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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 837 by tim, Wed Oct 29 00:19:10 2003 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    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
157    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
158    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
159    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
160 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
161 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
162 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
163  
164   protected:
165  
# Line 150 | Line 170 | template<typename T> class NPTi : public T{ (protected
170  
171    virtual void resetIntegrator( void );
172  
173 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
174 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
175 +  virtual void getPosScale(double pos[3], double COM[3],
176 +                           int index, double sc[3]) = 0;
177 +
178 +  virtual bool chiConverged( void );
179 +  virtual bool etaConverged( void ) = 0;
180 +
181 +  virtual void evolveChiA( void );
182 +  virtual void evolveEtaA( void ) = 0;
183 +  virtual void evolveChiB( void );
184 +  virtual void evolveEtaB( void ) = 0;
185 +
186 +  virtual void scaleSimBox( void ) = 0;
187 +
188 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
189 +
190    // chi and eta are the propagated degrees of freedom
191  
192 +  double oldChi;
193 +  double prevChi;
194    double chi;
156 –  double eta;
195    double NkBT;
196 +  double fkBT;
197  
198 <  // targetTemp, targetPressure, and tauBarostat must be set.  
198 >  double tt2, tb2;
199 >  double instaTemp, instaPress, instaVol;
200 >  double press[3][3];
201 >
202 >  int Nparticles;
203 >
204 >  double integralOfChidt;
205 >
206 >  // targetTemp, targetPressure, and tauBarostat must be set.
207    // One of qmass or tauThermostat must be set;
208  
209    double targetTemp;
# Line 167 | Line 214 | template<typename T> class NPTi : public T{ (protected
214    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
215    short int have_target_pressure;
216  
217 +  double *oldPos;
218 +  double *oldVel;
219 +  double *oldJi;
220 +
221 +  double chiTolerance;
222 +  short int have_chi_tolerance;
223 +  double posIterTolerance;
224 +  short int have_pos_iter_tolerance;
225 +  double etaTolerance;
226 +  short int have_eta_tolerance;
227 +
228   };
229  
230 < template<typename T> class NPTim : public T{
230 > template<typename T> class NPTi : public T{
231  
232   public:
233 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
234 +  ~NPTi();
235  
236 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
237 <  virtual ~NPTim() {};
238 <
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 <
236 >  virtual double getConservedQuantity(void);
237 >  virtual void resetIntegrator(void);
238 >  virtual string getAdditionalParameters(void);
239   protected:
240  
191 –  virtual void moveA( void );
192 –  virtual void moveB( void );
241  
194 –  virtual int readyCheck();
242  
243 <  virtual void resetIntegrator( void );
243 >  virtual void evolveEtaA(void);
244 >  virtual void evolveEtaB(void);
245  
246 <  Molecule* myMolecules;
199 <  Atom** myAtoms;
246 >  virtual bool etaConverged( void );
247  
248 <  // chi and eta are the propagated degrees of freedom
248 >  virtual void scaleSimBox( void );
249  
250 <  double chi;
251 <  double eta;
252 <  double NkBT;
250 >  virtual void getVelScaleA( double sc[3], double vel[3] );
251 >  virtual void getVelScaleB( double sc[3], int index );
252 >  virtual void getPosScale(double pos[3], double COM[3],
253 >                           int index, double sc[3]);
254  
255 <  // targetTemp, targetPressure, and tauBarostat must be set.  
208 <  // One of qmass or tauThermostat must be set;
209 <
210 <  double targetTemp;
211 <  double targetPressure;
212 <  double tauThermostat;
213 <  double tauBarostat;
214 <
215 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
216 <  short int have_target_pressure;
217 <
255 >  double eta, oldEta, prevEta;
256   };
257  
258   template<typename T> class NPTf : public T{
# Line 222 | Line 260 | template<typename T> class NPTf : public T{ (public)
260   public:
261  
262    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
263 <  virtual ~NPTf() {};
263 >  virtual ~NPTf();
264  
265 <  virtual void integrateStep( int calcPot, int calcStress ){
266 <    calcStress = 1;
267 <    T::integrateStep( calcPot, calcStress );
230 <  }
265 >  virtual double getConservedQuantity(void);
266 >  virtual string getAdditionalParameters(void);
267 >  virtual void resetIntegrator(void);
268  
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 –
269   protected:
270  
271 <  virtual void  moveA( void );
272 <  virtual void moveB( void );
271 >  virtual void evolveEtaA(void);
272 >  virtual void evolveEtaB(void);
273  
274 <  virtual void resetIntegrator( void );
274 >  virtual bool etaConverged( void );
275  
276 <  virtual int readyCheck();
276 >  virtual void scaleSimBox( void );
277  
278 <  // chi and eta are the propagated degrees of freedom
278 >  virtual void getVelScaleA( double sc[3], double vel[3] );
279 >  virtual void getVelScaleB( double sc[3], int index );
280 >  virtual void getPosScale(double pos[3], double COM[3],
281 >                           int index, double sc[3]);
282  
248 –  double chi;
283    double eta[3][3];
284 <  double NkBT;
285 <
252 <  // targetTemp, targetPressure, and tauBarostat must be set.  
253 <  // One of qmass or tauThermostat must be set;
254 <
255 <  double targetTemp;
256 <  double targetPressure;
257 <  double tauThermostat;
258 <  double tauBarostat;
259 <
260 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
261 <  short int have_target_pressure;
262 <
284 >  double oldEta[3][3];
285 >  double prevEta[3][3];
286   };
287  
288 < template<typename T> class NPTfm : public T{
288 > template<typename T> class NPTxyz : public T{
289  
290   public:
291  
292 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
293 <  virtual ~NPTfm() {};
292 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
293 >  virtual ~NPTxyz();
294  
295 <  virtual void integrateStep( int calcPot, int calcStress ){
296 <    calcStress = 1;
297 <    T::integrateStep( calcPot, calcStress );
275 <  }
295 >  virtual double getConservedQuantity(void);
296 >  virtual string getAdditionalParameters(void);
297 >  virtual void resetIntegrator(void);
298  
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 –
299   protected:
300  
301 <  virtual void  moveA( void );
302 <  virtual void moveB( void );
301 >  virtual void evolveEtaA(void);
302 >  virtual void evolveEtaB(void);
303  
304 <  virtual void resetIntegrator( void );
304 >  virtual bool etaConverged( void );
305  
306 <  virtual int readyCheck();
306 >  virtual void scaleSimBox( void );
307  
308 <  Molecule* myMolecules;
309 <  Atom** myAtoms;
308 >  virtual void getVelScaleA( double sc[3], double vel[3] );
309 >  virtual void getVelScaleB( double sc[3], int index );
310 >  virtual void getPosScale(double pos[3], double COM[3],
311 >                           int index, double sc[3]);
312  
294 –  // chi and eta are the propagated degrees of freedom
295 –
296 –  double chi;
313    double eta[3][3];
314 <  double NkBT;
315 <
300 <  // 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 <
314 >  double oldEta[3][3];
315 >  double prevEta[3][3];
316   };
317  
318  
314 – template<typename T> class NPTpr : public T{
315 –
316 – public:
317 –
318 –  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
319 –  virtual ~NPTpr() {};
320 –
321 –  virtual void integrateStep( int calcPot, int calcStress ){
322 –    calcStress = 1;
323 –    T::integrateStep( calcPot, calcStress );
324 –  }
325 –
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 –
331 – protected:
332 –
333 –  virtual void  moveA( void );
334 –  virtual void moveB( void );
335 –
336 –  virtual int readyCheck();
337 –
338 –  virtual void resetIntegrator( void );
339 –
340 –  // chi and eta are the propagated degrees of freedom
341 –
342 –  double chi;
343 –  double eta[3][3];
344 –  double NkBT;
345 –
346 –  // targetTemp, targetPressure, and tauBarostat must be set.  
347 –  // One of qmass or tauThermostat must be set;
348 –
349 –  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 –
357 – };
358 –
359 –
319   template<typename T> class ZConstraint : public T {
320 <  
321 <  public:
320 >
321 >  public:
322    class ForceSubtractionPolicy{
323      public:
324        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
325  
326 <      virtual void update() = 0;    
326 >      virtual void update() = 0;
327        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
328        virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
329        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
330        virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
331 <    
331 >
332     protected:
333 <     ZConstraint<T>* zconsIntegrator;;
333 >     ZConstraint<T>* zconsIntegrator;
334    };
335  
336    class PolicyByNumber : public ForceSubtractionPolicy{
337  
338      public:
339 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
340 <      virtual void update();    
339 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
340 >      virtual void update();
341        virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
342        virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
343        virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
344        virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
345 <    
345 >
346      private:
347 <    int totNumOfMovingAtoms;
347 >      int totNumOfMovingAtoms;
348    };
349  
350    class PolicyByMass : public ForceSubtractionPolicy{
351  
352      public:
353 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
354 <      
355 <      virtual void update();    
353 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
354 >
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);
# Line 407 | Line 366 | template<typename T> class ZConstraint : public T { (p
366  
367    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
368    ~ZConstraint();
369 <    
369 >
370    void setZConsTime(double time)                  {this->zconsTime = time;}
371    void getZConsTime()                             {return zconsTime;}
372 <  
372 >
373    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
374    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
375 <  
375 >
376    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
377    string getZConsOutput()                         {return zconsOutput;}
378 <  
378 >
379    virtual void integrate();
421 –  
380  
381 +
382   #ifdef IS_MPI
383    virtual void update();                      //which is called to indicate the molecules' migration
384   #endif
385  
386 +  enum ZConsState {zcsMoving, zcsFixed};
387 +
388 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
389 +  vector<ZConsState> states;                 //state of z-constraint molecules
390 +
391 +
392 +
393 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
394 +  double totalMassOfUncons;                //total mas of unconstraint molecules
395 +
396 +
397   protected:
398  
399 <  enum ZConsState {zcsMoving, zcsFixed};  
400 <
401 <  virtual void calcForce( int calcPot, int calcStress );
399 >
400 >
401 >  virtual void calcForce( int calcPot, int calcStress );
402    virtual void thermalize(void);
403 <  
403 >
404    void zeroOutVel();
405    void doZconstraintForce();
406    void doHarmonic();
# Line 448 | Line 418 | template<typename T> class ZConstraint : public T { (p
418    double zconsTol;                                 //tolerance of z-contratint
419    double zForceConst;                           //base force constant term
420                                                            //which is estimate by OOPSE
421 <  
422 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
423 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
421 >
422 >
423 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
424    vector<double> kz;                              //force constant array
425 <  vector<ZConsState> states;                 //state of z-constraint molecules
425 >
426    vector<double> zPos;                          //
427 <  
428 <  
427 >
428 >
429    vector<Molecule*> unconsMols;           //unconstraint molecules array
430    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
461 –  double totalMassOfUncons;                //total mas of unconstraint molecules
431  
432 +
433    vector<ZConsParaItem>* parameters; //
434 <  
434 >
435    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
436  
437 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
437 >  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
438    double* fz;
439    double* curZPos;
470 –  
471 –  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
440  
441 <  int whichDirection;                           //constraint direction
442 <  
441 >
442 >
443 >  int whichDirection;                           //constraint direction
444 >
445   private:
446 <  
446 >
447    string zconsOutput;                         //filename of zconstraint output
448    ZConsWriter* fzOut;                         //z-constraint writer
449  
450 <  double curZconsTime;                      
450 >  double curZconsTime;
451  
452    double calcMovingMolsCOMVel();
453    double calcSysCOMVel();
454    double calcTotalForce();
455 <  
455 >
456    ForceSubtractionPolicy* forcePolicy; //force subtraction policy
457    friend class ForceSubtractionPolicy;
458  

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