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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 747 by gezelter, Fri Sep 5 21:28:52 2003 UTC vs.
Revision 1057 by tim, Tue Feb 17 19:23:44 2004 UTC

# Line 27 | Line 27 | template<typename T = BaseIntegrator> class Integrator
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( DirectionalAtom* dAtom, 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
# Line 59 | Line 62 | template<typename T = BaseIntegrator> class Integrator
62  
63    int isConstrained; // boolean to know whether the systems contains
64           // constraints.
65 <  int nConstrained;  // counter for number of constraints
66 <  int *constrainedA; // the i of a constraint pair
67 <  int *constrainedB; // the j of a constraint pair
68 <  double *constrainedDsqr; // the square of the constraint distance
69 <  
65 >  int nConstrained;  // counter for number of constraints
66 >  int *constrainedA; // the i of a constraint pair
67 >  int *constrainedB; // the j of a constraint pair
68 >  double *constrainedDsqr; // the square of the constraint distance
69 >
70    int* moving; // tells whether we are moving atom i
71    int* moved;  // tells whether we have moved atom i
72 <  double* oldPos; // pre constrained positions
72 >  double* oldPos; // pre constrained positions
73  
74    short isFirst; /*boolean for the first time integrate is called */
75 <  
75 >
76    double dt;
77    double dt2;
78  
79    Thermo *tStats;
80    StatWriter*  statOut;
81    DumpWriter*  dumpOut;
82 <  
82 >
83   };
84  
85   typedef Integrator<BaseIntegrator> RealIntegrator;
# Line 86 | Line 89 | template<typename T> class NVE : public T { (public)
89   public:
90    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
91      T( theInfo, the_ff ){}
92 <  virtual ~NVE(){}  
92 >  virtual ~NVE(){}
93   };
94  
95  
# Line 95 | Line 98 | template<typename T> class NVT : public T { (public)
98   public:
99  
100    NVT ( SimInfo *theInfo, ForceFields* the_ff);
101 <  virtual ~NVT() {}
101 >  virtual ~NVT();
102  
103    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
104    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
105 +  void setChiTolerance(double tol) {chiTolerance = tol;}
106 +  virtual double  getConservedQuantity(void);
107 +  virtual string getAdditionalParameters(void);
108  
109   protected:
110  
# Line 113 | Line 119 | template<typename T> class NVT : public T { (public)
119  
120    double chi;
121  
122 +  //integral of chi(t)dt
123 +  double integralOfChidt;
124 +
125    // targetTemp must be set.  tauThermostat must also be set;
126  
127    double targetTemp;
128    double tauThermostat;
129 <  
129 >
130    short int have_tau_thermostat, have_target_temp;
131  
132 +  double *oldVel;
133 +  double *oldJi;
134 +
135 +  double chiTolerance;
136 +  short int have_chi_tolerance;
137 +
138   };
139  
140  
141  
142 < template<typename T> class NPTi : public T{
142 > template<typename T> class NPT : public T{
143  
144   public:
145  
146 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
147 <  virtual ~NPTi() {};
146 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
147 >  virtual ~NPT();
148  
149    virtual void integrateStep( int calcPot, int calcStress ){
150      calcStress = 1;
151      T::integrateStep( calcPot, calcStress );
152    }
153  
154 +  virtual double getConservedQuantity(void) = 0;
155 +  virtual string getAdditionalParameters(void) = 0;
156 +  
157 +  double myTauThermo( void ) { return tauThermostat; }
158 +  double myTauBaro( void ) { return tauBarostat; }
159 +
160    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
161    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
162    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
163    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
164 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
165 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
166 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
167  
168   protected:
169  
# Line 150 | Line 174 | template<typename T> class NPTi : public T{ (protected
174  
175    virtual void resetIntegrator( void );
176  
177 <  // chi and eta are the propagated degrees of freedom
177 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
178 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
179 >  virtual void getPosScale(double pos[3], double COM[3],
180 >                           int index, double sc[3]) = 0;
181  
182 <  double chi;
156 <  double eta;
157 <  double NkBT;
182 >  virtual void calcVelScale( void ) = 0;
183  
184 <  // targetTemp, targetPressure, and tauBarostat must be set.  
185 <  // One of qmass or tauThermostat must be set;
184 >  virtual bool chiConverged( void );
185 >  virtual bool etaConverged( void ) = 0;
186  
187 <  double targetTemp;
188 <  double targetPressure;
189 <  double tauThermostat;
190 <  double tauBarostat;
187 >  virtual void evolveChiA( void );
188 >  virtual void evolveEtaA( void ) = 0;
189 >  virtual void evolveChiB( void );
190 >  virtual void evolveEtaB( void ) = 0;
191  
192 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
168 <  short int have_target_pressure;
192 >  virtual void scaleSimBox( void ) = 0;
193  
194 < };
194 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
195  
172 – template<typename T> class NPTim : public T{
173 –
174 – public:
175 –
176 –  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
177 –  virtual ~NPTim() {};
178 –
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 –
189 – protected:
190 –
191 –  virtual void moveA( void );
192 –  virtual void moveB( void );
193 –
194 –  virtual int readyCheck();
195 –
196 –  virtual void resetIntegrator( void );
197 –
198 –  Molecule* myMolecules;
199 –  Atom** myAtoms;
200 –
196    // chi and eta are the propagated degrees of freedom
197  
198 +  double oldChi;
199 +  double prevChi;
200    double chi;
204 –  double eta;
201    double NkBT;
202 +  double fkBT;
203  
204 <  // targetTemp, targetPressure, and tauBarostat must be set.  
204 >  double tt2, tb2;
205 >  double instaTemp, instaPress, instaVol;
206 >  double press[3][3];
207 >
208 >  int Nparticles;
209 >
210 >  double integralOfChidt;
211 >
212 >  // targetTemp, targetPressure, and tauBarostat must be set.
213    // One of qmass or tauThermostat must be set;
214  
215    double targetTemp;
# Line 215 | Line 220 | template<typename T> class NPTim : public T{ (protecte
220    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
221    short int have_target_pressure;
222  
223 +  double *oldPos;
224 +  double *oldVel;
225 +  double *oldJi;
226 +
227 +  double chiTolerance;
228 +  short int have_chi_tolerance;
229 +  double posIterTolerance;
230 +  short int have_pos_iter_tolerance;
231 +  double etaTolerance;
232 +  short int have_eta_tolerance;
233 +
234   };
235  
236 < template<typename T> class NPTf : public T{
236 > template<typename T> class NPTi : public T{
237  
238   public:
239 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
240 +  ~NPTi();
241  
242 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
243 <  virtual ~NPTf() {};
244 <
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 <
242 >  virtual double getConservedQuantity(void);
243 >  virtual void resetIntegrator(void);
244 >  virtual string getAdditionalParameters(void);
245   protected:
246  
239 –  virtual void  moveA( void );
240 –  virtual void moveB( void );
247  
242 –  virtual void resetIntegrator( void );
248  
249 <  virtual int readyCheck();
249 >  virtual void evolveEtaA(void);
250 >  virtual void evolveEtaB(void);
251  
252 <  // chi and eta are the propagated degrees of freedom
252 >  virtual bool etaConverged( void );
253  
254 <  double chi;
249 <  double eta[3][3];
250 <  double NkBT;
254 >  virtual void scaleSimBox( void );
255  
256 <  // targetTemp, targetPressure, and tauBarostat must be set.  
257 <  // One of qmass or tauThermostat must be set;
256 >  virtual void getVelScaleA( double sc[3], double vel[3] );
257 >  virtual void getVelScaleB( double sc[3], int index );
258 >  virtual void getPosScale(double pos[3], double COM[3],
259 >                           int index, double sc[3]);
260  
261 <  double targetTemp;
256 <  double targetPressure;
257 <  double tauThermostat;
258 <  double tauBarostat;
261 >  virtual void calcVelScale( void );
262  
263 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
264 <  short int have_target_pressure;
262 <
263 >  double eta, oldEta, prevEta;
264 >  double vScale;
265   };
266  
267 < template<typename T> class NPTfm : public T{
267 > template<typename T> class NPTf : public T{
268  
269   public:
270  
271 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
272 <  virtual ~NPTfm() {};
271 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
272 >  virtual ~NPTf();
273  
274 <  virtual void integrateStep( int calcPot, int calcStress ){
275 <    calcStress = 1;
276 <    T::integrateStep( calcPot, calcStress );
275 <  }
274 >  virtual double getConservedQuantity(void);
275 >  virtual string getAdditionalParameters(void);
276 >  virtual void resetIntegrator(void);
277  
277 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
278 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
279 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
280 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
281 –
278   protected:
279  
280 <  virtual void  moveA( void );
281 <  virtual void moveB( void );
280 >  virtual void evolveEtaA(void);
281 >  virtual void evolveEtaB(void);
282  
283 <  virtual void resetIntegrator( void );
283 >  virtual bool etaConverged( void );
284  
285 <  virtual int readyCheck();
285 >  virtual void scaleSimBox( void );
286  
287 <  Molecule* myMolecules;
288 <  Atom** myAtoms;
287 >  virtual void getVelScaleA( double sc[3], double vel[3] );
288 >  virtual void getVelScaleB( double sc[3], int index );
289 >  virtual void getPosScale(double pos[3], double COM[3],
290 >                           int index, double sc[3]);
291  
292 <  // chi and eta are the propagated degrees of freedom
292 >  virtual void calcVelScale( void );
293  
296 –  double chi;
294    double eta[3][3];
295 <  double NkBT;
296 <
297 <  // targetTemp, targetPressure, and tauBarostat must be set.  
301 <  // One of qmass or tauThermostat must be set;
302 <
303 <  double targetTemp;
304 <  double targetPressure;
305 <  double tauThermostat;
306 <  double tauBarostat;
307 <
308 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
309 <  short int have_target_pressure;
310 <
295 >  double oldEta[3][3];
296 >  double prevEta[3][3];
297 >  double vScale[3][3];
298   };
299  
300 + template<typename T> class NPTxyz : public T{
301  
314 – template<typename T> class NPTpr : public T{
315 –
302   public:
303  
304 <  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
305 <  virtual ~NPTpr() {};
304 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
305 >  virtual ~NPTxyz();
306  
307 <  virtual void integrateStep( int calcPot, int calcStress ){
308 <    calcStress = 1;
309 <    T::integrateStep( calcPot, calcStress );
324 <  }
307 >  virtual double getConservedQuantity(void);
308 >  virtual string getAdditionalParameters(void);
309 >  virtual void resetIntegrator(void);
310  
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 –
311   protected:
312  
313 <  virtual void  moveA( void );
314 <  virtual void moveB( void );
313 >  virtual void evolveEtaA(void);
314 >  virtual void evolveEtaB(void);
315  
316 <  virtual int readyCheck();
316 >  virtual bool etaConverged( void );
317  
318 <  virtual void resetIntegrator( void );
318 >  virtual void scaleSimBox( void );
319  
320 <  // chi and eta are the propagated degrees of freedom
320 >  virtual void getVelScaleA( double sc[3], double vel[3] );
321 >  virtual void getVelScaleB( double sc[3], int index );
322 >  virtual void getPosScale(double pos[3], double COM[3],
323 >                           int index, double sc[3]);
324  
325 <  double chi;
343 <  double eta[3][3];
344 <  double NkBT;
325 >  virtual void calcVelScale( void );
326  
327 <  // targetTemp, targetPressure, and tauBarostat must be set.  
328 <  // One of qmass or tauThermostat must be set;
329 <
330 <  double targetTemp;
350 <  double targetPressure;
351 <  double tauThermostat;
352 <  double tauBarostat;
353 <
354 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
355 <  short int have_target_pressure;
356 <
327 >  double eta[3][3];
328 >  double oldEta[3][3];
329 >  double prevEta[3][3];
330 >  double vScale[3][3];
331   };
332  
333  
334   template<typename T> class ZConstraint : public T {
335 <  
336 <  public:
335 >
336 >  public:
337    class ForceSubtractionPolicy{
338      public:
339        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
340  
341 <      virtual void update() = 0;    
341 >      virtual void update() = 0;
342        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
343        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
344        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
345        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
346 <    
346 >
347     protected:
348 <     ZConstraint<T>* zconsIntegrator;;
348 >     ZConstraint<T>* zconsIntegrator;
349    };
350  
351    class PolicyByNumber : public ForceSubtractionPolicy{
352  
353      public:
354 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
355 <      virtual void update();    
354 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
355 >      virtual void update();
356        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
357        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
358        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
359        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
360 <    
360 >
361      private:
362 <    int totNumOfMovingAtoms;
362 >      int totNumOfMovingAtoms;
363    };
364  
365    class PolicyByMass : public ForceSubtractionPolicy{
366  
367      public:
368 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
369 <      
370 <      virtual void update();    
368 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
369 >
370 >      virtual void update();
371        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
372        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
373        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
# Line 407 | Line 381 | template<typename T> class ZConstraint : public T { (p
381  
382    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
383    ~ZConstraint();
384 <    
384 >
385    void setZConsTime(double time)                  {this->zconsTime = time;}
386    void getZConsTime()                             {return zconsTime;}
387 <  
387 >
388    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
389    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
390 <  
390 >
391    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
392    string getZConsOutput()                         {return zconsOutput;}
393 <  
393 >
394    virtual void integrate();
421 –  
395  
396 +
397   #ifdef IS_MPI
398    virtual void update();                      //which is called to indicate the molecules' migration
399   #endif
400  
401 +  enum ZConsState {zcsMoving, zcsFixed};
402 +
403 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
404 +  vector<ZConsState> states;                 //state of z-constraint molecules
405 +
406 +
407 +
408 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
409 +  double totalMassOfUncons;                //total mas of unconstraint molecules
410 +
411 +
412   protected:
413  
414 <  enum ZConsState {zcsMoving, zcsFixed};  
415 <
416 <  virtual void calcForce( int calcPot, int calcStress );
414 >
415 >
416 >  virtual void calcForce( int calcPot, int calcStress );
417    virtual void thermalize(void);
418 <  
418 >
419    void zeroOutVel();
420    void doZconstraintForce();
421    void doHarmonic();
# Line 448 | Line 433 | template<typename T> class ZConstraint : public T { (p
433    double zconsTol;                                 //tolerance of z-contratint
434    double zForceConst;                           //base force constant term
435                                                            //which is estimate by OOPSE
436 <  
437 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
438 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
436 >
437 >
438 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
439    vector<double> kz;                              //force constant array
440 <  vector<ZConsState> states;                 //state of z-constraint molecules
440 >
441    vector<double> zPos;                          //
442 <  
443 <  
442 >
443 >
444    vector<Molecule*> unconsMols;           //unconstraint molecules array
445    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
461 –  double totalMassOfUncons;                //total mas of unconstraint molecules
446  
447 +
448    vector<ZConsParaItem>* parameters; //
449 <  
449 >
450    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
451  
452 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
452 >  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
453    double* fz;
454    double* curZPos;
470 –  
471 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
455  
456 <  int whichDirection;                           //constraint direction
457 <  
456 >
457 >
458 >  int whichDirection;                           //constraint direction
459 >
460   private:
461 <  
461 >
462    string zconsOutput;                         //filename of zconstraint output
463    ZConsWriter* fzOut;                         //z-constraint writer
464  
465 <  double curZconsTime;                      
465 >  double curZconsTime;
466  
467    double calcMovingMolsCOMVel();
468    double calcSysCOMVel();
469    double calcTotalForce();
470 <  
470 >
471    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
472    friend class ForceSubtractionPolicy;
473  
474   };
475  
476 + class OOPSEMinimizerBase : public RealIntegrator {
477 +  public:
478 +
479 +    OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff );
480 +    virtual ~OOPSEMinimizerBase();
481 +    
482 +    double calcGradient(vector<double>& x, vector<double>& grad);
483 +    void setCoor(vector<double>& x);
484 +    vector<double> getCoor();
485 +    void output(vector<double>& x, int iteration);
486 +    int getDim() {return dim;}
487 +    void constraintMove();
488 +    void shakeF();
489 +    void shakeR();
490 +  protected:
491 +    
492 +    int dim;
493 +    void calcDim();
494 + };
495 +
496 + //template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
497 + //  public:
498 + //    void writeOutput();
499 + //};
500 +  
501   #endif

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