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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 576 by gezelter, Tue Jul 8 21:10:16 2003 UTC vs.
Revision 746 by mmeineke, Thu Sep 4 21:48:35 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  
17 – 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 31 | 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 <
39 <
49 >         double A[3][3] );
50 >        
51    ForceFields* myFF;
52  
53    SimInfo *info; // all the info we'll ever need
# Line 47 | 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 62 | Line 73 | class Integrator : public BaseIntegrator { (protected)
73    double dt;
74    double dt2;
75  
65 –  double* pos;
66 –  double* vel;
67 –  double* frc;
68 –  double* trq;
69 –  double* Amat;
70 –
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(){}
83 <
84 <  
85 <
88 >    T( theInfo, the_ff ){}
89 >  virtual ~NVE(){}  
90   };
91  
88 – 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 102 | 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 116 | Line 123 | class NPTi : public Integrator{
123   };
124  
125  
119 – class NPTi : public Integrator{
126  
127 + template<typename T> class NPTi : public T{
128 +
129   public:
130  
131    NPTi ( SimInfo *theInfo, ForceFields* the_ff);
132    virtual ~NPTi() {};
133  
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;}
# Line 135 | Line 148 | class NPTi : public Integrator{ (protected)
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 154 | Line 169 | class NPTf : public Integrator{
169  
170   };
171  
172 < class NPTf : public Integrator{
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 NPTf : public T{
221 +
222 + public:
223 +
224    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
225    virtual ~NPTf() {};
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;}
# Line 171 | Line 239 | class NPTf : public Integrator{ (protected)
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
247  
248    double chi;
249 <  double eta[9];
249 >  double eta[3][3];
250 >  double NkBT;
251 >
252 >  // targetTemp, targetPressure, and tauBarostat must be set.  
253 >  // One of qmass or tauThermostat must be set;
254 >
255 >  double targetTemp;
256 >  double targetPressure;
257 >  double tauThermostat;
258 >  double tauBarostat;
259 >
260 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
261 >  short int have_target_pressure;
262 >
263 > };
264 >
265 > template<typename T> class NPTfm : public T{
266 >
267 > public:
268 >
269 >  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
270 >  virtual ~NPTfm() {};
271 >
272 >  virtual void integrateStep( int calcPot, int calcStress ){
273 >    calcStress = 1;
274 >    T::integrateStep( calcPot, calcStress );
275 >  }
276 >
277 >  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
278 >  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
279 >  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
280 >  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
281 >
282 > protected:
283 >
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;
297 >  double eta[3][3];
298 >  double NkBT;
299 >
300 >  // targetTemp, targetPressure, and tauBarostat must be set.  
301 >  // One of qmass or tauThermostat must be set;
302 >
303 >  double targetTemp;
304 >  double targetPressure;
305 >  double tauThermostat;
306 >  double tauBarostat;
307 >
308 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
309 >  short int have_target_pressure;
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.  
# Line 192 | Line 356 | class NPTf : public Integrator{ (protected)
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 +    public:
379 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
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 +    int totNumOfMovingAtoms;
388 +  };
389 +
390 +  class PolicyByMass : public ForceSubtractionPolicy{
391 +    public:
392 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
393 +      
394 +      virtual void update();    
395 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
396 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
397 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
398 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
399 +
400 +   private:
401 +     double totMassOfMovingAtoms;
402 +  };
403 +
404 + public:
405 +
406 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
407 +  ~ZConstraint();
408 +    
409 +  void setZConsTime(double time)                  {this->zconsTime = time;}
410 +  void getZConsTime()                             {return zconsTime;}
411 +  
412 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
413 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
414 +  
415 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
416 +  string getZConsOutput()                         {return zconsOutput;}
417 +  
418 +  virtual void integrate();
419 +  
420 +
421 + #ifdef IS_MPI
422 +  virtual void update();                      //which is called to indicate the molecules' migration
423   #endif
424 +
425 + protected:
426 +
427 +  enum ZConsState {zcsMoving, zcsFixed};  
428 +
429 +  virtual void calcForce( int calcPot, int calcStress );
430 +  virtual void thermalize(void);
431 +  
432 +  void zeroOutVel();
433 +  void doZconstraintForce();
434 +  void doHarmonic();
435 +  bool checkZConsState();
436 +
437 +  bool haveFixedZMols();
438 +  bool haveMovingZMols();
439 +
440 +  double calcZSys();
441 +
442 +  int isZConstraintMol(Molecule* mol);
443 +
444 +
445 +  double zconsTime;                              //sample time
446 +  double zconsTol;                                 //tolerance of z-contratint
447 +  double zForceConst;                           //base force constant term
448 +                                                          //which is estimate by OOPSE
449 +  
450 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
451 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
452 +  vector<double> kz;                              //force constant array
453 +  vector<ZConsState> states;                 //state of z-constraint molecules
454 +  vector<double> zPos;                          //
455 +  
456 +  
457 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
458 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
459 +  double totalMassOfUncons;                //total mas of unconstraint molecules
460 +
461 +  vector<ZConsParaItem>* parameters; //
462 +  
463 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
464 +
465 +  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
466 +  double* fz;
467 +  double* curZPos;
468 +  
469 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
470 +
471 +  int whichDirection;                           //constraint direction
472 +  
473 + private:
474 +  
475 +  string zconsOutput;                         //filename of zconstraint output
476 +  ZConsWriter* fzOut;                         //z-constraint writer
477 +
478 +  double curZconsTime;                      
479 +
480 +  double calcMovingMolsCOMVel();
481 +  double calcSysCOMVel();
482 +  double calcTotalForce();
483 +  
484 +  ForceSubtractionPolicy* forcePolicy; //force substration policy
485 +  friend class ForceSubtractionPolicy;
486 +
487 + };
488 +
489 + #endif

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