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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 1254 by tim, Wed Jun 9 16:16:33 2004 UTC

# Line 4 | Line 4
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 12 | Line 13
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
# Line 20 | Line 22 | const double tol = 1.0e-6;
22   const int maxIteration = 300;
23   const double tol = 1.0e-6;
24  
25 <
25 > class RattleFramework;
26   template<typename T = BaseIntegrator> class Integrator : public T {
27  
28   public:
29    Integrator( SimInfo *theInfo, ForceFields* the_ff );
30    virtual ~Integrator();
31    void integrate( void );
32 +  virtual double  getConservedQuantity(void);
33 +  virtual string getAdditionalParameters(void);
34  
31 –
35   protected:
36 <  
36 >
37    virtual void integrateStep( int calcPot, int calcStress );
38 <  virtual void preMove( void );
38 >  //virtual void preMove( void );
39    virtual void moveA( void );
40    virtual void moveB( void );
41 <  virtual void constrainA( void );
42 <  virtual void constrainB( void );
41 >  //virtual void constrainA( void );
42 >  //virtual void constrainB( void );
43    virtual int  readyCheck( void ) { return 1; }
41 –  
42 –  void checkConstraints( void );
43 –  void rotate( int axes1, int axes2, double angle, double j[3],
44 –               double A[3][3] );
44  
45 +  virtual void resetIntegrator( void ) { }
46  
47 +  virtual void calcForce( int calcPot, int calcStress );
48 +  virtual void thermalize();
49 +
50 +  virtual bool stopIntegrator() {return false;}
51 +
52 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
53 +
54 +  //void checkConstraints( void );
55 +  void rotate( int axes1, int axes2, double angle, double j[3],
56 +         double A[3][3] );
57 +
58    ForceFields* myFF;
59  
60    SimInfo *info; // all the info we'll ever need
61 +  vector<StuntDouble*> integrableObjects;
62    int nAtoms;  /* the number of atoms */
63    int oldAtoms;
64    Atom **atoms; /* array of atom pointers */
65    Molecule* molecules;
66    int nMols;
67  
68 <  int isConstrained; // boolean to know whether the systems contains
57 <                     // constraints.
58 <  int nConstrained;  // counter for number of constraints
59 <  int *constrainedA; // the i of a constraint pair
60 <  int *constrainedB; // the j of a constraint pair
61 <  double *constrainedDsqr; // the square of the constraint distance
62 <  
63 <  int* moving; // tells whether we are moving atom i
64 <  int* moved;  // tells whether we have moved atom i
65 <  double* oldPos; // pre constrained positions
68 >  RattleFramework* rattle;
69  
70 +  //int isConstrained; // boolean to know whether the systems contains constraints.
71 +  //int nConstrained;  // counter for number of constraints
72 +  //int *constrainedA; // the i of a constraint pair
73 +  //int *constrainedB; // the j of a constraint pair
74 +  //double *constrainedDsqr; // the square of the constraint distance
75 +
76 +  //int* moving; // tells whether we are moving atom i
77 +  //int* moved;  // tells whether we have moved atom i
78 +  //double* oldPos; // pre constrained positions
79 +
80    short isFirst; /*boolean for the first time integrate is called */
81 <  
81 >
82    double dt;
83    double dt2;
84  
85    Thermo *tStats;
86    StatWriter*  statOut;
87    DumpWriter*  dumpOut;
88 <  
88 >
89   };
90  
91   typedef Integrator<BaseIntegrator> RealIntegrator;
92  
93 + // ansi instantiation
94 + template class Integrator<BaseIntegrator>;
95 +
96   template<typename T> class NVE : public T {
97  
98   public:
99    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
100      T( theInfo, the_ff ){}
101 <  virtual ~NVE(){}  
101 >  virtual ~NVE(){}
102   };
103  
104  
# Line 91 | Line 107 | template<typename T> class NVT : public T { (public)
107   public:
108  
109    NVT ( SimInfo *theInfo, ForceFields* the_ff);
110 <  virtual ~NVT() {}
110 >  virtual ~NVT();
111  
112    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
113    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
114 +  void setChiTolerance(double tol) {chiTolerance = tol;}
115 +  virtual double  getConservedQuantity(void);
116 +  virtual string getAdditionalParameters(void);
117  
118   protected:
119  
# Line 103 | Line 122 | template<typename T> class NVT : public T { (public)
122  
123    virtual int readyCheck();
124  
125 +  virtual void resetIntegrator( void );
126 +
127    // chi is a propagated degree of freedom.
128  
129    double chi;
130  
131 +  //integral of chi(t)dt
132 +  double integralOfChidt;
133 +
134    // targetTemp must be set.  tauThermostat must also be set;
135  
136    double targetTemp;
137    double tauThermostat;
138 <  
138 >
139    short int have_tau_thermostat, have_target_temp;
140  
141 +  double *oldVel;
142 +  double *oldJi;
143 +
144 +  double chiTolerance;
145 +  short int have_chi_tolerance;
146 +
147   };
148  
149  
150  
151 < template<typename T> class NPTi : public T{
151 > template<typename T> class NPT : public T{
152  
153   public:
154  
155 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
156 <  virtual ~NPTi() {};
155 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
156 >  virtual ~NPT();
157  
158    virtual void integrateStep( int calcPot, int calcStress ){
159      calcStress = 1;
160      T::integrateStep( calcPot, calcStress );
161    }
162  
163 +  virtual double getConservedQuantity(void) = 0;
164 +  virtual string getAdditionalParameters(void) = 0;
165 +  
166 +  double myTauThermo( void ) { return tauThermostat; }
167 +  double myTauBaro( void ) { return tauBarostat; }
168 +
169    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
170    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
171    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
172    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
173 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
174 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
175 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
176  
177   protected:
178  
# Line 142 | Line 181 | template<typename T> class NPTi : public T{ (protected
181  
182    virtual int readyCheck();
183  
184 <  // chi and eta are the propagated degrees of freedom
184 >  virtual void resetIntegrator( void );
185  
186 <  double chi;
187 <  double eta;
188 <  double NkBT;
186 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
187 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
188 >  virtual void getPosScale(double pos[3], double COM[3],
189 >                           int index, double sc[3]) = 0;
190  
191 <  // targetTemp, targetPressure, and tauBarostat must be set.  
152 <  // One of qmass or tauThermostat must be set;
191 >  virtual void calcVelScale( void ) = 0;
192  
193 <  double targetTemp;
194 <  double targetPressure;
156 <  double tauThermostat;
157 <  double tauBarostat;
193 >  virtual bool chiConverged( void );
194 >  virtual bool etaConverged( void ) = 0;
195  
196 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
197 <  short int have_target_pressure;
196 >  virtual void evolveChiA( void );
197 >  virtual void evolveEtaA( void ) = 0;
198 >  virtual void evolveChiB( void );
199 >  virtual void evolveEtaB( void ) = 0;
200  
201 < };
163 <
164 < template<typename T> class NPTim : public T{
165 <
166 < public:
167 <
168 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
169 <  virtual ~NPTim() {};
170 <
171 <  virtual void integrateStep( int calcPot, int calcStress ){
172 <    calcStress = 1;
173 <    T::integrateStep( calcPot, calcStress );
174 <  }
201 >  virtual void scaleSimBox( void ) = 0;
202  
203 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
177 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
178 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
179 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
203 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
204  
181 – protected:
182 –
183 –  virtual void moveA( void );
184 –  virtual void moveB( void );
185 –
186 –  virtual int readyCheck();
187 –
188 –  Molecule* myMolecules;
189 –  Atom** myAtoms;
190 –
205    // chi and eta are the propagated degrees of freedom
206  
207 +  double oldChi;
208 +  double prevChi;
209    double chi;
194 –  double eta;
210    double NkBT;
211 +  double fkBT;
212  
213 <  // targetTemp, targetPressure, and tauBarostat must be set.  
213 >  double tt2, tb2;
214 >  double instaTemp, instaPress, instaVol;
215 >  double press[3][3];
216 >
217 >  int Nparticles;
218 >
219 >  double integralOfChidt;
220 >
221 >  // targetTemp, targetPressure, and tauBarostat must be set.
222    // One of qmass or tauThermostat must be set;
223  
224    double targetTemp;
# Line 205 | Line 229 | template<typename T> class NPTim : public T{ (protecte
229    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
230    short int have_target_pressure;
231  
232 +  double *oldPos;
233 +  double *oldVel;
234 +  double *oldJi;
235 +
236 +  double chiTolerance;
237 +  short int have_chi_tolerance;
238 +  double posIterTolerance;
239 +  short int have_pos_iter_tolerance;
240 +  double etaTolerance;
241 +  short int have_eta_tolerance;
242 +
243   };
244  
245 < template<typename T> class NPTf : public T{
245 > template<typename T> class NPTi : public T{
246  
247   public:
248 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
249 +  ~NPTi();
250  
251 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
252 <  virtual ~NPTf() {};
251 >  virtual double getConservedQuantity(void);
252 >  virtual void resetIntegrator(void);
253 >  virtual string getAdditionalParameters(void);
254 > protected:
255  
217 –  virtual void integrateStep( int calcPot, int calcStress ){
218 –    calcStress = 1;
219 –    T::integrateStep( calcPot, calcStress );
220 –  }
256  
222 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
223 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
224 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
225 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
257  
258 < protected:
258 >  virtual void evolveEtaA(void);
259 >  virtual void evolveEtaB(void);
260  
261 <  virtual void  moveA( void );
230 <  virtual void moveB( void );
261 >  virtual bool etaConverged( void );
262  
263 <  virtual int readyCheck();
263 >  virtual void scaleSimBox( void );
264  
265 <  // chi and eta are the propagated degrees of freedom
265 >  virtual void getVelScaleA( double sc[3], double vel[3] );
266 >  virtual void getVelScaleB( double sc[3], int index );
267 >  virtual void getPosScale(double pos[3], double COM[3],
268 >                           int index, double sc[3]);
269  
270 <  double chi;
237 <  double eta[3][3];
238 <  double NkBT;
270 >  virtual void calcVelScale( void );
271  
272 <  // targetTemp, targetPressure, and tauBarostat must be set.  
273 <  // One of qmass or tauThermostat must be set;
272 >  double eta, oldEta, prevEta;
273 >  double vScale;
274 > };
275  
276 <  double targetTemp;
244 <  double targetPressure;
245 <  double tauThermostat;
246 <  double tauBarostat;
276 > template<typename T> class NPTf : public T{
277  
278 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
249 <  short int have_target_pressure;
278 > public:
279  
280 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
281 +  virtual ~NPTf();
282 +
283 +  virtual double getConservedQuantity(void);
284 +  virtual string getAdditionalParameters(void);
285 +  virtual void resetIntegrator(void);
286 +
287 + protected:
288 +
289 +  virtual void evolveEtaA(void);
290 +  virtual void evolveEtaB(void);
291 +
292 +  virtual bool etaConverged( void );
293 +
294 +  virtual void scaleSimBox( void );
295 +
296 +  virtual void getVelScaleA( double sc[3], double vel[3] );
297 +  virtual void getVelScaleB( double sc[3], int index );
298 +  virtual void getPosScale(double pos[3], double COM[3],
299 +                           int index, double sc[3]);
300 +
301 +  virtual void calcVelScale( void );
302 +
303 +  double eta[3][3];
304 +  double oldEta[3][3];
305 +  double prevEta[3][3];
306 +  double vScale[3][3];
307   };
308  
309 < template<typename T> class NPTfm : public T{
309 > template<typename T> class NPTxyz : public T{
310  
311   public:
312  
313 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
314 <  virtual ~NPTfm() {};
313 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
314 >  virtual ~NPTxyz();
315  
316 <  virtual void integrateStep( int calcPot, int calcStress ){
317 <    calcStress = 1;
318 <    T::integrateStep( calcPot, calcStress );
263 <  }
316 >  virtual double getConservedQuantity(void);
317 >  virtual string getAdditionalParameters(void);
318 >  virtual void resetIntegrator(void);
319  
265 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
266 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
267 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
268 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
269 –
320   protected:
321  
322 <  virtual void  moveA( void );
323 <  virtual void moveB( void );
322 >  virtual void evolveEtaA(void);
323 >  virtual void evolveEtaB(void);
324  
325 <  virtual int readyCheck();
325 >  virtual bool etaConverged( void );
326  
327 <  Molecule* myMolecules;
278 <  Atom** myAtoms;
327 >  virtual void scaleSimBox( void );
328  
329 <  // chi and eta are the propagated degrees of freedom
329 >  virtual void getVelScaleA( double sc[3], double vel[3] );
330 >  virtual void getVelScaleB( double sc[3], int index );
331 >  virtual void getPosScale(double pos[3], double COM[3],
332 >                           int index, double sc[3]);
333  
334 <  double chi;
334 >  virtual void calcVelScale( void );
335 >
336    double eta[3][3];
337 <  double NkBT;
337 >  double oldEta[3][3];
338 >  double prevEta[3][3];
339 >  double vScale[3][3];
340 > };
341  
286 –  // targetTemp, targetPressure, and tauBarostat must be set.  
287 –  // One of qmass or tauThermostat must be set;
342  
343 <  double targetTemp;
290 <  double targetPressure;
291 <  double tauThermostat;
292 <  double tauBarostat;
343 > template<typename T> class ZConstraint : public T {
344  
345 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
346 <  short int have_target_pressure;
345 >  public:
346 >  class ForceSubtractionPolicy{
347 >    public:
348 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
349  
350 < };
350 >      virtual void update() = 0;
351 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
352 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
353 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
354 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
355  
356 < template<typename T> class ZConstraint : public T {
356 >   protected:
357 >     ZConstraint<T>* zconsIntegrator;
358 >  };
359  
360 +  class PolicyByNumber : public ForceSubtractionPolicy{
361 +
362 +    public:
363 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
364 +      virtual void update();
365 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
366 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
367 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
368 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
369 +
370 +    private:
371 +      int totNumOfMovingAtoms;
372 +  };
373 +
374 +  class PolicyByMass : public ForceSubtractionPolicy{
375 +
376 +    public:
377 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
378 +
379 +      virtual void update();
380 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
381 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
382 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
383 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
384 +
385 +   private:
386 +     double totMassOfMovingAtoms;
387 +  };
388 +
389   public:
390  
391    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
392    ~ZConstraint();
393  
306 –  virtual void integrateStep( int calcPot, int calcStress );
307 –  
308 –  
394    void setZConsTime(double time)                  {this->zconsTime = time;}
395    void getZConsTime()                             {return zconsTime;}
396 <  
397 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
398 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
399 <  
400 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
396 >
397 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
398 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
399 >
400 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
401    string getZConsOutput()                         {return zconsOutput;}
402  
403 +  virtual void integrate();
404 +
405 +
406   #ifdef IS_MPI
407 <  virtual void update(); //which is called to indicate the molecules' migration
407 >  virtual void update();                      //which is called to indicate the molecules' migration
408   #endif
409  
410 +  enum ZConsState {zcsMoving, zcsFixed};
411 +
412 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
413 +  vector<ZConsState> states;                 //state of z-constraint molecules
414 +
415 +
416 +
417 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
418 +  double totalMassOfUncons;                //total mas of unconstraint molecules
419 +
420 +
421   protected:
422  
324 –  double zconsTime;
325 –  
326 –  void resetZ(void);
327 –  
328 –  vector<Molecule*> zconsMols;
329 –  vector<double> massOfZConsMols;
330 –  
331 –  vector<Molecule*> unconsMols;
332 –  vector<double> massOfUnconsMols;
333 –  double totalMassOfUncons;
423  
424 <  vector<double> allRefZ;    
425 <  vector<double> refZ;
426 <  
424 >
425 >  virtual void calcForce( int calcPot, int calcStress );
426 >  virtual void thermalize(void);
427 >
428 >  void zeroOutVel();
429 >  void doZconstraintForce();
430 >  void doHarmonic(vector<double>& resPos);
431 >  bool checkZConsState();
432 >
433 >  bool haveFixedZMols();
434 >  bool haveMovingZMols();
435 >
436 >  double calcZSys();
437 >
438 >  int isZConstraintMol(Molecule* mol);
439 >
440 >
441 >  double zconsTime;                              //sample time
442 >  double zconsTol;                                 //tolerance of z-contratint
443 >  double zForceConst;                           //base force constant term
444 >                                                          //which is estimate by OOPSE
445 >
446 >
447 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
448 >  vector<double> kz;                              //force constant array
449 >
450 >  vector<double> zPos;                          //
451 >
452 >
453 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
454 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
455 >
456 >
457 >  vector<ZConsParaItem>* parameters; //
458 >
459    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
460 <  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
461 <    
462 <  double* fz;
460 >
461 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
462 >  vector<double> fz;
463 >  vector<double> curZPos;
464 >
465 >  bool usingSMD;
466 >  vector<double> prevCantPos;
467 >  vector<double> cantPos;
468 >  vector<double> cantVel;
469 >
470 >  double zconsFixTime;  
471 >  double zconsGap;
472 >  bool hasZConsGap;
473 >  vector<double> endFixTime;
474    
475 +  int whichDirection;                           //constraint direction
476 +
477   private:
478  
479 <  int isZConstraintMol(Molecule* mol);
480 <  string zconsOutput;
481 <  ZConsWriter* fzOut;
479 >  string zconsOutput;                         //filename of zconstraint output
480 >  ZConsWriter* fzOut;                         //z-constraint writer
481 >
482 >  double curZconsTime;
483 >
484 >  double calcMovingMolsCOMVel();
485 >  double calcSysCOMVel();
486 >  double calcTotalForce();
487 >  void updateZPos();
488 >  void updateCantPos();
489 >  
490 >  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
491 >  friend class ForceSubtractionPolicy;
492 >
493   };
494  
495 +
496 + //Sympletic quaternion Scheme Integrator
497 + //Reference:
498 + // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
499 + //Symplectic quaternion Scheme for biophysical molecular dynamics
500 + //116(20), 8649, J. Chem. Phys. (2002)
501 + template<typename T> class SQSIntegrator : public T{
502 +  public:
503 +    virtual void moveA();
504 +    virtual void moveB();
505 +  protected:
506 +    void freeRotor();
507 +    void rotate(int k, double dt);
508 +    
509 + };
510   #endif

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