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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 782 by mmeineke, Tue Sep 23 20:34:31 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:
# Line 28 | Line 32 | template<typename T = BaseIntegrator> class Integrator
32    virtual ~Integrator();
33    void integrate( void );
34    virtual double  getConservedQuantity(void);
35 +  virtual string getAdditionalParameters(void);
36  
37   protected:
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; }
46  
47    virtual void resetIntegrator( void ) { }
48 <
49 <  virtual void calcForce( int calcPot, int calcStress );  
48 >
49 >  virtual void calcForce( int calcPot, int calcStress );
50    virtual void thermalize();
46 –  
47 –  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
51  
52 <  void checkConstraints( void );
53 <  void rotate( int axes1, int axes2, double angle, double j[3],
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 <        
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
63 <         // constraints.
64 <  int nConstrained;  // counter for number of constraints
65 <  int *constrainedA; // the i of a constraint pair
66 <  int *constrainedB; // the j of a constraint pair
67 <  double *constrainedDsqr; // the square of the constraint distance
68 <  
69 <  int* moving; // tells whether we are moving atom i
70 <  int* moved;  // tells whether we have moved atom i
71 <  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 103 | Line 119 | template<typename T> class NVT : public T { (public)
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 124 | Line 141 | template<typename T> class NVT : public T { (public)
141  
142    double targetTemp;
143    double tauThermostat;
144 <  
144 >
145    short int have_tau_thermostat, have_target_temp;
146  
147    double *oldVel;
# Line 143 | Line 160 | template<typename T> class NPT : public T{ (public)
160  
161    NPT ( SimInfo *theInfo, ForceFields* the_ff);
162    virtual ~NPT();
163 <  
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;}
# Line 170 | Line 191 | template<typename T> class NPT : public T{ (public)
191  
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],
194 >  virtual void getPosScale(double pos[3], double COM[3],
195                             int index, double sc[3]) = 0;
196  
197 +  virtual void calcVelScale( void ) = 0;
198 +
199    virtual bool chiConverged( void );
200    virtual bool etaConverged( void ) = 0;
201 <  
201 >
202    virtual void evolveChiA( void );
203    virtual void evolveEtaA( void ) = 0;
204    virtual void evolveChiB( void );
# Line 201 | Line 224 | template<typename T> class NPT : public T{ (public)
224  
225    double integralOfChidt;
226  
227 <  // targetTemp, targetPressure, and tauBarostat must be set.  
227 >  // targetTemp, targetPressure, and tauBarostat must be set.
228    // One of qmass or tauThermostat must be set;
229  
230    double targetTemp;
# Line 226 | Line 249 | template<typename T> class NPTi : public T{
249   };
250  
251   template<typename T> class NPTi : public T{
252 <  
252 >
253   public:
254    NPTi( SimInfo *theInfo, ForceFields* the_ff);
255    ~NPTi();
256  
257    virtual double getConservedQuantity(void);
258    virtual void resetIntegrator(void);
259 <
259 >  virtual string getAdditionalParameters(void);
260   protected:
261  
239 –
262  
263 +
264    virtual void evolveEtaA(void);
265    virtual void evolveEtaB(void);
266  
# Line 247 | Line 270 | template<typename T> class NPTi : public T{ (protected
270  
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],
273 >  virtual void getPosScale(double pos[3], double COM[3],
274                             int index, double sc[3]);
275  
276 +  virtual void calcVelScale( void );
277 +
278    double eta, oldEta, prevEta;
279 +  double vScale;
280   };
281  
282 < template<typename T> class NPTzm : public T{
282 > template<typename T> class NPTf : public T{
283  
284   public:
285  
286 <  NPTzm ( SimInfo *theInfo, ForceFields* the_ff);
287 <  virtual ~NPTzm() {};
286 >  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
287 >  virtual ~NPTf();
288  
289 <  virtual void integrateStep( int calcPot, int calcStress ){
290 <    calcStress = 1;
291 <    T::integrateStep( calcPot, calcStress );
266 <  }
289 >  virtual double getConservedQuantity(void);
290 >  virtual string getAdditionalParameters(void);
291 >  virtual void resetIntegrator(void);
292  
268 –  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
269 –  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
270 –  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
271 –  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
272 –
293   protected:
294  
295 <  virtual void moveA( void );
296 <  virtual void moveB( void );
295 >  virtual void evolveEtaA(void);
296 >  virtual void evolveEtaB(void);
297  
298 <  virtual int readyCheck();
298 >  virtual bool etaConverged( void );
299  
300 <  virtual void resetIntegrator( void );
300 >  virtual void scaleSimBox( void );
301  
302 <  Molecule* myMolecules;
303 <  Atom** myAtoms;
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 <  // chi and eta are the propagated degrees of freedom
307 >  virtual void calcVelScale( void );
308  
309 <  double chi;
310 <  double eta;
311 <  double etaZ;
312 <  double NkBT;
291 <
292 <  // targetTemp, targetPressure, and tauBarostat must be set.  
293 <  // One of qmass or tauThermostat must be set;
294 <
295 <  double targetTemp;
296 <  double targetPressure;
297 <  double tauThermostat;
298 <  double tauBarostat;
299 <
300 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
301 <  short int have_target_pressure;
302 <
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 NPTf : public T{
315 > template<typename T> class NPTxyz : public T{
316  
317   public:
318  
319 <  NPTf ( SimInfo *theInfo, ForceFields* the_ff);
320 <  virtual ~NPTf();
319 >  NPTxyz ( SimInfo *theInfo, ForceFields* the_ff);
320 >  virtual ~NPTxyz();
321  
322    virtual double getConservedQuantity(void);
323 +  virtual string getAdditionalParameters(void);
324    virtual void resetIntegrator(void);
325  
326   protected:
# Line 323 | Line 334 | template<typename T> class NPTf : public T{ (protected
334  
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],
337 >  virtual void getPosScale(double pos[3], double COM[3],
338                             int index, double sc[3]);
339  
340 +  virtual void calcVelScale( void );
341 +
342    double eta[3][3];
343    double oldEta[3][3];
344    double prevEta[3][3];
345 +  double vScale[3][3];
346   };
347  
334 – template<typename T> class NPTxym : public T{
348  
349 < public:
349 > template<typename T> class ZConstraint : public T {
350  
351 <  NPTxym ( SimInfo *theInfo, ForceFields* the_ff);
339 <  virtual ~NPTxym() {};
340 <
341 <  virtual void integrateStep( int calcPot, int calcStress ){
342 <    calcStress = 1;
343 <    T::integrateStep( calcPot, calcStress );
344 <  }
345 <
346 <  void setTauThermostat(double tt) {tauThermostat = tt; have_tau_thermostat=1;}
347 <  void setTauBarostat(double tb) {tauBarostat = tb; have_tau_barostat=1;}
348 <  void setTargetTemp(double tt) {targetTemp = tt; have_target_temp = 1;}
349 <  void setTargetPressure(double tp) {targetPressure = tp; have_target_pressure = 1;}
350 <
351 < protected:
352 <
353 <  virtual void moveA( void );
354 <  virtual void moveB( void );
355 <
356 <  virtual int readyCheck();
357 <
358 <  virtual void resetIntegrator( void );
359 <
360 <  Molecule* myMolecules;
361 <  Atom** myAtoms;
362 <
363 <  // chi and eta are the propagated degrees of freedom
364 <
365 <  double chi;
366 <  double eta;
367 <  double etaX;
368 <  double etaY;
369 <  double NkBT;
370 <
371 <  // targetTemp, targetPressure, and tauBarostat must be set.  
372 <  // One of qmass or tauThermostat must be set;
373 <
374 <  double targetTemp;
375 <  double targetPressure;
376 <  double tauThermostat;
377 <  double tauBarostat;
378 <
379 <  short int have_tau_thermostat, have_tau_barostat, have_target_temp;
380 <  short int have_target_pressure;
381 <
382 < };
383 <
384 < template<typename T> class ZConstraint : public T {
385 <  
386 <  public:
351 >  public:
352    class ForceSubtractionPolicy{
353      public:
354        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
355  
356 <      virtual void update() = 0;    
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 <    
361 >
362     protected:
363 <     ZConstraint<T>* zconsIntegrator;;
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();    
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 <    
375 >
376      private:
377        int totNumOfMovingAtoms;
378    };
# Line 415 | Line 380 | template<typename T> class ZConstraint : public T {
380    class PolicyByMass : public ForceSubtractionPolicy{
381  
382      public:
383 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
384 <      
385 <      virtual void update();    
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);
# Line 431 | Line 396 | template<typename T> class ZConstraint : public T {
396  
397    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
398    ~ZConstraint();
399 <    
399 >
400    void setZConsTime(double time)                  {this->zconsTime = time;}
401    void getZConsTime()                             {return zconsTime;}
402 <  
402 >
403    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
404    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
405 <  
405 >
406    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
407    string getZConsOutput()                         {return zconsOutput;}
408 <  
408 >
409    virtual void integrate();
445 –  
410  
411 +
412   #ifdef IS_MPI
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  
429 <  enum ZConsState {zcsMoving, zcsFixed};  
430 <
431 <  virtual void calcForce( int calcPot, int calcStress );
429 >
430 >
431 >  virtual void calcForce( int calcPot, int calcStress );
432    virtual void thermalize(void);
433 <  
433 >
434    void zeroOutVel();
435    void doZconstraintForce();
436 <  void doHarmonic();
436 >  void doHarmonic(vector<double>& resPos);
437    bool checkZConsState();
438  
439    bool haveFixedZMols();
# Line 472 | Line 448 | template<typename T> class ZConstraint : public T {
448    double zconsTol;                                 //tolerance of z-contratint
449    double zForceConst;                           //base force constant term
450                                                            //which is estimate by OOPSE
451 <  
452 <  vector<Molecule*> zconsMols;              //z-constraint molecules array
453 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
451 >
452 >
453 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
454    vector<double> kz;                              //force constant array
455 <  vector<ZConsState> states;                 //state of z-constraint molecules
455 >
456    vector<double> zPos;                          //
457 <  
458 <  
457 >
458 >
459    vector<Molecule*> unconsMols;           //unconstraint molecules array
460    vector<double> massOfUnconsMols;    //mass array of unconstraint molecules
485 –  double totalMassOfUncons;                //total mas of unconstraint molecules
461  
462 +
463    vector<ZConsParaItem>* parameters; //
464 <  
464 >
465    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
466  
467 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
468 <  double* fz;
469 <  double* curZPos;
494 <  
495 <  int totNumOfUnconsAtoms;              //total number of uncontraint atoms
467 >  vector<int> indexOfZConsMols;                   //index of local Z-Constraint Molecules
468 >  vector<double> fz;
469 >  vector<double> curZPos;
470  
471 <  int whichDirection;                           //constraint direction
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 <  
484 >
485    string zconsOutput;                         //filename of zconstraint output
486    ZConsWriter* fzOut;                         //z-constraint writer
487  
488 <  double curZconsTime;                      
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

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