magpie.data.materials

Class PrototypeDataset

java.lang.Object

magpie.data.Dataset

magpie.data.MultiPropertyDataset

magpie.data.materials.CompositionDataset

magpie.data.materials.PrototypeDataset

All Implemented Interfaces:

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

public class PrototypeDataset
extends CompositionDataset

Store data about compounds based on a single crystal structure prototype. User must specify the sites in the crystal, the number of atoms on each site, and which sites are equivalent. For example, this class could be used to represent a dataset composed of Heusler compounds, where there are 3 sites and two are equivalent.

Information about each site must be specified with a file in the following format:

<# of atoms on Site1> [-omit] [-equiv <site #s...>]
<# of atoms on Site2> [-omit] [-equiv <site #s...>]

Here sites (aka sublattices) can be occupied by a single kind of atom, and are treated as symmetrically distinct unless otherwise specified. Information about each site is used to calculate attributes unless otherwise indicated by an "-omit" flag. It is possible to mark equivalent sites using the "-equiv" flag.

The required format of data files is very similar to that of a CompositionDataset:

Identity [<property1 Name>] [<property2 Name>] [...]
<A site Element><B site Element><...> <property1 value> [...]
{<Composition of Site A>}{<Composition of Site B} <property1 value> [...]
[and so on]

It is important that you can define the identity of an crystal by either specifying the element present on each site, or by specifying the composition of the elements occupying that site. The latter option allows this class to handle mixing on a certain atomic site. Note that this does not consider the ordering (or lack there of) on that sublattice.

Usage: <Structure description filename>
Structure description filename: File containing description of atomic sites in structure

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected PrototypeSiteInformation	SiteInfo Stores information about each site

Fields inherited from class magpie.data.materials.CompositionDataset

DataDirectory, ElementalProperties, ElementNames, ElementPairProperties, OxidationStates, PairPropertyData, PropertyData, SortingOrder

Fields inherited from class magpie.data.Dataset

AttributeName, Entries, Expanders, Generators

Constructor Summary

Constructors

Constructor and Description
PrototypeDataset() Create a prototype dataset with default attribute
PrototypeDataset(boolean useDefaultGenerators) Create a prototype dataset.

Method Summary

Modifier and Type	Method and Description
PrototypeEntry	addEntry(java.lang.String input) A new entry by parsing an input string.
PrototypeDataset	emptyClone() Creates a new instance with the same class and attribute names, but without any entries.
PrototypeEntry	getEntry(int index) Retrieve a single entry from the dataset
PrototypeSiteInformation	getSiteInfo() Get information about each site in this prototype structure
void	importText(java.lang.String filename, java.lang.Object[] options) Read in an dataset from file.
int	NSites()
java.lang.String	printUsage() Print out required format for options.
void	readStructureInformation(java.lang.String filename) Read information about a prototype crystal structure from file.
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.
void	setSiteInfo(PrototypeSiteInformation SiteInfo) Define information about the prototypes contained by this dataset.

Methods inherited from class magpie.data.materials.CompositionDataset

addElementalProperty, addElementalPropertySet, addElementPairProperty, addGeneratedElementPairProperty, calculateAttributes, compositionCanFormIonic, createTemplate, getDataDirectory, getElementalProperties, getElementPairProperties, getOxidationStates, getPairPropertyLookupTable, getPropertyLookupTable, getSortingOrder, printEntryDescription, removeElementalProperty, removeElementPairProperty, runAttributeCommand, runCommand, runPairPropertyCommand, runPropertyCommand, saveCommand, setDataDirectory, useCompositionAsAttributes

Methods inherited from class magpie.data.MultiPropertyDataset

addEntries, addEntries, addEntry, addProperty, addProperty, clearPropertyData, combine, definePropertyNames, getClassNames, getMeasuredPropertyArray, getMeasuredPropertyArray, getPredictedPropertyArray, getPredictedPropertyArray, getPropertyClassCount, getPropertyClasses, getPropertyClasses, getPropertyIndex, getPropertyName, getPropertyNames, getTargetPropertyIndex, getTargetPropertyName, hasProperty, importEntryProperties, importPropertyNames, NClasses, NProperties, setClassNames, setPropertyClasses, setTargetProperty, setTargetProperty, toJSON, toString, usingPropertyAsClass

Methods inherited from class magpie.data.Dataset

about, addAttribute, addAttributeExpander, addAttributeGenerator, addAttributes, clearAttributeExpanders, clearAttributeGenerators, clearAttributes, clearData, clone, combine, combine, containsEntry, deleteMeasuredClasses, deletePredictedClasses, finalizeGeneration, generateAttributes, getAttributeArray, getAttributeExpanders, getAttributeGenerators, getAttributeIndex, getAttributeName, getAttributeNames, getCitations, getClassName, getClassProbabilityArray, getDistribution, getDistributionCount, getDuplicates, getEntries, getEntriesWriteAccess, getEntryArray, getMeasuredClassArray, getPredictedClassArray, getRandomSplit, getRandomSplit, getRandomSplit, getRandomSplit, getRandomSubset, getRandomSubset, getSingleAttributeArray, getSubset, getTrainingExamples, getUniqueEntries, loadState, matchEntries, NAttributes, NEntries, partition, partition, printAttributeDescription, printCommand, printDescription, printDistribution, printEntries, removeDuplicates, resolveDuplicates, restoreAttributes, runAttributeExpanders, runAttributeExpansionCommand, runAttributeGeneratorCommand, runAttributeGenerators, saveState, saveTemplate, setAttributeNames, setClassProbabilities, setMeasuredClasses, setPredictedClasses, splitForThreading, splitIntoFolds, splitIntoFolds, subtract, transferToWeka

Methods inherited from class java.lang.Object

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

Field Detail

SiteInfo

protected PrototypeSiteInformation SiteInfo

Stores information about each site

Constructor Detail

PrototypeDataset

public PrototypeDataset()

Create a prototype dataset with default attribute

PrototypeDataset

public PrototypeDataset(boolean useDefaultGenerators)

Create a prototype dataset. Gives user options of whether to use the "default" attribute generators for this class:

1. SingleSiteAttributeGenerator: Statistics about the properties of elements on each site.

Parameters:

useDefaultGenerators - Whether

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

Overrides:

setOptions in class Dataset

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

Overrides:

printUsage in class Dataset

Returns:

Usage for this function

emptyClone

public PrototypeDataset emptyClone()

Description copied from class: Dataset

Creates a new instance with the same class and attribute names, but without any entries.

Overrides:

emptyClone in class CompositionDataset

Returns:

Dataset with same properties, no entries

readStructureInformation

public void readStructureInformation(java.lang.String filename)
                              throws java.lang.Exception

Read information about a prototype crystal structure from file. See documentation for this class for format information.

Parameters:

filename - File containing structure information.

Throws:

java.lang.Exception - If file fails to parse

setSiteInfo

public void setSiteInfo(PrototypeSiteInformation SiteInfo)

Define information about the prototypes contained by this dataset.

NOTE: This will clear all existing data

Parameters:

SiteInfo - Object describing the number of atoms on each site, etc.

getSiteInfo

public PrototypeSiteInformation getSiteInfo()

Get information about each site in this prototype structure

Returns:

Site information for this dataset

importText

public void importText(java.lang.String filename,
                       java.lang.Object[] options)
                throws java.lang.Exception

Description copied from class: CompositionDataset

Read in an dataset from file. See documentation for format information.

Overrides:

importText in class CompositionDataset

Parameters:

filename - Path of file to be imported

options - Any options used to control import

Throws:

java.lang.Exception - If text import fails

NSites

public int NSites()

Returns:

Number of sites in prototype crystal

getEntry

public PrototypeEntry getEntry(int index)

Description copied from class: Dataset

Retrieve a single entry from the dataset

Overrides:

getEntry in class CompositionDataset

Parameters:

index - Index of entry

Returns:

Specified entry

addEntry

public PrototypeEntry addEntry(java.lang.String input)
                        throws java.lang.Exception

Description copied from class: Dataset

A new entry by parsing an input string. After using this operation, it may be necessary to recalculate attributes.

Overrides:

addEntry in class CompositionDataset

Parameters:

input - String describing the entry

Returns:

Entry representing the parsed string.

Throws:

java.lang.Exception - If conversion fails