ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/Integrator.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 755 by mmeineke, Tue Sep 9 20:35:25 2003 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 "Molecule.hpp"
8   #include "SRI.hpp"
9   #include "AbstractClasses.hpp"
10   #include "SimInfo.hpp"
11   #include "ForceFields.hpp"
12 < #include "ExtendedSystem.hpp"
12 > #include "Thermo.hpp"
13 > #include "ReadWrite.hpp"
14 > #include "ZConsWriter.hpp"
15  
16 < class Verlet : public Integrator {
16 > using namespace std;
17 > const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
18 > const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
19 > const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
20 > const int maxIteration = 300;
21 > const double tol = 1.0e-6;
22  
23 +
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27 <  Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es );
28 <  ~Verlet();
27 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
28 >  virtual ~Integrator();
29    void integrate( void );
30  
31 < private:
31 >
32 > protected:
33    
34 <  void move_a( double dt );
35 <  void move_b( double dt );
34 >  virtual void integrateStep( int calcPot, int calcStress );
35 >  virtual void preMove( void );
36 >  virtual void moveA( void );
37 >  virtual void moveB( void );
38 >  virtual void constrainA( void );
39 >  virtual void constrainB( void );
40 >  virtual int  readyCheck( void ) { return 1; }
41  
42 +  virtual void resetIntegrator( void ) { }
43 +
44 +  virtual void calcForce( int calcPot, int calcStress );  
45 +  virtual void thermalize();
46 +  
47 +  void checkConstraints( void );
48 +  void rotate( int axes1, int axes2, double angle, double j[3],
49 +         double A[3][3] );
50 +        
51    ForceFields* myFF;
24 –  ExtendedSystem* myES;
52  
53 <  SimInfo *entry_plug; // all the info we'll ever need
54 <  int c_natoms;  /* the number of atoms */
55 <  Atom **c_atoms; /* array of atom pointers */
53 >  SimInfo *info; // all the info we'll ever need
54 >  int nAtoms;  /* the number of atoms */
55 >  int oldAtoms;
56 >  Atom **atoms; /* array of atom pointers */
57    Molecule* molecules;
58    int nMols;
59  
60 <  int c_is_constrained; /*boolean to know whether the systems contains
61 <                          constraints. */
62 <  int c_n_constrained; /*counter for number of constraints */
63 <  int *c_constrained_i; /* the i of a constraint pair */
64 <  int *c_constrained_j; /* the j of a constraint pair */
65 <  double *c_constrained_dsqr; /* the square of the constraint distance */
66 <  double *c_mass; /* the array of masses */
67 <  short is_first; /*boolean for the first time integrate is called */
68 <  double c_box_x;
69 <  double c_box_y;
42 <  double c_box_z;
43 < };
60 >  int isConstrained; // boolean to know whether the systems contains
61 >         // constraints.
62 >  int nConstrained;  // counter for number of constraints
63 >  int *constrainedA; // the i of a constraint pair
64 >  int *constrainedB; // the j of a constraint pair
65 >  double *constrainedDsqr; // the square of the constraint distance
66 >  
67 >  int* moving; // tells whether we are moving atom i
68 >  int* moved;  // tells whether we have moved atom i
69 >  double* oldPos; // pre constrained positions
70  
71 < class Symplectic : public Integrator {
71 >  short isFirst; /*boolean for the first time integrate is called */
72    
73 +  double dt;
74 +  double dt2;
75 +
76 +  Thermo *tStats;
77 +  StatWriter*  statOut;
78 +  DumpWriter*  dumpOut;
79 +  
80 + };
81 +
82 + typedef Integrator<BaseIntegrator> RealIntegrator;
83 +
84 + template<typename T> class NVE : public T {
85 +
86   public:
87 <  Symplectic( SimInfo* the_entry_plug,  
88 <              ForceFields* the_ff,
89 <              ExtendedSystem* the_es);
90 <  ~Symplectic();
87 >  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
88 >    T( theInfo, the_ff ){}
89 >  virtual ~NVE(){}  
90 > };
91 >
92 >
93 > template<typename T> class NVT : public T {
94 >
95 > public:
96 >
97 >  NVT ( SimInfo *theInfo, ForceFields* the_ff);
98 >  virtual ~NVT() {}
99 >
100 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
101 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
102 >
103 > protected:
104 >
105 >  virtual void moveA( void );
106 >  virtual void moveB( void );
107 >
108 >  virtual int readyCheck();
109 >
110 >  virtual void resetIntegrator( void );
111 >
112 >  // chi is a propagated degree of freedom.
113 >
114 >  double chi;
115 >
116 >  // targetTemp must be set.  tauThermostat must also be set;
117 >
118 >  double targetTemp;
119 >  double tauThermostat;
120    
121 <  void integrate( void );
121 >  short int have_tau_thermostat, have_target_temp;
122  
123 < private:
123 > };
124  
57 –  void rotate( int axes1, int axes2, double angle, double j[3],
58 –               double A[3][3] );
125  
60 –  SimInfo* entry_plug;
61 –  ForceFields* myFF;
62 –  ExtendedSystem* myES;
126  
127 <  Molecule* molecules;
65 <  int nMols;
127 > template<typename T> class NPTi : public T{
128  
129 <  int is_constrained; /*boolean to know whether the systems contains
68 <                          constraints. */
69 <  int n_constrained; /*counter for number of constraints */
70 <  int *constrained_i; /* the i of a constraint pair */
71 <  int *constrained_j; /* the j of a constraint pair */
72 <  double *constrained_dsqr; /* the square of the constraint distance */
73 <  double *mass; /* the array of masses */
129 > public:
130  
131 <  short int isFirst;
131 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
132 >  virtual ~NPTi() {};
133  
134 <  SRI **srInteractions; /* array of SRI pointers */
135 <  int nSRI; /* the number of short range interactions */
134 >  virtual void integrateStep( int calcPot, int calcStress ){
135 >    calcStress = 1;
136 >    T::integrateStep( calcPot, calcStress );
137 >  }
138 >
139 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
140 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
141 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
142 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
143 >
144 > protected:
145 >
146 >  virtual void  moveA( void );
147 >  virtual void moveB( void );
148 >
149 >  virtual int readyCheck();
150 >
151 >  virtual void resetIntegrator( void );
152 >
153 >  // chi and eta are the propagated degrees of freedom
154 >
155 >  double chi;
156 >  double eta;
157 >  double NkBT;
158 >
159 >  // targetTemp, targetPressure, and tauBarostat must be set.  
160 >  // One of qmass or tauThermostat must be set;
161 >
162 >  double targetTemp;
163 >  double targetPressure;
164 >  double tauThermostat;
165 >  double tauBarostat;
166 >
167 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
168 >  short int have_target_pressure;
169 >
170 > };
171 >
172 > template<typename T> class NPTim : public T{
173 >
174 > public:
175 >
176 >  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
177 >  virtual ~NPTim() {};
178 >
179 >  virtual void integrateStep( int calcPot, int calcStress ){
180 >    calcStress = 1;
181 >    T::integrateStep( calcPot, calcStress );
182 >  }
183 >
184 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
185 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
186 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
187 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
188 >
189 > protected:
190 >
191 >  virtual void moveA( void );
192 >  virtual void moveB( void );
193 >
194 >  virtual int readyCheck();
195 >
196 >  virtual void resetIntegrator( void );
197 >
198 >  Molecule* myMolecules;
199 >  Atom** myAtoms;
200 >
201 >  // chi and eta are the propagated degrees of freedom
202 >
203 >  double chi;
204 >  double eta;
205 >  double NkBT;
206 >
207 >  // targetTemp, targetPressure, and tauBarostat must be set.  
208 >  // One of qmass or tauThermostat must be set;
209 >
210 >  double targetTemp;
211 >  double targetPressure;
212 >  double tauThermostat;
213 >  double tauBarostat;
214 >
215 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
216 >  short int have_target_pressure;
217 >
218 > };
219 >
220 > template<typename T> class NPTzm : public T{
221 >
222 > public:
223 >
224 >  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
225 >  virtual ~NPTzm() {};
226 >
227 >  virtual void integrateStep( int calcPot, int calcStress ){
228 >    calcStress = 1;
229 >    T::integrateStep( calcPot, calcStress );
230 >  }
231 >
232 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
233 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
234 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
235 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
236 >
237 > protected:
238 >
239 >  virtual void moveA( void );
240 >  virtual void moveB( void );
241 >
242 >  virtual int readyCheck();
243 >
244 >  virtual void resetIntegrator( void );
245 >
246 >  Molecule* myMolecules;
247 >  Atom** myAtoms;
248 >
249 >  // chi and eta are the propagated degrees of freedom
250 >
251 >  double chi;
252 >  double eta;
253 >  double etaZ;
254 >  double NkBT;
255 >
256 >  // targetTemp, targetPressure, and tauBarostat must be set.  
257 >  // One of qmass or tauThermostat must be set;
258 >
259 >  double targetTemp;
260 >  double targetPressure;
261 >  double tauThermostat;
262 >  double tauBarostat;
263 >
264 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
265 >  short int have_target_pressure;
266 >
267 > };
268 >
269 > template<typename T> class NPTf : public T{
270 >
271 > public:
272 >
273 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
274 >  virtual ~NPTf() {};
275 >
276 >  virtual void integrateStep( int calcPot, int calcStress ){
277 >    calcStress = 1;
278 >    T::integrateStep( calcPot, calcStress );
279 >  }
280 >
281 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
282 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
283 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
284 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
285 >
286 > protected:
287 >
288 >  virtual void  moveA( void );
289 >  virtual void moveB( void );
290 >
291 >  virtual void resetIntegrator( void );
292 >
293 >  virtual int readyCheck();
294 >
295 >  // chi and eta are the propagated degrees of freedom
296 >
297 >  double chi;
298 >  double eta[3][3];
299 >  double NkBT;
300 >
301 >  // targetTemp, targetPressure, and tauBarostat must be set.  
302 >  // One of qmass or tauThermostat must be set;
303 >
304 >  double targetTemp;
305 >  double targetPressure;
306 >  double tauThermostat;
307 >  double tauBarostat;
308 >
309 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
310 >  short int have_target_pressure;
311 >
312 > };
313 >
314 > template<typename T> class NPTxym : public T{
315 >
316 > public:
317 >
318 >  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
319 >  virtual ~NPTxym() {};
320 >
321 >  virtual void integrateStep( int calcPot, int calcStress ){
322 >    calcStress = 1;
323 >    T::integrateStep( calcPot, calcStress );
324 >  }
325 >
326 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
327 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
328 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
329 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
330 >
331 > protected:
332 >
333 >  virtual void moveA( void );
334 >  virtual void moveB( void );
335 >
336 >  virtual int readyCheck();
337 >
338 >  virtual void resetIntegrator( void );
339 >
340 >  Molecule* myMolecules;
341 >  Atom** myAtoms;
342 >
343 >  // chi and eta are the propagated degrees of freedom
344 >
345 >  double chi;
346 >  double eta;
347 >  double etaX;
348 >  double etaY;
349 >  double NkBT;
350 >
351 >  // targetTemp, targetPressure, and tauBarostat must be set.  
352 >  // One of qmass or tauThermostat must be set;
353 >
354 >  double targetTemp;
355 >  double targetPressure;
356 >  double tauThermostat;
357 >  double tauBarostat;
358 >
359 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
360 >  short int have_target_pressure;
361 >
362 > };
363 >
364 >
365 > template<typename T> class NPTfm : public T{
366 >
367 > public:
368 >
369 >  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
370 >  virtual ~NPTfm() {};
371 >
372 >  virtual void integrateStep( int calcPot, int calcStress ){
373 >    calcStress = 1;
374 >    T::integrateStep( calcPot, calcStress );
375 >  }
376 >
377 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
378 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
379 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
380 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
381 >
382 > protected:
383 >
384 >  virtual void  moveA( void );
385 >  virtual void moveB( void );
386 >
387 >  virtual void resetIntegrator( void );
388 >
389 >  virtual int readyCheck();
390 >
391 >  Molecule* myMolecules;
392 >  Atom** myAtoms;
393 >
394 >  // chi and eta are the propagated degrees of freedom
395 >
396 >  double chi;
397 >  double eta[3][3];
398 >  double NkBT;
399 >
400 >  // targetTemp, targetPressure, and tauBarostat must be set.  
401 >  // One of qmass or tauThermostat must be set;
402 >
403 >  double targetTemp;
404 >  double targetPressure;
405 >  double tauThermostat;
406 >  double tauBarostat;
407 >
408 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
409 >  short int have_target_pressure;
410 >
411 > };
412 >
413 >
414 > template<typename T> class NPTpr : public T{
415 >
416 > public:
417 >
418 >  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
419 >  virtual ~NPTpr() {};
420 >
421 >  virtual void integrateStep( int calcPot, int calcStress ){
422 >    calcStress = 1;
423 >    T::integrateStep( calcPot, calcStress );
424 >  }
425 >
426 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
427 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
428 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
429 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
430 >
431 > protected:
432 >
433 >  virtual void  moveA( void );
434 >  virtual void moveB( void );
435 >
436 >  virtual int readyCheck();
437 >
438 >  virtual void resetIntegrator( void );
439 >
440 >  // chi and eta are the propagated degrees of freedom
441 >
442 >  double chi;
443 >  double eta[3][3];
444 >  double NkBT;
445 >
446 >  // targetTemp, targetPressure, and tauBarostat must be set.  
447 >  // One of qmass or tauThermostat must be set;
448 >
449 >  double targetTemp;
450 >  double targetPressure;
451 >  double tauThermostat;
452 >  double tauBarostat;
453 >
454 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
455 >  short int have_target_pressure;
456 >
457 > };
458 >
459 >
460 > template<typename T> class ZConstraint : public T {
461    
462 +  public:
463 +  class ForceSubtractionPolicy{
464 +    public:
465 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
466 +
467 +      virtual void update() = 0;    
468 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
469 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
470 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
471 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
472 +    
473 +   protected:
474 +     ZConstraint<T>* zconsIntegrator;;
475 +  };
476 +
477 +  class PolicyByNumber : public ForceSubtractionPolicy{
478 +
479 +    public:
480 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
481 +      virtual void update();    
482 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
483 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
484 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
485 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
486 +    
487 +    private:
488 +    int totNumOfMovingAtoms;
489 +  };
490 +
491 +  class PolicyByMass : public ForceSubtractionPolicy{
492 +
493 +    public:
494 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
495 +      
496 +      virtual void update();    
497 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
498 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
499 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
500 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
501 +
502 +   private:
503 +     double totMassOfMovingAtoms;
504 +  };
505 +
506 + public:
507 +
508 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
509 +  ~ZConstraint();
510 +    
511 +  void setZConsTime(double time)                  {this->zconsTime = time;}
512 +  void getZConsTime()                             {return zconsTime;}
513 +  
514 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
515 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
516 +  
517 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
518 +  string getZConsOutput()                         {return zconsOutput;}
519 +  
520 +  virtual void integrate();
521 +  
522 +
523 + #ifdef IS_MPI
524 +  virtual void update();                      //which is called to indicate the molecules' migration
525 + #endif
526 +
527 + protected:
528 +
529 +  enum ZConsState {zcsMoving, zcsFixed};  
530 +
531 +  virtual void calcForce( int calcPot, int calcStress );
532 +  virtual void thermalize(void);
533 +  
534 +  void zeroOutVel();
535 +  void doZconstraintForce();
536 +  void doHarmonic();
537 +  bool checkZConsState();
538 +
539 +  bool haveFixedZMols();
540 +  bool haveMovingZMols();
541 +
542 +  double calcZSys();
543 +
544 +  int isZConstraintMol(Molecule* mol);
545 +
546 +
547 +  double zconsTime;                              //sample time
548 +  double zconsTol;                                 //tolerance of z-contratint
549 +  double zForceConst;                           //base force constant term
550 +                                                          //which is estimate by OOPSE
551 +  
552 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
553 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
554 +  vector<double> kz;                              //force constant array
555 +  vector<ZConsState> states;                 //state of z-constraint molecules
556 +  vector<double> zPos;                          //
557 +  
558 +  
559 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
560 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
561 +  double totalMassOfUncons;                //total mas of unconstraint molecules
562 +
563 +  vector<ZConsParaItem>* parameters; //
564 +  
565 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
566 +
567 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
568 +  double* fz;
569 +  double* curZPos;
570 +  
571 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
572 +
573 +  int whichDirection;                           //constraint direction
574 +  
575 + private:
576 +  
577 +  string zconsOutput;                         //filename of zconstraint output
578 +  ZConsWriter* fzOut;                         //z-constraint writer
579 +
580 +  double curZconsTime;                      
581 +
582 +  double calcMovingMolsCOMVel();
583 +  double calcSysCOMVel();
584 +  double calcTotalForce();
585 +  
586 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
587 +  friend class ForceSubtractionPolicy;
588 +
589   };
590  
591   #endif

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines