magpie.attributes.generators.composition

Class IonicCompoundProximityAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.composition.IonicCompoundProximityAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

public class IonicCompoundProximityAttributeGenerator
extends BaseAttributeGenerator

Generate attributes based on the distance of a composition from compositions that can form, charge-neutral ionic compounds.

This generator only computes a single attribute: the L₁ distance between the composition of an entry and the nearest ionic compound (determined using IonicCompoundFinder. For compound where it is not possible to form ionic compound (e.g., only metallic elements), the entry is assigned arbitrarily large distance (equal to the number of elements in the alloy).

The one adjustable parameter in this calculation is the maximum number of atoms per formula unit used when looking for ionic compounds. For binary compounds, the maximum conceivable number of elements in a formula unit is for a compound with a 9+ and a 5- species, which has 14 atoms in the formula unit. Consequently, we recommend using 14 or larger for this parameter.

Usage: <formula unit size>
formula unit size: Maximum number of formula unit size

See Also:

IonicCompoundFinder, CompositionDistanceFilter.computeDistance(CompositionEntry, CompositionEntry, int), Serialized Form

Constructor Summary

Constructors

Constructor and Description
IonicCompoundProximityAttributeGenerator()

Method Summary

Modifier and Type	Method and Description
void	addAttributes(Dataset dataPtr) Generate new attributes for a dataset.
java.lang.String	printDescription(boolean htmlFormat) Print out description of attributes.
java.lang.String	printUsage() Print out required format for options.
void	setMaxFormulaUnit(int size) Set the maximum formula unit size when searching for ionic compounds.
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

Constructor Detail

IonicCompoundProximityAttributeGenerator

public IonicCompoundProximityAttributeGenerator()

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.

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: ".

Returns:

Usage for this function

setMaxFormulaUnit

public void setMaxFormulaUnit(int size)

Set the maximum formula unit size when searching for ionic compounds.

Parameters:

size - Maximum size

See Also:

IonicCompoundFinder

addAttributes

public void addAttributes(Dataset dataPtr)
                   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:

dataPtr - 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