magpie.attributes.generators.crystal

Class ChemicalOrderingAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.crystal.ChemicalOrderingAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

public class ChemicalOrderingAttributeGenerator
extends BaseAttributeGenerator

Compute attributes based on chemical ordering of structure. Determines average Warren-Cowley ordering parameter for the bond network defined by the Voronoi tessellation of a structure.

For each atom in the structure, the average Warren-Cowley ordering parameter is determined by computing the average magnitude of ordering parameter for each type for all atoms in a structure. The ordering parameter is 0 for a perfectly-random distribution, so this average represents an average degree of "ordering" in the structure. This attribute is computed for several nearest-neighbor shells (1st, 2nd, and 3rd by default).

There are two options for computing order parameters: Weighted and unweighted. The former is computed by weighing the contribution of each neighboring atom by the fraction of surface area corresponding to boundaries between that atom and the central atom. The former considers all neighbors weighted equally, which means they are very sensitive to the introduction of small faces due to numerical problems inherent to the Voronoi tessellation. Full details is available in the Vassal documentation for VoronoiCellBasedAnalysis.getNeighborOrderingParameters(int, boolean).

Usage: [-unweighted] <shells...>
-unweighted: Do not weigh WC parameters with face areas.
shells: List of which nearest-neighbor shells to compute the mean WC parameter for (default: 1 2 3).

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
ChemicalOrderingAttributeGenerator() Create a default attribute generator.

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.
void	setShells(java.util.Collection<java.lang.Integer> shells) Define which nearest-neighbor shells to consider when generating attributes.
void	setWeighted(boolean weighted) Set whether to consider face sizes when computing ordering parameters.

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

ChemicalOrderingAttributeGenerator

public ChemicalOrderingAttributeGenerator()

Create a default attribute generator. Will compute WC parameters for the first, second and third nearest-neighbor shells.

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

setShells

public void setShells(java.util.Collection<java.lang.Integer> shells)

Define which nearest-neighbor shells to consider when generating attributes.

Parameters:

shells - List of shell indices

setWeighted

public void setWeighted(boolean weighted)

Set whether to consider face sizes when computing ordering parameters.

Parameters:

weighted - Whether to weigh using face sizes

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