Package ffx.algorithms.commands
Class ManyBody
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.ManyBody
The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.
Usage:
ffxc ManyBody [options] <filename>
Usage:
ffxc ManyBody [options] <filename>
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Field Summary
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
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Constructor Summary
ConstructorsConstructorDescriptionManyBody()
ManyBody Constructor.ManyBody
(FFXBinding binding) ManyBody Constructor.ManyBody constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptionGet ManyBodyOptions to access script parameters.Returns the potential energy of the active assembly.Returns a List of all Potential objects associated with this script.run()
Execute this Command.Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand
destroyPotentials, getActiveAssemblies, getActiveAssembly, init, saveDirFile, setActiveAssembly, setBaseDir, updateTitle
Methods inherited from class ffx.utilities.FFXCommand
getCommand, helpString, listCommands, setBinding
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Constructor Details
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ManyBody
public ManyBody()ManyBody Constructor. -
ManyBody
ManyBody Constructor.- Parameters:
binding
- The Binding to use.
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ManyBody
ManyBody constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Method Details
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run
Execute this Command.- Overrides:
run
in classFFXCommand
- Returns:
- The current FFXCommand.
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getManyBodyOptions
Get ManyBodyOptions to access script parameters. -
getPotential
Returns the potential energy of the active assembly. Used during testing assertions.- Returns:
- potentialEnergy Potential energy of the active assembly.
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getPotentials
Returns a List of all Potential objects associated with this script.- Overrides:
getPotentials
in classAlgorithmsCommand
- Returns:
- All Potentials. Sometimes empty, never null.
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