Package ffx.algorithms.commands

Class PhMinimize

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.PhMinimize

public class PhMinimize
extends AlgorithmsCommand

The MinimizePh command uses a limited-memory BFGS algorithm to minimize the energy of a CpHMD molecular system.
Usage:
ffxc test.MinimizePh [options] <filename [file2...]>

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

Method Summary

Modifier and Type	Method	Description
PhMinimize	run()	Execute this Command.

Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand

destroyPotentials, getActiveAssemblies, getActiveAssembly, getPotentials, 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

PhMinimize

public PhMinimize()

MinimizePh Constructor.

PhMinimize

public PhMinimize(FFXBinding binding)

MinimizePh Constructor.

Parameters:

binding - The Binding to use.

PhMinimize

public PhMinimize(String[] args)

MinimizePh constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public PhMinimize run()

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.