magpie.attributes.generators.crystal

Class PRDFAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.crystal.PRDFAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Citable, Commandable, Options

public class PRDFAttributeGenerator
extends BaseAttributeGenerator
implements Citable

Compute attributes based on the Pair Radial Distribution Function (PRDF). Based on work by Schutt et al..

Usage: <cutoff distance> <n steps> $<dataset>
cutoff distance: Maximum distance to consider
n steps: Number of distance points along axis to sample
dataset: CompositionDataset containing list of ElementList to be considered in PRDF. Usually, this is the dataset you will be computing attributes for

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected double	CutoffDistance Cutoff distance for PRDF
protected java.util.SortedSet<java.lang.Integer>	ElementList List of ElementList to use in PRDF
protected int	NPoints Number of distance points to evaluate

Constructor Summary

Constructors

Constructor and Description
PRDFAttributeGenerator()

Method Summary

Modifier and Type	Method and Description
void	addAttributes(Dataset data) Generate new attributes for a dataset.
void	addElement(int elem) Add element to list used when computing PRDF
void	addElement(java.lang.String elem) Add element to list used when computing PRDF
void	clearElementList() Clear list of elements used when computing PRDF
java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,Citation>>	getCitations() Return a list of citations for this object and any underlying objects.
java.lang.String	printDescription(boolean htmlFormat) Print out description of attributes.
java.lang.String	printUsage() Print out required format for options.
void	setCutoffDistance(double cutoffDistance) Define the maximum distance to consider when computing the PRDF
void	setElements(CompositionDataset data) Set the elements when computing PRDF
void	setNPoints(int NPoints) Define the number of points on each PRDF to store
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.

Methods inherited from class magpie.attributes.generators.BaseAttributeGenerator

runCommand

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CutoffDistance

protected double CutoffDistance

Cutoff distance for PRDF

NPoints

protected int NPoints

Number of distance points to evaluate

ElementList

protected final java.util.SortedSet<java.lang.Integer> ElementList

List of ElementList to use in PRDF

Constructor Detail

PRDFAttributeGenerator

public PRDFAttributeGenerator()

Method Detail

setOptions

public void setOptions(java.util.List<java.lang.Object> Options)
                throws java.lang.Exception

Description copied from interface: Options

Set any options for this object. If parsing the options fails, return an Exception with the usage as its message.

Specified by:

setOptions in interface Options

Parameters:

Options - Array of options as Objects - can be null

Throws:

java.lang.Exception - if problem with inputs

printUsage

public java.lang.String printUsage()

Description copied from interface: Options

Print out required format for options. For consistency, should start with "Usage: ".

Specified by:

printUsage in interface Options

Returns:

Usage for this function

setCutoffDistance

public void setCutoffDistance(double cutoffDistance)

Define the maximum distance to consider when computing the PRDF

Parameters:

cutoffDistance - Desired cutoff distance

setNPoints

public void setNPoints(int NPoints)

Define the number of points on each PRDF to store

Parameters:

NPoints - Number of evaluation points

clearElementList

public void clearElementList()

Clear list of elements used when computing PRDF

setElements

public void setElements(CompositionDataset data)

Set the elements when computing PRDF

Parameters:

data - Dataset containing each element to be

addElement

public void addElement(int elem)

Add element to list used when computing PRDF

Parameters:

elem - ID of element (Atomic number - 1)

addElement

public void addElement(java.lang.String elem)

Add element to list used when computing PRDF

Parameters:

elem - Abbreviation of element (e.g., "Al")

addAttributes

public void addAttributes(Dataset data)
                   throws java.lang.Exception

Description copied from class: BaseAttributeGenerator

Generate new attributes for a dataset. This operation must both add the new attribute names to the dataset and new values to each entry.

Specified by:

addAttributes in class BaseAttributeGenerator

Parameters:

data - Dataset to be added to

Throws:

java.lang.Exception

See Also:

Dataset.addAttribute(java.lang.String, double[])

printDescription

public java.lang.String printDescription(boolean htmlFormat)

Description copied from class: BaseAttributeGenerator

Print out description of attributes.

Implementation Notes

Format should look like

[Full Name of generator]: (Number of attributes) Text description of what these attributes are

For HTML format, omit the ":".

Specified by:

printDescription in class BaseAttributeGenerator

Parameters:

htmlFormat - Whether to print in HTML format

Returns:

Description of the attributes

getCitations

public java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,Citation>> getCitations()

Description copied from interface: Citable

Return a list of citations for this object and any underlying objects.

Specified by:

getCitations in interface Citable

Returns:

List of pairs: [Reason for Citation], [Citation]