Index (project API)

A B C D F G H I K L M N O P R S T V W Z _
All Classes and Interfaces|All Packages|Serialized Form

A

accept(File, String) - Method in class _global.tri.oxidationstates.util.VaspFileFilter
addEntry(String, String, IonFactory.Ion[], String[], double, double) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Add an entry to this data set
addMessage(String, boolean) - Method in class _global.tri.oxidationstates.webapi.PageData: This method can be used to set a message to be returned to the user, such as an error or warning encountered when generating the table.
addRemainingElementsForLastSeenState(HashMap<String, Double>) - Method in class _global.tri.oxidationstates.ion.filters.PolyatomicSubstitutionFilter: Given a composition map representing the polyatomic ion composition, adds the composition of monatomic ions according to the last state seen by this filter.
addWebIonsToData(Main.DataType, Main.DataType) - Static method in class _global.tri.oxidationstates.Main: The "web ions" are the polyatomic ions used in the manuscript and web site.
appendFile(String) - Method in class _global.tri.oxidationstates.fitting.CallableCalculator: Useful for debugging, appends information about the current fit to a file with the given name
assignBertosStates() - Static method in class _global.tri.oxidationstates.Main: Reads the states calculated by BERTOS based on composition and assigns them to sites in a way that minimizes the GII.

B

batchEntries(int) - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer: Divide the entries evenly into batches, each to be handled on its own thread
BondValenceCalculator - Class in _global.tri.oxidationstates.calculator: This is a simplified bond valence calculator that should be easier to use for this app than the one in the matsci oxidation analyzer.
BondValenceCalculator(Structure) - Constructor for class _global.tri.oxidationstates.calculator.BondValenceCalculator: Create a bond valence calculator for the given structure
boundariesToParameters(double[]) - Static method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Converts a set of oxidation state boundaries for an ion type into parameters

C

calcGIIForPymatgenStructs() - Static method in class _global.tri.oxidationstates.Main: Reads the states calculated by PyMatGen and assigns them to sites in a way that minimizes the GII.
call() - Method in class _global.tri.oxidationstates.fitting.CallableCalculator
CallableCalculator - Class in _global.tri.oxidationstates.fitting: This class is used for multi-threaded model fitting
CallableCalculator(OxidationStateData.Entry[]) - Constructor for class _global.tri.oxidationstates.fitting.CallableCalculator: Create a CallableCalculator that will work on the given subset of entries.
CAMD_DIR - Static variable in class _global.tri.oxidationstates.Main: This directory contains the data set from "Novel inorganic crystal structures predicted using autonomous simulation agents" (https://doi.org/10.1038/s41597-022-01438-8)
cleanDataGII(Main.DataType, Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Looks through all entries of the data set given by inType and determines whether the GII is lower than the GII for the ICSD (calculated by assinging ICSD states to sites in a way that minimizes the GII).
compareAssignments(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: This method prints out summary statistics comparing sets of oxidation states assignments (e.g.
compareStructures(Structure, Structure, boolean) - Static method in class _global.tri.oxidationstates.util.IonTools: Returns true if two structures are equivalent based on the standard mapping parameters set in IonTools.setMappingParams(_global.tri.structure.mapper.GeneralStructureMapper), and false otherwise.
compareTo(LikelihoodStateSet) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodStateSet
compareTo(TableRow) - Method in class _global.tri.oxidationstates.webapi.TableRow
Composition - Class in _global.tri.oxidationstates.util: A utility class to represent a composition
Composition(String) - Constructor for class _global.tri.oxidationstates.util.Composition: Create a composition from the given composition string
Composition(String[], double[]) - Constructor for class _global.tri.oxidationstates.util.Composition: Create a composition from the given symbols and counts.
Composition(String[], int[]) - Constructor for class _global.tri.oxidationstates.util.Composition: Create a composition from the given symbols and counts.
Composition(Map) - Constructor for class _global.tri.oxidationstates.util.Composition: Create a composition from a map in which the keys are ion type symbols and the values are amounts.
CompositionIonFinder - Class in _global.tri.oxidationstates.ion: Find networks of atoms that are polyatomic ions, where the composition of the network(per unit cell) can be found in a list of compositions.
CompositionIonFinder(Structure) - Constructor for class _global.tri.oxidationstates.ion.CompositionIonFinder: Initialize the composition finder for the given structure and find the ions
CompositionParseException - Exception in _global.tri.oxidationstates.util: This exception is thrown if there is a problem parsing a composition
CompositionParseException(String) - Constructor for exception _global.tri.oxidationstates.util.CompositionParseException: Creates a composition parse exception with the given message.
copy() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Returns a copy of this data set

D

dataKeepOnlyIons(Set<IonFactory.Ion>) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Only keep entries for which all ions are in the given set

F

findIons(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Looks through the training set for the given data type to extract polyatomic ions, as determined by the OxideIonFinder, ZintlIonFinder, or CompositionIonFinder
findRepresentativeStructure(List<Structure>, int, boolean) - Static method in class _global.tri.oxidationstates.util.IonTools: From a list of given structures, finds the one that is closest to the mean of random subset of the others based on the sum of the scores of the maps between the structures.
fitParameters(OxidationStateData, int, double, String, int) - Static method in class _global.tri.oxidationstates.Main: Fits the model parameters for all ions contained in the training data, randomly initializing the parameters to values between zero and 1
fitParameters(OxidationStateData, LikelihoodCalculator, int, double, String, int) - Static method in class _global.tri.oxidationstates.Main: Fits the model parameters for all ions contained in the training data, randomly initializing the parameters to values between zero and 1
FrequencyCalculator - Class in _global.tri.oxidationstates.calculator.frequency: Calculates the frequency score for possible sets of oxidation states
FrequencyCalculator(OxidationStateData) - Constructor for class _global.tri.oxidationstates.calculator.frequency.FrequencyCalculator: Initialize the frequency score calculator, generating frequencies per ion from the user-provided data
fromMappedPotential(double) - Method in class _global.tri.oxidationstates.webapi.PotentialMapper: Converts the mapped potential to the electronic chemical potential used internally by the oxidation analyzer.
fromMappedPotential(double[]) - Method in class _global.tri.oxidationstates.webapi.PotentialMapper: Converts the mapped potential to the electronic chemical potential used internally by the oxidation analyzer.

G

get(String) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns the ion matching the given symbol, or creates a new ion if no such ion exists.
get(String, double) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns an ion corresponding to the given ion type and oxidation state.
get(Element, double) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns an ion corresponding to the given element and oxidation state.
get(Species) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns an ion corresponding to the given species.
getActiveAtomIndex(String) - Method in class _global.tri.oxidationstates.ion.IonAssigner: This method is used to simplify the process of assigning oxidation states in a way that minimizes the GII for polyatomic ions.
getAllIons() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: The set of distinct ions in this entry
getAllKnownRepresentativeStructures(boolean) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns a map in which the keys are known ion types and the values are the corresponding representative structures.
getAllOxidationStates(Composition, double, int) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns an array possible oxidation state assignments for the given composition, subject to the given constraints.
getAllOxidationStates(String, double, int) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Get all possible oxidation state assignments for the given composition, subject to the given constraints.
getAllSources() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: The sources of data for this entry
getAtomicWeight() - Method in class _global.tri.oxidationstates.ion.IonFactory.IonType: Returns the atomic weight for this ion type.
getBondValenceCalculator() - Method in class _global.tri.oxidationstates.ion.IonAssigner: Returns the bond valence calculator used to calculate bond valence sums.
getBondValenceSums() - Method in class _global.tri.oxidationstates.calculator.BondValenceCalculator: Returns the calculated bond valence sums, with the array indices corresponding to the site indices in the provided structure.
getBoundaries(int) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Return all of the midpoint boundary values for the given ion type
getBoundaries(IonFactory.Ion) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Get the midpoint boundaries (lower and upper) for the given ion
getBoundaryPairs() - Method in class _global.tri.oxidationstates.webapi.TableRow: Returns the minimum and maximum boundaries for each ion in this row.
getBranchIndex(int[]) - Method in class _global.tri.oxidationstates.calculator.frequency.MaxFrequencyFilter
getBranchIndex(int[]) - Method in class _global.tri.oxidationstates.calculator.likelihood.MinAllowedLikelihoodFilter
getBranchIndex(int[]) - Method in class _global.tri.oxidationstates.calculator.MixedValenceChargeBalanceFilter
getBranchIndex(int[]) - Method in class _global.tri.oxidationstates.ion.filters.PolyatomicSubstitutionFilter
getCalculator() - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer.ParameterState: Returns the likelihood calculator containing the current parameters
getCAMDAssignments(Main.DataType, boolean) - Static method in class _global.tri.oxidationstates.Main: Assign oxidation states to the data set used in the CAMD search for new materials.
getCAMDDiscoveryCurve(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: This prints the data showing the percent of compositions with stable structures found vs the percent of total compositions evaluated using the CAMD data sorted by Likelihood score.
getCAMDHullHistogram(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Get the histogram of what percentage of structures are on the hull as a function of likelihood score for the CAMD data.
getCIFString() - Method in class _global.tri.oxidationstates.webapi.TableRow: Returns a string representation of a CIF file with all oxidation states assigned, or null if no such file could be generated.
getComposition() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: The composition of this entry
getComposition() - Method in class _global.tri.oxidationstates.webapi.PageData: Returns the composition of the material for which the oxidation states were generated.
getCompositionMap() - Method in class _global.tri.oxidationstates.util.Composition: Returns a map representation of this composition in which the keys are symbols and the values are amounts.
getCount(String) - Method in class _global.tri.oxidationstates.util.Composition: Returns the amount of the given symbol in this composition.
getCounts() - Method in class _global.tri.oxidationstates.ion.IonFactory.IonType: Returns the counts of each element in this ion type, in the same order as the array returned by IonFactory.IonType.getElements().
getCounts() - Method in class _global.tri.oxidationstates.webapi.TableRow: Returns an array of values indicating the count of each ion in a formula unit for the given material.
getCountsByIon() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Returns a map in which the keys are the ions contained in this data set and the values are the number of entries that contain the corresponding ion.
getData() - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer: Returns the training data
getData(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Return the data set for the given data type.
getDataFileName(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Return the file name for the given data set
getDistanceError(Structure, Structure) - Method in class _global.tri.oxidationstates.structure.StructureOptimizer: Calculates the mean squared ratios of the entries in the distance matrices for two structures, assuming the sites in the two structures are in the same order (e.g.
getDistinctElements() - Method in class _global.tri.oxidationstates.util.Composition: Returns the distinct elements in the compound represented by this composition.
getElementalComposition() - Method in class _global.tri.oxidationstates.util.Composition: Return the composition in terms of elements.
getElementalCompositionMap() - Method in class _global.tri.oxidationstates.util.Composition: Returns a map in which the keys are the distinct elements in the compound represented by this composition, and the values are the corresponding amounts.
getElements() - Method in class _global.tri.oxidationstates.ion.IonFactory.IonType: Returns the distinct elements in this ion type
getEnergiesAboveHull() - Static method in class _global.tri.oxidationstates.Main: Reads energies above the convex hull from a file extracted from the Materials Project and creates a Map (dictionary, for you Python folks) keyed by the icsd_id and with the energy above the hull as the value
getEnergyAboveHull() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: Returns the energy above the thermodynamic hull, in eV / atom, or Double.NaN if it is not available
getEntry(int) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Returns the "entryNum"'th entry in this data set.
getFailureReason() - Method in class _global.tri.oxidationstates.calculator.BondValenceCalculator: Returns the reason sums couldn't be calculated, if calculating sums failed.
getFoundIonMap(int) - Method in class _global.tri.oxidationstates.ion.KnownIonFinder: Returns a map that connecting the sites in the representative structure for the ion to sites in the given structure for the index'th found polyatomic ion.
getFoundIonType(int) - Method in class _global.tri.oxidationstates.ion.KnownIonFinder: Returns the ion type of the index'th found polyatomic ion.
getFoundPolyatomicIon(int) - Method in class _global.tri.oxidationstates.ion.CompositionIonFinder
getFoundPolyatomicIon(int) - Method in interface _global.tri.oxidationstates.ion.IIonFinder: Return the ionNum'th discovered polyatomic ion
getFoundPolyatomicIon(int) - Method in class _global.tri.oxidationstates.ion.KnownIonFinder
getFoundPolyatomicIon(int) - Method in class _global.tri.oxidationstates.ion.OxideIonFinder
getFoundPolyatomicIon(int) - Method in class _global.tri.oxidationstates.ion.ZintlIonFinder
getFrequency(IonFactory.Ion) - Method in class _global.tri.oxidationstates.calculator.frequency.FrequencyCalculator: Returns the frequency for a particular ion, where all frequencies for an ion type sum to 1.
getFrequencyScore(IonFactory.Ion[]) - Method in class _global.tri.oxidationstates.calculator.frequency.FrequencyCalculator: Calculates the frequency for a set of ions by multiplying the frequencies for all ionsin the set
getGivenCompositionString() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: The composition of this entry
getGivenStructure() - Method in class _global.tri.oxidationstates.ion.IonAssigner: Returns the structure provided in the constructor.
getGlobalInstabilityIndex() - Method in class _global.tri.oxidationstates.calculator.BondValenceCalculator: Returns the global instability index, based on the oxidations states of the provided structure and the calculated bond valence sums.
getGlobalInstabilityIndex() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: Returns the global instability index, or Double.NaN if it is not available
getGlobalInstabilityIndex() - Method in class _global.tri.oxidationstates.ion.IonAssigner: Returns the calculated global instability index for the assigned oxidation states.
getGlobalInstabilityIndex() - Method in class _global.tri.oxidationstates.webapi.TableRow: Returns the global instability index (gii) for the given set of oxidation states applied to a particular structure.
getGradient(double[]) - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer.ParameterState
getGradient(double[]) - Method in class _global.tri.oxidationstates.structure.LatticeOptimizer
getGradient(double[]) - Method in class _global.tri.oxidationstates.structure.StructureOptimizer
getICSDAssignments(Main.DataType, boolean) - Static method in class _global.tri.oxidationstates.Main: Assigns oxidation states to all of the structures in the given dataset using oxidation states provided in the ICSD.
getID() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: The structure ID for this entry.
getInitialTrainingData() - Static method in class _global.tri.oxidationstates.Main: Starting with a directory of CIF files extracted from the ICSD, select all charge calanced structures and use them to construct the initial training data file
getIntercept() - Method in class _global.tri.oxidationstates.webapi.PotentialMapper: Returns the "intercept" value in the equation mapped_potential = electronic_chemical_potential * slope + intercept, where the electronic chemical potential is the potential used internally by the oxidation analyzer.
getIon(double) - Method in class _global.tri.oxidationstates.ion.IonFactory.IonType: Returns the ion of this type with the given oxidation state.
getIon(int) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: Return the specNum'th ion in this entry
getIonComposition() - Method in class _global.tri.oxidationstates.ion.KnownIonFinder: Returns the composition in terms of found ions.
getIons() - Method in class _global.tri.oxidationstates.calculator.OxidationStateSet: Returns the set of ions
getIonStructureDirName(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Return the polyatomic ion structure directory name for the given data set
getIonSymbol(String, double) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Creates a standardized symbol for an ion from an ion type symbol and and oxidation state.
getIonType() - Method in class _global.tri.oxidationstates.ion.IonFactory.Ion: Returns the ion type for this ion.
getIonTypeComposition() - Method in class _global.tri.oxidationstates.ion.KnownIonFinder: Returns the composition in terms of found ion types (i.e.
getIonTypeIndex(String) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns the ion type index (used by this class) for ion types with the given symbol.
getIonTypeSymbol() - Method in class _global.tri.oxidationstates.webapi.RangeData: Returns the given symbol for the ion type (e.g.
getIonTypeSymbol(int) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Get the ion type symbol corresponding to the given index
getIonTypeSymbol(String) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns the ion type symbol corresponding to the given ion symbol.
getIsErrorMessage() - Method in class _global.tri.oxidationstates.webapi.Message: Returns true if this is an error message, false otherwise
getJSONFromComposition(String) - Method in class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Returns all combinations of oxidation states with optimal likelihood above the specified lower bound.
getJSONFromStructure(String) - Method in class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Returns a JSON-formatted string containing the data needed to generate the oxidation state table for the given structure.
getKnownIonComposition() - Method in class _global.tri.oxidationstates.util.Composition: Returns this composition in terms of known ion types, including polyatomic ions.
getKnownIonCompositionMap() - Method in class _global.tri.oxidationstates.util.Composition: Returns a composition in terms of known ion types, including polyatomic ions.
getKnownIons() - Method in class _global.tri.oxidationstates.ion.IonFactory.IonType: Return a map in which the keys are ion symbols and the values are the known ions of this type.
getKnownIonType(String) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns the ion type for the given symbol, or null if no such ion type exists.
getKnownIonTypes() - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns a map in which the keys are the ion type symbols and the values are the corresponding ion types for all known ion types, monatomic and polyatomic.
getKnownOxidationStates() - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Get a an array of all ions known to this calculator
getKnownOxidationStates() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Returns a map of oxidation states for each ion type in this data set.
getKnownRepresentativeStructures(String) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns a map in which the keys are integer oxidation states and the values are the representative structures for ions of the given ion type with the corresponding oxidation state.
getLastValidFermiLevel() - Method in class _global.tri.oxidationstates.calculator.likelihood.MinAllowedLikelihoodFilter: Returns the optimal electronic chemical potential for the last state to pass this filter.
getLastValidFrequencyScore() - Method in class _global.tri.oxidationstates.calculator.frequency.MaxFrequencyFilter: Get the last frequency score that passed this filter.
getLastValidLikelihood() - Method in class _global.tri.oxidationstates.calculator.likelihood.MinAllowedLikelihoodFilter: Returns the likelihood score of the last state to pass this filter.
getLattice() - Method in class _global.tri.oxidationstates.structure.LatticeOptimizer: Returns the optimized lattice
getLikelihood(double, IonFactory.Ion) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Return the likelihood score for a given ion at a give electronic chemical potential (fermiLevel)
getLikelihood(double, IonFactory.Ion[]) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Calculates the likelihood score for a given set of ions at a given electronic chemical potential
getLikelihoodCalculator(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Return a likelihood calculator for the given data type.
getLikelyOxidationStates(Composition) - Method in class _global.tri.oxidationstates.calculator.OxidationStateCalculator: Calculate the most likely oxidation states for the given composition
getLikelyOxidationStates(String) - Method in class _global.tri.oxidationstates.calculator.OxidationStateCalculator: Calculate the most likely oxidation states for the given composition
getLikelyOxidationStates(String[], double[]) - Method in class _global.tri.oxidationstates.calculator.frequency.FrequencyCalculator
getLikelyOxidationStates(String[], double[]) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator
getLikelyOxidationStates(String[], double[]) - Method in class _global.tri.oxidationstates.calculator.OxidationStateCalculator: Calculate the most likely oxidation states for the given ion types with the given composition.
getLikelyOxidationStates(Structure) - Method in class _global.tri.oxidationstates.calculator.OxidationStateCalculator: Calculate the most likely oxidation states for the elements in a given structure.
getMappedIndices(GeneralStructureMapper.Map) - Method in class _global.tri.oxidationstates.ion.IonAssigner: Returns an array of site indices correponding to the sites to which a polyatomic ion has been mapped in the given map.
getMaxBoundaryValue() - Method in class _global.tri.oxidationstates.webapi.PageData: Returns the maximum of boundary values for all possible ion types in terms of the mapped potential
getMaxIntegerOxidationState() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Gets the highest integer oxidation state in this data set, where any oxidation state within 0.01 of an integer is rounded to that integer.
getMaxKnownFrequencyScore() - Method in class _global.tri.oxidationstates.calculator.frequency.MaxFrequencyFilter: Returns the maximum frequency score for a valid state encountered so far, as set by the user.
getMaxLikelihood() - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator.PotentialOptimizer: Returns the likelihood score at the optimal electronic chemical potential (i.e.
getMaxLikelihood() - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodStateSet: Returns the likelihood score at the optimal electronic chemical potential
getMessages() - Method in class _global.tri.oxidationstates.webapi.PageData: Returns a list of messages (e.g.
getMessageString() - Method in class _global.tri.oxidationstates.webapi.Message: Returns the message content.
getMinAllowedLikelihood() - Method in class _global.tri.oxidationstates.calculator.likelihood.MinAllowedLikelihoodFilter: Returns the minimum allowed likelihood score.
getMinAllowedLikelihood() - Method in class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Returns the minimum allowed likelihood.
getMinAndMaxBoundary() - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns the minimum and maximum boundary values across all ion types
getMinBoundaryValue() - Method in class _global.tri.oxidationstates.webapi.PageData: Returns the minimum of boundary values for all possible ion types in terms of the mapped potential
getMinIntegerOxidationState() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Gets the lowest integer oxidation state in this data set, where any oxidation state within 0.01 of an integer is rounded to that integer.
getMinLikelihoodIndex(List<LikelihoodStateSet>) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Return the index of the state set with the minimum likelihood score from the given list
getOptimalFermiLevel() - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator.PotentialOptimizer: Returns the electronic chemical potential that maximizes the likelihood score
getOptimalFermiLevel() - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodStateSet: Returns the optimal electronic chemical potential (i.e.
getOptimalLikelihood() - Method in class _global.tri.oxidationstates.webapi.TableRow: Returns the likelihood at the optimal electronic chemical potential for the given set of oxidation states.
getOptimalMappedPotential() - Method in class _global.tri.oxidationstates.webapi.TableRow: Returns the value of the mapped potential that maximizes the likelihood of the set of oxidation states coexisting.
getOxidationState() - Method in class _global.tri.oxidationstates.ion.IonFactory.Ion: Returns the oxidation state for this ion.
getOxidationState(int, int) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns the stateNum'th oxidation state for the ion type with the given index
getOxidationState(String) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns the oxidation state of the ion with the given ion symbol.
getOxidationStateRangeData() - Method in class _global.tri.oxidationstates.webapi.PageData: Returns the information needed to generate the oxidation state ranges for the ions used in this table.
getOxidationStates() - Method in class _global.tri.oxidationstates.webapi.RangeData: Returns the oxidation states to be plotted.
getOxidationStates() - Method in class _global.tri.oxidationstates.webapi.TableRow: Returns the oxidation states for each ion in the material.
getOxidationStates(String) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns the oxidation states known to this calculator for the ion type with the given symbol
getOxidationString(double) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns a standardized string representation of the given oxidation state
getPageDataFromComposition(String) - Method in class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Returns all combinations of oxidation states with optimal likelihood above the specified lower bound.
getPageDataFromComposition(String, boolean) - Method in class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Returns all combinations of oxidation states with optimal likelihood above the provided lower bound.
getPageDataFromStructure(String) - Method in class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Returns an object containing the data needed to generate the web site pagefor the given structure.
getParameter(int, int) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Return the paramNumForMolecule'th parameter for the ion type with the given index
getParameters(double[]) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns the parameters for this calculator
getParameters(int) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns the parameters for the ion type with the given index
getParameterState(LikelihoodCalculator) - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer: Returns a state representing the parameters contained in the provided calculator.
getParameterState(String) - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer: Returns a state representing a set of parameters read from a file
getParamFileName(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Returns the name of the fitted parameter file for the given data type.
getPolyatomicIonDirName(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Return the name of directory of found polyatomic ions for the given data set
getPolyatomicTypes() - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns an array of known ion types for polyatomic ions.
getPotentialMapper() - Method in class _global.tri.oxidationstates.webapi.PageData: Returns a class that can transform the potentials used internally by the oxidation analyzer to and from mapped potentials
getRangeBoundaries() - Method in class _global.tri.oxidationstates.webapi.RangeData: Returns the boundaries of the oxidation states in terms of the mapped potential, starting from the left-most and ending with the right-most
getReducedComposition() - Method in class _global.tri.oxidationstates.util.Composition: For compositions with integer (or near-integer) counts for all symbols, returns the composition with all counts divided by their greater common factor.
getRegularizationParamaeter() - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer: Returns the regularization parameter
getRegularizer() - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer.ParameterState: Gets the regularization term, which is the regularization parameter times the sum of spreads
getRepresentativeStructure() - Method in class _global.tri.oxidationstates.ion.IonFactory.Ion: Returns the representative structure for this ion.
getSlope() - Method in class _global.tri.oxidationstates.webapi.PotentialMapper: Returns the "slope" value in the equation mapped_potential = electronic_chemical_potential * slope + intercept, where the electronic chemical potential is the potential used internally by the oxidation analyzer.
getStandardizedCompositionString() - Method in class _global.tri.oxidationstates.util.Composition: Returns a standardized string representation of this composition.
getStandardizedCompositionString(String) - Method in class _global.tri.oxidationstates.util.Composition: Returns a standardized string representation of this composition, using the given delimiter to separate terms.
getStructDir() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Returns the directory with atomic structure files for the entries
getStructure() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: The atomic structure of this entry.
getStructure() - Method in class _global.tri.oxidationstates.ion.IonAssigner: Return the structure with assigned oxidation states
getStructure() - Method in class _global.tri.oxidationstates.ion.KnownIonFinder: Return the structure in which we are searching for ions.
getStructure() - Method in class _global.tri.oxidationstates.structure.StructureOptimizer: Returns the optimized structure
getSumOfSpreads() - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Sum of the maximum boundaries for all ion types, subtract the sum of the minimum boundaries, and report the difference.
getSymbol() - Method in class _global.tri.oxidationstates.ion.IonFactory.Ion: Returns the symbol for this ion.
getSymbol() - Method in class _global.tri.oxidationstates.ion.IonFactory.IonType: Return the symbol for this ion type.
getSymbols() - Method in class _global.tri.oxidationstates.util.Composition: Returns the symbols for this composition
getSymbols() - Method in class _global.tri.oxidationstates.webapi.TableRow: Returns the symbols for each ion in the material.
getTableData() - Method in class _global.tri.oxidationstates.webapi.PageData: Returns the table data for this page.
getTableRows() - Method in class _global.tri.oxidationstates.webapi.TableData: Returns the array of rows in this table.
getTrainingAssigments(Main.DataType, boolean) - Static method in class _global.tri.oxidationstates.Main: Assigns oxidation states to all of the structures in the given dataset using the model trained on that dataset and writes out corresponding CIF files to a directory.
getUnboundedParameters(double[]) - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer.ParameterState
getUnboundedParameters(double[]) - Method in class _global.tri.oxidationstates.structure.LatticeOptimizer
getUnboundedParameters(double[]) - Method in class _global.tri.oxidationstates.structure.StructureOptimizer
getUniqueEntries(boolean) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: When entries with compositions written in terms of polyatomic ions are added to the data set, there will be two entries with the same ID: one with a composition written in terms of monatomic ions, and one with composition written in terms of polyatomic ions.
getValidationAssignments(Main.DataType, boolean) - Static method in class _global.tri.oxidationstates.Main: Assigns oxidation states calculated using 10-fold cross validation to all of the structures in the given dataset and writes out corresponding CIF files to a directory.
getValue() - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer.ParameterState
getValue() - Method in class _global.tri.oxidationstates.structure.LatticeOptimizer
getValue() - Method in class _global.tri.oxidationstates.structure.StructureOptimizer
getWebIonDirName() - Static method in class _global.tri.oxidationstates.Main: Returns the directory name for the polyatomic ions used for the paper and web site
getWeight(IonFactory.Ion) - Method in class _global.tri.oxidationstates.calculator.OxidationStateSet: Return the amount for the given ion
getWeights() - Method in class _global.tri.oxidationstates.calculator.OxidationStateSet: Returns the amounts of each of the ions, in the same order as the array returned by getIons()
GII_DIR - Static variable in class _global.tri.oxidationstates.Main: This subdirectory contains structures with assigned oxidation states, as assigned by different methods.
groupIons(Main.DataType, int, int) - Static method in class _global.tri.oxidationstates.Main: Places ions of the same composition into groups of structurally similar ions, where the atomic oxidation states of all ions in the set need to match.
groupIonsByOxidationState(double, boolean, int) - Static method in class _global.tri.oxidationstates.Main: Place the mean structures found by Main.groupIons(_global.tri.oxidationstates.Main.DataType,int,int) in groups by total oxidation state, calculated by adding the oxidation states of all atoms in the ion.

H

hasIntegerOxidationState() - Method in class _global.tri.oxidationstates.ion.IonFactory.Ion: Returns true if the oxidation state is within the oxidation tolerance (0.001 by default) of an integer, and false otherwise.
hasParametersForElement(Element) - Static method in class _global.tri.oxidationstates.calculator.BondValenceCalculator: Return true if this calculator has bond valence parameters or the given element, false otherwise.
hasParamsForElement(Element) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Whether this calculator has parameters for the given element
hasParamsForIon(IonFactory.Ion) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Whether this calculator has parameters for the given ion
hasParamsForIonType(String) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Whether this calculator has parameters for the given ion type
hasZeroSums() - Method in class _global.tri.oxidationstates.calculator.BondValenceCalculator: Returns true if some the bond valence sum for at least one site is zero, false otherwise

I

IIonFinder - Interface in _global.tri.oxidationstates.ion: This is a general interface for all ion finders
IonAssigner - Class in _global.tri.oxidationstates.ion: This class assigns ions to sites in a way that minimizes the global instability index
IonAssigner(KnownIonFinder, OxidationStateSet) - Constructor for class _global.tri.oxidationstates.ion.IonAssigner: Given an ionFinder (which identifies polyatomic ions) and a set of oxidation states, assign the oxidation states to atoms in a way that minimizes the GII.
IonAssigner(Structure, OxidationStateSet) - Constructor for class _global.tri.oxidationstates.ion.IonAssigner: Assign the given oxidation states to atom in the structure in a way that minimizes the GII.
IonFactory - Class in _global.tri.oxidationstates.ion: This class keeps track of available polyatomic and monatomci ions.
IonFactory() - Constructor for class _global.tri.oxidationstates.ion.IonFactory
IonFactory.Ion - Class in _global.tri.oxidationstates.ion: An Ion is a combination of an ion type (e.g.
IonFactory.IonType - Class in _global.tri.oxidationstates.ion: This class represents an ion type, which is an atom (or cluster of atoms) that can be assigned an oxidation state.
IonTools - Class in _global.tri.oxidationstates.util: This class contains some utility methods for identifying and working with polyatomic ions.
IonTools() - Constructor for class _global.tri.oxidationstates.util.IonTools
isChargeBalanced(double) - Method in class _global.tri.oxidationstates.util.Composition: Returns true if this composition is charge balanced within the given charge sum tolerance, or false if it is not.
isElement() - Method in class _global.tri.oxidationstates.ion.IonFactory.IonType: Returns true if this ion type is an element, and false if otherwise (e.g.
isErrorMessage() - Method in class _global.tri.oxidationstates.webapi.PageData: Returns an array of booleans, set to true if the corresponding messages returned by PageData.getMessages() contains an error that should be highlighted for the user, false otherwise.
isInPolyatomicIon(int) - Method in class _global.tri.oxidationstates.ion.KnownIonFinder: Returns true if the atom at the given site is contained within a polyatomic ion, and false otherwise.
isMixedValence() - Method in class _global.tri.oxidationstates.calculator.OxidationStateSet: Returns true if the same ion type has more than one oxidation state in this set, false otherwise.
isMixedValence() - Method in class _global.tri.oxidationstates.webapi.TableRow: Returns true if the generated oxidation states are "mixed valence", meaning the same element (or polyatomic ion type) is associated with more than one oxidation state.
isPolyatomic() - Method in class _global.tri.oxidationstates.ion.IonFactory.Ion: Returns true if this is a polyatomic ion (as determined by the representative structure), and false otherwise.

K

KnownIonFinder - Class in _global.tri.oxidationstates.ion: This class identifies known polyatomic ions in a given structure.
KnownIonFinder(Structure, boolean) - Constructor for class _global.tri.oxidationstates.ion.KnownIonFinder: Creates an ion finder and finds the ions.

L

LatticeOptimizer - Class in _global.tri.oxidationstates.structure: This class is used to find an "average" lattice given a set of target lattices.
LatticeOptimizer(BravaisLattice, BravaisLattice[]) - Constructor for class _global.tri.oxidationstates.structure.LatticeOptimizer: Initialize the lattice optimizer for a search starting from the initialLattice.
LikelihoodCalculator - Class in _global.tri.oxidationstates.calculator.likelihood: This is the main class for calculating likelihood scores
LikelihoodCalculator(String) - Constructor for class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Initialize a likelihood calculator from a parameters file.
LikelihoodCalculator(String, boolean) - Constructor for class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Initialize a likelihood calculator from a parameters file.
LikelihoodCalculator(HashMap<String, int[]>) - Constructor for class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Initialized the likelihood calculator from a map of molecule types to allowed oxidation states
LikelihoodCalculator.PotentialOptimizer - Class in _global.tri.oxidationstates.calculator.likelihood: This class is used to idnetify the electronic chemical potential that maximizes the likelihood score
LikelihoodStateSet - Class in _global.tri.oxidationstates.calculator.likelihood: An OxidationStateSet that keeps track of properties specific to the likelihood score, such as the likelihood score and electronic chemical potential.
LikelihoodStateSet(IonFactory.Ion[], double[], double, double) - Constructor for class _global.tri.oxidationstates.calculator.likelihood.LikelihoodStateSet: Initialize the LikelihoodStateSet
loadIonStructureFromFile(String) - Static method in class _global.tri.oxidationstates.util.IonTools: Reads an ion structure from a file written in the format defined by {2link writeIonStructure()}.
loadPolyatomicIons(String) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Loads into memory the polyatomic ions whose structure files are provided in the given top-level directory.
loadWebIons() - Static method in class _global.tri.oxidationstates.Main: Loads the polyatomic ions used for the web site and paper to the IonFactory.

M

main(String[]) - Static method in class _global.tri.oxidationstates.Main: This is the main entry point for the program.
Main - Class in _global.tri.oxidationstates: This is the main class containing the starting points for various oxidaiton analyzer routines.
Main() - Constructor for class _global.tri.oxidationstates.Main
makeRepresentativeStructure(String, int) - Static method in class _global.tri.oxidationstates.util.IonTools: Randomly samples POSCAR-formatted files from the given directory and creates an "average" structure from those files.
matches(Composition, double) - Method in class _global.tri.oxidationstates.util.Composition: Returns true if the given composition matches this one, within the given tolerance for amounts.
MaxFrequencyFilter - Class in _global.tri.oxidationstates.calculator.frequency: This is used to screen out families of oxidation state assignments that can't possibly be better than the best one found so far.
MaxFrequencyFilter(FrequencyCalculator, IonFactory.Ion[][]) - Constructor for class _global.tri.oxidationstates.calculator.frequency.MaxFrequencyFilter: Initialize the filter.
Message - Class in _global.tri.oxidationstates.webapi: This class represents an message to be returned to the user.
Message(String, boolean) - Constructor for class _global.tri.oxidationstates.webapi.Message
MinAllowedLikelihoodFilter - Class in _global.tri.oxidationstates.calculator.likelihood: This filter only allows combinations of oxidation states that have a likelihood score above a given threshold
MinAllowedLikelihoodFilter(LikelihoodCalculator, IonFactory.Ion[][], double) - Constructor for class _global.tri.oxidationstates.calculator.likelihood.MinAllowedLikelihoodFilter: Initialize the filter
minListLength() - Method in class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Return the minimum length of the list.
MixedValenceChargeBalanceFilter - Class in _global.tri.oxidationstates.calculator: Filters out all combinations of ions that aren't charge balanced, or could not be made charge balanced by allowing one ion to have mixed valence.
MixedValenceChargeBalanceFilter(IonFactory.Ion[][], double[]) - Constructor for class _global.tri.oxidationstates.calculator.MixedValenceChargeBalanceFilter: Initializes the filter.

N

normalizeWeights(double[], int) - Static method in class _global.tri.oxidationstates.ion.IonAssigner: Normalizes the given weights to that the sum of all weights is equal to the given ionTypeCount.
numEntries() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: The total number of entries in this data set.
numFoundPolyatomicIons() - Method in class _global.tri.oxidationstates.ion.CompositionIonFinder
numFoundPolyatomicIons() - Method in interface _global.tri.oxidationstates.ion.IIonFinder: Returns the total number of found polyatomic ions.
numFoundPolyatomicIons() - Method in class _global.tri.oxidationstates.ion.KnownIonFinder
numFoundPolyatomicIons() - Method in class _global.tri.oxidationstates.ion.OxideIonFinder
numFoundPolyatomicIons() - Method in class _global.tri.oxidationstates.ion.ZintlIonFinder
numIons() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData.Entry: THe number of distinct ions in this entry
numIonTypes() - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns the number of ion types known to this calculator
numOxidationStates(int) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns the number of oxidation states known to this calculator for the ion type with the given index
numParameters() - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns the total number of parameters used by this calculator
numParameters() - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer.ParameterState
numParameters() - Method in class _global.tri.oxidationstates.structure.LatticeOptimizer
numParameters() - Method in class _global.tri.oxidationstates.structure.StructureOptimizer
numPeriodicDimensions() - Method in class _global.tri.oxidationstates.ion.IonFactory.IonType: Some ions are crystalline.

O

optimizeLikelihood(OxidationStateData.Entry) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Determine the electronic chemical potential that maximizes the likelihood score for the given entry
optimizeLikelihood(IonFactory.Ion[]) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Finds the electronic chemical potential that maximizes the likelihood score for the given set of ions
optimizeLikelihood(IonFactory.Ion[], double) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Finds the electronic chemical potential that maximizes the likelihood score for the given set of ions
optimizeLikelihood(String[], double[]) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Determine the electronic chemical potential that maximizes the likelihood score for the given ion type IDS, where weights indicate the composition of each ion type.
optimizeLikelihood(Species[]) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Finds the electronic chemical potential that maximizes the likelihood score for the given set of species
oxidationCloseEnough(double, double) - Static method in class _global.tri.oxidationstates.ion.IonFactory: Returns true if two oxidation states are within a given tolerance, which by default is 0.001.
OxidationStateCalculator - Class in _global.tri.oxidationstates.calculator: A general class for calculating the most likely sets of oxidation states for a given set of ion types.
OxidationStateCalculator() - Constructor for class _global.tri.oxidationstates.calculator.OxidationStateCalculator
OxidationStateData - Class in _global.tri.oxidationstates.fitting: This is the main class for data sets (e.g.
OxidationStateData(String, boolean, double, boolean, boolean, String) - Constructor for class _global.tri.oxidationstates.fitting.OxidationStateData: Read a data set from a given file and remove entries according to the given options
OxidationStateData(String, String) - Constructor for class _global.tri.oxidationstates.fitting.OxidationStateData: Read a date set from a given file
OxidationStateData(Collection<OxidationStateData.Entry>, String) - Constructor for class _global.tri.oxidationstates.fitting.OxidationStateData: Create a data set with the provided entries
OxidationStateData.Entry - Class in _global.tri.oxidationstates.fitting: Represents a single data point in the data set
OxidationStateSet - Class in _global.tri.oxidationstates.calculator: Contains a set of oxidation states assigned to ion types (i.e.
OxidationStateSet(IonFactory.Ion[], double[]) - Constructor for class _global.tri.oxidationstates.calculator.OxidationStateSet: Create an OxidationStateSet from the given ions and weights
OxidationStateSet(Composition) - Constructor for class _global.tri.oxidationstates.calculator.OxidationStateSet: Initialize the OxidationStateSet from a given composition containing the ions and weights
OxideIonFinder - Class in _global.tri.oxidationstates.ion: This class finds polyatomic ions that are networks of atoms in consisting of oxygen atoms boudn to one of the following elements: boron, carbon, nitrogen, aluminum, silicon, germanium, tin, lead, phosphorus, sulfur, arsenic, selenium, chlorine, bromine, chromium, molybdenum, tungsten,
OxideIonFinder(Structure) - Constructor for class _global.tri.oxidationstates.ion.OxideIonFinder: Initialize the finder and find the oxide ions in the given strucutre.

P

PageData - Class in _global.tri.oxidationstates.webapi: This class contains all of the data that is needed to render a response to a request on the oxidation state app.
PageData(String, LikelihoodCalculator) - Constructor for class _global.tri.oxidationstates.webapi.PageData: Construct object containing data for this page
PageData(String, TableRow[], LikelihoodCalculator) - Constructor for class _global.tri.oxidationstates.webapi.PageData: Construct object containing data for this page
PARAMETER_DIR - Static variable in class _global.tri.oxidationstates.Main: This is where we store the model parameters (oxidation state boundaries)
parametersToBoundaries(double[]) - Static method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Converts a set of parameters for an ion type into oxidation state boundaries
ParamOptimizer - Class in _global.tri.oxidationstates.fitting: This class is used for optimizing the model parameters
ParamOptimizer(OxidationStateData) - Constructor for class _global.tri.oxidationstates.fitting.ParamOptimizer: Construct a parameter optimizer for a given set of training data
ParamOptimizer(OxidationStateData, int) - Constructor for class _global.tri.oxidationstates.fitting.ParamOptimizer: Construct a parameter optimizer for a given set of training data and number of threads
ParamOptimizer.ParameterState - Class in _global.tri.oxidationstates.fitting: This represents a snapshot of the parameters at one point in the optimization algorithm
PolyatomicSubstitutionFilter - Class in _global.tri.oxidationstates.ion.filters: This filter is used to consider possible combinations of polyatomic ions that can be created from an atomic composition.
PolyatomicSubstitutionFilter(double[], IonFactory.IonType[]) - Constructor for class _global.tri.oxidationstates.ion.filters.PolyatomicSubstitutionFilter: Initialize the filter
PotentialMapper - Class in _global.tri.oxidationstates.webapi: This class performs linear transformations between the electronic chemical potential and the mapped potential
PotentialMapper() - Constructor for class _global.tri.oxidationstates.webapi.PotentialMapper: Create a Potential Mapper with the default slope and intercept
PotentialMapper(double, double) - Constructor for class _global.tri.oxidationstates.webapi.PotentialMapper: Create a PotentialMapper with the given slope and intercept
prepareDataFromICSD(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Reads a directory of CIF files exported from the ICSD and builds an initial training data file for all ordered, charge-balanced structures.
printAllKnownStates(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Write all of the distinct oxidation states in a given data set
printElectrochemicalSeries(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Generate a table for the electrochemical series, consisting of boundaries for all redox pairs in the data set.
printNumEntriesByIon() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Prints to standard output the number of entries containing each ion in this data set.

R

RangeData - Class in _global.tri.oxidationstates.webapi: This class contains the data needed to generate the oxidation state range plots
RangeData(String, int[], double[]) - Constructor for class _global.tri.oxidationstates.webapi.RangeData: This constructor is used by the Jackson library to deserialize a JSON file containing the boundaries.
RangeData(String, LikelihoodCalculator) - Constructor for class _global.tri.oxidationstates.webapi.RangeData: Creates the data necessary to create the plot for a given ion type.
readParameters(String) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Read the parameters from a parameters file (the old format, not the JSON format).
readParametersFromBoundaryJSON(String) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Read parameters from a JSON-formatted boundaries file
removeEntries(OxidationStateData) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes the entries in the given set.
removeEntriesWithNonIntegerStates() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes all entries that contain oxidation states that are not within 0.01 of an integer.
removeEntriesWithNonIntegerStates(double) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes all entries that contain oxidation states that are not within "tolerance" of an integer.
removeEntriesWithZeroOxidationStates() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes all entries for which at least one of the ions has an oxidation state of zero.
removeEntriesWithZintlIons() - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes all entries with ZintlIons, as determined by the ZintlIonFinder.
removeGIIDecrease(String, String, LikelihoodCalculator) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes all entries for which the GII in structDirectory is less than the GII in refStructDirectory.
removeNonChargeBalancedStructures(String) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes all entries that do not have charge neutral structures, defined as structures for which all of the oxidation states of the atoms in each unit cell add up to zero.
removeRandomEntries(double) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes a random subset of this data set
removeRareIons(Main.DataType, Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Removes all entries with rare ions from a data set, where an ion is considered "rare" if it appears in fewer than 25 entries.
removeStructuresNotNearHull(double) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes all structures with energy above hull greater than the provided value.
removeUncommonIonsByCount(int) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes all entries that contain a rate ions, where "rare" ions are those that appear in fewer than minAllowedCount entries
removeUncommonOxidationStates(double) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes entries containing rare ions, where an ion is rare if the fraction of entries it appears in for its ion type is less than minAllowedFraction
removeUnstableEntries(double) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Removes all structures with energy above hull greater than the provided value.
ROOT_DIR - Static variable in class _global.tri.oxidationstates.Main: All input and output files should be contained under this directory

S

setCalculator(LikelihoodCalculator) - Method in class _global.tri.oxidationstates.fitting.CallableCalculator: Set the calculator to be used to calculate the likelihood score.
setCIFString(String) - Method in class _global.tri.oxidationstates.webapi.TableRow: Sets an optional string representation of a CIF file with all oxidation states assigned.
setEnergiesAboveHull(Map<String, Double>) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Sets the energies above the hull for entries in the given map.
setMappingParams(GeneralStructureMapper) - Static method in class _global.tri.oxidationstates.util.IonTools: Sets standard structure comparison parameters for the structure mapper
setMaxKnownFrequencyScore(double) - Method in class _global.tri.oxidationstates.calculator.frequency.MaxFrequencyFilter: The maximum valid frequency score found so far.
setMinAllowedLikelihood(double) - Method in class _global.tri.oxidationstates.calculator.likelihood.MinAllowedLikelihoodFilter: Set the minimum allowed likelihood score.
setMinAllowedLikelihood(double) - Method in class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Sets the minimum allowed likelihood.
setMinListLength(int) - Method in class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Set the minimum length of the list.
setParameters(double[]) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Returns a new calculator copied with this one, with parameters given by the provided parameters.
setRegularizationParameter(double) - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer: Sets the regularization parameter
setTableData(TableRow[]) - Method in class _global.tri.oxidationstates.webapi.PageData: Sets the table data to a new object containing the given rows
setUnboundedParameters(double[]) - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer.ParameterState
setUnboundedParameters(double[]) - Method in class _global.tri.oxidationstates.structure.LatticeOptimizer
setUnboundedParameters(double[]) - Method in class _global.tri.oxidationstates.structure.StructureOptimizer
splitData(int) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Randomly split the data into numSplits test sets.
splitData(OxidationStateData, int, String) - Static method in class _global.tri.oxidationstates.Main: Randomly splits the data for leave-k-out cross validation in a way that ensures that no composition appears in both the test and training set for any split.
stateSetFromBertosString(String) - Static method in class _global.tri.oxidationstates.Main: Reads an oxidation state prediction as output by BERTOS and converts it into an OxidationStateSet for use with this code.
STRUCT_DIR - Static variable in class _global.tri.oxidationstates.Main: This contains all of the structures from the broad ICSD data set
StructureOptimizer - Class in _global.tri.oxidationstates.structure: Finds a structure that is the average of a set of given structures, as determined by the mean squared log ratio of the elements of the minimum-distance matrices for the structures.
StructureOptimizer(Structure[]) - Constructor for class _global.tri.oxidationstates.structure.StructureOptimizer: Initialize the structure optimizer from a set of target structures.

T

TableData - Class in _global.tri.oxidationstates.webapi: This class contains all of the data required for the table in the web app.
TableData(TableRow[]) - Constructor for class _global.tri.oxidationstates.webapi.TableData: Construct the table data from an array of table rows.
TableRow - Class in _global.tri.oxidationstates.webapi: This class contains the data in a single row of the table on the web app
TableRow(LikelihoodCalculator, LikelihoodStateSet, double) - Constructor for class _global.tri.oxidationstates.webapi.TableRow: Constructs a row based on an OxidationStateSet (calculated by the oxidation state tool we've developed) and the global instability index (gii).
testWebAPI() - Static method in class _global.tri.oxidationstates.Main: This method provides an example of how to call the API to replicate the table-generating functionality of the web app.
toJSON() - Method in class _global.tri.oxidationstates.webapi.PageData: Returns a JSON-formatted string containing all of the information on this page.
toMappedPotential(double) - Method in class _global.tri.oxidationstates.webapi.PotentialMapper: Converts the mapped potential to the electronic chemical potential used internally by the oxidation analyzer.
toMappedPotential(double[]) - Method in class _global.tri.oxidationstates.webapi.PotentialMapper: Converts the mapped potential to the electronic chemical potential used internally by the oxidation analyzer.
toString() - Method in class _global.tri.oxidationstates.calculator.OxidationStateSet
toString() - Method in class _global.tri.oxidationstates.ion.IonFactory.Ion
toString() - Method in class _global.tri.oxidationstates.webapi.PageData
toString() - Method in class _global.tri.oxidationstates.webapi.RangeData
toString() - Method in class _global.tri.oxidationstates.webapi.TableData
toString() - Method in class _global.tri.oxidationstates.webapi.TableRow
TRAINING_DATA_DIR - Static variable in class _global.tri.oxidationstates.Main: This is where we store the training data sets
trainModel(String[]) - Static method in class _global.tri.oxidationstates.Main: This method is designed for use in a command-line interface to fit the model.

V

VaspFileFilter - Class in _global.tri.oxidationstates.util: Returns only files whose name ends with ".vasp".
VaspFileFilter() - Constructor for class _global.tri.oxidationstates.util.VaspFileFilter

W

WebOxidationAnalyzer - Class in _global.tri.oxidationstates.webapi: This is the primary class for the Web API.
WebOxidationAnalyzer(String, String) - Constructor for class _global.tri.oxidationstates.webapi.WebOxidationAnalyzer: Initializes the analyzer.
writeBoundaries(OutputStream) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write the boundaries to an output stream in a simple (non-JSON) format
writeBoundaries(String) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write the boundaries to a simple text file.
writeBoundaryJSON(Main.DataType) - Static method in class _global.tri.oxidationstates.Main: Write the JSON file containing the oxidation state boundaries.
writeBoundaryJSON(OutputStream) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write the boundaries in JSON format to an output stream.
writeBoundaryJSON(String) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write the boundaries to a JSON-formatted file.
writeDataFile(String, String, boolean) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write a file that can be used to visualize the boundaries for a particular ion type
writeDataFile(String, String, double, double, double, boolean) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write a file that can be used to visualize the boundaries for a particular ion type
writeDataFiles(String, boolean) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write files that can be used to visualize the boundaries
writeDataFiles(String, double, double, double, boolean) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write files that can be used to visualize the boundaries
writeDataFilesForVisualization(Main.DataType, boolean) - Static method in class _global.tri.oxidationstates.Main: Geneate the files we use to generate the wavy bar plots (or equivalent straight line plots).
writeFile(Writer) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Writes a file containing this data set
writeFile(String) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Writes a file containing this data set
writeFile(String) - Method in class _global.tri.oxidationstates.fitting.ParamOptimizer.ParameterState: Write the current parameters to a text file
writeIonStructure(Structure, String, String) - Static method in class _global.tri.oxidationstates.util.IonTools: Writes an ion structure to a special type of POSCAR-formatted file that contains information about the lattice vector periodicity in the first line of the file.
writeLikelihoods(LikelihoodCalculator, String) - Method in class _global.tri.oxidationstates.fitting.OxidationStateData: Writes the calculated likelihood scores, along with information about the composition and ions, for all entries in this data set to the given file.
writeParameters(OutputStream) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write the parameters to an output stream (not JSON formatted).
writeParameters(String) - Method in class _global.tri.oxidationstates.calculator.likelihood.LikelihoodCalculator: Write the parameters to a text file (not JSON formatted).
writeXYZFiles() - Static method in class _global.tri.oxidationstates.Main: Write files in xyz format for each of the polyatomic ions used for the web site nad paper

Z

ZintlIonFinder - Class in _global.tri.oxidationstates.ion: Finds possible Zintl ions in the given structure, where a possible Zintl ion is defined as a covalently bound network of ions containing one or more of boron, carbon, silicon, phosphorus, sulfur, gallium, germanium, arsenic, selenium, indium, tin, antimony, tellurium, lead, bismuth, polonium.
ZintlIonFinder(Structure) - Constructor for class _global.tri.oxidationstates.ion.ZintlIonFinder: Initializes a finder to search for ions in the given structure.

_

_global.tri.oxidationstates - package _global.tri.oxidationstates
_global.tri.oxidationstates.calculator - package _global.tri.oxidationstates.calculator
_global.tri.oxidationstates.calculator.frequency - package _global.tri.oxidationstates.calculator.frequency
_global.tri.oxidationstates.calculator.likelihood - package _global.tri.oxidationstates.calculator.likelihood
_global.tri.oxidationstates.fitting - package _global.tri.oxidationstates.fitting
_global.tri.oxidationstates.ion - package _global.tri.oxidationstates.ion
_global.tri.oxidationstates.ion.filters - package _global.tri.oxidationstates.ion.filters
_global.tri.oxidationstates.structure - package _global.tri.oxidationstates.structure
_global.tri.oxidationstates.util - package _global.tri.oxidationstates.util
_global.tri.oxidationstates.webapi - package _global.tri.oxidationstates.webapi

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