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#include "ReadWrite.hpp" |
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#include "ZConsWriter.hpp" |
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#include "Restraints.hpp" |
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+ |
#include "Quaternion.hpp" |
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#include "Mat4x4d.hpp" |
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|
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using namespace std; |
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const double kB = 8.31451e-7;// boltzmann constant amu*Ang^2*fs^-2/K |
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const int maxIteration = 300; |
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const double tol = 1.0e-6; |
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|
| 27 |
< |
class RattleFramework; |
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> |
class VelVerletConsFramework; |
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template<typename T = BaseIntegrator> class Integrator : public T { |
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public: |
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void rotate( int axes1, int axes2, double angle, double j[3], |
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double A[3][3] ); |
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|
| 60 |
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void printQuaternion(StuntDouble* sd); |
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Mat4x4d getS(const Quaternion& q); |
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|
| 63 |
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ForceFields* myFF; |
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|
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SimInfo *info; // all the info we'll ever need |
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Molecule* molecules; |
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int nMols; |
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|
| 73 |
< |
RattleFramework* rattle; |
| 73 |
> |
VelVerletConsFramework* consFramework; |
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|
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//int isConstrained; // boolean to know whether the systems contains constraints. |
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//int nConstrained; // counter for number of constraints |
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typedef Integrator<BaseIntegrator> RealIntegrator; |
| 97 |
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|
| 98 |
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// ansi instantiation |
| 99 |
< |
//template class Integrator<BaseIntegrator>; |
| 99 |
> |
// template class Integrator<BaseIntegrator>; |
| 100 |
> |
|
| 101 |
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|
| 102 |
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template<typename T> class NVE : public T { |
| 103 |
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|
| 497 |
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friend class ForceSubtractionPolicy; |
| 498 |
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|
| 499 |
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}; |
| 500 |
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|
| 501 |
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|
| 502 |
+ |
//Sympletic quaternion Scheme Integrator |
| 503 |
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//Reference: |
| 504 |
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// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna |
| 505 |
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//Symplectic quaternion Scheme for biophysical molecular dynamics |
| 506 |
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//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(); |
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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 |
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|
| 522 |
+ |
Vector4d p2j(const Vector4d& p, Mat4x4d& m); |
| 523 |
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Vector4d j2p(const Vector4d& j, Mat4x4d& m); |
| 524 |
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}; |
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#endif |
