magpie.attributes.generators.crystal

Class LatticeSimilarityAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.crystal.LatticeSimilarityAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

public class LatticeSimilarityAttributeGenerator
extends BaseAttributeGenerator

Compute similarity of structure to several simple lattices. Determined by comparing the shape of each coordination polyhedron in the structure (as determined using a Voronoi tessellation) to those in a reference lattice.

Similarity is computed by summing the difference in the number of faces with each number of edges between a certain Voronoi cell and that of the reference lattice. This difference is then normalized by the number of faces in the reference lattice, and averaged over all atoms to produce a "similarity index." In this form, structures based on the reference lattice have a match of 0, which becomes larger with increase dissimilarity.

For now we consider the BCC, FCC (which has the same coordination polyhedron shape as HCP), and SC lattices.

Usage: *No options*

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
LatticeSimilarityAttributeGenerator()

Method Summary

Modifier and Type	Method and Description
void	addAttributes(Dataset data) 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	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

LatticeSimilarityAttributeGenerator

public LatticeSimilarityAttributeGenerator()

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 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