magpie.attributes.generators.prototype

Class PairSiteAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.prototype.SingleSiteAttributeGenerator

magpie.attributes.generators.prototype.PairSiteAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

public class PairSiteAttributeGenerator
extends SingleSiteAttributeGenerator

Generate attributes based on the differences in properties between pairs of sites.

If there is only one site in a group, the mean elemental property of atoms on that site is used to describe it. If there are multiple sites in a group, then the maximum, mean, and minimum of that property is used to describe the site. The difference between all descriptions of each site group are used to compute attributes. Both the absolute value of the difference and the magnitude of the difference are generated.

Example: For a material with stoichiometry (AA')B₂ there are two groups of sites: (1) The group including the A and A' sites, and (2) the B site. This class will generate 3 attributes. B-min(AA'), B-mean(AA'), and B-max(AA')

Usage: *No options*

See Also:

PrototypeDataset, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected PrototypeSiteInformation	SiteInfo Information of this particular prototype

Fields inherited from class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator

ElementalProperties, MultipleSites, SingleSites

Constructor Summary

Constructors

Constructor and Description
PairSiteAttributeGenerator()

Method Summary

Modifier and Type	Method and Description
protected java.util.List<java.lang.String>	generateAttributeNames(PrototypeSiteInformation siteInfo) Generate names of attributes
protected void	generateAttributes(PrototypeSiteInformation siteInfo, PrototypeEntry entry, PrototypeDataset data, double[] attrs) Compute attributes for a single entry
java.lang.String	printDescription(boolean htmlFormat) Print out description of attributes.

Methods inherited from class magpie.attributes.generators.prototype.SingleSiteAttributeGenerator

addAttributes, printElementalProperties, printUsage, setOptions

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

SiteInfo

protected PrototypeSiteInformation SiteInfo

Information of this particular prototype

Constructor Detail

PairSiteAttributeGenerator

public PairSiteAttributeGenerator()

Method Detail

generateAttributeNames

protected java.util.List<java.lang.String> generateAttributeNames(PrototypeSiteInformation siteInfo)

Description copied from class: SingleSiteAttributeGenerator

Generate names of attributes

Overrides:

generateAttributeNames in class SingleSiteAttributeGenerator

Parameters:

siteInfo - Information about sites in this prototype structure

Returns:

List of attribute names

generateAttributes

protected void generateAttributes(PrototypeSiteInformation siteInfo,
                                  PrototypeEntry entry,
                                  PrototypeDataset data,
                                  double[] attrs)
                           throws java.lang.Exception

Description copied from class: SingleSiteAttributeGenerator

Compute attributes for a single entry

Overrides:

generateAttributes in class SingleSiteAttributeGenerator

Parameters:

siteInfo - Information each site in this protoype

entry - Entry being computed

data - Dataset (link to property lookup tables)

attrs - [out] Temporary storage for attributes (to avoid recreating N double[] arrays)

Throws:

java.lang.Exception

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 ":".

Overrides:

printDescription in class SingleSiteAttributeGenerator

Parameters:

htmlFormat - Whether to print in HTML format

Returns:

Description of the attributes