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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 596 by gezelter, Mon Jul 14 15:04:55 2003 UTC vs.
Revision 1330 by gezelter, Fri Jul 16 16:29:44 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"
11   #include "SimInfo.hpp"
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  
25 < class Integrator : public BaseIntegrator {
25 > class VelVerletConsFramework;
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  
25 –
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; }
35 –  
36 –  void checkConstraints( void );
37 –  void rotate( int axes1, int axes2, double angle, double j[3],
38 –               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
51 <                     // constraints.
52 <  int nConstrained;  // counter for number of constraints
53 <  int *constrainedA; // the i of a constraint pair
54 <  int *constrainedB; // the j of a constraint pair
55 <  double *constrainedDsqr; // the square of the constraint distance
56 <  
57 <  int* moving; // tells whether we are moving atom i
58 <  int* moved;  // tells whether we have moved atom i
59 <  double* oldPos; // pre constrained positions
68 >  VelVerletConsFramework* consFramework;
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  
66 –  double* pos;
67 –  double* vel;
68 –  double* frc;
69 –  double* trq;
70 –  double* Amat;
71 –
85    Thermo *tStats;
86    StatWriter*  statOut;
87    DumpWriter*  dumpOut;
88 <  
88 >
89   };
90  
91 < class NVE : public Integrator{
91 > typedef Integrator<BaseIntegrator> RealIntegrator;
92  
93 + // ansi instantiation
94 + // template class Integrator<BaseIntegrator>;
95 +
96 +
97 + template<typename T> class NVE : public T {
98 +
99   public:
100    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
101 <    Integrator( theInfo, the_ff ){}
101 >    T( theInfo, the_ff ){}
102    virtual ~NVE(){}
84 –
85 –  
86 –
103   };
104  
89 – class NVT : public Integrator{
105  
106 + template<typename T> class NVT : public T {
107 +
108   public:
109  
110    NVT ( SimInfo *theInfo, ForceFields* the_ff);
111 <  virtual ~NVT() {}
111 >  virtual ~NVT();
112  
113    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
114    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
115 +  void setChiTolerance(double tol) {chiTolerance = tol;}
116 +  virtual double  getConservedQuantity(void);
117 +  virtual string getAdditionalParameters(void);
118  
119   protected:
120  
# Line 103 | Line 123 | class NVT : public Integrator{ (protected)
123  
124    virtual int readyCheck();
125  
126 +  virtual void resetIntegrator( void );
127 +
128    // chi is a propagated degree of freedom.
129  
130    double chi;
131  
132 +  //integral of chi(t)dt
133 +  double integralOfChidt;
134 +
135    // targetTemp must be set.  tauThermostat must also be set;
136  
137    double targetTemp;
138    double tauThermostat;
139 <  
139 >
140    short int have_tau_thermostat, have_target_temp;
141  
142 +  double *oldVel;
143 +  double *oldJi;
144 +
145 +  double chiTolerance;
146 +  short int have_chi_tolerance;
147 +
148   };
149  
150  
120 – class NPTi : public Integrator{
151  
152 + template<typename T> class NPT : public T{
153 +
154   public:
155  
156 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
157 <  virtual ~NPTi() {};
156 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
157 >  virtual ~NPT();
158  
159    virtual void integrateStep( int calcPot, int calcStress ){
160      calcStress = 1;
161 <    Integrator::integrateStep( calcPot, calcStress );
161 >    T::integrateStep( calcPot, calcStress );
162    }
163  
164 +  virtual double getConservedQuantity(void) = 0;
165 +  virtual string getAdditionalParameters(void) = 0;
166 +  
167 +  double myTauThermo( void ) { return tauThermostat; }
168 +  double myTauBaro( void ) { return tauBarostat; }
169 +
170    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
171    void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
172    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
173    void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
174 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
175 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
176 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
177  
178   protected:
179  
# Line 141 | Line 182 | class NPTi : public Integrator{ (protected)
182  
183    virtual int readyCheck();
184  
185 +  virtual void resetIntegrator( void );
186 +
187 +  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
188 +  virtual void getVelScaleB( double sc[3], int index ) = 0;
189 +  virtual void getPosScale(double pos[3], double COM[3],
190 +                           int index, double sc[3]) = 0;
191 +
192 +  virtual void calcVelScale( void ) = 0;
193 +
194 +  virtual bool chiConverged( void );
195 +  virtual bool etaConverged( void ) = 0;
196 +
197 +  virtual void evolveChiA( void );
198 +  virtual void evolveEtaA( void ) = 0;
199 +  virtual void evolveChiB( void );
200 +  virtual void evolveEtaB( void ) = 0;
201 +
202 +  virtual void scaleSimBox( void ) = 0;
203 +
204 +  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
205 +
206    // chi and eta are the propagated degrees of freedom
207  
208 +  double oldChi;
209 +  double prevChi;
210    double chi;
147 –  double eta;
211    double NkBT;
212 +  double fkBT;
213  
214 <  // targetTemp, targetPressure, and tauBarostat must be set.  
214 >  double tt2, tb2;
215 >  double instaTemp, instaPress, instaVol;
216 >  double press[3][3];
217 >
218 >  int Nparticles;
219 >
220 >  double integralOfChidt;
221 >
222 >  // targetTemp, targetPressure, and tauBarostat must be set.
223    // One of qmass or tauThermostat must be set;
224  
225    double targetTemp;
# Line 158 | Line 230 | class NPTi : public Integrator{ (protected)
230    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
231    short int have_target_pressure;
232  
233 +  double *oldPos;
234 +  double *oldVel;
235 +  double *oldJi;
236 +
237 +  double chiTolerance;
238 +  short int have_chi_tolerance;
239 +  double posIterTolerance;
240 +  short int have_pos_iter_tolerance;
241 +  double etaTolerance;
242 +  short int have_eta_tolerance;
243 +
244   };
245  
246 < class NPTim : public Integrator{
246 > template<typename T> class NPTi : public T{
247  
248   public:
249 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
250 +  ~NPTi();
251  
252 <  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
253 <  virtual ~NPTim() {};
254 <
170 <  virtual void integrateStep( int calcPot, int calcStress ){
171 <    calcStress = 1;
172 <    Integrator::integrateStep( calcPot, calcStress );
173 <  }
174 <
175 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
176 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
177 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
178 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
179 <
252 >  virtual double getConservedQuantity(void);
253 >  virtual void resetIntegrator(void);
254 >  virtual string getAdditionalParameters(void);
255   protected:
256  
182 –  virtual void  moveA( void );
183 –  virtual void moveB( void );
257  
185 –  virtual int readyCheck();
258  
259 <  // chi and eta are the propagated degrees of freedom
259 >  virtual void evolveEtaA(void);
260 >  virtual void evolveEtaB(void);
261  
262 <  double chi;
190 <  double eta;
191 <  double NkBT;
262 >  virtual bool etaConverged( void );
263  
264 <  // targetTemp, targetPressure, and tauBarostat must be set.  
194 <  // One of qmass or tauThermostat must be set;
264 >  virtual void scaleSimBox( void );
265  
266 <  double targetTemp;
267 <  double targetPressure;
268 <  double tauThermostat;
269 <  double tauBarostat;
266 >  virtual void getVelScaleA( double sc[3], double vel[3] );
267 >  virtual void getVelScaleB( double sc[3], int index );
268 >  virtual void getPosScale(double pos[3], double COM[3],
269 >                           int index, double sc[3]);
270  
271 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
202 <  short int have_target_pressure;
271 >  virtual void calcVelScale( void );
272  
273 +  double eta, oldEta, prevEta;
274 +  double vScale;
275   };
276  
277 < class NPTf : public Integrator{
277 > template<typename T> class NPTf : public T{
278  
279   public:
280  
281    NPTf ( SimInfo *theInfo, ForceFields* the_ff);
282 <  virtual ~NPTf() {};
282 >  virtual ~NPTf();
283  
284 <  virtual void integrateStep( int calcPot, int calcStress ){
285 <    calcStress = 1;
286 <    Integrator::integrateStep( calcPot, calcStress );
216 <  }
284 >  virtual double getConservedQuantity(void);
285 >  virtual string getAdditionalParameters(void);
286 >  virtual void resetIntegrator(void);
287  
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;}
222 –
288   protected:
289  
290 <  virtual void  moveA( void );
291 <  virtual void moveB( void );
290 >  virtual void evolveEtaA(void);
291 >  virtual void evolveEtaB(void);
292  
293 <  virtual int readyCheck();
293 >  virtual bool etaConverged( void );
294  
295 <  // chi and eta are the propagated degrees of freedom
295 >  virtual void scaleSimBox( void );
296  
297 <  double chi;
298 <  double eta[3][3];
299 <  double NkBT;
297 >  virtual void getVelScaleA( double sc[3], double vel[3] );
298 >  virtual void getVelScaleB( double sc[3], int index );
299 >  virtual void getPosScale(double pos[3], double COM[3],
300 >                           int index, double sc[3]);
301  
302 <  // targetTemp, targetPressure, and tauBarostat must be set.  
237 <  // One of qmass or tauThermostat must be set;
302 >  virtual void calcVelScale( void );
303  
304 <  double targetTemp;
305 <  double targetPressure;
306 <  double tauThermostat;
307 <  double tauBarostat;
304 >  double eta[3][3];
305 >  double oldEta[3][3];
306 >  double prevEta[3][3];
307 >  double vScale[3][3];
308 > };
309  
310 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
245 <  short int have_target_pressure;
310 > template<typename T> class NPTxyz : public T{
311  
312 + public:
313 +
314 +  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
315 +  virtual ~NPTxyz();
316 +
317 +  virtual double getConservedQuantity(void);
318 +  virtual string getAdditionalParameters(void);
319 +  virtual void resetIntegrator(void);
320 +
321 + protected:
322 +
323 +  virtual void evolveEtaA(void);
324 +  virtual void evolveEtaB(void);
325 +
326 +  virtual bool etaConverged( void );
327 +
328 +  virtual void scaleSimBox( void );
329 +
330 +  virtual void getVelScaleA( double sc[3], double vel[3] );
331 +  virtual void getVelScaleB( double sc[3], int index );
332 +  virtual void getPosScale(double pos[3], double COM[3],
333 +                           int index, double sc[3]);
334 +
335 +  virtual void calcVelScale( void );
336 +
337 +  double eta[3][3];
338 +  double oldEta[3][3];
339 +  double prevEta[3][3];
340 +  double vScale[3][3];
341   };
342  
249 – class NPTfm : public Integrator{
343  
344 + template<typename T> class ZConstraint : public T {
345 +
346 +  public:
347 +  class ForceSubtractionPolicy{
348 +    public:
349 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
350 +
351 +      virtual void update() = 0;
352 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
353 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
354 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
355 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
356 +
357 +   protected:
358 +     ZConstraint<T>* zconsIntegrator;
359 +  };
360 +
361 +  class PolicyByNumber : public ForceSubtractionPolicy{
362 +
363 +    public:
364 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
365 +      virtual void update();
366 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
367 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
368 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
369 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
370 +
371 +    private:
372 +      int totNumOfMovingAtoms;
373 +  };
374 +
375 +  class PolicyByMass : public ForceSubtractionPolicy{
376 +
377 +    public:
378 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(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 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
393 <  virtual ~NPTfm() {};
392 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
393 >  ~ZConstraint();
394  
395 <  virtual void integrateStep( int calcPot, int calcStress ){
396 <    calcStress = 1;
258 <    Integrator::integrateStep( calcPot, calcStress );
259 <  }
395 >  void setZConsTime(double time)                  {this->zconsTime = time;}
396 >  void getZConsTime()                             {return zconsTime;}
397  
398 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
399 <  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;}
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 +  enum ZConsState {zcsMoving, zcsFixed};
412 +
413 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
414 +  vector<ZConsState> states;                 //state of z-constraint molecules
415 +
416 +
417 +
418 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
419 +  double totalMassOfUncons;                //total mas of unconstraint molecules
420 +
421 +
422   protected:
423  
268 –  virtual void  moveA( void );
269 –  virtual void moveB( void );
424  
271 –  virtual int readyCheck();
425  
426 <  // chi and eta are the propagated degrees of freedom
426 >  virtual void calcForce( int calcPot, int calcStress );
427 >  virtual void thermalize(void);
428  
429 <  double chi;
430 <  double eta[3][3];
431 <  double NkBT;
429 >  void zeroOutVel();
430 >  void doZconstraintForce();
431 >  void doHarmonic(vector<double>& resPos);
432 >  bool checkZConsState();
433  
434 <  // targetTemp, targetPressure, and tauBarostat must be set.  
435 <  // One of qmass or tauThermostat must be set;
434 >  bool haveFixedZMols();
435 >  bool haveMovingZMols();
436  
437 <  double targetTemp;
283 <  double targetPressure;
284 <  double tauThermostat;
285 <  double tauBarostat;
437 >  double calcZSys();
438  
439 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
288 <  short int have_target_pressure;
439 >  int isZConstraintMol(Molecule* mol);
440  
441 +
442 +  double zconsTime;                              //sample time
443 +  double zconsTol;                                 //tolerance of z-contratint
444 +  double zForceConst;                           //base force constant term
445 +                                                          //which is estimate by OOPSE
446 +
447 +
448 +  vector<double> massOfZConsMols;       //mass of z-constraint molecule
449 +  vector<double> kz;                              //force constant array
450 +
451 +  vector<double> zPos;                          //
452 +
453 +
454 +  vector<Molecule*> unconsMols;           //unconstraint molecules array
455 +  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
456 +
457 +
458 +  vector<ZConsParaItem>* parameters; //
459 +
460 +  vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
461 +
462 +  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
463 +  vector<double> fz;
464 +  vector<double> curZPos;
465 +
466 +  bool usingSMD;
467 +  vector<double> prevCantPos;
468 +  vector<double> cantPos;
469 +  vector<double> cantVel;
470 +
471 +  double zconsFixTime;  
472 +  double zconsGap;
473 +  bool hasZConsGap;
474 +  vector<double> endFixTime;
475 +  
476 +  int whichDirection;                           //constraint direction
477 +
478 + private:
479 +
480 +  string zconsOutput;                         //filename of zconstraint output
481 +  ZConsWriter* fzOut;                         //z-constraint writer
482 +
483 +  double curZconsTime;
484 +
485 +  double calcMovingMolsCOMVel();
486 +  double calcSysCOMVel();
487 +  double calcTotalForce();
488 +  void updateZPos();
489 +  void updateCantPos();
490 +  
491 +  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
492 +  friend class ForceSubtractionPolicy;
493 +
494   };
495  
496 +
497 + //Sympletic quaternion Scheme Integrator
498 + //Reference:
499 + // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
500 + //Symplectic quaternion Scheme for biophysical molecular dynamics
501 + //116(20), 8649, J. Chem. Phys. (2002)
502 + template<typename T> class SQSIntegrator : public T{
503 +  public:
504 +    virtual void moveA();
505 +    virtual void moveB();
506 +  protected:
507 +    void freeRotor();
508 +    void rotate(int k, double dt);
509 +    
510 + };
511   #endif

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