magpie.attributes.generators.crystal

Class CoulombMatrixAttributeGenerator

java.lang.Object

magpie.attributes.generators.BaseAttributeGenerator

magpie.attributes.generators.crystal.CoulombMatrixAttributeGenerator

All Implemented Interfaces:

java.io.Serializable, Citable, Commandable, Options

public class CoulombMatrixAttributeGenerator
extends BaseAttributeGenerator
implements Citable

Compute attributes using the Coulomb Sine Matrix representation. Based on work by Faber et al..

This method works by computing an approximation for the Coulomb matrix that considers periodicity. Specifically, we use the Coulomb Sine matrix, which is described in detail in the Faber et al.. For molecules, the Coloumb matrix is defined as

The eigenvalues of this matrix are then used as attributes. In order to provided a fixed number of attributes, the first N attributes are defined to be the N eigenvalues from the Coulomb matrix. The remaining attributes are defined to be zero.

Note: The Coulomb Matrix attributes are dependant on unit cell choice. Please consider transforming your input crystal structures to the primitive cell before using these attributes.

Usage: <n eigenvalues>
n eigenvalues: Maximum number of Coulomb matrix eigenvalues to use as attributes

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected int	NEigenvalues Maximum number of atoms to consider.

Constructor Summary

Constructors

Constructor and Description
CoulombMatrixAttributeGenerator()

Method Summary

Modifier and Type	Method and Description
void	addAttributes(Dataset data) Generate new attributes for a dataset.
java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,Citation>>	getCitations() Return a list of citations for this object and any underlying objects.
java.lang.String	printDescription(boolean htmlFormat) Print out description of attributes.
java.lang.String	printUsage() Print out required format for options.
void	setNEigenvalues(int x) Set the number of eigenvalues used in representation
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

NEigenvalues

protected int NEigenvalues

Maximum number of atoms to consider. Defines number of attributes

Constructor Detail

CoulombMatrixAttributeGenerator

public CoulombMatrixAttributeGenerator()

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.

Specified by:

setOptions in interface Options

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: ".

Specified by:

printUsage in interface Options

Returns:

Usage for this function

setNEigenvalues

public void setNEigenvalues(int x)

Set the number of eigenvalues used in representation

Parameters:

x - Desired numbers

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

getCitations

public java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,Citation>> getCitations()

Description copied from interface: Citable

Return a list of citations for this object and any underlying objects.

Specified by:

getCitations in interface Citable

Returns:

List of pairs: [Reason for Citation], [Citation]