| 22 |
|
const int maxIteration = 300; |
| 23 |
|
const double tol = 1.0e-6; |
| 24 |
|
|
| 25 |
+ |
class VelVerletConsFramework; |
| 26 |
|
template<typename T = BaseIntegrator> class Integrator : public T { |
| 27 |
|
|
| 28 |
|
public: |
| 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 ) { } |
| 51 |
|
|
| 52 |
|
virtual void rotationPropagation( StuntDouble* sd, double ji[3] ); |
| 53 |
|
|
| 54 |
< |
void checkConstraints( void ); |
| 54 |
> |
//void checkConstraints( void ); |
| 55 |
|
void rotate( int axes1, int axes2, double angle, double j[3], |
| 56 |
|
double A[3][3] ); |
| 57 |
|
|
| 65 |
|
Molecule* molecules; |
| 66 |
|
int nMols; |
| 67 |
|
|
| 68 |
< |
int isConstrained; // boolean to know whether the systems contains |
| 68 |
< |
// constraints. |
| 69 |
< |
int nConstrained; // counter for number of constraints |
| 70 |
< |
int *constrainedA; // the i of a constraint pair |
| 71 |
< |
int *constrainedB; // the j of a constraint pair |
| 72 |
< |
double *constrainedDsqr; // the square of the constraint distance |
| 68 |
> |
VelVerletConsFramework* consFramework; |
| 69 |
|
|
| 70 |
< |
int* moving; // tells whether we are moving atom i |
| 71 |
< |
int* moved; // tells whether we have moved atom i |
| 72 |
< |
double* oldPos; // pre constrained positions |
| 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 |
|
|
| 82 |
|
double dt; |
| 91 |
|
typedef Integrator<BaseIntegrator> RealIntegrator; |
| 92 |
|
|
| 93 |
|
// ansi instantiation |
| 94 |
< |
template class Integrator<BaseIntegrator>; |
| 94 |
> |
// template class Integrator<BaseIntegrator>; |
| 95 |
|
|
| 96 |
+ |
|
| 97 |
|
template<typename T> class NVE : public T { |
| 98 |
|
|
| 99 |
|
public: |
| 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 |
