MDLJ_Simulation Class Reference

Inheritance diagram for MDLJ_Simulation:

[legend]Collaboration diagram for MDLJ_Simulation:

[legend]List of all members.

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Detailed Description

This performs a Molecular-dynamic Lennard-Jones simulation on a cluster.

Note:

Ideas adopted from Allen and Tildesley.

Author:

John Schneiderman

Definition at line 30 of file mdljsimulation.h.

Public Member Functions
void	clear ()
	MDLJ_Simulation (const ConfigurationDatabase &conf)
double	reducedKineticEnergy () const
double	reducedPotentialEnergy () const
double	reducedTotalEnergy () const
virtual void	run (Cluster &cluster, string currentRun, string prevRun)
Protected Member Functions
void	adjustPosCenMass (Cluster &cluster) const
void	calculateAccelerations (Cluster &cluster) const
void	calculatePositions (Cluster &cluster) const
void	calculateVelocities (Cluster &cluster) const
virtual double	findLastStep (string baseName) const
Private Attributes
double	m_reducedEnergyTotal
double	m_reducedKineticEnergy
double	m_reducedPotentialEnergy

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Constructor & Destructor Documentation

MDLJ_Simulation::MDLJ_Simulation (  const ConfigurationDatabase &  conf  )

General constructor. Parameters: conf  is the default configuration values. Definition at line 33 of file mdljsimulation.cpp. References m_reducedEnergyTotal, m_reducedKineticEnergy, and m_reducedPotentialEnergy.

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Member Function Documentation

void MDLJ_Simulation::adjustPosCenMass (  Cluster &  cluster  )  const [protected]

Adjusts the positions of a cluster according to its centre of mass. Parameters: cluster  is the cluster to adjust. Definition at line 222 of file mdljsimulation.cpp. References Cluster::positionCentreMass(), and Cluster::size(). Here is the call graph for this function:

void MDLJ_Simulation::calculateAccelerations (  Cluster &  cluster  )  const [protected]

Calculates the accelerations, and the total potential energy of the simulation. Parameters: cluster  is the cluster whose accelerations are adjusted for the simulation. Definition at line 185 of file mdljsimulation.cpp. References Cluster::potentialEnergyTotal(), Cluster::setPotentialEnergyTotal(), Cluster::size(), Coordinate::x, Coordinate::y, and Coordinate::z. Referenced by run(). Here is the call graph for this function:

void MDLJ_Simulation::calculatePositions (  Cluster &  cluster  )  const [protected]

Moves the positions of a cluster during the simulation. Parameters: cluster  is the cluster whose positions are adjusted for the simulation. Definition at line 153 of file mdljsimulation.cpp. References BaseSimulation::m_changeInStep, and Cluster::size(). Referenced by run(). Here is the call graph for this function:

void MDLJ_Simulation::calculateVelocities (  Cluster &  cluster  )  const [protected]

Calculates the velocity of a cluster during a the simulation and calcultes the total kinetic energy. Parameters: cluster  is the cluster whose velocities are adjusted for the simulation. Definition at line 169 of file mdljsimulation.cpp. References BaseSimulation::m_changeInStep, Cluster::setKineticEnergyTotal(), and Cluster::size(). Referenced by run(). Here is the call graph for this function:

void MDLJ_Simulation::clear (   )

Clears the mdljSimulation. Reimplemented from MD_Simulation. Definition at line 147 of file mdljsimulation.cpp. References MD_Simulation::clear(), m_reducedEnergyTotal, m_reducedKineticEnergy, and m_reducedPotentialEnergy. Here is the call graph for this function:

double MDLJ_Simulation::findLastStep (  string  baseName  )  const [protected, virtual]

Finds the last step in the a series of simulations. Parameters: baseName  is the name of the file that is the direct previous run. Returns: the last time value in the series of runs. If there is not a previous run, returns zero. Implements BaseSimulation. Definition at line 233 of file mdljsimulation.cpp. Referenced by run().

double MDLJ_Simulation::reducedKineticEnergy (   )  const

An accessor to the reduced kinetic energy. Returns: the reduced kinetic energy. Definition at line 43 of file mdljsimulation.cpp. References m_reducedKineticEnergy.

double MDLJ_Simulation::reducedPotentialEnergy (   )  const

An accessor to the reduced potential energy. Returns: the reduced potential energy. Definition at line 38 of file mdljsimulation.cpp. References m_reducedPotentialEnergy.

double MDLJ_Simulation::reducedTotalEnergy (   )  const

An accessor to the reduced total energy. Returns: the reduced total energy. Definition at line 48 of file mdljsimulation.cpp. References m_reducedEnergyTotal.

void MDLJ_Simulation::run (  Cluster &  cluster, string  currentRun, string  prevRun )  [virtual]

Runs a molecular dynamics simulation using the Lennard-Jones model. During the run, a run file and a miscellaneous file have been created. The run file (currentRun.run) has the information pulled from each step of the run. The miscellaneous file (currentRun.msc) has various information regarding the run. Parameters: cluster  is the cluster that is ready to be manipulated during the simulation. currentRun  is the base name for the current run. prevRun  is the base name of the previous run files. Implements BaseSimulation. Definition at line 53 of file mdljsimulation.cpp. References KineticEnergyHistogram::acquire(), PotentialEnergyHistogram::acquire(), RadialDistributionFunction::acquire(), RadialDensityHistogram::acquire(), calculateAccelerations(), Cluster::calculateCentreMass(), Cluster::calculateKineticEnergy(), calculatePositions(), Cluster::calculatePotentialEnergy(), calculateVelocities(), findLastStep(), Cluster::kineticEnergyTotal(), MD_Simulation::m_accumEnergySQ, MD_Simulation::m_accumEnergyTotal, MD_Simulation::m_accumKineticSQ, MD_Simulation::m_accumKineticTotal, MD_Simulation::m_accumPotentialSQ, MD_Simulation::m_accumPotentialTotal, BaseSimulation::m_changeInStep, BaseSimulation::m_kineticEnergyHistogram, BaseSimulation::m_potentialEnergyHistogram, BaseSimulation::m_printInterval, BaseSimulation::m_radialDensityHistogram, BaseSimulation::m_radialDistributionFunction, m_reducedEnergyTotal, m_reducedKineticEnergy, m_reducedPotentialEnergy, BaseSimulation::m_runSteps, BaseSimulation::m_stepStart, MD_Simulation::m_temperature, MD_Simulation::m_timeStep, Cluster::potentialEnergyTotal(), Cluster::PRECISION, BaseHistogram::pullingInterval(), Cluster::size(), Cluster::WIDTH, PotentialEnergyHistogram::write(), KineticEnergyHistogram::write(), RadialDistributionFunction::write(), RadialDensityHistogram::write(), and MD_Simulation::writeAverages(). Here is the call graph for this function:

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Member Data Documentation

double MDLJ_Simulation::m_reducedEnergyTotal [private]

Parameters: reducedEnergyTotal  is the reduced total energy of the system. Definition at line 102 of file mdljsimulation.h. Referenced by clear(), MDLJ_Simulation(), reducedTotalEnergy(), and run().

double MDLJ_Simulation::m_reducedKineticEnergy [private]

Parameters: m_reducedKineticEnergy  is the reduced kinetic energy of the system. Definition at line 100 of file mdljsimulation.h. Referenced by clear(), MDLJ_Simulation(), reducedKineticEnergy(), and run().

double MDLJ_Simulation::m_reducedPotentialEnergy [private]

Parameters: m_reducedPotentialEnergy  is the reduced potential energy of the system. Definition at line 98 of file mdljsimulation.h. Referenced by clear(), MDLJ_Simulation(), reducedPotentialEnergy(), and run().

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The documentation for this class was generated from the following files:

• simulations/mdljsimulation.h
• simulations/mdljsimulation.cpp

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