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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 597 by mmeineke, Mon Jul 14 21:28:54 2003 UTC vs.
Revision 1268 by tim, Fri Jun 11 17:16:21 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[9] );
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 + template<typename T> class NVE : public T {
97 +
98   public:
99    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
100 <    Integrator( theInfo, the_ff ){}
100 >    T( theInfo, the_ff ){}
101    virtual ~NVE(){}
84 –
85 –  
86 –
102   };
103  
89 – class NVT : public Integrator{
104  
105 + template<typename T> class NVT : public T {
106 +
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 | class NVT : public Integrator{ (protected)
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  
120 – class NPTi : public Integrator{
150  
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 <    Integrator::integrateStep( calcPot, calcStress );
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 141 | Line 181 | class NPTi : public Integrator{ (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.  
151 <  // One of qmass or tauThermostat must be set;
191 >  virtual void calcVelScale( void ) = 0;
192  
193 <  double targetTemp;
194 <  double targetPressure;
155 <  double tauThermostat;
156 <  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 < };
201 >  virtual void scaleSimBox( void ) = 0;
202  
203 < class NPTim : public Integrator{
203 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
204  
165 – public:
166 –
167 –  NPTim ( SimInfo *theInfo, ForceFields* the_ff);
168 –  virtual ~NPTim() {};
169 –
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 –
180 – protected:
181 –
182 –  virtual void  moveA( void );
183 –  virtual void moveB( void );
184 –
185 –  virtual int readyCheck();
186 –
205    // chi and eta are the propagated degrees of freedom
206  
207 +  double oldChi;
208 +  double prevChi;
209    double chi;
190 –  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 201 | Line 229 | class NPTim : public Integrator{ (protected)
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 < class NPTf : public Integrator{
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  
213 –  virtual void integrateStep( int calcPot, int calcStress ){
214 –    calcStress = 1;
215 –    Integrator::integrateStep( calcPot, calcStress );
216 –  }
256  
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;}
257  
258 +  virtual void evolveEtaA(void);
259 +  virtual void evolveEtaB(void);
260 +
261 +  virtual bool etaConverged( void );
262 +
263 +  virtual void scaleSimBox( void );
264 +
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 +  virtual void calcVelScale( void );
271 +
272 +  double eta, oldEta, prevEta;
273 +  double vScale;
274 + };
275 +
276 + template<typename T> class NPTf : public T{
277 +
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  moveA( void );
290 <  virtual void moveB( void );
289 >  virtual void evolveEtaA(void);
290 >  virtual void evolveEtaB(void);
291  
292 <  virtual int readyCheck();
292 >  virtual bool etaConverged( void );
293  
294 <  // chi and eta are the propagated degrees of freedom
294 >  virtual void scaleSimBox( void );
295  
296 <  double chi;
297 <  double eta[3][3];
298 <  double NkBT;
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 <  // targetTemp, targetPressure, and tauBarostat must be set.  
237 <  // One of qmass or tauThermostat must be set;
301 >  virtual void calcVelScale( void );
302  
303 <  double targetTemp;
304 <  double targetPressure;
305 <  double tauThermostat;
306 <  double tauBarostat;
303 >  double eta[3][3];
304 >  double oldEta[3][3];
305 >  double prevEta[3][3];
306 >  double vScale[3][3];
307 > };
308  
309 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
245 <  short int have_target_pressure;
309 > template<typename T> class NPTxyz : public T{
310  
311 + public:
312 +
313 +  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
314 +  virtual ~NPTxyz();
315 +
316 +  virtual double getConservedQuantity(void);
317 +  virtual string getAdditionalParameters(void);
318 +  virtual void resetIntegrator(void);
319 +
320 + protected:
321 +
322 +  virtual void evolveEtaA(void);
323 +  virtual void evolveEtaB(void);
324 +
325 +  virtual bool etaConverged( void );
326 +
327 +  virtual void scaleSimBox( void );
328 +
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 +  virtual void calcVelScale( void );
335 +
336 +  double eta[3][3];
337 +  double oldEta[3][3];
338 +  double prevEta[3][3];
339 +  double vScale[3][3];
340   };
341  
249 – class NPTfm : public Integrator{
342  
343 + template<typename T> class ZConstraint : public T {
344 +
345 +  public:
346 +  class ForceSubtractionPolicy{
347 +    public:
348 +      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
349 +
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 +   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 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
392 <  virtual ~NPTfm() {};
391 >  ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
392 >  ~ZConstraint();
393  
394 <  virtual void integrateStep( int calcPot, int calcStress ){
395 <    calcStress = 1;
258 <    Integrator::integrateStep( calcPot, calcStress );
259 <  }
394 >  void setZConsTime(double time)                  {this->zconsTime = time;}
395 >  void getZConsTime()                             {return zconsTime;}
396  
397 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
398 <  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;}
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
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  
268 –  virtual void  moveA( void );
269 –  virtual void moveB( void );
423  
271 –  virtual int readyCheck();
424  
425 <  // chi and eta are the propagated degrees of freedom
425 >  virtual void calcForce( int calcPot, int calcStress );
426 >  virtual void thermalize(void);
427  
428 <  double chi;
429 <  double eta[3][3];
430 <  double NkBT;
428 >  void zeroOutVel();
429 >  void doZconstraintForce();
430 >  void doHarmonic(vector<double>& resPos);
431 >  bool checkZConsState();
432  
433 <  // targetTemp, targetPressure, and tauBarostat must be set.  
434 <  // One of qmass or tauThermostat must be set;
433 >  bool haveFixedZMols();
434 >  bool haveMovingZMols();
435  
436 <  double targetTemp;
283 <  double targetPressure;
284 <  double tauThermostat;
285 <  double tauBarostat;
436 >  double calcZSys();
437  
438 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
288 <  short int have_target_pressure;
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 +
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 +  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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