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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 542 by mmeineke, Fri May 30 21:31:48 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 < class Integrator : public BaseIntegrator {
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 <  Symplectic( SimInfo &theInfo, ForceFields* the_ff );
28 <  virtual ~Symplectic();
27 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
28 >  virtual ~Integrator();
29    void integrate( void );
30  
31  
32   protected:
21 –
33    
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    
29 –  
47    void checkConstraints( void );
48    void rotate( int axes1, int axes2, double angle, double j[3],
49 <               double A[3][3] );
50 <
34 <
49 >         double A[3][3] );
50 >        
51    ForceFields* myFF;
52  
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 isConstrained; /*boolean to know whether the systems contains
61 <                       constraints. */
62 <  int nConstrained; /*counter for number of constraints */
63 <  int *constrainedI; /* the i of a constraint pair */
64 <  int *constrainedJ; /* the j of a constraint pair */
65 <  double *constrainedDsqr; /* the square of the constraint distance */
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    short isFirst; /*boolean for the first time integrate is called */
72    
73    double dt;
74    double dt2;
53 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
75  
55 –  
56 –  double* pos;
57 –  double* vel;
58 –  double* frc;
59 –  double* trq;
60 –  double* Amat;
61 –  
62 –
63 –
76    Thermo *tStats;
77    StatWriter*  statOut;
78    DumpWriter*  dumpOut;
79    
80   };
81  
82 + typedef Integrator<BaseIntegrator> RealIntegrator;
83  
84 < class NVT : public Integrator{
84 > template<typename T> class NVE : public T {
85  
86 <  NVT ( void );
87 <  virtual ~NVT();
86 > public:
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 <  virtual moveA( void );
105 <  virtual moveB( void );
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 >  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;
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 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;}
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 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[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.  
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 +    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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