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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 561 by mmeineke, Fri Jun 20 20:29:36 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  
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);
98    virtual ~NVT() {}
99  
95 –  void setQmass(double q) {qmass = q; have_qmass = 1;}
100    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
101    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
102  
# Line 103 | Line 107 | class NVT : public Integrator{ (protected)
107  
108    virtual int readyCheck();
109  
110 <  // zeta is a propagated degree of freedom.
110 >  virtual void resetIntegrator( void );
111  
112 <  double zeta;
112 >  // chi is a propagated degree of freedom.
113  
114 <  // targetTemp must be set.  One of qmass or tauThermostat must be set;
114 >  double chi;
115  
116 <  double qmass;
116 >  // targetTemp must be set.  tauThermostat must also be set;
117 >
118    double targetTemp;
119    double tauThermostat;
120 +  
121 +  short int have_tau_thermostat, have_target_temp;
122  
123 + };
124 +
125 +
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;}
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;
117 –  
118 –  short int have_tau_thermostat, have_target_temp, have_qmass;
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 < class NPT : public Integrator{
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 <  NPT ( SimInfo *theInfo, ForceFields* the_ff);
225 <  virtual ~NPT();
224 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
225 >  virtual ~NPTf() {};
226  
227 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
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 138 | Line 239 | class NPT : 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 <  Atom** atoms;
246 >  // chi and eta are the propagated degrees of freedom
247  
248 <  // zeta and epsilonDot are the propagated degrees of freedom.
248 >  double chi;
249 >  double eta[3][3];
250 >  double NkBT;
251  
252 <  double zeta;
253 <  double epsilonDot;
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  
153 –  double qmass;
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, have_qmass;
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.  
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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