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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 560 by gezelter, Fri Jun 20 16:49:33 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"
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 <  Integrator( SimInfo &theInfo, ForceFields* the_ff );
27 >  Integrator( SimInfo *theInfo, ForceFields* the_ff );
28    virtual ~Integrator();
29    void integrate( void );
30  
# Line 26 | 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 <
34 <
47 >         double A[3][3] );
48 >        
49    ForceFields* myFF;
50  
51    SimInfo *info; // all the info we'll ever need
# Line 42 | 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 50 | Line 64 | class Integrator : public BaseIntegrator { (protected)
64    
65    int* moving; // tells whether we are moving atom i
66    int* moved;  // tells whether we have moved atom i
67 <  double* prePos; // pre constrained positions
67 >  double* oldPos; // pre constrained positions
68  
69    short isFirst; /*boolean for the first time integrate is called */
70    
71    double dt;
72    double dt2;
73  
60 –  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
61 –  const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
62 –  const int maxIteration = 300;
63 –  const double tol = 1.0e-6;
64 –  
65 –  double* pos;
66 –  double* vel;
67 –  double* frc;
68 –  double* trq;
69 –  double* Amat;
70 –
74    Thermo *tStats;
75    StatWriter*  statOut;
76    DumpWriter*  dumpOut;
77    
78   };
79  
80 < class NVE : public Integrator{
80 > typedef Integrator<BaseIntegrator> RealIntegrator;
81  
82 <  NVE ( void ):
80 <    Integrator( theInfo, the_ff ){}
81 <  virtual ~NVE(){}
82 > template<typename T> class NVE : public T {
83  
84 + public:
85 +  NVE ( SimInfo *theInfo, ForceFields* the_ff ):
86 +    T( theInfo, the_ff ){}
87 +  virtual ~NVE(){}  
88 + };
89 +
90 +
91 + template<typename T> class NVT : public T {
92 +
93 + public:
94 +
95 +  NVT ( SimInfo *theInfo, ForceFields* the_ff);
96 +  virtual ~NVT() {}
97 +
98 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
99 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
100 +
101 + protected:
102 +
103 +  virtual void moveA( void );
104 +  virtual void moveB( void );
105 +
106 +  virtual int readyCheck();
107 +
108 +  // chi is a propagated degree of freedom.
109 +
110 +  double chi;
111 +
112 +  // targetTemp must be set.  tauThermostat must also be set;
113 +
114 +  double targetTemp;
115 +  double tauThermostat;
116    
117 +  short int have_tau_thermostat, have_target_temp;
118  
119   };
120  
87 – class NVT : public Integrator{
121  
122 +
123 + template<typename T> class NPTi : public T{
124 +
125   public:
126  
127 <  NVT ( SimInfo &theInfo, ForceFields* the_ff) :
128 <    Integrator( theInfo, the_ff );
93 <  virtual ~NVT();
127 >  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
128 >  virtual ~NPTi() {};
129  
130 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
130 >  virtual void integrateStep( int calcPot, int calcStress ){
131 >    calcStress = 1;
132 >    T::integrateStep( calcPot, calcStress );
133 >  }
134 >
135    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
136 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
137    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
138 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
139  
140   protected:
141  
142 <  virtual moveA( void );
143 <  virtual moveB( void );
142 >  virtual void  moveA( void );
143 >  virtual void moveB( void );
144  
145 <  int readyCheck();
145 >  virtual int readyCheck();
146  
147 <  Atom** atoms;
147 >  // chi and eta are the propagated degrees of freedom
148  
149 <  // zeta is a propagated degree of freedom.
149 >  double chi;
150 >  double eta;
151 >  double NkBT;
152  
153 <  double zeta;
153 >  // targetTemp, targetPressure, and tauBarostat must be set.  
154 >  // One of qmass or tauThermostat must be set;
155  
112 –  // targetTemp must be set.  One of qmass or tauThermostat must be set;
113 –
114 –  double qmass;
156    double targetTemp;
157 +  double targetPressure;
158    double tauThermostat;
159 +  double tauBarostat;
160  
161 <  short int have_tau_thermostat, have_target_temp, have_qmass;
161 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
162 >  short int have_target_pressure;
163  
164   };
165  
166 + template<typename T> class NPTim : public T{
167  
168 < class NPT : public Integrator{
168 > public:
169  
170 +  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
171 +  virtual ~NPTim() {};
172 +
173 +  virtual void integrateStep( int calcPot, int calcStress ){
174 +    calcStress = 1;
175 +    T::integrateStep( calcPot, calcStress );
176 +  }
177 +
178 +  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
179 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
180 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
181 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
182 +
183 + protected:
184 +
185 +  virtual void moveA( void );
186 +  virtual void moveB( void );
187 +
188 +  virtual int readyCheck();
189 +
190 +  Molecule* myMolecules;
191 +  Atom** myAtoms;
192 +
193 +  // chi and eta are the propagated degrees of freedom
194 +
195 +  double chi;
196 +  double eta;
197 +  double NkBT;
198 +
199 +  // targetTemp, targetPressure, and tauBarostat must be set.  
200 +  // One of qmass or tauThermostat must be set;
201 +
202 +  double targetTemp;
203 +  double targetPressure;
204 +  double tauThermostat;
205 +  double tauBarostat;
206 +
207 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
208 +  short int have_target_pressure;
209 +
210 + };
211 +
212 + template<typename T> class NPTf : public T{
213 +
214   public:
215  
216 <  NPT ( SimInfo &theInfo, ForceFields* the_ff) :
217 <    Integrator( theInfo, the_ff );
129 <  virtual ~NPT();
216 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
217 >  virtual ~NPTf() {};
218  
219 <  void setQmass(double q) {qmass = q; have_qmass = 1;}
219 >  virtual void integrateStep( int calcPot, int calcStress ){
220 >    calcStress = 1;
221 >    T::integrateStep( calcPot, calcStress );
222 >  }
223 >
224    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
225    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
226    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
# Line 136 | Line 228 | class NPT : public Integrator{ (protected)
228  
229   protected:
230  
231 <  virtual moveA( void );
232 <  virtual moveB( void );
231 >  virtual void  moveA( void );
232 >  virtual void moveB( void );
233  
234 <  int readyCheck();
234 >  virtual int readyCheck();
235  
236 <  Atom** atoms;
236 >  // chi and eta are the propagated degrees of freedom
237  
238 <  // zeta and epsilonDot are the propagated degrees of freedom.
238 >  double chi;
239 >  double eta[3][3];
240 >  double NkBT;
241  
242 <  double zeta;
243 <  double epsilonDot;
242 >  // targetTemp, targetPressure, and tauBarostat must be set.  
243 >  // One of qmass or tauThermostat must be set;
244 >
245 >  double targetTemp;
246 >  double targetPressure;
247 >  double tauThermostat;
248 >  double tauBarostat;
249 >
250 >  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
251 >  short int have_target_pressure;
252 >
253 > };
254 >
255 > template<typename T> class NPTfm : public T{
256 >
257 > public:
258 >
259 >  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
260 >  virtual ~NPTfm() {};
261  
262 +  virtual void integrateStep( int calcPot, int calcStress ){
263 +    calcStress = 1;
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  
154 –  double qmass;
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, have_qmass;
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;}
315 +  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
316 +  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
317 +  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
318 +
319 + protected:
320 +
321 +  virtual void  moveA( void );
322 +  virtual void moveB( void );
323 +
324 +  virtual int readyCheck();
325 +
326 +  // chi and eta are the propagated degrees of freedom
327 +
328 +  double chi;
329 +  double eta[3][3];
330 +  double NkBT;
331 +
332 +  // targetTemp, targetPressure, and tauBarostat must be set.  
333 +  // One of qmass or tauThermostat must be set;
334 +
335 +  double targetTemp;
336 +  double targetPressure;
337 +  double tauThermostat;
338 +  double tauBarostat;
339 +
340 +  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
341 +  short int have_target_pressure;
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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