Package ffx.algorithms.commands
Class Minimize
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.Minimize
The Minimize script uses a limited-memory BFGS algorithm to minimize the energy of a molecular system.
Usage:
ffxc Minimize [options] <filename> [file2...]
Usage:
ffxc Minimize [options] <filename> [file2...]
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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
ConstructorsConstructorDescriptionMinimize()
Minimize Constructor.Minimize
(FFXBinding binding) Minimize Constructor.Minimize constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptiondouble
Get the final energy after minimization.Get the list of energies recorded during minimization.Returns a List of all Potential objects associated with this script.double
Get the final RMS gradient after minimization.run()
Execute this Command.toString()
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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Minimize
public Minimize()Minimize Constructor. -
Minimize
Minimize Constructor.- Parameters:
binding
- The Binding to use.
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Minimize
Minimize 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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toString
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getEnergyList
Get the list of energies recorded during minimization.- Returns:
- A List of Double energies, or null if minimization was not run.
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getRMSGradient
public double getRMSGradient()Get the final RMS gradient after minimization.- Returns:
- The final RMS gradient or NaN if minimization was not run.
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getEnergy
public double getEnergy()Get the final energy after minimization.- Returns:
- The final energy or NaN if minimization was not run.
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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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