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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 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 < class Verlet : public Integrator {
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 + template<typename T = BaseIntegrator> class Integrator : public T {
26 +
27   public:
28 <  Verlet( SimInfo &info, ForceFields* the_ff );
29 <  ~Verlet();
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  
34 < private:
18 <  
19 <  void move_a( double dt );
20 <  void move_b( double dt );
34 > protected:
35  
36 +  virtual void integrateStep( int calcPot, int calcStress );
37 +  virtual void preMove( void );
38 +  virtual void moveA( void );
39 +  virtual void moveB( void );
40 +  virtual void constrainA( void );
41 +  virtual void constrainB( void );
42 +  virtual int  readyCheck( void ) { return 1; }
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 *entry_plug; // all the info we'll ever need
60 <  int c_natoms;  /* the number of atoms */
61 <  Atom **c_atoms; /* array of atom pointers */
62 <  SRI **c_sr_interactions; /* array of SRI pointers */
63 <  int c_n_SRI; /* the number of short range interactions */
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 */
64 >  Molecule* molecules;
65 >  int nMols;
66  
67 <  int c_is_constrained; /*boolean to know whether the systems contains
68 <                          constraints. */
69 <  int c_n_constrained; /*counter for number of constraints */
70 <  int *c_constrained_i; /* the i of a constraint pair */
71 <  int *c_constrained_j; /* the j of a constraint pair */
72 <  double *c_constrained_dsqr; /* the square of the constraint distance */
73 <  double *c_mass; /* the array of masses */
74 <  short is_first; /*boolean for the first time integrate is called */
75 <  double c_box_x;
76 <  double c_box_y;
77 <  double c_box_z;
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 >
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
77 >
78 >  short isFirst; /*boolean for the first time integrate is called */
79 >
80 >  double dt;
81 >  double dt2;
82 >
83 >  Thermo *tStats;
84 >  StatWriter*  statOut;
85 >  DumpWriter*  dumpOut;
86 >
87 >  int i; // just an int
88   };
89  
90 < class Symplectic : public Integrator {
91 <  
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 <  Symplectic( SimInfo* the_entry_plug,  ForceFields* the_ff );
99 <  ~Symplectic();
98 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
99 >    T( theInfo, the_ff ){}
100 >  virtual ~NVE(){}
101 > };
102 >
103 >
104 > template<typename T> class NVT : public T {
105 >
106 > public:
107 >
108 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
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 >
119 >  virtual void moveA( void );
120 >  virtual void moveB( void );
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 >
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 >
149 >
150 > template<typename T> class NPT : public T{
151 >
152 > public:
153 >
154 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
155 >  virtual ~NPT();
156 >
157 >  virtual void integrateStep( int calcPot, int calcStress ){
158 >    calcStress = 1;
159 >    T::integrateStep( calcPot, calcStress );
160 >  }
161 >
162 >  virtual double getConservedQuantity(void) = 0;
163 >  virtual string getAdditionalParameters(void) = 0;
164    
165 <  void integrate( void );
165 >  double myTauThermo( void ) { return tauThermostat; }
166 >  double myTauBaro( void ) { return tauBarostat; }
167  
168 < private:
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 <  void rotate( int axes1, int axes2, double angle, double j[3],
54 <               double A[3][3] );
176 > protected:
177  
178 <  SimInfo* entry_plug;
179 <  ForceFields* myFF;
178 >  virtual void  moveA( void );
179 >  virtual void moveB( void );
180  
181 <  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 */
181 >  virtual int readyCheck();
182  
183 <  short int isFirst;
183 >  virtual void resetIntegrator( void );
184  
185 <  SRI **srInteractions; /* array of SRI pointers */
186 <  int nSRI; /* the number of short range interactions */
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;
209 >  double NkBT;
210 >  double fkBT;
211 >
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;
224 >  double targetPressure;
225 >  double tauThermostat;
226 >  double tauBarostat;
227 >
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 > template<typename T> class NPTi : public T{
245 >
246 > public:
247 >  NPTi( SimInfo *theInfo, ForceFields* the_ff);
248 >  ~NPTi();
249 >
250 >  virtual double getConservedQuantity(void);
251 >  virtual void resetIntegrator(void);
252 >  virtual string getAdditionalParameters(void);
253 > protected:
254 >
255 >
256 >
257 >  virtual void evolveEtaA(void);
258 >  virtual void evolveEtaB(void);
259 >
260 >  virtual bool etaConverged( void );
261 >
262 >  virtual void scaleSimBox( void );
263 >
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 >  virtual void calcVelScale( void );
270 >
271 >  double eta, oldEta, prevEta;
272 >  double vScale;
273 > };
274 >
275 > template<typename T> class NPTf : public T{
276 >
277 > public:
278 >
279 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
280 >  virtual ~NPTf();
281 >
282 >  virtual double getConservedQuantity(void);
283 >  virtual string getAdditionalParameters(void);
284 >  virtual void resetIntegrator(void);
285 >
286 > protected:
287 >
288 >  virtual void evolveEtaA(void);
289 >  virtual void evolveEtaB(void);
290 >
291 >  virtual bool etaConverged( void );
292 >
293 >  virtual void scaleSimBox( void );
294 >
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 oldEta[3][3];
304 >  double prevEta[3][3];
305 >  double vScale[3][3];
306 > };
307 >
308 > template<typename T> class NPTxyz : public T{
309 >
310 > public:
311 >
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 >
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 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
391 >  ~ZConstraint();
392 >
393 >  void setZConsTime(double time)                  {this->zconsTime = time;}
394 >  void getZConsTime()                             {return zconsTime;}
395 >
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 >
422 >
423 >
424 >  virtual void calcForce( int calcPot, int calcStress );
425 >  virtual void thermalize(void);
426 >
427 >  void zeroOutVel();
428 >  void doZconstraintForce();
429 >  void doHarmonic(vector<double>& resPos);
430 >  bool checkZConsState();
431 >
432 >  bool haveFixedZMols();
433 >  bool haveMovingZMols();
434 >
435 >  double calcZSys();
436 >
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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