magpie.attributes.generators.crystal

Class EffectiveCoordinationNumberAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.crystal.EffectiveCoordinationNumberAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

public class EffectiveCoordinationNumberAttributeGenerator
extends BaseAttributeGenerator

Compute attributes based on the effective coordination number. The effective coordination number can be thought of as a face-size-weighted coordination number. It is computed by the formula N_eff = 1 / sum[(f_i / SA)²] where f_i is the area of face i and SA is the surface area of the entire cell.

The effective coordination number has major benefit: stability against the additional of a very small face. Small perturbations in atomic positions can break symmetry in a crystal, and lead to the introduction of small faces. The conventional coordination number treats all faces equally, so the coordination number changes even when one of these small faces is added.

One approach in the literature is to first apply a screen on small faces (e.g., remove any smaller than 1% of the total face area), which still runs into problems with discontinuity for larger displacements.

Our approach is differentiable with respect to the additional of a small face (ask Logan if you want the math), and also captures another interesting effect small coordination numbers for Voronoi cells with a dispersity in face sizes. For example, BCC has 14 faces on its voronoi cell. 8 large faces, and 6 small ones. Our effective face size identifies a face size of closer to 8, the commonly-accepted value of the BCC coordination number, than 14 reported by the conventional measure. Additional, for systems with equal-sized faces (e.g., FCC), this measure agrees exactly with conventional reports.

Usage: *No options*

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
EffectiveCoordinationNumberAttributeGenerator()

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

EffectiveCoordinationNumberAttributeGenerator

public EffectiveCoordinationNumberAttributeGenerator()

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