magpie.data.materials

Class CompositionEntry

java.lang.Object

magpie.data.BaseEntry

magpie.data.MultiPropertyEntry

magpie.data.materials.CompositionEntry

All Implemented Interfaces:

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

Direct Known Subclasses:

CrystalStructureEntry, PrototypeEntry

public class CompositionEntry
extends MultiPropertyEntry

Stores several properties about a compound and its composition. Can store information regarding multiple properties of the material represented by the composition.

Equality is computed based on the composition, and the attributes. In most cases, entries with the same composition will have the same attributes. However, one may introduce properties as attributes PropertyAsAttributeGenerator, which can cause entries witht the same composition to have different attributes.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected int[]	Element Elements present in composition
protected java.lang.String[]	ElementNames Names of each element
protected double[]	Fraction Fraction of each element
boolean	HTMLFormat Whether to print composition in HTML Format
protected double	NumberInCell Number of atoms in cell (used to convert when printing)
protected int[]	SortingOrder Rank of each element (used in display order)

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	CompositionEntry() Allows the creation of arbitrary constructors for superclasses.
	CompositionEntry(int[] Element, double[] Amount) Given the element numbers (probably Z-1) and fractions, create an entry
	CompositionEntry(java.lang.String Composition) Make a new instance by parsing the composition of an object, provided by a string.

Method Summary

Modifier and Type	Method and Description
CompositionEntry	clone() Generates a clone of an entry.
void	combineCompositions(java.util.Map<java.lang.Integer,java.lang.Double> totalComp, java.util.Map<java.lang.Integer,java.lang.Double> addComp, double multiplier) Add composition from one map to another
int	compare(java.lang.Object A_obj, java.lang.Object B_obj)
boolean	equals(java.lang.Object other)
double	getAverageDeviation(double[] Lookup) Calculate the mean deviation of a property from the average.
double	getAverageDeviation(double[] Lookup, double mean) Calculate the mean deviation of a property from the average.
double	getElementFraction(int element) Return the fraction of a certain element found in an entry
double	getElementFraction(java.lang.String elem) Return the fraction of a certain element found in an entry
int[]	getElements()
double[]	getFractions()
double	getMaxDifference(double[] Lookup) Calculate maximum difference between the properties of two elements that are present in this entry
double	getMaximum(double[] Lookup) Get the maximum of an elemental property
double	getMean(double[] Lookup) Calculate the alloy mean of a property
double	getMinimum(double[] Lookup) Get the minimum of an elemental property
double	getMost(double[] Lookup) Get the elemental property of the most-prevalent element.
int[]	getSortingOrder()
int	hashCode()
static java.lang.String[]	printNumber(double[] fraction, double NInFormulaUnit) Print out the number of atoms in a formula unit for each element given its fraction
void	rectifyEntry(boolean toSort) Makes sure this entry is in a proper format.
protected void	setComposition(int[] elements, double[] amount, boolean toSort) Set the composition of this entry.
java.lang.String	toHTMLString() Print entry in a HTML-friendly format.
org.json.JSONObject	toJSON() Print entry as a JSON object
java.lang.String	toString()

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, reduceMemoryFootprint, 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

Field Detail

HTMLFormat

public boolean HTMLFormat

Whether to print composition in HTML Format

ElementNames

protected java.lang.String[] ElementNames

Names of each element

SortingOrder

protected int[] SortingOrder

Rank of each element (used in display order)

Element

protected int[] Element

Elements present in composition

Fraction

protected double[] Fraction

Fraction of each element

NumberInCell

protected double NumberInCell

Number of atoms in cell (used to convert when printing)

Constructor Detail

CompositionEntry

protected CompositionEntry()

Allows the creation of arbitrary constructors for superclasses.

CompositionEntry

public CompositionEntry(java.lang.String Composition)
                 throws java.lang.Exception

Make a new instance by parsing the composition of an object, provided by a string.

First splits using the regex [A-Z][^A-Z] to separate each component of the alloy. This assumes that capitalization is used property. Then, splits each component into the Alphabetical part (assumed to be the element name) and the numeric part (amount of element). If no numeric part is present, 1 is assumed. An element can be appear more than once.

Parameters:

Composition - Composition of entry

Throws:

java.lang.Exception - If parse fails

CompositionEntry

public CompositionEntry(int[] Element,
                        double[] Amount)

Given the element numbers (probably Z-1) and fractions, create an entry

Parameters:

Element - Numbers of element in ElementList

Amount - Amount of each element present

Method Detail

printNumber

public static java.lang.String[] printNumber(double[] fraction,
                                             double NInFormulaUnit)

Print out the number of atoms in a formula unit for each element given its fraction

Parameters:

fraction - Fractions to be printed

NInFormulaUnit - Number of atoms in a formula unit

Returns:

Result formatted as a string

combineCompositions

public void combineCompositions(java.util.Map<java.lang.Integer,java.lang.Double> totalComp,
                                java.util.Map<java.lang.Integer,java.lang.Double> addComp,
                                double multiplier)

Add composition from one map to another

Parameters:

totalComp - Composition to be added to

addComp - Composition to add

multiplier - Multiplier for added part

setComposition

protected final void setComposition(int[] elements,
                                    double[] amount,
                                    boolean toSort)

Set the composition of this entry.

Checks to make sure all elements have positive amounts.

Parameters:

elements - Elements in sample (listed by index in LookupData.ElementNames)

amount - Amount of each element

toSort - Whether to store elements in sorted order

clone

public CompositionEntry 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 MultiPropertyEntry

Returns:

Clone

getSortingOrder

public int[] getSortingOrder()

Returns:

Order in which elements listed during printing

getElements

public int[] getElements()

Returns:

List of elements contained in an entry

getFractions

public double[] getFractions()

Returns:

Fractions of each element in array in same order as getElements()

getElementFraction

public double getElementFraction(java.lang.String elem)

Return the fraction of a certain element found in an entry

Parameters:

elem - Abbreviation of element

Returns:

Fraction of that element present in this entry

getElementFraction

public double getElementFraction(int element)

Return the fraction of a certain element found in an entry

Parameters:

element - Index of element (usually: AtomicNumber - 1)

Returns:

Fraction of that element present in this entry

compare

public int compare(java.lang.Object A_obj,
                   java.lang.Object B_obj)

Specified by:

compare in interface java.util.Comparator

Overrides:

compare in class BaseEntry

hashCode

public int hashCode()

Overrides:

hashCode in class BaseEntry

equals

public boolean equals(java.lang.Object other)

Specified by:

equals in interface java.util.Comparator

Overrides:

equals in class BaseEntry

rectifyEntry

public final void rectifyEntry(boolean toSort)

Makes sure this entry is in a proper format. Must be run from constructor

Performs the following operations:

• Optional: Ensure Element and Fraction are sorted according to the order listed in SortingOrder.
• Ensure that the sum of Fraction is equal to 1.
• Set NumberInCell is equal to the original sum of Fraction.

Parameters:

toSort - Whether to sort elements in "Sorting order"

getMean

public double getMean(double[] Lookup)

Calculate the alloy mean of a property

Parameters:

Lookup - Lookup table of elemental properties

Returns:

Alloy mean of that property

getMaxDifference

public double getMaxDifference(double[] Lookup)

Calculate maximum difference between the properties of two elements that are present in this entry

Parameters:

Lookup - Lookup table of elemental properties

Returns:

Maximum difference between

getAverageDeviation

public double getAverageDeviation(double[] Lookup)

Calculate the mean deviation of a property from the average. This is computed as: df = sum[ xi * (fi - fmean) ]

Parameters:

Lookup - Lookup table of elemental properties

Returns:

Average deviation of property from mean

getAverageDeviation

public double getAverageDeviation(double[] Lookup,
                                  double mean)

Calculate the mean deviation of a property from the average. This is computed as: df = sum[ xi * (fi - fmean) ]

Parameters:

Lookup - Lookup table of elemental properties

mean - Mean as computed using "getMean"

Returns:

Average deviation of property from mean

getMaximum

public double getMaximum(double[] Lookup)

Get the maximum of an elemental property

Parameters:

Lookup - Lookup table of elemental properties

Returns:

Maximum of the property amongst all elements in the composition

getMinimum

public double getMinimum(double[] Lookup)

Get the minimum of an elemental property

Parameters:

Lookup - Lookup table of elemental properties

Returns:

Minimum of the property amongst all elements in the compound

getMost

public double getMost(double[] Lookup)

Get the elemental property of the most-prevalent element. If multiple elements are equally prevalent, returns the average of their properties.

Parameters:

Lookup - Lookup table of elemental properties

Returns:

Property of the most-prevalent element

toString

public java.lang.String toString()

Overrides:

toString in class BaseEntry

toHTMLString

public java.lang.String toHTMLString()

Description copied from class: BaseEntry

Print entry in a HTML-friendly format.

Overrides:

toHTMLString in class BaseEntry

Returns:

Entry as a string

toJSON

public org.json.JSONObject toJSON()

Description copied from class: BaseEntry

Print entry as a JSON object

Overrides:

toJSON in class MultiPropertyEntry

Returns:

JSON object