magpie.utility.tools

Class OxidationStateGuesser

java.lang.Object

magpie.utility.tools.OxidationStateGuesser

All Implemented Interfaces:

java.io.Serializable, Commandable, Options

public class OxidationStateGuesser
extends java.lang.Object
implements Commandable, Options, java.io.Serializable

Given a composition, guess the most-likely oxidation states for each element.

Works by finding all combinations non-zero oxidation states for each element, computing which are the most reasonable, and finding which of those have the minimum value of

sum_i,j[ (Χ_i - Χ_j) (c_i - c_j) ] for i < j where Χ_i is the electronegativity and c_i is the oxidation. This biases the selection towards the more electronegative elements being more negatively charged.

Implemented Command

run <composition> - Find all ionic compounds possible at this composition
composition: Composition
Prints a list of charges to the screen where the first is the most favored based on the electronegative elements having the greatest charge.

Usage: [<oxidation states>] [<en>]
lookup table: Path oxidation states lookup table
en: Path to electronegativity lookup table
Lookup tables must files where each line is contains either the allowed oxidation states or electronegativity for each element. Lines must be ordered by atomic number (H, He, ...). By default, looks in "./lookup-data/".

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
OxidationStateGuesser()

Method Summary

Modifier and Type	Method and Description
java.util.List<int[]>	getPossibleStates(CompositionEntry comp) Get list of possible charge states.
protected java.lang.String	printStates(int[] elems, int[] charges) Print out the elements and charges in a nice way.
java.lang.String	printUsage() Print out required format for options.
java.lang.Object	runCommand(java.util.List<java.lang.Object> Command) Process some command described by a list of Objects.
void	setElectronegativity(double[] values) Set the lookup table for electronegativity values.
void	setElectronegativity(java.lang.String path) Set the lookup table for electronegativity values.
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.
void	setOxidationStates(double[][] states) Set the oxidation states
void	setOxidationStates(int[][] states) Set the oxidation states
void	setOxidationStates(java.lang.String path) Set the oxidation states

Methods inherited from class java.lang.Object

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

Constructor Detail

OxidationStateGuesser

public OxidationStateGuesser()

Method Detail

setOptions

public void setOptions(java.util.List<java.lang.Object> Options)
                throws java.lang.Exception

Description copied from interface: Options

Set any options for this object. If parsing the options fails, return an Exception with the usage as its message.

Specified by:

setOptions in interface Options

Parameters:

Options - Array of options as Objects - can be null

Throws:

java.lang.Exception - if problem with inputs

printUsage

public java.lang.String printUsage()

Description copied from interface: Options

Print out required format for options. For consistency, should start with "Usage: ".

Specified by:

printUsage in interface Options

Returns:

Usage for this function

setElectronegativity

public void setElectronegativity(double[] values)

Set the lookup table for electronegativity values.

Parameters:

values - Electronegativity for each element (ordered by Z)

setElectronegativity

public void setElectronegativity(java.lang.String path)
                          throws java.io.IOException

Set the lookup table for electronegativity values.

Parameters:

path - Path to file containing electronegativity for each element, on lines ordered by Z.

Throws:

java.io.IOException

setOxidationStates

public void setOxidationStates(int[][] states)

Set the oxidation states

Parameters:

states - Allowed oxidation states. Each row contains the allowed oxidation states for each element (ordered by Z).

setOxidationStates

public void setOxidationStates(double[][] states)

Set the oxidation states

Parameters:

states - Allowed oxidation states. Each row contains the allowed oxidation states for each element (ordered by Z).

setOxidationStates

public void setOxidationStates(java.lang.String path)
                        throws java.lang.Exception

Set the oxidation states

Parameters:

path - Path to lookup file. Each line must contain the allowed oxidation states for each element (ordered by Z).

Throws:

java.lang.Exception

getPossibleStates

public java.util.List<int[]> getPossibleStates(CompositionEntry comp)

Get list of possible charge states.

Parameters:

comp - Composition of allegedly ionic compound

Returns:

List of possible oxidation states, same order as CompositionEntry.getElements(). Listed such that most likely is first.

See Also:

OxidationStateGuesser

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

printStates

protected java.lang.String printStates(int[] elems,
                                       int[] charges)

Print out the elements and charges in a nice way.

Parameters:

elems - Element indices (Z-1)

charges - Oxidation state of each element

Returns:

Human-readable string of oxidation state guesses