Package ffx.algorithms.commands

Class Thermodynamics

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.Thermodynamics

Direct Known Subclasses:

RepexThermo

public class Thermodynamics
extends AlgorithmsCommand

The Thermodynamics script uses the Transition-Tempered Orthogonal Space Random Walk algorithm to estimate a free energy.
Usage:
ffxc Thermodynamics [options] <filename> [file2...]

Field Summary

Fields

Modifier and Type	Field	Description
org.apache.commons.configuration2.Configuration	additionalProperties
AlchemicalOptions	alchemicalOptions
BarostatOptions	barostatOptions
DynamicsOptions	dynamicsOptions
List<String>	filenames	The final argument(s) should be one or more filenames.
LambdaParticleOptions	lambdaParticleOptions
MultiDynamicsOptions	multiDynamicsOptions
OrthogonalSpaceTempering	orthogonalSpaceTempering
OSTOptions	ostOptions
CrystalPotential	potential
RandomUnitCellOptions	randomSymopOptions
ThermodynamicsOptions	thermodynamicsOptions
MolecularAssembly[]	topologies
TopologyOptions	topologyOptions
boolean	verbose	-v or --verbose Log additional information (primarily for MC-OST).
WriteoutOptions	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
Thermodynamics()	Thermodynamics Constructor.
Thermodynamics(FFXBinding binding)	Thermodynamics Constructor.
Thermodynamics(String[] args)	Thermodynamics constructor that sets the command line arguments.

Method Summary

Modifier and Type	Method	Description
boolean	destroyPotentials()	Reclaims resources associated with all Potential objects associated with this script.
OrthogonalSpaceTempering	getOST()
CrystalPotential	getPotential()
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this script.
Thermodynamics	run()	Execute this Command.
void	setProperties(org.apache.commons.configuration2.Configuration additionalProps)	Sets an optional Configuration with additional properties.

Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand

getActiveAssemblies, getActiveAssembly, init, saveDirFile, setActiveAssembly, 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

Field Details

dynamicsOptions

public DynamicsOptions dynamicsOptions

barostatOptions

public BarostatOptions barostatOptions

randomSymopOptions

public RandomUnitCellOptions randomSymopOptions

alchemicalOptions

public AlchemicalOptions alchemicalOptions

topologyOptions

public TopologyOptions topologyOptions

writeoutOptions

public WriteoutOptions writeoutOptions

thermodynamicsOptions

public ThermodynamicsOptions thermodynamicsOptions

ostOptions

public OSTOptions ostOptions

lambdaParticleOptions

public LambdaParticleOptions lambdaParticleOptions

multiDynamicsOptions

public MultiDynamicsOptions multiDynamicsOptions

verbose

public boolean verbose

-v or --verbose Log additional information (primarily for MC-OST).

filenames

public List<String> filenames

The final argument(s) should be one or more filenames.

topologies

public MolecularAssembly[] topologies

potential

public CrystalPotential potential

orthogonalSpaceTempering

public OrthogonalSpaceTempering orthogonalSpaceTempering

additionalProperties

public org.apache.commons.configuration2.Configuration additionalProperties

Constructor Details

Thermodynamics

public Thermodynamics()

Thermodynamics Constructor.

Thermodynamics

public Thermodynamics(FFXBinding binding)

Thermodynamics Constructor.

Parameters:

binding - The Binding to use.

Thermodynamics

public Thermodynamics(String[] args)

Thermodynamics constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

setProperties

public void setProperties(org.apache.commons.configuration2.Configuration additionalProps)

Sets an optional Configuration with additional properties.

Parameters:

additionalProps - Additional properties configuration

run

public Thermodynamics run()

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

getOST

public OrthogonalSpaceTempering getOST()

getPotential

public CrystalPotential getPotential()

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 AlgorithmsCommand

Returns:

All Potentials. Sometimes empty, never null.

destroyPotentials

public boolean destroyPotentials()

Description copied from class: AlgorithmsCommand

Reclaims resources associated with all Potential objects associated with this script.

Overrides:

destroyPotentials in class AlgorithmsCommand

Returns:

If all Potentials had resources reclaimed.