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#include "Thermo.hpp" |
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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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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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class VelVerletConsFramework; |
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template<typename T = BaseIntegrator> class Integrator : public T { |
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public: |
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protected: |
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virtual void integrateStep( int calcPot, int calcStress ); |
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virtual void preMove( void ); |
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//virtual void preMove( void ); |
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virtual void moveA( void ); |
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virtual void moveB( void ); |
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virtual void constrainA( void ); |
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virtual void constrainB( void ); |
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//virtual void constrainA( void ); |
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//virtual void constrainB( void ); |
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virtual int readyCheck( void ) { return 1; } |
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virtual void resetIntegrator( void ) { } |
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virtual void rotationPropagation( StuntDouble* sd, double ji[3] ); |
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void checkConstraints( void ); |
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//void checkConstraints( void ); |
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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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void printQuaternion(StuntDouble* sd); |
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Mat4x4d getS(const Quaternion& q); |
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ForceFields* myFF; |
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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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int isConstrained; // boolean to know whether the systems contains |
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// constraints. |
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int nConstrained; // counter for number of constraints |
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int *constrainedA; // the i of a constraint pair |
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int *constrainedB; // the j of a constraint pair |
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double *constrainedDsqr; // the square of the constraint distance |
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VelVerletConsFramework* consFramework; |
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int* moving; // tells whether we are moving atom i |
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int* moved; // tells whether we have moved atom i |
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double* oldPos; // pre constrained positions |
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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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//int *constrainedA; // the i of a constraint pair |
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//int *constrainedB; // the j of a constraint pair |
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//double *constrainedDsqr; // the square of the constraint distance |
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//int* moving; // tells whether we are moving atom i |
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//int* moved; // tells whether we have moved atom i |
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//double* oldPos; // pre constrained positions |
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short isFirst; /*boolean for the first time integrate is called */ |
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double dt; |
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typedef Integrator<BaseIntegrator> RealIntegrator; |
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// ansi instantiation |
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// template class Integrator<BaseIntegrator>; |
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template<typename T> class NVE : public T { |
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public: |
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}; |
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/* |
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template<typename T> class SingleZConstrain : public T{ |
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}; |
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*/ |
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template<typename T> class NonEquMD : public T { |
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//Sympletic quaternion Scheme Integrator |
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//Reference: |
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// T.F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns and G.J. Martyna |
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//Symplectic quaternion Scheme for biophysical molecular dynamics |
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//116(20), 8649, J. Chem. Phys. (2002) |
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template<typename T> class SQSIntegrator : public T{ |
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public: |
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}; |
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// |
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template<typename T> class SingleZConstraint : public T{ |
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public: |
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SingleZConstraint(SimInfo *theInfo, ForceFields* the_ff); |
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~SingleZConstraint(); |
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bool stopIntegrator(); |
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SQSIntegrator( SimInfo *theInfo, ForceFields* the_ff ); |
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virtual void moveA(); |
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virtual void moveB(); |
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protected: |
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}; |
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//Steered Molecular Dynamics, curret implement only support one steered molecule |
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template<typename T> class SMD : public T{ |
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public: |
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SMD( SimInfo *theInfo, ForceFields* the_ff); |
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~SMD(); |
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virtual void integrate(); |
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virtual void calcForce( int calcPot, int calcStress ); |
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bool stopIntegrator(); |
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void freeRotor(double dt, Quaternion& q, Vector4d& qdot, Vector3d& I); |
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void rotate(int k, double dt, Quaternion& q, Vector4d& qdot, double Ik); |
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private: |
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}; |
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Quaternion getPk(int i, const Vector4d& q); |
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Mat4x4d getS(const Quaternion& q); |
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vector<Quaternion> q; |
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vector<Vector4d> p_qua; |
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vector<double> I0; |
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//By using state pattern, Coordinate Drive is responsible for switching back and forth between |
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//Driven Molecular Dynamics and ZConstraint Method. |
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< |
template<typename T> class CoordinateDriver : public T { |
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public: |
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typedef T ParentIntegrator; |
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CoordinateDriver(SimInfo*, ForceFields*, BaseIntegrator*, BaseIntegrator*); |
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~CoordinateDriver(); |
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virtual void integrate(); |
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private: |
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BaseIntegrator* zconsIntegrator; |
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< |
BaseIntegrator* drivenIntegrator; |
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Vector4d p2j(const Vector4d& p, Mat4x4d& m); |
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Vector4d j2p(const Vector4d& j, Mat4x4d& m); |
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}; |
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#endif |
