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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 645 by tim, Tue Jul 22 19:54:52 2003 UTC vs.
Revision 1198 by tim, Thu May 27 00:48:12 2004 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 "StuntDouble.hpp"
8   #include "Molecule.hpp"
9   #include "SRI.hpp"
10   #include "AbstractClasses.hpp"
# Line 9 | Line 12
12   #include "ForceFields.hpp"
13   #include "Thermo.hpp"
14   #include "ReadWrite.hpp"
15 + #include "ZConsWriter.hpp"
16 + #include "Restraints.hpp"
17  
18 + using namespace std;
19   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
20   const double eConvert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
21   const double p_convert = 1.63882576e8; //converts amu*fs^-2*Ang^-1 -> atm
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
19 –
25   template<typename T = BaseIntegrator> class Integrator : public T {
26  
27   public:
28    Integrator( SimInfo *theInfo, ForceFields* the_ff );
29    virtual ~Integrator();
30    void integrate( void );
31 +  virtual double  getConservedQuantity(void);
32 +  virtual string getAdditionalParameters(void);
33  
27 –
34   protected:
35 <  
35 >
36    virtual void integrateStep( int calcPot, int calcStress );
37    virtual void preMove( void );
38    virtual void moveA( void );
# Line 34 | Line 40 | template<typename T = BaseIntegrator> class Integrator
40    virtual void constrainA( void );
41    virtual void constrainB( void );
42    virtual int  readyCheck( void ) { return 1; }
37 –  
38 –  void checkConstraints( void );
39 –  void rotate( int axes1, int axes2, double angle, double j[3],
40 –               double A[3][3] );
43  
44 +  virtual void resetIntegrator( void ) { }
45  
46 +  virtual void calcForce( int calcPot, int calcStress );
47 +  virtual void thermalize();
48 +
49 +  virtual bool stopIntegrator() {return false;}
50 +
51 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
52 +
53 +  void checkConstraints( void );
54 +  void rotate( int axes1, int axes2, double angle, double j[3],
55 +         double A[3][3] );
56 +
57    ForceFields* myFF;
58  
59    SimInfo *info; // all the info we'll ever need
60 +  vector<StuntDouble*> integrableObjects;
61    int nAtoms;  /* the number of atoms */
62    int oldAtoms;
63    Atom **atoms; /* array of atom pointers */
# Line 50 | Line 65 | template<typename T = BaseIntegrator> class Integrator
65    int nMols;
66  
67    int isConstrained; // boolean to know whether the systems contains
68 <                     // constraints.
69 <  int nConstrained;  // counter for number of constraints
70 <  int *constrainedA; // the i of a constraint pair
71 <  int *constrainedB; // the j of a constraint pair
72 <  double *constrainedDsqr; // the square of the constraint distance
73 <  
68 >         // constraints.
69 >  int nConstrained;  // counter for number of constraints
70 >  int *constrainedA; // the i of a constraint pair
71 >  int *constrainedB; // the j of a constraint pair
72 >  double *constrainedDsqr; // the square of the constraint distance
73 >
74    int* moving; // tells whether we are moving atom i
75    int* moved;  // tells whether we have moved atom i
76 <  double* oldPos; // pre constrained positions
76 >  double* oldPos; // pre constrained positions
77  
78    short isFirst; /*boolean for the first time integrate is called */
79 <  
79 >
80    double dt;
81    double dt2;
82  
83    Thermo *tStats;
84    StatWriter*  statOut;
85    DumpWriter*  dumpOut;
86 <  
86 >
87   };
88  
89   typedef Integrator<BaseIntegrator> RealIntegrator;
90  
91 + // ansi instantiation
92 + template class Integrator<BaseIntegrator>;
93 +
94   template<typename T> class NVE : public T {
95  
96   public:
97    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
98      T( theInfo, the_ff ){}
99 <  virtual ~NVE(){}  
99 >  virtual ~NVE(){}
100   };
101  
102  
# Line 87 | Line 105 | template<typename T> class NVT : public T { (public)
105   public:
106  
107    NVT ( SimInfo *theInfo, ForceFields* the_ff);
108 <  virtual ~NVT() {}
108 >  virtual ~NVT();
109  
110    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
111    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
112 +  void setChiTolerance(double tol) {chiTolerance = tol;}
113 +  virtual double  getConservedQuantity(void);
114 +  virtual string getAdditionalParameters(void);
115  
116   protected:
117  
# Line 99 | Line 120 | template<typename T> class NVT : public T { (public)
120  
121    virtual int readyCheck();
122  
123 +  virtual void resetIntegrator( void );
124 +
125    // chi is a propagated degree of freedom.
126  
127    double chi;
128  
129 +  //integral of chi(t)dt
130 +  double integralOfChidt;
131 +
132    // targetTemp must be set.  tauThermostat must also be set;
133  
134    double targetTemp;
135    double tauThermostat;
136 <  
136 >
137    short int have_tau_thermostat, have_target_temp;
138  
139 +  double *oldVel;
140 +  double *oldJi;
141 +
142 +  double chiTolerance;
143 +  short int have_chi_tolerance;
144 +
145   };
146  
147  
148  
149 < template<typename T> class NPTi : public T{
149 > template<typename T> class NPT : public T{
150  
151   public:
152  
153 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
154 <  virtual ~NPTi() {};
153 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
154 >  virtual ~NPT();
155  
156    virtual void integrateStep( int calcPot, int calcStress ){
157      calcStress = 1;
158      T::integrateStep( calcPot, calcStress );
159    }
160  
161 +  virtual double getConservedQuantity(void) = 0;
162 +  virtual string getAdditionalParameters(void) = 0;
163 +  
164 +  double myTauThermo( void ) { return tauThermostat; }
165 +  double myTauBaro( void ) { return tauBarostat; }
166 +
167    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
168    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
169    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
170    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
171 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
172 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
173 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
174  
175   protected:
176  
# Line 138 | Line 179 | template<typename T> class NPTi : public T{ (protected
179  
180    virtual int readyCheck();
181  
182 <  // chi and eta are the propagated degrees of freedom
182 >  virtual void resetIntegrator( void );
183  
184 <  double chi;
185 <  double eta;
186 <  double NkBT;
184 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
185 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
186 >  virtual void getPosScale(double pos[3], double COM[3],
187 >                           int index, double sc[3]) = 0;
188  
189 <  // targetTemp, targetPressure, and tauBarostat must be set.  
148 <  // One of qmass or tauThermostat must be set;
189 >  virtual void calcVelScale( void ) = 0;
190  
191 <  double targetTemp;
192 <  double targetPressure;
152 <  double tauThermostat;
153 <  double tauBarostat;
191 >  virtual bool chiConverged( void );
192 >  virtual bool etaConverged( void ) = 0;
193  
194 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
195 <  short int have_target_pressure;
194 >  virtual void evolveChiA( void );
195 >  virtual void evolveEtaA( void ) = 0;
196 >  virtual void evolveChiB( void );
197 >  virtual void evolveEtaB( void ) = 0;
198  
199 < };
199 >  virtual void scaleSimBox( void ) = 0;
200  
201 < template<typename T> class NPTim : public T{
161 <
162 < public:
163 <
164 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
165 <  virtual ~NPTim() {};
166 <
167 <  virtual void integrateStep( int calcPot, int calcStress ){
168 <    calcStress = 1;
169 <    T::integrateStep( calcPot, calcStress );
170 <  }
201 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
202  
172 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
173 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
174 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
175 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
176 –
177 – protected:
178 –
179 –  virtual void moveA( void );
180 –  virtual void moveB( void );
181 –
182 –  virtual int readyCheck();
183 –
184 –  Molecule* myMolecules;
185 –  Atom** myAtoms;
186 –
203    // chi and eta are the propagated degrees of freedom
204  
205 +  double oldChi;
206 +  double prevChi;
207    double chi;
190 –  double eta;
208    double NkBT;
209 +  double fkBT;
210  
211 <  // targetTemp, targetPressure, and tauBarostat must be set.  
211 >  double tt2, tb2;
212 >  double instaTemp, instaPress, instaVol;
213 >  double press[3][3];
214 >
215 >  int Nparticles;
216 >
217 >  double integralOfChidt;
218 >
219 >  // targetTemp, targetPressure, and tauBarostat must be set.
220    // One of qmass or tauThermostat must be set;
221  
222    double targetTemp;
# Line 201 | Line 227 | template<typename T> class NPTim : public T{ (protecte
227    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
228    short int have_target_pressure;
229  
230 +  double *oldPos;
231 +  double *oldVel;
232 +  double *oldJi;
233 +
234 +  double chiTolerance;
235 +  short int have_chi_tolerance;
236 +  double posIterTolerance;
237 +  short int have_pos_iter_tolerance;
238 +  double etaTolerance;
239 +  short int have_eta_tolerance;
240 +
241   };
242  
243 < template<typename T> class NPTf : public T{
243 > template<typename T> class NPTi : public T{
244  
245   public:
246 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
247 +  ~NPTi();
248  
249 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
250 <  virtual ~NPTf() {};
249 >  virtual double getConservedQuantity(void);
250 >  virtual void resetIntegrator(void);
251 >  virtual string getAdditionalParameters(void);
252 > protected:
253  
213 –  virtual void integrateStep( int calcPot, int calcStress ){
214 –    calcStress = 1;
215 –    T::integrateStep( calcPot, calcStress );
216 –  }
254  
218 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
219 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
220 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
221 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
255  
256 < protected:
256 >  virtual void evolveEtaA(void);
257 >  virtual void evolveEtaB(void);
258  
259 <  virtual void  moveA( void );
226 <  virtual void moveB( void );
259 >  virtual bool etaConverged( void );
260  
261 <  virtual int readyCheck();
261 >  virtual void scaleSimBox( void );
262  
263 <  // chi and eta are the propagated degrees of freedom
263 >  virtual void getVelScaleA( double sc[3], double vel[3] );
264 >  virtual void getVelScaleB( double sc[3], int index );
265 >  virtual void getPosScale(double pos[3], double COM[3],
266 >                           int index, double sc[3]);
267  
268 <  double chi;
233 <  double eta[3][3];
234 <  double NkBT;
268 >  virtual void calcVelScale( void );
269  
270 <  // targetTemp, targetPressure, and tauBarostat must be set.  
271 <  // One of qmass or tauThermostat must be set;
270 >  double eta, oldEta, prevEta;
271 >  double vScale;
272 > };
273  
274 <  double targetTemp;
240 <  double targetPressure;
241 <  double tauThermostat;
242 <  double tauBarostat;
274 > template<typename T> class NPTf : public T{
275  
276 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
277 <  short int have_target_pressure;
276 > public:
277 >
278 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
279 >  virtual ~NPTf();
280 >
281 >  virtual double getConservedQuantity(void);
282 >  virtual string getAdditionalParameters(void);
283 >  virtual void resetIntegrator(void);
284 >
285 > protected:
286 >
287 >  virtual void evolveEtaA(void);
288 >  virtual void evolveEtaB(void);
289 >
290 >  virtual bool etaConverged( void );
291 >
292 >  virtual void scaleSimBox( void );
293 >
294 >  virtual void getVelScaleA( double sc[3], double vel[3] );
295 >  virtual void getVelScaleB( double sc[3], int index );
296 >  virtual void getPosScale(double pos[3], double COM[3],
297 >                           int index, double sc[3]);
298  
299 +  virtual void calcVelScale( void );
300 +
301 +  double eta[3][3];
302 +  double oldEta[3][3];
303 +  double prevEta[3][3];
304 +  double vScale[3][3];
305   };
306  
307 < template<typename T> class NPTfm : public T{
307 > template<typename T> class NPTxyz : public T{
308  
309   public:
310  
311 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
312 <  virtual ~NPTfm() {};
311 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
312 >  virtual ~NPTxyz();
313  
314 <  virtual void integrateStep( int calcPot, int calcStress ){
315 <    calcStress = 1;
316 <    T::integrateStep( calcPot, calcStress );
259 <  }
314 >  virtual double getConservedQuantity(void);
315 >  virtual string getAdditionalParameters(void);
316 >  virtual void resetIntegrator(void);
317  
261 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
262 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
263 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
264 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
265 –
318   protected:
319  
320 <  virtual void  moveA( void );
321 <  virtual void moveB( void );
320 >  virtual void evolveEtaA(void);
321 >  virtual void evolveEtaB(void);
322  
323 <  virtual int readyCheck();
323 >  virtual bool etaConverged( void );
324  
325 <  Molecule* myMolecules;
274 <  Atom** myAtoms;
325 >  virtual void scaleSimBox( void );
326  
327 <  // chi and eta are the propagated degrees of freedom
327 >  virtual void getVelScaleA( double sc[3], double vel[3] );
328 >  virtual void getVelScaleB( double sc[3], int index );
329 >  virtual void getPosScale(double pos[3], double COM[3],
330 >                           int index, double sc[3]);
331  
332 <  double chi;
332 >  virtual void calcVelScale( void );
333 >
334    double eta[3][3];
335 <  double NkBT;
335 >  double oldEta[3][3];
336 >  double prevEta[3][3];
337 >  double vScale[3][3];
338 > };
339  
282 –  // targetTemp, targetPressure, and tauBarostat must be set.  
283 –  // One of qmass or tauThermostat must be set;
340  
341 <  double targetTemp;
286 <  double targetPressure;
287 <  double tauThermostat;
288 <  double tauBarostat;
341 > template<typename T> class ZConstraint : public T {
342  
343 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
344 <  short int have_target_pressure;
343 >  public:
344 >  class ForceSubtractionPolicy{
345 >    public:
346 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
347  
348 +      virtual void update() = 0;
349 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
350 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
351 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
353 +
354 +   protected:
355 +     ZConstraint<T>* zconsIntegrator;
356 +  };
357 +
358 +  class PolicyByNumber : public ForceSubtractionPolicy{
359 +
360 +    public:
361 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
362 +      virtual void update();
363 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
364 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
365 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
366 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
367 +
368 +    private:
369 +      int totNumOfMovingAtoms;
370 +  };
371 +
372 +  class PolicyByMass : public ForceSubtractionPolicy{
373 +
374 +    public:
375 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
376 +
377 +      virtual void update();
378 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
379 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
380 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
381 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
382 +
383 +   private:
384 +     double totMassOfMovingAtoms;
385 +  };
386 +
387 + public:
388 +
389 +  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
390 +  ~ZConstraint();
391 +
392 +  void setZConsTime(double time)                  {this->zconsTime = time;}
393 +  void getZConsTime()                             {return zconsTime;}
394 +
395 +  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
396 +  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
397 +
398 +  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
399 +  string getZConsOutput()                         {return zconsOutput;}
400 +
401 +  virtual void integrate();
402 +
403 +
404 + #ifdef IS_MPI
405 +  virtual void update();                      //which is called to indicate the molecules' migration
406 + #endif
407 +
408 +  enum ZConsState {zcsMoving, zcsFixed};
409 +
410 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
411 +  vector<ZConsState> states;                 //state of z-constraint molecules
412 +
413 +
414 +
415 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
416 +  double totalMassOfUncons;                //total mas of unconstraint molecules
417 +
418 +
419 + protected:
420 +
421 +
422 +
423 +  virtual void calcForce( int calcPot, int calcStress );
424 +  virtual void thermalize(void);
425 +
426 +  void zeroOutVel();
427 +  void doZconstraintForce();
428 +  void doHarmonic(vector<double>& resPos);
429 +  bool checkZConsState();
430 +
431 +  bool haveFixedZMols();
432 +  bool haveMovingZMols();
433 +
434 +  double calcZSys();
435 +
436 +  int isZConstraintMol(Molecule* mol);
437 +
438 +
439 +  double zconsTime;                              //sample time
440 +  double zconsTol;                                 //tolerance of z-contratint
441 +  double zForceConst;                           //base force constant term
442 +                                                          //which is estimate by OOPSE
443 +
444 +
445 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
446 +  vector<double> kz;                              //force constant array
447 +
448 +  vector<double> zPos;                          //
449 +
450 +
451 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
452 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
453 +
454 +
455 +  vector<ZConsParaItem>* parameters; //
456 +
457 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
458 +
459 +  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
460 +  vector<double> fz;
461 +  vector<double> curZPos;
462 +
463 +  bool usingSMD;
464 +  vector<double> prevCantPos;
465 +  vector<double> cantPos;
466 +  vector<double> cantVel;
467 +
468 +  double zconsFixTime;  
469 +  double zconsGap;
470 +  bool hasZConsGap;
471 +  vector<double> endFixTime;
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 +  void updateZPos();
486 +  void updateCantPos();
487 +  
488 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
489 +  friend class ForceSubtractionPolicy;
490 +
491   };
492  
493   #endif

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