ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.

ProtoMol::DihedralHMCIntegrator Class Reference

#include <DihedralHMCIntegrator.h>

Inheritance diagram for ProtoMol::DihedralHMCIntegrator:

List of all members.


Public Member Functions
	DihedralHMCIntegrator ()
	DihedralHMCIntegrator (int cycles, Real initialTemperature, bool randomCycLen, bool dihset, std::string dsetfile, bool angset, std::string asetfile, ForceGroup overloadedForces, StandardIntegrator nextIntegrator)
virtual	~DihedralHMCIntegrator ()
virtual std::string	getIdNoAlias () const
virtual void	getParameters (std::vector< Parameter > &parameters) const
virtual unsigned int	getParameterSize () const
virtual void	initialize (GenericTopology topo, Vector3DBlock positions, Vector3DBlock velocities, ScalarStructure energies)
virtual void	run (int numTimesteps)
Static Public Attributes
const std::string	keyword
Protected Member Functions
bool	metropolisTest (Real newEnergy, Real oldEnergy, Real theTemperature, Real &acceptProb)
void	saveValues ()
void	restoreValues ()
Protected Attributes
Vector3DBlock *	myOldPositions
Vector3DBlock *	myOldVelocities
ScalarStructure *	myOldEnergies
Real	myInitialTemperature
bool	myRandomCycLen
bool	myDihedralsSet
std::string	myDhmcDiSetFile
bool	myAnglesSet
std::string	myDhmcAnSetFile
int	myDihedralIndex
std::vector< int > *	myDihedrals
std::vector< Real > *	myAngles
Private Member Functions
virtual MTSIntegrator *	doMake (std::string &errMsg, const std::vector< Value > &values, ForceGroup fg, StandardIntegrator nextIntegrator) const

Constructor & Destructor Documentation

ProtoMol::DihedralHMCIntegrator::DihedralHMCIntegrator ( )

ProtoMol::DihedralHMCIntegrator::DihedralHMCIntegrator ( int cycles,

Real initialTemperature,

bool randomCycLen,

bool dihset,

std::string dsetfile,

bool angset,

std::string asetfile,

ForceGroup * overloadedForces,

StandardIntegrator * nextIntegrator

)

ProtoMol::DihedralHMCIntegrator::~DihedralHMCIntegrator ( ) [virtual]

Member Function Documentation

virtual MTSIntegrator* ProtoMol::DihedralHMCIntegrator::doMake ( std::string & errMsg,

const std::vector< Value > & values,

ForceGroup * fg,

StandardIntegrator * nextIntegrator

) const [private, virtual]

Implements ProtoMol::MTSIntegrator.

virtual std::string ProtoMol::DihedralHMCIntegrator::getIdNoAlias ( ) const [inline, virtual]

Implements ProtoMol::Makeable.

void ProtoMol::DihedralHMCIntegrator::getParameters ( std::vector< Parameter > & parameters ) const [virtual]

retrieve all parameters

Reimplemented from ProtoMol::MTSIntegrator.

virtual unsigned int ProtoMol::DihedralHMCIntegrator::getParameterSize ( ) const [inline, virtual]

number of parameters

Reimplemented from ProtoMol::MTSIntegrator.

void ProtoMol::DihedralHMCIntegrator::initialize ( GenericTopology * topo,

Vector3DBlock * positions,

Vector3DBlock * velocities,

ScalarStructure * energies

) [virtual]

Set the integrator up. This method can be called at any time, and should perform any starting force evaluations the integrator needs in order to run correctly. The simulation data should be kept in the given structures.
Reimplemented from ProtoMol::MTSIntegrator.

bool ProtoMol::DihedralHMCIntegrator::metropolisTest ( Real newEnergy,

Real oldEnergy,

Real theTemperature,

Real & acceptProb

) [protected]

void ProtoMol::DihedralHMCIntegrator::restoreValues ( ) [protected]

void ProtoMol::DihedralHMCIntegrator::run ( int numTimesteps ) [virtual]

Run the integrator for the certain number of timesteps. It can be assumed that the topology and forces have not changed since the last time the integrator was initialized.
Reimplemented from ProtoMol::StandardIntegrator.