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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC vs.
Revision 1323 by gezelter, Wed Jul 14 20:11:29 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 VelVerletConsFramework;
26   template<typename T = BaseIntegrator> class Integrator : public T {
27  
28   public:
# Line 28 | Line 30 | template<typename T = BaseIntegrator> class Integrator
30    virtual ~Integrator();
31    void integrate( void );
32    virtual double  getConservedQuantity(void);
33 +  virtual string getAdditionalParameters(void);
34  
35   protected:
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; }
44  
45    virtual void resetIntegrator( void ) { }
46 <
47 <  virtual void calcForce( int calcPot, int calcStress );  
46 >
47 >  virtual void calcForce( int calcPot, int calcStress );
48    virtual void thermalize();
46 –  
47 –  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
49  
50 <  void checkConstraints( void );
51 <  void rotate( int axes1, int axes2, double angle, double j[3],
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 <        
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
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
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  
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 103 | Line 113 | template<typename T> class NVT : public T { (public)
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 124 | Line 135 | template<typename T> class NVT : public T { (public)
135  
136    double targetTemp;
137    double tauThermostat;
138 <  
138 >
139    short int have_tau_thermostat, have_target_temp;
140  
141    double *oldVel;
# Line 143 | Line 154 | template<typename T> class NPT : public T{ (public)
154  
155    NPT ( SimInfo *theInfo, ForceFields* the_ff);
156    virtual ~NPT();
157 <  
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;}
# Line 170 | Line 185 | template<typename T> class NPT : public T{ (public)
185  
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],
188 >  virtual void getPosScale(double pos[3], double COM[3],
189                             int index, double sc[3]) = 0;
190  
191 +  virtual void calcVelScale( void ) = 0;
192 +
193    virtual bool chiConverged( void );
194    virtual bool etaConverged( void ) = 0;
195 <  
195 >
196    virtual void evolveChiA( void );
197    virtual void evolveEtaA( void ) = 0;
198    virtual void evolveChiB( void );
# Line 201 | Line 218 | template<typename T> class NPT : public T{ (public)
218  
219    double integralOfChidt;
220  
221 <  // targetTemp, targetPressure, and tauBarostat must be set.  
221 >  // targetTemp, targetPressure, and tauBarostat must be set.
222    // One of qmass or tauThermostat must be set;
223  
224    double targetTemp;
# Line 226 | Line 243 | template<typename T> class NPTi : public T{
243   };
244  
245   template<typename T> class NPTi : public T{
246 <  
246 >
247   public:
248    NPTi( SimInfo *theInfo, ForceFields* the_ff);
249    ~NPTi();
250  
251    virtual double getConservedQuantity(void);
252    virtual void resetIntegrator(void);
253 <
253 >  virtual string getAdditionalParameters(void);
254   protected:
255  
239 –
256  
257 +
258    virtual void evolveEtaA(void);
259    virtual void evolveEtaB(void);
260  
# Line 247 | Line 264 | template<typename T> class NPTi : public T{
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],
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{
# Line 261 | Line 281 | template<typename T> class NPTf : public T{ (public)
281    virtual ~NPTf();
282  
283    virtual double getConservedQuantity(void);
284 +  virtual string getAdditionalParameters(void);
285    virtual void resetIntegrator(void);
286  
287   protected:
# Line 274 | Line 295 | template<typename T> class NPTf : public T{ (public)
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],
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 NPTxyz : public T{
# Line 290 | Line 314 | template<typename T> class NPTxyz : public T{ (public)
314    virtual ~NPTxyz();
315  
316    virtual double getConservedQuantity(void);
317 +  virtual string getAdditionalParameters(void);
318    virtual void resetIntegrator(void);
319  
320   protected:
# Line 303 | Line 328 | template<typename T> class NPTxyz : public T{ (public)
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],
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  
342  
343   template<typename T> class ZConstraint : public T {
344 <  
345 <  public:
344 >
345 >  public:
346    class ForceSubtractionPolicy{
347      public:
348        ForceSubtractionPolicy(ZConstraint<T>* integrator) {zconsIntegrator = integrator;}
349  
350 <      virtual void update() = 0;    
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 <    
355 >
356     protected:
357       ZConstraint<T>* zconsIntegrator;
358    };
# Line 332 | Line 360 | template<typename T> class ZConstraint : public T {
360    class PolicyByNumber : public ForceSubtractionPolicy{
361  
362      public:
363 <      PolicyByNumber(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}    
364 <      virtual void update();    
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 <    
369 >
370      private:
371        int totNumOfMovingAtoms;
372    };
# Line 346 | Line 374 | template<typename T> class ZConstraint : public T {
374    class PolicyByMass : public ForceSubtractionPolicy{
375  
376      public:
377 <      PolicyByMass(ZConstraint<T>* integrator) :ForceSubtractionPolicy(integrator) {}  
378 <      
379 <      virtual void update();    
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);
# Line 362 | Line 390 | template<typename T> class ZConstraint : public T {
390  
391    ZConstraint( SimInfo *theInfo, ForceFields* the_ff);
392    ~ZConstraint();
393 <    
393 >
394    void setZConsTime(double time)                  {this->zconsTime = time;}
395    void getZConsTime()                             {return zconsTime;}
396 <  
396 >
397    void setIndexOfAllZConsMols(vector<int> index) {indexOfAllZConsMols = index;}
398    void getIndexOfAllZConsMols()                  {return indexOfAllZConsMols;}
399 <  
399 >
400    void setZConsOutput(const char * fileName)          {zconsOutput = fileName;}
401    string getZConsOutput()                         {return zconsOutput;}
402 <  
402 >
403    virtual void integrate();
376 –  
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};  
410 >  enum ZConsState {zcsMoving, zcsFixed};
411  
412    vector<Molecule*> zconsMols;              //z-constraint molecules array
413    vector<ZConsState> states;                 //state of z-constraint molecules
414  
387 –
415  
416 +
417    int totNumOfUnconsAtoms;              //total number of uncontraint atoms
418    double totalMassOfUncons;                //total mas of unconstraint molecules
419  
# Line 393 | Line 421 | template<typename T> class ZConstraint : public T {
421   protected:
422  
423  
424 <
425 <  virtual void calcForce( int calcPot, int calcStress );
424 >
425 >  virtual void calcForce( int calcPot, int calcStress );
426    virtual void thermalize(void);
427 <  
427 >
428    void zeroOutVel();
429    void doZconstraintForce();
430 <  void doHarmonic();
430 >  void doHarmonic(vector<double>& resPos);
431    bool checkZConsState();
432  
433    bool haveFixedZMols();
# Line 414 | Line 442 | template<typename T> class ZConstraint : public T {
442    double zconsTol;                                 //tolerance of z-contratint
443    double zForceConst;                           //base force constant term
444                                                            //which is estimate by OOPSE
417 –  
445  
446 <  vector<double> massOfZConsMols;       //mass of z-constraint molecule
446 >
447 >  vector<double> massOfZConsMols;       //mass of z-constraint molecule
448    vector<double> kz;                              //force constant array
449  
450    vector<double> zPos;                          //
451 <  
452 <  
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 <  
458 >
459    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
460  
461 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules  
462 <  double* fz;
463 <  double* curZPos;
436 <  
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 <  int whichDirection;                           //constraint direction
470 >  double zconsFixTime;  
471 >  double zconsGap;
472 >  bool hasZConsGap;
473 >  vector<double> endFixTime;
474    
475 +  int whichDirection;                           //constraint direction
476 +
477   private:
478 <  
478 >
479    string zconsOutput;                         //filename of zconstraint output
480    ZConsWriter* fzOut;                         //z-constraint writer
481  
482 <  double curZconsTime;                      
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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