Package ffx.algorithms.commands

Class MinimizeCrystals

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.MinimizeCrystals

public class MinimizeCrystals
extends AlgorithmsCommand

The MinimizeCrystals script uses a limited-memory BFGS algorithm to minimize the energy of a crystal, including both coordinates and unit cell parameters.
Usage:
ffxc MinimizeCrystals [options] <filename>

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

Constructor Summary

Constructors

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

Method Summary

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

Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand

destroyPotentials, 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

MinimizeCrystals

public MinimizeCrystals()

CrystalMin Constructor.

MinimizeCrystals

public MinimizeCrystals(FFXBinding binding)

CrystalMin Constructor.

Parameters:

binding - The Binding to use.

MinimizeCrystals

public MinimizeCrystals(String[] args)

MinimizeCrystals constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public MinimizeCrystals run()

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

getPotentials

public List<Potential> getPotentials()

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

Overrides:

getPotentials in class AlgorithmsCommand

Returns:

All Potentials. Sometimes empty, never null.