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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 596 by gezelter, Mon Jul 14 15:04:55 2003 UTC vs.
Revision 1180 by chrisfen, Thu May 20 20:24:07 2004 UTC

# Line 1 | Line 1
1   #ifndef _INTEGRATOR_H_
2   #define _INTEGRATOR_H_
3  
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"
11   #include "SimInfo.hpp"
12   #include "ForceFields.hpp"
13   #include "Thermo.hpp"
14   #include "ReadWrite.hpp"
15 + #include "ZConsWriter.hpp"
16 + #include "Restraints.hpp"
17  
18 + using namespace std;
19   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
20   const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
21   const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
25 < class Integrator : public BaseIntegrator {
25 > template<typename T = BaseIntegrator> class Integrator : public T {
26  
27   public:
28    Integrator( SimInfo *theInfo, ForceFields* the_ff );
29    virtual ~Integrator();
30    void integrate( void );
31 +  virtual double  getConservedQuantity(void);
32 +  virtual string getAdditionalParameters(void);
33  
25 –
34   protected:
35 <  
35 >
36    virtual void integrateStep( int calcPot, int calcStress );
37    virtual void preMove( void );
38    virtual void moveA( void );
# Line 32 | Line 40 | class Integrator : public BaseIntegrator { (protected)
40    virtual void constrainA( void );
41    virtual void constrainB( void );
42    virtual int  readyCheck( void ) { return 1; }
35 –  
36 –  void checkConstraints( void );
37 –  void rotate( int axes1, int axes2, double angle, double j[3],
38 –               double A[3][3] );
43  
44 +  virtual void resetIntegrator( void ) { }
45  
46 +  virtual void calcForce( int calcPot, int calcStress );
47 +  virtual void thermalize();
48 +
49 +  virtual bool stopIntegrator() {return false;}
50 +
51 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
52 +
53 +  void checkConstraints( void );
54 +  void rotate( int axes1, int axes2, double angle, double j[3],
55 +         double A[3][3] );
56 +
57    ForceFields* myFF;
58  
59    SimInfo *info; // all the info we'll ever need
60 +  vector<StuntDouble*> integrableObjects;
61    int nAtoms;  /* the number of atoms */
62    int oldAtoms;
63    Atom **atoms; /* array of atom pointers */
# Line 48 | Line 65 | class Integrator : public BaseIntegrator { (protected)
65    int nMols;
66  
67    int isConstrained; // boolean to know whether the systems contains
68 <                     // constraints.
69 <  int nConstrained;  // counter for number of constraints
70 <  int *constrainedA; // the i of a constraint pair
71 <  int *constrainedB; // the j of a constraint pair
72 <  double *constrainedDsqr; // the square of the constraint distance
73 <  
68 >         // constraints.
69 >  int nConstrained;  // counter for number of constraints
70 >  int *constrainedA; // the i of a constraint pair
71 >  int *constrainedB; // the j of a constraint pair
72 >  double *constrainedDsqr; // the square of the constraint distance
73 >
74    int* moving; // tells whether we are moving atom i
75    int* moved;  // tells whether we have moved atom i
76 <  double* oldPos; // pre constrained positions
76 >  double* oldPos; // pre constrained positions
77  
78    short isFirst; /*boolean for the first time integrate is called */
79 <  
79 >
80    double dt;
81    double dt2;
82  
66 –  double* pos;
67 –  double* vel;
68 –  double* frc;
69 –  double* trq;
70 –  double* Amat;
71 –
83    Thermo *tStats;
84    StatWriter*  statOut;
85    DumpWriter*  dumpOut;
86 <  
86 >
87 >  int i; // just an int
88   };
89  
90 < class NVE : public Integrator{
90 > typedef Integrator<BaseIntegrator> RealIntegrator;
91  
92 + // ansi instantiation
93 + template class Integrator<BaseIntegrator>;
94 +
95 + template<typename T> class NVE : public T {
96 +
97   public:
98    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
99 <    Integrator( theInfo, the_ff ){}
99 >    T( theInfo, the_ff ){}
100    virtual ~NVE(){}
84 –
85 –  
86 –
101   };
102  
89 – class NVT : public Integrator{
103  
104 + template<typename T> class NVT : public T {
105 +
106   public:
107  
108    NVT ( SimInfo *theInfo, ForceFields* the_ff);
109 <  virtual ~NVT() {}
109 >  virtual ~NVT();
110  
111    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
112    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
113 +  void setChiTolerance(double tol) {chiTolerance = tol;}
114 +  virtual double  getConservedQuantity(void);
115 +  virtual string getAdditionalParameters(void);
116  
117   protected:
118  
# Line 103 | Line 121 | class NVT : public Integrator{ (protected)
121  
122    virtual int readyCheck();
123  
124 +  virtual void resetIntegrator( void );
125 +
126    // chi is a propagated degree of freedom.
127  
128    double chi;
129  
130 +  //integral of chi(t)dt
131 +  double integralOfChidt;
132 +
133    // targetTemp must be set.  tauThermostat must also be set;
134  
135    double targetTemp;
136    double tauThermostat;
137 <  
137 >
138    short int have_tau_thermostat, have_target_temp;
139  
140 +  double *oldVel;
141 +  double *oldJi;
142 +
143 +  double chiTolerance;
144 +  short int have_chi_tolerance;
145 +
146   };
147  
148  
120 – class NPTi : public Integrator{
149  
150 + template<typename T> class NPT : public T{
151 +
152   public:
153  
154 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
155 <  virtual ~NPTi() {};
154 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
155 >  virtual ~NPT();
156  
157    virtual void integrateStep( int calcPot, int calcStress ){
158      calcStress = 1;
159 <    Integrator::integrateStep( calcPot, calcStress );
159 >    T::integrateStep( calcPot, calcStress );
160    }
161  
162 +  virtual double getConservedQuantity(void) = 0;
163 +  virtual string getAdditionalParameters(void) = 0;
164 +  
165 +  double myTauThermo( void ) { return tauThermostat; }
166 +  double myTauBaro( void ) { return tauBarostat; }
167 +
168    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
169    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
170    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
171    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
172 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
173 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
174 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
175  
176   protected:
177  
# Line 141 | Line 180 | class NPTi : public Integrator{ (protected)
180  
181    virtual int readyCheck();
182  
183 +  virtual void resetIntegrator( void );
184 +
185 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
186 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
187 +  virtual void getPosScale(double pos[3], double COM[3],
188 +                           int index, double sc[3]) = 0;
189 +
190 +  virtual void calcVelScale( void ) = 0;
191 +
192 +  virtual bool chiConverged( void );
193 +  virtual bool etaConverged( void ) = 0;
194 +
195 +  virtual void evolveChiA( void );
196 +  virtual void evolveEtaA( void ) = 0;
197 +  virtual void evolveChiB( void );
198 +  virtual void evolveEtaB( void ) = 0;
199 +
200 +  virtual void scaleSimBox( void ) = 0;
201 +
202 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
203 +
204    // chi and eta are the propagated degrees of freedom
205  
206 +  double oldChi;
207 +  double prevChi;
208    double chi;
147 –  double eta;
209    double NkBT;
210 +  double fkBT;
211  
212 <  // targetTemp, targetPressure, and tauBarostat must be set.  
212 >  double tt2, tb2;
213 >  double instaTemp, instaPress, instaVol;
214 >  double press[3][3];
215 >
216 >  int Nparticles;
217 >
218 >  double integralOfChidt;
219 >
220 >  // targetTemp, targetPressure, and tauBarostat must be set.
221    // One of qmass or tauThermostat must be set;
222  
223    double targetTemp;
# Line 158 | Line 228 | class NPTi : public Integrator{ (protected)
228    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
229    short int have_target_pressure;
230  
231 +  double *oldPos;
232 +  double *oldVel;
233 +  double *oldJi;
234 +
235 +  double chiTolerance;
236 +  short int have_chi_tolerance;
237 +  double posIterTolerance;
238 +  short int have_pos_iter_tolerance;
239 +  double etaTolerance;
240 +  short int have_eta_tolerance;
241 +
242   };
243  
244 < class NPTim : public Integrator{
244 > template<typename T> class NPTi : public T{
245  
246   public:
247 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
248 +  ~NPTi();
249  
250 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
251 <  virtual ~NPTim() {};
252 <
170 <  virtual void integrateStep( int calcPot, int calcStress ){
171 <    calcStress = 1;
172 <    Integrator::integrateStep( calcPot, calcStress );
173 <  }
174 <
175 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
176 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
177 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
178 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
179 <
250 >  virtual double getConservedQuantity(void);
251 >  virtual void resetIntegrator(void);
252 >  virtual string getAdditionalParameters(void);
253   protected:
254  
182 –  virtual void  moveA( void );
183 –  virtual void moveB( void );
255  
185 –  virtual int readyCheck();
256  
257 <  // chi and eta are the propagated degrees of freedom
257 >  virtual void evolveEtaA(void);
258 >  virtual void evolveEtaB(void);
259  
260 <  double chi;
190 <  double eta;
191 <  double NkBT;
260 >  virtual bool etaConverged( void );
261  
262 <  // targetTemp, targetPressure, and tauBarostat must be set.  
194 <  // One of qmass or tauThermostat must be set;
262 >  virtual void scaleSimBox( void );
263  
264 <  double targetTemp;
265 <  double targetPressure;
266 <  double tauThermostat;
267 <  double tauBarostat;
264 >  virtual void getVelScaleA( double sc[3], double vel[3] );
265 >  virtual void getVelScaleB( double sc[3], int index );
266 >  virtual void getPosScale(double pos[3], double COM[3],
267 >                           int index, double sc[3]);
268  
269 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
202 <  short int have_target_pressure;
269 >  virtual void calcVelScale( void );
270  
271 +  double eta, oldEta, prevEta;
272 +  double vScale;
273   };
274  
275 < class NPTf : public Integrator{
275 > template<typename T> class NPTf : public T{
276  
277   public:
278  
279    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
280 <  virtual ~NPTf() {};
280 >  virtual ~NPTf();
281  
282 <  virtual void integrateStep( int calcPot, int calcStress ){
283 <    calcStress = 1;
284 <    Integrator::integrateStep( calcPot, calcStress );
216 <  }
282 >  virtual double getConservedQuantity(void);
283 >  virtual string getAdditionalParameters(void);
284 >  virtual void resetIntegrator(void);
285  
218 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
219 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
220 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
221 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
222 –
286   protected:
287  
288 <  virtual void  moveA( void );
289 <  virtual void moveB( void );
288 >  virtual void evolveEtaA(void);
289 >  virtual void evolveEtaB(void);
290  
291 <  virtual int readyCheck();
291 >  virtual bool etaConverged( void );
292  
293 <  // chi and eta are the propagated degrees of freedom
293 >  virtual void scaleSimBox( void );
294  
295 <  double chi;
295 >  virtual void getVelScaleA( double sc[3], double vel[3] );
296 >  virtual void getVelScaleB( double sc[3], int index );
297 >  virtual void getPosScale(double pos[3], double COM[3],
298 >                           int index, double sc[3]);
299 >
300 >  virtual void calcVelScale( void );
301 >
302    double eta[3][3];
303 <  double NkBT;
303 >  double oldEta[3][3];
304 >  double prevEta[3][3];
305 >  double vScale[3][3];
306 > };
307  
308 <  // targetTemp, targetPressure, and tauBarostat must be set.  
237 <  // One of qmass or tauThermostat must be set;
308 > template<typename T> class NPTxyz : public T{
309  
310 <  double targetTemp;
240 <  double targetPressure;
241 <  double tauThermostat;
242 <  double tauBarostat;
310 > public:
311  
312 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
313 <  short int have_target_pressure;
312 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
313 >  virtual ~NPTxyz();
314  
315 +  virtual double getConservedQuantity(void);
316 +  virtual string getAdditionalParameters(void);
317 +  virtual void resetIntegrator(void);
318 +
319 + protected:
320 +
321 +  virtual void evolveEtaA(void);
322 +  virtual void evolveEtaB(void);
323 +
324 +  virtual bool etaConverged( void );
325 +
326 +  virtual void scaleSimBox( void );
327 +
328 +  virtual void getVelScaleA( double sc[3], double vel[3] );
329 +  virtual void getVelScaleB( double sc[3], int index );
330 +  virtual void getPosScale(double pos[3], double COM[3],
331 +                           int index, double sc[3]);
332 +
333 +  virtual void calcVelScale( void );
334 +
335 +  double eta[3][3];
336 +  double oldEta[3][3];
337 +  double prevEta[3][3];
338 +  double vScale[3][3];
339   };
340  
249 – class NPTfm : public Integrator{
341  
342 + template<typename T> class ZConstraint : public T {
343 +
344 +  public:
345 +  class ForceSubtractionPolicy{
346 +    public:
347 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
348 +
349 +      virtual void update() = 0;
350 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
351 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
352 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
353 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
354 +
355 +   protected:
356 +     ZConstraint<T>* zconsIntegrator;
357 +  };
358 +
359 +  class PolicyByNumber : public ForceSubtractionPolicy{
360 +
361 +    public:
362 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
363 +      virtual void update();
364 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
365 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
366 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
367 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
368 +
369 +    private:
370 +      int totNumOfMovingAtoms;
371 +  };
372 +
373 +  class PolicyByMass : public ForceSubtractionPolicy{
374 +
375 +    public:
376 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
377 +
378 +      virtual void update();
379 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
380 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
381 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
382 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
383 +
384 +   private:
385 +     double totMassOfMovingAtoms;
386 +  };
387 +
388   public:
389  
390 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
391 <  virtual ~NPTfm() {};
390 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
391 >  ~ZConstraint();
392  
393 <  virtual void integrateStep( int calcPot, int calcStress ){
394 <    calcStress = 1;
258 <    Integrator::integrateStep( calcPot, calcStress );
259 <  }
393 >  void setZConsTime(double time)                  {this->zconsTime = time;}
394 >  void getZConsTime()                             {return zconsTime;}
395  
396 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
397 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
263 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
264 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
396 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
397 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
398  
399 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
400 +  string getZConsOutput()                         {return zconsOutput;}
401 +
402 +  virtual void integrate();
403 +
404 +
405 + #ifdef IS_MPI
406 +  virtual void update();                      //which is called to indicate the molecules' migration
407 + #endif
408 +
409 +  enum ZConsState {zcsMoving, zcsFixed};
410 +
411 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
412 +  vector<ZConsState> states;                 //state of z-constraint molecules
413 +
414 +
415 +
416 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
417 +  double totalMassOfUncons;                //total mas of unconstraint molecules
418 +
419 +
420   protected:
421  
268 –  virtual void  moveA( void );
269 –  virtual void moveB( void );
422  
271 –  virtual int readyCheck();
423  
424 <  // chi and eta are the propagated degrees of freedom
424 >  virtual void calcForce( int calcPot, int calcStress );
425 >  virtual void thermalize(void);
426  
427 <  double chi;
428 <  double eta[3][3];
429 <  double NkBT;
427 >  void zeroOutVel();
428 >  void doZconstraintForce();
429 >  void doHarmonic(vector<double>& resPos);
430 >  bool checkZConsState();
431  
432 <  // targetTemp, targetPressure, and tauBarostat must be set.  
433 <  // One of qmass or tauThermostat must be set;
432 >  bool haveFixedZMols();
433 >  bool haveMovingZMols();
434  
435 <  double targetTemp;
283 <  double targetPressure;
284 <  double tauThermostat;
285 <  double tauBarostat;
435 >  double calcZSys();
436  
437 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
288 <  short int have_target_pressure;
437 >  int isZConstraintMol(Molecule* mol);
438  
439 +
440 +  double zconsTime;                              //sample time
441 +  double zconsTol;                                 //tolerance of z-contratint
442 +  double zForceConst;                           //base force constant term
443 +                                                          //which is estimate by OOPSE
444 +
445 +
446 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
447 +  vector<double> kz;                              //force constant array
448 +
449 +  vector<double> zPos;                          //
450 +
451 +
452 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
453 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
454 +
455 +
456 +  vector<ZConsParaItem>* parameters; //
457 +
458 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
459 +
460 +  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
461 +  vector<double> fz;
462 +  vector<double> curZPos;
463 +
464 +  bool usingSMD;
465 +  vector<double> prevCantPos;
466 +  vector<double> cantPos;
467 +  vector<double> cantVel;
468 +
469 +  double zconsFixTime;  
470 +  double zconsGap;
471 +  bool hasZConsGap;
472 +  vector<double> endFixTime;
473 +  
474 +  int whichDirection;                           //constraint direction
475 +
476 + private:
477 +
478 +  string zconsOutput;                         //filename of zconstraint output
479 +  ZConsWriter* fzOut;                         //z-constraint writer
480 +
481 +  double curZconsTime;
482 +
483 +  double calcMovingMolsCOMVel();
484 +  double calcSysCOMVel();
485 +  double calcTotalForce();
486 +  void updateZPos();
487 +  void updateCantPos();
488 +  
489 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
490 +  friend class ForceSubtractionPolicy;
491 +
492   };
493  
494 + /*
495 + template<typename T> class SingleZConstrain : public T{
496 +
497 +
498 + };
499 + */
500 +
501 + template<typename T> class NonEquMD : public T {
502 +  public:
503 +    
504 +
505 +
506 + };
507 +
508 +
509 + //
510 + template<typename T> class SingleZConstraint : public T{
511 +  public:
512 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
513 +    ~SingleZConstraint();
514 +    
515 +    bool stopIntegrator();
516 +    
517 +  protected:
518 +    
519 + };
520 +
521 + //Steered Molecular Dynamics, curret implement only support one steered molecule
522 + template<typename T> class SMD : public T{
523 +  public:
524 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
525 +    ~SMD();
526 +  
527 +    virtual void integrate();
528 +    virtual void calcForce( int calcPot, int calcStress );  
529 +    bool stopIntegrator();
530 +  private:
531 +    
532 + };
533 +
534 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
535 + //Driven Molecular Dynamics and ZConstraint Method.
536 + template<typename T> class CoordinateDriver : public T {
537 +  public:
538 +    typedef T ParentIntegrator;
539 +
540 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
541 +    ~CoordinateDriver();
542 +    
543 +    virtual void integrate();
544 +
545 +  private:    
546 +    BaseIntegrator* zconsIntegrator;
547 +    BaseIntegrator* drivenIntegrator;
548 +    
549 + };
550 +
551   #endif

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