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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 423 by mmeineke, Thu Mar 27 20:12:15 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 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  
17 < class Verlet : public Integrator {
17 > using namespace std;
18 > const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
19 > const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
20 > const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
21 > const int maxIteration = 300;
22 > const double tol = 1.0e-6;
23  
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27 <  Verlet( SimInfo &info, ForceFields* the_ff );
28 <  ~Verlet();
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  
33 < private:
18 <  
19 <  void move_a( double dt );
20 <  void move_b( double dt );
33 > protected:
34  
35 +  virtual void integrateStep( int calcPot, int calcStress );
36 +  virtual void preMove( void );
37 +  virtual void moveA( void );
38 +  virtual void moveB( void );
39 +  virtual void constrainA( void );
40 +  virtual void constrainB( void );
41 +  virtual int  readyCheck( void ) { return 1; }
42 +
43 +  virtual void resetIntegrator( void ) { }
44 +
45 +  virtual void calcForce( int calcPot, int calcStress );
46 +  virtual void thermalize();
47 +
48 +  virtual bool stopIntegrator() {return false;}
49 +
50 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
51 +
52 +  void checkConstraints( void );
53 +  void rotate( int axes1, int axes2, double angle, double j[3],
54 +         double A[3][3] );
55 +
56    ForceFields* myFF;
57  
58 <  SimInfo *entry_plug; // all the info we'll ever need
59 <  int c_natoms;  /* the number of atoms */
60 <  Atom **c_atoms; /* array of atom pointers */
58 >  SimInfo *info; // all the info we'll ever need
59 >  vector<StuntDouble*> integrableObjects;
60 >  int nAtoms;  /* the number of atoms */
61 >  int oldAtoms;
62 >  Atom **atoms; /* array of atom pointers */
63    Molecule* molecules;
64    int nMols;
65  
66 <  int c_is_constrained; /*boolean to know whether the systems contains
67 <                          constraints. */
68 <  int c_n_constrained; /*counter for number of constraints */
69 <  int *c_constrained_i; /* the i of a constraint pair */
70 <  int *c_constrained_j; /* the j of a constraint pair */
71 <  double *c_constrained_dsqr; /* the square of the constraint distance */
72 <  double *c_mass; /* the array of masses */
73 <  short is_first; /*boolean for the first time integrate is called */
74 <  double c_box_x;
75 <  double c_box_y;
76 <  double c_box_z;
66 >  int isConstrained; // boolean to know whether the systems contains
67 >         // constraints.
68 >  int nConstrained;  // counter for number of constraints
69 >  int *constrainedA; // the i of a constraint pair
70 >  int *constrainedB; // the j of a constraint pair
71 >  double *constrainedDsqr; // the square of the constraint distance
72 >
73 >  int* moving; // tells whether we are moving atom i
74 >  int* moved;  // tells whether we have moved atom i
75 >  double* oldPos; // pre constrained positions
76 >
77 >  short isFirst; /*boolean for the first time integrate is called */
78 >
79 >  double dt;
80 >  double dt2;
81 >
82 >  Thermo *tStats;
83 >  StatWriter*  statOut;
84 >  DumpWriter*  dumpOut;
85 >
86   };
87  
88 < class Symplectic : public Integrator {
89 <  
88 > typedef Integrator<BaseIntegrator> RealIntegrator;
89 >
90 > template<typename T> class NVE : public T {
91 >
92   public:
93 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
94 <  ~Symplectic();
93 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
94 >    T( theInfo, the_ff ){}
95 >  virtual ~NVE(){}
96 > };
97 >
98 >
99 > template<typename T> class NVT : public T {
100 >
101 > public:
102 >
103 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
104 >  virtual ~NVT();
105 >
106 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
107 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
108 >  void setChiTolerance(double tol) {chiTolerance = tol;}
109 >  virtual double  getConservedQuantity(void);
110 >  virtual string getAdditionalParameters(void);
111 >
112 > protected:
113 >
114 >  virtual void moveA( void );
115 >  virtual void moveB( void );
116 >
117 >  virtual int readyCheck();
118 >
119 >  virtual void resetIntegrator( void );
120 >
121 >  // chi is a propagated degree of freedom.
122 >
123 >  double chi;
124 >
125 >  //integral of chi(t)dt
126 >  double integralOfChidt;
127 >
128 >  // targetTemp must be set.  tauThermostat must also be set;
129 >
130 >  double targetTemp;
131 >  double tauThermostat;
132 >
133 >  short int have_tau_thermostat, have_target_temp;
134 >
135 >  double *oldVel;
136 >  double *oldJi;
137 >
138 >  double chiTolerance;
139 >  short int have_chi_tolerance;
140 >
141 > };
142 >
143 >
144 >
145 > template<typename T> class NPT : public T{
146 >
147 > public:
148 >
149 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
150 >  virtual ~NPT();
151 >
152 >  virtual void integrateStep( int calcPot, int calcStress ){
153 >    calcStress = 1;
154 >    T::integrateStep( calcPot, calcStress );
155 >  }
156 >
157 >  virtual double getConservedQuantity(void) = 0;
158 >  virtual string getAdditionalParameters(void) = 0;
159    
160 <  void integrate( void );
160 >  double myTauThermo( void ) { return tauThermostat; }
161 >  double myTauBaro( void ) { return tauBarostat; }
162  
163 < private:
163 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
164 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
165 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
166 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
167 >  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
168 >  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
169 >  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
170  
171 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 <               double A[3][3] );
171 > protected:
172  
173 <  SimInfo* entry_plug;
174 <  ForceFields* myFF;
173 >  virtual void  moveA( void );
174 >  virtual void moveB( void );
175  
176 <  Molecule* molecules;
60 <  int nMols;
176 >  virtual int readyCheck();
177  
178 <  int is_constrained; /*boolean to know whether the systems contains
63 <                          constraints. */
64 <  int n_constrained; /*counter for number of constraints */
65 <  int *constrained_i; /* the i of a constraint pair */
66 <  int *constrained_j; /* the j of a constraint pair */
67 <  double *constrained_dsqr; /* the square of the constraint distance */
68 <  double *mass; /* the array of masses */
178 >  virtual void resetIntegrator( void );
179  
180 <  short int isFirst;
180 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
181 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
182 >  virtual void getPosScale(double pos[3], double COM[3],
183 >                           int index, double sc[3]) = 0;
184  
185 <  SRI **srInteractions; /* array of SRI pointers */
186 <  int nSRI; /* the number of short range interactions */
185 >  virtual void calcVelScale( void ) = 0;
186 >
187 >  virtual bool chiConverged( void );
188 >  virtual bool etaConverged( void ) = 0;
189 >
190 >  virtual void evolveChiA( void );
191 >  virtual void evolveEtaA( void ) = 0;
192 >  virtual void evolveChiB( void );
193 >  virtual void evolveEtaB( void ) = 0;
194 >
195 >  virtual void scaleSimBox( void ) = 0;
196 >
197 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
198 >
199 >  // chi and eta are the propagated degrees of freedom
200 >
201 >  double oldChi;
202 >  double prevChi;
203 >  double chi;
204 >  double NkBT;
205 >  double fkBT;
206 >
207 >  double tt2, tb2;
208 >  double instaTemp, instaPress, instaVol;
209 >  double press[3][3];
210 >
211 >  int Nparticles;
212 >
213 >  double integralOfChidt;
214 >
215 >  // targetTemp, targetPressure, and tauBarostat must be set.
216 >  // One of qmass or tauThermostat must be set;
217 >
218 >  double targetTemp;
219 >  double targetPressure;
220 >  double tauThermostat;
221 >  double tauBarostat;
222 >
223 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
224 >  short int have_target_pressure;
225 >
226 >  double *oldPos;
227 >  double *oldVel;
228 >  double *oldJi;
229 >
230 >  double chiTolerance;
231 >  short int have_chi_tolerance;
232 >  double posIterTolerance;
233 >  short int have_pos_iter_tolerance;
234 >  double etaTolerance;
235 >  short int have_eta_tolerance;
236 >
237 > };
238 >
239 > template<typename T> class NPTi : public T{
240 >
241 > public:
242 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
243 >  ~NPTi();
244 >
245 >  virtual double getConservedQuantity(void);
246 >  virtual void resetIntegrator(void);
247 >  virtual string getAdditionalParameters(void);
248 > protected:
249 >
250 >
251 >
252 >  virtual void evolveEtaA(void);
253 >  virtual void evolveEtaB(void);
254 >
255 >  virtual bool etaConverged( void );
256 >
257 >  virtual void scaleSimBox( void );
258 >
259 >  virtual void getVelScaleA( double sc[3], double vel[3] );
260 >  virtual void getVelScaleB( double sc[3], int index );
261 >  virtual void getPosScale(double pos[3], double COM[3],
262 >                           int index, double sc[3]);
263 >
264 >  virtual void calcVelScale( void );
265 >
266 >  double eta, oldEta, prevEta;
267 >  double vScale;
268 > };
269 >
270 > template<typename T> class NPTf : public T{
271 >
272 > public:
273 >
274 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
275 >  virtual ~NPTf();
276 >
277 >  virtual double getConservedQuantity(void);
278 >  virtual string getAdditionalParameters(void);
279 >  virtual void resetIntegrator(void);
280 >
281 > protected:
282 >
283 >  virtual void evolveEtaA(void);
284 >  virtual void evolveEtaB(void);
285 >
286 >  virtual bool etaConverged( void );
287 >
288 >  virtual void scaleSimBox( void );
289 >
290 >  virtual void getVelScaleA( double sc[3], double vel[3] );
291 >  virtual void getVelScaleB( double sc[3], int index );
292 >  virtual void getPosScale(double pos[3], double COM[3],
293 >                           int index, double sc[3]);
294 >
295 >  virtual void calcVelScale( void );
296 >
297 >  double eta[3][3];
298 >  double oldEta[3][3];
299 >  double prevEta[3][3];
300 >  double vScale[3][3];
301 > };
302 >
303 > template<typename T> class NPTxyz : public T{
304 >
305 > public:
306 >
307 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
308 >  virtual ~NPTxyz();
309 >
310 >  virtual double getConservedQuantity(void);
311 >  virtual string getAdditionalParameters(void);
312 >  virtual void resetIntegrator(void);
313 >
314 > protected:
315 >
316 >  virtual void evolveEtaA(void);
317 >  virtual void evolveEtaB(void);
318 >
319 >  virtual bool etaConverged( void );
320 >
321 >  virtual void scaleSimBox( void );
322 >
323 >  virtual void getVelScaleA( double sc[3], double vel[3] );
324 >  virtual void getVelScaleB( double sc[3], int index );
325 >  virtual void getPosScale(double pos[3], double COM[3],
326 >                           int index, double sc[3]);
327 >
328 >  virtual void calcVelScale( void );
329 >
330 >  double eta[3][3];
331 >  double oldEta[3][3];
332 >  double prevEta[3][3];
333 >  double vScale[3][3];
334 > };
335 >
336 >
337 > template<typename T> class ZConstraint : public T {
338 >
339 >  public:
340 >  class ForceSubtractionPolicy{
341 >    public:
342 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
343 >
344 >      virtual void update() = 0;
345 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
346 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
347 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
348 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
349 >
350 >   protected:
351 >     ZConstraint<T>* zconsIntegrator;
352 >  };
353 >
354 >  class PolicyByNumber : public ForceSubtractionPolicy{
355 >
356 >    public:
357 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
358 >      virtual void update();
359 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
360 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
361 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
362 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
363 >
364 >    private:
365 >      int totNumOfMovingAtoms;
366 >  };
367 >
368 >  class PolicyByMass : public ForceSubtractionPolicy{
369 >
370 >    public:
371 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
372 >
373 >      virtual void update();
374 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
375 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
376 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
377 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
378 >
379 >   private:
380 >     double totMassOfMovingAtoms;
381 >  };
382 >
383 > public:
384 >
385 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
386 >  ~ZConstraint();
387 >
388 >  void setZConsTime(double time)                  {this->zconsTime = time;}
389 >  void getZConsTime()                             {return zconsTime;}
390 >
391 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
392 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
393 >
394 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
395 >  string getZConsOutput()                         {return zconsOutput;}
396 >
397 >  virtual void integrate();
398 >
399 >
400 > #ifdef IS_MPI
401 >  virtual void update();                      //which is called to indicate the molecules' migration
402 > #endif
403 >
404 >  enum ZConsState {zcsMoving, zcsFixed};
405 >
406 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
407 >  vector<ZConsState> states;                 //state of z-constraint molecules
408 >
409 >
410 >
411 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
412 >  double totalMassOfUncons;                //total mas of unconstraint molecules
413 >
414 >
415 > protected:
416 >
417 >
418 >
419 >  virtual void calcForce( int calcPot, int calcStress );
420 >  virtual void thermalize(void);
421 >
422 >  void zeroOutVel();
423 >  void doZconstraintForce();
424 >  void doHarmonic(vector<double>& resPos);
425 >  bool checkZConsState();
426 >
427 >  bool haveFixedZMols();
428 >  bool haveMovingZMols();
429 >
430 >  double calcZSys();
431 >
432 >  int isZConstraintMol(Molecule* mol);
433 >
434 >
435 >  double zconsTime;                              //sample time
436 >  double zconsTol;                                 //tolerance of z-contratint
437 >  double zForceConst;                           //base force constant term
438 >                                                          //which is estimate by OOPSE
439 >
440 >
441 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
442 >  vector<double> kz;                              //force constant array
443 >
444 >  vector<double> zPos;                          //
445 >
446 >
447 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
448 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
449 >
450 >
451 >  vector<ZConsParaItem>* parameters; //
452 >
453 >  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
454 >
455 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
456 >  vector<double> fz;
457 >  vector<double> curZPos;
458 >
459 >  bool usingSMD;
460 >  vector<double> cantPos;
461 >  vector<double> cantVel;
462 >
463 >  double zconsFixTime;  
464 >  double zconsGap;
465 >  bool hasZConsGap;
466 >  vector<double> endFixTime;
467    
468 +  int whichDirection;                           //constraint direction
469 +
470 + private:
471 +
472 +  string zconsOutput;                         //filename of zconstraint output
473 +  ZConsWriter* fzOut;                         //z-constraint writer
474 +
475 +  double curZconsTime;
476 +
477 +  double calcMovingMolsCOMVel();
478 +  double calcSysCOMVel();
479 +  double calcTotalForce();
480 +  void updateZPos();
481 +  void updateCantPos();
482 +  
483 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
484 +  friend class ForceSubtractionPolicy;
485 +
486   };
487  
488 + /*
489 + template<typename T> class SingleZConstrain : public T{
490 +
491 +
492 + };
493 + */
494 +
495 + template<typename T> class NonEquMD : public T {
496 +  public:
497 +    
498 +
499 +
500 + };
501 +
502 +
503 + //
504 + template<typename T> class SingleZConstraint : public T{
505 +  public:
506 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
507 +    ~SingleZConstraint();
508 +    
509 +    bool stopIntegrator();
510 +    
511 +  protected:
512 +    
513 + };
514 +
515 + //Steered Molecular Dynamics, curret implement only support one steered molecule
516 + template<typename T> class SMD : public T{
517 +  public:
518 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
519 +    ~SMD();
520 +  
521 +    virtual void integrate();
522 +    virtual void calcForce( int calcPot, int calcStress );  
523 +    bool stopIntegrator();
524 +  private:
525 +    
526 + };
527 +
528 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
529 + //Driven Molecular Dynamics and ZConstraint Method.
530 + template<typename T> class CoordinateDriver : public T {
531 +  public:
532 +    typedef T ParentIntegrator;
533 +
534 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
535 +    ~CoordinateDriver();
536 +    
537 +    virtual void integrate();
538 +
539 +  private:    
540 +    BaseIntegrator* zconsIntegrator;
541 +    BaseIntegrator* drivenIntegrator;
542 +    
543 + };
544 +
545   #endif

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