magpie.data.materials.util

Class PrototypeSiteInformation

java.lang.Object

magpie.data.materials.util.PrototypeSiteInformation

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class PrototypeSiteInformation
extends java.lang.Object
implements java.io.Serializable, java.lang.Cloneable

Stores information about all sites in a prototype crystal structure. Has the capacity to store the following information:

1. Number of atoms on each site
2. Which groups are used to calculate attributes
3. Which sites in the crystal are equivalent

Example for the double perovskite structure: This structure has 5 sites, and a stoichiometry of (AA')(BB')O₆. The A and A' sites, and the B and B' are each interchangable. So, the site information file for a double perovskite would be:

1 -equiv 1
1 -equiv 0
1 -equiv 3
1 -equiv 2
6

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PrototypeSiteInformation()

Method Summary

Modifier and Type	Method and Description
void	addSite(double NAtoms, boolean isIncluded, java.util.List<java.lang.Integer> equivalentSites) Add a new crystallographic site.
protected java.lang.Object	clone()
boolean	equals(java.lang.Object obj)
java.util.List<int[]>	getEquivalentArragements() Get all equivalent orders of sites.
java.lang.String	getGroupLabel(int index) Generate a label for a certain group of sites.
java.util.Set<java.lang.Integer>	getSiteGroup(int group) Get indices of sites in a particular group.
boolean	groupIsIncludedInAttributes(int index) Determine whether a group sites of should be included in attributes.
int	hashCode()
int	NGroups() Get the number of groups of equivalent sites.
double	NOnSite(int index) Get number of atoms on a certain site
int	NSites() Get the number of sites.
static PrototypeSiteInformation	readFromFile(java.lang.String filename) Read site information from a specially-formatted file.
void	setGroupIncludedInAttribute(int index, boolean isIncluded) Define whether a group of sites should be included when generating attributes.
boolean	siteIsIncludedInAttributes(int index)

Methods inherited from class java.lang.Object

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

Constructor Detail

PrototypeSiteInformation

public PrototypeSiteInformation()

Method Detail

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

readFromFile

public static PrototypeSiteInformation readFromFile(java.lang.String filename)
                                             throws java.lang.Exception

Read site information from a specially-formatted file. See PrototypeDataset for format.

Parameters:

filename - Path to site information file

Returns:

New site information object

Throws:

java.lang.Exception - If file fails to parse

clone

protected java.lang.Object clone()

Overrides:

clone in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

NSites

public int NSites()

Get the number of sites. Note: this is different than the number of groups of equivalent sites

Returns:

Number of sites

See Also:

NGroups()

NGroups

public int NGroups()

Get the number of groups of equivalent sites.

Returns:

Number of groups

See Also:

NSites()

getSiteGroup

public java.util.Set<java.lang.Integer> getSiteGroup(int group)

Get indices of sites in a particular group.

Parameters:

group - Index of group

Returns:

Set of indicies corresponding to sites that are equivalent

getEquivalentArragements

public java.util.List<int[]> getEquivalentArragements()

Get all equivalent orders of sites. For example, if sites B and C are equivalent in a prototype with three sites: ABC and ACB are equivalent.

Returns:

List of equivalent arragments

NOnSite

public double NOnSite(int index)

Get number of atoms on a certain site

Parameters:

index - Index of desired site

Returns:

Number of atoms on that site

siteIsIncludedInAttributes

public boolean siteIsIncludedInAttributes(int index)

Parameters:

index - Index of desired site

Returns:

Whether to include this site when generating attributes

groupIsIncludedInAttributes

public boolean groupIsIncludedInAttributes(int index)

Determine whether a group sites of should be included in attributes. This is only true if none of the individual sites are marked as omitted.

Parameters:

index - Index of desired group

Returns:

Whether to include this group when generating attributes

setGroupIncludedInAttribute

public void setGroupIncludedInAttribute(int index,
                                        boolean isIncluded)

Define whether a group of sites should be included when generating attributes.

Parameters:

index - Index of desired group

isIncluded - Whether to include it when generating statistics

getGroupLabel

public java.lang.String getGroupLabel(int index)

Generate a label for a certain group of sites.

Parameters:

index - Index of desired group

Returns:

Appropriate label (ex. AB for a group containing only sites 1 and 2)

addSite

public void addSite(double NAtoms,
                    boolean isIncluded,
                    java.util.List<java.lang.Integer> equivalentSites)

Add a new crystallographic site.

Parameters:

NAtoms - Number of atoms on this site

isIncluded - Whether this site should be included when generating attributes

equivalentSites - List of sites that are equivalent to this one (can be empty)