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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 682 by tim, Tue Aug 12 17:51:33 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 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( StuntDouble* sd, 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
57 +  vector<StuntDouble*> integrableObjects;
58    int nAtoms;  /* the number of atoms */
59    int oldAtoms;
60    Atom **atoms; /* array of atom pointers */
# Line 56 | Line 62 | template<typename T = BaseIntegrator> class Integrator
62    int nMols;
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 <  
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 >
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 84 | 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 93 | 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 105 | Line 114 | template<typename T> class NVT : public T { (public)
114  
115    virtual int readyCheck();
116  
117 +  virtual void resetIntegrator( void );
118 +
119    // chi is a propagated degree of freedom.
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 144 | Line 173 | template<typename T> class NPTi : public T{ (protected
173  
174    virtual int readyCheck();
175  
176 <  // chi and eta are the propagated degrees of freedom
176 >  virtual void resetIntegrator( void );
177  
178 <  double chi;
179 <  double eta;
180 <  double NkBT;
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 <  // targetTemp, targetPressure, and tauBarostat must be set.  
154 <  // One of qmass or tauThermostat must be set;
183 >  virtual void calcVelScale( void ) = 0;
184  
185 <  double targetTemp;
186 <  double targetPressure;
158 <  double tauThermostat;
159 <  double tauBarostat;
185 >  virtual bool chiConverged( void );
186 >  virtual bool etaConverged( void ) = 0;
187  
188 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
189 <  short int have_target_pressure;
188 >  virtual void evolveChiA( void );
189 >  virtual void evolveEtaA( void ) = 0;
190 >  virtual void evolveChiB( void );
191 >  virtual void evolveEtaB( void ) = 0;
192  
193 < };
193 >  virtual void scaleSimBox( void ) = 0;
194  
195 < template<typename T> class NPTim : public T{
167 <
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;
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;
196 –  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 207 | Line 221 | template<typename T> class NPTim : public T{ (protecte
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 NPTf : public T{
237 > template<typename T> class NPTi : public T{
238  
239   public:
240 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
241 +  ~NPTi();
242  
243 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
244 <  virtual ~NPTf() {};
243 >  virtual double getConservedQuantity(void);
244 >  virtual void resetIntegrator(void);
245 >  virtual string getAdditionalParameters(void);
246 > protected:
247  
219 –  virtual void integrateStep( int calcPot, int calcStress ){
220 –    calcStress = 1;
221 –    T::integrateStep( calcPot, calcStress );
222 –  }
248  
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;}
249  
250 < protected:
250 >  virtual void evolveEtaA(void);
251 >  virtual void evolveEtaB(void);
252  
253 <  virtual void  moveA( void );
232 <  virtual void moveB( void );
253 >  virtual bool etaConverged( void );
254  
255 <  virtual int readyCheck();
255 >  virtual void scaleSimBox( void );
256  
257 <  // chi and eta are the propagated degrees of freedom
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 <  double chi;
239 <  double eta[3][3];
240 <  double NkBT;
262 >  virtual void calcVelScale( void );
263  
264 <  // targetTemp, targetPressure, and tauBarostat must be set.  
265 <  // One of qmass or tauThermostat must be set;
264 >  double eta, oldEta, prevEta;
265 >  double vScale;
266 > };
267  
268 <  double targetTemp;
246 <  double targetPressure;
247 <  double tauThermostat;
248 <  double tauBarostat;
268 > template<typename T> class NPTf : public T{
269  
270 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
251 <  short int have_target_pressure;
270 > public:
271  
272 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
273 +  virtual ~NPTf();
274 +
275 +  virtual double getConservedQuantity(void);
276 +  virtual string getAdditionalParameters(void);
277 +  virtual void resetIntegrator(void);
278 +
279 + protected:
280 +
281 +  virtual void evolveEtaA(void);
282 +  virtual void evolveEtaB(void);
283 +
284 +  virtual bool etaConverged( void );
285 +
286 +  virtual void scaleSimBox( void );
287 +
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 +  virtual void calcVelScale( void );
294 +
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 NPTfm : public T{
301 > template<typename T> class NPTxyz : public T{
302  
303   public:
304  
305 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
306 <  virtual ~NPTfm() {};
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 );
265 <  }
266 <
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;}
308 >  virtual double getConservedQuantity(void);
309 >  virtual string getAdditionalParameters(void);
310 >  virtual void resetIntegrator(void);
311  
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 <  Molecule* myMolecules;
280 <  Atom** myAtoms;
319 >  virtual void scaleSimBox( void );
320  
321 <  // chi and eta are the propagated degrees of freedom
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 <  double chi;
326 >  virtual void calcVelScale( void );
327 >
328    double eta[3][3];
329 <  double NkBT;
329 >  double oldEta[3][3];
330 >  double prevEta[3][3];
331 >  double vScale[3][3];
332 > };
333  
288 –  // targetTemp, targetPressure, and tauBarostat must be set.  
289 –  // One of qmass or tauThermostat must be set;
334  
335 <  double targetTemp;
292 <  double targetPressure;
293 <  double tauThermostat;
294 <  double tauBarostat;
335 > template<typename T> class ZConstraint : public T {
336  
337 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
338 <  short int have_target_pressure;
337 >  public:
338 >  class ForceSubtractionPolicy{
339 >    public:
340 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
341  
342 < };
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  
348 < template<typename T> class ZConstraint : public T {
348 >   protected:
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();
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 +
362 +    private:
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();
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);
375 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
376 +
377 +   private:
378 +     double totMassOfMovingAtoms;
379 +  };
380 +
381   public:
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 <  
389 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
390 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
391 <  
392 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
388 >
389 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
390 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
391 >
392 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
393    string getZConsOutput()                         {return zconsOutput;}
394 <  
394 >
395    virtual void integrate();
318 –  
396  
397 +
398   #ifdef IS_MPI
399 <  virtual void update(); //which is called to indicate the molecules' migration
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  
326 –  enum ZConsState {zcsMoving, zcsFixed};
415  
416  
417 <
330 <  virtual void calcForce( int calcPot, int calcStress );
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 343 | Line 430 | template<typename T> class ZConstraint : public T { (p
430    int isZConstraintMol(Molecule* mol);
431  
432  
433 <  double zconsTime;
434 <  double zconsTol;
435 <  double zForceConst;
436 <  
350 <  vector<Molecule*> zconsMols;
351 <  vector<double> massOfZConsMols;
352 <  vector<double> kz;
353 <  vector<ZConsState> states;
354 <  vector<double> zPos;
355 <  
356 <  
357 <  vector<Molecule*> unconsMols;
358 <  vector<double> massOfUnconsMols;
359 <  double totalMassOfUncons;
433 >  double zconsTime;                              //sample time
434 >  double zconsTol;                                 //tolerance of z-contratint
435 >  double zForceConst;                           //base force constant term
436 >                                                          //which is estimate by OOPSE
437  
438 <  vector<ZConsParaItem>* parameters;
439 <  
438 >
439 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
440 >  vector<double> kz;                              //force constant array
441 >
442 >  vector<double> zPos;                          //
443 >
444 >
445 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
446 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
447 >
448 >
449 >  vector<ZConsParaItem>* parameters; //
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 <  
368 <  int totNumOfUnconsAtoms;
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:
373 –  
374 –  string zconsOutput;
375 –  ZConsWriter* fzOut;
469  
470 +  string zconsOutput;                         //filename of zconstraint output
471 +  ZConsWriter* fzOut;                         //z-constraint writer
472  
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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