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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 1097 by gezelter, Mon Apr 12 20:32:20 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 void rotationPropagation( StuntDouble* sd, double ji[3] );
49 >
50    void checkConstraints( void );
51 <  void rotate( int axes1, int axes2, double angle, double j[3],
51 >  void rotate( int axes1, int axes2, double angle, double j[3],
52           double A[3][3] );
53 <        
53 >
54    ForceFields* myFF;
55  
56    SimInfo *info; // all the info we'll ever need
57 +  vector<StuntDouble*> integrableObjects;
58    int nAtoms;  /* the number of atoms */
59    int oldAtoms;
60    Atom **atoms; /* array of atom pointers */
# Line 59 | Line 63 | template<typename T = BaseIntegrator> class Integrator
63  
64    int isConstrained; // boolean to know whether the systems contains
65           // constraints.
66 <  int nConstrained;  // counter for number of constraints
67 <  int *constrainedA; // the i of a constraint pair
68 <  int *constrainedB; // the j of a constraint pair
69 <  double *constrainedDsqr; // the square of the constraint distance
70 <  
66 >  int nConstrained;  // counter for number of constraints
67 >  int *constrainedA; // the i of a constraint pair
68 >  int *constrainedB; // the j of a constraint pair
69 >  double *constrainedDsqr; // the square of the constraint distance
70 >
71    int* moving; // tells whether we are moving atom i
72    int* moved;  // tells whether we have moved atom i
73 <  double* oldPos; // pre constrained positions
73 >  double* oldPos; // pre constrained positions
74  
75    short isFirst; /*boolean for the first time integrate is called */
76 <  
76 >
77    double dt;
78    double dt2;
79  
80    Thermo *tStats;
81    StatWriter*  statOut;
82    DumpWriter*  dumpOut;
83 <  
83 >
84   };
85  
86   typedef Integrator<BaseIntegrator> RealIntegrator;
# Line 86 | Line 90 | template<typename T> class NVE : public T { (public)
90   public:
91    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
92      T( theInfo, the_ff ){}
93 <  virtual ~NVE(){}  
93 >  virtual ~NVE(){}
94   };
95  
96  
# Line 95 | Line 99 | template<typename T> class NVT : public T { (public)
99   public:
100  
101    NVT ( SimInfo *theInfo, ForceFields* the_ff);
102 <  virtual ~NVT() {}
102 >  virtual ~NVT();
103  
104    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
105    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
106 +  void setChiTolerance(double tol) {chiTolerance = tol;}
107 +  virtual double  getConservedQuantity(void);
108 +  virtual string getAdditionalParameters(void);
109  
110   protected:
111  
# Line 113 | Line 120 | template<typename T> class NVT : public T { (public)
120  
121    double chi;
122  
123 +  //integral of chi(t)dt
124 +  double integralOfChidt;
125 +
126    // targetTemp must be set.  tauThermostat must also be set;
127  
128    double targetTemp;
129    double tauThermostat;
130 <  
130 >
131    short int have_tau_thermostat, have_target_temp;
132  
133 +  double *oldVel;
134 +  double *oldJi;
135 +
136 +  double chiTolerance;
137 +  short int have_chi_tolerance;
138 +
139   };
140  
141  
142  
143 < template<typename T> class NPTi : public T{
143 > template<typename T> class NPT : public T{
144  
145   public:
146  
147 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
148 <  virtual ~NPTi() {};
147 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
148 >  virtual ~NPT();
149  
150    virtual void integrateStep( int calcPot, int calcStress ){
151      calcStress = 1;
152      T::integrateStep( calcPot, calcStress );
153    }
154  
155 +  virtual double getConservedQuantity(void) = 0;
156 +  virtual string getAdditionalParameters(void) = 0;
157 +  
158 +  double myTauThermo( void ) { return tauThermostat; }
159 +  double myTauBaro( void ) { return tauBarostat; }
160 +
161    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
162    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
163    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
164    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
165 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
166 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
167 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
168  
169   protected:
170  
# Line 150 | Line 175 | template<typename T> class NPTi : public T{ (protected
175  
176    virtual void resetIntegrator( void );
177  
178 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
179 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
180 +  virtual void getPosScale(double pos[3], double COM[3],
181 +                           int index, double sc[3]) = 0;
182 +
183 +  virtual void calcVelScale( void ) = 0;
184 +
185 +  virtual bool chiConverged( void );
186 +  virtual bool etaConverged( void ) = 0;
187 +
188 +  virtual void evolveChiA( void );
189 +  virtual void evolveEtaA( void ) = 0;
190 +  virtual void evolveChiB( void );
191 +  virtual void evolveEtaB( void ) = 0;
192 +
193 +  virtual void scaleSimBox( void ) = 0;
194 +
195 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
196 +
197    // chi and eta are the propagated degrees of freedom
198  
199 +  double oldChi;
200 +  double prevChi;
201    double chi;
156 –  double eta;
202    double NkBT;
203 +  double fkBT;
204  
205 <  // targetTemp, targetPressure, and tauBarostat must be set.  
205 >  double tt2, tb2;
206 >  double instaTemp, instaPress, instaVol;
207 >  double press[3][3];
208 >
209 >  int Nparticles;
210 >
211 >  double integralOfChidt;
212 >
213 >  // targetTemp, targetPressure, and tauBarostat must be set.
214    // One of qmass or tauThermostat must be set;
215  
216    double targetTemp;
# Line 167 | Line 221 | template<typename T> class NPTi : public T{ (protected
221    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
222    short int have_target_pressure;
223  
224 +  double *oldPos;
225 +  double *oldVel;
226 +  double *oldJi;
227 +
228 +  double chiTolerance;
229 +  short int have_chi_tolerance;
230 +  double posIterTolerance;
231 +  short int have_pos_iter_tolerance;
232 +  double etaTolerance;
233 +  short int have_eta_tolerance;
234 +
235   };
236  
237 < template<typename T> class NPTim : public T{
237 > template<typename T> class NPTi : public T{
238  
239   public:
240 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
241 +  ~NPTi();
242  
243 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
244 <  virtual ~NPTim() {};
245 <
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 <
243 >  virtual double getConservedQuantity(void);
244 >  virtual void resetIntegrator(void);
245 >  virtual string getAdditionalParameters(void);
246   protected:
247  
191 –  virtual void moveA( void );
192 –  virtual void moveB( void );
248  
194 –  virtual int readyCheck();
249  
250 <  virtual void resetIntegrator( void );
250 >  virtual void evolveEtaA(void);
251 >  virtual void evolveEtaB(void);
252  
253 <  Molecule* myMolecules;
199 <  Atom** myAtoms;
253 >  virtual bool etaConverged( void );
254  
255 <  // chi and eta are the propagated degrees of freedom
255 >  virtual void scaleSimBox( void );
256  
257 <  double chi;
258 <  double eta;
259 <  double NkBT;
257 >  virtual void getVelScaleA( double sc[3], double vel[3] );
258 >  virtual void getVelScaleB( double sc[3], int index );
259 >  virtual void getPosScale(double pos[3], double COM[3],
260 >                           int index, double sc[3]);
261  
262 <  // targetTemp, targetPressure, and tauBarostat must be set.  
208 <  // One of qmass or tauThermostat must be set;
262 >  virtual void calcVelScale( void );
263  
264 <  double targetTemp;
265 <  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 <
264 >  double eta, oldEta, prevEta;
265 >  double vScale;
266   };
267  
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 –
268   template<typename T> class NPTf : public T{
269  
270   public:
271  
272    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
273 <  virtual ~NPTf() {};
273 >  virtual ~NPTf();
274  
275 <  virtual void integrateStep( int calcPot, int calcStress ){
276 <    calcStress = 1;
277 <    T::integrateStep( calcPot, calcStress );
279 <  }
275 >  virtual double getConservedQuantity(void);
276 >  virtual string getAdditionalParameters(void);
277 >  virtual void resetIntegrator(void);
278  
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 –
279   protected:
280  
281 <  virtual void  moveA( void );
282 <  virtual void moveB( void );
281 >  virtual void evolveEtaA(void);
282 >  virtual void evolveEtaB(void);
283  
284 <  virtual void resetIntegrator( void );
284 >  virtual bool etaConverged( void );
285  
286 <  virtual int readyCheck();
286 >  virtual void scaleSimBox( void );
287  
288 <  // chi and eta are the propagated degrees of freedom
288 >  virtual void getVelScaleA( double sc[3], double vel[3] );
289 >  virtual void getVelScaleB( double sc[3], int index );
290 >  virtual void getPosScale(double pos[3], double COM[3],
291 >                           int index, double sc[3]);
292  
293 <  double chi;
298 <  double eta[3][3];
299 <  double NkBT;
293 >  virtual void calcVelScale( void );
294  
295 <  // targetTemp, targetPressure, and tauBarostat must be set.  
296 <  // One of qmass or tauThermostat must be set;
297 <
298 <  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 <
295 >  double eta[3][3];
296 >  double oldEta[3][3];
297 >  double prevEta[3][3];
298 >  double vScale[3][3];
299   };
300  
301 < template<typename T> class NPTxym : public T{
301 > template<typename T> class NPTxyz : public T{
302  
303   public:
304  
305 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
306 <  virtual ~NPTxym() {};
305 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
306 >  virtual ~NPTxyz();
307  
308 <  virtual void integrateStep( int calcPot, int calcStress ){
309 <    calcStress = 1;
310 <    T::integrateStep( calcPot, calcStress );
324 <  }
308 >  virtual double getConservedQuantity(void);
309 >  virtual string getAdditionalParameters(void);
310 >  virtual void resetIntegrator(void);
311  
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 –
312   protected:
313  
314 <  virtual void moveA( void );
315 <  virtual void moveB( void );
314 >  virtual void evolveEtaA(void);
315 >  virtual void evolveEtaB(void);
316  
317 <  virtual int readyCheck();
317 >  virtual bool etaConverged( void );
318  
319 <  virtual void resetIntegrator( void );
319 >  virtual void scaleSimBox( void );
320  
321 <  Molecule* myMolecules;
322 <  Atom** myAtoms;
321 >  virtual void getVelScaleA( double sc[3], double vel[3] );
322 >  virtual void getVelScaleB( double sc[3], int index );
323 >  virtual void getPosScale(double pos[3], double COM[3],
324 >                           int index, double sc[3]);
325  
326 <  // chi and eta are the propagated degrees of freedom
326 >  virtual void calcVelScale( void );
327  
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;
328    double eta[3][3];
329 <  double NkBT;
330 <
331 <  // 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 <
329 >  double oldEta[3][3];
330 >  double prevEta[3][3];
331 >  double vScale[3][3];
332   };
333  
334  
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 –
335   template<typename T> class ZConstraint : public T {
336 <  
337 <  public:
336 >
337 >  public:
338    class ForceSubtractionPolicy{
339      public:
340        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
341  
342 <      virtual void update() = 0;    
342 >      virtual void update() = 0;
343        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
344        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
345        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
347 <    
347 >
348     protected:
349 <     ZConstraint<T>* zconsIntegrator;;
349 >     ZConstraint<T>* zconsIntegrator;
350    };
351  
352    class PolicyByNumber : public ForceSubtractionPolicy{
353  
354      public:
355 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
356 <      virtual void update();    
355 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
356 >      virtual void update();
357        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
358        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
359        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
360        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
361 <    
361 >
362      private:
363 <    int totNumOfMovingAtoms;
363 >      int totNumOfMovingAtoms;
364    };
365  
366    class PolicyByMass : public ForceSubtractionPolicy{
367  
368      public:
369 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
370 <      
371 <      virtual void update();    
369 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
370 >
371 >      virtual void update();
372        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
373        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
374        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 507 | Line 382 | template<typename T> class ZConstraint : public T { (p
382  
383    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
384    ~ZConstraint();
385 <    
385 >
386    void setZConsTime(double time)                  {this->zconsTime = time;}
387    void getZConsTime()                             {return zconsTime;}
388 <  
388 >
389    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
390    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
391 <  
391 >
392    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
393    string getZConsOutput()                         {return zconsOutput;}
394 <  
394 >
395    virtual void integrate();
521 –  
396  
397 +
398   #ifdef IS_MPI
399    virtual void update();                      //which is called to indicate the molecules' migration
400   #endif
401  
402 +  enum ZConsState {zcsMoving, zcsFixed};
403 +
404 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
405 +  vector<ZConsState> states;                 //state of z-constraint molecules
406 +
407 +
408 +
409 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
410 +  double totalMassOfUncons;                //total mas of unconstraint molecules
411 +
412 +
413   protected:
414  
415 <  enum ZConsState {zcsMoving, zcsFixed};  
416 <
417 <  virtual void calcForce( int calcPot, int calcStress );
415 >
416 >
417 >  virtual void calcForce( int calcPot, int calcStress );
418    virtual void thermalize(void);
419 <  
419 >
420    void zeroOutVel();
421    void doZconstraintForce();
422 <  void doHarmonic();
422 >  void doHarmonic(vector<double>& resPos);
423    bool checkZConsState();
424  
425    bool haveFixedZMols();
# Line 548 | Line 434 | template<typename T> class ZConstraint : public T { (p
434    double zconsTol;                                 //tolerance of z-contratint
435    double zForceConst;                           //base force constant term
436                                                            //which is estimate by OOPSE
437 <  
438 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
439 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
437 >
438 >
439 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
440    vector<double> kz;                              //force constant array
441 <  vector<ZConsState> states;                 //state of z-constraint molecules
441 >
442    vector<double> zPos;                          //
443 <  
444 <  
443 >
444 >
445    vector<Molecule*> unconsMols;           //unconstraint molecules array
446    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
561 –  double totalMassOfUncons;                //total mas of unconstraint molecules
447  
448 +
449    vector<ZConsParaItem>* parameters; //
450 <  
450 >
451    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
452  
453 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
454 <  double* fz;
455 <  double* curZPos;
570 <  
571 <  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
453 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
454 >  vector<double> fz;
455 >  vector<double> curZPos;
456  
457 <  int whichDirection;                           //constraint direction
457 >  bool usingSMD;
458 >  vector<double> cantPos;
459 >  vector<double> cantVel;
460 >
461 >  double zconsFixTime;  
462 >  double zconsGap;
463 >  bool hasZConsGap;
464 >  vector<double> endFixTime;
465    
466 +  int whichDirection;                           //constraint direction
467 +
468   private:
469 <  
469 >
470    string zconsOutput;                         //filename of zconstraint output
471    ZConsWriter* fzOut;                         //z-constraint writer
472  
473 <  double curZconsTime;                      
473 >  double curZconsTime;
474  
475    double calcMovingMolsCOMVel();
476    double calcSysCOMVel();
477    double calcTotalForce();
478 +  void updateZPos();
479 +  void updateCantPos();
480    
481    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
482    friend class ForceSubtractionPolicy;
483  
484   };
485  
486 + /*
487 + //Steered Molecular Dynamics
488 + template<typename T> class SMD : public T{
489 +  public:
490 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
491 +    ~SMD();
492 +  
493 +   virtual void integrate();
494 +  virtual void calcForce( int calcPot, int calcStress );  
495 + };
496 + */
497   #endif

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