magpie.attributes.generators.crystal

Class StructuralHeterogeneityAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.crystal.StructuralHeterogeneityAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

public class StructuralHeterogeneityAttributeGenerator
extends BaseAttributeGenerator

Compute attributes based on heterogeneity in structure. Measures variance in bond lengths (both for a single atom and between different atoms) and atomic volumes. Also considers the number of unique coordination polyhedron shapes.

Bond lengths, atomic volumes, and coordination polyhedra are based on the Voronoi tessellation of the structure.

Current attributes:

1. Mean absolute deviation in average bond length for each atom, normalized by mean for all atoms
2. Minimum in average bond length, normalized by mean for all atoms
3. Maximum in average bond length, normalized by mean for all atoms
4. Mean bond length variance between bonds across all atom
5. Mean absolute deviation in bond length variance
6. Minimum bond length variance
7. Maximum bond length variance
8. Mean absolute deviation in atomic volume, normalized by mean atomic volume

Here, bond length variation for a single atom is defined as:

\(\hat{l}=\langle l_i - \bar{l} \rangle\)

where \(l_i\) is the distance between an atom and one of its neighbors.

Usage: *No options*

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
StructuralHeterogeneityAttributeGenerator()

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

StructuralHeterogeneityAttributeGenerator

public StructuralHeterogeneityAttributeGenerator()

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