magpie.utility.tools

Class IonicCompoundFinder

java.lang.Object

magpie.utility.tools.IonicCompoundFinder

All Implemented Interfaces:

Commandable

public class IonicCompoundFinder
extends java.lang.Object
implements Commandable

Given a nominal composition, find nearby compositions that can be charge neutral.

Works by finding all combinations of elements in the supplied composition that are within a certain distance of the target composition with less than a certain number of atoms per unit cell.

Distance is computed as the L₁ distance of the composition vector. Example: Fe3Al and FeAl are 0.5 apart.

Implemented Command

run <composition> <distance> <size> - Find all neutral compounds within a certain distance of a target
composition: Target composition
distance: Maximum allowed distance
size: Maximum number of atoms in formula unit.

Constructor Summary

Constructors

Constructor and Description
IonicCompoundFinder()

Method Summary

Modifier and Type	Method and Description
java.util.List<CompositionEntry>	findAllCompounds() Locate all ionic compounds within a certain distance of the target composition.
java.lang.Object	runCommand(java.util.List<java.lang.Object> Command) Process some command described by a list of Objects.
void	setLookupPath(java.lang.String dir) Set where to look for oxidation state data
void	setMaxFormulaUnitSize(int size) Set maximum number of atoms in formula unit.
void	setMaximumDistance(double dist) Set the maximum allowed distance from the target value.
void	setNominalComposition(CompositionEntry comp) Set the target composition of the ionic compound.

Methods inherited from class java.lang.Object

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

Constructor Detail

IonicCompoundFinder

public IonicCompoundFinder()

Method Detail

setNominalComposition

public void setNominalComposition(CompositionEntry comp)
                           throws java.lang.Exception

Set the target composition of the ionic compound.

Parameters:

comp - Desired nominal composition

Throws:

java.lang.Exception

setMaximumDistance

public void setMaximumDistance(double dist)

Set the maximum allowed distance from the target value. Note, distance is computed as the L₁ norm of the composition vector assuming one of the elements is a balance (i.e., only sum the difference for N-1 elements).

Parameters:

dist - Maximum allowed distance

setMaxFormulaUnitSize

public void setMaxFormulaUnitSize(int size)

Set maximum number of atoms in formula unit. Example: NaCl has 2

Parameters:

size - Maximum allowed size

setLookupPath

public void setLookupPath(java.lang.String dir)

Set where to look for oxidation state data

Parameters:

dir - Path to lookup-data directory

findAllCompounds

public java.util.List<CompositionEntry> findAllCompounds()
                                                  throws java.lang.Exception

Locate all ionic compounds within a certain distance of the target composition. Subject to the constraints set by setMaximumDistance(double) and setMaxFormulaUnitSize(int).

Returns:

List of possible compositions, sorted by L_1 distance to the target composition

Throws:

java.lang.Exception

runCommand

public java.lang.Object runCommand(java.util.List<java.lang.Object> Command)
                            throws java.lang.Exception

Description copied from interface: Commandable

Process some command described by a list of Objects.

Specified by:

runCommand in interface Commandable

Parameters:

Command - Command as a list of objects

Returns:

Any output (null if no output generated by command)

Throws:

java.lang.Exception - If something goes wrong