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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC vs.
Revision 1010 by tim, Tue Feb 3 20:43:08 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 39 | Line 40 | template<typename T = BaseIntegrator> class Integrator
40    virtual void constrainB( void );
41    virtual int  readyCheck( void ) { return 1; }
42  
43 <  virtual void calcForce( int calcPot, int calcStress );  
43 >  virtual void resetIntegrator( void ) { }
44 >
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],
52 <               double A[3][3] );
53 <              
51 >  void rotate( int axes1, int axes2, double angle, double j[3],
52 >         double A[3][3] );
53 >
54    ForceFields* myFF;
55  
56    SimInfo *info; // all the info we'll ever need
# Line 56 | Line 61 | template<typename T = BaseIntegrator> class Integrator
61    int nMols;
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 <  
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 >
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 84 | 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 93 | 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 105 | Line 113 | template<typename T> class NVT : public T { (public)
113  
114    virtual int readyCheck();
115  
116 +  virtual void resetIntegrator( void );
117 +
118    // chi is a propagated degree of freedom.
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 144 | Line 172 | template<typename T> class NPTi : public T{ (protected
172  
173    virtual int readyCheck();
174  
175 <  // chi and eta are the propagated degrees of freedom
175 >  virtual void resetIntegrator( void );
176  
177 <  double chi;
178 <  double eta;
179 <  double NkBT;
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 <  // targetTemp, targetPressure, and tauBarostat must be set.  
154 <  // One of qmass or tauThermostat must be set;
182 >  virtual void calcVelScale( void ) = 0;
183  
184 <  double targetTemp;
185 <  double targetPressure;
158 <  double tauThermostat;
159 <  double tauBarostat;
184 >  virtual bool chiConverged( void );
185 >  virtual bool etaConverged( void ) = 0;
186  
187 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
188 <  short int have_target_pressure;
187 >  virtual void evolveChiA( void );
188 >  virtual void evolveEtaA( void ) = 0;
189 >  virtual void evolveChiB( void );
190 >  virtual void evolveEtaB( void ) = 0;
191  
192 < };
192 >  virtual void scaleSimBox( void ) = 0;
193  
194 < template<typename T> class NPTim : public T{
194 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
195  
168 – public:
169 –
170 –  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
171 –  virtual ~NPTim() {};
172 –
173 –  virtual void integrateStep( int calcPot, int calcStress ){
174 –    calcStress = 1;
175 –    T::integrateStep( calcPot, calcStress );
176 –  }
177 –
178 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
179 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
180 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
181 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
182 –
183 – protected:
184 –
185 –  virtual void moveA( void );
186 –  virtual void moveB( void );
187 –
188 –  virtual int readyCheck();
189 –
190 –  Molecule* myMolecules;
191 –  Atom** myAtoms;
192 –
196    // chi and eta are the propagated degrees of freedom
197  
198 +  double oldChi;
199 +  double prevChi;
200    double chi;
196 –  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 207 | 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() {};
242 >  virtual double getConservedQuantity(void);
243 >  virtual void resetIntegrator(void);
244 >  virtual string getAdditionalParameters(void);
245 > protected:
246  
219 –  virtual void integrateStep( int calcPot, int calcStress ){
220 –    calcStress = 1;
221 –    T::integrateStep( calcPot, calcStress );
222 –  }
247  
224 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
225 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
226 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
227 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
248  
249 < protected:
249 >  virtual void evolveEtaA(void);
250 >  virtual void evolveEtaB(void);
251  
252 <  virtual void  moveA( void );
232 <  virtual void moveB( void );
252 >  virtual bool etaConverged( void );
253  
254 <  virtual int readyCheck();
254 >  virtual void scaleSimBox( void );
255  
256 <  // chi and eta are the propagated degrees of freedom
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 chi;
239 <  double eta[3][3];
240 <  double NkBT;
261 >  virtual void calcVelScale( void );
262  
263 <  // targetTemp, targetPressure, and tauBarostat must be set.  
264 <  // One of qmass or tauThermostat must be set;
263 >  double eta, oldEta, prevEta;
264 >  double vScale;
265 > };
266  
267 <  double targetTemp;
246 <  double targetPressure;
247 <  double tauThermostat;
248 <  double tauBarostat;
267 > template<typename T> class NPTf : public T{
268  
269 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
251 <  short int have_target_pressure;
269 > public:
270  
271 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
272 +  virtual ~NPTf();
273 +
274 +  virtual double getConservedQuantity(void);
275 +  virtual string getAdditionalParameters(void);
276 +  virtual void resetIntegrator(void);
277 +
278 + protected:
279 +
280 +  virtual void evolveEtaA(void);
281 +  virtual void evolveEtaB(void);
282 +
283 +  virtual bool etaConverged( void );
284 +
285 +  virtual void scaleSimBox( void );
286 +
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 +  virtual void calcVelScale( void );
293 +
294 +  double eta[3][3];
295 +  double oldEta[3][3];
296 +  double prevEta[3][3];
297 +  double vScale[3][3];
298   };
299  
300 < template<typename T> class NPTfm : public T{
300 > template<typename T> class NPTxyz : public T{
301  
302   public:
303  
304 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
305 <  virtual ~NPTfm() {};
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 );
265 <  }
307 >  virtual double getConservedQuantity(void);
308 >  virtual string getAdditionalParameters(void);
309 >  virtual void resetIntegrator(void);
310  
267 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
268 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
269 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
270 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
271 –
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 <  Molecule* myMolecules;
280 <  Atom** myAtoms;
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;
285 <  double eta[3][3];
286 <  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;
292 <  double targetPressure;
293 <  double tauThermostat;
294 <  double tauBarostat;
295 <
296 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
297 <  short int have_target_pressure;
298 <
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:      
337 <  class ForceSubstractionPolicy{
335 >
336 >  public:
337 >  class ForceSubtractionPolicy{
338      public:
339 <      ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
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 <                
347 <         protected:
348 <           ZConstraint<T>* zconsIntegrator;;
344 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
345 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
346 >
347 >   protected:
348 >     ZConstraint<T>* zconsIntegrator;
349    };
350  
351 <  class PolicyByNumber : ForceSubstractionPolicy{
351 >  class PolicyByNumber : public ForceSubtractionPolicy{
352 >
353      public:
354 <                PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(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 <                
358 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
359 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
360 >
361      private:
362 <                int totNumOfMovingAtoms;
362 >      int totNumOfMovingAtoms;
363    };
364  
365 <  class PolicyByMass :ForceSubstractionPolicy{
365 >  class PolicyByMass : public ForceSubtractionPolicy{
366 >
367      public:
368 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(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);
374 <                virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
373 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
374 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
375  
376 <         private:
377 <           double totMassOfMovingAtoms;
376 >   private:
377 >     double totMassOfMovingAtoms;
378    };
379  
380   public:
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 <  
388 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
389 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
390 <  
391 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
387 >
388 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
389 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
390 >
391 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
392    string getZConsOutput()                         {return zconsOutput;}
393 <  
393 >
394    virtual void integrate();
360 –  
395  
396 +
397   #ifdef IS_MPI
398 <  virtual void update(); //which is called to indicate the molecules' migration
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  
368 –  enum ZConsState {zcsMoving, zcsFixed};
414  
415  
416 <
372 <  virtual void calcForce( int calcPot, int calcStress );
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 385 | Line 429 | template<typename T> class ZConstraint : public T { (p
429    int isZConstraintMol(Molecule* mol);
430  
431  
432 <  double zconsTime;
433 <  double zconsTol;
434 <  double zForceConst;
435 <  
392 <  vector<Molecule*> zconsMols;
393 <  vector<double> massOfZConsMols;
394 <  vector<double> kz;
395 <  vector<ZConsState> states;
396 <  vector<double> zPos;
397 <  
398 <  
399 <  vector<Molecule*> unconsMols;
400 <  vector<double> massOfUnconsMols;
401 <  double totalMassOfUncons;
432 >  double zconsTime;                              //sample time
433 >  double zconsTol;                                 //tolerance of z-contratint
434 >  double zForceConst;                           //base force constant term
435 >                                                          //which is estimate by OOPSE
436  
437 <  vector<ZConsParaItem>* parameters;
438 <  
437 >
438 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
439 >  vector<double> kz;                              //force constant array
440 >
441 >  vector<double> zPos;                          //
442 >
443 >
444 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
445 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
446 >
447 >
448 >  vector<ZConsParaItem>* parameters; //
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;
410 –  
411 –  int totNumOfUnconsAtoms;
455  
456 <  int whichDirection;                           //constraint direction
457 <  
456 >
457 >
458 >  int whichDirection;                           //constraint direction
459 >
460   private:
416 –  
417 –  string zconsOutput;
418 –  ZConsWriter* fzOut;
461  
462 +  string zconsOutput;                         //filename of zconstraint output
463 +  ZConsWriter* fzOut;                         //z-constraint writer
464 +
465    double curZconsTime;
466  
467    double calcMovingMolsCOMVel();
468    double calcSysCOMVel();
469    double calcTotalForce();
425 –        
426 –  ForceSubstractionPolicy* forcePolicy;
427 –  friend class ForceSubstractionPolicy;
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 setOptCoor(vector<double>& x);
484 +    void getOptCoor(vector<double>& x);
485 +    void output();
486 +    
487 + };
488 +
489 + template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{
490 +  public:
491 +    void writeOutput();
492 + };
493 +  
494   #endif

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