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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Integrator.hpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Integrator.hpp (file contents), Revision 1161 by tim, Tue May 11 21:44:05 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 */
61 <  SRI **c_sr_interactions; /* array of SRI pointers */
62 <  int c_n_SRI; /* the number of short range interactions */
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 > // ansi instantiation
91 > template class Integrator<BaseIntegrator>;
92 >
93 > template<typename T> class NVE : public T {
94 >
95   public:
96 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
97 <  ~Symplectic();
96 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
97 >    T( theInfo, the_ff ){}
98 >  virtual ~NVE(){}
99 > };
100 >
101 >
102 > template<typename T> class NVT : public T {
103 >
104 > public:
105 >
106 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
107 >  virtual ~NVT();
108 >
109 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
110 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
111 >  void setChiTolerance(double tol) {chiTolerance = tol;}
112 >  virtual double  getConservedQuantity(void);
113 >  virtual string getAdditionalParameters(void);
114 >
115 > protected:
116 >
117 >  virtual void moveA( void );
118 >  virtual void moveB( void );
119 >
120 >  virtual int readyCheck();
121 >
122 >  virtual void resetIntegrator( void );
123 >
124 >  // chi is a propagated degree of freedom.
125 >
126 >  double chi;
127 >
128 >  //integral of chi(t)dt
129 >  double integralOfChidt;
130 >
131 >  // targetTemp must be set.  tauThermostat must also be set;
132 >
133 >  double targetTemp;
134 >  double tauThermostat;
135 >
136 >  short int have_tau_thermostat, have_target_temp;
137 >
138 >  double *oldVel;
139 >  double *oldJi;
140 >
141 >  double chiTolerance;
142 >  short int have_chi_tolerance;
143 >
144 > };
145 >
146 >
147 >
148 > template<typename T> class NPT : public T{
149 >
150 > public:
151 >
152 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
153 >  virtual ~NPT();
154 >
155 >  virtual void integrateStep( int calcPot, int calcStress ){
156 >    calcStress = 1;
157 >    T::integrateStep( calcPot, calcStress );
158 >  }
159 >
160 >  virtual double getConservedQuantity(void) = 0;
161 >  virtual string getAdditionalParameters(void) = 0;
162    
163 <  void integrate( void );
163 >  double myTauThermo( void ) { return tauThermostat; }
164 >  double myTauBaro( void ) { return tauBarostat; }
165  
166 < private:
166 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
167 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
168 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
169 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
170 >  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
171 >  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
172 >  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
173  
174 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 <               double A[3][3] );
174 > protected:
175  
176 <  SimInfo* entry_plug;
177 <  ForceFields* myFF;
176 >  virtual void  moveA( void );
177 >  virtual void moveB( void );
178  
179 <  int is_constrained; /*boolean to know whether the systems contains
60 <                          constraints. */
61 <  int n_constrained; /*counter for number of constraints */
62 <  int *constrained_i; /* the i of a constraint pair */
63 <  int *constrained_j; /* the j of a constraint pair */
64 <  double *constrained_dsqr; /* the square of the constraint distance */
65 <  double *mass; /* the array of masses */
179 >  virtual int readyCheck();
180  
181 <  short int isFirst;
181 >  virtual void resetIntegrator( void );
182  
183 <  SRI **srInteractions; /* array of SRI pointers */
184 <  int nSRI; /* the number of short range interactions */
183 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
184 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
185 >  virtual void getPosScale(double pos[3], double COM[3],
186 >                           int index, double sc[3]) = 0;
187 >
188 >  virtual void calcVelScale( void ) = 0;
189 >
190 >  virtual bool chiConverged( void );
191 >  virtual bool etaConverged( void ) = 0;
192 >
193 >  virtual void evolveChiA( void );
194 >  virtual void evolveEtaA( void ) = 0;
195 >  virtual void evolveChiB( void );
196 >  virtual void evolveEtaB( void ) = 0;
197 >
198 >  virtual void scaleSimBox( void ) = 0;
199 >
200 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
201 >
202 >  // chi and eta are the propagated degrees of freedom
203 >
204 >  double oldChi;
205 >  double prevChi;
206 >  double chi;
207 >  double NkBT;
208 >  double fkBT;
209 >
210 >  double tt2, tb2;
211 >  double instaTemp, instaPress, instaVol;
212 >  double press[3][3];
213 >
214 >  int Nparticles;
215 >
216 >  double integralOfChidt;
217 >
218 >  // targetTemp, targetPressure, and tauBarostat must be set.
219 >  // One of qmass or tauThermostat must be set;
220 >
221 >  double targetTemp;
222 >  double targetPressure;
223 >  double tauThermostat;
224 >  double tauBarostat;
225 >
226 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
227 >  short int have_target_pressure;
228 >
229 >  double *oldPos;
230 >  double *oldVel;
231 >  double *oldJi;
232 >
233 >  double chiTolerance;
234 >  short int have_chi_tolerance;
235 >  double posIterTolerance;
236 >  short int have_pos_iter_tolerance;
237 >  double etaTolerance;
238 >  short int have_eta_tolerance;
239 >
240 > };
241 >
242 > template<typename T> class NPTi : public T{
243 >
244 > public:
245 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
246 >  ~NPTi();
247 >
248 >  virtual double getConservedQuantity(void);
249 >  virtual void resetIntegrator(void);
250 >  virtual string getAdditionalParameters(void);
251 > protected:
252 >
253 >
254 >
255 >  virtual void evolveEtaA(void);
256 >  virtual void evolveEtaB(void);
257 >
258 >  virtual bool etaConverged( void );
259 >
260 >  virtual void scaleSimBox( void );
261 >
262 >  virtual void getVelScaleA( double sc[3], double vel[3] );
263 >  virtual void getVelScaleB( double sc[3], int index );
264 >  virtual void getPosScale(double pos[3], double COM[3],
265 >                           int index, double sc[3]);
266 >
267 >  virtual void calcVelScale( void );
268 >
269 >  double eta, oldEta, prevEta;
270 >  double vScale;
271 > };
272 >
273 > template<typename T> class NPTf : public T{
274 >
275 > public:
276 >
277 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
278 >  virtual ~NPTf();
279 >
280 >  virtual double getConservedQuantity(void);
281 >  virtual string getAdditionalParameters(void);
282 >  virtual void resetIntegrator(void);
283 >
284 > protected:
285 >
286 >  virtual void evolveEtaA(void);
287 >  virtual void evolveEtaB(void);
288 >
289 >  virtual bool etaConverged( void );
290 >
291 >  virtual void scaleSimBox( void );
292 >
293 >  virtual void getVelScaleA( double sc[3], double vel[3] );
294 >  virtual void getVelScaleB( double sc[3], int index );
295 >  virtual void getPosScale(double pos[3], double COM[3],
296 >                           int index, double sc[3]);
297 >
298 >  virtual void calcVelScale( void );
299 >
300 >  double eta[3][3];
301 >  double oldEta[3][3];
302 >  double prevEta[3][3];
303 >  double vScale[3][3];
304 > };
305 >
306 > template<typename T> class NPTxyz : public T{
307 >
308 > public:
309 >
310 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
311 >  virtual ~NPTxyz();
312 >
313 >  virtual double getConservedQuantity(void);
314 >  virtual string getAdditionalParameters(void);
315 >  virtual void resetIntegrator(void);
316 >
317 > protected:
318 >
319 >  virtual void evolveEtaA(void);
320 >  virtual void evolveEtaB(void);
321 >
322 >  virtual bool etaConverged( void );
323 >
324 >  virtual void scaleSimBox( void );
325 >
326 >  virtual void getVelScaleA( double sc[3], double vel[3] );
327 >  virtual void getVelScaleB( double sc[3], int index );
328 >  virtual void getPosScale(double pos[3], double COM[3],
329 >                           int index, double sc[3]);
330 >
331 >  virtual void calcVelScale( void );
332 >
333 >  double eta[3][3];
334 >  double oldEta[3][3];
335 >  double prevEta[3][3];
336 >  double vScale[3][3];
337 > };
338 >
339 >
340 > template<typename T> class ZConstraint : public T {
341 >
342 >  public:
343 >  class ForceSubtractionPolicy{
344 >    public:
345 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
346 >
347 >      virtual void update() = 0;
348 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
349 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
350 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
351 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
352 >
353 >   protected:
354 >     ZConstraint<T>* zconsIntegrator;
355 >  };
356 >
357 >  class PolicyByNumber : public ForceSubtractionPolicy{
358 >
359 >    public:
360 >      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
361 >      virtual void update();
362 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
363 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
364 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
365 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
366 >
367 >    private:
368 >      int totNumOfMovingAtoms;
369 >  };
370 >
371 >  class PolicyByMass : public ForceSubtractionPolicy{
372 >
373 >    public:
374 >      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
375 >
376 >      virtual void update();
377 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
378 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
379 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
380 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
381 >
382 >   private:
383 >     double totMassOfMovingAtoms;
384 >  };
385 >
386 > public:
387 >
388 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
389 >  ~ZConstraint();
390 >
391 >  void setZConsTime(double time)                  {this->zconsTime = time;}
392 >  void getZConsTime()                             {return zconsTime;}
393 >
394 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
395 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
396 >
397 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
398 >  string getZConsOutput()                         {return zconsOutput;}
399 >
400 >  virtual void integrate();
401 >
402 >
403 > #ifdef IS_MPI
404 >  virtual void update();                      //which is called to indicate the molecules' migration
405 > #endif
406 >
407 >  enum ZConsState {zcsMoving, zcsFixed};
408 >
409 >  vector<Molecule*> zconsMols;              //z-constraint molecules array
410 >  vector<ZConsState> states;                 //state of z-constraint molecules
411 >
412 >
413 >
414 >  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
415 >  double totalMassOfUncons;                //total mas of unconstraint molecules
416 >
417 >
418 > protected:
419 >
420 >
421 >
422 >  virtual void calcForce( int calcPot, int calcStress );
423 >  virtual void thermalize(void);
424 >
425 >  void zeroOutVel();
426 >  void doZconstraintForce();
427 >  void doHarmonic(vector<double>& resPos);
428 >  bool checkZConsState();
429 >
430 >  bool haveFixedZMols();
431 >  bool haveMovingZMols();
432 >
433 >  double calcZSys();
434 >
435 >  int isZConstraintMol(Molecule* mol);
436 >
437 >
438 >  double zconsTime;                              //sample time
439 >  double zconsTol;                                 //tolerance of z-contratint
440 >  double zForceConst;                           //base force constant term
441 >                                                          //which is estimate by OOPSE
442 >
443 >
444 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
445 >  vector<double> kz;                              //force constant array
446 >
447 >  vector<double> zPos;                          //
448 >
449 >
450 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
451 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
452 >
453 >
454 >  vector<ZConsParaItem>* parameters; //
455 >
456 >  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
457 >
458 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
459 >  vector<double> fz;
460 >  vector<double> curZPos;
461 >
462 >  bool usingSMD;
463 >  vector<double> prevCantPos;
464 >  vector<double> cantPos;
465 >  vector<double> cantVel;
466 >
467 >  double zconsFixTime;  
468 >  double zconsGap;
469 >  bool hasZConsGap;
470 >  vector<double> endFixTime;
471    
472 +  int whichDirection;                           //constraint direction
473 +
474 + private:
475 +
476 +  string zconsOutput;                         //filename of zconstraint output
477 +  ZConsWriter* fzOut;                         //z-constraint writer
478 +
479 +  double curZconsTime;
480 +
481 +  double calcMovingMolsCOMVel();
482 +  double calcSysCOMVel();
483 +  double calcTotalForce();
484 +  void updateZPos();
485 +  void updateCantPos();
486 +  
487 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
488 +  friend class ForceSubtractionPolicy;
489 +
490   };
491  
492 + /*
493 + template<typename T> class SingleZConstrain : public T{
494 +
495 +
496 + };
497 + */
498 +
499 + template<typename T> class NonEquMD : public T {
500 +  public:
501 +    
502 +
503 +
504 + };
505 +
506 +
507 + //
508 + template<typename T> class SingleZConstraint : public T{
509 +  public:
510 +    SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff);
511 +    ~SingleZConstraint();
512 +    
513 +    bool stopIntegrator();
514 +    
515 +  protected:
516 +    
517 + };
518 +
519 + //Steered Molecular Dynamics, curret implement only support one steered molecule
520 + template<typename T> class SMD : public T{
521 +  public:
522 +    SMD( SimInfo *theInfo, ForceFields* the_ff);
523 +    ~SMD();
524 +  
525 +    virtual void integrate();
526 +    virtual void calcForce( int calcPot, int calcStress );  
527 +    bool stopIntegrator();
528 +  private:
529 +    
530 + };
531 +
532 + //By using state pattern, Coordinate Drive is responsible for switching back and forth between
533 + //Driven Molecular Dynamics and ZConstraint Method.
534 + template<typename T> class CoordinateDriver : public T {
535 +  public:
536 +    typedef T ParentIntegrator;
537 +
538 +    CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*);
539 +    ~CoordinateDriver();
540 +    
541 +    virtual void integrate();
542 +
543 +  private:    
544 +    BaseIntegrator* zconsIntegrator;
545 +    BaseIntegrator* drivenIntegrator;
546 +    
547 + };
548 +
549   #endif

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