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root/group/trunk/OOPSE/libmdtools/Integrator.hpp
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Comparing trunk/OOPSE/libmdtools/Integrator.hpp (file contents):
Revision 837 by tim, Wed Oct 29 00:19:10 2003 UTC vs.
Revision 1330 by gezelter, Fri Jul 16 16:29:44 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 33 | Line 35 | template<typename T = BaseIntegrator> class Integrator
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 ) { }
# Line 45 | Line 47 | template<typename T = BaseIntegrator> class Integrator
47    virtual void calcForce( int calcPot, int calcStress );
48    virtual void thermalize();
49  
50 <  virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] );
50 >  virtual bool stopIntegrator() {return false;}
51  
52 <  void checkConstraints( void );
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
69 <         // constraints.
70 <  int nConstrained;  // counter for number of constraints
71 <  int *constrainedA; // the i of a constraint pair
72 <  int *constrainedB; // the j of a constraint pair
73 <  double *constrainedDsqr; // the square of the constraint distance
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
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  
# Line 84 | Line 90 | typedef Integrator<BaseIntegrator> RealIntegrator;
90  
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:
# Line 153 | Line 163 | template<typename T> class NPT : public T{ (public)
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;}
# Line 175 | Line 189 | template<typename T> class NPT : public T{ (public)
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  
# Line 251 | Line 267 | template<typename T> class NPTi : public T{ (protected
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 +  virtual void calcVelScale( void );
272  
273    double eta, oldEta, prevEta;
274 +  double vScale;
275   };
276  
277   template<typename T> class NPTf : public T{
# Line 280 | Line 299 | template<typename T> class NPTf : public T{ (protected
299    virtual void getPosScale(double pos[3], double COM[3],
300                             int index, double sc[3]);
301  
302 +  virtual void calcVelScale( void );
303 +
304    double eta[3][3];
305    double oldEta[3][3];
306    double prevEta[3][3];
307 +  double vScale[3][3];
308   };
309  
310   template<typename T> class NPTxyz : public T{
# Line 310 | Line 332 | template<typename T> class NPTxyz : public T{ (protect
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  
343  
# Line 403 | Line 428 | template<typename T> class ZConstraint : public T { (p
428  
429    void zeroOutVel();
430    void doZconstraintForce();
431 <  void doHarmonic();
431 >  void doHarmonic(vector<double>& resPos);
432    bool checkZConsState();
433  
434    bool haveFixedZMols();
# Line 434 | Line 459 | template<typename T> class ZConstraint : public T { (p
459  
460    vector<int> indexOfAllZConsMols;     //index of All Z-Constraint Molecuels
461  
462 <  int* indexOfZConsMols;                   //index of local Z-Constraint Molecules
463 <  double* fz;
464 <  double* curZPos;
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 <
471 >  double zconsFixTime;  
472 >  double zconsGap;
473 >  bool hasZConsGap;
474 >  vector<double> endFixTime;
475 >  
476    int whichDirection;                           //constraint direction
477  
478   private:
# Line 452 | Line 485 | template<typename T> class ZConstraint : public T { (p
485    double calcMovingMolsCOMVel();
486    double calcSysCOMVel();
487    double calcTotalForce();
488 <
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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