Package ffx.xray.commands.test

Class Gradient

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.xray.commands.test.Gradient

public class Gradient
extends AlgorithmsCommand

The Gradient script evaluates the consistency of the energy and gradient.
Usage:
ffxc test.Gradient [options] <filename>

Field Summary

Fields

Modifier and Type	Field	Description
double	dx	-d or --dx Finite-difference step size.
String	gradientParams	--params or --gradientAtoms Ranges of degrees of freedom to test [ALL, NONE, Range(s): 1-3,6-N].
int	nFailures
double	tolerance	--tol or --tolerance Gradient error tolerance.

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
Gradient()	Gradient constructor.
Gradient(FFXBinding binding)	Gradient constructor.
Gradient(String[] args)	Gradient 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.
Gradient	run()	Execute the script.

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

Field Details

dx

public double dx

-d or --dx Finite-difference step size.

tolerance

public double tolerance

--tol or --tolerance Gradient error tolerance.

gradientParams

public String gradientParams

--params or --gradientAtoms Ranges of degrees of freedom to test [ALL, NONE, Range(s): 1-3,6-N].

nFailures

public int nFailures

Constructor Details

Gradient

public Gradient()

Gradient constructor.

Gradient

public Gradient(FFXBinding binding)

Gradient constructor.

Parameters:

binding - The Binding to use.

Gradient

public Gradient(String[] args)

Gradient constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public Gradient run()

Execute the script.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

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.