magpie.models.regression.crystal

Class PRDFRegression

java.lang.Object

magpie.models.BaseModel

magpie.models.regression.BaseRegression

magpie.models.regression.crystal.StructureKRRBasedRegression

magpie.models.regression.crystal.PRDFRegression

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, AbstractRegressionModel, Citable, Commandable, Options, Printable, Savable

public class PRDFRegression
extends StructureKRRBasedRegression

Uses the partial radial distribution function to perform regression. Each material is represented by a matrix containing the PRDF between each element type. Distance between structures are computed as Frobenius norm of the difference between their PRDF matrices. If you use this method, please cite Schutt, Glawe, et al. PRB (2015).

Usage: <lambda> <sigma> <cutoff> <bins>
lambda: Regularization parameter
sigma: Normalization parameter in kernel function.
cutoff: Distance cutoff used for PRDF (Angstroms)
bins: Number of bins used in PRDF

See Also:

Serialized Form

Field Summary

Fields inherited from class magpie.models.BaseModel

AttributeSelector, trained, TrainingStats, validated, ValidationStats

Constructor Summary

Constructors

Constructor and Description
PRDFRegression()

Method Summary

Modifier and Type	Method and Description
java.lang.Object	computeRepresentation(vassal.data.Cell strc) Compute the pair distribution function
protected double	computeSimiliarity(java.lang.Object strc1, java.lang.Object strc2) Compute similarity between two crystal structures.
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	printUsage() Print out required format for options.
void	setCutoff(double cutoff) Set the cutoff distance used when computing the PRDF
void	setNBins(int nBins) Set the number of bins used when computing the PRDF.
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.
void	setSigma(double sigma) Set the normalization parameter in the kernel function.

Methods inherited from class magpie.models.regression.crystal.StructureKRRBasedRegression

clone, findClosestEntries, getNFittingParameters, printModel_protected, run_protected, runCommand, setLambda, train_protected

Methods inherited from class magpie.models.regression.BaseRegression

doRobustRegression, getRobustRegressionQ, robustTraining, setRobustRegressionQ

Methods inherited from class magpie.models.BaseModel

about, crossValidate, crossValidate, crossValidate, done, externallyValidate, getAttributeSelector, getFilter, getTrainTime, getValidationMethod, handleSetCommand, isTrained, isValidated, loadState, printCommand, printDescription, printModel, printModelDescriptionDetails, resetModel, run, saveCommand, saveState, setAttributeSelector, setComponent, setFilter, train, train

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PRDFRegression

public PRDFRegression()

Method Detail

setSigma

public void setSigma(double sigma)

Set the normalization parameter in the kernel function.

Parameters:

sigma - Desired normalization parameter.

setNBins

public void setNBins(int nBins)

Set the number of bins used when computing the PRDF.

Parameters:

nBins - Number of bins (>1)

setCutoff

public void setCutoff(double cutoff)

Set the cutoff distance used when computing the PRDF

Parameters:

cutoff - Cutoff distance (>0 Angstrom)

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

computeSimiliarity

protected double computeSimiliarity(java.lang.Object strc1,
                                    java.lang.Object strc2)

Description copied from class: StructureKRRBasedRegression

Compute similarity between two crystal structures.

Specified by:

computeSimiliarity in class StructureKRRBasedRegression

Parameters:

strc1 - Representation of structure #1

strc2 - Representation of structure #2

Returns:

Similarity between two structures

computeRepresentation

public java.lang.Object computeRepresentation(vassal.data.Cell strc)

Compute the pair distribution function

Specified by:

computeRepresentation in class StructureKRRBasedRegression

Parameters:

strc - Structure to be evaluated

Returns:

Map where the key is (Z_a,Z_b) and the value is the PRDF

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

Overrides:

getCitations in class BaseModel

Returns:

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