magpie.data.utilities.generators

Class CombinatorialSubstitutionGenerator

java.lang.Object

magpie.data.utilities.generators.BaseEntryGenerator

magpie.data.utilities.generators.CombinatorialSubstitutionGenerator

All Implemented Interfaces:

java.lang.Iterable<BaseEntry>, Options

public class CombinatorialSubstitutionGenerator
extends BaseEntryGenerator

Generate new crystalline compound by substituting elements onto all sites of a known prototype.

Usage: [-voro] -style [all|permutations|combinations] [-ignore <elems to ignore>] $<prototypes> <elements...>
-voro: Compute Voronoi tessellation of the prototype before creating derivatives.
-style: How to choose new combinations of elements. "all" all permutations with replacements, "permutations" all permutations without replacement, "combinations" all combinations without replacement
elems to ignore: List of elements that should not be replaced in the prototype (e.g., use this to generate all ABO₃ compounds)
prototypes: CrystalStructureDataset containing prototype structures (as entries).
elements: List of elements to substitute

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CombinatorialSubstitutionGenerator.EnumerationType Types of enumeration

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	ComputeVoronoi Whether to compute the Voronoi tessellation before generation
protected java.util.Set<java.lang.String>	Elements List of elements to substitute
protected java.util.Set<java.lang.String>	ElementsToIgnore List of elements ignore during substitution
protected CombinatorialSubstitutionGenerator.EnumerationType	EnumerationStyle Enumeration type for generating new compounds
protected java.util.List<CrystalStructureEntry>	Prototypes List of prototype structures

Constructor Summary

Constructors

Constructor and Description
CombinatorialSubstitutionGenerator()

Method Summary

Modifier and Type	Method and Description
protected void	checkElements(java.util.Collection<java.lang.String> elements) Given list of element abbreviations, make sure all are known elements
protected java.util.Iterator<java.util.List<java.lang.String>>	getReplacementIterator(CrystalStructureEntry entry) Get an iterator over all possible combinations of elements on each site of this structure
java.util.Iterator<BaseEntry>	iterator()
java.lang.String	printUsage() Print out required format for options.
void	setComputeVoronoi(boolean input) Set whether to compute the Voronoi tessellation before generating entries.
void	setElementsToIgnore(java.util.Collection<java.lang.String> elements) Set list of elements that, if present, will not be replaced
void	setElementsToSubstitute(java.util.Collection<java.lang.String> elements) Set list of elements to use for substitutions.
void	setEnumerationStyle(CombinatorialSubstitutionGenerator.EnumerationType type) Set method used to enumerate different sets of elements
void	setOptions(java.util.List<java.lang.Object> Options) Set any options for this object.
void	setPrototypes(CrystalStructureDataset data) Define the list of prototype structures used to create entries.
void	setPrototypes(java.util.List<CrystalStructureEntry> prototypes) Define the list of prototype structures to use to create entries.

Methods inherited from class magpie.data.utilities.generators.BaseEntryGenerator

addEntriesToDataset, generateEntries, train

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

Elements

protected final java.util.Set<java.lang.String> Elements

List of elements to substitute

ElementsToIgnore

protected final java.util.Set<java.lang.String> ElementsToIgnore

List of elements ignore during substitution

Prototypes

protected final java.util.List<CrystalStructureEntry> Prototypes

List of prototype structures

EnumerationStyle

protected CombinatorialSubstitutionGenerator.EnumerationType EnumerationStyle

Enumeration type for generating new compounds

ComputeVoronoi

protected boolean ComputeVoronoi

Whether to compute the Voronoi tessellation before generation

Constructor Detail

CombinatorialSubstitutionGenerator

public CombinatorialSubstitutionGenerator()

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.

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: ".

Returns:

Usage for this function

setElementsToSubstitute

public void setElementsToSubstitute(java.util.Collection<java.lang.String> elements)

Set list of elements to use for substitutions.

Parameters:

elements - List of element abbreviations

checkElements

protected void checkElements(java.util.Collection<java.lang.String> elements)
                      throws java.lang.IllegalArgumentException

Given list of element abbreviations, make sure all are known elements

Parameters:

elements - List of element abbreviation

Throws:

java.lang.IllegalArgumentException - If an element is not of a known type

setElementsToIgnore

public void setElementsToIgnore(java.util.Collection<java.lang.String> elements)

Set list of elements that, if present, will not be replaced

Parameters:

elements - Collection of element abbreviations

setPrototypes

public void setPrototypes(java.util.List<CrystalStructureEntry> prototypes)

Define the list of prototype structures to use to create entries.

Parameters:

prototypes - List containing prototype structures

setPrototypes

public void setPrototypes(CrystalStructureDataset data)

Define the list of prototype structures used to create entries.

Parameters:

data - Dataset containing list of prototype structures

setEnumerationStyle

public void setEnumerationStyle(CombinatorialSubstitutionGenerator.EnumerationType type)

Set method used to enumerate different sets of elements

Parameters:

type - Enumeration style

setComputeVoronoi

public void setComputeVoronoi(boolean input)

Set whether to compute the Voronoi tessellation before generating entries. Allows for faster attribute generation with CrystalStructureDataset.

Parameters:

input - Desired setting.

iterator

public java.util.Iterator<BaseEntry> iterator()

getReplacementIterator

protected java.util.Iterator<java.util.List<java.lang.String>> getReplacementIterator(CrystalStructureEntry entry)

Get an iterator over all possible combinations of elements on each site of this structure

Parameters:

entry - Entry to make the iterator for

Returns:

Iterator over all combinations