magpie.data.materials

Class CrystalStructureDataset

java.lang.Object

magpie.data.Dataset

magpie.data.MultiPropertyDataset

magpie.data.materials.CompositionDataset

magpie.data.materials.CrystalStructureDataset

All Implemented Interfaces:

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

public class CrystalStructureDataset
extends CompositionDataset

Holds a entries that represent crystal structures.

How to Import Files:

Rather than importing data from a single file with the importText(java.lang.String, java.lang.Object[]) operation, this class imports all the files in a given directory. These files must be VASP 5 POSCAR files. Any files that are not in this format will be ignored.

In order to provide properties about these structures, add a "properties.txt" file to the POSCAR-containing directory. This file should be in the following format

filename <property #1 name> <...>
<name of POSCAR> <property #1 of that structure> <...>

This file follows similar rules to that of CompositionDataset

Implemented Save Formats

poscar - Save dataset as a directory full of POSCARs.
Properties of each entry will be saved in a file in that directory named "properties.txt"

Usage: *No options*

See Also:

Serialized Form

Field Summary

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
CrystalStructureDataset() Create a instance with the default attribute generators
CrystalStructureDataset(boolean useDefaultGenerators) Create a new instance.

Method Summary

Modifier and Type	Method and Description
CrystalStructureEntry	addEntry(java.lang.String input) A new entry by parsing an input string.
CrystalStructureDataset	clone() Creates a new instance of this dataset, and clones of each entry.
CrystalStructureDataset	emptyClone() Creates a new instance with the same class and attribute names, but without any entries.
CrystalStructureEntry	getEntry(int index) Retrieve a single entry from the dataset
void	importText(java.lang.String directory, java.lang.Object[] options) Import all structure files in a directory.
void	runAttributeGenerators() Expand the list of attributes using the currently-set list of attribute generators.
java.lang.String	saveCommand(java.lang.String Basename, java.lang.String Format) Handles complicated saving commands.
void	writePOSCARs(java.lang.String directory) Save dataset as a directory full of POSCARs.

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, 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, 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, printUsage, removeDuplicates, resolveDuplicates, restoreAttributes, runAttributeExpanders, runAttributeExpansionCommand, runAttributeGeneratorCommand, saveState, saveTemplate, setAttributeNames, setClassProbabilities, setMeasuredClasses, setOptions, setPredictedClasses, splitForThreading, splitIntoFolds, splitIntoFolds, subtract, transferToWeka

Methods inherited from class java.lang.Object

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

Constructor Detail

CrystalStructureDataset

public CrystalStructureDataset()

Create a instance with the default attribute generators

See Also:

CrystalStructureDataset(boolean)

CrystalStructureDataset

public CrystalStructureDataset(boolean useDefaultGenerators)

Create a new instance.

Default attribute generators are:

1. EffectiveCoordinationNumberAttributeGenerator
2. StructuralHeterogeneityAttributeGenerator
3. ChemicalOrderingAttributeGenerator
4. PackingEfficiencyAttributeGenerator
5. LocalPropertyDifferenceAttributeGenerator
6. Default generators from CompositionDataset.CompositionDataset(boolean)

Parameters:

useDefaultGenerators - Whether to use the default attribute generators

Method Detail

clone

public CrystalStructureDataset clone()

Description copied from class: Dataset

Creates a new instance of this dataset, and clones of each entry.

Overrides:

clone in class Dataset

Returns:

Clone of this dataset

emptyClone

public CrystalStructureDataset 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

importText

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

Import all structure files in a directory.

Overrides:

importText in class CompositionDataset

Parameters:

directory - Directory containing VASP5-formatted files

options - No options

Throws:

java.lang.Exception - If parsing fails

getEntry

public CrystalStructureEntry 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 CrystalStructureEntry 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

runAttributeGenerators

public void runAttributeGenerators()
                            throws java.lang.Exception

Description copied from class: Dataset

Expand the list of attributes using the currently-set list of attribute generators.

Overrides:

runAttributeGenerators in class Dataset

Throws:

java.lang.Exception

See Also:

Dataset.getAttributeGenerators()

saveCommand

public java.lang.String saveCommand(java.lang.String Basename,
                                    java.lang.String Format)
                             throws java.lang.Exception

Description copied from interface: Savable

Handles complicated saving commands.

Dev Note: Make sure to add save format to Javadoc. See Dataset as an example. Required format:

<save><p><b>format<b> - Description
<br>Optional room to talk more about format </save>

Specified by:

saveCommand in interface Savable

Overrides:

saveCommand in class CompositionDataset

Parameters:

Basename - Name of file without extension

Format - Command specifying format in which to print

Returns:

Filename Path to output file

Throws:

java.lang.Exception - If command not understood

writePOSCARs

public void writePOSCARs(java.lang.String directory)
                  throws java.lang.Exception

Save dataset as a directory full of POSCARs. Will delete directory at the specified path if it exists. File names: [Entry #]-[Composition].vasp Also writes out the measured and predicted class of these entries to a file named "properties.txt" in this directory

Parameters:

directory - Path to output directory

Throws:

java.lang.Exception - if writing fails