magpie.attributes.generators.composition

Class ChargeDependentAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.composition.ChargeDependentAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Citable, Commandable, Options

public class ChargeDependentAttributeGenerator
extends BaseAttributeGenerator
implements Citable

Attributes derived from the oxidation states of elements in a material. Based on work by Deml et al.:

Deml et al.. PRB. 93 (2016), 085142

These attributes are based on the formal charges of materials determined using the OxidationStateGuesser. Currently implemented attributes:

1. Statistics of formal charges (min, max, range, mean, variance)
2. Cumulative ionization energies / electron affinities
3. Difference in electronegativity between cation and anion.

For materials that the algorithm fails to find an charge states, NaN is set for all attributes.

Usage: *No options*

See Also:

http://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.085142, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected OxidationStateGuesser	ChargeGuesser Tool used to compute electronegativity
protected double[][]	IonizationEnergies Ionization energies of each element

Constructor Summary

Constructors

Constructor and Description
ChargeDependentAttributeGenerator()

Method Summary

Modifier and Type	Method and Description
void	addAttributes(Dataset data) Generate new attributes for a dataset.
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	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

ChargeGuesser

protected OxidationStateGuesser ChargeGuesser

Tool used to compute electronegativity

IonizationEnergies

protected double[][] IonizationEnergies

Ionization energies of each element

Constructor Detail

ChargeDependentAttributeGenerator

public ChargeDependentAttributeGenerator()

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

addAttributes

public void addAttributes(Dataset data)

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

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]