ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/Integrator.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC vs.
Revision 1452 by tim, Mon Aug 23 15:11:36 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 + #include "Quaternion.hpp"
18 + #include "Mat4x4d.hpp"
19  
20   using namespace std;
21   const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K
# Line 20 | Line 24 | const double tol = 1.0e-6;
24   const int maxIteration = 300;
25   const double tol = 1.0e-6;
26  
27 <
27 > class VelVerletConsFramework;
28   template<typename T = BaseIntegrator> class Integrator : public T {
29  
30   public:
31    Integrator( SimInfo *theInfo, ForceFields* the_ff );
32    virtual ~Integrator();
33    void integrate( void );
34 +  virtual double  getConservedQuantity(void);
35 +  virtual string getAdditionalParameters(void);
36  
31 –
37   protected:
38 <  
38 >
39    virtual void integrateStep( int calcPot, int calcStress );
40 <  virtual void preMove( void );
40 >  //virtual void preMove( void );
41    virtual void moveA( void );
42    virtual void moveB( void );
43 <  virtual void constrainA( void );
44 <  virtual void constrainB( void );
43 >  //virtual void constrainA( void );
44 >  //virtual void constrainB( void );
45    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] );
46  
47 +  virtual void resetIntegrator( void ) { }
48  
49 +  virtual void calcForce( int calcPot, int calcStress );
50 +  virtual void thermalize();
51 +
52 +  virtual bool stopIntegrator() {return false;}
53 +
54 +  virtual void rotationPropagation( StuntDouble* sd, double ji[3] );
55 +
56 +  //void checkConstraints( void );
57 +  void rotate( int axes1, int axes2, double angle, double j[3],
58 +         double A[3][3] );
59 +
60 +  void printQuaternion(StuntDouble* sd);
61 +  Mat4x4d getS(const Quaternion& q);
62 +
63    ForceFields* myFF;
64  
65    SimInfo *info; // all the info we'll ever need
66 +  vector<StuntDouble*> integrableObjects;
67    int nAtoms;  /* the number of atoms */
68    int oldAtoms;
69    Atom **atoms; /* array of atom pointers */
70    Molecule* molecules;
71    int nMols;
72  
73 <  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
73 >  VelVerletConsFramework* consFramework;
74  
75 +  //int isConstrained; // boolean to know whether the systems contains constraints.
76 +  //int nConstrained;  // counter for number of constraints
77 +  //int *constrainedA; // the i of a constraint pair
78 +  //int *constrainedB; // the j of a constraint pair
79 +  //double *constrainedDsqr; // the square of the constraint distance
80 +
81 +  //int* moving; // tells whether we are moving atom i
82 +  //int* moved;  // tells whether we have moved atom i
83 +  //double* oldPos; // pre constrained positions
84 +
85    short isFirst; /*boolean for the first time integrate is called */
86 <  
86 >
87    double dt;
88    double dt2;
89  
90    Thermo *tStats;
91    StatWriter*  statOut;
92    DumpWriter*  dumpOut;
93 <  
93 >
94   };
95  
96   typedef Integrator<BaseIntegrator> RealIntegrator;
97  
98 + // ansi instantiation
99 + // template class Integrator<BaseIntegrator>;
100 +
101 +
102   template<typename T> class NVE : public T {
103  
104   public:
105    NVE ( SimInfo *theInfo, ForceFields* the_ff ):
106      T( theInfo, the_ff ){}
107 <  virtual ~NVE(){}  
107 >  virtual ~NVE(){}
108   };
109  
110  
# Line 91 | Line 113 | template<typename T> class NVT : public T { (public)
113   public:
114  
115    NVT ( SimInfo *theInfo, ForceFields* the_ff);
116 <  virtual ~NVT() {}
116 >  virtual ~NVT();
117  
118    void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
119    void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
120 +  void setChiTolerance(double tol) {chiTolerance = tol;}
121 +  virtual double  getConservedQuantity(void);
122 +  virtual string getAdditionalParameters(void);
123  
124   protected:
125  
# Line 103 | Line 128 | template<typename T> class NVT : public T { (public)
128  
129    virtual int readyCheck();
130  
131 +  virtual void resetIntegrator( void );
132 +
133    // chi is a propagated degree of freedom.
134  
135    double chi;
136  
137 +  //integral of chi(t)dt
138 +  double integralOfChidt;
139 +
140    // targetTemp must be set.  tauThermostat must also be set;
141  
142    double targetTemp;
143    double tauThermostat;
144 <  
144 >
145    short int have_tau_thermostat, have_target_temp;
146  
147 +  double *oldVel;
148 +  double *oldJi;
149 +
150 +  double chiTolerance;
151 +  short int have_chi_tolerance;
152 +
153   };
154  
155  
156  
157 < template<typename T> class NPTi : public T{
157 > template<typename T> class NPT : public T{
158  
159   public:
160  
161 <  NPTi ( SimInfo *theInfo, ForceFields* the_ff);
162 <  virtual ~NPTi() {};
161 >  NPT ( SimInfo *theInfo, ForceFields* the_ff);
162 >  virtual ~NPT();
163  
164    virtual void integrateStep( int calcPot, int calcStress ){
165      calcStress = 1;
166      T::integrateStep( calcPot, calcStress );
167    }
168  
169 +  virtual double getConservedQuantity(void) = 0;
170 +  virtual string getAdditionalParameters(void) = 0;
171 +  
172 +  double myTauThermo( void ) { return tauThermostat; }
173 +  double myTauBaro( void ) { return tauBarostat; }
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 +  void setChiTolerance(double tol) {chiTolerance = tol; have_chi_tolerance = 1;}
180 +  void setPosIterTolerance(double tol) {posIterTolerance = tol; have_pos_iter_tolerance = 1;}
181 +  void setEtaTolerance(double tol) {etaTolerance = tol; have_eta_tolerance = 1;}
182  
183   protected:
184  
# Line 142 | Line 187 | template<typename T> class NPTi : public T{ (protected
187  
188    virtual int readyCheck();
189  
190 <  // chi and eta are the propagated degrees of freedom
190 >  virtual void resetIntegrator( void );
191  
192 <  double chi;
193 <  double eta;
194 <  double NkBT;
192 >  virtual void getVelScaleA( double sc[3], double vel[3] ) = 0;
193 >  virtual void getVelScaleB( double sc[3], int index ) = 0;
194 >  virtual void getPosScale(double pos[3], double COM[3],
195 >                           int index, double sc[3]) = 0;
196  
197 <  // targetTemp, targetPressure, and tauBarostat must be set.  
152 <  // One of qmass or tauThermostat must be set;
197 >  virtual void calcVelScale( void ) = 0;
198  
199 <  double targetTemp;
200 <  double targetPressure;
156 <  double tauThermostat;
157 <  double tauBarostat;
199 >  virtual bool chiConverged( void );
200 >  virtual bool etaConverged( void ) = 0;
201  
202 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
203 <  short int have_target_pressure;
202 >  virtual void evolveChiA( void );
203 >  virtual void evolveEtaA( void ) = 0;
204 >  virtual void evolveChiB( void );
205 >  virtual void evolveEtaB( void ) = 0;
206  
207 < };
207 >  virtual void scaleSimBox( void ) = 0;
208  
209 < 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 <  }
209 >  void accIntegralOfChidt(void) { integralOfChidt += dt * chi;}
210  
176 –  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;}
180 –
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 –
211    // chi and eta are the propagated degrees of freedom
212  
213 +  double oldChi;
214 +  double prevChi;
215    double chi;
194 –  double eta;
216    double NkBT;
217 +  double fkBT;
218  
219 <  // targetTemp, targetPressure, and tauBarostat must be set.  
219 >  double tt2, tb2;
220 >  double instaTemp, instaPress, instaVol;
221 >  double press[3][3];
222 >
223 >  int Nparticles;
224 >
225 >  double integralOfChidt;
226 >
227 >  // targetTemp, targetPressure, and tauBarostat must be set.
228    // One of qmass or tauThermostat must be set;
229  
230    double targetTemp;
# Line 205 | Line 235 | template<typename T> class NPTim : public T{ (protecte
235    short int have_tau_thermostat, have_tau_barostat, have_target_temp;
236    short int have_target_pressure;
237  
238 +  double *oldPos;
239 +  double *oldVel;
240 +  double *oldJi;
241 +
242 +  double chiTolerance;
243 +  short int have_chi_tolerance;
244 +  double posIterTolerance;
245 +  short int have_pos_iter_tolerance;
246 +  double etaTolerance;
247 +  short int have_eta_tolerance;
248 +
249   };
250  
251 < template<typename T> class NPTf : public T{
251 > template<typename T> class NPTi : public T{
252  
253   public:
254 +  NPTi( SimInfo *theInfo, ForceFields* the_ff);
255 +  ~NPTi();
256  
257 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
258 <  virtual ~NPTf() {};
257 >  virtual double getConservedQuantity(void);
258 >  virtual void resetIntegrator(void);
259 >  virtual string getAdditionalParameters(void);
260 > protected:
261  
217 –  virtual void integrateStep( int calcPot, int calcStress ){
218 –    calcStress = 1;
219 –    T::integrateStep( calcPot, calcStress );
220 –  }
262  
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;}
263  
264 < protected:
264 >  virtual void evolveEtaA(void);
265 >  virtual void evolveEtaB(void);
266  
267 <  virtual void  moveA( void );
230 <  virtual void moveB( void );
267 >  virtual bool etaConverged( void );
268  
269 <  virtual int readyCheck();
269 >  virtual void scaleSimBox( void );
270  
271 <  // chi and eta are the propagated degrees of freedom
271 >  virtual void getVelScaleA( double sc[3], double vel[3] );
272 >  virtual void getVelScaleB( double sc[3], int index );
273 >  virtual void getPosScale(double pos[3], double COM[3],
274 >                           int index, double sc[3]);
275  
276 <  double chi;
237 <  double eta[3][3];
238 <  double NkBT;
276 >  virtual void calcVelScale( void );
277  
278 <  // targetTemp, targetPressure, and tauBarostat must be set.  
279 <  // One of qmass or tauThermostat must be set;
278 >  double eta, oldEta, prevEta;
279 >  double vScale;
280 > };
281  
282 <  double targetTemp;
244 <  double targetPressure;
245 <  double tauThermostat;
246 <  double tauBarostat;
282 > template<typename T> class NPTf : public T{
283  
284 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
249 <  short int have_target_pressure;
284 > public:
285  
286 +  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
287 +  virtual ~NPTf();
288 +
289 +  virtual double getConservedQuantity(void);
290 +  virtual string getAdditionalParameters(void);
291 +  virtual void resetIntegrator(void);
292 +
293 + protected:
294 +
295 +  virtual void evolveEtaA(void);
296 +  virtual void evolveEtaB(void);
297 +
298 +  virtual bool etaConverged( void );
299 +
300 +  virtual void scaleSimBox( void );
301 +
302 +  virtual void getVelScaleA( double sc[3], double vel[3] );
303 +  virtual void getVelScaleB( double sc[3], int index );
304 +  virtual void getPosScale(double pos[3], double COM[3],
305 +                           int index, double sc[3]);
306 +
307 +  virtual void calcVelScale( void );
308 +
309 +  double eta[3][3];
310 +  double oldEta[3][3];
311 +  double prevEta[3][3];
312 +  double vScale[3][3];
313   };
314  
315 < template<typename T> class NPTfm : public T{
315 > template<typename T> class NPTxyz : public T{
316  
317   public:
318  
319 <  NPTfm ( SimInfo *theInfo, ForceFields* the_ff);
320 <  virtual ~NPTfm() {};
259 <
260 <  virtual void integrateStep( int calcPot, int calcStress ){
261 <    calcStress = 1;
262 <    T::integrateStep( calcPot, calcStress );
263 <  }
319 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
320 >  virtual ~NPTxyz();
321  
322 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
323 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
324 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
268 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
322 >  virtual double getConservedQuantity(void);
323 >  virtual string getAdditionalParameters(void);
324 >  virtual void resetIntegrator(void);
325  
326   protected:
327  
328 <  virtual void  moveA( void );
329 <  virtual void moveB( void );
328 >  virtual void evolveEtaA(void);
329 >  virtual void evolveEtaB(void);
330  
331 <  virtual int readyCheck();
331 >  virtual bool etaConverged( void );
332  
333 <  Molecule* myMolecules;
278 <  Atom** myAtoms;
333 >  virtual void scaleSimBox( void );
334  
335 <  // chi and eta are the propagated degrees of freedom
335 >  virtual void getVelScaleA( double sc[3], double vel[3] );
336 >  virtual void getVelScaleB( double sc[3], int index );
337 >  virtual void getPosScale(double pos[3], double COM[3],
338 >                           int index, double sc[3]);
339  
340 <  double chi;
340 >  virtual void calcVelScale( void );
341 >
342    double eta[3][3];
343 <  double NkBT;
343 >  double oldEta[3][3];
344 >  double prevEta[3][3];
345 >  double vScale[3][3];
346 > };
347  
286 –  // targetTemp, targetPressure, and tauBarostat must be set.  
287 –  // One of qmass or tauThermostat must be set;
348  
349 <  double targetTemp;
290 <  double targetPressure;
291 <  double tauThermostat;
292 <  double tauBarostat;
349 > template<typename T> class ZConstraint : public T {
350  
351 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
352 <  short int have_target_pressure;
351 >  public:
352 >  class ForceSubtractionPolicy{
353 >    public:
354 >      ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
355  
356 < };
356 >      virtual void update() = 0;
357 >      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
358 >      virtual double getZFOfMovingMols(Atom* atom, double totalForce) = 0;
359 >      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) = 0;
360 >      virtual double getHFOfUnconsMols(Atom* atom, double totalForce) = 0;
361  
362 < template<typename T> class ZConstraint : public T {
362 >   protected:
363 >     ZConstraint<T>* zconsIntegrator;
364 >  };
365  
366 +  class PolicyByNumber : public ForceSubtractionPolicy{
367 +
368 +    public:
369 +      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
370 +      virtual void update();
371 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
372 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
373 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
374 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
375 +
376 +    private:
377 +      int totNumOfMovingAtoms;
378 +  };
379 +
380 +  class PolicyByMass : public ForceSubtractionPolicy{
381 +
382 +    public:
383 +      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}
384 +
385 +      virtual void update();
386 +      virtual double getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce) ;
387 +      virtual double getZFOfMovingMols(Atom* atom, double totalForce) ;
388 +      virtual double getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce);
389 +      virtual double getHFOfUnconsMols(Atom* atom, double totalForce);
390 +
391 +   private:
392 +     double totMassOfMovingAtoms;
393 +  };
394 +
395   public:
396  
397    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
398    ~ZConstraint();
399  
306 –  virtual void integrateStep( int calcPot, int calcStress );
307 –  
308 –  
400    void setZConsTime(double time)                  {this->zconsTime = time;}
401    void getZConsTime()                             {return zconsTime;}
402 <  
403 <  void setIndexOfAllZConsMols(vector<int> index)  {indexOfAllZConsMols = index;}
404 <  void getIndexOfAllZConsMols()                   {return indexOfAllZConsMols;}
405 <  
406 <  void setZConsOutput(const char * fileName)      {zconsOutput = fileName;}
402 >
403 >  void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
404 >  void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
405 >
406 >  void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
407    string getZConsOutput()                         {return zconsOutput;}
408  
409 +  virtual void integrate();
410 +
411 +
412   #ifdef IS_MPI
413 <  virtual void update(); //which is called to indicate the molecules' migration
413 >  virtual void update();                      //which is called to indicate the molecules' migration
414   #endif
415  
416 +  enum ZConsState {zcsMoving, zcsFixed};
417 +
418 +  vector<Molecule*> zconsMols;              //z-constraint molecules array
419 +  vector<ZConsState> states;                 //state of z-constraint molecules
420 +
421 +
422 +
423 +  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
424 +  double totalMassOfUncons;                //total mas of unconstraint molecules
425 +
426 +
427   protected:
428  
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;
429  
430 <  vector<double> allRefZ;    
431 <  vector<double> refZ;
432 <  
430 >
431 >  virtual void calcForce( int calcPot, int calcStress );
432 >  virtual void thermalize(void);
433 >
434 >  void zeroOutVel();
435 >  void doZconstraintForce();
436 >  void doHarmonic(vector<double>& resPos);
437 >  bool checkZConsState();
438 >
439 >  bool haveFixedZMols();
440 >  bool haveMovingZMols();
441 >
442 >  double calcZSys();
443 >
444 >  int isZConstraintMol(Molecule* mol);
445 >
446 >
447 >  double zconsTime;                              //sample time
448 >  double zconsTol;                                 //tolerance of z-contratint
449 >  double zForceConst;                           //base force constant term
450 >                                                          //which is estimate by OOPSE
451 >
452 >
453 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
454 >  vector<double> kz;                              //force constant array
455 >
456 >  vector<double> zPos;                          //
457 >
458 >
459 >  vector<Molecule*> unconsMols;           //unconstraint molecules array
460 >  vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
461 >
462 >
463 >  vector<ZConsParaItem>* parameters; //
464 >
465    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
466 <  int* indexOfZConsMols;               //index of local Z-Constraint Molecules
467 <    
468 <  double* fz;
466 >
467 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
468 >  vector<double> fz;
469 >  vector<double> curZPos;
470 >
471 >  bool usingSMD;
472 >  vector<double> prevCantPos;
473 >  vector<double> cantPos;
474 >  vector<double> cantVel;
475 >
476 >  double zconsFixTime;  
477 >  double zconsGap;
478 >  bool hasZConsGap;
479 >  vector<double> endFixTime;
480    
481 +  int whichDirection;                           //constraint direction
482 +
483   private:
484  
485 <  int isZConstraintMol(Molecule* mol);
486 <  string zconsOutput;
487 <  ZConsWriter* fzOut;
485 >  string zconsOutput;                         //filename of zconstraint output
486 >  ZConsWriter* fzOut;                         //z-constraint writer
487 >
488 >  double curZconsTime;
489 >
490 >  double calcMovingMolsCOMVel();
491 >  double calcSysCOMVel();
492 >  double calcTotalForce();
493 >  void updateZPos();
494 >  void updateCantPos();
495 >  
496 >  ForceSubtractionPolicy* forcePolicy; //force subtraction policy
497 >  friend class ForceSubtractionPolicy;
498 >
499   };
500  
501 +
502 + //Sympletic quaternion Scheme Integrator
503 + //Reference:
504 + // T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna
505 + //Symplectic quaternion Scheme for biophysical molecular dynamics
506 + //116(20), 8649, J. Chem. Phys. (2002)
507 + template<typename T> class SQSIntegrator : public T{
508 +  public:
509 +    SQSIntegrator( SimInfo *theInfo, ForceFields* the_ff );
510 +    virtual void moveA();
511 +    virtual void moveB();
512 +  protected:
513 +    void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I);
514 +    void rotate(int k, double dt,  Quaternion& q,  Vector4d& qdot, double Ik);
515 +  private:
516 +    Quaternion getPk(int i, const Vector4d& q);
517 +    Mat4x4d getS(const Quaternion& q);
518 +    vector<Quaternion> q;
519 +    vector<Vector4d> p_qua;
520 +    vector<double> I0;
521 +
522 +                Vector4d p2j(const Vector4d& p, Mat4x4d& m);    
523 +                Vector4d j2p(const Vector4d& j, Mat4x4d& m);
524 + };
525   #endif

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines