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

ProtoMol::PaulTrapIntegrator Class Reference

#include <PaulTrapIntegrator.h>

Inheritance diagram for ProtoMol::PaulTrapIntegrator:

List of all members.


Public Member Functions
	PaulTrapIntegrator ()
	PaulTrapIntegrator (Real timestep, Real temperature, Real thermalInertia, Real bathPosition, Real bathVelocity, ThermostatType nvttype, Real part, const std::vector< Real > &time, const std::vector< Real > &t, ForceGroup *overloadedForces)
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)
Static Public Attributes
const std::string	keyword
Protected Member Functions
virtual void	doDrift ()
Private Member Functions
void	init ()
virtual void	doUncache ()
virtual STSIntegrator *	doMake (std::string &errMsg, const std::vector< Value > &values, ForceGroup *fg) const
Private Attributes
bool	myCached
const Real	myTemperature
const Real	myThermalInertia
Real	myBathPosition
Real	myBathVelocity
ThermostatType	myThermostatType
Real	myPart
Real	myPartReal
unsigned int	myCount
bool	myRemoveAngularMotion
bool	myRemoveCommonMotion
std::vector< Real >	myTime
std::vector< Real >	myT
std::vector< int >	myKeep
std::vector< std::vector< int > >	myLayer

Constructor & Destructor Documentation

ProtoMol::PaulTrapIntegrator::PaulTrapIntegrator ( )

ProtoMol::PaulTrapIntegrator::PaulTrapIntegrator ( Real timestep,

Real temperature,

Real thermalInertia,

Real bathPosition,

Real bathVelocity,

ThermostatType nvttype,

Real part,

const std::vector< Real > & time,

const std::vector< Real > & t,

ForceGroup * overloadedForces

)

Member Function Documentation

void ProtoMol::PaulTrapIntegrator::doDrift ( ) [protected, virtual]

Reimplemented from ProtoMol::STSIntegrator.

virtual STSIntegrator* ProtoMol::PaulTrapIntegrator::doMake ( std::string & errMsg,

const std::vector< Value > & values,

ForceGroup * fg

) const [private, virtual]

Implements ProtoMol::STSIntegrator.

void ProtoMol::PaulTrapIntegrator::doUncache ( ) [private, virtual]

Integrator specific details of uncache.

Reimplemented from ProtoMol::Integrator.

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

Implements ProtoMol::Makeable.

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

retrieve all parameters

Reimplemented from ProtoMol::STSIntegrator.

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

number of parameters

Implements ProtoMol::Makeable.

void ProtoMol::PaulTrapIntegrator::init ( ) [private]

void ProtoMol::PaulTrapIntegrator::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::STSIntegrator.