magpie.data.materials

Class CrystalStructureEntry

java.lang.Object

magpie.data.BaseEntry

magpie.data.MultiPropertyEntry

magpie.data.materials.CompositionEntry

magpie.data.materials.CrystalStructureEntry

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable, java.util.Comparator

public class CrystalStructureEntry
extends CompositionEntry

Represents a crystal structure.

See Also:

Serialized Form

Field Summary

Fields inherited from class magpie.data.materials.CompositionEntry

Element, ElementNames, Fraction, HTMLFormat, NumberInCell, SortingOrder

Constructor Summary

Constructors

Constructor and Description
CrystalStructureEntry(vassal.data.Cell structure, java.lang.String name, double[] radii) Create an entry given its crystal structure

Method Summary

Modifier and Type	Method and Description
java.util.List<CrystalStructureEntry>	changeComposition(CompositionEntry composition) Redecorate a structure with a new composition.
void	clearRepresentations() Clear out the representations used when computing attributes.
CrystalStructureEntry	clone() Generates a clone of an entry.
int	compare(java.lang.Object A, java.lang.Object B)
vassal.analysis.VoronoiCellBasedAnalysis	computeVoronoiTessellation() Compute the Voronoi tessellation of this structure.
boolean	equals(java.lang.Object other)
CompositionEntry	getComposition() Get the composition of this entry.
java.lang.String	getName() Get name of this entry
vassal.data.Cell	getStructure() Get link to structure
int	hashCode()
void	reduceMemoryFootprint() Delete any cached information stored within this entry.
CrystalStructureEntry	replaceElements(java.util.Map<java.lang.String,java.lang.String> replacements) Create a new entry by replacing elements on this entry
org.json.JSONObject	toJSON() Print entry as a JSON object
java.lang.String	toString()

Methods inherited from class magpie.data.materials.CompositionEntry

combineCompositions, getAverageDeviation, getAverageDeviation, getElementFraction, getElementFraction, getElements, getFractions, getMaxDifference, getMaximum, getMean, getMinimum, getMost, getSortingOrder, printNumber, rectifyEntry, setComposition, toHTMLString

Methods inherited from class magpie.data.MultiPropertyEntry

addProperty, addProperty, addProperty, clearPropertyData, deleteMeasuredClass, deletePredictedClass, getClassProbilities, getMeasuredClass, getMeasuredProperties, getMeasuredProperty, getPredictedClass, getPredictedProperty, getPropertyClassProbabilties, getTargetProperty, hasClassProbabilities, hasMeasuredProperty, hasMeasurement, hasPredictedProperty, hasPrediction, hasPropertyClassProbabilities, NProperties, setClassProbabilities, setMeasuredClass, setMeasuredProperties, setMeasuredProperty, setNProperties, setPredictedClass, setPredictedProperty, setPredictedProperty, setTargetProperty, usingPropertyAsClass

Methods inherited from class magpie.data.BaseEntry

addAttribute, addAttributes, clearAttributes, compareTo, getAttribute, getAttributes, NAttributes, setAttribute, setAttributes

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Comparator

comparing, comparing, comparingDouble, comparingInt, comparingLong, naturalOrder, nullsFirst, nullsLast, reversed, reverseOrder, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Constructor Detail

CrystalStructureEntry

public CrystalStructureEntry(vassal.data.Cell structure,
                             java.lang.String name,
                             double[] radii)

Create an entry given its crystal structure

Parameters:

structure - Structure of this entry

radii - Radii to use for each element (null to leave radii unchanged)

name - Name of structure (used for debugging purposes)

Method Detail

replaceElements

public CrystalStructureEntry replaceElements(java.util.Map<java.lang.String,java.lang.String> replacements)

Create a new entry by replacing elements on this entry

Parameters:

replacements - Map of elements to replace. Key: Old element, Value: New element

Returns:

New entry

changeComposition

public java.util.List<CrystalStructureEntry> changeComposition(CompositionEntry composition)

Redecorate a structure with a new composition. Creates a list of possible structures given a new composition.

Note that this operation may create structures which have different atomic positions, but are symmetrically equivalent.

Parameters:

composition - Desired composition

Returns:

List of possible structures. Empty list if stoichiometry of input composition does not match up with structure

clone

public CrystalStructureEntry clone()

Description copied from class: BaseEntry

Generates a clone of an entry. It creates a new list to store the attributes. So, the attribute data is preserved, but you can change the list as desired.

Overrides:

clone in class CompositionEntry

Returns:

Clone

equals

public boolean equals(java.lang.Object other)

Specified by:

equals in interface java.util.Comparator

Overrides:

equals in class CompositionEntry

compare

public int compare(java.lang.Object A,
                   java.lang.Object B)

Specified by:

compare in interface java.util.Comparator

Overrides:

compare in class CompositionEntry

hashCode

public int hashCode()

Overrides:

hashCode in class CompositionEntry

getStructure

public vassal.data.Cell getStructure()

Get link to structure

Returns:

Structure this entry represents

getComposition

public CompositionEntry getComposition()

Get the composition of this entry.

Returns:

The composition as a CompositionEntry object

getName

public java.lang.String getName()

Get name of this entry

Returns:

Name

computeVoronoiTessellation

public vassal.analysis.VoronoiCellBasedAnalysis computeVoronoiTessellation()
                                                                    throws java.lang.Exception

Compute the Voronoi tessellation of this structure.

Returns:

Tool used to query properties of the tessellation

Throws:

java.lang.Exception

clearRepresentations

public void clearRepresentations()

Clear out the representations used when computing attributes.

reduceMemoryFootprint

public void reduceMemoryFootprint()

Description copied from class: BaseEntry

Delete any cached information stored within this entry.

Overrides:

reduceMemoryFootprint in class BaseEntry

toString

public java.lang.String toString()

Overrides:

toString in class CompositionEntry

toJSON

public org.json.JSONObject toJSON()

Description copied from class: BaseEntry

Print entry as a JSON object

Overrides:

toJSON in class CompositionEntry

Returns:

JSON object