magpie.attributes.generators.crystal

Class LocalPropertyDifferenceAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.crystal.LocalPropertyDifferenceAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

Direct Known Subclasses:

LocalPropertyVarianceAttributeGenerator

public class LocalPropertyDifferenceAttributeGenerator
extends BaseAttributeGenerator

Compute attributes based on the difference in elemental properties between neighboring atoms. For an atom, its "local property difference" is computed by:
\(\frac{\sum_{n}{f_{n} * \left|p_{atom}-p_{n}\right|}}{\sum_{n}{f_n}}\)

where \(f_n\) is the area of the face associated with neighbor n, \(p_{atom}\) the the elemental property of the central atom, and \(p_n\) is the elemental property of the neighbor atom.

For shells past the 1st nearest neighbor shell, the neighbors are identified by finding all of the unique faces on the outside of the polyhedron formed by the previous neighbor shell. This list of faces will faces corresponding to all of the atoms in the desired shell and the total weight for each atom is defined by the total area of the faces corresponding to that atom (there may be more than one).

By default, this class considers the only the 1st nearest neighbor shell.

This parameter is computed for all elemental properties stored in CompositionDataset.ElementalProperties.

Usage: <shells...>
shells: Which nearest neighbor shells to consider

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	AttrDescription Property description (used in description output)
protected java.lang.String	AttrName Property name

Constructor Summary

Constructors

Constructor and Description
LocalPropertyDifferenceAttributeGenerator() Create Default attribute generator.
LocalPropertyDifferenceAttributeGenerator(int... shells) Create attribute generator that considers a certain list of shells.

Method Summary

Modifier and Type	Method and Description
void	addAttributes(Dataset data) Generate new attributes for a dataset.
void	addShell(int shell) Add shell to list of used when computing attributes
void	addShells(java.util.Collection<java.lang.Integer> shells) Add several shells to list of used when computing attributes
void	clearShells() Clear list of shells to use when computing attributes
protected java.util.List<java.lang.String>	createNames() Create names for the attributes
protected double[]	getAtomProperties(vassal.analysis.VoronoiCellBasedAnalysis voro, org.apache.commons.lang3.tuple.Pair<int[][],double[][]> faceInfo, double[] propValues) Provided the Voronoi tessellation and properties of each atom type, compute the properties of a certain neighbor cell for each atom.
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

Field Detail

AttrName

protected java.lang.String AttrName

Property name

AttrDescription

protected java.lang.String AttrDescription

Property description (used in description output)

Constructor Detail

LocalPropertyDifferenceAttributeGenerator

public LocalPropertyDifferenceAttributeGenerator()

Create Default attribute generator. Will consider 1st and 2nd shells

LocalPropertyDifferenceAttributeGenerator

public LocalPropertyDifferenceAttributeGenerator(int... shells)

Create attribute generator that considers a certain list of shells.

Parameters:

shells - List of shells to be considered

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

clearShells

public void clearShells()

Clear list of shells to use when computing attributes

addShell

public final void addShell(int shell)

Add shell to list of used when computing attributes

Parameters:

shell - Index of nearest neighbor shell

addShells

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

Add several shells to list of used when computing attributes

Parameters:

shells - Indices of nearest neighbor shells

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[])

getAtomProperties

protected double[] getAtomProperties(vassal.analysis.VoronoiCellBasedAnalysis voro,
                                     org.apache.commons.lang3.tuple.Pair<int[][],double[][]> faceInfo,
                                     double[] propValues)

Provided the Voronoi tessellation and properties of each atom type, compute the properties of a certain neighbor cell for each atom.

For LocalPropertyDifferenceAttributeGenerator, this produces the local property difference for each atom.

Parameters:

voro - Voronoi tessellation

faceInfo - Areas and types on outside of each face for desired shell. Computed using VoronoiCellBasedAnalysis.getNeighborShellWeights(int)

propValues - Properties of each atom type

Returns:

Properties of each atom

createNames

protected java.util.List<java.lang.String> createNames()

Create names for the attributes

Returns:

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