MD_Simulation Class Reference

Inheritance diagram for MD_Simulation:

[legend]Collaboration diagram for MD_Simulation:

[legend]List of all members.

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Detailed Description

This is the base class for all molecular dynamic simulations.

Author:

John Schneiderman

Definition at line 30 of file mdsimulation.h.

Public Member Functions
void	clear ()
	MD_Simulation (const ConfigurationDatabase &conf)
Protected Member Functions
void	writeAverages (ostream &out, const Cluster &cluster)
Protected Attributes
double	m_accumEnergySQ
double	m_accumEnergyTotal
double	m_accumKineticSQ
double	m_accumKineticTotal
double	m_accumPotentialSQ
double	m_accumPotentialTotal
double	m_temperature
double	m_timeStep

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Constructor & Destructor Documentation

MD_Simulation::MD_Simulation (  const ConfigurationDatabase &  conf  )

General constructor. Parameters: conf  is the default configuration values. Definition at line 28 of file mdsimulation.cpp. References m_accumEnergySQ, m_accumEnergyTotal, m_accumKineticSQ, m_accumKineticTotal, m_accumPotentialSQ, m_accumPotentialTotal, m_temperature, and m_timeStep.

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Member Function Documentation

void MD_Simulation::clear (   )

Clears the simulation. Reimplemented from BaseSimulation. Reimplemented in MDLJ_Simulation. Definition at line 35 of file mdsimulation.cpp. References BaseSimulation::clear(), m_accumEnergySQ, m_accumEnergyTotal, m_accumKineticSQ, m_accumKineticTotal, m_accumPotentialSQ, m_accumPotentialTotal, m_temperature, and m_timeStep. Referenced by MDLJ_Simulation::clear(). Here is the call graph for this function:

void MD_Simulation::writeAverages (  ostream &  out, const Cluster &  cluster )  [protected]

Calculates the simulation averages and writes them out. Parameters: out  is the source to write the averages to. cluster  is the cluster that ran in the simulation. Definition at line 43 of file mdsimulation.cpp. References m_accumEnergySQ, m_accumEnergyTotal, m_accumKineticSQ, m_accumKineticTotal, m_accumPotentialSQ, m_accumPotentialTotal, BaseSimulation::m_changeInStep, BaseSimulation::m_runSteps, m_timeStep, and Cluster::size(). Referenced by MDLJ_Simulation::run(). Here is the call graph for this function:

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Member Data Documentation

double MD_Simulation::m_accumEnergySQ [protected]

Parameters: m_accumEnergySQ  is the total energy accumulator squared. Definition at line 75 of file mdsimulation.h. Referenced by clear(), MD_Simulation(), MDLJ_Simulation::run(), and writeAverages().

double MD_Simulation::m_accumEnergyTotal [protected]

Parameters: m_accumEnergyTotal  is the total energy accumulator. Definition at line 63 of file mdsimulation.h. Referenced by clear(), MD_Simulation(), MDLJ_Simulation::run(), and writeAverages().

double MD_Simulation::m_accumKineticSQ [protected]

Parameters: m_accumKineticSQ  is the kinetic energy accumulator squared. Definition at line 71 of file mdsimulation.h. Referenced by clear(), MD_Simulation(), MDLJ_Simulation::run(), and writeAverages().

double MD_Simulation::m_accumKineticTotal [protected]

Parameters: m_accumKineticTotal  is the total kinetic energy accumulator. Definition at line 59 of file mdsimulation.h. Referenced by clear(), MD_Simulation(), MDLJ_Simulation::run(), and writeAverages().

double MD_Simulation::m_accumPotentialSQ [protected]

Parameters: m_accumPotentialSQ  is the potential energy accumulator squared. Definition at line 67 of file mdsimulation.h. Referenced by clear(), MD_Simulation(), MDLJ_Simulation::run(), and writeAverages().

double MD_Simulation::m_accumPotentialTotal [protected]

Parameters: m_accumPotentialTotal  is the total potential energy accumulator. Definition at line 55 of file mdsimulation.h. Referenced by clear(), MD_Simulation(), MDLJ_Simulation::run(), and writeAverages().

double MD_Simulation::m_temperature [protected]

Parameters: m_temperature  is the temperature of the system. Definition at line 47 of file mdsimulation.h. Referenced by clear(), MD_Simulation(), and MDLJ_Simulation::run().

double MD_Simulation::m_timeStep [protected]

Parameters: m_timeStep  is the current step for the simulation. Definition at line 51 of file mdsimulation.h. Referenced by clear(), MD_Simulation(), MDLJ_Simulation::run(), and writeAverages().

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

• simulations/mdsimulation.h
• simulations/mdsimulation.cpp

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