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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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– |
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template<typename T = BaseIntegrator> class Integrator : public T { |
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public: |
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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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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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StatWriter* statOut; |
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DumpWriter* dumpOut; |
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int i; // just an int |
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}; |
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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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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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/* |
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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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public: |
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OOPSEMinimizerBase ( SimInfo *theInfo, ForceFields* the_ff ); |
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virtual ~OOPSEMinimizerBase(); |
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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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double calcGradient(const vector<double>& x, vector<double>& grad); |
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void setOptCoor(vector<double>& x); |
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void getOptCoor(vector<double>& x); |
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void output(); |
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bool stopIntegrator(); |
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protected: |
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}; |
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template<typename TMinimizer> class OOPSEMinimizer : public OOPSEMinimizerBase, TMinimizer{ |
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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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private: |
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}; |
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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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}; |
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#endif |
