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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 597 by mmeineke, Mon Jul 14 21:28:54 2003 UTC vs.
Revision 747 by gezelter, Fri Sep 5 21:28:52 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 "Thermo.hpp"
13   #include "ReadWrite.hpp"
14 + #include "ZConsWriter.hpp"
15  
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  
18 – class Integrator : public BaseIntegrator {
23  
24 + template<typename T = BaseIntegrator> class Integrator : public T {
25 +
26   public:
27    Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
# Line 32 | Line 38 | class Integrator : public BaseIntegrator { (protected)
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[9] );
50 <
40 <
49 >         double A[3][3] );
50 >        
51    ForceFields* myFF;
52  
53    SimInfo *info; // all the info we'll ever need
# Line 48 | Line 58 | class Integrator : public BaseIntegrator { (protected)
58    int nMols;
59  
60    int isConstrained; // boolean to know whether the systems contains
61 <                     // constraints.
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
# Line 63 | Line 73 | class Integrator : public BaseIntegrator { (protected)
73    double dt;
74    double dt2;
75  
66 –  double* pos;
67 –  double* vel;
68 –  double* frc;
69 –  double* trq;
70 –  double* Amat;
71 –
76    Thermo *tStats;
77    StatWriter*  statOut;
78    DumpWriter*  dumpOut;
79    
80   };
81  
82 < class NVE : public Integrator{
82 > typedef Integrator<BaseIntegrator> RealIntegrator;
83  
84 + template<typename T> class NVE : public T {
85 +
86   public:
87    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
88 <    Integrator( theInfo, the_ff ){}
89 <  virtual ~NVE(){}
84 <
85 <  
86 <
88 >    T( theInfo, the_ff ){}
89 >  virtual ~NVE(){}  
90   };
91  
89 – class NVT : public Integrator{
92  
93 + template<typename T> class NVT : public T {
94 +
95   public:
96  
97    NVT ( SimInfo *theInfo, ForceFields* the_ff);
# Line 103 | Line 107 | class NVT : public Integrator{ (protected)
107  
108    virtual int readyCheck();
109  
110 +  virtual void resetIntegrator( void );
111 +
112    // chi is a propagated degree of freedom.
113  
114    double chi;
# Line 117 | Line 123 | class NPTi : public Integrator{
123   };
124  
125  
120 – class NPTi : public Integrator{
126  
127 + template<typename T> class NPTi : public T{
128 +
129   public:
130  
131    NPTi ( SimInfo *theInfo, ForceFields* the_ff);
# Line 126 | Line 133 | class NPTi : public Integrator{ (public)
133  
134    virtual void integrateStep( int calcPot, int calcStress ){
135      calcStress = 1;
136 <    Integrator::integrateStep( calcPot, calcStress );
136 >    T::integrateStep( calcPot, calcStress );
137    }
138  
139    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 141 | Line 148 | class NPTi : public Integrator{ (public)
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;
# Line 160 | Line 169 | class NPTim : public Integrator{
169  
170   };
171  
172 < class NPTim : public Integrator{
172 > template<typename T> class NPTim : public T{
173  
174   public:
175  
# Line 169 | Line 178 | class NPTim : public Integrator{ (public)
178  
179    virtual void integrateStep( int calcPot, int calcStress ){
180      calcStress = 1;
181 <    Integrator::integrateStep( calcPot, calcStress );
181 >    T::integrateStep( calcPot, calcStress );
182    }
183  
184    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 179 | Line 188 | class NPTim : public Integrator{ (public)
188  
189   protected:
190  
191 <  virtual void  moveA( void );
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;
# Line 203 | Line 217 | class NPTf : public Integrator{
217  
218   };
219  
220 < class NPTf : public Integrator{
220 > template<typename T> class NPTf : public T{
221  
222   public:
223  
# Line 212 | Line 226 | class NPTf : public Integrator{ (public)
226  
227    virtual void integrateStep( int calcPot, int calcStress ){
228      calcStress = 1;
229 <    Integrator::integrateStep( calcPot, calcStress );
229 >    T::integrateStep( calcPot, calcStress );
230    }
231  
232    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 225 | Line 239 | class NPTf : public Integrator{ (public)
239    virtual void  moveA( void );
240    virtual void moveB( void );
241  
242 +  virtual void resetIntegrator( void );
243 +
244    virtual int readyCheck();
245  
246    // chi and eta are the propagated degrees of freedom
# Line 246 | Line 262 | class NPTfm : public Integrator{
262  
263   };
264  
265 < class NPTfm : public Integrator{
265 > template<typename T> class NPTfm : public T{
266  
267   public:
268  
# Line 255 | Line 271 | class NPTfm : public Integrator{ (public)
271  
272    virtual void integrateStep( int calcPot, int calcStress ){
273      calcStress = 1;
274 <    Integrator::integrateStep( calcPot, calcStress );
274 >    T::integrateStep( calcPot, calcStress );
275    }
276  
277    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 268 | Line 284 | class NPTfm : public Integrator{ (public)
284    virtual void  moveA( void );
285    virtual void moveB( void );
286  
287 +  virtual void resetIntegrator( void );
288 +
289    virtual int readyCheck();
290  
291 +  Molecule* myMolecules;
292 +  Atom** myAtoms;
293 +
294    // chi and eta are the propagated degrees of freedom
295  
296    double chi;
# Line 289 | Line 310 | class NPTfm : public Integrator{ (public)
310  
311   };
312  
313 +
314 + template<typename T> class NPTpr : public T{
315 +
316 + public:
317 +
318 +  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
319 +  virtual ~NPTpr() {};
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 +  // chi and eta are the propagated degrees of freedom
341 +
342 +  double chi;
343 +  double eta[3][3];
344 +  double NkBT;
345 +
346 +  // targetTemp, targetPressure, and tauBarostat must be set.  
347 +  // One of qmass or tauThermostat must be set;
348 +
349 +  double targetTemp;
350 +  double targetPressure;
351 +  double tauThermostat;
352 +  double tauBarostat;
353 +
354 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
355 +  short int have_target_pressure;
356 +
357 + };
358 +
359 +
360 + template<typename T> class ZConstraint : public T {
361 +  
362 +  public:
363 +  class ForceSubtractionPolicy{
364 +    public:
365 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
366 +
367 +      virtual void update() = 0;    
368 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
369 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
370 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
371 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
372 +    
373 +   protected:
374 +     ZConstraint<T>* zconsIntegrator;;
375 +  };
376 +
377 +  class PolicyByNumber : public ForceSubtractionPolicy{
378 +
379 +    public:
380 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
381 +      virtual void update();    
382 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
383 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
384 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
385 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
386 +    
387 +    private:
388 +    int totNumOfMovingAtoms;
389 +  };
390 +
391 +  class PolicyByMass : public ForceSubtractionPolicy{
392 +
393 +    public:
394 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
395 +      
396 +      virtual void update();    
397 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
398 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
399 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
400 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
401 +
402 +   private:
403 +     double totMassOfMovingAtoms;
404 +  };
405 +
406 + public:
407 +
408 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
409 +  ~ZConstraint();
410 +    
411 +  void setZConsTime(double time)                  {this->zconsTime = time;}
412 +  void getZConsTime()                             {return zconsTime;}
413 +  
414 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
415 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
416 +  
417 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
418 +  string getZConsOutput()                         {return zconsOutput;}
419 +  
420 +  virtual void integrate();
421 +  
422 +
423 + #ifdef IS_MPI
424 +  virtual void update();                      //which is called to indicate the molecules' migration
425   #endif
426 +
427 + protected:
428 +
429 +  enum ZConsState {zcsMoving, zcsFixed};  
430 +
431 +  virtual void calcForce( int calcPot, int calcStress );
432 +  virtual void thermalize(void);
433 +  
434 +  void zeroOutVel();
435 +  void doZconstraintForce();
436 +  void doHarmonic();
437 +  bool checkZConsState();
438 +
439 +  bool haveFixedZMols();
440 +  bool haveMovingZMols();
441 +
442 +  double calcZSys();
443 +
444 +  int isZConstraintMol(Molecule* mol);
445 +
446 +
447 +  double zconsTime;                              //sample time
448 +  double zconsTol;                                 //tolerance of z-contratint
449 +  double zForceConst;                           //base force constant term
450 +                                                          //which is estimate by OOPSE
451 +  
452 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
453 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
454 +  vector<double> kz;                              //force constant array
455 +  vector<ZConsState> states;                 //state of z-constraint molecules
456 +  vector<double> zPos;                          //
457 +  
458 +  
459 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
460 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
461 +  double totalMassOfUncons;                //total mas of unconstraint molecules
462 +
463 +  vector<ZConsParaItem>* parameters; //
464 +  
465 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
466 +
467 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
468 +  double* fz;
469 +  double* curZPos;
470 +  
471 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
472 +
473 +  int whichDirection;                           //constraint direction
474 +  
475 + private:
476 +  
477 +  string zconsOutput;                         //filename of zconstraint output
478 +  ZConsWriter* fzOut;                         //z-constraint writer
479 +
480 +  double curZconsTime;                      
481 +
482 +  double calcMovingMolsCOMVel();
483 +  double calcSysCOMVel();
484 +  double calcTotalForce();
485 +  
486 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
487 +  friend class ForceSubtractionPolicy;
488 +
489 + };
490 +
491 + #endif

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