi;
203    double chi;
156 –  double eta;
204    double NkBT;
205 +  double fkBT;
206  
207 <  // targetTemp, targetPressure, and tauBarostat must be set.  
207 >  double tt2, tb2;
208 >  double instaTemp, instaPress, instaVol;
209 >  double press[3][3];
210 >
211 >  int Nparticles;
212 >
213 >  double integralOfChidt;
214 >
215 >  // targetTemp, targetPressure, and tauBarostat must be set.
216    // One of qmass or tauThermostat must be set;
217  
218    double targetTemp;
# Line 167 | Line 223 | template<typename T> class NPTi : public T{ (protected
223    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
224    short int have_target_pressure;
225  
226 +  double *oldPos;
227 +  double *oldVel;
228 +  double *oldJi;
229 +
230 +  double chiTolerance;
231 +  short int have_chi_tolerance;
232 +  double posIterTolerance;
233 +  short int have_pos_iter_tolerance;
234 +  double etaTolerance;
235 +  short int have_eta_tolerance;
236 +
237   };
238  
239 < template<typename T> class NPTim : public T{
239 > template<typename T> class NPTi : public T{
240  
241   public:
242 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
243 +  ~NPTi();
244  
245 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
246 <  virtual ~NPTim() {};
247 <
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 <
245 >  virtual double getConservedQuantity(void);
246 >  virtual void resetIntegrator(void);
247 >  virtual string getAdditionalParameters(void);
248   protected:
249  
191 –  virtual void moveA( void );
192 –  virtual void moveB( void );
250  
194 –  virtual int readyCheck();
251  
252 <  virtual void resetIntegrator( void );
252 >  virtual void evolveEtaA(void);
253 >  virtual void evolveEtaB(void);
254  
255 <  Molecule* myMolecules;
199 <  Atom** myAtoms;
255 >  virtual bool etaConverged( void );
256  
257 <  // chi and eta are the propagated degrees of freedom
257 >  virtual void scaleSimBox( void );
258  
259 <  double chi;
260 <  double eta;
261 <  double NkBT;
259 >  virtual void getVelScaleA( double sc[3], double vel[3] );
260 >  virtual void getVelScaleB( double sc[3], int index );
261 >  virtual void getPosScale(double pos[3], double COM[3],
262 >                           int index, double sc[3]);
263  
264 <  // targetTemp, targetPressure, and tauBarostat must be set.  
208 <  // One of qmass or tauThermostat must be set;
264 >  virtual void calcVelScale( void );
265  
266 <  double targetTemp;
267 <  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 <
266 >  double eta, oldEta, prevEta;
267 >  double vScale;
268   };
269  
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 –
270   template<typename T> class NPTf : public T{
271  
272   public:
273  
274    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
275 <  virtual ~NPTf() {};
275 >  virtual ~NPTf();
276  
277 <  virtual void integrateStep( int calcPot, int calcStress ){
278 <    calcStress = 1;
279 <    T::integrateStep( calcPot, calcStress );
279 <  }
277 >  virtual double getConservedQuantity(void);
278 >  virtual string getAdditionalParameters(void);
279 >  virtual void resetIntegrator(void);
280  
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 –
281   protected:
282  
283 <  virtual void  moveA( void );
284 <  virtual void moveB( void );
283 >  virtual void evolveEtaA(void);
284 >  virtual void evolveEtaB(void);
285  
286 <  virtual void resetIntegrator( void );
286 >  virtual bool etaConverged( void );
287  
288 <  virtual int readyCheck();
288 >  virtual void scaleSimBox( void );
289  
290 <  // chi and eta are the propagated degrees of freedom
290 >  virtual void getVelScaleA( double sc[3], double vel[3] );
291 >  virtual void getVelScaleB( double sc[3], int index );
292 >  virtual void getPosScale(double pos[3], double COM[3],
293 >                           int index, double sc[3]);
294  
295 <  double chi;
298 <  double eta[3][3];
299 <  double NkBT;
295 >  virtual void calcVelScale( void );
296  
297 <  // targetTemp, targetPressure, and tauBarostat must be set.  
298 <  // One of qmass or tauThermostat must be set;
299 <
300 <  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 <
297 >  double eta[3][3];
298 >  double oldEta[3][3];
299 >  double prevEta[3][3];
300 >  double vScale[3][3];
301   };
302  
303 < template<typename T> class NPTxym : public T{
303 > template<typename T> class NPTxyz : public T{
304  
305   public:
306  
307 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
308 <  virtual ~NPTxym() {};
307 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
308 >  virtual ~NPTxyz();
309  
310 <  virtual void integrateStep( int calcPot, int calcStress ){
311 <    calcStress = 1;
312 <    T::integrateStep( calcPot, calcStress );
324 <  }
310 >  virtual double getConservedQuantity(void);
311 >  virtual string getAdditionalParameters(void);
312 >  virtual void resetIntegrator(void);
313  
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 –
314   protected:
315  
316 <  virtual void moveA( void );
317 <  virtual void moveB( void );
316 >  virtual void evolveEtaA(void);
317 >  virtual void evolveEtaB(void);
318  
319 <  virtual int readyCheck();
319 >  virtual bool etaConverged( void );
320  
321 <  virtual void resetIntegrator( void );
321 >  virtual void scaleSimBox( void );
322  
323 <  Molecule* myMolecules;
324 <  Atom** myAtoms;
323 >  virtual void getVelScaleA( double sc[3], double vel[3] );
324 >  virtual void getVelScaleB( double sc[3], int index );
325 >  virtual void getPosScale(double pos[3], double COM[3],
326 >                           int index, double sc[3]);
327  
328 <  // chi and eta are the propagated degrees of freedom
328 >  virtual void calcVelScale( void );
329  
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;
330    double eta[3][3];
331 <  double NkBT;
332 <
333 <  // 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 <
331 >  double oldEta[3][3];
332 >  double prevEta[3][3];
333 >  double vScale[3][3];
334   };
335  
336  
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 –
337   template<typename T> class ZConstraint : public T {
338 <  
339 <  public:
338 >
339 >  public:
340    class ForceSubtractionPolicy{
341      public:
342        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
343  
344 <      virtual void update() = 0;    
344 >      virtual void update() = 0;
345        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
347        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
348        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
349 <    
349 >
350     protected:
351 <     ZConstraint<T>* zconsIntegrator;;
351 >     ZConstraint<T>* zconsIntegrator;
352    };
353  
354    class PolicyByNumber : public ForceSubtractionPolicy{
355  
356      public:
357 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
358 <      virtual void update();    
357 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358 >      virtual void update();
359        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
360        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
361        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
362        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
363 <    
363 >
364      private:
365 <    int totNumOfMovingAtoms;
365 >      int totNumOfMovingAtoms;
366    };
367  
368    class PolicyByMass : public ForceSubtractionPolicy{
369  
370      public:
371 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
372 <      
373 <      virtual void update();    
371 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
372 >
373 >      virtual void update();
374        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
375        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
376        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 507 | Line 384 | template<typename T> class ZConstraint : public T { (p
384  
385    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
386    ~ZConstraint();
387 <    
387 >
388    void setZConsTime(double time)                  {this->zconsTime = time;}
389    void getZConsTime()                             {return zconsTime;}
390 <  
390 >
391    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
392    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
393 <  
393 >
394    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
395    string getZConsOutput()                         {return zconsOutput;}
396 <  
396 >
397    virtual void integrate();
521 –  
398  
399 +
400   #ifdef IS_MPI
401    virtual void update();                      //which is called to indicate the molecules' migration
402   #endif
403  
404 +  enum ZConsState {zcsMoving, zcsFixed};
405 +
406 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
407 +  vector<ZConsState> states;                 //state of z-constraint molecules
408 +
409 +
410 +
411 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
412 +  double totalMassOfUncons;                //total mas of unconstraint molecules
413 +
414 +
415   protected:
416  
417 <  enum ZConsState {zcsMoving, zcsFixed};  
418 <
419 <  virtual void calcForce( int calcPot, int calcStress );
417 >
418 >
419 >  virtual void calcForce( int calcPot, int calcStress );
420    virtual void thermalize(void);
421 <  
421 >
422    void zeroOutVel();
423    void doZconstraintForce();
424 <  void doHarmonic();
424 >  void doHarmonic(vector<double>& resPos);
425    bool checkZConsState();
426  
427    bool haveFixedZMols();
# Line 548 | Line 436 | template<typename T> class ZConstraint : public T { (p
436    double zconsTol;                                 //tolerance of z-contratint
437    double zForceConst;                           //base force constant term
438                                                            //which is estimate by OOPSE
439 <  
440 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
441 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
439 >
440 >
441 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
442    vector<double> kz;                              //force constant array
443 <  vector<ZConsState> states;                 //state of z-constraint molecules
443 >
444    vector<double> zPos;                          //
445 <  
446 <  
445 >
446 >
447    vector<Molecule*> unconsMols;           //unconstraint molecules array
448    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
561 –  double totalMassOfUncons;                //total mas of unconstraint molecules
449  
450 +
451    vector<ZConsParaItem>* parameters; //
452 <  
452 >
453    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
454  
455 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
456 <  double* fz;
457 <  double* curZPos;
570 <  
571 <  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
455 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
456 >  vector<double> fz;
457 >  vector<double> curZPos;
458  
459 <  int whichDirection;                           //constraint direction
459 >  bool usingSMD;
460 >  vector<double> prevCantPos;
461 >  vector<double> cantPos;
462 >  vector<double> cantVel;
463 >
464 >  double zconsFixTime;  
465 >  double zconsGap;
466 >  bool hasZConsGap;
467 >  vector<double> endFixTime;
468    
469 +  int whichDirection;                           //constraint direction
470 +
471   private:
472 <  
472 >
473    string zconsOutput;                         //filename of zconstraint output
474    ZConsWriter* fzOut;                         //z-constraint writer
475  
476 <  double curZconsTime;                      
476 >  double curZconsTime;
477  
478    double calcMovingMolsCOMVel();
479    double calcSysCOMVel();
480    double calcTotalForce();
481 +  void updateZPos();
482 +  void updateCantPos();
483    
484    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
485    friend class ForceSubtractionPolicy;
486  
487   };
488  
489 + /*
490 + template<typename T> class SingleZConstrain : public T{
491 +
492 +
493 + };
494 + */
495 +
496 + template<typename T> class NonEquMD : public T {
497 +  public:
498 +    
499 +
500 +
501 + };
502 +
503 +
504 + //
505 + template<typename T> class SingleZConstraint : public T{
506 +  public:
507 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
508 +    ~SingleZConstraint();
509 +    
510 +    bool stopIntegrator();
511 +    
512 +  protected:
513 +    
514 + };
515 +
516 + //Steered Molecular Dynamics, curret implement only support one steered molecule
517 + template<typename T> class SMD : public T{
518 +  public:
519 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
520 +    ~SMD();
521 +  
522 +    virtual void integrate();
523 +    virtual void calcForce( int calcPot, int calcStress );  
524 +    bool stopIntegrator();
525 +  private:
526 +    
527 + };
528 +
529 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
530 + //Driven Molecular Dynamics and ZConstraint Method.
531 + template<typename T> class CoordinateDriver : public T {
532 +  public:
533 +    typedef T ParentIntegrator;
534 +
535 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
536 +    ~CoordinateDriver();
537 +    
538 +    virtual void integrate();
539 +
540 +  private:    
541 +    BaseIntegrator* zconsIntegrator;
542 +    BaseIntegrator* drivenIntegrator;
543 +    
544 + };
545 +
546   #endif

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