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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC vs.
Revision 718 by gezelter, Mon Aug 25 21:51:30 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"
# Line 9 | Line 11
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  
19 – 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 33 | 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 calcForce( int calcPot, int calcStress );  
43 +  virtual void thermalize();
44    
45    void checkConstraints( void );
46    void rotate( int axes1, int axes2, double angle, double j[3],
47 <               double A[3][3] );
48 <
41 <
47 >         double A[3][3] );
48 >        
49    ForceFields* myFF;
50  
51    SimInfo *info; // all the info we'll ever need
# Line 49 | Line 56 | class Integrator : public BaseIntegrator { (protected)
56    int nMols;
57  
58    int isConstrained; // boolean to know whether the systems contains
59 <                     // constraints.
59 >         // constraints.
60    int nConstrained;  // counter for number of constraints
61    int *constrainedA; // the i of a constraint pair
62    int *constrainedB; // the j of a constraint pair
# Line 70 | Line 77 | class NVE : public Integrator{
77    
78   };
79  
80 < class NVE : public Integrator{
80 > typedef Integrator<BaseIntegrator> RealIntegrator;
81  
82 + template<typename T> class NVE : public T {
83 +
84   public:
85    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
86 <    Integrator( theInfo, the_ff ){}
87 <  virtual ~NVE(){}
79 <
80 <  
81 <
86 >    T( theInfo, the_ff ){}
87 >  virtual ~NVE(){}  
88   };
89  
84 – class NVT : public Integrator{
90  
91 + template<typename T> class NVT : public T {
92 +
93   public:
94  
95    NVT ( SimInfo *theInfo, ForceFields* the_ff);
# Line 112 | Line 119 | class NPTi : public Integrator{
119   };
120  
121  
115 – class NPTi : public Integrator{
122  
123 + template<typename T> class NPTi : public T{
124 +
125   public:
126  
127    NPTi ( SimInfo *theInfo, ForceFields* the_ff);
# Line 121 | Line 129 | class NPTi : public Integrator{ (public)
129  
130    virtual void integrateStep( int calcPot, int calcStress ){
131      calcStress = 1;
132 <    Integrator::integrateStep( calcPot, calcStress );
132 >    T::integrateStep( calcPot, calcStress );
133    }
134  
135    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 155 | Line 163 | class NPTim : public Integrator{
163  
164   };
165  
166 < class NPTim : public Integrator{
166 > template<typename T> class NPTim : public T{
167  
168   public:
169  
# Line 164 | Line 172 | class NPTim : public Integrator{ (public)
172  
173    virtual void integrateStep( int calcPot, int calcStress ){
174      calcStress = 1;
175 <    Integrator::integrateStep( calcPot, calcStress );
175 >    T::integrateStep( calcPot, calcStress );
176    }
177  
178    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 201 | Line 209 | class NPTf : public Integrator{
209  
210   };
211  
212 < class NPTf : public Integrator{
212 > template<typename T> class NPTf : public T{
213  
214   public:
215  
# Line 210 | Line 218 | class NPTf : public Integrator{ (public)
218  
219    virtual void integrateStep( int calcPot, int calcStress ){
220      calcStress = 1;
221 <    Integrator::integrateStep( calcPot, calcStress );
221 >    T::integrateStep( calcPot, calcStress );
222    }
223  
224    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 244 | Line 252 | class NPTfm : public Integrator{
252  
253   };
254  
255 < class NPTfm : public Integrator{
255 > template<typename T> class NPTfm : public T{
256  
257   public:
258  
# Line 253 | Line 261 | class NPTfm : public Integrator{ (public)
261  
262    virtual void integrateStep( int calcPot, int calcStress ){
263      calcStress = 1;
264 <    Integrator::integrateStep( calcPot, calcStress );
264 >    T::integrateStep( calcPot, calcStress );
265 >  }
266 >
267 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
268 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
269 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
270 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
271 >
272 > protected:
273 >
274 >  virtual void  moveA( void );
275 >  virtual void moveB( void );
276 >
277 >  virtual int readyCheck();
278 >
279 >  Molecule* myMolecules;
280 >  Atom** myAtoms;
281 >
282 >  // chi and eta are the propagated degrees of freedom
283 >
284 >  double chi;
285 >  double eta[3][3];
286 >  double NkBT;
287 >
288 >  // targetTemp, targetPressure, and tauBarostat must be set.  
289 >  // One of qmass or tauThermostat must be set;
290 >
291 >  double targetTemp;
292 >  double targetPressure;
293 >  double tauThermostat;
294 >  double tauBarostat;
295 >
296 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
297 >  short int have_target_pressure;
298 >
299 > };
300 >
301 >
302 > template<typename T> class NPTpr : public T{
303 >
304 > public:
305 >
306 >  NPTpr ( SimInfo *theInfo, ForceFields* the_ff);
307 >  virtual ~NPTpr() {};
308 >
309 >  virtual void integrateStep( int calcPot, int calcStress ){
310 >    calcStress = 1;
311 >    T::integrateStep( calcPot, calcStress );
312    }
313  
314    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
# Line 287 | Line 342 | class NPTfm : public Integrator{ (public)
342  
343   };
344  
345 +
346 + template<typename T> class ZConstraint : public T {
347 +  
348 +  public:
349 +  class ForceSubstractionPolicy{
350 +    public:
351 +      ForceSubstractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
352 +
353 +      virtual void update() = 0;    
354 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
355 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
356 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
357 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
358 +    
359 +   protected:
360 +     ZConstraint<T>* zconsIntegrator;;
361 +  };
362 +
363 +  class PolicyByNumber : ForceSubstractionPolicy{
364 +    public:
365 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}    
366 +      virtual void update();    
367 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
368 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
369 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
370 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
371 +    
372 +    private:
373 +    int totNumOfMovingAtoms;
374 +  };
375 +
376 +  class PolicyByMass :ForceSubstractionPolicy{
377 +    public:
378 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubstractionPolicy(integrator) {}  
379 +      
380 +      virtual void update();    
381 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
382 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
383 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
384 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
385 +
386 +   private:
387 +     double totMassOfMovingAtoms;
388 +  };
389 +
390 + public:
391 +
392 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
393 +  ~ZConstraint();
394 +    
395 +  void setZConsTime(double time)                  {this->zconsTime = time;}
396 +  void getZConsTime()                             {return zconsTime;}
397 +  
398 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
399 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
400 +  
401 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
402 +  string getZConsOutput()                         {return zconsOutput;}
403 +  
404 +  virtual void integrate();
405 +  
406 +
407 + #ifdef IS_MPI
408 +  virtual void update();                      //which is called to indicate the molecules' migration
409   #endif
410 +
411 + protected:
412 +
413 +  enum ZConsState {zcsMoving, zcsFixed};  
414 +
415 +  virtual void calcForce( int calcPot, int calcStress );
416 +  virtual void thermalize(void);
417 +  
418 +  void zeroOutVel();
419 +  void doZconstraintForce();
420 +  void doHarmonic();
421 +  bool checkZConsState();
422 +
423 +  bool haveFixedZMols();
424 +  bool haveMovingZMols();
425 +
426 +  double calcZSys();
427 +
428 +  int isZConstraintMol(Molecule* mol);
429 +
430 +
431 +  double zconsTime;                              //sample time
432 +  double zconsTol;                                 //tolerance of z-contratint
433 +  double zForceConst;                           //base force constant term
434 +                                                          //which is estimate by OOPSE
435 +  
436 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
437 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
438 +  vector<double> kz;                              //force constant array
439 +  vector<ZConsState> states;                 //state of z-constraint molecules
440 +  vector<double> zPos;                          //
441 +  
442 +  
443 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
444 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
445 +  double totalMassOfUncons;                //total mas of unconstraint molecules
446 +
447 +  vector<ZConsParaItem>* parameters; //
448 +  
449 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
450 +
451 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
452 +  double* fz;
453 +  double* curZPos;
454 +  
455 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
456 +
457 +  int whichDirection;                           //constraint direction
458 +  
459 + private:
460 +  
461 +  string zconsOutput;                         //filename of zconstraint output
462 +  ZConsWriter* fzOut;                         //z-constraint writer
463 +
464 +  double curZconsTime;                      
465 +
466 +  double calcMovingMolsCOMVel();
467 +  double calcSysCOMVel();
468 +  double calcTotalForce();
469 +  
470 +  ForceSubstractionPolicy* forcePolicy; //force substration policy
471 +  friend class ForceSubstractionPolicy;
472 +
473 + };
474 +
475 + #endif

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