Package ffx.potential.commands.test

Class LambdaGradient

java.lang.Object

ffx.utilities.FFXCommand

ffx.potential.cli.PotentialCommand

ffx.potential.commands.test.LambdaGradient

public class LambdaGradient
extends PotentialCommand

The LambdaGradient script tests numeric gradients w.r.t. lambda against numeric, finite-difference gradients
Usage:
ffxc test.LambdaGradient [options] <filename> [file2...]

Field Summary

Fields

Modifier and Type	Field	Description
double	e0
double	e1
int	nd2EdL2Failures
int	ndEdLFailures
int	ndEdXdLFailures
int	ndEdXFailures

Fields inherited from class ffx.potential.cli.PotentialCommand

activeAssembly, baseDir, potentialFunctions

Fields inherited from class ffx.utilities.FFXCommand

args, binding, color, help, logger, parseResult, version

Constructor Summary

Constructors

Constructor	Description
LambdaGradient()	LambdaGradient Constructor
LambdaGradient(FFXBinding binding)	LambdaGradient Constructor
LambdaGradient(String[] args)	LambdaGradient 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 command.
LambdaGradient	run()	Script run method.

Methods inherited from class ffx.potential.cli.PotentialCommand

createOutputFile, destroyPotentials, getActiveAssemblies, getActiveAssembly, getActiveAssembly, getBaseDirString, getPotentialsFromAssemblies, init, parseFilePath, saveByExtension, saveByExtension, saveByOriginalExtension, saveByOriginalExtension, setActiveAssembly

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

ndEdLFailures

public int ndEdLFailures

ndEdXFailures

public int ndEdXFailures

nd2EdL2Failures

public int nd2EdL2Failures

ndEdXdLFailures

public int ndEdXdLFailures

e0

public double e0

e1

public double e1

Constructor Details

LambdaGradient

public LambdaGradient()

LambdaGradient Constructor

LambdaGradient

public LambdaGradient(FFXBinding binding)

LambdaGradient Constructor

Parameters:

binding - Binding to use.

LambdaGradient

public LambdaGradient(String[] args)

LambdaGradient constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public LambdaGradient run()

Script run method.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

getPotentials

public List<Potential> getPotentials()

Description copied from class: PotentialCommand

Returns a List of all Potential objects associated with this command. Should be written to tolerate nulls, as many tests run help() and exit without instantiating their Potentials.

Overrides:

getPotentials in class PotentialCommand

Returns:

All Potentials. Sometimes empty, never null.