magpie.attributes.generators.prototype

Class SingleSiteAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.prototype.SingleSiteAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

Direct Known Subclasses:

PairSiteAttributeGenerator

public class SingleSiteAttributeGenerator
extends BaseAttributeGenerator

Create attributes based on the properties of elements on each group of equivalent sites in a crystal. For an example, check out this paper by Pilania et al.

If there is only one site in a group, the mean elemental property of atoms on that site is used. If there are multiple sites, then the maximum, minimum, mean, mean absolute deviation, and range are reported (following a similar strategy to ElementalPropertyAttributeGenerator).

Usage: *No options*

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.List<java.lang.String>	ElementalProperties List of properties used to compute attributes
protected java.util.List<java.lang.String>	MultipleSites List of groups with a multiple site
protected java.util.List<java.lang.String>	SingleSites List of groups with a single site

Constructor Summary

Constructors

Constructor and Description
SingleSiteAttributeGenerator()

Method Summary

Modifier and Type	Method and Description
void	addAttributes(Dataset dataPtr) Generate new attributes for a dataset.
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.
protected java.lang.String	printElementalProperties(boolean htmlFormat) Print list of elemental properties used in computing 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

ElementalProperties

protected java.util.List<java.lang.String> ElementalProperties

List of properties used to compute attributes

SingleSites

protected java.util.List<java.lang.String> SingleSites

List of groups with a single site

MultipleSites

protected java.util.List<java.lang.String> MultipleSites

List of groups with a multiple site

Constructor Detail

SingleSiteAttributeGenerator

public SingleSiteAttributeGenerator()

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

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[])

generateAttributes

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

Compute attributes for a single entry

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

generateAttributeNames

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

Generate names of attributes

Parameters:

siteInfo - Information about sites in this prototype structure

Returns:

List of attribute names

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

printElementalProperties

protected java.lang.String printElementalProperties(boolean htmlFormat)

Print list of elemental properties used in computing attributes

Parameters:

htmlFormat - Whether to use HTML format

Returns:

List of attributes