magpie.attributes.generators.crystal

Class CoordinationNumberAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.crystal.CoordinationNumberAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

public class CoordinationNumberAttributeGenerator
extends BaseAttributeGenerator

Compute attributes based on the coordination number. Uses the Voronoi tessellation to define the coordination network.

DEV NOTE (LW 15Jul15): Could benefit from adding a face size cutoff, where atoms are only defined as coordinated if the face between them is larger than a certain fraction of the surface area of both cells. Otherwise faces on the cells that are only present to numerical issues will be counted as neighbors. Metallic glass community commonly removes any faces smaller than 1% of the total surface area of a cell.

Usage: *No options*

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
CoordinationNumberAttributeGenerator()

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

CoordinationNumberAttributeGenerator

public CoordinationNumberAttributeGenerator()

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