Package ffx.algorithms.commands.test

Class RepexThermo

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.Thermodynamics

ffx.algorithms.commands.test.RepexThermo

public class RepexThermo
extends Thermodynamics

The RepexThermo command uses the Orthogonal Space Tempering with histogram replica exchange to estimate a free energy difference.
Usage:
ffxc test.RepexThermo [options] <filename> [file2...];

Field Summary

Fields inherited from class ffx.algorithms.commands.Thermodynamics

additionalProperties, alchemicalOptions, barostatOptions, dynamicsOptions, filenames, lambdaParticleOptions, multiDynamicsOptions, orthogonalSpaceTempering, ostOptions, potential, randomSymopOptions, thermodynamicsOptions, topologies, topologyOptions, verbose, writeoutOptions

Fields inherited from class ffx.algorithms.cli.AlgorithmsCommand

activeAssembly, algorithmFunctions, algorithmListener, baseDir

Fields inherited from class ffx.utilities.FFXCommand

args, binding, color, help, logger, parseResult, version

Constructor Summary

Constructors

Constructor	Description
RepexThermo()	RepexThermo Constructor.
RepexThermo(FFXBinding binding)	RepexThermo Constructor.
RepexThermo(String[] args)	RepexThermo constructor that sets the command line arguments.

Method Summary

Modifier and Type	Method	Description
OrthogonalSpaceTempering	getOST()
CrystalPotential	getPotential()
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this script.
RepexThermo	run()	Execute this Command.

Methods inherited from class ffx.algorithms.commands.Thermodynamics

destroyPotentials, setProperties

Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand

getActiveAssemblies, getActiveAssembly, getPotentialsFromAssemblies, init, saveDirFile, setBaseDir, updateTitle

Methods inherited from class ffx.utilities.FFXCommand

getCommand, helpString, listCommands, setBinding

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

RepexThermo

public RepexThermo()

RepexThermo Constructor.

RepexThermo

public RepexThermo(FFXBinding binding)

RepexThermo Constructor.

Parameters:

binding - The Binding to use.

RepexThermo

public RepexThermo(String[] args)

RepexThermo constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public RepexThermo run()

Execute this Command.

Overrides:

run in class Thermodynamics

Returns:

The current FFXCommand.

getOST

public OrthogonalSpaceTempering getOST()

Overrides:

getOST in class Thermodynamics

getPotential

public CrystalPotential getPotential()

Overrides:

getPotential in class Thermodynamics

getPotentials

public List<Potential> getPotentials()

Description copied from class: AlgorithmsCommand

Returns a List of all Potential objects associated with this script.

Overrides:

getPotentials in class Thermodynamics

Returns:

All Potentials. Sometimes empty, never null.