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#include <string> |
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#include <vector> |
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#include "Atom.hpp" |
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#include "StuntDouble.hpp" |
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#include "Molecule.hpp" |
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#include "SRI.hpp" |
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#include "AbstractClasses.hpp" |
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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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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 RattleFramework; |
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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 calcForce( int calcPot, int calcStress ); |
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virtual void thermalize(); |
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virtual void rotationPropagation( DirectionalAtom* dAtom, double ji[3] ); |
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virtual bool stopIntegrator() {return false;} |
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void checkConstraints( 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 rotate( int axes1, int axes2, double angle, double j[3], |
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double A[3][3] ); |
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ForceFields* myFF; |
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SimInfo *info; // all the info we'll ever need |
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vector<StuntDouble*> integrableObjects; |
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int nAtoms; /* the number of atoms */ |
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int oldAtoms; |
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Atom **atoms; /* array of atom pointers */ |
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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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RattleFramework* rattle; |
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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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void zeroOutVel(); |
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void doZconstraintForce(); |
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void doHarmonic(); |
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void doHarmonic(vector<double>& resPos); |
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bool checkZConsState(); |
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bool haveFixedZMols(); |
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vector<int> indexOfAllZConsMols; //index of All Z-Constraint Molecuels |
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int* indexOfZConsMols; //index of local Z-Constraint Molecules |
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double* fz; |
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double* curZPos; |
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vector<int> indexOfZConsMols; //index of local Z-Constraint Molecules |
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vector<double> fz; |
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vector<double> curZPos; |
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bool usingSMD; |
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vector<double> prevCantPos; |
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vector<double> cantPos; |
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vector<double> cantVel; |
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double zconsFixTime; |
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double zconsGap; |
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bool hasZConsGap; |
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vector<double> endFixTime; |
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int whichDirection; //constraint direction |
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private: |
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double calcMovingMolsCOMVel(); |
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double calcSysCOMVel(); |
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double calcTotalForce(); |
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void updateZPos(); |
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void updateCantPos(); |
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ForceSubtractionPolicy* forcePolicy; //force subtraction policy |
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friend class ForceSubtractionPolicy; |
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}; |
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class OOPSEMinimizerBase : public RealIntegrator { |
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public: |
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OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff ); |
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virtual ~OOPSEMinimizerBase(); |
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double calcGradient(vector<double>& x, vector<double>& grad); |
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void setOptCoor(vector<double>& x); |
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vector<double> getOptCoor(); |
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void output(vector<double>& x, int iteration); |
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int getDim() {return dim;} |
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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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virtual void moveA(); |
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virtual void moveB(); |
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protected: |
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void freeRotor(); |
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void rotate(int k, double dt); |
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int dim; |
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void calcDim(); |
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}; |
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//template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{ |
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// public: |
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// void writeOutput(); |
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//}; |
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#endif |