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

ProtoMol::DMDLeapfrogIntegrator Class Reference

#include <DMDLeapfrogIntegrator.h>

Inheritance diagram for ProtoMol::DMDLeapfrogIntegrator:

List of all members.


Public Member Functions
	DMDLeapfrogIntegrator ()
	DMDLeapfrogIntegrator (Real timestep, int numIter, Real gamma, Real initialTemperature, int seed, ForceGroup *overloadedForces)
	~DMDLeapfrogIntegrator ()
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
virtual void	doHalfKick ()
Private Member Functions
void	calculateDissipativeForces ()
void	calculateDissipativeAndRandomForces ()
void	doHalfKickVhat ()
void	doHalfKickIterate ()
virtual STSIntegrator *	doMake (std::string &errMsg, const std::vector< Value > &values, ForceGroup *fg) const
Private Attributes
Vector3DBlock *	myDissipativeForces
Vector3DBlock *	myRandomForces
Vector3DBlock *	myVhat
Real	myDissipativeCutoff
Real	myGamma
Real	myTemperature
int	myNumIter
Real	mySigma
int	mySeed

Detailed Description

For Dissipative MD, and it is self-consistent

Constructor & Destructor Documentation

ProtoMol::DMDLeapfrogIntegrator::DMDLeapfrogIntegrator ( )

ProtoMol::DMDLeapfrogIntegrator::DMDLeapfrogIntegrator ( Real timestep,

int numIter,

Real gamma,

Real initialTemperature,

int seed,

ForceGroup * overloadedForces

)

Specify the the forces to evaluate. Also sigma, the noise level control parameter, a constant and numIter, the count of iterations to be made in the "self-consistency" loop. The desired temperature in Kelvin is used to get the drag coefficient, gamma. sigma^2 = 2 * gamma * BOLZMAN * Temperature. the gamma is passed in assuming unit of (ps^-1). Internally, it is used in the unit of (fs^-1), a factor of 0.001

ProtoMol::DMDLeapfrogIntegrator::~DMDLeapfrogIntegrator ( )

Member Function Documentation

void ProtoMol::DMDLeapfrogIntegrator::calculateDissipativeAndRandomForces ( ) [private]

void ProtoMol::DMDLeapfrogIntegrator::calculateDissipativeForces ( ) [private]

void ProtoMol::DMDLeapfrogIntegrator::doHalfKick ( ) [protected, virtual]

Reimplemented from ProtoMol::StandardIntegrator.

void ProtoMol::DMDLeapfrogIntegrator::doHalfKickIterate ( ) [private]

void ProtoMol::DMDLeapfrogIntegrator::doHalfKickVhat ( ) [private]

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

const std::vector< Value > & values,

ForceGroup * fg

) const [private, virtual]

Implements ProtoMol::STSIntegrator.

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

Implements ProtoMol::Makeable.

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

retrieve all parameters

Reimplemented from ProtoMol::STSIntegrator.

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

number of parameters

Implements ProtoMol::Makeable.

void ProtoMol::DMDLeapfrogIntegrator::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.

void ProtoMol::DMDLeapfrogIntegrator::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.