CASM Namespace Reference

Detailed Description

Main CASM namespace.

Cluster expansion class.

Namespaces
	adapter
	api_impl
	BasisSet_impl
	bset_impl
	CASM_TMP
	clex_SimpleStructureTools_impl
	ClexBasis_impl
	ClexBasisWriter_impl
	ClexParamPack_impl
	Clexulator_impl
	ClusterSpecs_impl
	ClusterSpecs_json_io_impl
	ComparePTLeaf
	Completer
	ConfigDoFIsEquivalent
	Namespace containing DoF comparison functors.
	ConfigEnumIO
	ConfigEnumSiteDoFsInterface_impl
	ConfigEnumStrainInterface_impl
	ConfigIO
	Contains ConfigIO classes and functions.
	ConfigIO_impl
	ConfigMapping
	DataStream_impl
	DB
	DiffClexParamPack_impl
	DoF
	DoF_impl
	DoFSpace_impl
	DoFSpaceIO
	DoFType
	FunctionLabel_impl
	Hull_impl
	HungarianMethod_impl
	Local
	local_impl
	make_report_impl
	Monte
	multivector_impl
	normal_form_impl
	Orbit_impl
	parse_OccupationDoFSpecs_impl
	ParsingDictionary_impl
	query_impl
	QueryIO
	ref_impl
	ScelIO
	SharedPrim_dataformatter_impl
	simpleformatter
	strain
	SubOrbits_impl
	SupercellSymInfo_dataformatter_impl
	sym
	SymRepBuilder
	SymRepTools
	SymRepTools_v2
	VaspIO
	Functions and classes related to VASP input/output.
	xtal

Classes
class	APICommandBase
class	APICommand
class	BsetCommand
	'casm enum' implementation More...
struct	CommandArgs
	Data structure holding basic CASM command info. More...
class	InterfaceBase
	Base class for generic use of algorithms through the API. More...
struct	ClexDescription
	Specifies a particular cluster expansion. More...
class	CLIParse
struct	QueryTraits
class	DirectoryStructure
	Specification of CASM project directory structure. More...
struct	ConfigEnumData
struct	ConfigEnumOptions
	Options for the enumerate_configurations function. More...
struct	EnumerateSupercellsOptions
	Options for the enumerate_supercells function. More...
class	EnumInterfaceBase
class	InputParser
class	ConfigEnumAllOccupationsInterface
	Interface for ConfigEnumAllOccupations. More...
class	ConfigEnumRandomLocalInterface
	Interface for ConfigEnumRandomLocal. More...
class	ConfigEnumRandomOccupationsInterface
	Interface for ConfigEnumRandomOccupations. More...
class	ConfigEnumSiteDoFsInterface
	Interface for ConfigEnumSiteDoFs. More...
class	ConfigEnumStrainInterface
	Interface for ConfigEnumStrain. More...
class	ScelEnumInterface
	Interface for ScelEnum. More...
class	SuperConfigEnumInterface
	Interface for SuperConfigEnum. More...
class	EnumCommand
class	EnumeratorHandler
class	runtime_error
class	FileEnumerator
	Lists all files in a CASM project, for use with 'casm files' command. More...
class	ParsingDictionary
	Parsing dictionary for obtaining the correct MoleculeAttribute given a name. More...
class	HamiltonianModules
class	ImportCommandImpl
class	ImportCommand
class	InfoInterfaceBase
class	NeighborListInfoInterface
	Interface for neighbor list info. More...
class	PrimInfoInterface
	Interface for prim info. More...
class	SupercellInfoInterface
	Interface for supercell info. More...
class	InfoCommand
class	QueryHandler
class	ProjectSettings
struct	jsonConstructor
	Helper struct for constructing objects that need additional data. More...
struct	jsonConstructor< ProjectSettings >
struct	QueryData
class	QueryCommandImpl
class	QueryCommand
class	RmCommandImpl
class	RmCommand
class	SelectCommandImpl
class	SelectCommand
class	SymCommand
class	UpdateCommandImpl
class	UpdateCommand
class	SparseTensor
class	Function
class	InnerProduct
class	FunctionOperation
class	DoFSpecs
struct	BasisFunctionSpecs
	Specify how to construct basis functions. More...
class	BasisSet
class	OccupantDoF
class	DiscreteDoF
class	ContinuousDoF
class	DoFIsEquivalent
	Class for checking equivalence of two DoFSet objects, with respect to symmetry transformations. More...
class	OccupantDoFIsEquivalent
	Class for checking equivalence of two OccupantDoF objects, with respect to symmetry transformations. More...
struct	DoFSetInfo
class	DoFSet
class	Array
	Basic std::vector like container (deprecated) More...
class	FunctionVisitor
class	OccFuncLabeler
class	OccFuncBasisIndexer
class	OccFuncEvaluator
	Evaluates. More...
class	VariableLabeler
class	SubExpressionLabeler
class	OccupantFunction
class	OccOccOperation
class	PolynomialFunction
class	BasicPolyPolyScalarProd
class	PolyPolyOperation
class	PolyVarOperation
class	PolyOccOperation
class	Variable
class	BasicVarVarScalarProd
class	VarVarOperation
class	DataFormatter
	Extract data from objects of 'DataObject' class. More...
class	BaseDatumFormatter
	Abstract base class from which all other DatumFormatter<DataObject> classes inherit. More...
class	FormattedPrintable
	Abstract base class to enable generic formatting. More...
struct	DictionaryConverter
class	DataFormatterDictionary
	Parsing dictionary for constructing a DataFormatter<DataObject> object. More...
class	DataFormatterOperator
	DataFormatters that operate on the results of other DataFormatters. More...
class	DatumFormatterAlias
	Implements a DatumFormatter that is an alias for a combination of others. More...
class	ConstantValueFormatter
	Prints a string value specified at construction. A header string can also be passed. More...
class	BaseValueFormatter
	Base class for creating scalar DatumFormatter. More...
class	GenericDatumFormatter
	A DatumFormatter that returns a value of specified type, via functions that may be specified at runtime. More...
class	Base1DDatumFormatter
	Abstract base class for creating 1D DatumFormatter. More...
class	Generic1DDatumFormatter
	A DatumFormatter that returns a 1D value of specified type, via functions that may be specified at runtime. More...
class	Base2DDatumFormatter
	A DatumFormatter that returns a value of specified 2d container. More...
class	Generic2DDatumFormatter
	A DatumFormatter that returns a 2D value of specified type, via functions that may be specified at runtime. More...
struct	DataFormatterFilter
class	DataStream
class	CountDataStream
class	ValueDataStream
class	VectorDataStream
class	DatumFormatterAdapter
class	MatrixXdDataStream
class	LabeledMatrixXdDataStream
struct	FormattedDataFileOptions
class	FormattedDataFile
struct	traits
class	FileData
	Interface class to check and/or store path and last_write_time of file on disk. Used to determine if files have been updated or deleted. More...
class	FormatFlag
struct	KwargsParser
class	ParentInputParser
class	jsonFile
	Slightly more compact construction of jsonParser from file. More...
class	jsonParserIterator
class	jsonParser
struct	jsonMake
	Helper struct for constructing objects that need additional data. More...
struct	jsonConstructor< std::optional< T > >
	Helper struct for constructing std::optional<T> objects. More...
struct	LogText
struct	LogParagraph
struct	LogVerbatim
class	Log
class	FixedLog
	A Log whose underlying ostream* cannot be reset. More...
class	OStringStreamLog
class	ScopedLogging
class	ScopedNullLogging
class	ScopedStringStreamLogging
class	SafeOfstream
	Write to a temporary file to ensure a good write, then rename. More...
class	BasicClexParamKey
class	BasicClexParamPack
	Abstract base class for reading/writing clexulator parameters Parameters are assume be naturally representable as 1D or 2D arrays. More...
struct	ValAccess< double >
struct	traits< BasicClexParamPack::EvalMode >
class	Calculable
struct	ChemicalReferenceState
	Stores the composition and energy in a single reference state. More...
class	ChemicalReference
struct	ChemicalReferencePrinter
	BasicStructure to help print ChemicalReference. More...
struct	Clex
	Pair of Clexulator and ECIContainer. More...
class	ClexBasis
struct	ClexBasisSpecs
	Provides parameters for constructing a cluster expansion basis (ClexBasis) More...
class	ClexBasisWriter
struct	ValAccess
class	ParamPackMixIn
	ParamPackMixIn is interface class to control ClexParamPack portion of Clexulator printing Used primarily by ClexBasisWriter. More...
class	ClexParamKey
	Key for indexing clexulator parameters Contains pointer to implementation of the Key. More...
class	ClexParamPack
	Abstract base class for reading/writing clexulator parameters Parameters are assumed to be stored as, or at least sliceable into, 2D or 1D arrays in order to standardize read/write interface via Eigen types Arrays are layed out along two dimensions to form (m x N) or (m x 1) matrices where 'N' is the number of sites in the neighborhood of a unit cell, and 'm' is the intrinsic dimension of a particular parameter. Macroscopic or homogeneous properties of the crystal, such as evaluated crystal basis functions or homogeneous strain, which are not associated with individual sites, are represented as a (m x 1) array. The length of the 'm' dimension of a parameter array is referred do as 'dim' and the length of the N' dimension is referred to as 'size'. More...
class	Clexulator
	Evaluates correlations. More...
struct	CompositionAxes
class	CompositionConverter
	Convert between number of species per unit cell and parametric composition. More...
class	GenericConfigCompare
	Class for less than comparison of Configurations implemented via a ConfigTypeIsEqual class that also stores the less than result. More...
class	ConfigDoF
class	ConfigDoFCompare
	Wrapper class for generic less than comparison of ConfigDoF. More...
class	ConfigDoFValues
class	LocalDiscreteConfigDoFValues
class	LocalContinuousConfigDoFValues
class	GlobalContinuousConfigDoFValues
class	ConfigEnumAllOccupations
class	ConfigEnumByPermutation
	Enumerate all equivalent Configurations obtained by permuations in a Supercell. More...
struct	ConfigEnumRandomLocalParams
	Parameters controlling ConfigEnumRandomLocal. More...
class	ConfigEnumRandomLocal
	Enumerate random values for continuous degrees of freedom. More...
struct	ConfigEnumRandomOccupationsParams
	Parameters controlling ConfigEnumRandomOccupations. More...
class	ConfigEnumRandomOccupations
	Enumerate n random occupations in a particular Supercell. More...
struct	ConfigEnumSiteDoFsParams
class	ConfigEnumSiteDoFs
struct	ConfigEnumStrainParams
class	ConfigEnumStrain
class	Norm
class	ConfigIsEquivalent
	Class for comparison of Configurations (with the same Supercell) More...
class	PrimStrucMapCalculator
struct	ConfigMapperResult
	Data structure holding results of ConfigMapper algorithm. More...
class	ConfigMapper
class	Configuration
struct	ConfigInsertResult
	Holds results of Configuration::insert. More...
struct	RefToCanonicalPrim
	Operations that transform a canonical primitive configuration to any equivalent. More...
struct	traits< Configuration >
class	DiffClexParamKey
	Abstract base class for all keys that interact with DiffClexParamPack DiffClexParamPack values are assumed to be 1D, 2D, or to be naturally accessed via 2D slices Standalone values are assumed to be 1D or 2D (for example, a 3xN displacement field) Derived values typically have more dimensions (for example, the derivative of the Mx1 correlation vector with respect to the displacement field has 3 indices, whild the second derivative wrt the displacement field has 5 indices). Derivatives are always asociated with the first independent standalone value in the key name. The key "diff/corr/disp_var" would be associated with "disp_var", which is a 3xN Matrix, and thus the resulting derived value (which is the first derifative of correlations with respect to displacements) will be sliced into 3xN slices. Each slice corresponds to a particular entry in the Mx1 correlation vector (i.e., slice 'j' is the gradient of correlation value j with respect to the entire set of displacement variables). The 'j' index that specifies the particular slice is called a 'secondary identifier', and it can be specified via ClexParamKey::set_identifiers(). More...
struct	DiffScalarContainer
	container struct for storing a standalone value as 2D arrays of both autodiff Scalars doubles More...
class	DiffClexParamPack
	Class for managing the set of all dependent and independent paramters used/generated by clexulator. More...
class	DiffClexParamValKey
class	DiffClexParamGradKey
class	DiffClexParamHessKey
struct	traits< DiffClexParamPack::EvalMode >
struct	ValAccess< typename DiffClexParamPack::DiffScalar >
class	ECIContainer
	A sparse container of ECI values and their corresponding orbit indices. More...
class	FillSupercell
class	FilteredConfigIterator
class	CanonicalForm
	Implements canonical form finding when using SymCompare. More...
class	ConfigCanonicalForm
	Implements canonical form finding for Configuration and DiffTransConfiguration. More...
class	SupercellCanonicalForm
class	HasPrimClex
	Implements PrimClex dependent functions. More...
class	HasSupercell
	Implements PrimClex dependent functions. More...
struct	jsonConstructor< HyperPlaneReference >
struct	jsonConstructor< ChemicalReference >
	Read chemical reference from JSON. More...
struct	jsonMake< ConfigDoF >
struct	jsonConstructor< ConfigDoF >
struct	jsonConstructor< Configuration >
struct	jsonMake< Configuration >
struct	ProtoFuncsPrinter
	Print Orbit<SymCompareType> & ClexBasis, including prototypes and prototype basis functions. More...
class	ClexBasisFunctionPrinter
struct	MappedProperties
class	ScoreMappedProperties
class	PrimNeighborList
	The PrimNeighborList gives the coordinates of UnitCell that are neighbors of the origin UnitCell. More...
class	SuperNeighborList
class	NormPerUnitCell
class	NormPerSpecies
class	ClexBasisBuilder
class	OrbitFunctionTraits
	virtual base class for printing orbit functions of type specified by implementation. More...
class	InvariantPolyBasisBuilder
class	InvariantPolyOrbitFunctionTraits
class	ParamComposition
class	PrimClex
	PrimClex is the top-level data structure for a CASM project. More...
class	ConstantReference
	Maps all Configurations to the same value. More...
class	HyperPlaneReferenceBase
	Maps a Configuration to a scalar value via a hyperplane. More...
class	HyperPlaneReference
	Maps a Configuration to a scalar value via a hyperplane. More...
class	ScelEnumByProps
class	ScelEnumEquivalents
	Enumerate equivalent Supercell. More...
class	ScelCanonicalGenerator
	Functor to find the canonical generating element for an orbit in a Supercell. More...
struct	ScelIsCanonical
	Functor to find to check if element is in canonical form. More...
class	ConfigIterator
class	Supercell
	Represents a supercell of the primitive parent crystal structure. More...
struct	traits< Supercell >
class	SuperConfigEnum
	Given a selection of Configurations, enumerate all tilings into some supercell. More...
class	ClusterInvariants
	Stores cluster invariants: number of sites and site distances. More...
class	WithinScelClusterInvariants
	Stores cluster invariants: number of sites and site distances (using robust_min_dist) More...
struct	OrbitGenerators
	Data structure that holds canonical generating elements and can then make sorted orbits. More...
struct	IntegralClusterOrbitGenerator
class	OrbitBranchSpecs
	Store data used to generate an orbit branch of IntegralCluster. More...
class	ClusterSpecs
class	PeriodicMaxLengthClusterSpecs
class	LocalMaxLengthClusterSpecs
	Parameters most commonly used for local orbit generation. More...
class	GenericPeriodicClusterSpecs
class	GenericLocalClusterSpecs
class	ClusterSymCompare
	CRTP Base class for common cluster symmetry and comparison implementations. More...
class	AperiodicSymCompare< Element >
	Comparisons of clusters using aperiodic symmetry. More...
class	PrimPeriodicSymCompare< Element >
	Comparisons of clusters using prim periodic symmetry. More...
class	ScelPeriodicSymCompare< Element >
	Comparisons of clusters using supercell periodic symmetry, but without periodic images. More...
class	AperiodicSymCompare
	Template class to be specialized for comparisons with aperiodic symmetry. More...
class	PrimPeriodicSymCompare
	Template class to be specialized for comparisons with periodic symmetry of the primitive lattice. More...
class	ScelPeriodicSymCompare
	Template class to be specialized for comparisons with periodic symmetry of the supercell lattice. More...
class	GenericCluster
	A CRTP base class for a cluster of anything. More...
struct	traits< IntegralCluster >
	traits, required for GenericCluster More...
class	IntegralCluster
struct	IntegralClusterSymCompareTraits
struct	traits< AperiodicSymCompare< IntegralCluster > >
struct	traits< PrimPeriodicSymCompare< IntegralCluster > >
struct	traits< ScelPeriodicSymCompare< IntegralCluster > >
struct	jsonConstructor< IntegralCluster >
struct	OrbitPrinterOptions
struct	jsonConstructor< OrbitPrinterOptions >
struct	PrinterBase
struct	Printer
struct	Printer< IntegralCluster >
struct	OrbitPrinter
struct	OrbitPrinter< _Element, ORBIT_PRINT_MODE::PROTO >
	Print Orbit<SymCompareType>, including only prototypes. More...
struct	OrbitPrinter< _Element, ORBIT_PRINT_MODE::FULL >
	Print Orbit<SymCompareType>, including all equivalents. More...
class	SubClusterGenerator
	Generates subclusters of a cluster with an iterator-like interface. More...
struct	ClusterSiteIndicesCompare
	Sort std::set<Index> by size, then value (lexicographical compare) More...
class	ReturnArray
class	ArraySizeLessThan
class	CounterValueIterator
class	BaseCounter
	A Counter allows looping over many incrementing variables in one loop. More...
struct	ContainerTraits
	Specialize container traits Expects: More...
struct	ContainerTraits< std::vector< _value_type, Allocator > >
struct	ContainerTraits< Eigen::Matrix< _value_type, a, b, c, d, e > >
	Eigen::MatrixXd container traits. More...
class	Counter
	A Counter allows looping over many incrementing variables in one loop. More...
struct	traits< Counter< _Container, _value_type, _size_type, _Access, _Compare > >
class	IsoCounter
	A IsoCounter allows looping over many incrementing variables in one loop. More...
struct	traits< IsoCounter< _Container, _value_type, _size_type, _Access, _Compare > >
class	MultiCounter
class	CounterValueIterator< MultiCounter< SubCounterType > >
struct	multivector
	Shortcut for multidimensional vector (std::vector< std::vector< ...) More...
class	Permutation
class	PolyTrie
class	PTNode
class	PTLeaf
class	PTIterator
class	GramSchmidt
class	DynamicMatrix
class	ReturnTensor
class	Tensor
class	TensorBasis
class	AnisoValTraits
	Specifies traits of (possibly) anisotropic crystal properties. More...
struct	jsonConstructor< xtal::AtomPosition >
struct	jsonConstructor< xtal::Molecule >
struct	jsonConstructor< xtal::Site >
struct	jsonConstructor< xtal::SiteDoFSet >
struct	jsonConstructor< xtal::DoFSet >
class	SimpleJSonSiteStructure
	Used to construct a BasicStructure from a 'properties.calc.json' object. More...
struct	jsonConstructor< xtal::ScelEnumProps >
	Make a ScelEnumProps object from JSON input. More...
class	LatticeEnumEquivalents
	Enumerate equivalent Lattics, given a SymGroup. More...
class	Structure
	Structure specifies the lattice and atomic basis of a crystal. More...
class	SymRepBuilderInterface
	Abstract base class that provides interface for converting cartesian isometry to specialized transformation matrix Given a symmetry operation as a 3x3 orthogonal matrix acting on Cartesian space, a 3x1 Cartesian translation, and a time-reversal flag (true indicates +t goes to -t and false indicates +t goes to +t), returns a particular NxN matrix transformation whose dimension and value depends on the underlying implementation. More...
class	TemplateSymRepBuilderBase
class	NullSymRepBuilder
	Un-cloneable class for specifying absence of valid SymRepBuilder. More...
class	CartesianSymRepBuilder
	Builds symmetry representation as the Cartesian matrix of povided SymOp. More...
class	KroneckerSymRepBuilder
	Builds symmetry representation as the Kronecker product of two other representations. More...
class	IdentitySymRepBuilder
	Builds symmetry representation as the 'dim' x 'dim' identity matrix, regardless of symop. More...
class	AngularMomentumSymRepBuilder
	Builds symmetry representation that is the angular momentum symmetry representation of provided symop. More...
class	TimeReversalSymRepBuilder
	Builds symmetry representation that is 'dim'x'dim' +Identity (-Identity) matrix if time_reversal is false (true) More...
class	Rank2TensorSymRepBuilder
	Build 6x6 symmetry representation for a rank 2 Cartesian tensor represented in Kelvin notation. More...
class	TimeReversalSwapSymRepBuilder
class	dOrbitalOccupationSymRepBuilder
class	dOrbitalOccupationSpinPolarizedSymRepBuilder
class	CopyApplyWithPrim_crtp
struct	traits< CASM::xtal::UnitCellCoord >
struct	traits< DB::jsonDB >
class	ConfigEnumInput
class	DoFSpace
class	make_symmetry_adapted_dof_space_error
struct	VectorSpaceMixingInfo
	A struct which gives out the mixing information of given column_vector_space and a subspace. More...
class	EnumeratorBase
	Abstract base class for enumerators. More...
class	ValEnumerator
class	EnumIteratorBase
class	ValEnumIterator
class	InputEnumeratorBase
	Base class for implementing specialized input enumerators. More...
class	InputEnumIterator
class	InputEnumIteratorBase
class	InputEnumerator
	Generic input enumerator. More...
struct	jsonConstructor< ConfigEnumInput >
	Read ConfigEnumInput from JSON. More...
struct	jsonConstructor< DoFSpace >
struct	jsonMake< DoFSpace >
struct	AxesCounterParams
	Data structure used for continuous DoF enumeration IO. More...
class	RandomAccessEnumIterator
	The iterator type for RandomAccessEnumerator. More...
class	RandomAccessEnumeratorBase
	Base class for implementing specialized random access enumerators. More...
class	RandomAccessEnumerator
	Generic random access enumerator. More...
class	RandomAccessEnumIteratorBase
	RandomAccessEnumIterator implemenation. More...
class	UnaryCompare_f
class	libcasm_runtime_error
class	Hull
	Generate and inspect the convex hull generated from a selection of Configurations. More...
struct	FloatCompare
class	FilterIterator
class	HallOfFame
	A container for storing best scoring objects. More...
class	HierarchyID
class	DerivedID
class	PCA
	Principle component analysis. More...
struct	Validator
	Data structure to hold error and warning messages. More...
struct	jsonConstructor< Monte::OccCandidate >
struct	jsonConstructor< Monte::OccSwap >
class	StrainConverter
class	EnumEquivalents
	Enumerate over all equivalents. More...
struct	traits< EnumEquivalents< ObjectType, SymOpIterator, SymOpType, SymOpCompare > >
struct	jsonConstructor< SymInfoOptions >
struct	SymInfoOptions
	Options for printing SymInfo. More...
class	Orbit
	An Orbit of Element. More...
struct	GetPrototype
struct	GetInvariants
class	SymCompare
	CRTP base class for implementing element and orbit comparison. More...
struct	OrbitGeneratorCompare
	Compare concept functor for canonical generating elements. More...
struct	CanonicalGenerator
	Functor to find the canonical generating element for an orbit. More...
struct	IsCanonical
	Functor to find to check if element is in canonical form. More...
class	PermuteIterator
struct	jsonConstructor< PermuteIterator >
class	SimpleOrbit
class	MakeSubOrbitGenerators
	Output the orbit generators necessary to construct the sub-orbits corresponding to group -> subgroup symmetry breaking. More...
class	SupercellSymInfo
	A class that collects all symmetry information for for performing symmetry transformations on the site indices, site DoFs, and global DoFs of a Supercell or Configuration. More...
class	SymBasisPermute
	SymBasisPermute describes how a symmetry operation permutes atoms in a basis. More...
class	SymGroup
	SymGroup is a collection of symmetry operations that satisfy the group property The symmetry operations are stored as their coordinate representation, as described by the SymOp class i.e., if SymOps 'A' and 'B' are in SymGroup, C=A*B is also in SymGroup if 'A' is in SymGroup, then A.inverse() is in SymGroup SymGroup always contains an identity operation. More...
class	MasterSymGroup
class	SymGroupRep
	SymGroupRep is an alternative representation of a SymGroup for something other than real space. There is a one-to-one correspondence of SymOps in some SymGroup with the SymOpRepresentations in SymGroupRep SymGroupRep does not know or care about the specifics of what the SymOpRepresentations describe or how they are implemented. More...
class	SymGroupRepHandle
class	SymGroupRepID
	Type-safe ID object for communicating and accessing Symmetry representation info. More...
struct	SymInfo
	Simple struct to be used as return type for SymOp::info(). More...
class	SymMatrixXd
	Generalized symmetry matrix representation for arbitrary dimension Can be used to describe application of symmetry to N-dimensional vector spaces Use for 3-dimensional transformations if they do not describe coordinate transformations. More...
class	SymOp
	SymOp is the Coordinate representation of a symmetry operation it keeps fraction (FRAC) and Cartesian (CART) information about how a symetry operation transforms 3D spatial coordinates. More...
class	SymOpRepresentation
	SymOpRepresentation is the base class for anything describes a symmetry operation. More...
struct	SymRepIndexCompare
class	SymPermutation
	SymPermutation describes how a symmetry operation permutes a list of 'things' For example, Coordinates in a Cluster, basis atoms in a Structure, Clusters in an Orbit, etc. More...
struct	VectorSpaceSymReport
	Summary of data associated with the action of a symmetry group on a vector space. More...
class	VectorSymCompare
class	VectorInvariants
class	DirectionSymCompare
struct	traits< DirectionSymCompare< _Element, _SymApply > >
	Traits class for DirectionSymCompare. More...
class	SubspaceSymCompare
struct	traits< SubspaceSymCompare< _Element, _SymApply > >
	Traits class for SubspaceSymCompare. More...
struct	traits< VectorSymCompare< Base > >
	Traits class for VectorSymCompare. More...
class	EigenSymCompare
	CRTP Base class for Vector comparisons. More...
class	EigenSymRepApply
class	Popen
	Remember how to use popen. More...
class	runtime_lib_compile_error
class	runtime_lib_shared_error
class	RuntimeLibrary
	Write, compile, load and use code at runtime. More...
class	ImportCommandImplBase
	Defaults used if DataObject type doesn't matter or not given. More...
class	QueryCommandImplBase
	Defaults used if DataObject type doesn't matter or not given. More...
class	RmCommandImplBase
	Defaults used if DataObject type doesn't matter or not given. More...
class	SelectCommandImplBase
	Defaults used if DataObject type doesn't matter or not given. More...
struct	PrintDetails
class	UpdateCommandImplBase
	Defaults used if DataObject type doesn't matter or not given. More...
struct	WriteBasisSetDataImpl
	Write clust.json, basis.json, and clexulator source code, given orbits. More...
struct	PolyWriter

Typedefs
typedef std::function< int(const CommandArgs &)>	Command
typedef std::map< std::string, Command >	CommandMap
template<typename OptionType >
using	InterfaceMap = notstd::unique_cloneable_map< std::string, InterfaceBase< OptionType > >
	Used to hold a list of all algorithms that may be accessed via the API. More...
typedef std::vector< notstd::cloneable_ptr< EnumInterfaceBase > >	EnumInterfaceVector
typedef std::vector< notstd::cloneable_ptr< InfoInterfaceBase > >	InfoInterfaceVector
template<typename DataObject >
using	StringAttribute = BaseValueFormatter< std::string, DataObject >
	Template alias for BaseValueFormatter returning std::string. More...
template<typename DataObject >
using	StringAttributeDictionary = DataFormatterDictionary< DataObject, StringAttribute< DataObject > >
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
using	BooleanAttribute = BaseValueFormatter< bool, DataObject >
	Template alias for BaseValueFormatter returning bool. More...
template<typename DataObject >
using	BooleanAttributeDictionary = DataFormatterDictionary< DataObject, BooleanAttribute< DataObject > >
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
using	IntegerAttribute = BaseValueFormatter< Index, DataObject >
	Template alias for BaseValueFormatter returning Index. More...
template<typename DataObject >
using	IntegerAttributeDictionary = DataFormatterDictionary< DataObject, IntegerAttribute< DataObject > >
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
using	ScalarAttribute = BaseValueFormatter< double, DataObject >
	Template alias for BaseValueFormatter returning double. More...
template<typename DataObject >
using	ScalarAttributeDictionary = DataFormatterDictionary< DataObject, ScalarAttribute< DataObject > >
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
using	VectorXiAttribute = Base1DDatumFormatter< Eigen::VectorXi, DataObject >
	Template alias for BaseValueFormatter returning Eigen::VectorXi. More...
template<typename DataObject >
using	VectorXiAttributeDictionary = DataFormatterDictionary< DataObject, VectorXiAttribute< DataObject > >
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
using	VectorXdAttribute = Base1DDatumFormatter< Eigen::VectorXd, DataObject >
	Template alias for BaseValueFormatter returning Eigen::VectorXd. More...
template<typename DataObject >
using	VectorXdAttributeDictionary = DataFormatterDictionary< DataObject, VectorXdAttribute< DataObject > >
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
using	MatrixXdAttribute = Base2DDatumFormatter< Eigen::MatrixXd, DataObject >
	Template alias for BaseValueFormatter returning Eigen::MatrixXd. More...
template<typename DataObject >
using	MatrixXdAttributeDictionary = DataFormatterDictionary< DataObject, MatrixXdAttribute< DataObject > >
	Template to be specialized for constructing dictionaries for particular DataObject. More...
using	ConfigCompare = GenericConfigCompare< Configuration, ConfigIsEquivalent >
typedef ConfigCanonicalForm< HasSupercell< Comparisons< Calculable< CRTPBase< Configuration > > > > >	ConfigurationBase
typedef ScalarAttribute< Configuration >	Reference
typedef std::function< bool(xtal::Site)>	SiteFilterFunction
typedef std::function< bool(IntegralCluster)>	ClusterFilterFunction
typedef std::function< std::vector< xtal::UnitCellCoord >Structure const &, SiteFilterFunction)>	CandidateSitesFunction
template<typename Element , typename U = void>
using	LocalSymCompare = AperiodicSymCompare< Element, U >
template<typename Element >
using	AperiodicOrbit = Orbit< AperiodicSymCompare< Element > >
template<typename Element >
using	LocalOrbit = AperiodicOrbit< Element >
template<typename Element >
using	ScelPeriodicOrbit = Orbit< ScelPeriodicSymCompare< Element > >
template<typename Element >
using	PrimPeriodicOrbit = Orbit< PrimPeriodicSymCompare< Element > >
typedef AperiodicOrbit< IntegralCluster >	AperiodicIntegralClusterOrbit
typedef LocalOrbit< IntegralCluster >	LocalIntegralClusterOrbit
typedef PrimPeriodicOrbit< IntegralCluster >	PrimPeriodicIntegralClusterOrbit
typedef ScelPeriodicOrbit< IntegralCluster >	ScelPeriodicIntegralClusterOrbit
typedef Printer< IntegralCluster >	SitesPrinter
template<typename _Element >
using	PrototypePrinter = OrbitPrinter< _Element, ORBIT_PRINT_MODE::PROTO >
typedef PrototypePrinter< IntegralCluster >	ProtoSitesPrinter
template<typename _Element >
using	FullOrbitPrinter = OrbitPrinter< _Element, ORBIT_PRINT_MODE::FULL >
typedef FullOrbitPrinter< IntegralCluster >	FullSitesPrinter
template<typename EigenType >
using	EigenCounter = Counter< EigenType, typename EigenType::Scalar, typename EigenType::Index, CASM_TMP::ParenthesesAccess< EigenType, typename EigenType::Scalar, typename EigenType::Index > >
typedef EigenCounter< Eigen::VectorXd >	EigenVectorXdCounter
	Counter for Eigen::VectorXd. More...
typedef EigenCounter< Eigen::MatrixXd >	EigenMatrixXdCounter
	Counter for Eigen::MatrixXd. More...
typedef EigenCounter< Eigen::Matrix3d >	EigenMatrix3dCounter
	Counter for Eigen::Matrix3d. More...
typedef EigenCounter< Eigen::Vector3d >	EigenVector3dCounter
	Counter for Eigen::Vector3d. More...
typedef EigenCounter< Eigen::Vector3i >	EigenVector3iCounter
	Counter for Eigen::Vector3i. More...
typedef EigenCounter< Eigen::VectorXi >	EigenVectorXiCounter
	Counter for Eigen::VectorXi. More...
typedef EigenCounter< Eigen::MatrixXi >	EigenMatrixXiCounter
	Counter for Eigen::MatrixXd. More...
typedef EigenCounter< Eigen::Matrix3i >	EigenMatrix3iCounter
	Counter for Eigen::MatrixXd. More...
typedef std::string	DoFKey
using	SymRepBuilderBase = TemplateSymRepBuilderBase< false >
using	TimeReversalSymRepBuilderBase = TemplateSymRepBuilderBase< true >
typedef unsigned int	uint
typedef unsigned long int	ulint
typedef long int	lint
typedef INDEX_TYPE	Index
	For long integer indexing: More...
typedef Eigen::MatrixXd::Index	EigenIndex
template<bool B, class T = void>
using	enable_if_t = typename std::enable_if< B, T >::type
template<typename Base >
using	Comparisons = notstd::Comparisons< Base >
template<typename MostDerived >
using	CRTPBase = notstd::CRTPBase< MostDerived >
typedef Eigen::VectorXd	VectorXd
typedef Eigen::MatrixXd	MatrixXd
typedef Eigen::Matrix3d	Matrix3d
typedef strain::METRIC	STRAIN_METRIC
template<typename OrbitIterator >
using	PrototypeIterator = boost::transform_iterator< GetPrototype, OrbitIterator >
template<typename OrbitIterator >
using	InvariantsIterator = boost::transform_iterator< GetInvariants, OrbitIterator >
template<typename OrbitType >
using	OrbitGeneratorSet = std::set< typename OrbitType::Element, OrbitGeneratorCompare< OrbitType > >
	An std::set of Orbit. More...
typedef ArgHandler::ARG_TYPE	ARG_TYPE

Enumerations
enum class	PARAM_PACK_TYPE { DEFAULT , DIFF }
enum class	DatumFormatterClass { Property , Operator }
enum class	JustificationType { Left , Right , Center , Full }
enum	COMPOSITION_TYPE { PARAM_COMP = 0 , NUMBER_ATOMS = 1 }
enum class	CLUSTER_PERIODICITY_TYPE : int {   PRIM_PERIODIC = 0 , APERIODIC = 1 , LOCAL = 1 , WITHIN_SCEL = 2 ,   SCEL_PERIODIC = 3 }
enum class	ORBIT_PRINT_MODE { PROTO , FULL }
enum class	COORD_TYPE { FRAC , CART , INTEGRAL , COORD_DEFAULT }
enum class	PERIODICITY_TYPE : int { PERIODIC = 0 , APERIODIC = 1 , LOCAL = 1 , PERIODICITY_DEFAULT = 2 }
enum class	EQUIVALENCE_TYPE { PRIM , SCEL , CONFIG }
enum class	CELL_TYPE { PRIM , SCEL }
enum class	OnError { THROW , WARN , CONTINUE }
enum class	symmetry_type {   identity_op , mirror_op , glide_op , rotation_op ,   screw_op , inversion_op , rotoinversion_op , invalid_op }

Functions
template<typename CommandType >
std::unique_ptr< CommandType >	make_api_command (CommandArgs const &args, typename CommandType::OptionType &opt)
	Parse command line options and make API command. Throws for parsing errors. More...
template<typename CommandType >
std::unique_ptr< CommandType >	make_api_command (std::string cli_str, PrimClex &primclex, typename CommandType::OptionType &opt)
	Parse command line options and make API command. Throws for parsing errors. More...
template<typename CommandType >
int	run_api_command (const CommandArgs &args)
	Standardizes how 'casm X' api commands are executed and implemented. More...
void	print_splash (std::ostream &out)
CommandMap &	command_map ()
	Return static CommandMap containing all CASM API commands. More...
int	casm_api (const CommandArgs &args)
	Executes CASM commands specified by args. More...
PrimClex &	make_primclex_if_not (const CommandArgs &args, std::unique_ptr< PrimClex > &uniq_primclex)
	If !_primclex, construct new PrimClex stored in uniq_primclex, then return reference to existing or constructed PrimClex. More...
std::ostream &	make_ostream_if (bool output, std::ostream &sout, std::unique_ptr< std::ostream > &fout, fs::path out_path, bool gzip)
	Return a reference to proper std::ostream. More...
int	help_command (const CommandArgs &args)
	Print CASM help info to log() More...
int	version_command (const CommandArgs &args)
template<typename OptionType >
std::unique_ptr< InterfaceMap< OptionType > >	make_interface_map ()
	Use to construct an InterfaceMap. More...
ClexDescription	default_configuration_clex ()
bool	operator< (const ClexDescription &A, const ClexDescription &B)
	Compare using name strings: A.name < B.name. More...
jsonParser &	to_json (const ClexDescription &desc, jsonParser &json)
void	from_json (ClexDescription &desc, const jsonParser &json)
bool	clex_exists (const DirectoryStructure &dir, const ClexDescription &desc)
bool	new_dir (const DirectoryStructure &dir, ClexDescription const &desc)
void	parse_args (Completer::OptionHandlerBase &opt, std::string args)
int	composition_command (const CommandArgs &args)
template<typename MakeEnumeratorFunction , typename InputNameValuePairIterator , typename ConfigEnumDataType >
void	enumerate_configurations (PrimClex const &primclex, ConfigEnumOptions const &options, MakeEnumeratorFunction make_enumerator_f, InputNameValuePairIterator name_value_pairs_begin, InputNameValuePairIterator name_value_pairs_end, DataFormatter< ConfigEnumDataType > const &formatter)
	Enumerate configurations. More...
template<typename EnumeratorType >
void	enumerate_supercells (EnumerateSupercellsOptions const &options, EnumeratorType &enumerator, DB::Database< Supercell > &supercell_db)
jsonParser &	to_json (const Completer::EnumOption &enum_opt, jsonParser &json)
	Convert casm enum CLI input to JSON. More...
ParentInputParser	make_enum_parent_parser (Log &log, jsonParser const &json_options, jsonParser const &cli_options_as_json)
	Combine –input / –settings JSON with CLI options. More...
std::string	dry_run_msg (bool dry_run)
jsonParser	combine_configuration_enum_json_options (jsonParser const &json_options, jsonParser const &cli_options_as_json)
void	parse (InputParser< ConfigEnumOptions > &parser, std::string method_name, PrimClex const &primclex, DataFormatterDictionary< Configuration > const &dict)
jsonParser	combine_supercell_enum_json_options (jsonParser const &json_options, jsonParser const &cli_options_as_json)
void	parse (InputParser< EnumerateSupercellsOptions > &parser, std::string method_name, PrimClex const &primclex, DataFormatterDictionary< Supercell > const &dict)
template<typename PermuteIteratorIt >
void	print_dof_space (Log &log, DoFSpace const &dof_space, std::string const &identifier, ConfigEnumInput const &input_state, PermuteIteratorIt permute_begin, PermuteIteratorIt permute_end, bool sym_axes, bool calc_wedges)
	Print DoFSpace information. More...
template<typename NamedInitialStatesType >
void	print_initial_states (Log &log, NamedInitialStatesType const &named_initial_states)
void	print_options (Log &log, ConfigEnumOptions const &options)
std::string	standard_ConfigEnumInput_help ()
EnumInterfaceVector	make_standard_enumerator_interfaces ()
template<typename EnumInterfaceVectorInserter , typename RuntimeLibInserter >
std::pair< EnumInterfaceVectorInserter, RuntimeLibInserter >	load_enumerator_plugins (ProjectSettings const &set, EnumInterfaceVectorInserter enum_it, RuntimeLibInserter lib_it)
	Load enumerator plugins from a CASM project. More...
int	files_command (const CommandArgs &args)
int	format_command (const CommandArgs &args)
template<>
HamiltonianModules::SymRepBuilderDictionary	make_parsing_dictionary< SymRepBuilderInterface > ()
template<typename DoFDictInserter , typename RuntimeLibInserter >
std::pair< DoFDictInserter, RuntimeLibInserter >	load_dof_plugins (const ProjectSettings &set, DoFDictInserter dict_it, RuntimeLibInserter lib_it)
	Load DoF plugins from a CASM project. More...
template<typename SymRepBuilderDictInserter , typename RuntimeLibInserter >
std::pair< SymRepBuilderDictInserter, RuntimeLibInserter >	load_symrep_builder_plugins (const ProjectSettings &set, SymRepBuilderDictInserter dict_it, RuntimeLibInserter lib_it)
	Load SymRepBuilder plugins from a CASM project. More...
InfoInterfaceVector	make_standard_info_method_interfaces ()
	A vector containing casm info method interfaces. More...
int	init_command (const CommandArgs &args)
void	write_lat (Supercell const &supercell, DirectoryStructure const &dir)
void	write_pos (Configuration const &configuration, DirectoryStructure const &dir)
	Write configuration "POS" file (VASP POSCAR) to standard location. More...
void	write_structure_json (Configuration const &configuration, DirectoryStructure const &dir)
void	write_config_json (Configuration const &configuration, DirectoryStructure const &dir)
template<typename OptionType >
jsonParser	make_json_input (const OptionType &opt)
jsonParser &	combine_json_options (std::map< std::string, std::string > const &source_to_combined_keys, jsonParser const &json_source, jsonParser &json_combined)
	Copy from json_source to json_combined More...
std::shared_ptr< RuntimeLibrary >	log_make_shared_runtime_lib (std::string filename_base, std::string compile_options, std::string so_options, std::string compile_msg)
	Make shared_ptr<RuntimeLibrary>, logging progress and errors. More...
int	monte_command (const CommandArgs &args)
void	build_project (ProjectSettings const &project_settings, Structure const &prim)
ProjectSettings	make_default_project_settings (xtal::BasicStructure const &prim, std::string project_name)
ProjectSettings	make_default_project_settings (xtal::BasicStructure const &prim, std::string project_name, fs::path root_dir)
Eigen::Matrix3l	default_nlist_weight_matrix (xtal::BasicStructure const &prim, double tol)
std::set< int >	default_nlist_sublat_indices (xtal::BasicStructure const &prim)
bool	is_valid_project_name (std::string project_name)
void	throw_if_project_name_is_not_valid (std::string project_name)
	Throw if project name is invalid. More...
bool	create_all_directories (ProjectSettings const &set)
void	print_compiler_settings_summary (ProjectSettings const &set, Log &log)
	Print summary of compiler settings, as for 'casm settings -l'. More...
void	print_summary (ProjectSettings const &set, Log &log)
	Print summary of ProjectSettings, as for 'casm settings -l'. More...
jsonParser &	to_json (const ProjectSettings &set, jsonParser &json)
	Serialize ProjectSettings to JSON. More...
void	write_project_settings (ProjectSettings const &set, fs::path project_settings_path)
ProjectSettings	read_project_settings (fs::path project_settings_path)
void	commit (ProjectSettings const &set)
ProjectSettings	open_project_settings (fs::path path_in_project)
template<typename DataFormatterDictInserter , typename RuntimeLibInserter >
std::pair< DataFormatterDictInserter, RuntimeLibInserter >	load_query_plugins (const ProjectSettings &set, DataFormatterDictInserter dict_it, RuntimeLibInserter lib_it)
	Load enumerator plugins from a CASM project. More...
int	ref_command (const CommandArgs &args)
int	run_command (const CommandArgs &args)
int	settings_command (const CommandArgs &args)
int	status_command (const CommandArgs &args)
int	super_command (const CommandArgs &args)
std::string	dof_space_analysis_desc ()
	Describe DoF space analysis input. More...
void	dof_space_analysis (PrimClex &primclex, jsonParser const &json_options, jsonParser const &cli_options_as_json)
	Perform DoF space analysis. More...
jsonParser &	to_json (const Completer::SymOption &sym_opt, jsonParser &json)
	Convert casm sym CLI input to JSON. More...
std::string	symmetrize_desc ()
	Describe the symmetrize method. More...
void	symmetrize (PrimClex &primclex, jsonParser const &json_options, jsonParser const &cli_options_as_json)
	Adjust a structure's lattice and basis to increase factor group symmetry. More...
std::string	write_prim_symmetry_desc ()
	Describe the default casm sym option. More...
void	write_prim_symmetry (PrimClex &primclex, jsonParser const &json_options, jsonParser const &cli_options_as_json)
	Write/print prim symmetry. More...
int	view_command (const CommandArgs &args)
jsonParser &	to_json (const Function *func, jsonParser &json)
template<typename DoFSpecsType >
DoFSpecsType const &	get (DoFKey const &key, BasisFunctionSpecs const &basis_function_specs)
jsonParser &	to_json (const BasisSet &bset, jsonParser &json)
void	from_json (BasisSet &bset, const jsonParser &json)
BasisSet	operator* (const SymOp &LHS, const BasisSet &RHS)
BasisSet	direct_sum (BasisSet::ArgList const &_subs)
bool	compare_no_value (ContinuousDoF const &A, ContinuousDoF const &B)
bool	operator== (DoFSet const &A, DoFSet const &B)
bool	operator!= (DoFSet const &A, DoFSet const &B)
void	parse (InputParser< BasisFunctionSpecs > &parser, Structure const &prim, ParsingDictionary< DoFType::Traits > const *dof_dict)
jsonParser &	to_json (const BasisFunctionSpecs &basis_function_specs, jsonParser &json, Structure const &prim, ParsingDictionary< DoFType::Traits > const *dof_dict)
void	parse (InputParser< DoF_impl::MagSpinDoFSpecs > &parser, const Structure &prim)
void	to_json (const DoF_impl::MagSpinDoFSpecs &occ_specs, jsonParser &json)
jsonParser &	to_json (const OccupantFunction &func, jsonParser &json)
void	from_json (OccupantFunction &func, const jsonParser &json)
void	parse (InputParser< DoF_impl::OccupationDoFSpecs > &parser, const Structure &prim)
void	to_json (const DoF_impl::OccupationDoFSpecs &occupation_dof_specs, jsonParser &json)
jsonParser &	to_json (const Variable &var, jsonParser &json)
void	from_json (Variable &var, const jsonParser &json)
template<typename T , typename... Args>
jsonParser &	to_json (const Array< T > &value, jsonParser &json, Args &&... args)
template<typename T , typename... Args>
void	from_json (Array< T > &value, const jsonParser &json, Args &&... args)
	This requires that 'T::T()' exists, if not, you must do this by hand. More...
template<class T >
std::istream &	operator>> (std::istream &_in, std::vector< T > &vec)
std::pair< std::vector< long >, std::vector< long > >	index_expression_to_bounds (const std::string &_expr)
void	split_formatter_expression (const std::string &input_expr, std::vector< std::string > &tag_names, std::vector< std::string > &sub_exprs)
template<typename DataObject >
DataFormatterDictionary< DataObject >	make_attribute_dictionary ()
	Dictionary of all AttributeFormatter (i.e. BaseValueFormatter<V, DataObject>) More...
template<typename DataObject >
DataFormatterDictionary< DataObject >	make_operator_dictionary ()
	Dictionary of all DatumFormatterOperator. More...
template<typename DataObject >
DataFormatterDictionary< DataObject >	make_dictionary ()
	Template to can be specialized for constructing dictionaries for particular DataObject. More...
jsonParser &	to_json (const FormattedPrintable &_obj, jsonParser &json)
std::ostream &	operator<< (std::ostream &_stream, const FormattedPrintable &_formatted)
DataStream &	operator<< (DataStream &_stream, const FormattedPrintable &_formatted)
template<typename T >
bool	always_true (const T &)
template<typename DataObject >
StringAttributeDictionary< DataObject >	make_string_dictionary ()
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
BooleanAttributeDictionary< DataObject >	make_boolean_dictionary ()
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
IntegerAttributeDictionary< DataObject >	make_integer_dictionary ()
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
ScalarAttributeDictionary< DataObject >	make_scalar_dictionary ()
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
VectorXiAttributeDictionary< DataObject >	make_vectorxi_dictionary ()
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
VectorXdAttributeDictionary< DataObject >	make_vectorxd_dictionary ()
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
MatrixXdAttributeDictionary< DataObject >	make_matrixxd_dictionary ()
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
DataFormatterDictionary< DataObject, BaseValueFormatter< jsonParser, DataObject > >	make_json_dictionary ()
	Template to be specialized for constructing dictionaries for particular DataObject. More...
template<typename DataObject >
DataFormatterFilter< DataObject >	make_data_formatter_filter (std::string const &filter_expr, DataFormatterDictionary< DataObject > const &_dict)
template<typename DataObject >
DataFormatterFilter< DataObject >	make_data_formatter_filter (std::vector< std::string > const &filter_expr, DataFormatterDictionary< DataObject > const &_dict)
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_add ()
	Makes a DataFormatterOperator that adds two or more numbers. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_sub ()
	Makes a DataFormatterOperator that subtracts two numbers. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_mult ()
	Makes a DataFormatterOperator that returns the product of two or more numbers. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_div ()
	Makes a DataFormatterOperator that divides two numbers. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_rms ()
	Makes a DataFormatterOperator that returns the root-mean-square value of 0 or more elements. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_pnorm ()
	Makes a DataFormatterOperator that returns the root-mean-square value of 0 or more elements. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_max ()
	Makes a DataFormatterOperator that returns the maximum of two or more numbers. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_min ()
	Makes a DataFormatterOperator that returns the minimum of two or more numbers. More...
template<typename DataObject >
DataFormatterOperator< long, double, DataObject >	format_operator_imax ()
	Makes a DataFormatterOperator that returns the index (from 0) of the maximum of two or more numbers. More...
template<typename DataObject >
DataFormatterOperator< long, double, DataObject >	format_operator_imin ()
	Makes a DataFormatterOperator that returns the index (from 0) of the minimum of two or more numbers. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_exp ()
	Makes a DataFormatterOperator that returns the exponential of a number. More...
template<typename DataObject >
DataFormatterOperator< bool, std::string, DataObject >	format_operator_re ()
	Makes a DataFormatterOperator that checks if a string matches a regular expression. More...
template<typename DataObject >
DataFormatterOperator< bool, std::string, DataObject >	format_operator_rs ()
	Makes a DataFormatterOperator that checks if a string contains a regular expression. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_sq ()
	Makes a DataFormatterOperator that returns the square of a number. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_sqrt ()
	Makes a DataFormatterOperator that returns the square root of a number. More...
template<typename DataObject >
DataFormatterOperator< double, double, DataObject >	format_operator_neg ()
	Makes a DataFormatterOperator that returns the negative of a number. More...
template<typename DataObject >
DataFormatterOperator< bool, bool, DataObject >	format_operator_and ()
	Makes a DataFormatterOperator that returns the boolean AND for a sequence of boolean values. More...
template<typename DataObject >
DataFormatterOperator< bool, bool, DataObject >	format_operator_or ()
	Makes a DataFormatterOperator that returns the boolean OR for a sequence of boolean values. More...
template<typename DataObject >
DataFormatterOperator< bool, bool, DataObject >	format_operator_xor ()
	Makes a DataFormatterOperator that returns the boolean NOT for a single boolean value. More...
template<typename DataObject >
DataFormatterOperator< bool, bool, DataObject >	format_operator_not ()
template<typename DataObject >
DataFormatterOperator< bool, double, DataObject >	format_operator_eq ()
	Makes a DataFormatterOperator for equality comparison of two numbers. More...
template<typename DataObject >
DataFormatterOperator< bool, double, DataObject >	format_operator_lt ()
	Makes a DataFormatterOperator for less-than comparison of two numbers. More...
template<typename DataObject >
DataFormatterOperator< bool, double, DataObject >	format_operator_le ()
	Makes a DataFormatterOperator for less-than-or-equal comparison of two numbers. More...
template<typename DataObject >
DataFormatterOperator< bool, double, DataObject >	format_operator_gt ()
	Makes a DataFormatterOperator for greater-than comparison of two numbers. More...
template<typename DataObject >
DataFormatterOperator< bool, double, DataObject >	format_operator_ge ()
	Makes a DataFormatterOperator for greater-than-or-equal comparison of two numbers. More...
template<typename DataObject >
DatumFormatterAlias< DataObject >	datum_formatter_alias (const std::string &_name, const std::string &_command, const DataFormatterDictionary< DataObject > &_dict, const std::string &_help="")
	Make a DatumFormatterAlias. More...
template<typename DataObject >
DatumFormatterAlias< DataObject >	datum_formatter_alias (const std::string &_name, const BaseDatumFormatter< DataObject > &_inside, const std::string &_help="")
	Make a DatumFormatterAlias. More...
template<typename DataObject >
GenericDatumFormatter< std::string, DataObject >	name ()
template<typename DataObject >
GenericDatumFormatter< std::string, DataObject >	alias ()
template<typename DataObject >
GenericDatumFormatter< std::string, DataObject >	alias_or_name ()
DataStream &	operator<< (DataStream &_stream, int i)
DataStream &	operator<< (DataStream &_stream, float f)
DataStream &	operator<< (DataStream &_stream, unsigned int i)
DataStream &	operator<< (DataStream &_stream, unsigned long i)
template<class T >
DataStream &	operator<< (DataStream &_stream, const std::vector< T > &vec)
template<typename ExternalType , typename InternalType >
DatumFormatterAdapter< ExternalType, InternalType >	make_datum_formatter_adapter (BaseDatumFormatter< InternalType > const &_base_formatter)
template<typename ENUM >
std::string	to_string (ENUM val)
	Return string representation of enum class. More...
template<typename ENUM >
std::string	multiline_enum_help ()
	Print help message describing recognized strings for allowed enum values. More...
template<typename StringContainer >
std::string	standard_singleline_help (StringContainer options, std::string _default="")
	Print short help message describing recognized strings for allowed enum values. More...
template<typename ENUM >
std::string	standard_singleline_enum_help (std::string _default="", std::string other="")
	Print short help message describing recognized strings for allowed enum values. More...
template<typename ENUM >
std::string	singleline_enum_help ()
	Print short help message describing recognized strings for allowed enum values. More...
template<typename ENUM >
void	invalid_enum_string (std::string val)
	Throw invalid_argument error for unrecognized strings. More...
template<typename ENUM >
std::set< ENUM >	matches (const std::string &val)
	Return all matching enum class members from string representation. More...
template<typename ENUM >
ENUM	from_string (const std::string &val)
	Return enum class object from string representation. More...
std::ostream &	operator<< (std::ostream &_stream, const FormatFlag &flag)
template<typename T >
std::string	multiline_help ()
	Help message for reading a type T from input. More...
template<typename T >
std::string	singleline_help ()
	Help message for reading a type T from input. More...
template<typename T >
std::string	help ()
	Uses 'multiline_help<T>()' by default. More...
int	parse_verbosity (KwargsParser &parser, int default_verbosity=10)
void	parse (InputParser< std::nullptr_t > &parser)
	Temporary – enables compilation of legacy code. More...
template<typename T >
void	parse (InputParser< T > &parser)
void	print_warnings (KwargsParser const &parser, Log &log, std::string header="Warnings")
	Formatted print warning messages, including all subparsers. More...
void	print_errors (KwargsParser const &parser, Log &log, std::string header="Errors")
	Formatted print error messages, including all subparsers. More...
jsonParser	make_report (KwargsParser const &parser)
	Return parser.input with error and warning messages added in place. More...
template<typename ErrorType >
void	report_and_throw_if_invalid (KwargsParser const &parser, Log &log, ErrorType error)
std::ostream &	operator<< (std::ostream &stream, const jsonParser &json)
std::istream &	operator>> (std::istream &stream, jsonParser &json)
jsonParser &	to_json (bool value, jsonParser &json)
	To JSON for basic types. More...
jsonParser &	to_json (int value, jsonParser &json)
jsonParser &	to_json (unsigned int value, jsonParser &json)
jsonParser &	to_json (long int value, jsonParser &json)
jsonParser &	to_json (unsigned long int value, jsonParser &json)
jsonParser &	to_json (double value, jsonParser &json)
jsonParser &	to_json (const std::string &value, jsonParser &json)
jsonParser &	to_json (const char *value, jsonParser &json)
jsonParser &	to_json (const jsonParser &value, jsonParser &json)
template<typename T >
T	from_json (const jsonParser &json)
	From JSON for basic types. More...
template<typename T >
std::unique_ptr< T >	make_from_json (const jsonParser &json)
	Make from JSON for basic types. More...
template<>
bool	from_json< bool > (const jsonParser &json)
template<>
int	from_json< int > (const jsonParser &json)
template<>
unsigned int	from_json< unsigned int > (const jsonParser &json)
template<>
long int	from_json< long int > (const jsonParser &json)
template<>
unsigned long int	from_json< unsigned long int > (const jsonParser &json)
template<>
double	from_json< double > (const jsonParser &json)
template<>
std::string	from_json< std::string > (const jsonParser &json)
template<>
jsonParser	from_json< jsonParser > (const jsonParser &json)
void	from_json (bool &value, const jsonParser &json)
	From JSON for basic types. More...
void	from_json (int &value, const jsonParser &json)
void	from_json (unsigned int &value, const jsonParser &json)
void	from_json (long int &value, const jsonParser &json)
void	from_json (unsigned long int &value, const jsonParser &json)
void	from_json (double &value, const jsonParser &json)
void	from_json (std::string &value, const jsonParser &json)
void	from_json (jsonParser &value, const jsonParser &json)
void	from_json (std::istream &stream, const jsonParser &json)
void	from_json (fs::path &value, const jsonParser &json)
void	to_json (std::istream &stream, jsonParser &json)
	Create a jsonParser from a stream. More...
void	to_json (fs::path file_path, jsonParser &json)
	Create a jsonParser by reading a file. More...
template<typename T >
jsonParser &	to_json (const std::complex< T > &value, jsonParser &json)
	To JSON for complex. More...
template<typename T >
void	from_json (std::complex< T > &value, const jsonParser &json)
	From JSON for complex. More...
template<typename Key , typename T >
jsonParser &	to_json (const std::pair< Key, T > &value, jsonParser &json)
	To JSON for std::pair<std::string, T> More...
template<typename Key , typename T >
void	from_json (std::pair< Key, T > &value, const jsonParser &json)
	From JSON for std::pair<std::string, T> More...
template<typename T , typename... Args>
void	make_from_json (std::unique_ptr< T > &ptr, const jsonParser &json, Args &&... args)
	Make from JSON for basic types. More...
fs::path	find_diff (const jsonParser &A, const jsonParser &B)
	Return the location at which jsonParser 'A' != 'B' as a fs::path. More...
fs::path	find_diff (const jsonParser &A, const jsonParser &B, double tol)
template<typename T >
jsonParser	json_pair (const std::string &key, const T &value)
	Create pair/value json object without intermediate temporary. More...
template<typename T , typename... Args>
jsonParser &	to_json (std::optional< T > const &value, jsonParser &json)
template<typename T , typename... Args>
void	from_json (std::optional< T > &value, jsonParser const &json, Args &&... args)
template<typename T >
Log &	operator<< (Log &log, const T &msg_details)
Log &	operator<< (Log &log, std::ostream &(*fptr)(std::ostream &))
Log &	default_log ()
Log &	default_err_log ()
Log &	log ()
Log &	err_log ()
Log &	cout_log ()
Log &	cerr_log ()
Log &	null_log ()
std::string	to_string (const std::string &s, std::string begin="\"", std::string end="\"")
template<typename T1 , typename T2 >
std::string	to_string (const std::pair< T1, T2 > &value)
template<typename Iterator >
std::string	container_to_string (Iterator begin_it, Iterator end_it, std::string begin="[", std::string end="]", std::string delim=", ")
template<class T >
std::string	to_string (const std::vector< T > &container, std::string begin="[", std::string end="]", std::string delim=", ")
template<class T , class Compare >
std::string	to_string (const std::set< T, Compare > &container, std::string begin="[", std::string end="]", std::string delim=", ")
template<class Key , class T , class Compare >
std::string	to_string (const std::map< T, Key, Compare > &container, std::string begin="{", std::string end="}", std::string delim=", ")
template<typename ConfigType >
bool	is_calculated (const ConfigType &config, std::string calctype="")
	Return true if all required properties have been been calculated for the configuration. More...
template<typename ConfigType >
void	reset_properties (ConfigType &config)
template<typename ConfigType >
std::string	calc_status (const ConfigType &_config, std::string calctype="")
	Status of calculation. More...
template<typename ConfigType >
std::string	failure_type (const ConfigType &config, std::string calctype="")
template<typename ConfigType >
bool	has_calc_status (const ConfigType &config, std::string calctype="")
template<typename ConfigType >
bool	has_failure_type (const ConfigType &config, std::string calctype="")
template<typename ConfigType >
std::string	calc_properties_path (const ConfigType &config, std::string calctype="")
template<typename ConfigType >
std::string	pos_path (const ConfigType &config, std::string calctype="")
template<typename ConfigType >
std::string	calc_status_path (const ConfigType &config, std::string calctype="")
bool	is_calculated (const MappedProperties &calc_properties, const std::vector< std::string > &required_properties)
	Return true if all required properties are included in the JSON. More...
std::string	calc_properties_path (const PrimClex &primclex, const std::string &configname, std::string calctype="")
std::string	pos_path (const PrimClex &primclex, const std::string &configname)
std::string	calc_status_path (const PrimClex &primclex, const std::string &configname, std::string calctype="")
Index	print_clust_basis (std::ostream &stream, BasisSet _clust_basis, IntegralCluster const &_prototype, Index func_ind=0, int space=18, char delim='\n')
template<typename OrbitType >
void	print_proto_clust_funcs (ClexBasis const &_clex_basis, std::ostream &out, BasicStructure const &_prim, std::vector< OrbitType > const &_tree)
template<typename OrbitType >
Index	_orbit_max_poly_order (OrbitType const &orbit, BasisFunctionSpecs const &basis_function_specs)
	allow basis_function_specs to specify max_poly_order by branch, orbit, etc. More...
template<typename OutputIterator >
OutputIterator	standard_composition_axes (ParamComposition::AllowedOccupants _allowed_occs, OutputIterator result)
	Generate CompositionConverter specifying standard composition axes for a prim Structure. More...
void	display_composition_axes (std::ostream &stream, const std::map< std::string, CompositionConverter > &map)
	Pretty-print map of name/CompositionConverter pairs. More...
void	display_comp (std::ostream &stream, const CompositionConverter &f, int indent=0)
	Pretty-print comp in terms of comp_n. More...
void	display_comp_n (std::ostream &stream, const CompositionConverter &f, int indent=0)
	Pretty-print comp_n in terms of comp. More...
void	display_param_chem_pot (std::ostream &stream, const CompositionConverter &f, int indent=0)
	Pretty-print param_chem_pot in terms of chem_pot. More...
Eigen::MatrixXd	end_members (const ParamComposition::AllowedOccupants &_allowed_occs)
	Serialize CompositionConverter to JSON. More...
Eigen::MatrixXd	composition_space (const ParamComposition::AllowedOccupants &_allowed_occs, double tol=1e-14)
	Return the composition space of a ParamComposition::AllowedOccupants. More...
Eigen::MatrixXd	null_composition_space (const ParamComposition::AllowedOccupants &_allowed_occs, double tol=1e-14)
	Return the null composition space of a ParamComposition::AllowedOccupants. More...
void	swap (ConfigDoF &A, ConfigDoF &B)
void	reset_properties (ConfigDoF &_dof)
ConfigDoF	make_configdof (Structure const &prim, Index volume)
	Construct zero-valued ConfigDoF. More...
ConfigDoF	make_configdof (Structure const &prim, Index volume, double tol)
	Construct zero-valued ConfigDoF. More...
std::unique_ptr< ConfigDoF >	make_unique_configdof (Structure const &prim, Index volume)
	Construct zero-valued std::unique_ptr<ConfigDoF> More...
std::unique_ptr< ConfigDoF >	make_unique_configdof (Structure const &prim, Index volume, double tol)
	Construct zero-valued std::unique_ptr<ConfigDoF> More...
ConfigDoF	make_configdof (Supercell const &supercell)
	Construct zero-valued ConfigDoF. More...
ConfigDoF	make_configdof (Supercell const &supercell, double tol)
	Construct zero-valued ConfigDoF. More...
std::unique_ptr< ConfigDoF >	make_unique_configdof (Supercell const &supercell)
	Construct zero-valued std::unique_ptr<ConfigDoF> More...
std::unique_ptr< ConfigDoF >	make_unique_configdof (Supercell const &supercell, double tol)
	Construct zero-valued std::unique_ptr<ConfigDoF> More...
template<>
bool	is_guaranteed_for_database_insert (ConfigEnumAllOccupations const &enumerator)
template<>
StringAttributeDictionary< Configuration >	make_string_dictionary< Configuration > ()
template<>
BooleanAttributeDictionary< Configuration >	make_boolean_dictionary< Configuration > ()
template<>
IntegerAttributeDictionary< Configuration >	make_integer_dictionary< Configuration > ()
template<>
ScalarAttributeDictionary< Configuration >	make_scalar_dictionary< Configuration > ()
template<>
VectorXdAttributeDictionary< Configuration >	make_vectorxd_dictionary< Configuration > ()
template<>
MatrixXdAttributeDictionary< Configuration >	make_matrixxd_dictionary< Configuration > ()
MappingNode	copy_apply (PermuteIterator const &_it, MappingNode const &_node, bool transform_cost_mat=true)
	Reorders the permutation and compounds the spatial isometry (rotation. More...
std::pair< ConfigDoF, std::set< std::string > >	to_configdof (SimpleStructure const &_child_struc, Supercell const &_scel)
	Initializes configdof of Supercell '_scel' corresponding to an idealized child structure (encoded by _child_struc) _child_struc is assumed to have been idealized via structure-mapping or to be the result of converting a configuration to a SimpleStructure. result.second gives list of properties that were utilized in the course of building the configdof. More...
Configuration	sub_configuration (std::shared_ptr< Supercell const > sub_scel_ptr, const Configuration &super_config, const UnitCell &origin=UnitCell(0, 0, 0))
	Returns the sub-configuration that fills a particular Supercell. More...
Configuration	make_configuration (const PrimClex &primclex, std::string name)
	Make Configuration from name string. More...
Eigen::VectorXd	correlations (const Configuration &config, Clexulator const &clexulator)
	Returns correlations using 'clexulator'. More...
Eigen::VectorXd	corr_contribution (Index linear_unitcell_index, const Configuration &config, Clexulator const &clexulator)
	Returns correlation contribution from a single unit cell, not normalized. More...
Eigen::VectorXd	point_corr (Index linear_unitcell_index, Index neighbor_index, const Configuration &config, Clexulator const &clexulator)
	Returns point correlations from a single site, normalized by cluster orbit size. More...
Eigen::MatrixXd	gradcorrelations (const Configuration &config, Clexulator const &clexulator, DoFKey &key)
	Returns gradient correlations using 'clexulator', with respect to DoF 'dof_type'. More...
Eigen::VectorXd	comp (const Configuration &config)
	Returns parametric composition, as calculated using PrimClex::param_comp. More...
Eigen::VectorXd	comp_n (const Configuration &config)
	Returns the composition, as number of each species per unit cell. More...
double	n_vacancy (const Configuration &config)
	Returns the vacancy composition, as number per unit cell. More...
double	n_species (const Configuration &config)
	Returns the total number species per unit cell. More...
Eigen::VectorXd	species_frac (const Configuration &config)
	Returns the composition as species fraction, with [Va] = 0.0, in the order of Structure::get_struc_molecule. More...
Eigen::VectorXd	site_frac (const Configuration &config)
	Returns the composition as site fraction, in the order of Structure::get_struc_molecule. More...
double	energy (const Configuration &config)
	Returns the energy, normalized per unit cell. More...
double	energy_per_species (const Configuration &config)
	Returns the energy, normalized per species. More...
double	reference_energy (const Configuration &config)
	Returns the reference energy, normalized per unit cell. More...
double	reference_energy_per_species (const Configuration &config)
	Returns the reference energy, normalized per species. More...
double	formation_energy (const Configuration &config)
	Returns the formation energy, normalized per unit cell. More...
double	formation_energy_per_species (const Configuration &config)
	Returns the formation energy, normalized per species. More...
double	clex_formation_energy (const Configuration &config)
	Returns the formation energy, normalized per unit cell. More...
double	clex_formation_energy_per_species (const Configuration &config)
	Returns the formation energy, normalized per species. More...
double	rms_force (const Configuration &_config)
	Root-mean-square forces of relaxed configurations, determined from DFT (eV/Angstr.) More...
double	atomic_deformation (const Configuration &_config)
	Cost function that describes the degree to which basis sites have relaxed. More...
double	lattice_deformation (const Configuration &_config)
	Cost function that describes the degree to which lattice has relaxed. More...
double	volume_relaxation (const Configuration &_config)
	Change in volume due to relaxation, expressed as the ratio V/V_0. More...
double	relaxed_magmom (const Configuration &_config)
	Returns the relaxed magnetic moment, normalized per unit cell. More...
double	relaxed_magmom_per_species (const Configuration &_config)
	Returns the relaxed magnetic moment, normalized per species. More...
Eigen::MatrixXd	relaxed_forces (const Configuration &_config)
	relaxed forces of configuration, determined from DFT (eV/Angstr.), as a 3xN matrix More...
IntegralCluster	config_diff (const Configuration &_config1, const Configuration &_config2)
	Returns an Integral Cluster representing the perturbed sites between the configs. More...
Configuration	closest_setting (const Configuration &_config1, const Configuration &_config2)
Configuration	config_clip (const Configuration &_config, const Configuration &_bg, IntegralCluster &_clust)
	Returns a Configuration with the sites in _clust clipped from _config and placed in _bg. More...
bool	is_primitive (const Configuration &_config)
	returns true if _config describes primitive cell of the configuration it describes More...
bool	is_canonical (const Configuration &_config)
	returns true if no symmetry transformation applied to _config will increase its lexicographic order More...
bool	is_diff_trans_endpoint (const Configuration &_config)
	returns true if _config is an endpoint of any existing diff_trans_config More...
std::string	diff_trans_endpoint_of (const Configuration &_config)
	returns which diff_trans _config is an endpoint of More...
bool	has_energy (const Configuration &_config)
bool	has_reference_energy (const Configuration &_config)
bool	has_formation_energy (const Configuration &_config)
bool	has_rms_force (const Configuration &_config)
bool	has_atomic_deformation (const Configuration &_config)
bool	has_lattice_deformation (const Configuration &_config)
bool	has_volume_relaxation (const Configuration &_config)
bool	has_relaxed_magmom (const Configuration &_config)
bool	has_relaxed_mag_basis (const Configuration &_config)
Eigen::VectorXd	correlations (const ConfigDoF &configdof, const Supercell &scel, Clexulator const &clexulator)
	Returns correlations using 'clexulator'. Supercell needs a correctly populated neighbor list. More...
Eigen::VectorXd	corr_contribution (Index linear_unitcell_index, const ConfigDoF &configdof, const Supercell &scel, Clexulator const &clexulator)
	Returns correlation contribution from a single unit cell, not normalized. More...
Eigen::VectorXd	point_corr (Index linear_unitcell_index, Index neighbor_index, const ConfigDoF &configdof, const Supercell &scel, Clexulator const &clexulator)
	Returns point correlations from a single site, normalized by cluster orbit size. More...
Eigen::MatrixXd	gradcorrelations (const ConfigDoF &configdof, const Supercell &scel, Clexulator const &clexulator, DoFKey &key)
	Returns gradient correlations using 'clexulator', with respect to DoF 'dof_type'. More...
Eigen::VectorXi	num_each_molecule (const ConfigDoF &configdof, const Supercell &scel)
	Returns num_each_molecule(molecule_type), where 'molecule_type' is ordered as Structure::get_struc_molecule() More...
Eigen::VectorXd	comp_n (const ConfigDoF &configdof, const Supercell &scel)
	Returns comp_n, the number of each molecule per primitive cell, ordered as Structure::get_struc_molecule() More...
double	operator* (const ECIContainer &_eci, const Eigen::VectorXd &_corr)
	Evaluate property given an ECIContainer and correlations. More...
double	operator* (const ECIContainer &_eci, double const *_corr_begin)
	Evaluate property given an ECIContainer and pointer to beginning of range of correlation. More...
bool	is_valid_sub_configuration (xtal::Lattice const &sub_configuration_lattice, Supercell const &supercell)
Configuration	fill_supercell (Configuration const &motif, std::shared_ptr< Supercell const > const &shared_supercell)
Configuration	fill_supercell (Configuration const &motif, Supercell const &supercell)
Configuration	fill_supercell (SymOp const &symop, Configuration const &motif, std::shared_ptr< Supercell const > const &shared_supercell)
Configuration	fill_supercell (SymOp const &symop, Configuration const &motif, Supercell const &supercell)
template<typename ConfigOutputIterator >
ConfigOutputIterator	make_all_super_configurations (Configuration const &configuration, std::shared_ptr< Supercell const > shared_supercell, ConfigOutputIterator result)
	Make all super configurations that fill a particular supercell. More...
template<typename IteratorType >
void	swap (FilteredConfigIterator< IteratorType > &a, FilteredConfigIterator< IteratorType > &b)
	Definitions. More...
template<typename IteratorType , typename DataObject >
FilteredConfigIterator< IteratorType >	filter_begin (const IteratorType &it, const IteratorType &it_end, const std::vector< std::string > &filter_expr, const DataFormatterDictionary< DataObject > &_dict)
template<typename IteratorType >
FilteredConfigIterator< IteratorType >	filter_end (const IteratorType &it_end)
ChemicalReference	read_chemical_reference (fs::path filename, BasicStructure const &prim, double tol)
	Read chemical reference states from JSON file. More...
void	write_chemical_reference (const ChemicalReference &chem_ref, fs::path filename)
	Write chemical reference states to JSON file. More...
CompositionAxes	read_composition_axes (fs::path _filename)
void	write_composition_axes (fs::path _filename, CompositionAxes const &composition_axes)
	Write CompositionAxes to file. More...
void	parse (InputParser< ClexBasisSpecs > &parser, std::shared_ptr< Structure const > shared_prim, ParsingDictionary< DoFType::Traits > const *dof_dict)
jsonParser &	to_json (ClexBasisSpecs const &basis_set_specs, jsonParser &json, Structure const &prim, ParsingDictionary< DoFType::Traits > const *dof_dict)
void	from_json (CompositionAxes &composition_axes, const jsonParser &json)
jsonParser &	to_json (CompositionAxes const &composition_axes, jsonParser &json)
	Write CompositionAxes to JSON. More...
jsonParser &	to_json (const CompositionConverter &f, jsonParser &json)
	Serialize CompositionConverter to JSON. More...
void	from_json (CompositionConverter &f, const jsonParser &json)
	Deserialize CompositionConverter from JSON. More...
jsonParser &	to_json (const ConfigDoF &configdof, jsonParser &json)
void	from_json (ConfigDoF &configdof, const jsonParser &json)
	Read ConfigDoF from JSON. More...
jsonParser &	to_json (ConfigMapping::Settings const &_set, jsonParser &_json)
jsonParser const &	from_json (ConfigMapping::Settings &_set, jsonParser const &_json)
jsonParser &	to_json (Configuration const &configuration, jsonParser &json)
	Insert Configuration to JSON. More...
void	from_json (Configuration &configuration, jsonParser const &json)
	Read Configuration from JSON. More...
void	parse (InputParser< ECIContainer > &parser)
	Make ECIContainer from JSON (eci.json file) More...
void	print_tex_tabular_cluster_sites (Log &out, IntegralCluster const &cluster, xtal::BasicStructure const &prim, COORD_TYPE mode)
	Print prototype cluster sites as a tex tabular. More...
void	print_site_basis_funcs (std::shared_ptr< const Structure > prim_ptr, ClexBasis const &clex_basis, Log &out, Index indent_space=6, COORD_TYPE mode=FRAC)
	Print site basis functions, as for 'casm bset –functions'. More...
void	print_aligned_site_basis_funcs (std::shared_ptr< const Structure > prim_ptr, ClexBasis const &clex_basis, Log &out, Index indent_space=6, COORD_TYPE mode=FRAC)
	Print aligned site basis functions, as for 'casm bset –functions –align'. More...
void	write_site_basis_funcs (std::shared_ptr< const Structure > prim_ptr, ClexBasis const &clex_basis, jsonParser &json)
void	print_basis_functions (Log &log, std::shared_ptr< Structure const > const &shared_prim, ClexBasisSpecs const &basis_set_specs, bool align, OrbitPrinterOptions opt=OrbitPrinterOptions())
	Pretty-print basis functions – generate, then print. More...
void	print_basis_functions (Log &log, PrimClex const &primclex, std::string basis_set_name, bool align, OrbitPrinterOptions opt=OrbitPrinterOptions())
	Pretty-print basis functions – read clusters from existing clust.json file. More...
void	print_poscar (Configuration const &configuration, std::ostream &sout)
jsonParser &	to_json (const MappedProperties &prop, jsonParser &json)
jsonParser const &	from_json (MappedProperties &prop, const jsonParser &json)
jsonParser &	to_json (const ScoreMappedProperties &score, jsonParser &json)
jsonParser const &	from_json (ScoreMappedProperties &score, const jsonParser &json)
MappedProperties	copy_apply (PermuteIterator const &op, MappedProperties const &props)
void	write_basis_set_data (std::shared_ptr< Structure const > shared_prim, ProjectSettings const &settings, std::string const &basis_set_name, ClexBasisSpecs const &basis_set_specs, PrimNeighborList &prim_neighbor_list)
Clexulator	make_clexulator (ProjectSettings const &settings, std::string const &basis_set_name, PrimNeighborList &prim_neighbor_list)
template<>
bool	is_guaranteed_for_database_insert (ScelEnumByProps const &enumerator)
	Always true for ScelEnumByProps. More...
xtal::SimpleStructure	make_simple_structure (Supercell const &_scel, ConfigDoF const &_dof, std::vector< DoFKey > const &_which_dofs={})
	Construct from ConfigDoF _dof belonging to provided Supercell _scel. More...
xtal::SimpleStructure	make_simple_structure (Configuration const &_config, std::vector< DoFKey > const &_which_dofs={}, bool relaxed=false)
	Construct SimpleStructure from Configuration. More...
xtal::SimpleStructure	make_simple_structure (Supercell const &_scel, ConfigDoF const &_dof, MappedProperties const &_props, std::vector< DoFKey > const &_which_dofs={}, bool relaxed=false)
	Construct from ConfigDoF _dof belonging to provided Supercell _scel and using calculated properties. More...
std::vector< std::set< Index > >	atom_site_compatibility (xtal::SimpleStructure const &sstruc, Configuration const &_config)
	Determine which sites of a Configuration can host each atom of a SimpleStructure result[i] is set of site indices in. More...
std::vector< std::set< Index > >	mol_site_compatibility (xtal::SimpleStructure const &sstruc, Configuration const &_config)
	Determine which sites of a Configuration can host each molecule of a SimpleStructure result[i] is set of site indices in. More...
std::string	make_supercell_name (Structure const &prim, xtal::Superlattice const &superlattice)
	Make the supercell name from a Superlattice. More...
std::string	make_canonical_supercell_name (Structure const &prim, xtal::Superlattice const &superlattice)
	Make the canonical supercell name from a Superlattice. More...
xtal::Superlattice	make_superlattice_from_supercell_name (Structure const &prim, std::string supercell_name)
	Construct a Superlattice from the supercell name. More...
Supercell &	apply (const SymOp &op, Supercell &scel)
	Apply symmetry operation to Supercell. More...
Supercell	copy_apply (const SymOp &op, const Supercell &scel)
	Copy and apply symmetry operation to Supercell. More...
const Supercell &	make_supercell (const PrimClex &primclex, std::string name)
std::shared_ptr< Supercell >	make_shared_supercell (const PrimClex &primclex, std::string name)
Eigen::Matrix3l	transf_mat (const Lattice &prim_lat, const Lattice &super_lat)
std::string	generate_name (const Eigen::Matrix3l &transf_mat)
	Make hermite normal form name [deprecated]. More...
std::string	scelname (const Structure &prim, const Lattice &superlat)
	Make supercell name name [deprecated]. More...
std::string	canonical_scelname (const Structure &prim, const Lattice &superlat)
	Make canonical supercell name name [deprecated]. More...
template<>
StringAttributeDictionary< Supercell >	make_string_dictionary< Supercell > ()
template<>
BooleanAttributeDictionary< Supercell >	make_boolean_dictionary< Supercell > ()
template<>
IntegerAttributeDictionary< Supercell >	make_integer_dictionary< Supercell > ()
template<>
ScalarAttributeDictionary< Supercell >	make_scalar_dictionary< Supercell > ()
template<>
VectorXiAttributeDictionary< Supercell >	make_vectorxi_dictionary< Supercell > ()
template<>
VectorXdAttributeDictionary< Supercell >	make_vectorxd_dictionary< Supercell > ()
bool	almost_equal (ClusterInvariants const &A, ClusterInvariants const &B, double tol)
	Check if ClusterInvariants are equal. More...
bool	compare (ClusterInvariants const &A, ClusterInvariants const &B, double tol)
	Compare ClusterInvariants. More...
bool	almost_equal (WithinScelClusterInvariants const &A, WithinScelClusterInvariants const &B, double tol)
	Check if WithinScelClusterInvariants are equal. More...
bool	compare (WithinScelClusterInvariants const &A, WithinScelClusterInvariants const &B, double tol)
	Compare WithinScelClusterInvariants. More...
template<typename OutputIterator >
OutputIterator	neighborhood (Structure const &unit, double max_radius, SiteFilterFunction site_filter, OutputIterator result, double xtal_tol)
	Output the neighborhood of UnitCellCoord within max_radius of any sites in unit cell. More...
template<typename OutputIterator >
OutputIterator	neighborhood (IntegralCluster const &phenomenal, double cutoff_radius, SiteFilterFunction site_filter, bool include_phenomenal_sites, OutputIterator result, double xtal_tol)
	Output the neighborhood of sites within cutoff_radius of any sites in the phenomenal. More...
template<typename OrbitType , typename OutputIterator >
OutputIterator	local_orbit_neighborhood (const OrbitType &orbit, OutputIterator result)
	Iterate over all sites in an orbit and insert a UnitCellCoord. More...
template<typename ClusterOrbitIterator , typename OutputIterator >
OutputIterator	local_neighborhood (ClusterOrbitIterator begin, ClusterOrbitIterator end, OutputIterator result)
	Iterate over all sites in all orbits and insert a UnitCellCoord. More...
template<typename OrbitType >
bool	has_local_neighborhood_overlap (std::vector< OrbitType > &local_orbits, const Eigen::Matrix3i &transf_mat)
	Check if periodic images of sites in an orbit are overlapping in supercells defined by the given superlattice transformation matrix. More...
template<typename OrbitType >
std::vector< Eigen::Matrix3i >	viable_supercells (std::vector< OrbitType > &local_orbits, const std::vector< Eigen::Matrix3i > &transf_mat)
	Return superlattice transf. matrices for which has_local_neighborhood_overlap is false. More...
template<typename OrbitType >
OrbitGenerators< OrbitType > &	insert_subcluster_generators (typename OrbitType::Element cluster, OrbitGenerators< OrbitType > &generators)
	Given a cluster, generate all subcluster generators. More...
template<typename OrbitIterator >
std::pair< OrbitIterator, OrbitIterator >	orbit_branch (OrbitIterator begin, OrbitIterator end, Index size)
	Returns the first range containing orbits of the requested orbit branch in the given range of Orbit. More...
template<typename OrbitType , typename OrbitOutputIterator >
OrbitOutputIterator	make_asymmetric_unit (const OrbitBranchSpecs< OrbitType > &specs, OrbitOutputIterator result, std::ostream &status)
	Generate the asymmetric unit, using OrbitBranchSpecs. More...
template<typename OrbitType , typename OrbitInputIterator , typename OrbitOutputIterator >
OrbitOutputIterator	make_next_orbitbranch (OrbitInputIterator begin, OrbitInputIterator end, const OrbitBranchSpecs< OrbitType > &specs, OrbitOutputIterator result, std::ostream &status)
	Use orbits of size n to generate orbits of size n+1. More...
template<typename OrbitBranchSpecsIterator , typename OrbitOutputIterator >
OrbitOutputIterator	make_orbits (OrbitBranchSpecsIterator begin, OrbitBranchSpecsIterator end, const std::vector< IntegralClusterOrbitGenerator > &custom_generators, OrbitOutputIterator result, std::ostream &status)
	Generate orbits of IntegralCluster using OrbitBranchSpecs. More...
template<typename OutputIterator >
OutputIterator	prim_periodic_orbit_neighborhood (const PrimPeriodicOrbit< IntegralCluster > &orbit, OutputIterator result)
	Iterate over all sites in an orbit and insert a UnitCellCoord. More...
template<typename ClusterOrbitIterator , typename OutputIterator >
OutputIterator	prim_periodic_neighborhood (ClusterOrbitIterator begin, ClusterOrbitIterator end, OutputIterator result)
	Iterate over all sites in all orbits and insert a UnitCellCoord. More...
template<typename OutputIterator , typename OrbitType >
OutputIterator	flower_neighborhood (OrbitType const &orbit, OutputIterator result)
	Iterate over all sites in an orbit and insert a UnitCellCoord. More...
template<typename ClusterOrbitIterator , typename OutputIterator >
OutputIterator	flower_neighborhood (ClusterOrbitIterator begin, ClusterOrbitIterator end, OutputIterator result)
	Iterate over all sites in all orbits and insert a UnitCellCoord. More...
template<typename OrbitType >
bool	has_local_neighborhood_overlap (std::vector< OrbitType > const &local_orbits, Eigen::Matrix3i const &transf_mat)
	Check if periodic images of sites in an orbit are overlapping in supercells defined by the given superlattice transformation matrix. More...
template<typename FunctorType >
void	for_all_orbits (ClusterSpecs const &cluster_specs, std::vector< IntegralCluster > const &generating_elements, FunctorType const &f)
template<typename FunctorType >
void	for_all_orbits (ClusterSpecs const &cluster_specs, std::ostream &status, FunctorType const &f)
bool	all_sites_filter (const xtal::Site &site)
	Generate clusters using all Site. More...
bool	alloy_sites_filter (const xtal::Site &site)
	Generate clusters using Site with site_occupant.size() > 1. More...
SiteFilterFunction	dof_sites_filter (const std::vector< DoFKey > &dofs={})
	Generate clusters using Site with specified DoF. More...
ClusterFilterFunction	all_clusters_filter ()
	Accept all clusters. More...
ClusterFilterFunction	max_length_cluster_filter (double max_length)
	Accept clusters with max pair distance less than max_length. More...
CandidateSitesFunction	empty_neighborhood ()
	No sites (for null orbit, or global dof only) More...
CandidateSitesFunction	origin_neighborhood ()
	Only sites in the origin unit cell {b, 0, 0, 0}. More...
CandidateSitesFunction	max_length_neighborhood (double max_length)
CandidateSitesFunction	cutoff_radius_neighborhood (IntegralCluster const &phenomenal, double cutoff_radius, bool include_phenomenal_sites=false)
	Sites within cutoff_radius distance to any site in the phenomenal cluster. More...
jsonParser &	to_json (const IntegralClusterOrbitGenerator &orbit_generator, jsonParser &json)
	Write custom orbit specs to JSON. More...
void	parse (InputParser< std::vector< IntegralClusterOrbitGenerator >> &parser, Structure const &prim)
	Parse custom orbit specs from JSON. More...
void	parse (InputParser< PeriodicMaxLengthClusterSpecs > &parser, const std::shared_ptr< Structure const > &shared_prim, const SymGroup &super_group)
	Parse PeriodicMaxLengthClusterSpecs from JSON. More...
void	parse (InputParser< LocalMaxLengthClusterSpecs > &parser, const std::shared_ptr< Structure const > &shared_prim, const SymGroup &super_group)
	Parse LocalMaxLengthClusterSpecs from JSON. More...
void	parse (InputParser< ClusterSpecs > &parser, const std::shared_ptr< Structure const > &shared_prim)
	Parse PeriodicMaxLengthClusterSpecs or LocalMaxLengthClusterSpecs from JSON & validate. More...
void	parse (InputParser< ClusterSpecs > &parser, const std::shared_ptr< Structure const > &shared_prim, const SymGroup &super_group)
	Parse ClusterSpecs from JSON & validate. More...
jsonParser &	to_json (const PeriodicMaxLengthClusterSpecs &cspecs, jsonParser &json)
	Write PeriodicMaxLengthClusterSpecs to JSON. More...
jsonParser &	to_json (const LocalMaxLengthClusterSpecs &cspecs, jsonParser &json)
	Write LocalMaxLengthClusterSpecs to JSON. More...
jsonParser &	to_json (const ClusterSpecs &cspecs, jsonParser &json)
	Write PeriodicMaxLengthClusterSpecs or LocalMaxLengthClusterSpecs to JSON. More...
jsonParser &	to_json (IntegralCluster const &clust, jsonParser &json)
	Write IntegralCluster to JSON object. More...
void	from_json (IntegralCluster &clust, jsonParser const &json)
	Read from JSON. More...
void	parse (InputParser< IntegralCluster > &parser, Structure const &prim)
	Parse IntegralCluster from JSON. More...
jsonParser &	to_json (const OrbitPrinterOptions &opt, jsonParser &json)
void	from_json (OrbitPrinterOptions &opt, const jsonParser &json)
	Read from JSON. More...
template<typename ClusterOrbitIterator , typename OrbitPrinter >
void	print_clust (ClusterOrbitIterator begin, ClusterOrbitIterator end, Log &out, OrbitPrinter printer)
	Print IntegralCluster orbits. More...
template<typename ClusterOrbitIterator >
void	print_clust (ClusterOrbitIterator begin, ClusterOrbitIterator end, Log &out, const OrbitPrinterOptions &opt=OrbitPrinterOptions())
	Print IntegralCluster orbits. More...
template<typename ClusterOutputIterator , typename SymCompareType >
ClusterOutputIterator	read_clust (ClusterOutputIterator result, const jsonParser &json, const Structure &prim, const SymGroup &generating_grp, const SymCompareType &sym_compare)
	Read JSON containing Orbit<SymCompareType> prototypes. More...
template<typename ClusterOutputIterator >
ClusterOutputIterator	read_clust (ClusterOutputIterator result, const jsonParser &json, const Structure &prim)
	Read JSON containing IntegralCluster prototypes, as IntegralCluster. More...
template<typename ClusterOrbitIterator , typename Printer >
jsonParser &	write_clust (ClusterOrbitIterator begin, ClusterOrbitIterator end, jsonParser &json, Printer printer)
	Write Orbit<SymCompareType> to JSON. More...
template<typename ClusterOrbitIterator >
jsonParser &	write_clust (ClusterOrbitIterator begin, ClusterOrbitIterator end, jsonParser &json, const OrbitPrinterOptions &opt=OrbitPrinterOptions())
	Write Orbit<SymCompareType> to JSON. More...
template<typename ClusterOrbitIterator , typename Printer >
jsonParser &	write_clust (ClusterOrbitIterator begin, ClusterOrbitIterator end, jsonParser &json, Printer printer, const jsonParser &bspecs)
	Write Orbit<SymCompareType> to JSON, including 'bspecs'. More...
template<typename OrbitPrinter , typename Element >
void	print_coordinates (OrbitPrinter &printer, const Element &element, Log &out)
std::ostream &	operator<< (std::ostream &sout, ClusterInvariants const &invariants)
	Print ClusterInvariants. More...
std::ostream &	operator<< (std::ostream &sout, WithinScelClusterInvariants const &invariants)
	Print WithinScelClusterInvariants. More...
std::ostream &	operator<< (std::ostream &sout, const IntegralCluster &clust)
	Print IntegralCluster to stream, using default Printer<IntegralCluster> More...
std::set< Index >	make_cluster_site_indices (IntegralCluster const &cluster, SupercellSymInfo const &sym_info)
	Return site indices of cluster sites. More...
IntegralCluster	make_cluster (std::set< Index > const &cluster_site_indices, Structure const &prim, SupercellSymInfo const &sym_info)
	Return cluster from cluster site indices. More...
template<typename PermuteIteratorIt >
std::vector< Permutation >	make_inverse_permutations (PermuteIteratorIt begin, PermuteIteratorIt end)
	Make inverse permutations. More...
std::set< Index >	permute_cluster_site_indices (Permutation const &inverse_permute, std::set< Index > const &cluster_site_indices)
	Rather than permute values, here we want to permute cluster site indices. More...
template<typename InversePermutationIterator >
std::set< Index >	make_canonical_cluster_site_indices (InversePermutationIterator inverse_permutations_begin, InversePermutationIterator inverse_permutations_end, std::set< Index > const &cluster_site_indices)
template<typename InversePermutationIterator , typename ElementIterator >
std::set< std::set< Index >, ClusterSiteIndicesCompare >	make_orbit_generators_under_periodic_boundary_conditions (SupercellSymInfo const &sym_info, InversePermutationIterator inverse_permutations_begin, InversePermutationIterator inverse_permutations_end, ElementIterator element_begin, ElementIterator element_end)
	Return "within_scel" orbit generators, as sets of cluster site indices. More...
std::string	dry_run_help ()
std::string	coordinate_mode_help ()
std::string	indent_space_help ()
std::string	orbit_print_mode_help ()
std::string	prec_help (std::string what, int default_prec)
std::string	verbosity_help ()
template<typename T >
std::vector< T >	sequence (T first, T last)
template<typename T >
std::vector< T >	sequence (T first, T inc, T last)
template<class T >
Array< T >	array_cat (const Array< T > &A1, const Array< T > &A2)
template<class T >
std::ostream &	operator<< (std::ostream &out, const Array< T > &array_out)
template<typename T >
void	swap (Array< T > &A1, Array< T > &A2)
jsonParser &	to_json (const Permutation &value, jsonParser &json)
void	from_json (Permutation &value, const jsonParser &json)
std::ostream &	operator<< (std::ostream &, const Permutation &)
template<class T >
Tensor< T >	operator* (const T &LHS, const Tensor< T > &RHS)
template<class T >
Tensor< T >	operator* (const SymOp &LHS, const Tensor< T > &RHS)
template<class T >
std::ostream &	operator<< (std::ostream &stream, const Tensor< T > &RHS)
template<class T >
std::istream &	operator>> (std::istream &stream, Tensor< T > &RHS)
template<class T >
T	dot (const Tensor< T > &LHS, const Tensor< T > &RHS)
template<class T >
T	norm (const Tensor< T > &ttens)
template<>
ParsingDictionary< AnisoValTraits >	make_parsing_dictionary< AnisoValTraits > ()
bool	identical (AnisoValTraits const &A, AnisoValTraits const &B)
jsonParser const &	from_json (xtal::SpeciesAttribute &_attr, jsonParser const &json)
	Read SpeciesAttribute from json. More...
jsonParser &	to_json (xtal::SpeciesAttribute const &_attr, jsonParser &json)
	From SpeciesAttribute to json. More...
jsonParser &	to_json (const xtal::AtomPosition &apos, jsonParser &json, Eigen::Ref< const Eigen::Matrix3d > const &cart2frac)
	Print AtomPosition to json after applying affine transformation cart2frac*cart()+trans. More...
void	from_json (xtal::AtomPosition &apos, const jsonParser &json, Eigen::Ref< const Eigen::Matrix3d > const &frac2cart, ParsingDictionary< AnisoValTraits > const &_aniso_val_dict)
	Read AtomPosition from json and then apply affine transformation cart2frac*cart() More...
jsonParser &	to_json (const xtal::Molecule &mol, jsonParser &json, Eigen::Ref< const Eigen::Matrix3d > const &c2f_mat)
void	from_json (xtal::Molecule &mol, const jsonParser &json, Eigen::Ref< const Eigen::Matrix3d > const &f2c_mat, ParsingDictionary< AnisoValTraits > const &_aniso_val_dict)
jsonParser &	to_json (const xtal::Site &value, jsonParser &json, COORD_TYPE coordtype)
void	from_json (xtal::Site &value, const jsonParser &json, xtal::Lattice const &_home, COORD_TYPE coordtype, std::map< std::string, xtal::Molecule > const &mol_map, ParsingDictionary< AnisoValTraits > const &_aniso_val_dict)
xtal::BasicStructure	read_prim (fs::path filename, double xtal_tol, ParsingDictionary< AnisoValTraits > const *_aniso_val_dict=nullptr)
xtal::BasicStructure	read_prim (const jsonParser &json, double xtal_tol, ParsingDictionary< AnisoValTraits > const *_aniso_val_dict)
	Read prim.json. More...
void	write_prim (const xtal::BasicStructure &prim, fs::path filename, COORD_TYPE mode, bool include_va=false)
	Write prim.json to file. More...
void	write_prim (const xtal::BasicStructure &prim, jsonParser &json, COORD_TYPE mode, bool include_va=false)
	Write prim.json as JSON. More...
void	from_json (xtal::BasicStructure &prim, jsonParser const &json, double xtal_tol, ParsingDictionary< AnisoValTraits > const *_aniso_val_dict=nullptr)
jsonParser &	to_json (const xtal::BasicStructure &prim, jsonParser &json, COORD_TYPE mode, bool include_va=false)
template<>
DataFormatterDictionary< std::shared_ptr< const Structure > >	make_attribute_dictionary< std::shared_ptr< const Structure > > ()
jsonParser &	to_json (xtal::SiteDoFSet const &_dof, jsonParser &json)
jsonParser &	to_json (xtal::DoFSet const &_dof, jsonParser &json)
jsonParser &	to_json (const xtal::Lattice &lat, jsonParser &json)
void	from_json (xtal::Lattice &lat, const jsonParser &json, double xtal_tol)
jsonParser &	to_json (xtal::SimpleStructure const &simple_structure, jsonParser &json, std::set< std::string > const &excluded_species={"Va", "VA", "va"}, COORD_TYPE coordinate_mode=CART)
	Output SimpleStructure to JSON. More...
void	from_json (xtal::SimpleStructure &simple_structure, const jsonParser &json)
	Read SimpleStructure from JSON. More...
jsonParser &	to_json (const xtal::ScelEnumProps &props, jsonParser &json)
void	from_json (xtal::ScelEnumProps &props, const jsonParser &json)
	Make a ScelEnumProps object from JSON input. More...
void	parse (InputParser< xtal::ScelEnumProps > &parser)
	Make a ScelEnumProps object from JSON input. More...
jsonParser &	to_json (const xtal::UnitCellCoord &ucc_val, jsonParser &fill_json)
	Print to json as [b, i, j, k]. More...
void	from_json (xtal::UnitCellCoord &fill_value, const jsonParser &read_json)
	Read from json [b, i, j, k]. More...
template<>
std::string	singleline_enum_help< DB::SELECTION_TYPE > ()
template<typename Inserter >
Inserter	select_cluster_sites (ConfigEnumInput const &reference_config_enum_input, std::vector< PrimPeriodicIntegralClusterOrbit > const &orbits, Inserter result)
std::vector< PermuteIterator >	make_invariant_subgroup (ConfigEnumInput const &config_enum_input)
template<typename PermuteIteratorIt >
std::vector< PermuteIterator >	make_invariant_subgroup (ConfigEnumInput const &config_enum_input, PermuteIteratorIt group_begin, PermuteIteratorIt group_end)
bool	is_valid_dof_space (Configuration const &config, DoFSpace const &dof_space)
void	throw_if_invalid_dof_space (Configuration const &config, DoFSpace const &dof_space)
	Throw if !is_valid_dof_space(config, dof_space) More...
Eigen::VectorXd	get_normal_coordinate (Configuration const &config, DoFSpace const &dof_space)
	Return config DoF value as a coordinate in the DoFSpace basis. More...
void	set_dof_value (Configuration &config, DoFSpace const &dof_space, Eigen::VectorXd const &normal_coordinate)
	Set config DoF value from a coordinate in the DoFSpace basis. More...
Index	get_dof_space_dimension (DoFKey dof_key, xtal::BasicStructure const &prim, std::optional< Eigen::Matrix3l > const &transformation_matrix_to_super=std::nullopt, std::optional< std::set< Index >> const &sites=std::nullopt)
	Return dimension of DoFSpace. More...
std::vector< std::string >	make_dof_space_axis_glossary (DoFKey dof_key, xtal::BasicStructure const &prim, std::optional< Eigen::Matrix3l > const &transformation_matrix_to_super=std::nullopt, std::optional< std::set< Index >> const &sites=std::nullopt)
	Make DoFSpace axis glossary. More...
void	make_dof_space_axis_info (DoFKey dof_key, xtal::BasicStructure const &prim, std::optional< Eigen::Matrix3l > const &transformation_matrix_to_super, std::optional< std::set< Index >> const &sites, std::vector< std::string > &axis_glossary, std::optional< std::vector< Index >> &axis_site_index, std::optional< std::vector< Index >> &axis_dof_component)
	Make DoFSpace axis glossary, axis site index, and axis dof component. More...
DoFSpace	make_dof_space (DoFKey dof_key, ConfigEnumInput const &input_state, std::optional< Eigen::MatrixXd > const &basis=std::nullopt)
SymGroupRep const &	make_dof_space_symrep (DoFSpace const &dof_space, SupercellSymInfo const &sym_info, std::vector< PermuteIterator > const &group, MasterSymGroup &symrep_master_group, SymGroupRepID &id)
	Make a SymGroupRep for a DoFSpace. More...
VectorSpaceSymReport	vector_space_sym_report (DoFSpace const &dof_space, SupercellSymInfo const &sym_info, std::vector< PermuteIterator > const &group, bool calc_wedges=false)
	Make VectorSpaceSymReport. More...
SymRepTools_v2::VectorSpaceSymReport	vector_space_sym_report_v2 (DoFSpace const &dof_space, SupercellSymInfo const &sym_info, std::vector< PermuteIterator > const &group, bool calc_wedges=false)
	Make VectorSpaceSymReport. More...
DoFSpace	make_symmetry_adapted_dof_space (DoFSpace const &dof_space, SupercellSymInfo const &sym_info, std::vector< PermuteIterator > const &group, bool calc_wedges, std::optional< VectorSpaceSymReport > &symmetry_report)
	Make DoFSpace with symmetry adapated basis. More...
DoFSpace	make_symmetry_adapted_dof_space_v2 (DoFSpace const &dof_space, SupercellSymInfo const &sym_info, std::vector< PermuteIterator > const &group, bool calc_wedges, std::optional< SymRepTools_v2::VectorSpaceSymReport > &symmetry_report)
	Make DoFSpace with symmetry adapated basis. More...
DoFSpace	exclude_homogeneous_mode_space (DoFSpace const &dof_space)
	Removes the homogeneous mode space from the DoFSpace basis. More...
Eigen::MatrixXd	make_homogeneous_mode_space (DoFSpace const &dof_space)
	Make the homogeneous mode space of a local DoFSpace. More...
template<typename EnumeratorType >
bool	is_guaranteed_for_database_insert (EnumeratorType const &enumerator)
jsonParser &	to_json (ConfigEnumInput const &config_enum_input, jsonParser &json)
	Output ConfigEnumInput to JSON. More...
void	parse (InputParser< ConfigEnumInput > &parser, std::shared_ptr< Structure const > const &shared_prim)
	Read ConfigEnumInput from JSON. More...
void	from_json (std::vector< std::pair< std::string, ConfigEnumInput >> &config_enum_input, jsonParser const &json, std::shared_ptr< Structure const > shared_prim, PrimClex const *primclex, DB::Database< Supercell > &supercell_db, DB::Database< Configuration > &configuration_db)
void	parse (InputParser< xtal::ScelEnumProps > &parser, DB::Database< Supercell > &supercell_db)
std::string	parse_ConfigEnumInput_desc ()
	A string describing the JSON format for parsing named ConfigEnumInput. More...
void	parse (InputParser< std::vector< std::pair< std::string, ConfigEnumInput >>> &parser, std::shared_ptr< Structure const > shared_prim, PrimClex const *primclex, DB::Database< Supercell > &supercell_db, DB::Database< Configuration > &configuration_db)
void	from_json (DoFSpace &dofspace, jsonParser const &json, std::shared_ptr< Structure const > const &shared_prim)
jsonParser &	to_json (DoFSpace const &dofspace, jsonParser &json, std::optional< std::string > const &identifier=std::nullopt, std::optional< ConfigEnumInput > const &input_state=std::nullopt, std::optional< VectorSpaceSymReport > const &sym_report=std::nullopt)
jsonParser &	to_json (DoFSpace const &dofspace, jsonParser &json, std::optional< std::string > const &identifier, std::optional< ConfigEnumInput > const &input_state, std::optional< SymRepTools_v2::VectorSpaceSymReport > const &sym_report)
void	parse (InputParser< AxesCounterParams > &parser, Index dof_space_dimension)
bool	valid_index (Index i)
template<typename Object , typename Transform , typename... Args>
Object &	apply (const Transform &f, Object &obj, Args &&... args)
template<typename Object , typename Transform , typename... Args>
Object	copy_apply (const Transform &f, Object obj, Args &&... args)
template<typename Iterator , typename T , typename BinaryCompare >
Iterator	find (Iterator begin, Iterator end, const T &value, BinaryCompare q)
	Equivalent to std::find(begin, end, value), but with custom comparison. More...
template<typename Iterator , typename T >
Index	find_index (Iterator begin, Iterator end, const T &value)
	Equivalent to std::distance(begin, std::find(begin, end, value)) More...
template<typename Iterator , typename T , typename BinaryCompare >
Index	find_index (Iterator begin, Iterator end, const T &value, BinaryCompare q)
	Equivalent to std::distance(begin, find(begin, end, value, q)) More...
template<typename Container , typename T , typename BinaryCompare >
Index	find_index (const Container &container, const T &value, BinaryCompare q)
	Equivalent to std::distance(container.begin(), find(container.begin(), container.end(), value,q)) More...
template<typename Container , typename T >
Index	find_index (const Container &container, const T &value)
	Equivalent to std::distance(container.begin(), std::find(container.begin(), container.end(), value)) More...
template<typename Iterator , typename UnaryPredicate >
Index	find_index_if (Iterator begin, Iterator end, UnaryPredicate p)
	Equivalent to std::distance(begin, std::find_if(begin, end, p)) More...
template<typename Container , typename UnaryPredicate >
Index	find_index_if (const Container &container, UnaryPredicate p)
	Equivalent to std::distance(container.begin(), std::find_if(container.begin(), container.end(), p)) More...
template<typename Iterator , typename UnaryPredicate >
Index	find_index_if_not (Iterator begin, Iterator end, UnaryPredicate q)
	Equivalent to std::distance(begin, std::find_if_not(begin, end, q)) More...
template<typename Container , typename UnaryPredicate >
Index	find_index_if_not (const Container &container, UnaryPredicate q)
	Equivalent to std::distance(container.begin(), std::find_if_not(container.begin(), container.end(), p)) More...
template<typename Container , typename T >
bool	contains (const Container &container, const T &value)
	Equivalent to container.end() != std::find(container.begin(), container.end(), value) More...
template<typename Container , typename T , typename BinaryCompare >
bool	contains (const Container &container, const T &value, BinaryCompare q)
	Equivalent to container.end() != find(container.begin(), container.end(), value, q) More...
template<typename Container , typename UnaryPredicate >
bool	contains_if (const Container &container, UnaryPredicate p)
	Equivalent to container.end() != std::find_if(container.begin(), container.end(), p) More...
template<typename Container , typename UnaryPredicate >
bool	contains_if_not (const Container &container, UnaryPredicate q)
	Equivalent to container.end() != std::find_if_not(container.begin(), container.end(), q) More...
template<typename Container1 , typename Container2 >
bool	contains_all (const Container1 &container, const Container2 &values)
	Returns true if each elements of 'values' is contained in 'container'. More...
template<typename Container1 , typename Container2 , typename BinaryCompare >
bool	contains_all (const Container1 &container, const Container2 &values, BinaryCompare q)
	Returns true if each elements of 'values' is contained in 'container', using comparison functor 'q'. More...
template<typename Container >
Container::value_type	sum (const Container &container, typename Container::value_type init_val=0)
template<typename T >
T *	end_ptr (std::vector< T > &container)
	Return pointer one past end of vector. Equivalent to convainer.data()+container.size() More...
template<typename T >
T const *	end_ptr (std::vector< T > const &container)
	Return const pointer one past end of vector. Equivalent to convainer.data()+container.size() More...
Index	which_unique_combination (const Array< Index > &input, const Array< Index >::X2 &unique, const Array< Index >::X2 &ind_equiv)
Index	which_unique_combination (const Array< Index > &input, const Array< Index >::X2 &unique)
int	lcm (const Array< int > &series)
	Find least common multiple. More...
ReturnArray< Array< int > >	get_prime_factors (int target)
template<typename IntType >
IntType	multinomial_coeff (const Array< IntType > &exponents)
template<typename IntType >
IntType	multinomial_coeff (const Array< IntType > &exponents, const Array< Index > &sublist)
template<typename T >
bool	almost_equal (const Array< T > &A, const Array< T > &B, double tol=TOL)
template<typename T >
ReturnArray< T >	cum_sum (const Array< T > &arr)
template<typename Derived >
ReturnArray< Index >	partition_distinct_values (const Eigen::MatrixBase< Derived > &value, double tol=TOL)
bool	float_lexicographical_compare (const Eigen::Ref< const Eigen::MatrixXd > &A, const Eigen::Ref< const Eigen::MatrixXd > &B, double tol)
	Floating point lexicographical comparison with tol. More...
template<typename Derived >
bool	colmajor_lex_compare (const Eigen::MatrixBase< Derived > &A, const Eigen::MatrixBase< Derived > &B, double tol)
	Floating point lexicographical comparison with tol. More...
template<typename Derived >
Derived::PlainObject	reduced_column_echelon (Eigen::MatrixBase< Derived > const &M, double _tol)
Eigen::VectorXd	eigen_vector_from_string (const std::string &tstr, const int &size)
double	hungarian_method (const Eigen::MatrixXd &cost_matrix, std::vector< Index > &optimal_assignments, const double _tol)
template<typename Derived >
Derived::Scalar *	end_ptr (Eigen::PlainObjectBase< Derived > &container)
	Return pointer one past end of vector. Equivalent to convainer.data()+container.size() More...
template<typename Derived >
Derived::Scalar const *	end_ptr (Eigen::PlainObjectBase< Derived > const &container)
	Return const pointer one past end of vector. Equivalent to convainer.data()+container.size() More...
void	get_Hermitian (Eigen::MatrixXcd &original_mat, Eigen::MatrixXcd &hermitian_mat, Eigen::MatrixXcd &antihermitian_mat)
bool	is_Hermitian (Eigen::MatrixXcd &mat)
std::pair< Eigen::MatrixXi, Eigen::MatrixXi >	hermite_normal_form (const Eigen::MatrixXi &M)
	Return the hermite normal form, M == H*V. More...
double	angle (const Eigen::Ref< const Eigen::Vector3d > &a, const Eigen::Ref< const Eigen::Vector3d > &b)
	Get angle, in radians, between two vectors on range [0,pi]. More...
double	signed_angle (const Eigen::Ref< const Eigen::Vector3d > &a, const Eigen::Ref< const Eigen::Vector3d > &b, const Eigen::Ref< const Eigen::Vector3d > &pos_ref)
	signed angle, in radians, between -pi and pi that describe separation in direction of two vectors More...
Eigen::MatrixXd	pretty (const Eigen::MatrixXd &M, double tol)
	Round entries that are within tol of being integer to that integer value. More...
template<typename Derived >
Derived::Scalar	triple_product (const Derived &vec0, const Derived &vec1, const Derived &vec2)
template<typename Derived >
bool	is_integer (const Eigen::MatrixBase< Derived > &M, double tol)
	Check if Eigen::Matrix is integer. More...
template<typename Derived >
bool	is_unimodular (const Eigen::MatrixBase< Derived > &M, double tol)
	Check if Eigen::Matrix is unimodular. More...
template<typename Derived >
bool	is_diagonal (const Eigen::MatrixBase< Derived > &M, double tol=TOL)
	Check if Eigen::Matrix is diagonal. More...
template<typename Derived >
Eigen::CwiseUnaryOp< decltype(Local::round_l< typename Derived::Scalar >), const Derived >	round (const Eigen::MatrixBase< Derived > &val)
	Round Eigen::MatrixXd. More...
template<typename Derived >
Eigen::CwiseUnaryOp< decltype(Local::iround_l< typename Derived::Scalar >), const Derived >	iround (const Eigen::MatrixBase< Derived > &val)
	Round Eigen::MatrixXd to Eigen::MatrixXi. More...
template<typename Derived >
Eigen::CwiseUnaryOp< decltype(Local::lround_l< typename Derived::Scalar >), const Derived >	lround (const Eigen::MatrixBase< Derived > &val)
	Round Eigen::MatrixXd to Eigen::MatrixXl. More...
template<typename Derived >
Derived::Scalar	matrix_minor (const Eigen::MatrixBase< Derived > &M, int row, int col)
	Return the minor of integer Matrix M element row, col. More...
template<typename Derived >
Eigen::Matrix< typename Derived::Scalar, Derived::RowsAtCompileTime, Derived::ColsAtCompileTime >	cofactor (const Eigen::MatrixBase< Derived > &M)
	Return cofactor matrix. More...
template<typename Derived >
Eigen::Matrix< typename Derived::Scalar, Derived::RowsAtCompileTime, Derived::ColsAtCompileTime >	adjugate (const Eigen::MatrixBase< Derived > &M)
	Return adjugate matrix. More...
template<typename Derived >
Eigen::Matrix< typename Derived::Scalar, Derived::RowsAtCompileTime, Derived::ColsAtCompileTime >	inverse (const Eigen::MatrixBase< Derived > &M)
	Return the integer inverse matrix of an invertible integer matrix. More...
template<typename DerivedIn , typename DerivedOut >
void	smith_normal_form (const Eigen::MatrixBase< DerivedIn > &M, Eigen::MatrixBase< DerivedOut > &U, Eigen::MatrixBase< DerivedOut > &S, Eigen::MatrixBase< DerivedOut > &V)
	Return the smith normal form, M == U*S*V. More...
Eigen::Matrix3d	polar_decomposition (Eigen::Matrix3d const &mat)
std::vector< Eigen::Matrix3i >	_unimodular_matrices (bool positive, bool negative, int range=1)
const std::vector< Eigen::Matrix3i > &	positive_unimodular_matrices ()
const std::vector< Eigen::Matrix3i > &	negative_unimodular_matrices ()
template<int range = 1>
const std::vector< Eigen::Matrix3i > &	unimodular_matrices ()
int	round (double val)
template<typename T >
T	min (const T &A, const T &B)
template<typename T >
T	max (const T &A, const T &B)
template<typename T , typename std::enable_if< std::is_floating_point< T >::value, T >::type * = nullptr>
bool	almost_zero (const T &val, double tol=TOL)
	If T is not integral, use std::abs(val) < tol;. More...
template<typename T , typename std::enable_if< std::is_floating_point< T >::value, T >::type * = nullptr>
bool	almost_zero (const std::complex< T > &val, double tol=TOL)
	If std::complex<T>, use std::abs(val) < tol;. More...
template<typename T , typename std::enable_if<!std::is_integral< T >::value, T >::type * = nullptr>
bool	almost_equal (const T &val1, const T &val2, double tol=TOL)
	If T is not integral, use almost_zero(val1 - val2, tol);. More...
template<typename T , typename std::enable_if< std::is_floating_point< T >::value, T >::type * = nullptr>
bool	compare (const T &A, const T &B, double tol)
	Floating point comparison with tol, return A < B. More...
template<class InputIt1 , class InputIt2 >
bool	float_lexicographical_compare (InputIt1 first1, InputIt1 last1, InputIt2 first2, InputIt2 last2, double tol)
	Floating point lexicographical comparison with tol. More...
template<typename T , typename std::enable_if< std::is_integral< T >::value, T >::type * = nullptr>
int	sgn (T val)
template<typename T , typename std::enable_if< std::is_floating_point< T >::value, T >::type * = nullptr>
int	float_sgn (T val, double compare_tol=TOL)
template<typename IntType >
IntType	nchoosek (IntType n, IntType k)
template<typename IntType >
std::vector< IntType >	index_to_kcombination (IntType ind, IntType k)
int	dl_string_dist (const std::string &a, const std::string &b)
	Computes the Damerescau-Levenshtein distance – the number of edits (deletions, insertions, transpositions) to go from string 'a' to string 'b'. More...
double	ran0 (int &idum)
int	gcf (int i1, int i2)
	Find greatest common factor. More...
int	lcm (int i1, int i2)
	Find least common multiple. More...
template<typename IntType >
IntType	extended_gcf (IntType i1, IntType i2, IntType &p1, IntType &p2)
	Calculate greatest common factor of two integers, and bezout coefficients. More...
double	gaussian (double a, double x, double b, double c)
double	gaussian_moment (int expon, double sigma)
double	gaussian_moment (int expon, double sigma, double x0)
void	nearest_rational_number (double val, long &numerator, long &denominator, double tol=TOL)
std::string	irrational_to_tex_string (double val, int lim, int max_pow=2)
std::string	to_sequential_string (Index i, Index max_i, char prepend_char='0')
int	mod (int a, int b)
double	cuberoot (double number)
template<typename IteratorType >
void	swap (FilterIterator< IteratorType > &a, FilterIterator< IteratorType > &b)
	Definitions. More...
template<typename IteratorType , typename DataObject >
FilterIterator< IteratorType >	filter_begin (IteratorType const &it, IteratorType const &it_end, std::function< bool(typename FilterIterator< IteratorType >::reference)> filter_function)
template<typename IteratorType >
FilterIterator< IteratorType >	filter_end (IteratorType const &it_end)
template<typename T >
ParsingDictionary< T >	make_parsing_dictionary ()
Eigen::MatrixXd	pad (const Eigen::MatrixXd &M, int n)
	Construct a matrix consisting of blocks M and Identity(n,n) More...
template<typename T >
std::string	type_name ()
template<typename Element , typename OpIterator , typename SymCompareType , typename OpOutputIterator >
OpOutputIterator	make_invariant_subgroup (Element const &element, OpIterator group_begin, OpIterator group_end, SymCompareType const &sym_compare, OpOutputIterator result)
	Construct the subgroup that leaves an element unchanged. More...
template<typename Element , typename SymCompareType , typename OutputIterator >
OutputIterator	make_invariant_subgroup (Element const &element, PermuteIterator permute_begin, PermuteIterator permute_end, SymCompareType const &sym_compare, OutputIterator result)
	Construct the subgroup (PermuteIterator) that leaves an element unchanged. More...
template<typename Element , typename SymCompareType >
SymGroup	make_invariant_subgroup (const Element &element, const SymGroup &generating_grp, const SymCompareType &sym_compare)
	Construct the subgroup that leaves an element unchanged. More...
template<typename OrbitType >
SymGroup	make_invariant_subgroup (const OrbitType &orbit, Index element_index=0)
	Construct the subgroup that leaves an element of the orbit unchanged. More...
template<>
DataFormatterDictionary< SupercellSymInfo >	make_attribute_dictionary< SupercellSymInfo > ()
void	write_symop (SymGroup const &grp, Index i, jsonParser &j)
void	write_symgroup (SymGroup const &grp, jsonParser &json)
void	write_basis_permutation_rep (SymGroup const &grp, jsonParser &group_rep_json, SymGroupRepID symgrouprep_id)
	Describes how integral site coordinates transform under application of symmetry. More...
void	write_occ_permutation_rep (SymGroup const &grp, jsonParser &json, std::vector< SymGroupRepID > occupant_symrep_IDs)
void	write_matrix_rep (SymGroupRepHandle const &grp, jsonParser &json)
jsonParser &	to_json (const SymInfoOptions &opt, jsonParser &json)
void	from_json (SymInfoOptions &opt, const jsonParser &json)
	Read from JSON. More...
void	to_json (const SymInfo &info, jsonParser &json)
	Adds to existing JSON object. More...
jsonParser &	to_json (SymRepTools::IrrepInfo const &irrep, jsonParser &json)
jsonParser &	to_json (SymRepTools::SubWedge const &wedge, jsonParser &json)
jsonParser &	to_json (VectorSpaceSymReport const &obj, jsonParser &json)
jsonParser &	to_json (SymRepTools_v2::IrrepInfo const &irrep, jsonParser &json)
jsonParser &	to_json (SymRepTools_v2::SubWedge const &wedge, jsonParser &json)
jsonParser &	to_json (SymRepTools_v2::VectorSpaceSymReport const &obj, jsonParser &json)
void	print_sym_info (Log &log, const SymInfo &info, SymInfoOptions opt=SymInfoOptions())
	Print SymInfo. More...
std::string	to_string (const SymInfo &info, SymInfoOptions opt=SymInfoOptions())
	Print SymInfo to string. More...
std::string	to_brief_unicode (const SymInfo &info, SymInfoOptions opt=SymInfoOptions())
	Print symmetry symbol to string. More...
std::string	description (const SymOp &op, const xtal::Lattice &lat, SymInfoOptions opt=SymInfoOptions())
	Print SymInfo to string. More...
void	description (Log &log, const SymGroup &g, const xtal::Lattice &lat, SymInfoOptions opt=SymInfoOptions())
	Print SymGroup with matrix / tau. More...
std::string	brief_description (const SymOp &op, const xtal::Lattice &lat, SymInfoOptions opt=SymInfoOptions())
	Print SymInfo to brief string. More...
void	brief_description (Log &log, const SymGroup &g, const xtal::Lattice &lat, SymInfoOptions opt=SymInfoOptions())
	Print SymGroup with brief string. More...
SymRepTools_v2::IrrepDecomposition	make_irrep_decomposition (SymGroupRep const &rep, SymGroup const &head_group, Eigen::MatrixXd const &_init_subspace, bool allow_complex)
	Make an IrrepDecompotion using CASM::SymGroupRep and CASM::SymGroup. More...
template<typename GeneratorIterator , typename SymCompareType , typename OrbitOutputIterator >
OrbitOutputIterator	make_orbits (GeneratorIterator gen_begin, GeneratorIterator gen_end, const SymGroup &generating_group, const SymCompareType &sym_compare, OrbitOutputIterator result)
	Iterator over Generators (potential prototypes) and insert resulting orbits into 'result' iterator. More...
template<typename OrbitIterator , typename Element >
OrbitIterator	find_orbit (OrbitIterator begin, OrbitIterator end, Element e)
	Find orbit containing an element in a range of Orbit. More...
template<typename OrbitIterator >
PrototypeIterator< OrbitIterator >	prototype_iterator (OrbitIterator orbit_it)
	Convert an Orbit iterator to a prototype iterator. More...
template<typename OrbitIterator >
InvariantsIterator< OrbitIterator >	invariants_iterator (OrbitIterator orbit_it)
	Convert an Orbit iterator to an invariants iterator. More...
template<typename SymCompareType >
std::vector< Orbit< SymCompareType > >	generate_orbits (std::vector< typename SymCompareType::Element > const &generating_elements, SymGroup const &generating_group, SymCompareType const &sym_compare)
	Construct orbits from a vector of generating elements. More...
template<typename GroupOpIterator , typename SubgroupOpIterator >
MakeSubOrbitGenerators< GroupOpIterator, SubgroupOpIterator >	make_suborbit_generators_f (GroupOpIterator group_begin, GroupOpIterator group_end, SubgroupOpIterator subgroup_begin, SubgroupOpIterator subgroup_end)
template<typename GroupOpIterator , typename SubgroupOpIterator , typename ElementIterator , typename SymCompareType , typename ElementOutputIterator >
ElementOutputIterator	make_suborbit_generators (GroupOpIterator group_begin, GroupOpIterator group_end, SubgroupOpIterator subgroup_begin, SubgroupOpIterator subgroup_end, ElementIterator element_begin, ElementIterator element_end, SymCompareType const &sym_compare, ElementOutputIterator result)
std::string	hermite_normal_form_name (const Eigen::Matrix3l &matrix)
Eigen::Matrix3l	make_hermite_normal_form (std::string hermite_normal_form_name)
std::string	make_supercell_name (SymGroup const &point_group, Lattice const &prim_lattice, Lattice const &supercell_lattice)
	Make the supercell name. More...
std::string	make_canonical_supercell_name (SymGroup const &point_group, Lattice const &prim_lattice, Lattice const &supercell_lattice)
	Make the canonical supercell name. More...
xtal::Superlattice	make_superlattice_from_supercell_name (SymGroup const &factor_group, Lattice const &prim_lattice, std::string supercell_name)
	Construct a Superlattice from the supercell name. More...
std::pair< MasterSymGroup, SymGroupRepID >	make_collective_dof_symrep (std::set< Index > const &site_indices, SupercellSymInfo const &_syminfo, DoFKey const &_key, std::vector< PermuteIterator > const &_group)
	Make the matrix representation for group '_group' describing the transformation of DoF '_key' among a subset of sites. More...
std::map< std::string, std::string >	point_group_info (SymGroup const &group)
	return dictionary of point group info: result["centricity"] : "Centric" or "Acentric" result["crystal_system"] : cubic, hexagonal, etc result["international_name"] : Hermann-Mauguin point group name result["name"] : Schoenflies name result["latex_name"] : Schoenflies name (in LaTeX markup) result["space_group_range"] : range of possible space group numbers If group is magnetic, then point group name has form "G1(G2)" where G1 is point group name of entire group (with time-reversal turned of) and G2 is the subgroup of operations that do not effect time reversal. If G1 is identical to G2 (every operation has a time-reversed partner), then the name is G1' does not work for icosahedral groups More...
SymGroup	molecular_point_group (std::map< int, std::vector< Eigen::Vector3d >> coord_map)
MasterSymGroup	make_master_sym_group (SymGroup const &_group, Lattice const &_lattice)
bool	compare_periodic (const SymOp &a, const SymOp &b, const Lattice &lat, PERIODICITY_TYPE periodicity, double _tol)
SymOp	within_cell (const SymOp &a, const Lattice &lat, PERIODICITY_TYPE periodicity)
const SymOp::matrix_type &	get_matrix (const SymOp &op)
const SymOp::vector_type &	get_translation (const SymOp &op)
bool	get_time_reversal (const SymOp &op)
void	print_matrix_tau_col (Log &log, const SymOp &op, Index prec)
	Print formatted SymOp matrix and tau. More...
VectorSpaceSymReport	vector_space_sym_report (SymGroupRep const &_rep, SymGroup const &head_group, Eigen::Ref< const Eigen::MatrixXd > const &_subspace, bool calc_wedges=false)
	Construct the VectorSpaceSymReport for. More...
multivector< Eigen::VectorXcd >::X< 2 >	special_irrep_directions (SymGroupRep const &_rep, SymGroup const &head_group, double vec_compare_tol)
	Assuming that _rep is an irrep of head_group, find high-symmetry directions throws if _rep is not an irrep. More...
multivector< Eigen::VectorXcd >::X< 2 >	special_irrep_directions (SymGroupRep const &_rep, SymGroup const &head_group, Eigen::Ref< const Eigen::MatrixXcd > const &_subspace, double vec_compare_tol, bool all_subgroups=false)
	Assuming that _rep is an irrep of head_group, find high-symmetry directions throws if _rep is not an irrep. More...
SymRepTools::Symmetrizer	irrep_symmetrizer (SymGroupRep const &_rep, const SymGroup &head_group, double vec_compare_tol)
SymRepTools::Symmetrizer	irrep_symmetrizer (SymGroupRep const &_rep, const SymGroup &head_group, Eigen::Ref< const Eigen::MatrixXcd > const &_subspace, double vec_compare_tol)
Index	num_blocks (SymGroupRep const &_rep, const SymGroup &head_group)
	counts number of nonzero blocks in matrix representation of head_group as specified by _rep Reveals number of invariant subspaces (with respect to head_group) that comprise the vector space supporting _rep More...
Eigen::MatrixXd	full_trans_mat (std::vector< SymRepTools::IrrepInfo > const &irreps)
	Assumes that irreps are real, and concatenates their individual trans_mats to form larger trans_mat. More...
multivector< Eigen::VectorXd >::X< 3 >	special_total_directions (SymGroupRep const &_rep, const SymGroup &head_group)
	finds high-symmetry directions within vector space supporting _rep, wrt symmetry of head_group More...
std::vector< std::vector< Eigen::MatrixXd > >	special_subspaces (SymGroupRep const &_rep, const SymGroup &head_group)
	finds high-symmetry subspaces within vector space supporting _rep, wrt symmetry of head_group High-symmetry subspaces are closed under the action of a nontrivial subgroup of head_group, without spanning the entire vector space supporting _rep More...
std::vector< SymGroupRepID >	irrep_IDs (SymGroupRep const &_rep, const SymGroup &head_group)
	Find irrep decomposition of _rep wrt group head_group and returns it as a list of SymGroupRepIDs corresponding to representtions of master_group. More...
bool	is_irrep (SymGroupRep const &_rep, const SymGroup &head_group)
	Returns true if _rep is irreducible wrt head_group (does not use character table information) More...
Eigen::MatrixXd	irrep_trans_mat (SymGroupRep const &_rep, const SymGroup &head_group)
	Finds the transformation matrix that block-diagonalizes this representation of head_group into irrep blocks It does not rely on the character table, but instead utilizes a brute-force method This routine additionally orients the resulting basis vectors along high-symmetry directions of the vector space on which they are defined. More...
std::pair< Eigen::MatrixXd, std::vector< Eigen::VectorXcd > >	irrep_trans_mat_and_characters (SymGroupRep const &_rep, const SymGroup &head_group, SymRepTools::SymmetrizerFunction symmetrizer_func)
	Finds the transformation matrix that block-diagonalizes this representation of head_group into irrep blocks It does not rely on the character table, but instead utilizes a brute-force method. More...
std::vector< SymRepTools::IrrepInfo >	irrep_decomposition (SymGroupRep const &_rep, SymGroup const &head_group, bool allow_complex)
	Finds irreducible subspaces that comprise an underlying subspace It does not rely on the character table, but instead utilizes a brute-force method. More...
std::vector< SymRepTools::IrrepInfo >	irrep_decomposition (SymGroupRep const &_rep, SymGroup const &head_group, Eigen::Ref< const Eigen::MatrixXd > const &_subspace, bool allow_complex)
	Finds irreducible subspaces that comprise an underlying subspace It does not rely on the character table, but instead utilizes a brute-force method. More...
std::vector< SymRepTools::IrrepInfo >	irrep_decomposition (SymGroupRep const &_rep, SymGroup const &head_group, SymRepTools::SymmetrizerFunction const &symmetrizer_func, bool allow_complex)
	Finds irreducible subspaces that comprise an underlying subspace It does not rely on the character table, but instead utilizes a brute-force method. More...
std::vector< SymRepTools::IrrepInfo >	irrep_decomposition (SymGroupRep const &_rep, SymGroup const &head_group, SymRepTools::SymmetrizerFunction const &symmetrizer_func, Eigen::MatrixXd subspace, bool allow_complex)
	Finds irreducible subspaces that comprise an underlying subspace It does not rely on the character table, but instead utilizes a brute-force method. More...
SymGroupRep	subset_permutation_rep (const SymGroupRep &permute_rep, const std::vector< std::set< Index >> &subsets)
SymGroupRep	permuted_direct_sum_rep (const SymGroupRep &permute_rep, const std::vector< SymGroupRep const * > &sum_reps)
SymGroupRep	kron_rep (const SymGroupRep &LHS, const SymGroupRep &RHS)
template<typename GeneratorIterator , typename SymCompareType , typename OrbitOutputIterator >
OrbitOutputIterator	make_orbits (GeneratorIterator gen_begin, GeneratorIterator gen_end, const SymGroup &generating_group, const SymCompareType &sym_compare, OrbitOutputIterator result, std::ostream &status)
	Generate Orbit<IntegralVector> using OrbitBranchSpecs. More...
SymRepTools_v2::VectorSpaceSymReport	vector_space_sym_report_v2 (SymGroupRep const &rep, SymGroup const &head_group, Eigen::MatrixXd const &subspace, bool calc_wedges=false)
	Construct VectorSpaceSymReport, using CASM::SymGroupRep and CASM::SymGroup. More...
bool	almost_equal (VectorInvariants const &A_invariants, VectorInvariants const &B_invariants, double tol)
	Check if VectorInvariants are equal. More...
bool	compare (VectorInvariants const &A_invariants, VectorInvariants const &B_invariants, double tol)
	Compare ClusterInvariants. More...
bool	almost_equal (SymRepTools_v2::VectorInvariants const &A_invariants, SymRepTools_v2::VectorInvariants const &B_invariants, double tol)
bool	compare (SymRepTools_v2::VectorInvariants const &A_invariants, SymRepTools_v2::VectorInvariants const &B_invariants, double tol)
std::string	include_path (const fs::path &dir)
std::string	link_path (const fs::path &dir)
const std::string &	version ()
void	display (std::ostream &sout, const CompositionAxes &comp_axes)
void	throw_if_no_root_dir (DirectoryStructure const &dir)
void	parse (InputParser< ConfigEnumRandomLocalParams > &parser, MTRand &mtrand)
void	parse (InputParser< ConfigEnumRandomOccupationsParams > &parser, MTRand &mtrand)
void	parse (InputParser< ConfigEnumSiteDoFsParams > &parser, ConfigEnumInput const &initial_state, AxesCounterParams &axes_params, bool sym_axes_option, bool exclude_homogeneous_modes)
	Parse the ConfigEnumSiteDoFsParams JSON input. More...
void	require_all_input_have_the_same_number_of_selected_sites (InputParser< std::vector< std::pair< std::string, ConfigEnumInput >>> &parser)
void	parse (InputParser< ConfigEnumStrainParams > &parser, ConfigEnumInput const &initial_state, AxesCounterParams &axes_params, bool sym_axes_option)
void	require_valid_sub_configurations (ParentInputParser &parser, DB::Selection< Configuration > const &config_selection, Supercell const &supercell)
template std::pair< enum_it_type, runtimelib_it_type >	load_enumerator_plugins (ProjectSettings const &set, enum_it_type enum_it, runtimelib_it_type lib_it)
std::tuple< std::string, std::string, BasicStructure >	standardize_prim (BasicStructure const &prim, bool force)
void	print_runtime_lib_options_help (std::ostream &sout)
void	print_monte_help (std::ostream &sout, const po::options_description &desc)
void	print_monte_desc (std::ostream &sout, const po::options_description &desc)
template<typename MCType >
int	_initial_POSCAR (PrimClex &primclex, const CommandArgs &args, const Completer::MonteOption &monte_opt)
template<typename MCType >
int	_final_POSCAR (PrimClex &primclex, const CommandArgs &args, const Completer::MonteOption &monte_opt)
template<typename MCType >
int	_traj_POSCAR (PrimClex &primclex, const CommandArgs &args, const Completer::MonteOption &monte_opt)
template<typename MCType >
int	_driver (PrimClex &primclex, const CommandArgs &args, const Completer::MonteOption &monte_opt)
int	_run_GrandCanonical (PrimClex &primclex, const Monte::MonteSettings &monte_settings, const CommandArgs &args, const Completer::MonteOption &monte_opt)
int	_run_Canonical (PrimClex &primclex, const Monte::MonteSettings &monte_settings, const CommandArgs &args, const Completer::MonteOption &monte_opt)
int	perturb_command (const CommandArgs &args)
template<typename DataObject >
void	_update_query_dict (DataFormatterDictionary< QueryData< DataObject >> &query_dict)
template<>
void	_update_query_dict< Configuration > (DataFormatterDictionary< QueryData< Configuration >> &query_dict)
template<typename DataObject >
void	_query_equivalents (DataFormatter< QueryData< DataObject >> &formatter, jsonParser &json, PrimClex const &primclex, DataObject const &object)
template<>
void	_query_equivalents (DataFormatter< QueryData< Configuration >> &formatter, jsonParser &json, PrimClex const &primclex, Configuration const &object)
template<typename DataObject >
void	_query_equivalents (DataFormatter< QueryData< DataObject >> &formatter, std::ostream &stream, PrimClex const &primclex, DataObject const &object)
template<>
void	_query_equivalents (DataFormatter< QueryData< Configuration >> &formatter, std::ostream &stream, PrimClex const &primclex, Configuration const &object)
void	status_unitialized (const CommandArgs &args)
void	composition_unselected (const CommandArgs &args)
void	supercells_ungenerated (const CommandArgs &args)
void	configs_ungenerated (const CommandArgs &args)
void	configs_uncalculated (const CommandArgs &args)
void	references_unset (const CommandArgs &args)
void	bset_uncalculated (const CommandArgs &args)
void	eci_uncalculated (const CommandArgs &args)
void	montecarlo (const CommandArgs &args)
void	write_prim_symmetry_impl (Structure const &prim, DirectoryStructure const &dir, COORD_TYPE coordtype, bool brief, Log &log, bool print_lattice_point_group, bool print_factor_group, bool print_crystal_point_group)
template<>
DoFType::TraitsDictionary	make_parsing_dictionary< DoFType::Traits > ()
std::vector< std::string >	parse_label_template (std::string const &_template)
std::string::const_iterator	end_of_literal (std::string::const_iterator it, std::string::const_iterator end_it)
template<bool IsConst>
void	swap (jsonParserIterator< IsConst > &a, jsonParserIterator< IsConst > &b)
template void	swap< true > (jsonParserIterator< true > &, jsonParserIterator< true > &)
template void	swap< false > (jsonParserIterator< false > &, jsonParserIterator< false > &)
std::vector< int >	rand_unique (int n, int c, MTRand &mtrand)
	Choose c random unique numbers in [0,n) More...
template<typename ConfigType >
std::string	pos_path (const ConfigType &config)
Eigen::MatrixXd	_composition_space (const ParamComposition::AllowedOccupants &_allowed_occs, double tol)
	Non-orthogonal composition space. More...
template<>
VectorXiAttributeDictionary< Configuration >	make_vectorxi_dictionary< Configuration > ()
template<>
DataFormatterDictionary< Configuration, BaseValueFormatter< jsonParser, Configuration > >	make_json_dictionary< Configuration > ()
std::ostream &	operator<< (std::ostream &sout, const Configuration &c)
template<>
ChemicalReferenceState	from_json (const jsonParser &json)
	Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'. More...
BasicStructure	read_prim (ProjectSettings const &project_settings)
std::shared_ptr< Structure const >	read_shared_prim (ProjectSettings const &project_settings)
Eigen::Matrix3l	transf_mat (const Lattice &prim_lat, const Lattice &super_lat, double tol)
	Make superlattice transformation matrix [deprecated]. More...
template<>
DataFormatterDictionary< Supercell, BaseValueFormatter< jsonParser, Supercell > >	make_json_dictionary< Supercell > ()
std::vector< std::string >	make_axis_glossary (DoFKey dof_key, xtal::BasicStructure const &prim, std::optional< Eigen::Matrix3l > const &transformation_matrix_to_super, std::optional< std::set< Index >> const &sites)
	The axis_glossary gives names to an un-symmetrized coordinate system. More...
void	parse (InputParser< DoFSpace > &parser, std::shared_ptr< Structure const > const &shared_prim)
void	parse_axes_counter_range (InputParser< AxesCounterParams > &parser)
void	parse_axes_from_object (InputParser< AxesCounterParams > &parser, Index dof_space_dimension)
void	parse_axes_from_array (InputParser< AxesCounterParams > &parser, Index dof_space_dimension)
void	parse_dof_space_axes (InputParser< AxesCounterParams > &parser, Index dof_space_dimension)
Index	which_unique_combination (const Array< Index > &input, const Array< Array< Index > > &unique, const Array< Array< Index > > &ind_equiv)
Index	which_unique_combination (const Array< Index > &input, const Array< Array< Index > > &unique)
std::string	sym_line (const xtal::Coordinate &axis, const xtal::Coordinate &point, SymInfoOptions opt)
	Use axis and invariant point to return line in '0, y, 0'-type notation. More...
std::string	sym_plane (const xtal::Coordinate &v1, const xtal::Coordinate &v2, const xtal::Coordinate &point, SymInfoOptions opt)
	Use two perpendicular vectors in plane and invariant point to return plane in 'x, y, 0'-type notation. More...
std::string	sym_plane (const xtal::Coordinate &axis, const xtal::Coordinate &point, SymInfoOptions opt)
	Use axis and invariant point to return plane in 'x, y, 0'-type notation. More...
template SymGroup	make_sym_group (PermuteIterator begin, PermuteIterator end, const Lattice &supercell_lattice)
template SymGroup	make_sym_group (std::vector< PermuteIterator >::const_iterator begin, std::vector< PermuteIterator >::const_iterator end, const Lattice &supercell_lattice)
template SymGroup	make_sym_group (std::vector< PermuteIterator >::iterator begin, std::vector< PermuteIterator >::iterator end, const Lattice &supercell_lattice)
template SymGroup	make_point_group (PermuteIterator begin, PermuteIterator end, const Lattice &supercell_lattice)
template SymGroup	make_point_group (std::vector< PermuteIterator >::const_iterator begin, std::vector< PermuteIterator >::const_iterator end, const Lattice &supercell_lattice)
template SymGroup	make_point_group (std::vector< PermuteIterator >::iterator begin, std::vector< PermuteIterator >::iterator end, const Lattice &supercell_lattice)
void	swap (PermuteIterator &a, PermuteIterator &b)
std::vector< Permutation >	make_translation_permutations (const Eigen::Matrix3l &transformation_matrix, int basis_sites_in_prim)
SymGroupRepID	make_permutation_representation (const SymGroup &group, const xtal::UnitCellCoordIndexConverter &bijk_index_converter, const Lattice &prim_lattice, const SymGroupRepID &prim_symrep_ID)
std::string	recast (ARG_TYPE atype)
void	subopt_test ()
void	opt_test ()
void	opt_test2 ()
void	po_test ()
Option	generate_option (std::string postfix, char beginshort)
void	engine_test ()
void	argtype_test ()
void	property_test ()
fs::path	find_casmroot (const fs::path &cwd)
fs::path	relative_casmroot (const fs::path &cwd)
void	recurs_rm_files (fs::path p, bool dry_run, Log &log)
	Remove files recursively. More...
Index	recurs_cp_files (const fs::path &from_dir, const fs::path &to_dir, bool dry_run, Log &log)
	Copy files recursively, and returns a count of copied files. More...
void	throw_if_no_basis_set_specs (std::string basis_set_name, DirectoryStructure const &dir)
void	throw_if_no_clexulator_src (std::string project_name, std::string basis_set_name, DirectoryStructure const &dir)
template<typename K , typename V >
jsonParser &	to_json (const std::map< K, V > &map, jsonParser &json)
	Converts to a JSON object. More...
template<typename K , typename V >
void	from_json (std::map< K, V > &map, const jsonParser &json)
template<typename T , typename... Args>
jsonParser &	to_json (const std::map< std::string, T > &map, jsonParser &json, Args &&... args)
	Converts to a JSON object. More...
template<typename T , typename... Args>
void	from_json (std::map< std::string, T > &map, const jsonParser &json, Args &&... args)
template<typename T , typename... Args>
jsonParser &	to_json (const std::vector< T > &vec, jsonParser &json, Args &&... args)
	Converts to a JSON array. More...
template<typename T , typename... Args>
void	from_json (std::vector< T > &vec, const jsonParser &json, Args &&... args)
template<typename T >
void	from_json (std::vector< T > &vec, const jsonParser &json, const T &initial)
template<typename T , std::size_t N>
jsonParser &	to_json (const std::array< T, N > &arr, jsonParser &json)
	Converts to a JSON array. More...
template<typename T , std::size_t N>
void	from_json (std::array< T, N > &arr, const jsonParser &json)
template<typename T , typename Compare >
jsonParser &	to_json (const std::set< T, Compare > &set, jsonParser &json)
	Converts to a JSON array. More...
template<typename T , typename Compare , typename... Args>
void	from_json (std::set< T, Compare > &set, const jsonParser &json, Args &&... args)
template<typename T , typename Compare >
jsonParser &	to_json (const std::unordered_set< T, Compare > &set, jsonParser &json)
	Converts to a JSON array. More...
template<typename T , typename Compare , typename... Args>
void	from_json (std::unordered_set< T, Compare > &set, const jsonParser &json, Args &&... args)
template<typename Derived >
CASM::jsonParser &	to_json (const Eigen::MatrixBase< Derived > &value, CASM::jsonParser &json)
	Write Eigen Matrix/Vector to JSON. More...
template<typename Derived >
CASM::jsonParser &	to_json (const Eigen::MatrixBase< Derived > &value, CASM::jsonParser &json, CASM::jsonParser::as_array)
	Write Eigen Matrix/Vector to JSON. More...
template<typename Derived >
CASM::jsonParser &	to_json (const Eigen::MatrixBase< Derived > &value, CASM::jsonParser &json, CASM::jsonParser::as_flattest)
	Write Eigen Matrix/Vector to JSON. More...
template<typename Derived >
CASM::jsonParser &	to_json_array (const Eigen::MatrixBase< Derived > &value, CASM::jsonParser &json)
	Write Eigen Matrix with 1 row or 1 column to JSON array. More...
template<typename Derived >
CASM::jsonParser	to_json_array (const Eigen::MatrixBase< Derived > &value)
	Write Eigen Matrix with 1 row or 1 column to JSON array. More...
template<typename Derived >
void	from_json (Eigen::MatrixBase< Derived > &value, const CASM::jsonParser &json)
	Read Eigen Matrix/Vector from JSON. More...
std::ostream &	operator<< (std::ostream &sout, const BasicClexParamPack::EvalMode &val)
std::istream &	operator>> (std::istream &sin, BasicClexParamPack::EvalMode &val)
ChemicalReference	auto_chemical_reference (const PrimClex &primclex, double lin_alg_tol)
	Automatically set ChemicalReference using calculated Configurations with 'extreme' compositions. More...
std::ostream &	operator<< (std::ostream &sout, const DiffClexParamPack::EvalMode &val)
std::istream &	operator>> (std::istream &sin, DiffClexParamPack::EvalMode &val)
jsonParser &	to_json (const ChemicalReferenceState &ref_state, jsonParser &json)
	Write ChemicalReferenceState to: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'. More...
template<>
ChemicalReferenceState	from_json< ChemicalReferenceState > (const jsonParser &json)
	Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'. More...
void	from_json (ChemicalReferenceState &ref_state, const jsonParser &json)
	Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'. More...
jsonParser &	to_json (const HyperPlaneReference &ref, jsonParser &json)
void	from_json (HyperPlaneReference &ref, const jsonParser &json, HyperPlaneReference::InputFunction f)
jsonParser &	to_json (const ChemicalReference &ref, jsonParser &json)
	Write chemical reference. More...
std::pair< Eigen::VectorXd, std::vector< ChemicalReferenceState > >	one_chemical_reference_from_json (xtal::BasicStructure const &prim, jsonParser const &json)
	Read chemical reference from one of 3 alternative forms. More...
void	from_json (ChemicalReference &ref, jsonParser const &json, xtal::BasicStructure const &prim, double tol=1e-14)
	Read chemical reference from JSON. More...
template<typename CounterType >
std::ostream &	operator<< (std::ostream &stream, const MultiCounter< CounterType > &counter)
template<bool IsConst>
void	from_json (const SimpleJSonSiteStructure< IsConst > &jstruc, const jsonParser &json)
template<bool IsConst>
jsonParser &	to_json (const SimpleJSonSiteStructure< IsConst > &jstruc, jsonParser &json)
SimpleJSonSiteStructure< true >	simple_json (const BasicStructure &struc, const std::string &prefix)
SimpleJSonSiteStructure< false >	simple_json (BasicStructure &struc, const std::string &prefix)
std::vector< std::vector< Index > >	make_index_converter (const Structure &struc, std::vector< xtal::Molecule > mol_list)
std::vector< std::vector< Index > >	make_index_converter (const Structure &struc, std::vector< std::string > mol_name_list)
std::vector< std::vector< Index > >	make_index_converter_inverse (const Structure &struc, std::vector< std::string > mol_name_list)
std::map< DoFKey, CASM::DoFSetInfo >	global_dof_info (Structure const &_struc)
std::map< DoFKey, std::vector< CASM::DoFSetInfo > >	local_dof_info (Structure const &_struc)
SupercellSymInfo	make_supercell_sym_info (Structure const &prim, Lattice const &super_lattice)
template<typename IterType >
IterType	begin_next_fg_op (IterType it, IterType end)
template<typename PermuteIteratorContainer >
SymGroup	make_point_group (const PermuteIteratorContainer &container, const Lattice &supercell_lattice)
	Returns a SymGroup generated from a container of PermuteIterator. More...
template<typename PermuteIteratorIt >
SymGroup	make_point_group (PermuteIteratorIt begin, PermuteIteratorIt end, const Lattice &supercell_lattice)
	Returns a SymGroup generated from a range of PermuteIterator. More...
template<typename PermuteIteratorContainer >
SymGroup	make_sym_group (const PermuteIteratorContainer &container, const Lattice &supercell_lattice)
	Returns a SymGroup generated from a container of PermuteIterator. More...
template<typename PermuteIteratorIt >
SymGroup	make_sym_group (PermuteIteratorIt begin, PermuteIteratorIt end, const Lattice &supercell_lattice)
	Returns a SymGroup generated from a range of PermuteIterator. More...
template<typename PermuteIteratorContainer >
std::unique_ptr< SymGroup >	make_unique_sym_group (const PermuteIteratorContainer &container, const Lattice &supercell_lattice)
	Returns a std::unique_ptr<SymGroup> generated from a container of PermuteIterator. More...
template<typename PermuteIteratorIt >
std::unique_ptr< SymGroup >	make_unique_sym_group (PermuteIteratorIt begin, PermuteIteratorIt end, const Lattice &supercell_lattice)
	Returns a SymGroup generated from a range of PermuteIterator. More...
bool	site_indices_are_invariant (PermuteIterator const &permute_it, std::set< Index > const &site_indices)
	Return true if the permutation does not mix given sites and other sites. More...
jsonParser &	to_json (const PermuteIterator &clust, jsonParser &json)
SymGroupRep	coord_transformed_copy (SymGroupRep const &_rep, const Eigen::MatrixXd &trans_mat)
	Make a copy of representation on vector space 'V' that is transformed into a representation on vector space 'W' 'trans_mat' is the unitary matrix that isomorphically maps 'V'->'W' (i.e., [w = trans_mat * v] and [v = trans_mat.transpose() * w] ) If the original representation to be transformed is just a temporary standalone SymGroupRep, be sure to delete it before falling out of scope. More...
bool	operator== (SymGroupRepID const &a, SymGroupRepID const &b)
	Compares true if group_index() and rep_index() are equal. More...
bool	operator!= (SymGroupRepID const &a, SymGroupRepID const &b)
	Compares false if group_index() and rep_index() are equal. More...
bool	operator< (SymGroupRepID const &a, SymGroupRepID const &b)
	Less-than comparison for use in STL containers (std::set, std::map, etc) More...
jsonParser &	to_json (SymGroupRepID const &_id, jsonParser &json)
jsonParser const &	from_json (SymGroupRepID &_id, jsonParser const &json)
std::ostream &	operator<< (std::ostream &out, SymGroupRepID const &_id)

Variables
const double	TOL = 0.00001
const double	KB = 8.6173423E-05
const double	PLANCK = 4.135667516E-15
const COORD_TYPE	FRAC = COORD_TYPE::FRAC
const COORD_TYPE	CART = COORD_TYPE::CART
const COORD_TYPE	INTEGRAL = COORD_TYPE::INTEGRAL
const COORD_TYPE	COORD_DEFAULT = COORD_TYPE::COORD_DEFAULT
const PERIODICITY_TYPE	PERIODIC = PERIODICITY_TYPE::PERIODIC
const PERIODICITY_TYPE	LOCAL = PERIODICITY_TYPE::LOCAL
const PERIODICITY_TYPE	PERIODICITY_DEFAULT
const CELL_TYPE	PRIM = CELL_TYPE::PRIM
const CELL_TYPE	SCEL = CELL_TYPE::SCEL
const std::string	subproject_opt = "sub"
const std::string	write_prim_opt = "write-prim"
const std::string	relaxed_opt = "relaxed"
const std::string	molecule_opt = "as-molecules"
const std::string	include_va_opt = "include-va"

Typedef Documentation

AperiodicIntegralClusterOrbit

typedef AperiodicOrbit<IntegralCluster> CASM::AperiodicIntegralClusterOrbit

Definition at line 65 of file IntegralClusterSymCompareTraits.hh.

AperiodicOrbit

template<typename Element >

using CASM::AperiodicOrbit = typedef Orbit<AperiodicSymCompare<Element> >

Definition at line 38 of file ClusterSymCompareDecl.hh.

ARG_TYPE

typedef ArgHandler::ARG_TYPE CASM::ARG_TYPE

Definition at line 10 of file complete_tests.cpp.

CandidateSitesFunction

typedef std::function<std::vector<xtal::UnitCellCoord>Structure const &, SiteFilterFunction)> CASM::CandidateSitesFunction

A CandidateSitesFunction generates a vector of UnitCellCoord from a Structure and SiteFilterFuntion

Definition at line 47 of file ClusterOrbits.hh.

ClusterFilterFunction

typedef std::function<bool(IntegralCluster)> CASM::ClusterFilterFunction

A ClusterFilterFunction returns true if an IntegralCluster should be included and false if it should be excluded

Definition at line 41 of file ClusterOrbits.hh.

Comparisons

template<typename Base >

using CASM::Comparisons = typedef notstd::Comparisons<Base>

Definition at line 51 of file Comparisons.hh.

ConfigCompare

using CASM::ConfigCompare = typedef GenericConfigCompare<Configuration, ConfigIsEquivalent>

Definition at line 35 of file Configuration.hh.

CRTPBase

template<typename MostDerived >

using CASM::CRTPBase = typedef notstd::CRTPBase<MostDerived>

Definition at line 24 of file CRTPBase.hh.

DoFKey

typedef std::string CASM::DoFKey

Definition at line 7 of file DoFDecl.hh.

EigenIndex

typedef Eigen::MatrixXd::Index CASM::EigenIndex

Definition at line 7 of file eigen.hh.

enable_if_t

template<bool B, class T = void>

using CASM::enable_if_t = typedef typename std::enable_if<B, T>::type

Definition at line 18 of file CASM_TMP.hh.

EnumInterfaceVector

typedef std::vector<notstd::cloneable_ptr<EnumInterfaceBase> > CASM::EnumInterfaceVector

Definition at line 13 of file standard_enumerator_interfaces.hh.

FullOrbitPrinter

template<typename _Element >

using CASM::FullOrbitPrinter = typedef OrbitPrinter<_Element, ORBIT_PRINT_MODE::FULL>

Definition at line 155 of file OrbitPrinter.hh.

FullSitesPrinter

typedef FullOrbitPrinter<IntegralCluster> CASM::FullSitesPrinter

Definition at line 157 of file OrbitPrinter.hh.

Index

typedef INDEX_TYPE CASM::Index

For long integer indexing:

Definition at line 39 of file definitions.hh.

InfoInterfaceVector

typedef std::vector<notstd::cloneable_ptr<InfoInterfaceBase> > CASM::InfoInterfaceVector

Definition at line 13 of file standard_info_method_interfaces.hh.

InvariantsIterator

template<typename OrbitIterator >

using CASM::InvariantsIterator = typedef boost::transform_iterator<GetInvariants, OrbitIterator>

Definition at line 223 of file Orbit.hh.

lint

typedef long int CASM::lint

Definition at line 27 of file definitions.hh.

LocalIntegralClusterOrbit

typedef LocalOrbit<IntegralCluster> CASM::LocalIntegralClusterOrbit

Definition at line 66 of file IntegralClusterSymCompareTraits.hh.

LocalOrbit

template<typename Element >

using CASM::LocalOrbit = typedef AperiodicOrbit<Element>

Definition at line 41 of file ClusterSymCompareDecl.hh.

LocalSymCompare

template<typename Element , typename U = void>

using CASM::LocalSymCompare = typedef AperiodicSymCompare<Element, U>

Definition at line 25 of file ClusterSymCompareDecl.hh.

Matrix3d

typedef Eigen::Matrix3d CASM::Matrix3d

Definition at line 31 of file StrainConverter.hh.

MatrixXd

typedef Eigen::MatrixXd CASM::MatrixXd

Definition at line 30 of file StrainConverter.hh.

PrimPeriodicIntegralClusterOrbit

typedef PrimPeriodicOrbit<IntegralCluster> CASM::PrimPeriodicIntegralClusterOrbit

Definition at line 67 of file IntegralClusterSymCompareTraits.hh.

PrimPeriodicOrbit

template<typename Element >

using CASM::PrimPeriodicOrbit = typedef Orbit<PrimPeriodicSymCompare<Element> >

Definition at line 47 of file ClusterSymCompareDecl.hh.

ProtoSitesPrinter

typedef PrototypePrinter<IntegralCluster> CASM::ProtoSitesPrinter

Definition at line 133 of file OrbitPrinter.hh.

PrototypeIterator

template<typename OrbitIterator >

using CASM::PrototypeIterator = typedef boost::transform_iterator<GetPrototype, OrbitIterator>

Definition at line 205 of file Orbit.hh.

PrototypePrinter

template<typename _Element >

using CASM::PrototypePrinter = typedef OrbitPrinter<_Element, ORBIT_PRINT_MODE::PROTO>

Definition at line 131 of file OrbitPrinter.hh.

Reference

typedef ScalarAttribute<Configuration> CASM::Reference

Definition at line 18 of file Reference.hh.

ScelPeriodicIntegralClusterOrbit

typedef ScelPeriodicOrbit<IntegralCluster> CASM::ScelPeriodicIntegralClusterOrbit

Definition at line 68 of file IntegralClusterSymCompareTraits.hh.

ScelPeriodicOrbit

template<typename Element >

using CASM::ScelPeriodicOrbit = typedef Orbit<ScelPeriodicSymCompare<Element> >

Definition at line 44 of file ClusterSymCompareDecl.hh.

SiteFilterFunction

typedef std::function<bool(xtal::Site)> CASM::SiteFilterFunction

A SiteFilterFunction returns true if a Site should be included and false if it should be excluded

Definition at line 37 of file ClusterOrbits.hh.

SitesPrinter

typedef Printer<IntegralCluster> CASM::SitesPrinter

Definition at line 106 of file OrbitPrinter.hh.

STRAIN_METRIC

typedef strain::METRIC CASM::STRAIN_METRIC

Definition at line 35 of file StrainConverter.hh.

SymRepBuilderBase

using CASM::SymRepBuilderBase = typedef TemplateSymRepBuilderBase<false>

Definition at line 82 of file SymRepBuilder.hh.

TimeReversalSymRepBuilderBase

using CASM::TimeReversalSymRepBuilderBase = typedef TemplateSymRepBuilderBase<true>

Definition at line 84 of file SymRepBuilder.hh.

uint

typedef unsigned int CASM::uint

Definition at line 25 of file definitions.hh.

ulint

typedef unsigned long int CASM::ulint

Definition at line 26 of file definitions.hh.

VectorXd

typedef Eigen::VectorXd CASM::VectorXd

Definition at line 29 of file StrainConverter.hh.

Enumeration Type Documentation

CELL_TYPE

enum CASM::CELL_TYPE

strong

Enumerator
PRIM
SCEL

Definition at line 27 of file enum.hh.

CLUSTER_PERIODICITY_TYPE

enum CASM::CLUSTER_PERIODICITY_TYPE : int

strong

Enumerator
PRIM_PERIODIC
APERIODIC
LOCAL
WITHIN_SCEL
SCEL_PERIODIC

Definition at line 8 of file ClusterSymCompareDecl.hh.

COMPOSITION_TYPE

enum CASM::COMPOSITION_TYPE

Enumerator
PARAM_COMP
NUMBER_ATOMS

Definition at line 12 of file ParamComposition.hh.

COORD_TYPE

enum CASM::COORD_TYPE

strong

Enumerator
FRAC
CART
INTEGRAL
COORD_DEFAULT

Definition at line 6 of file enum.hh.

DatumFormatterClass

enum CASM::DatumFormatterClass

strong

Enumerator
Property
Operator

Definition at line 321 of file DataFormatter.hh.

EQUIVALENCE_TYPE

enum CASM::EQUIVALENCE_TYPE

strong

Enumerator
PRIM
SCEL
CONFIG

Definition at line 25 of file enum.hh.

JustificationType

enum CASM::JustificationType

strong

Enumerator
Left
Right
Center
Full

Definition at line 17 of file Log.hh.

OnError

enum CASM::OnError

strong

Standard Error handling options:

THROW: Throw an exception WARN: Print warning message, and continue CONTINUE: Continue quietly

Enumerator
THROW
WARN
CONTINUE

Definition at line 37 of file enum.hh.

ORBIT_PRINT_MODE

enum CASM::ORBIT_PRINT_MODE

strong

Enumerator
PROTO
FULL

Definition at line 18 of file OrbitPrinter.hh.

PARAM_PACK_TYPE

enum CASM::PARAM_PACK_TYPE

strong

Specify the Clexulator underlying data structure type.

Choices:

• DEFAULT: For BasisClexParamPack, the default.
• DIFF: For DiffClexParamPack, to make use of FADBAD++ automatic differentiation library

Enumerator
DEFAULT
DIFF

Definition at line 22 of file BasisFunctionSpecs.hh.

PERIODICITY_TYPE

enum CASM::PERIODICITY_TYPE : int

strong

Enumerator
PERIODIC
APERIODIC
LOCAL
PERIODICITY_DEFAULT

Definition at line 13 of file enum.hh.

Function Documentation

_composition_space()

Eigen::MatrixXd CASM::_composition_space	(	const ParamComposition::AllowedOccupants &	_allowed_occs,
		double	tol
	)

Non-orthogonal composition space.

Definition at line 578 of file CompositionConverter.cc.

_driver()

template<typename MCType >

int CASM::_driver	(	PrimClex &	primclex,
		const CommandArgs &	args,
		const Completer::MonteOption &	monte_opt
	)

Definition at line 292 of file monte.cc.

_final_POSCAR()

template<typename MCType >

int CASM::_final_POSCAR	(	PrimClex &	primclex,
		const CommandArgs &	args,
		const Completer::MonteOption &	monte_opt
	)

Definition at line 250 of file monte.cc.

_initial_POSCAR()

template<typename MCType >

int CASM::_initial_POSCAR	(	PrimClex &	primclex,
		const CommandArgs &	args,
		const Completer::MonteOption &	monte_opt
	)

Definition at line 229 of file monte.cc.

_orbit_max_poly_order()

template<typename OrbitType >

Index CASM::_orbit_max_poly_order	(	OrbitType const &	orbit,
		BasisFunctionSpecs const &	basis_function_specs
	)

allow basis_function_specs to specify max_poly_order by branch, orbit, etc.

Definition at line 21 of file ClexBasis_impl.hh.

_query_equivalents() [1/4]

template<>

void CASM::_query_equivalents	(	DataFormatter< QueryData< Configuration >> &	formatter,
		jsonParser &	json,
		PrimClex const &	primclex,
		Configuration const &	object
	)

Definition at line 389 of file query.cc.

_query_equivalents() [2/4]

template<>

void CASM::_query_equivalents	(	DataFormatter< QueryData< Configuration >> &	formatter,
		std::ostream &	stream,
		PrimClex const &	primclex,
		Configuration const &	object
	)

Definition at line 414 of file query.cc.

_query_equivalents() [3/4]

template<typename DataObject >

void CASM::_query_equivalents	(	DataFormatter< QueryData< DataObject >> &	formatter,
		jsonParser &	json,
		PrimClex const &	primclex,
		DataObject const &	object
	)

Definition at line 379 of file query.cc.

_query_equivalents() [4/4]

template<typename DataObject >

void CASM::_query_equivalents	(	DataFormatter< QueryData< DataObject >> &	formatter,
		std::ostream &	stream,
		PrimClex const &	primclex,
		DataObject const &	object
	)

Definition at line 404 of file query.cc.

_run_Canonical()

int CASM::_run_Canonical	(	PrimClex &	primclex,
		const Monte::MonteSettings &	monte_settings,
		const CommandArgs &	args,
		const Completer::MonteOption &	monte_opt
	)

Definition at line 434 of file monte.cc.

_run_GrandCanonical()

int CASM::_run_GrandCanonical	(	PrimClex &	primclex,
		const Monte::MonteSettings &	monte_settings,
		const CommandArgs &	args,
		const Completer::MonteOption &	monte_opt
	)

Definition at line 308 of file monte.cc.

_traj_POSCAR()

template<typename MCType >

int CASM::_traj_POSCAR	(	PrimClex &	primclex,
		const CommandArgs &	args,
		const Completer::MonteOption &	monte_opt
	)

Definition at line 271 of file monte.cc.

_update_query_dict()

template<typename DataObject >

void CASM::_update_query_dict

(

DataFormatterDictionary< QueryData< DataObject >> &

query_dict

)

Definition at line 224 of file query.cc.

_update_query_dict< Configuration >()

template<>

void CASM::_update_query_dict< Configuration >

(

DataFormatterDictionary< QueryData< Configuration >> &

query_dict

)

Definition at line 228 of file query.cc.

alias()

template<typename DataObject >

GenericDatumFormatter<std::string, DataObject> CASM::alias

(

)

Definition at line 931 of file DataFormatterTools.hh.

alias_or_name()

template<typename DataObject >

GenericDatumFormatter<std::string, DataObject> CASM::alias_or_name

(

)

Definition at line 944 of file DataFormatterTools.hh.

all_clusters_filter()

ClusterFilterFunction CASM::all_clusters_filter

(

)

Accept all clusters.

Definition at line 493 of file ClusterSpecs.cc.

all_sites_filter()

bool CASM::all_sites_filter

(

const xtal::Site &

site

)

Generate clusters using all Site.

Definition at line 476 of file ClusterSpecs.cc.

alloy_sites_filter()

bool CASM::alloy_sites_filter

(

const xtal::Site &

site

)

Generate clusters using Site with site_occupant.size() > 1.

Definition at line 479 of file ClusterSpecs.cc.

almost_equal() [1/6]

bool CASM::almost_equal	(	ClusterInvariants const &	A,
		ClusterInvariants const &	B,
		double	tol
	)

Check if ClusterInvariants are equal.

Definition at line 36 of file ClusterInvariants.cc.

almost_equal() [2/6]

template<typename T >

bool CASM::almost_equal	(	const Array< T > &	A,
		const Array< T > &	B,
		double	tol = TOL
	)

Definition at line 76 of file CASM_Array_math.hh.

almost_equal() [3/6]

template<typename T , typename std::enable_if<!std::is_integral< T >::value, T >::type * = nullptr>

bool CASM::almost_equal	(	const T &	val1,
		const T &	val2,
		double	tol = TOL
	)

If T is not integral, use almost_zero(val1 - val2, tol);.

If T is integral type, use val1 == val2;.

Definition at line 127 of file CASM_math.hh.

almost_equal() [4/6]

bool CASM::almost_equal	(	SymRepTools_v2::VectorInvariants const &	A_invariants,
		SymRepTools_v2::VectorInvariants const &	B_invariants,
		double	tol
	)

Definition at line 19 of file VectorSymCompare_v2.cc.

almost_equal() [5/6]

bool CASM::almost_equal	(	VectorInvariants const &	A_invariants,
		VectorInvariants const &	B_invariants,
		double	tol
	)

Check if VectorInvariants are equal.

Definition at line 12 of file VectorSymCompare.cc.

almost_equal() [6/6]

bool CASM::almost_equal	(	WithinScelClusterInvariants const &	A,
		WithinScelClusterInvariants const &	B,
		double	tol
	)

Check if WithinScelClusterInvariants are equal.

Check if ClusterInvariants are equal.

Definition at line 113 of file ClusterInvariants.cc.

almost_zero() [1/2]

template<typename T , typename std::enable_if< std::is_floating_point< T >::value, T >::type * = nullptr>

bool CASM::almost_zero ( const std::complex< T > &  val, double  tol = TOL  )

inline

If std::complex<T>, use std::abs(val) < tol;.

Definition at line 111 of file CASM_math.hh.

almost_zero() [2/2]

template<typename T , typename std::enable_if< std::is_floating_point< T >::value, T >::type * = nullptr>

bool CASM::almost_zero ( const T &  val, double  tol = TOL  )

inline

If T is not integral, use std::abs(val) < tol;.

If T is integral, val == 0;.

Definition at line 104 of file CASM_math.hh.

always_true()

template<typename T >

bool CASM::always_true

(

const T &

)

Definition at line 29 of file DataFormatterDecl.hh.

apply()

template<typename Object , typename Transform , typename... Args>

Object& CASM::apply	(	const Transform &	f,
		Object &	obj,
		Args &&...	args
	)

Apply a transformation, in place

• Default is equivalent to

  obj.apply_sym(f, args...) 

Definition at line 83 of file definitions.hh.

argtype_test()

void CASM::argtype_test

(

)

Definition at line 187 of file complete_tests.cpp.

atom_site_compatibility()

std::vector< std::set< Index > > CASM::atom_site_compatibility	(	xtal::SimpleStructure const &	sstruc,
		Configuration const &	_config
	)

Determine which sites of a Configuration can host each atom of a SimpleStructure result[i] is set of site indices in.

Parameters

_config	that can host atom 'i' of
sstruc

Definition at line 111 of file SimpleStructureTools.cc.

auto_chemical_reference()

ChemicalReference CASM::auto_chemical_reference	(	const PrimClex &	primclex,
		double	lin_alg_tol
	)

Automatically set ChemicalReference using calculated Configurations with 'extreme' compositions.

Definition at line 405 of file ChemicalReference.cc.

begin_next_fg_op()

template<typename IterType >

IterType CASM::begin_next_fg_op	(	IterType	it,
		IterType	end
	)

Iterator to next beginning of next factor group operation skipping all of the intervening operations that differ only by a translation

Definition at line 165 of file PermuteIterator.hh.

brief_description() [1/2]

std::string CASM::brief_description	(	const SymOp &	op,
		const xtal::Lattice &	lat,
		SymInfoOptions	opt = SymInfoOptions()
	)

Print SymInfo to brief string.

Definition at line 489 of file SymInfo_stream_io.cc.

brief_description() [2/2]

void CASM::brief_description	(	Log &	log,
		const SymGroup &	g,
		const xtal::Lattice &	lat,
		SymInfoOptions	opt
	)

Print SymGroup with brief string.

Print SymGroup with brief strings.

Uses indexing starting at 1 Format: <group index> (master group index): <symmetry operation> The master group index is only printed when some differ from the group index.

Definition at line 501 of file SymInfo_stream_io.cc.

bset_uncalculated()

void CASM::bset_uncalculated

(

const CommandArgs &

args

)

Definition at line 232 of file status.cc.

build_project()

void CASM::build_project	(	ProjectSettings const &	project_settings,
		Structure const &	prim
	)

Build a CASM project directory tree and populate with standard files

Notes:

• The project is built at project_settings.root_dir()
• Throws if !project_settings.has_dir()
• Throws if a CASM project already exists at that location (subprojects are OK)

Definition at line 21 of file ProjectBuilder.cc.

calc_properties_path() [1/2]

template<typename ConfigType >

std::string CASM::calc_properties_path	(	const ConfigType &	config,
		std::string	calctype = ""
	)

Definition at line 197 of file Calculable.cc.

calc_properties_path() [2/2]

std::string CASM::calc_properties_path	(	const PrimClex &	primclex,
		const std::string &	configname,
		std::string	calctype = ""
	)

Definition at line 228 of file Calculable.cc.

calc_status()

template<typename ConfigType >

std::string CASM::calc_status	(	const ConfigType &	_config,
		std::string	calctype = ""
	)

Status of calculation.

Definition at line 153 of file Calculable.cc.

calc_status_path() [1/2]

template<typename ConfigType >

std::string CASM::calc_status_path	(	const ConfigType &	config,
		std::string	calctype = ""
	)

Definition at line 211 of file Calculable.cc.

calc_status_path() [2/2]

std::string CASM::calc_status_path	(	const PrimClex &	primclex,
		const std::string &	configname,
		std::string	calctype = ""
	)

Definition at line 241 of file Calculable.cc.

cerr_log()

Log& CASM::cerr_log ( )

inline

Definition at line 433 of file Log.hh.

clex_exists()

bool CASM::clex_exists	(	const DirectoryStructure &	dir,
		const ClexDescription &	desc
	)

Definition at line 71 of file ClexDescription.cc.

colmajor_lex_compare()

template<typename Derived >

bool CASM::colmajor_lex_compare	(	const Eigen::MatrixBase< Derived > &	A,
		const Eigen::MatrixBase< Derived > &	B,
		double	tol
	)

Floating point lexicographical comparison with tol.

Definition at line 54 of file CASM_Eigen_math.hh.

combine_configuration_enum_json_options()

jsonParser CASM::combine_configuration_enum_json_options	(	jsonParser const &	json_options,
		jsonParser const &	cli_options_as_json
	)

A standard approach to combine CLI options with user JSON options into one JSON document

A standard approach to combine CLI options with user JSON options into one JSON document

Not all configuration enumerator interfaces need to incorporate the CLI output using this method, but it is the most common way to do so.

"min": <int, min supercell volume to do enumerations>, "max": <int, max supercell volume to do enumerations>, "scelnames": <array of string, list of supercell names, context dependent usage>, "confignames": <array of string, list of config names, context dependent usage>, "all": <bool, use all existing supercells for enumeration, ignore other inputs>, "filter": <array of string, filter query/select expression, save configs if evaluates true>, "verbosity": <string, to be read by Log::verbosity_level>, "dry_run": <bool, print/return method results but do not save results>

"min": <int, min supercell volume to do enumerations>, "max": <int, max supercell volume to do enumerations>, "scelnames": <array of string, list of supercell names, context dependent usage>, "confignames": <array of string, list of config names, context dependent usage>, "all": <bool, use all existing supercells for enumeration, ignore other inputs>, "filter": <array of string, filter query/select expression, save configs if evaluates true>, "verbosity": <string, to be read by Log::verbosity_level>, "dry_run": <bool, print/return method results but do not save results>

Definition at line 16 of file enumerate_configurations_json_io.cc.

combine_json_options()

jsonParser & CASM::combine_json_options	(	std::map< std::string, std::string > const &	source_to_combined_keys,
		jsonParser const &	json_source,
		jsonParser &	json_combined
	)

Copy from json_source to json_combined

Definition at line 8 of file json_io.cc.

combine_supercell_enum_json_options()

jsonParser CASM::combine_supercell_enum_json_options	(	jsonParser const &	json_options,
		jsonParser const &	cli_options_as_json
	)

A standard approach to combine CLI options with user JSON options into one JSON document

A standard approach to combine CLI options with user JSON options into one JSON document

Not all supercell enumerator interfaces need to incorporate the CLI output using this method, but it is the most common way to do so (only way currently).

Definition at line 16 of file enumerate_supercells_json_io.cc.

compare() [1/5]

bool CASM::compare	(	ClusterInvariants const &	A,
		ClusterInvariants const &	B,
		double	tol
	)

Compare ClusterInvariants.

Returns

True if A < B, to specified tolerance

• First compares by number of sites in cluster
• Then compare all displacements, from longest to shortest

Definition at line 52 of file ClusterInvariants.cc.

compare() [2/5]

template<typename T , typename std::enable_if< std::is_floating_point< T >::value, T >::type * = nullptr>

bool CASM::compare	(	const T &	A,
		const T &	B,
		double	tol
	)

Floating point comparison with tol, return A < B.

Implements:

if(!almost_equal(A,B,tol)) { return A < B; }
return false;

Definition at line 149 of file CASM_math.hh.

compare() [3/5]

bool CASM::compare	(	SymRepTools_v2::VectorInvariants const &	A_invariants,
		SymRepTools_v2::VectorInvariants const &	B_invariants,
		double	tol
	)

Definition at line 26 of file VectorSymCompare_v2.cc.

compare() [4/5]

bool CASM::compare	(	VectorInvariants const &	A_invariants,
		VectorInvariants const &	B_invariants,
		double	tol
	)

Compare ClusterInvariants.

Definition at line 18 of file VectorSymCompare.cc.

compare() [5/5]

bool CASM::compare	(	WithinScelClusterInvariants const &	A,
		WithinScelClusterInvariants const &	B,
		double	tol
	)

Compare WithinScelClusterInvariants.

Returns

True if A < B, to specified tolerance

• First compares by number of sites in cluster
• Then compare all displacements, from longest to shortest

Definition at line 129 of file ClusterInvariants.cc.

compare_no_value()

bool CASM::compare_no_value ( ContinuousDoF const &  A, ContinuousDoF const &  B  )

inline

Definition at line 412 of file DoF.hh.

composition_command()

int CASM::composition_command

(

const CommandArgs &

args

)

–help option

–help option

Definition at line 69 of file composition.cc.

composition_space()

Eigen::MatrixXd CASM::composition_space	(	const ParamComposition::AllowedOccupants &	_allowed_occs,
		double	tol
	)

Return the composition space of a ParamComposition::AllowedOccupants.

Return the composition space of a BasicStructure.

Parameters

_allowed_occs	A BasicStructure to find the standard composition space for (does not check if it is actually primitive).
tol	tolerance for checking rank (default 1e-14)

• Each column corresponds to an orthogonal vector in atom fraction space
• Each row corresponds to a Molecule, ordered as from BasicStructure::struc_molecule

Definition at line 615 of file CompositionConverter.cc.

composition_unselected()

void CASM::composition_unselected

(

const CommandArgs &

args

)

Definition at line 80 of file status.cc.

configs_uncalculated()

void CASM::configs_uncalculated

(

const CommandArgs &

args

)

Definition at line 133 of file status.cc.

configs_ungenerated()

void CASM::configs_ungenerated

(

const CommandArgs &

args

)

Definition at line 108 of file status.cc.

container_to_string()

template<typename Iterator >

std::string CASM::container_to_string	(	Iterator	begin_it,
		Iterator	end_it,
		std::string	begin = "[",
		std::string	end = "]",
		std::string	delim = ", "
	)

Definition at line 23 of file string_io.hh.

contains() [1/2]

template<typename Container , typename T >

bool CASM::contains	(	const Container &	container,
		const T &	value
	)

Equivalent to container.end() != std::find(container.begin(), container.end(), value)

Definition at line 83 of file algorithm.hh.

contains() [2/2]

template<typename Container , typename T , typename BinaryCompare >

bool CASM::contains	(	const Container &	container,
		const T &	value,
		BinaryCompare	q
	)

Equivalent to container.end() != find(container.begin(), container.end(), value, q)

Definition at line 91 of file algorithm.hh.

contains_all() [1/2]

template<typename Container1 , typename Container2 >

bool CASM::contains_all	(	const Container1 &	container,
		const Container2 &	values
	)

Returns true if each elements of 'values' is contained in 'container'.

Definition at line 112 of file algorithm.hh.

contains_all() [2/2]

template<typename Container1 , typename Container2 , typename BinaryCompare >

bool CASM::contains_all	(	const Container1 &	container,
		const Container2 &	values,
		BinaryCompare	q
	)

Returns true if each elements of 'values' is contained in 'container', using comparison functor 'q'.

Definition at line 122 of file algorithm.hh.

contains_if()

template<typename Container , typename UnaryPredicate >

bool CASM::contains_if	(	const Container &	container,
		UnaryPredicate	p
	)

Equivalent to container.end() != std::find_if(container.begin(), container.end(), p)

Definition at line 98 of file algorithm.hh.

contains_if_not()

template<typename Container , typename UnaryPredicate >

bool CASM::contains_if_not	(	const Container &	container,
		UnaryPredicate	q
	)

Equivalent to container.end() != std::find_if_not(container.begin(), container.end(), q)

Definition at line 105 of file algorithm.hh.

coord_transformed_copy()

SymGroupRep CASM::coord_transformed_copy	(	SymGroupRep const &	_rep,
		const Eigen::MatrixXd &	trans_mat
	)

Make a copy of representation on vector space 'V' that is transformed into a representation on vector space 'W' 'trans_mat' is the unitary matrix that isomorphically maps 'V'->'W' (i.e., [w = trans_mat * v] and [v = trans_mat.transpose() * w] ) If the original representation to be transformed is just a temporary standalone SymGroupRep, be sure to delete it before falling out of scope.

Definition at line 175 of file SymGroupRep.cc.

coordinate_mode_help()

std::string CASM::coordinate_mode_help

(

)

Definition at line 17 of file help.cc.

copy_apply() [1/3]

template<typename Object , typename Transform , typename... Args>

Object CASM::copy_apply	(	const Transform &	f,
		Object	obj,
		Args &&...	args
	)

Copy and apply a transformation

• We can also include a specialization for cloneable objects, via SFINAE
• Default is equivalent to

  Object result(obj); apply(f, obj, args...)

Definition at line 93 of file definitions.hh.

copy_apply() [2/3]

MappingNode CASM::copy_apply	(	PermuteIterator const &	_it,
		MappingNode const &	_node,
		bool	transform_cost_mat = true
	)

Reorders the permutation and compounds the spatial isometry (rotation.

• translation) of _node with that of _it

Definition at line 174 of file ConfigMapping.cc.

copy_apply() [3/3]

MappedProperties CASM::copy_apply	(	PermuteIterator const &	op,
		MappedProperties const &	props
	)

Definition at line 8 of file MappedPropertiesTools.cc.

cout_log()

Log& CASM::cout_log ( )

inline

Definition at line 428 of file Log.hh.

cuberoot()

double CASM::cuberoot

(

double

number

)

Definition at line 272 of file CASM_math.cc.

cum_sum()

template<typename T >

ReturnArray<T> CASM::cum_sum

(

const Array< T > &

arr

)

Definition at line 87 of file CASM_Array_math.hh.

cutoff_radius_neighborhood()

CandidateSitesFunction CASM::cutoff_radius_neighborhood	(	IntegralCluster const &	phenomenal,
		double	cutoff_radius,
		bool	include_phenomenal_sites = false
	)

Sites within cutoff_radius distance to any site in the phenomenal cluster.

Definition at line 519 of file ClusterSpecs.cc.

default_configuration_clex()

ClexDescription CASM::default_configuration_clex

(

)

Create default configuration ClexDescription

Using:

• name,property="formation_energy"
• calctype,ref,bset,eci="default"

Definition at line 26 of file ClexDescription.cc.

default_err_log()

Log& CASM::default_err_log ( )

inline

Definition at line 419 of file Log.hh.

default_log()

Log& CASM::default_log ( )

inline

Definition at line 414 of file Log.hh.

default_nlist_sublat_indices()

std::set< int > CASM::default_nlist_sublat_indices

(

xtal::BasicStructure const &

prim

)

Make default list of sublattice indices that will be included in the neighbor list

Includes sublattices with either:

• 2 or more occupants (Site::occupant_dof().size() >= 2)
• Continuous degrees of freedom (Site::dof_size() > 0)

Definition at line 114 of file ProjectBuilder.cc.

default_nlist_weight_matrix()

Eigen::Matrix3l CASM::default_nlist_weight_matrix	(	xtal::BasicStructure const &	prim,
		double	tol
	)

Make default weight matrix for approximately spherical neighborhood in Cartesian coordinates

Equivalent to:

PrimNeighborList::make_weight_matrix(prim.lattice().lat_column_mat(), 10,
tol()); 

Definition at line 108 of file ProjectBuilder.cc.

description() [1/2]

std::string CASM::description	(	const SymOp &	op,
		const xtal::Lattice &	lat,
		SymInfoOptions	opt = SymInfoOptions()
	)

Print SymInfo to string.

Definition at line 454 of file SymInfo_stream_io.cc.

description() [2/2]

void CASM::description	(	Log &	log,
		const SymGroup &	g,
		const xtal::Lattice &	lat,
		SymInfoOptions	opt
	)

Print SymGroup with matrix / tau.

Print SymGroup info.

Uses indexing starting at 1

Definition at line 462 of file SymInfo_stream_io.cc.

direct_sum()

BasisSet CASM::direct_sum

(

BasisSet::ArgList const &

_subs

)

Definition at line 1324 of file BasisSet.cc.

display()

void CASM::display	(	std::ostream &	sout,
		const CompositionAxes &	comp_axes
	)

Definition at line 20 of file composition.cc.

display_comp()

void CASM::display_comp	(	std::ostream &	stream,
		const CompositionConverter &	f,
		int	indent
	)

Pretty-print comp in terms of comp_n.

Example:

comp(a) = c00*(comp_n(A) - 1) + c01*comp_n(B) + ...
comp(b) = c00*comp_n(A) + c01*(comp_n(B) - 2) + ...
...

Definition at line 522 of file CompositionConverter.cc.

display_comp_n()

void CASM::display_comp_n	(	std::ostream &	stream,
		const CompositionConverter &	f,
		int	indent
	)

Pretty-print comp_n in terms of comp.

Pretty-print comp in terms of comp_n.

Example:

comp_n(A) = nAo + c00*comp(a) + c01*comp(b) + ...
comp_n(B) = nBo + c10*comp(a) + c11*comp(b) + ...
...

Definition at line 537 of file CompositionConverter.cc.

display_composition_axes()

void CASM::display_composition_axes	(	std::ostream &	stream,
		const std::map< std::string, CompositionConverter > &	map
	)

Pretty-print map of name/CompositionConverter pairs.

Parameters

stream	Output stream
map	Map of name/CompositionConverter pairs
name	Name for this set of composition axes

Definition at line 472 of file CompositionConverter.cc.

display_param_chem_pot()

void CASM::display_param_chem_pot	(	std::ostream &	stream,
		const CompositionConverter &	f,
		int	indent
	)

Pretty-print param_chem_pot in terms of chem_pot.

Example:

param_chem_pot(a) = c00*chem_pot(A) + c01*chem_pot(B) + ...
param_chem_pot(b) = c10*chem_pot(A) + c11*chem_pot(B) + ...
...

Definition at line 552 of file CompositionConverter.cc.

dl_string_dist()

int CASM::dl_string_dist	(	const std::string &	a,
		const std::string &	b
	)

Computes the Damerescau-Levenshtein distance – the number of edits (deletions, insertions, transpositions) to go from string 'a' to string 'b'.

Definition at line 45 of file CASM_math.cc.

dof_sites_filter()

SiteFilterFunction CASM::dof_sites_filter

(

std::vector< DoFKey > const &

dofs

)

Generate clusters using Site with specified DoF.

If dofs is empty, return true if Site has any continuous DoF or >1 allowed occupant DoF If dofs is not empty, return true if Site has any of the DoF types included. Use "occ" for / Site with >1 occupant allowed

Definition at line 488 of file ClusterSpecs.cc.

dof_space_analysis()

void CASM::dof_space_analysis	(	PrimClex &	primclex,
		jsonParser const &	json_options,
		jsonParser const &	cli_options_as_json
	)

Perform DoF space analysis.

Perform DoF space analysis

Usage:

• Specify one or more DoF spaces and a symmetry group via selection of configurations, sites within the configurations, DoF type, and DoF subspace.
  • The supercell, selected sites, DoF type, and subspace determine the DoF space
  • The subgroup of the configuration factor group that leaves selected sites invariant is used for symmetry analysis
• The analysis finds irreducible representations of the DoF vector space and optionally calculates the symmetrically unique wedges in that space
• See dof_space_analysis_desc() for JSON and CLI input options

Definition at line 205 of file dof_space_analysis.cc.

dof_space_analysis_desc()

std::string CASM::dof_space_analysis_desc

(

)

Describe DoF space analysis input.

Describe DoF space analysis.

Definition at line 73 of file dof_space_analysis.cc.

dry_run_help()

std::string CASM::dry_run_help

(

)

Definition at line 7 of file help.cc.

dry_run_msg()

std::string CASM::dry_run_msg ( bool  dry_run )

inline

Standardized string that can prepended to method output to make clear that method results are not going to be committed

Definition at line 76 of file EnumInterface.hh.

eci_uncalculated()

void CASM::eci_uncalculated

(

const CommandArgs &

args

)

Definition at line 249 of file status.cc.

eigen_vector_from_string()

Eigen::VectorXd CASM::eigen_vector_from_string	(	const std::string &	tstr,
		const int &	size
	)

Definition at line 10 of file CASM_Eigen_math.cc.

empty_neighborhood()

CandidateSitesFunction CASM::empty_neighborhood

(

)

No sites (for null orbit, or global dof only)

Definition at line 503 of file ClusterSpecs.cc.

end_members()

Eigen::MatrixXd CASM::end_members

(

const ParamComposition::AllowedOccupants &

_allowed_occs

)

Serialize CompositionConverter to JSON.

Generate a column matrix containing all the possible molecular end members.

Generate a column matrix containing all the possible molecular end members

Parameters

_allowed_occs

A BasicStructure to find the end members of (does not check if it is actually primitive).

• Each column corresponds to a point in composition space (specifying number of each Molecule per prim)
• Each row corresponds to a Molecule, ordered as from BasicStructure::struc_molecule, with units number Molecule / prim

Definition at line 570 of file CompositionConverter.cc.

end_of_literal()

std::string::const_iterator CASM::end_of_literal	(	std::string::const_iterator	it,
		std::string::const_iterator	end_it
	)

Definition at line 47 of file DataFormatter.cc.

end_ptr() [1/4]

template<typename Derived >

Derived::Scalar* CASM::end_ptr

(

Eigen::PlainObjectBase< Derived > &

container

)

Return pointer one past end of vector. Equivalent to convainer.data()+container.size()

Definition at line 114 of file CASM_Eigen_math.hh.

end_ptr() [2/4]

template<typename Derived >

Derived::Scalar const* CASM::end_ptr

(

Eigen::PlainObjectBase< Derived > const &

container

)

Return const pointer one past end of vector. Equivalent to convainer.data()+container.size()

Definition at line 121 of file CASM_Eigen_math.hh.

end_ptr() [3/4]

template<typename T >

T* CASM::end_ptr

(

std::vector< T > &

container

)

Return pointer one past end of vector. Equivalent to convainer.data()+container.size()

Definition at line 142 of file algorithm.hh.

end_ptr() [4/4]

template<typename T >

T const* CASM::end_ptr

(

std::vector< T > const &

container

)

Return const pointer one past end of vector. Equivalent to convainer.data()+container.size()

Definition at line 149 of file algorithm.hh.

engine_test()

void CASM::engine_test

(

)

Definition at line 166 of file complete_tests.cpp.

enumerate_configurations()

template<typename MakeEnumeratorFunction , typename InputNameValuePairIterator , typename ConfigEnumDataType >

void CASM::enumerate_configurations	(	PrimClex const &	primclex,
		ConfigEnumOptions const &	options,
		MakeEnumeratorFunction	make_enumerator_f,
		InputNameValuePairIterator	name_value_pairs_begin,
		InputNameValuePairIterator	name_value_pairs_end,
		DataFormatter< ConfigEnumDataType > const &	formatter
	)

Enumerate configurations.

Enumerate configurations

This method enumerates configurations given a rage of starting values, typically a range of supercells or initial configurations, possibly with particular sites selected for enumeration, represented using ConfigEnumInput.

A pseudo-code outline of the method is:

for name_value_pair in range [name_value_pairs_begin, name_value_pairs_end):
  print "Enumerate configuration for " + name_value_pair.first + "..."
  auto enumerator = make_enumerator_f(name_value_pair.first,
  name_value_pair.second); for configuration generated by enumerator:
    make ConfigEnumDataType data
    if options.filter and !options.filter(configuration):
      do not insert configuration
    else
      if is_guaranteed_for_database_insert(enumerator):
        insert configuration in configuration_db
      else:
        make primitive canonical configuration and insert in
        configuration_db if !options.primitive_only:
          make non-primitive canonical configuration and insert in
          configuration_db
    if options.output_enumerated_configurations:
      formatter(data)
if !options.dry_run:
  commit supercell_db
  commit configuration_db
  if options.output_enumerated_configurations:
    write formatted data to options.output_path

Note:

• To avoid unnecessary configuration canonicalization, specialize the following method: template<> bool is_guaranteed_for_database_insert(EnumeratorType const &);

Parameters

primclex	PrimClex provides access to project database and other data
options	See ConfigEnumOptions for method options
make_enumerator_f	A function that constructs a Configuration enumerator of type EnumeratorType for each value in the range [name_value_pairs_begin, name_value_pairs_end). Requires signature: EnumeratorType make_enumerator_f(Index initial_state_index, std::string initial_state_name, InitialStateType const &initial_state);
name_value_pairs_begin,name_value_pairs_end	A range of pairs of name (for printing progress) to InitialStateType value (typically, but not necessarily InputType = ConfigEnumInput). The value InputType is used as the argument to make_enumerator_f to construct a series of enumerators which are executed in turn.
formatter	DataFormatter used to record enumerated configurations. See ConfigEnumOptions for output options. The ConfigEnumDataType should follow the example of ConfigEnumData which provides the minimum required interface.

Note:

• Uses CASM::log() for logging progress

Use while transitioning Supercell to no longer need a PrimClex const *

Use while transitioning Supercell to no longer need a PrimClex const *

Definition at line 80 of file enumerate_configurations_impl.hh.

enumerate_supercells()

template<typename EnumeratorType >

void CASM::enumerate_supercells	(	EnumerateSupercellsOptions const &	options,
		EnumeratorType &	enumerator,
		DB::Database< Supercell > &	supercell_db
	)

Enumerate supercells

Note:

• To avoid unnecessary supercell canonicalization, specialize the following method: template<> bool is_guaranteed_for_database_insert(EnumeratorType const &);

Parameters

options	See EnumerateSupercellsOptions for method options
enumerator	A supercell enumerator.
supercell_db	Will commit any new Supercell if options.dry_run==false.

Note:

• Uses CASM::log() for logging progress

Use while transitioning Supercell to no longer need a PrimClex const *

Use while transitioning Supercell to no longer need a PrimClex const *

Definition at line 30 of file enumerate_supercells_impl.hh.

err_log()

Log& CASM::err_log ( )

inline

Definition at line 426 of file Log.hh.

exclude_homogeneous_mode_space()

DoFSpace CASM::exclude_homogeneous_mode_space

(

DoFSpace const &

dof_space

)

Removes the homogeneous mode space from the DoFSpace basis.

Removes the homogeneous mode space from the local continuous DoFSpace basis.

Parameters

dof_space

DoF space to remove the homogeneous mode space from. Must be a DoF space for a local continuous DoF and include all sites in the supercell (dof_space.includes_all_sites==true), else will throw.

Returns

A copy of dof_space with basis modified to remove homogeneous modes.

Definition at line 673 of file DoFSpace.cc.

extended_gcf()

template<typename IntType >

IntType CASM::extended_gcf	(	IntType	i1,
		IntType	i2,
		IntType &	p1,
		IntType &	p2
	)

Calculate greatest common factor of two integers, and bezout coefficients.

Returns

greatest common factor

Parameters

	i1,i2	two integers for which to find greatest common factor
[out]	p1,p2	bezout coefficients such that p1*i1 + p2*i2 = gcf(abs(i1),abs(i2));

See also

smith_normal_form

Definition at line 277 of file CASM_math.hh.

failure_type()

template<typename ConfigType >

std::string CASM::failure_type	(	const ConfigType &	config,
		std::string	calctype = ""
	)

Definition at line 167 of file Calculable.cc.

files_command()

int CASM::files_command

(

const CommandArgs &

args

)

Set command line options using boost program_options

–help option

Set command line options using boost program_options

–help option

Definition at line 47 of file files.cc.

fill_supercell() [1/4]

Configuration CASM::fill_supercell	(	Configuration const &	motif,
		std::shared_ptr< Supercell const > const &	shared_supercell
	)

Create a super configuration by tiling the motif Configuration into the supercell.

Note:

• This overload finds the first SymOp in the prim factor group such that apply(symop, motif) can be used to fill the Supercell. If none can be found, it throws.

Definition at line 33 of file FillSupercell.cc.

fill_supercell() [2/4]

Configuration CASM::fill_supercell	(	Configuration const &	motif,
		Supercell const &	supercell
	)

Create a super configuration by tiling the motif Configuration into the supercell.

Note:

• Prefer to use std::shared_ptr<Supercell const> overload if possible
• This overload finds the first SymOp in the prim factor group such that apply(symop, motif) can be used to fill the Supercell. If none can be found, it throws.

Definition at line 48 of file FillSupercell.cc.

fill_supercell() [3/4]

Configuration CASM::fill_supercell	(	SymOp const &	symop,
		Configuration const &	motif,
		std::shared_ptr< Supercell const > const &	shared_supercell
	)

Create a super configuration by tiling the apply(symop, motif) Configuration into the supercell

Note:

• Will throw if apply(symop, motif) cannot be tiled into the supercell

Definition at line 59 of file FillSupercell.cc.

fill_supercell() [4/4]

Configuration CASM::fill_supercell	(	SymOp const &	symop,
		Configuration const &	motif,
		Supercell const &	supercell
	)

Create a super configuration by tiling the apply(symop, motif) Configuration into the supercell

Note:

• Prefer to use std::shared_ptr<Supercell const> overload if possible
• Will throw if apply(symop, motif) cannot be tiled into the supercell

Definition at line 72 of file FillSupercell.cc.

filter_begin() [1/2]

template<typename IteratorType , typename DataObject >

FilteredConfigIterator<IteratorType> CASM::filter_begin	(	const IteratorType &	it,
		const IteratorType &	it_end,
		const std::vector< std::string > &	filter_expr,
		const DataFormatterDictionary< DataObject > &	_dict
	)

Definition at line 114 of file FilteredConfigIterator.hh.

filter_begin() [2/2]

template<typename IteratorType , typename DataObject >

FilterIterator<IteratorType> CASM::filter_begin	(	IteratorType const &	it,
		IteratorType const &	it_end,
		std::function< bool(typename FilterIterator< IteratorType >::reference)>	filter_function
	)

Definition at line 79 of file FilterIterator.hh.

filter_end() [1/2]

template<typename IteratorType >

FilteredConfigIterator<IteratorType> CASM::filter_end

(

const IteratorType &

it_end

)

Definition at line 122 of file FilteredConfigIterator.hh.

filter_end() [2/2]

template<typename IteratorType >

FilterIterator<IteratorType> CASM::filter_end

(

IteratorType const &

it_end

)

Definition at line 87 of file FilterIterator.hh.

find()

template<typename Iterator , typename T , typename BinaryCompare >

Iterator CASM::find	(	Iterator	begin,
		Iterator	end,
		const T &	value,
		BinaryCompare	q
	)

Equivalent to std::find(begin, end, value), but with custom comparison.

Definition at line 16 of file algorithm.hh.

find_casmroot()

fs::path CASM::find_casmroot

(

const fs::path &

cwd

)

return path to current or parent directory containing ".casm" directory if none found, return empty path

Definition at line 14 of file DirectoryStructure.cc.

find_index() [1/4]

template<typename Container , typename T >

Index CASM::find_index	(	const Container &	container,
		const T &	value
	)

Equivalent to std::distance(container.begin(), std::find(container.begin(), container.end(), value))

Definition at line 46 of file algorithm.hh.

find_index() [2/4]

template<typename Container , typename T , typename BinaryCompare >

Index CASM::find_index	(	const Container &	container,
		const T &	value,
		BinaryCompare	q
	)

Equivalent to std::distance(container.begin(), find(container.begin(), container.end(), value,q))

Definition at line 38 of file algorithm.hh.

find_index() [3/4]

template<typename Iterator , typename T >

Index CASM::find_index	(	Iterator	begin,
		Iterator	end,
		const T &	value
	)

Equivalent to std::distance(begin, std::find(begin, end, value))

Definition at line 24 of file algorithm.hh.

find_index() [4/4]

template<typename Iterator , typename T , typename BinaryCompare >

Index CASM::find_index	(	Iterator	begin,
		Iterator	end,
		const T &	value,
		BinaryCompare	q
	)

Equivalent to std::distance(begin, find(begin, end, value, q))

Definition at line 30 of file algorithm.hh.

find_index_if() [1/2]

template<typename Container , typename UnaryPredicate >

Index CASM::find_index_if	(	const Container &	container,
		UnaryPredicate	p
	)

Equivalent to std::distance(container.begin(), std::find_if(container.begin(), container.end(), p))

Definition at line 60 of file algorithm.hh.

find_index_if() [2/2]

template<typename Iterator , typename UnaryPredicate >

Index CASM::find_index_if	(	Iterator	begin,
		Iterator	end,
		UnaryPredicate	p
	)

Equivalent to std::distance(begin, std::find_if(begin, end, p))

Definition at line 53 of file algorithm.hh.

find_index_if_not() [1/2]

template<typename Container , typename UnaryPredicate >

Index CASM::find_index_if_not	(	const Container &	container,
		UnaryPredicate	q
	)

Equivalent to std::distance(container.begin(), std::find_if_not(container.begin(), container.end(), p))

Definition at line 75 of file algorithm.hh.

find_index_if_not() [2/2]

template<typename Iterator , typename UnaryPredicate >

Index CASM::find_index_if_not	(	Iterator	begin,
		Iterator	end,
		UnaryPredicate	q
	)

Equivalent to std::distance(begin, std::find_if_not(begin, end, q))

Definition at line 67 of file algorithm.hh.

find_orbit()

template<typename OrbitIterator , typename Element >

OrbitIterator CASM::find_orbit	(	OrbitIterator	begin,
		OrbitIterator	end,
		Element	e
	)

Find orbit containing an element in a range of Orbit.

Find orbit containing an element in a range of Orbit<ClusterType>

Parameters

begin,end	Range of Orbit
e	Element to find

Returns

Iterator to Orbit containing e, or end if not found

• Expects typename std::iterator_traits<OrbitIterator>::value_type to be the Orbit<SymCompareType> type
• Expects e to be prepared via SymCompareType::prepare
• Assume range of orbit is sorted according to SymCompareType::invariants_compare
• Uses SymCompareType::compare (via Orbit::contains) to check for element in orbit

Definition at line 295 of file Orbit_impl.hh.

float_lexicographical_compare() [1/2]

bool CASM::float_lexicographical_compare ( const Eigen::Ref< const Eigen::MatrixXd > &  A, const Eigen::Ref< const Eigen::MatrixXd > &  B, double  tol  )

inline

Floating point lexicographical comparison with tol.

Definition at line 45 of file CASM_Eigen_math.hh.

float_lexicographical_compare() [2/2]

template<class InputIt1 , class InputIt2 >

bool CASM::float_lexicographical_compare	(	InputIt1	first1,
		InputIt1	last1,
		InputIt2	first2,
		InputIt2	last2,
		double	tol
	)

Floating point lexicographical comparison with tol.

Definition at line 169 of file CASM_math.hh.

float_sgn()

template<typename T , typename std::enable_if< std::is_floating_point< T >::value, T >::type * = nullptr>

int CASM::float_sgn	(	T	val,
		double	compare_tol = TOL
	)

Definition at line 188 of file CASM_math.hh.

for_all_orbits() [1/2]

template<typename FunctorType >

void CASM::for_all_orbits	(	ClusterSpecs const &	cluster_specs,
		std::ostream &	status,
		FunctorType const &	f
	)

Call functor for orbits generated by ClusterSpecs

Selects the correct make_X_orbits method and then calls f for all orbits, as with:

auto orbits = cluster_specs.make_X_orbits(status); f(orbits);

The FunctorType should have the template method:

template<typename OrbitVecType>
void FunctorType::operator()(OrbitVecType const &orbits) const;

Definition at line 38 of file ClusterSpecs_impl.hh.

for_all_orbits() [2/2]

template<typename FunctorType >

void CASM::for_all_orbits	(	ClusterSpecs const &	cluster_specs,
		std::vector< IntegralCluster > const &	generating_elements,
		FunctorType const &	f
	)

Call functor for orbits generated by ClusterSpecs

Selects the correct make_X_orbits method and then calls f for all orbits, as with:

 auto orbits = cluster_specs.make_X_orbits(generating_elements);
f(orbits);

The FunctorType should have the template method:

template<typename OrbitVecType>
void FunctorType::operator()(OrbitVecType const &orbits) const;

Definition at line 13 of file ClusterSpecs_impl.hh.

format_command()

int CASM::format_command

(

const CommandArgs &

args

)

–help option

–help option

Definition at line 46 of file format.cc.

format_operator_not()

template<typename DataObject >

DataFormatterOperator<bool, bool, DataObject> CASM::format_operator_not

(

)

Definition at line 417 of file DataFormatterTools.hh.

from_json() [1/34]

template<typename T , typename... Args>

void CASM::from_json	(	Array< T > &	value,
		const jsonParser &	json,
		Args &&...	args
	)

This requires that 'T::T()' exists, if not, you must do this by hand.

re-throw exceptions

Definition at line 27 of file json_io.hh.

from_json() [2/34]

void CASM::from_json	(	BasisSet &	bset,
		const jsonParser &	json
	)

from_json() [3/34]

void CASM::from_json	(	ChemicalReference &	ref,
		jsonParser const &	json,
		xtal::BasicStructure const &	prim,
		double	tol = 1e-14
	)

Read chemical reference from JSON.

Definition at line 287 of file ChemicalReference_json_io.cc.

from_json() [4/34]

void CASM::from_json	(	ChemicalReferenceState &	ref_state,
		const jsonParser &	json
	)

Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'.

Definition at line 49 of file ChemicalReference_json_io.cc.

from_json() [5/34]

void CASM::from_json	(	ClexDescription &	desc,
		const jsonParser &	json
	)

Definition at line 52 of file ClexDescription.cc.

from_json() [6/34]

void CASM::from_json	(	CompositionAxes &	composition_axes,
		const jsonParser &	json
	)

Definition at line 9 of file CompositionAxes_json_io.cc.

from_json() [7/34]

void CASM::from_json	(	CompositionConverter &	f,
		const jsonParser &	json
	)

Deserialize CompositionConverter from JSON.

Definition at line 24 of file CompositionConverter_json_io.cc.

from_json() [8/34]

void CASM::from_json	(	ConfigDoF &	configdof,
		const jsonParser &	json
	)

Read ConfigDoF from JSON.

Definition at line 145 of file ConfigDoF_json_io.cc.

from_json() [9/34]

jsonParser const & CASM::from_json	(	ConfigMapping::Settings &	_set,
		jsonParser const &	_json
	)

Definition at line 31 of file ConfigMapping_json_io.cc.

from_json() [10/34]

void CASM::from_json	(	Configuration &	configuration,
		jsonParser const &	json
	)

Read Configuration from JSON.

Read Configuration from JSON

Note:

• See to_json(Configuration const &configuration, jsonParser &json) for expected format.
• The attribute "transformation_matrix_to_super" must be present. If "supercell_name" is present it is ignored.
• The constructed Configuration is not necessarily canonical, nor is its Supercell.
• The constructed Configuration has a shared Supercell (std::shared_ptr<Supercell const>) that is not owned by any Supercell database.
• Use DB::in_canonical_supercell to make the canonical equivalent configuration with the canonical supercell from the Supercell database, without inserting the configuration in the Configuration database.
• Use DB::make_canonical_and_insert to make the equivalent configuration with the canonical supercell from the Supercell database and insert the canonical equivalent configuration in the Configuration database.

Definition at line 120 of file Configuration_json_io.cc.

from_json() [11/34]

template<>

ChemicalReferenceState CASM::from_json

(

const jsonParser &

json

)

Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'.

Definition at line 21 of file ChemicalReference_json_io.cc.

from_json() [12/34]

template<bool IsConst>

void CASM::from_json	(	const SimpleJSonSiteStructure< IsConst > &	jstruc,
		const jsonParser &	json
	)

Definition at line 114 of file jsonStruc.hh.

from_json() [13/34]

void CASM::from_json	(	DoFSpace &	dofspace,
		jsonParser const &	json,
		std::shared_ptr< Structure const > const &	shared_prim
	)

Definition at line 51 of file DoFSpace.cc.

from_json() [14/34]

void CASM::from_json	(	HyperPlaneReference &	ref,
		const jsonParser &	json,
		HyperPlaneReference::InputFunction	f
	)

Definition at line 71 of file ChemicalReference_json_io.cc.

from_json() [15/34]

void CASM::from_json	(	IntegralCluster &	clust,
		const jsonParser &	json
	)

Read from JSON.

Read IntegralCluster from JSON.

Format:

{
  "min_length" : number,
  "max_length" : number,
  "coordinate_mode" : ("FRAC", "CART", "INT" (default)) (optional)
  "sites" : [
    [b, i, j, k],
    ...
  ]
}

• Also accepts "prototype" in place of "sites"

Definition at line 61 of file IntegralCluster_json_io.cc.

from_json() [16/34]

jsonParser const & CASM::from_json	(	MappedProperties &	prop,
		const jsonParser &	json
	)

Definition at line 66 of file MappedProperties.cc.

from_json() [17/34]

void CASM::from_json	(	OccupantFunction &	func,
		const jsonParser &	json
	)

from_json() [18/34]

void CASM::from_json	(	OrbitPrinterOptions &	opt,
		const jsonParser &	json
	)

Read from JSON.

Definition at line 33 of file OrbitPrinter.cc.

from_json() [19/34]

void CASM::from_json	(	Permutation &	value,
		const jsonParser &	json
	)

re-throw exceptions

re-throw exceptions

Definition at line 22 of file PermutationIO.cc.

from_json() [20/34]

jsonParser const & CASM::from_json	(	ScoreMappedProperties &	score,
		const jsonParser &	json
	)

Definition at line 175 of file MappedProperties.cc.

from_json() [21/34]

template<typename T , typename... Args>

void CASM::from_json	(	std::optional< T > &	value,
		jsonParser const &	json,
		Args &&...	args
	)

Definition at line 21 of file optional.hh.

from_json() [22/34]

void CASM::from_json	(	std::vector< std::pair< std::string, ConfigEnumInput >> &	config_enum_input,
		jsonParser const &	json,
		std::shared_ptr< Structure const >	shared_prim,
		PrimClex const *	primclex,
		DB::Database< Supercell > &	supercell_db,
		DB::Database< Configuration > &	configuration_db
	)

Read std::map<std::string, ConfigEnumInput> from JSON input, allowing queries from databases

Read std::vector<ConfigEnumInput> from JSON input, allowing queries from databases

Note: See parse for JSON documentation

Definition at line 58 of file ConfigEnumInput_json_io.cc.

from_json() [23/34]

jsonParser const & CASM::from_json	(	SymGroupRepID &	_id,
		jsonParser const &	json
	)

Definition at line 20 of file SymGroupRepID.cc.

from_json() [24/34]

void CASM::from_json	(	SymInfoOptions &	opt,
		const jsonParser &	json
	)

Read from JSON.

Definition at line 23 of file SymInfo_json_io.cc.

from_json() [25/34]

void CASM::from_json	(	Variable &	var,
		const jsonParser &	json
	)

from_json() [26/34]

void CASM::from_json	(	xtal::AtomPosition &	apos,
		const jsonParser &	json,
		Eigen::Ref< const Eigen::Matrix3d > const &	frac2cart,
		ParsingDictionary< AnisoValTraits > const &	_aniso_val_dict
	)

Read AtomPosition from json and then apply affine transformation cart2frac*cart()

Definition at line 44 of file BasicStructureIO.cc.

from_json() [27/34]

void CASM::from_json	(	xtal::BasicStructure &	prim,
		jsonParser const &	json,
		double	xtal_tol,
		ParsingDictionary< AnisoValTraits > const *	_aniso_val_dict = nullptr
	)

Definition at line 507 of file BasicStructureIO.cc.

from_json() [28/34]

void CASM::from_json	(	xtal::Lattice &	lat,
		const jsonParser &	json,
		double	xtal_tol
	)

re-throw exceptions

re-throw exceptions

Definition at line 18 of file LatticeIO.cc.

from_json() [29/34]

void CASM::from_json	(	xtal::Molecule &	mol,
		const jsonParser &	json,
		Eigen::Ref< const Eigen::Matrix3d > const &	f2c_mat,
		ParsingDictionary< AnisoValTraits > const &	_aniso_val_dict
	)

Definition at line 108 of file BasicStructureIO.cc.

from_json() [30/34]

void CASM::from_json	(	xtal::ScelEnumProps &	props,
		const jsonParser &	json
	)

Make a ScelEnumProps object from JSON input.

Definition at line 43 of file SuperlatticeEnumeratorIO.cc.

from_json() [31/34]

void CASM::from_json	(	xtal::SimpleStructure &	simple_structure,
		const jsonParser &	json
	)

Read SimpleStructure from JSON.

Read SimpleStructure from JSON

Parameters

simple_structure	xtal::SimpleStructure to read from JSON
json	A JSON object, from which the xtal::SimpleStructure JSON is read. Expects JSON formatted either i) as documented for to_json for xtal::SimpleStructure or ii) if the "atoms_per_type" attribute exists, using the legacy properties.calc.json format as documented for from_json_legacy.

Note:

• This is the expected format for properties.calc.json

Definition at line 387 of file SimpleStructureIO.cc.

from_json() [32/34]

void CASM::from_json	(	xtal::Site &	value,
		const jsonParser &	json,
		xtal::Lattice const &	_home,
		COORD_TYPE	coordtype,
		std::map< std::string, xtal::Molecule > const &	mol_map,
		ParsingDictionary< AnisoValTraits > const &	_aniso_val_dict
	)

Definition at line 184 of file BasicStructureIO.cc.

from_json() [33/34]

jsonParser const & CASM::from_json	(	xtal::SpeciesAttribute &	_attr,
		jsonParser const &	json
	)

Read SpeciesAttribute from json.

Definition at line 18 of file BasicStructureIO.cc.

from_json() [34/34]

void CASM::from_json	(	xtal::UnitCellCoord &	fill_value,
		const jsonParser &	read_json
	)

Read from json [b, i, j, k].

Read from json [b, i, j, k], assuming fill_value.unit() is already set.

Definition at line 19 of file UnitCellCoordIO.cc.

from_json< ChemicalReferenceState >()

template<>

ChemicalReferenceState CASM::from_json< ChemicalReferenceState >

(

const jsonParser &

json

)

Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'.

full_trans_mat()

Eigen::MatrixXd CASM::full_trans_mat

(

std::vector< SymRepTools::IrrepInfo > const &

irreps

)

Assumes that irreps are real, and concatenates their individual trans_mats to form larger trans_mat.

Definition at line 447 of file SymRepTools.cc.

gaussian()

double CASM::gaussian	(	double	a,
		double	x,
		double	b,
		double	c
	)

Definition at line 120 of file CASM_math.cc.

gaussian_moment() [1/2]

double CASM::gaussian_moment	(	int	expon,
		double	sigma
	)

Definition at line 130 of file CASM_math.cc.

gaussian_moment() [2/2]

double CASM::gaussian_moment	(	int	expon,
		double	sigma,
		double	x0
	)

Definition at line 149 of file CASM_math.cc.

gcf()

int CASM::gcf	(	int	i1,
		int	i2
	)

Find greatest common factor.

Definition at line 94 of file CASM_math.cc.

generate_option()

Option CASM::generate_option	(	std::string	postfix,
		char	beginshort
	)

Definition at line 137 of file complete_tests.cpp.

generate_orbits()

template<typename SymCompareType >

std::vector<Orbit<SymCompareType> > CASM::generate_orbits	(	std::vector< typename SymCompareType::Element > const &	generating_elements,
		SymGroup const &	generating_group,
		SymCompareType const &	sym_compare
	)

Construct orbits from a vector of generating elements.

Definition at line 56 of file OrbitGeneration_impl.hh.

get()

template<typename DoFSpecsType >

DoFSpecsType const & CASM::get	(	DoFKey const &	key,
		BasisFunctionSpecs const &	basis_function_specs
	)

Find DoFSpecs and static_cast to DoFSpecsType, or throw exception if not found

Definition at line 169 of file BasisFunctionSpecs.hh.

get_dof_space_dimension()

Index CASM::get_dof_space_dimension	(	DoFKey	dof_key,
		xtal::BasicStructure const &	prim,
		std::optional< Eigen::Matrix3l > const &	transformation_matrix_to_super = std::nullopt,
		std::optional< std::set< Index >> const &	sites = std::nullopt
	)

Return dimension of DoFSpace.

Definition at line 359 of file DoFSpace.cc.

get_normal_coordinate()

Eigen::VectorXd CASM::get_normal_coordinate	(	Configuration const &	config,
		DoFSpace const &	dof_space
	)

Return config DoF value as a coordinate in the DoFSpace basis.

Return config DoF value as a coordinate in the DoFSpace basis

TODO: handle DoF values not in the basis subspace

Definition at line 284 of file DoFSpace.cc.

get_prime_factors()

ReturnArray< Array< int > > CASM::get_prime_factors

(

int

target

)

Definition at line 72 of file CASM_Array_math.cc.

global_dof_info()

std::map< DoFKey, DoFSetInfo > CASM::global_dof_info

(

Structure const &

_struc

)

Definition at line 384 of file Structure.cc.

has_calc_status()

template<typename ConfigType >

bool CASM::has_calc_status	(	const ConfigType &	config,
		std::string	calctype = ""
	)

Definition at line 181 of file Calculable.cc.

has_failure_type()

template<typename ConfigType >

bool CASM::has_failure_type	(	const ConfigType &	config,
		std::string	calctype = ""
	)

Definition at line 189 of file Calculable.cc.

has_local_neighborhood_overlap() [1/2]

template<typename OrbitType >

bool CASM::has_local_neighborhood_overlap	(	std::vector< OrbitType > &	local_orbits,
		const Eigen::Matrix3i &	transf_mat
	)

Check if periodic images of sites in an orbit are overlapping in supercells defined by the given superlattice transformation matrix.

has_local_neighborhood_overlap() [2/2]

template<typename OrbitType >

bool CASM::has_local_neighborhood_overlap	(	std::vector< OrbitType > const &	local_orbits,
		Eigen::Matrix3i const &	transf_mat
	)

Check if periodic images of sites in an orbit are overlapping in supercells defined by the given superlattice transformation matrix.

Parameters

local_orbits	Vector of IntegralCluster orbits defining the local neighborhood
transf_mat	A supercell transformation matrix

Definition at line 195 of file ClusterOrbits_impl.hh.

help()

template<typename T >

std::string CASM::help

(

)

Uses 'multiline_help<T>()' by default.

Definition at line 22 of file Help.hh.

hermite_normal_form_name()

std::string CASM::hermite_normal_form_name

(

const Eigen::Matrix3l &

matrix

)

Definition at line 217 of file SupercellSymInfo.cc.

hungarian_method()

double CASM::hungarian_method	(	const Eigen::MatrixXd &	cost_matrix,
		std::vector< Index > &	optimal_assignments,
		const double	_tol
	)

Definition at line 458 of file CASM_Eigen_math.cc.

identical()

bool CASM::identical ( AnisoValTraits const &  A, AnisoValTraits const &  B  )

inline

Check for equivalence of AnisoValTraits

Compares: name(), standard_var_names(), options(), symrep_builder_name(), incompatible(), must_apply_before(), must_apply_after(), and is_default()

Definition at line 245 of file AnisoValTraits.hh.

include_path()

std::string CASM::include_path

(

const fs::path &

dir

)

Definition at line 401 of file RuntimeLibrary.cc.

indent_space_help()

std::string CASM::indent_space_help

(

)

Definition at line 12 of file help.cc.

index_expression_to_bounds()

std::pair< std::vector< long >, std::vector< long > > CASM::index_expression_to_bounds

(

const std::string &

_expr

)

Definition at line 14 of file DataFormatter.cc.

index_to_kcombination()

template<typename IntType >

std::vector<IntType> CASM::index_to_kcombination	(	IntType	ind,
		IntType	k
	)

Definition at line 228 of file CASM_math.hh.

init_command()

int CASM::init_command

(

const CommandArgs &

args

)

Set command line options using boost program_options

–help option

Set command line options using boost program_options

–help option

Definition at line 139 of file init.cc.

invariants_iterator()

template<typename OrbitIterator >

InvariantsIterator<OrbitIterator> CASM::invariants_iterator

(

OrbitIterator

orbit_it

)

Convert an Orbit iterator to an invariants iterator.

Definition at line 228 of file Orbit.hh.

irrational_to_tex_string()

std::string CASM::irrational_to_tex_string	(	double	val,
		int	lim,
		int	max_pow = 2
	)

Definition at line 199 of file CASM_math.cc.

irrep_decomposition() [1/4]

std::vector< SymRepTools::IrrepInfo > CASM::irrep_decomposition	(	SymGroupRep const &	_rep,
		SymGroup const &	head_group,
		bool	allow_complex
	)

Finds irreducible subspaces that comprise an underlying subspace It does not rely on the character table, but instead utilizes a brute-force method.

Parameters

_rep	matrix representation of head_group, this defines group action on the underlying vector space
head_group	group for which the irreps are to be found
allow_complex	if true, irreps may be complex-valued, if false, complex irreps would be combined to form real representations

Returns

vector of IrrepInfo objects. Irreps are ordered by dimension, with identity first (if present) repeated irreps are sequential, and are distinguished by IrrepInfo::index

Definition at line 761 of file SymRepTools.cc.

irrep_decomposition() [2/4]

std::vector< SymRepTools::IrrepInfo > CASM::irrep_decomposition	(	SymGroupRep const &	_rep,
		SymGroup const &	head_group,
		Eigen::Ref< const Eigen::MatrixXd > const &	_subspace,
		bool	allow_complex
	)

Finds irreducible subspaces that comprise an underlying subspace It does not rely on the character table, but instead utilizes a brute-force method.

Parameters

_rep	matrix representation of head_group, this defines group action on the underlying vector space
head_group	group for which the irreps are to be found
allow_complex	if true, irreps may be complex-valued, if false, complex irreps would be combined to form real representations

Returns

vector of IrrepInfo objects. Irreps are ordered by dimension, with identity first (if present) repeated irreps are sequential, and are distinguished by IrrepInfo::index

Definition at line 770 of file SymRepTools.cc.

irrep_decomposition() [3/4]

std::vector< SymRepTools::IrrepInfo > CASM::irrep_decomposition	(	SymGroupRep const &	_rep,
		SymGroup const &	head_group,
		SymRepTools::SymmetrizerFunction const &	symmetrizer_func,
		bool	allow_complex
	)

Finds irreducible subspaces that comprise an underlying subspace It does not rely on the character table, but instead utilizes a brute-force method.

Parameters

_rep	matrix representation of head_group, this defines group action on the underlying vector space
head_group	group for which the irreps are to be found
allow_complex	if true, irreps may be complex-valued, if false, complex irreps would be combined to form real representations

Returns

vector of IrrepInfo objects. Irreps are ordered by dimension, with identity first (if present) repeated irreps are sequential, and are distinguished by IrrepInfo::index

Definition at line 842 of file SymRepTools.cc.

irrep_decomposition() [4/4]

std::vector< SymRepTools::IrrepInfo > CASM::irrep_decomposition	(	SymGroupRep const &	_rep,
		SymGroup const &	head_group,
		SymRepTools::SymmetrizerFunction const &	symmetrizer_func,
		Eigen::MatrixXd	subspace,
		bool	allow_complex
	)

Finds irreducible subspaces that comprise an underlying subspace It does not rely on the character table, but instead utilizes a brute-force method.

Parameters

_rep	matrix representation of head_group, this defines group action on the underlying vector space
head_group	group for which the irreps are to be found
allow_complex	if true, irreps may be complex-valued, if false, complex irreps would be combined to form real representations

Returns

vector of IrrepInfo objects. Irreps are ordered by dimension, with identity first (if present) repeated irreps are sequential, and are distinguished by IrrepInfo::index

Definition at line 787 of file SymRepTools.cc.

irrep_IDs()

std::vector<SymGroupRepID> CASM::irrep_IDs	(	SymGroupRep const &	_rep,
		const SymGroup &	head_group
	)

Find irrep decomposition of _rep wrt group head_group and returns it as a list of SymGroupRepIDs corresponding to representtions of master_group.

irrep_symmetrizer() [1/2]

SymRepTools::Symmetrizer CASM::irrep_symmetrizer	(	SymGroupRep const &	_rep,
		const SymGroup &	head_group,
		double	vec_compare_tol
	)

Find a new coordinate system oriented along high-symmetry directions in underlying vector space

Parameters

_rep	matrix representation specifying group action on underlying vector space
head_group	subgroup of operations in _rep to be used for symmetry analysis
vec_compare_tol	tolerance for elementwise floating-point comparisons of vectors The ROWS of result.first are the new basis vectors in terms of the old such that new_symrep_matrix = result.first * old_symrep_matrix * result.first.transpose();

Definition at line 420 of file SymRepTools.cc.

irrep_symmetrizer() [2/2]

SymRepTools::Symmetrizer CASM::irrep_symmetrizer	(	SymGroupRep const &	_rep,
		const SymGroup &	head_group,
		Eigen::Ref< const Eigen::MatrixXcd > const &	_subspace,
		double	vec_compare_tol
	)

Find a new coordinate system oriented along high-symmetry directions in vector space spanned by columns of

Parameters

_subspace
_rep	matrix representation specifying group action on underlying vector space
head_group	subgroup of operations in _rep to be used for symmetry analysis
_subspace	matrix such that _subspace.rows()==_rep.dim() and whose columns specify a subspace of underlying vector space
vec_compare_tol	tolerance for elementwise floating-point comparisons of vectors The ROWS of result.first are the new basis vectors in terms of the old such that new_symrep_matrix = result.first * old_symrep_matrix * result.first.transpose();

Definition at line 431 of file SymRepTools.cc.

irrep_trans_mat()

Eigen::MatrixXd CASM::irrep_trans_mat	(	SymGroupRep const &	_rep,
		const SymGroup &	head_group
	)

Finds the transformation matrix that block-diagonalizes this representation of head_group into irrep blocks It does not rely on the character table, but instead utilizes a brute-force method This routine additionally orients the resulting basis vectors along high-symmetry directions of the vector space on which they are defined.

Parameters

head_group

The group with respect to which irreps are determined, which may be a subset of all operations in this representation

Returns

Transformation matrix with the ROWS comprising the new basis vectors in terms of the old such that new_symrep_matrix = trans_mat * old_symrep_matrix * trans_mat.transpose();

Definition at line 1128 of file SymRepTools.cc.

irrep_trans_mat_and_characters()

std::pair<Eigen::MatrixXd, std::vector<Eigen::VectorXcd> > CASM::irrep_trans_mat_and_characters	(	SymGroupRep const &	_rep,
		const SymGroup &	head_group,
		SymRepTools::SymmetrizerFunction	symmetrizer_func
	)

Finds the transformation matrix that block-diagonalizes this representation of head_group into irrep blocks It does not rely on the character table, but instead utilizes a brute-force method.

Parameters

head_group	The group with respect to which irreps are determined, which may be a subset of all operations in this representation
symmetrizer_func,a	function object that takes an unsymmetrized irrep subspace and returns its Symmetrizer object

Returns

Pair, with result.first being the transformation matrix with the ROWS comprising the new basis vectors in terms of the old such that new_symrep_matrix = trans_mat * old_symrep_matrix * trans_mat.transpose(); result.second contains the complex character vectors of the irreducible subspaces, in same order as they appear in result.first

is_calculated() [1/2]

template<typename ConfigType >

bool CASM::is_calculated	(	const ConfigType &	config,
		std::string	calctype = ""
	)

Return true if all required properties have been been calculated for the configuration.

Return true if all required properties have been been calculated for the configuration in the calctype specified (current calctype if none specified)

Definition at line 137 of file Calculable.cc.

is_calculated() [2/2]

bool CASM::is_calculated	(	const MappedProperties &	calc_properties,
		const std::vector< std::string > &	required_properties
	)

Return true if all required properties are included in the JSON.

Definition at line 219 of file Calculable.cc.

is_guaranteed_for_database_insert()

template<>

bool CASM::is_guaranteed_for_database_insert

(

ScelEnumByProps const &

enumerator

)

Always true for ScelEnumByProps.

Definition at line 13 of file ScelEnum.cc.

is_irrep()

bool CASM::is_irrep	(	SymGroupRep const &	_rep,
		const SymGroup &	head_group
	)

Returns true if _rep is irreducible wrt head_group (does not use character table information)

Definition at line 708 of file SymRepTools.cc.

is_valid_dof_space()

bool CASM::is_valid_dof_space	(	Configuration const &	config,
		DoFSpace const &	dof_space
	)

Return true if dof_space is valid for config

Checks that:

• The prim are equivalent
• For local DoF, that the transformation_matrix_to_super are equivalent

Definition at line 257 of file DoFSpace.cc.

is_valid_sub_configuration()

bool CASM::is_valid_sub_configuration	(	xtal::Lattice const &	sub_configuration_lattice,
		Supercell const &	supercell
	)

Return true if a configuration (in any equivalent orientation) can be tiled into a supercell

Note:

• This will return true if, for any SymOp in the prim factor group, apply(symop, sub_configuration_lattice) can be used used to fill the Supercell. Otherwise it will return false.

Return true if a configuration (in any equivalent orientation) can be tiled into a supercell

Note:

• This will return true if, any SymOp in the prim factor group, apply(symop, configuration) can be used used to fill the Supercell. Otherwise it will return false.

Definition at line 20 of file FillSupercell.cc.

kron_rep()

SymGroupRep CASM::kron_rep	(	const SymGroupRep &	LHS,
		const SymGroupRep &	RHS
	)

Build a large matrix representation by forming kronecker products of a matrix from

Parameters

LHS	with a matrix from
RHS

Definition at line 1256 of file SymRepTools.cc.

lcm() [1/2]

int CASM::lcm

(

const Array< int > &

series

)

Find least common multiple.

Definition at line 62 of file CASM_Array_math.cc.

lcm() [2/2]

int CASM::lcm	(	int	i1,
		int	i2
	)

Find least common multiple.

Definition at line 113 of file CASM_math.cc.

link_path()

std::string CASM::link_path

(

const fs::path &

dir

)

Definition at line 408 of file RuntimeLibrary.cc.

load_dof_plugins()

template<typename DoFDictInserter , typename RuntimeLibInserter >

std::pair< DoFDictInserter, RuntimeLibInserter > CASM::load_dof_plugins	(	const ProjectSettings &	set,
		DoFDictInserter	dict_it,
		RuntimeLibInserter	lib_it
	)

Load DoF plugins from a CASM project.

Definition at line 14 of file HamiltonianModules_impl.hh.

load_enumerator_plugins() [1/2]

template std::pair<enum_it_type, runtimelib_it_type> CASM::load_enumerator_plugins	(	ProjectSettings const &	set,
		enum_it_type	enum_it,
		runtimelib_it_type	lib_it
	)

load_enumerator_plugins() [2/2]

template<typename EnumInterfaceVectorInserter , typename RuntimeLibInserter >

std::pair< EnumInterfaceVectorInserter, RuntimeLibInserter > CASM::load_enumerator_plugins	(	ProjectSettings const &	set,
		EnumInterfaceVectorInserter	enum_it,
		RuntimeLibInserter	lib_it
	)

Load enumerator plugins from a CASM project.

Parameters

set	CASM project settings to read enumerator plugins from
enum_it	Inserter to EnumInterfaceVector where the plugins should be stored
lib_it	Inserter to container of pair<std::string, std::shared_ptr<RuntimeLibrary> > holding the libraries with the enumerator plugins

• Checks the directory primclex.dir().enumerator_plugins() for ENUMNAME.cc files
• All *.cc files found are compiled and linked, and the base of the filename (ENUMNAME) is assumed to be the enumerator name
• An extern C function named make_ENUMNAME_interface is assumed to exist with signature: CASM::EnumInterfaceBase* make_ENUMNAME_interface(), that returns a pointer which owns a CASM::EnumInterfaceBase-derived object

Note

The lifetime of the RuntimeLibrary must be longer than the lifetime of the EnumInterface

Definition at line 36 of file EnumeratorHandler_impl.hh.

load_query_plugins()

template<typename DataFormatterDictInserter , typename RuntimeLibInserter >

std::pair< DataFormatterDictInserter, RuntimeLibInserter > CASM::load_query_plugins	(	const ProjectSettings &	set,
		DataFormatterDictInserter	dict_it,
		RuntimeLibInserter	lib_it
	)

Load enumerator plugins from a CASM project.

Definition at line 105 of file QueryHandler_impl.hh.

load_symrep_builder_plugins()

template<typename SymRepBuilderDictInserter , typename RuntimeLibInserter >

std::pair< SymRepBuilderDictInserter, RuntimeLibInserter > CASM::load_symrep_builder_plugins	(	const ProjectSettings &	set,
		SymRepBuilderDictInserter	dict_it,
		RuntimeLibInserter	lib_it
	)

Load SymRepBuilder plugins from a CASM project.

Definition at line 66 of file HamiltonianModules_impl.hh.

local_dof_info()

std::map< DoFKey, std::vector< DoFSetInfo > > CASM::local_dof_info

(

Structure const &

_struc

)

Definition at line 395 of file Structure.cc.

log()

Log& CASM::log ( )

inline

Definition at line 424 of file Log.hh.

log_make_shared_runtime_lib()

std::shared_ptr< RuntimeLibrary > CASM::log_make_shared_runtime_lib	(	std::string	filename_base,
		std::string	compile_options,
		std::string	so_options,
		std::string	compile_msg
	)

Make shared_ptr<RuntimeLibrary>, logging progress and errors.

Definition at line 19 of file LogRuntimeLibrary.cc.

make_all_super_configurations()

template<typename ConfigOutputIterator >

ConfigOutputIterator CASM::make_all_super_configurations	(	Configuration const &	configuration,
		std::shared_ptr< Supercell const >	shared_supercell,
		ConfigOutputIterator	result
	)

Make all super configurations that fill a particular supercell.

Make all equivalent configurations with respect to the prim factor group that fill a supercell

Method:

• Generate primitive of "configuration"
• Find all non-equivalent ways (w.r.t. supercell factor group) to fill "shared_supercell" with the primitive configuration
• For each, use ConfigEnumByPermutation to generate all equivalents (w.r.t. supercell factor group) in "shared_supercell"

Note:

• Does not check if "shared_supercell" can be tiled by configuration. To do this check with is_valid_sub_configuration.

Definition at line 27 of file FillSupercell_impl.hh.

make_api_command() [1/2]

template<typename CommandType >

std::unique_ptr< CommandType > CASM::make_api_command	(	CommandArgs const &	args,
		typename CommandType::OptionType &	opt
	)

Parse command line options and make API command. Throws for parsing errors.

Definition at line 13 of file APICommand_impl.hh.

make_api_command() [2/2]

template<typename CommandType >

std::unique_ptr< CommandType > CASM::make_api_command	(	std::string	cli_str,
		PrimClex &	primclex,
		typename CommandType::OptionType &	opt
	)

Parse command line options and make API command. Throws for parsing errors.

Parse command line options and make API command. Throws for parsing errors.

Parameters

cli_str	CLI args string, ex: 'casm X ...'
primclex	Existing PrimClex

Definition at line 27 of file APICommand_impl.hh.

make_asymmetric_unit()

template<typename OrbitType , typename OrbitOutputIterator >

OrbitOutputIterator CASM::make_asymmetric_unit ( const OrbitBranchSpecs< OrbitType > &  specs, OrbitOutputIterator  result, std::ostream &  status  )

related

Generate the asymmetric unit, using OrbitBranchSpecs.

make_attribute_dictionary()

template<typename DataObject >

DataFormatterDictionary< DataObject > CASM::make_attribute_dictionary

(

)

Dictionary of all AttributeFormatter (i.e. BaseValueFormatter<V, DataObject>)

Dictionary of all Attribute.

Dictionary of all Attribute types of DataObject.

Default includes String, Boolean, Integer, Scalar, and VectorXd attributes

Definition at line 1182 of file DataFormatterTools.hh.

make_attribute_dictionary< std::shared_ptr< const Structure > >()

template<>

DataFormatterDictionary< std::shared_ptr< const Structure > > CASM::make_attribute_dictionary< std::shared_ptr< const Structure > >

(

)

Definition at line 1 of file SharedPrim_data_io.cc.

make_attribute_dictionary< SupercellSymInfo >()

template<>

DataFormatterDictionary< SupercellSymInfo > CASM::make_attribute_dictionary< SupercellSymInfo >

(

)

Definition at line 1 of file SupercellSymInfo_data_io.cc.

make_axis_glossary()

std::vector<std::string> CASM::make_axis_glossary	(	DoFKey	dof_key,
		xtal::BasicStructure const &	prim,
		std::optional< Eigen::Matrix3l > const &	transformation_matrix_to_super,
		std::optional< std::set< Index >> const &	sites
	)

The axis_glossary gives names to an un-symmetrized coordinate system.

Definition at line 388 of file DoFSpace.cc.

make_boolean_dictionary< Supercell >()

template<>

BooleanAttributeDictionary< Supercell > CASM::make_boolean_dictionary< Supercell >

(

)

Definition at line 19 of file SupercellIO.cc.

make_canonical_cluster_site_indices()

template<typename InversePermutationIterator >

std::set< Index > CASM::make_canonical_cluster_site_indices	(	InversePermutationIterator	inverse_permutations_begin,
		InversePermutationIterator	inverse_permutations_end,
		std::set< Index > const &	cluster_site_indices
	)

Apply inverse permutations and return the maximum equivalent cluster_site_indices

Definition at line 26 of file SupercellClusterOrbits_impl.hh.

make_canonical_supercell_name()

std::string CASM::make_canonical_supercell_name	(	SymGroup const &	point_group,
		Lattice const &	prim_lattice,
		Lattice const &	supercell_lattice
	)

Make the canonical supercell name.

Make the canonical supercell name from SupercellSymInfo.

Definition at line 300 of file SupercellSymInfo.cc.

make_cluster()

IntegralCluster CASM::make_cluster	(	std::set< Index > const &	cluster_site_indices,
		Structure const &	prim,
		SupercellSymInfo const &	sym_info
	)

Return cluster from cluster site indices.

Definition at line 28 of file SupercellClusterOrbits.cc.

make_cluster_site_indices()

std::set< Index > CASM::make_cluster_site_indices	(	IntegralCluster const &	cluster,
		SupercellSymInfo const &	sym_info
	)

Return site indices of cluster sites.

Definition at line 17 of file SupercellClusterOrbits.cc.

make_collective_dof_symrep()

std::pair< MasterSymGroup, SymGroupRepID > CASM::make_collective_dof_symrep	(	std::set< Index > const &	site_indices,
		SupercellSymInfo const &	_syminfo,
		DoFKey const &	_key,
		std::vector< PermuteIterator > const &	_group
	)

Make the matrix representation for group '_group' describing the transformation of DoF '_key' among a subset of sites.

Parameters

site_indices	Set of site indices that define subset of sites of interest
_syminfo	SupercellSymInfo object that defines all symmetry properties of supercell
_key	DoFKey specifying which local DoF is of interest
_group	vector of PermuteIterators forming the group that is to be represented (this may be larger than a crystallographic factor group)

Returns

A std::pair containing a MasterSymGroup instantiation of _group and a SymGroupRepID that can be used to access the 'collective_dof_symrep' within the returned MasterSymGroup

Definition at line 372 of file SupercellSymInfo.cc.

make_configdof() [1/4]

ConfigDoF CASM::make_configdof	(	Structure const &	prim,
		Index	volume
	)

Construct zero-valued ConfigDoF.

Definition at line 10 of file ConfigDoFTools.cc.

make_configdof() [2/4]

ConfigDoF CASM::make_configdof	(	Structure const &	prim,
		Index	volume,
		double	tol
	)

Construct zero-valued ConfigDoF.

Definition at line 17 of file ConfigDoFTools.cc.

make_configdof() [3/4]

ConfigDoF CASM::make_configdof

(

Supercell const &

supercell

)

Construct zero-valued ConfigDoF.

Definition at line 39 of file ConfigDoFTools.cc.

make_configdof() [4/4]

ConfigDoF CASM::make_configdof	(	Supercell const &	supercell,
		double	tol
	)

Construct zero-valued ConfigDoF.

Definition at line 44 of file ConfigDoFTools.cc.

make_data_formatter_filter() [1/2]

template<typename DataObject >

DataFormatterFilter< DataObject > CASM::make_data_formatter_filter	(	std::string const &	filter_expr,
		DataFormatterDictionary< DataObject > const &	_dict
	)

Definition at line 24 of file DataFormatterFilter_impl.hh.

make_data_formatter_filter() [2/2]

template<typename DataObject >

DataFormatterFilter< DataObject > CASM::make_data_formatter_filter	(	std::vector< std::string > const &	filter_expr,
		DataFormatterDictionary< DataObject > const &	_dict
	)

Definition at line 31 of file DataFormatterFilter_impl.hh.

make_datum_formatter_adapter()

template<typename ExternalType , typename InternalType >

DatumFormatterAdapter<ExternalType, InternalType> CASM::make_datum_formatter_adapter

(

BaseDatumFormatter< InternalType > const &

_base_formatter

)

Definition at line 122 of file DatumFormatterAdapter.hh.

make_default_project_settings() [1/2]

ProjectSettings CASM::make_default_project_settings	(	xtal::BasicStructure const &	prim,
		std::string	project_name
	)

Construct default project settings for a given prim structure, without setting a root dir

Notes:

• Uses default_nlist_weight_matrix and default_nlist_sublat_indices
• Create default clex using default_configuration_clex
• Sets required_properties for Configuration to "energy"

Definition at line 88 of file ProjectBuilder.cc.

make_default_project_settings() [2/2]

ProjectSettings CASM::make_default_project_settings	(	xtal::BasicStructure const &	prim,
		std::string	project_name,
		fs::path	root_dir
	)

Construct default project settings for a given prim structure, including a root dir

Notes:

• Uses default_nlist_weight_matrix and default_nlist_sublat_indices
• Create default clex using default_configuration_clex
• Sets required_properties for Configuration to "energy"
• Sets root dir in project settings

Definition at line 100 of file ProjectBuilder.cc.

make_dictionary()

template<typename DataObject >

DataFormatterDictionary<DataObject> CASM::make_dictionary

(

)

Template to can be specialized for constructing dictionaries for particular DataObject.

Default includes the make_attribute_dictionary() and make_operator_dictionary()

Definition at line 732 of file DataFormatter.hh.

make_dof_space()

DoFSpace CASM::make_dof_space	(	DoFKey	dof_key,
		ConfigEnumInput const &	input_state,
		std::optional< Eigen::MatrixXd > const &	basis = std::nullopt
	)

Make DoFSpace using dof_key, transformation matrix and sites from input_state, and basis

Definition at line 487 of file DoFSpace.cc.

make_dof_space_axis_glossary()

std::vector<std::string> CASM::make_dof_space_axis_glossary	(	DoFKey	dof_key,
		xtal::BasicStructure const &	prim,
		std::optional< Eigen::Matrix3l > const &	transformation_matrix_to_super = std::nullopt,
		std::optional< std::set< Index >> const &	sites = std::nullopt
	)

Make DoFSpace axis glossary.

make_dof_space_axis_info()

void CASM::make_dof_space_axis_info	(	DoFKey	dof_key,
		xtal::BasicStructure const &	prim,
		std::optional< Eigen::Matrix3l > const &	transformation_matrix_to_super,
		std::optional< std::set< Index >> const &	sites,
		std::vector< std::string > &	axis_glossary,
		std::optional< std::vector< Index >> &	axis_site_index,
		std::optional< std::vector< Index >> &	axis_dof_component
	)

Make DoFSpace axis glossary, axis site index, and axis dof component.

The axis_glossary gives names to an un-symmetrized coordinate system.

Definition at line 429 of file DoFSpace.cc.

make_dof_space_symrep()

SymGroupRep const & CASM::make_dof_space_symrep	(	DoFSpace const &	dof_space,
		SupercellSymInfo const &	sym_info,
		std::vector< PermuteIterator > const &	group,
		MasterSymGroup &	symrep_master_group,
		SymGroupRepID &	id
	)

Make a SymGroupRep for a DoFSpace.

Make a SymGroupRep for a DoFSpace

Usage:

    DoFSpace dof_space = ... ;
    SupercellSymInfo const &sym_info = ... ;
    std::vector<PermuteIterator> invariant_group = ... ;
    MasterSymGroup symrep_master_group;
    SymGroupRepID id;
    SymGroupRep const &rep = make_dof_space_symrep(
       dof_space, sym_info, invariant_group, symrep_master_group, id);
    for (SymOp const &op : group) {
      Eigen::MatrixXd matrix_rep = *(rep.MatrixXd(op));
      // transformed_dof_values = matrix_rep * dof_values_in_dof_space_basis;
// }

Definition at line 513 of file DoFSpace.cc.

make_enum_parent_parser()

ParentInputParser CASM::make_enum_parent_parser	(	Log &	log,
		jsonParser const &	json_options,
		jsonParser const &	cli_options_as_json
	)

Combine –input / –settings JSON with CLI options.

Definition at line 78 of file EnumInterface.cc.

make_hermite_normal_form()

Eigen::Matrix3l CASM::make_hermite_normal_form

(

std::string

hermite_normal_form_name

)

Definition at line 231 of file SupercellSymInfo.cc.

make_homogeneous_mode_space()

Eigen::MatrixXd CASM::make_homogeneous_mode_space

(

DoFSpace const &

dof_space

)

Make the homogeneous mode space of a local DoFSpace.

Make the homogeneous mode space of a local DoFSpace

Parameters

dof_space

DoF space to find the homogeneous mode space of. Should be a DoF space for a local continuous DoF and include all sites in the supercell.

Returns

The column vector space of allowed homogeneous modes (i.e. allowed rigid translations)

The prim DoF basis may not be either equal to the standard DoF basis, or the same on all sublattices. The homoegeneous mode space then is limited to the common part of dof_info.basis() for each site in the prim.

Ex: most typical, all displacements allowed on all sites: prim_dof_info[0].basis(): [[dx], [dy], [dz]], prim_dof_info[1].basis(): [[dx], [dy], [dz]] Common basis: Rigid translations in [[dx], [dy], [dz]]

Ex: 2d displacements: prim_dof_info[0].basis(): [[dx], [dy]], prim_dof_info[1].basis(): [[dx], [dy]] Common basis: Rigid translations are only allowed in [[dx], [dy]]

Ex: 2d displacements of differing orientation, 1d common basis: prim_dof_info[0].basis(): [[dx, dy], [dz]], prim_dof_info[1].basis(): [[-dx, dy], [dz]] Common basis: Rigid translations are only allowed in [[dz]]

Ex: some fixed sites: prim_dof_info[0].basis(): <not allowed>, prim_dof_info[1].basis(): [[dx], [dy], [dz]] Common basis: No rigid translations allowed

The common basis, in the standard DoF basis, is: common_standard_basis = nullspace( Prod_i P(i) - I ), where projector P(i), is: P(i) = prim_dof_info[i].basis() * prim_dof_info[i].inv_basis()

If the common_standard_basis is not empty, the homogeneous mode space is the column vector space constructed by transforming the common_standard_basis back into the basis for each site in the DoFSpace:

[[ sites_dof_info[0].inv_basis() * common_standard_basis ],
 [ sites_dof_info[1].inv_basis() * common_standard_basis ],
 ...,
 [ sites_dof_info[n_sites-1].inv_basis() * common_standard_basis ]]

Note that the lines above represent blocks equal to the dimension of the DoF basis on each site.

DoFSetInfo for each sublattice

DoFSetInfo for each site in the DoFSpace with 'dof_key'

DoFSetInfo for each sublattice

DoFSetInfo for each site in the DoFSpace with 'dof_key'

Definition at line 740 of file DoFSpace.cc.

make_index_converter() [1/2]

std::vector< std::vector< Index > > CASM::make_index_converter	(	const Structure &	struc,
		std::vector< std::string >	mol_name_list
	)

Returns 'converter' which converts site_occupant indices to 'mol_name_list' indices: mol_name_list_index = converter[basis_site][site_occupant_index]

Returns 'converter' which converts Site::site_occupant indices to 'mol_name_list' indices: mol_name_list_index = converter[basis_site][site_occupant_index]

Definition at line 341 of file Structure.cc.

make_index_converter() [2/2]

std::vector<std::vector<Index> > CASM::make_index_converter	(	const Structure &	struc,
		std::vector< xtal::Molecule >	mol_list
	)

Returns 'converter' which converts site_occupant indices to 'mol_list' indices: mol_list_index = converter[basis_site][site_occupant_index]

Returns 'converter' which converts Site::site_occupant indices to 'mol_list' indices: mol_list_index = converter[basis_site][site_occupant_index]

Definition at line 322 of file Structure.cc.

make_index_converter_inverse()

std::vector< std::vector< Index > > CASM::make_index_converter_inverse	(	const Structure &	struc,
		std::vector< std::string >	mol_name_list
	)

Returns 'converter_inverse' which converts 'mol_name_list' indices to Site::site_occupant indices: site_occupant_index = converter_inverse[basis_site][mol_name_list_index]

Returns 'converter_inverse' which converts 'mol_name_list' indices to Site::site_occupant indices: site_occupant_index = converter_inverse[basis_site][mol_name_list_index]

If mol is not allowed on basis_site, return struc.basis()[basis_site].occupant_dof().size()

Definition at line 363 of file Structure.cc.

make_integer_dictionary< Supercell >()

template<>

IntegerAttributeDictionary< Supercell > CASM::make_integer_dictionary< Supercell >

(

)

Definition at line 19 of file SupercellIO.cc.

make_invariant_subgroup() [1/4]

template<typename Element , typename SymCompareType >

SymGroup CASM::make_invariant_subgroup	(	const Element &	element,
		const SymGroup &	generating_grp,
		const SymCompareType &	sym_compare
	)

Construct the subgroup that leaves an element unchanged.

Includes translations as determined from 'sym_compare'

Implementation is equivalent to:

Element e {sym_compare.prepare(element)};
SymGroup result = generating_grp;
result.clear();
for(const auto &op : generating_grp) {
  if(sym_compare.equal(e, sym_compare.prepare(sym_compare.copy_apply(op,
  e)))) {
   result.push_back(sym_compare.spatial_transform()*op);
  }
}
return result;

Definition at line 92 of file InvariantSubgroup_impl.hh.

make_invariant_subgroup() [2/4]

template<typename OrbitType >

SymGroup CASM::make_invariant_subgroup	(	const OrbitType &	orbit,
		Index	element_index
	)

Construct the subgroup that leaves an element of the orbit unchanged.

Does not include translations as determined from 'sym_compare'

The equivalence map is: element(i) compares equivalent to prototype().copy_apply(equivalence_map[i][j]) for all j

The subgroup that leaves element 'i' of the orbit unchanged is, for all j: eq_map[i][0]*eq_map[0][j]*eq_map[i][0].inverse()

Definition at line 118 of file InvariantSubgroup_impl.hh.

make_invariant_subgroup() [3/4]

template<typename Element , typename OpIterator , typename SymCompareType , typename OpOutputIterator >

OpOutputIterator CASM::make_invariant_subgroup	(	Element const &	element,
		OpIterator	group_begin,
		OpIterator	group_end,
		SymCompareType const &	sym_compare,
		OpOutputIterator	result
	)

Construct the subgroup that leaves an element unchanged.

Construct the subgroup that leaves an element unchanged

Includes translations as determined from 'sym_compare'

Implementation is equivalent to:

Element e {sym_compare.prepare(element)};
for(auto group_it=group_begin; group_it!=group_end; ++group_it) {
  if(sym_compare.equal(e, sym_compare.prepare(sym_compare.copy_apply(*it,
  e)))) {
    *result++ = sym_compare.spatial_transform() * (*it);
  }
}
return result;

Definition at line 29 of file InvariantSubgroup_impl.hh.

make_invariant_subgroup() [4/4]

template<typename Element , typename SymCompareType , typename OutputIterator >

OutputIterator CASM::make_invariant_subgroup	(	Element const &	element,
		PermuteIterator	permute_begin,
		PermuteIterator	permute_end,
		SymCompareType const &	sym_compare,
		OutputIterator	result
	)

Construct the subgroup (PermuteIterator) that leaves an element unchanged.

Construct the subgroup (PermuteIterator) that leaves an element unchanged

Implementation is equivalent to:

Element e {sym_compare.prepare(element)};
for(auto permute_it=permute_begin; permute_it!=permute_end; ++permute_it) {
  if(sym_compare.equal(e,
  sym_compare.prepare(sym_compare.copy_apply(permute_it->sym_op(), e)))) {
    *result++ = permute_it;
  }
}
return result;

Definition at line 58 of file InvariantSubgroup_impl.hh.

make_inverse_permutations()

template<typename PermuteIteratorIt >

std::vector< Permutation > CASM::make_inverse_permutations	(	PermuteIteratorIt	begin,
		PermuteIteratorIt	end
	)

Make inverse permutations.

Make inverse permutations

Inverse permutations allow fast permutation of cluster site indices. For the details see permute_cluster_site_indices.

Definition at line 14 of file SupercellClusterOrbits_impl.hh.

make_irrep_decomposition()

SymRepTools_v2::IrrepDecomposition CASM::make_irrep_decomposition	(	SymGroupRep const &	rep,
		SymGroup const &	head_group,
		Eigen::MatrixXd const &	_init_subspace,
		bool	allow_complex
	)

Make an IrrepDecompotion using CASM::SymGroupRep and CASM::SymGroup.

Definition at line 150 of file IrrepDecomposition.cc.

make_json_dictionary< Configuration >()

template<>

DataFormatterDictionary<Configuration, BaseValueFormatter<jsonParser, Configuration> > CASM::make_json_dictionary< Configuration >

(

)

Definition at line 43 of file ConfigIO.cc.

make_json_dictionary< Supercell >()

template<>

DataFormatterDictionary<Supercell, BaseValueFormatter<jsonParser, Supercell> > CASM::make_json_dictionary< Supercell >

(

)

Definition at line 19 of file SupercellIO.cc.

make_json_input()

template<typename OptionType >

jsonParser CASM::make_json_input

(

const OptionType &

opt

)

Check for –settings, then –input and return JSON input. Else return empty JSON object.

Definition at line 11 of file json_io_impl.hh.

make_operator_dictionary()

template<typename DataObject >

DataFormatterDictionary< DataObject > CASM::make_operator_dictionary

(

)

Dictionary of all DatumFormatterOperator.

Definition at line 514 of file DataFormatterTools.hh.

make_orbit_generators_under_periodic_boundary_conditions()

template<typename InversePermutationIterator , typename ElementIterator >

std::set< std::set< Index >, ClusterSiteIndicesCompare > CASM::make_orbit_generators_under_periodic_boundary_conditions	(	SupercellSymInfo const &	sym_info,
		InversePermutationIterator	inverse_permutations_begin,
		InversePermutationIterator	inverse_permutations_end,
		ElementIterator	element_begin,
		ElementIterator	element_end
	)

Return "within_scel" orbit generators, as sets of cluster site indices.

Return orbit generators, as sets of cluster site indices, under periodic boundary conditions

Given a range of elements (IntegralCluster), convert to sets of cluster site indices, and apply permute group operations (using inverse permutations to permute site indices instead of site values) to identify unique cluster site indices under periodic boundary conditions

Note:

• A supercell/configuration may have lower symmetry than the prim, resulting in orbit breaking. The input elements must have been generated using the supercell/configuration symmetry in order to generate all the unique orbit generating elements under periodic boundary conditions. Using "prim_periodic" orbit prototypes is allowed, but then the output of this method will not reflect any symmetry breaking do to the supercell/configuration.

Parameters

sym_info	SupercellSymInfo for the supercell in which cluster orbits are generated
inverse_permutations_begin,inverse_permutations_end	The inverse permutations of the permute group that will be used to generate cluster orbits in the supercell (i.e the result of make_inverse_permutations for the range [sym_info.permute_begin(), sym_info.permute_end()) or a subgroup (i.e. Configuration::factor_group()).
element_begin,element_end	Iterators that provide orbit elements (IntegralCluster).

Definition at line 72 of file SupercellClusterOrbits_impl.hh.

make_orbits() [1/3]

template<typename GeneratorIterator , typename SymCompareType , typename OrbitOutputIterator >

OrbitOutputIterator CASM::make_orbits	(	GeneratorIterator	gen_begin,
		GeneratorIterator	gen_end,
		const SymGroup &	generating_group,
		const SymCompareType &	sym_compare,
		OrbitOutputIterator	result
	)

Iterator over Generators (potential prototypes) and insert resulting orbits into 'result' iterator.

Definition at line 179 of file Orbit.hh.

make_orbits() [2/3]

template<typename GeneratorIterator , typename SymCompareType , typename OrbitOutputIterator >

OrbitOutputIterator CASM::make_orbits	(	GeneratorIterator	gen_begin,
		GeneratorIterator	gen_end,
		const SymGroup &	generating_group,
		const SymCompareType &	sym_compare,
		OrbitOutputIterator	result,
		std::ostream &	status
	)

Generate Orbit<IntegralVector> using OrbitBranchSpecs.

Definition at line 19 of file VectorOrbits.hh.

make_orbits() [3/3]

template<typename OrbitBranchSpecsIterator , typename OrbitOutputIterator >

OrbitOutputIterator CASM::make_orbits	(	OrbitBranchSpecsIterator	begin,
		OrbitBranchSpecsIterator	end,
		const std::vector< IntegralClusterOrbitGenerator > &	custom_generators,
		OrbitOutputIterator	result,
		std::ostream &	status
	)

Generate orbits of IntegralCluster using OrbitBranchSpecs.

Generate Orbit<IntegralCluster> using OrbitBranchSpecs.

Parameters

begin,end	A range of OrbitBranchSpecs, starting with the null branch
custom_generators	A vector of custom orbit generating clusters
result	An output iterator for Orbit
status	Stream for status messages

Definition at line 479 of file ClusterOrbits_impl.hh.

make_parsing_dictionary()

template<typename T >

ParsingDictionary<T> CASM::make_parsing_dictionary

(

)

make_parsing_dictionary< AnisoValTraits >()

template<>

ParsingDictionary< AnisoValTraits > CASM::make_parsing_dictionary< AnisoValTraits >

(

)

Definition at line 1 of file AnisoValTraits.cc.

make_parsing_dictionary< DoFType::Traits >()

template<>

DoFType::TraitsDictionary CASM::make_parsing_dictionary< DoFType::Traits >

(

)

Definition at line 26 of file DoFTraits.cc.

make_parsing_dictionary< SymRepBuilderInterface >()

template<>

HamiltonianModules::SymRepBuilderDictionary CASM::make_parsing_dictionary< SymRepBuilderInterface >

(

)

Definition at line 7 of file HamiltonianModules.cc.

make_permutation_representation()

SymGroupRepID CASM::make_permutation_representation	(	const SymGroup &	group,
		const xtal::UnitCellCoordIndexConverter &	bijk_index_converter,
		const Lattice &	prim_lattice,
		const SymGroupRepID &	prim_symrep_ID
	)

Definition at line 103 of file SupercellSymInfo.cc.

make_point_group() [1/5]

template<typename PermuteIteratorContainer >

SymGroup CASM::make_point_group	(	const PermuteIteratorContainer &	container,
		const Lattice &	supercell_lattice
	)

Returns a SymGroup generated from a container of PermuteIterator.

Parameters

container

A container of PermuteIterator

• The result is sorted

Definition at line 179 of file PermuteIterator.hh.

make_point_group() [2/5]

template SymGroup CASM::make_point_group	(	PermuteIterator	begin,
		PermuteIterator	end,
		const Lattice &	supercell_lattice
	)

make_point_group() [3/5]

template<typename PermuteIteratorIt >

SymGroup CASM::make_point_group	(	PermuteIteratorIt	begin,
		PermuteIteratorIt	end,
		const Lattice &	supercell_lattice
	)

Returns a SymGroup generated from a range of PermuteIterator.

Parameters

begin,end

A range of PermuteIterator

• The result is sorted
• The result uses the Supercell lattice for periodic comparisons

Definition at line 236 of file PermuteIterator.cc.

make_point_group() [4/5]

template SymGroup CASM::make_point_group	(	std::vector< PermuteIterator >::const_iterator	begin,
		std::vector< PermuteIterator >::const_iterator	end,
		const Lattice &	supercell_lattice
	)

make_point_group() [5/5]

template SymGroup CASM::make_point_group	(	std::vector< PermuteIterator >::iterator	begin,
		std::vector< PermuteIterator >::iterator	end,
		const Lattice &	supercell_lattice
	)

make_report()

jsonParser CASM::make_report

(

KwargsParser const &

parser

)

Return parser.input with error and warning messages added in place.

Return parser.input with error and warning messages added in place, including all subparsers

Definition at line 214 of file InputParser.cc.

make_scalar_dictionary< Supercell >()

template<>

ScalarAttributeDictionary< Supercell > CASM::make_scalar_dictionary< Supercell >

(

)

Definition at line 19 of file SupercellIO.cc.

make_simple_structure() [1/3]

xtal::SimpleStructure CASM::make_simple_structure	(	Configuration const &	_config,
		std::vector< DoFKey > const &	_which_dofs = {},
		bool	relaxed = false
	)

Construct SimpleStructure from Configuration.

Parameters

_config	Configuration used as source data
_which_dofs	List of DoF type-names that specify which DoF values to utilize from _config when building the result. If empty, all DoFs are used. To exclude all DoFs from conversion, pass _which_dofs={"none"}.
relaxed	Flag specifying to use relaxed coordinates and parameters (if true) or to only use the imposed DoFs (if false).

Note:

• If (relaxed==true && is_calculated(_config):
  • MappedProperties from _config.calc_properties() are applied.
  • Relaxed coordinates are obtained from _config.calc_properties().site.at("coordinate")
  • Relaxed lattice vectors are obtained from _config.calc_properties().global.at("latvec")
  • It is expected, but not checked, that there exist no DoF whose application further affects the coordinates or lattice vectors
• Otherwise: no MappedProperties are applied.

Definition at line 33 of file SimpleStructureTools.cc.

make_simple_structure() [2/3]

xtal::SimpleStructure CASM::make_simple_structure	(	Supercell const &	_scel,
		ConfigDoF const &	_dof,
		MappedProperties const &	_props,
		std::vector< DoFKey > const &	_which_dofs = {},
		bool	relaxed = false
	)

Construct from ConfigDoF _dof belonging to provided Supercell _scel and using calculated properties.

Parameters

_props	Record of calculated properties to use during conversion
relaxed	flag specifying to use _props argument during conversion (if true)

Note:

• If relaxed==true:
  • Relaxed coordinates are obtained from _config.calc_properties().site.at("coordinate")
  • Relaxed lattice vectors are obtained from _config.calc_properties().global.at("latvec")
  • It is expected, but not checked, that there exist no DoF whose application further affects the coordinates or lattice vectors.
• Otherwise: no MappedProperties are applied.

If not, initialize it

If not, initialize it

Definition at line 45 of file SimpleStructureTools.cc.

make_simple_structure() [3/3]

xtal::SimpleStructure CASM::make_simple_structure	(	Supercell const &	_scel,
		ConfigDoF const &	_dof,
		std::vector< DoFKey > const &	_which_dofs = {}
	)

Construct from ConfigDoF _dof belonging to provided Supercell _scel.

Parameters

_which_dofs

List of DoF type-names that specify which DoF values to utilize from _config when building the result if empty, all DoFs are used. To exclude all DoFs from conversion, pass _which_dofs={"none"}

Definition at line 26 of file SimpleStructureTools.cc.

make_standard_enumerator_interfaces()

EnumInterfaceVector CASM::make_standard_enumerator_interfaces

(

)

A map containing interfaces that allow casm enum to run the enumeration methods in libcasm

Definition at line 19 of file standard_enumerator_interfaces.cc.

make_standard_info_method_interfaces()

InfoInterfaceVector CASM::make_standard_info_method_interfaces

(

)

A vector containing casm info method interfaces.

Definition at line 14 of file standard_info_method_interfaces.cc.

make_string_dictionary< Supercell >()

template<>

StringAttributeDictionary< Supercell > CASM::make_string_dictionary< Supercell >

(

)

Definition at line 19 of file SupercellIO.cc.

make_suborbit_generators()

template<typename GroupOpIterator , typename SubgroupOpIterator , typename ElementIterator , typename SymCompareType , typename ElementOutputIterator >

ElementOutputIterator CASM::make_suborbit_generators	(	GroupOpIterator	group_begin,
		GroupOpIterator	group_end,
		SubgroupOpIterator	subgroup_begin,
		SubgroupOpIterator	subgroup_end,
		ElementIterator	element_begin,
		ElementIterator	element_end,
		SymCompareType const &	sym_compare,
		ElementOutputIterator	result
	)

Definition at line 143 of file SubOrbits_impl.hh.

make_suborbit_generators_f()

template<typename GroupOpIterator , typename SubgroupOpIterator >

MakeSubOrbitGenerators<GroupOpIterator, SubgroupOpIterator> CASM::make_suborbit_generators_f	(	GroupOpIterator	group_begin,
		GroupOpIterator	group_end,
		SubgroupOpIterator	subgroup_begin,
		SubgroupOpIterator	subgroup_end
	)

Definition at line 50 of file SubOrbits.hh.

make_supercell_name()

std::string CASM::make_supercell_name	(	SymGroup const &	point_group,
		Lattice const &	prim_lattice,
		Lattice const &	supercell_lattice
	)

Make the supercell name.

Make the supercell name from SupercellSymInfo

For supercells that are equivalent to the canonical supercell:

• The supercell name is SCELV_A_B_C_D_E_F, where 'V' is supercell volume (number of unit cells), and 'A-F' are the six non-zero elements of the hermite normal form of the canonical supercell transformation matrix (T00, T11, T22, T12, T02, T01)

For supercells that are not equivalent to the canonical supercell:

• The supercell name is $CANON_SCELNAME.$FG_INDEX where CANON_SCELNAME is the supercell name for the canonical equivalent supercell and FG_INDEX is the lowest index prim factor group operation which can be applied to the canonical supercell lattice to construct a lattice equivalent to the input supercell lattice.

Definition at line 278 of file SupercellSymInfo.cc.

make_supercell_sym_info()

SupercellSymInfo CASM::make_supercell_sym_info	(	Structure const &	prim,
		Lattice const &	super_lattice
	)

Definition at line 419 of file Structure.cc.

make_superlattice_from_supercell_name()

xtal::Superlattice CASM::make_superlattice_from_supercell_name	(	SymGroup const &	factor_group,
		Lattice const &	prim_lattice,
		std::string	supercell_name
	)

Construct a Superlattice from the supercell name.

Definition at line 311 of file SupercellSymInfo.cc.

make_sym_group() [1/5]

template<typename PermuteIteratorContainer >

SymGroup CASM::make_sym_group	(	const PermuteIteratorContainer &	container,
		const Lattice &	supercell_lattice
	)

Returns a SymGroup generated from a container of PermuteIterator.

Parameters

container

A container of PermuteIterator

• The result is sorted

Definition at line 196 of file PermuteIterator.hh.

make_sym_group() [2/5]

template SymGroup CASM::make_sym_group	(	PermuteIterator	begin,
		PermuteIterator	end,
		const Lattice &	supercell_lattice
	)

make_sym_group() [3/5]

template<typename PermuteIteratorIt >

SymGroup CASM::make_sym_group	(	PermuteIteratorIt	begin,
		PermuteIteratorIt	end,
		const Lattice &	supercell_lattice
	)

Returns a SymGroup generated from a range of PermuteIterator.

Parameters

begin,end

A range of PermuteIterator

• The result is sorted
• The result uses the Supercell lattice for periodic comparisons

Definition at line 262 of file PermuteIterator.cc.

make_sym_group() [4/5]

template SymGroup CASM::make_sym_group	(	std::vector< PermuteIterator >::const_iterator	begin,
		std::vector< PermuteIterator >::const_iterator	end,
		const Lattice &	supercell_lattice
	)

make_sym_group() [5/5]

template SymGroup CASM::make_sym_group	(	std::vector< PermuteIterator >::iterator	begin,
		std::vector< PermuteIterator >::iterator	end,
		const Lattice &	supercell_lattice
	)

make_symmetry_adapted_dof_space()

DoFSpace CASM::make_symmetry_adapted_dof_space	(	DoFSpace const &	dof_space,
		SupercellSymInfo const &	sym_info,
		std::vector< PermuteIterator > const &	group,
		bool	calc_wedges,
		std::optional< VectorSpaceSymReport > &	symmetry_report
	)

Make DoFSpace with symmetry adapated basis.

Definition at line 604 of file DoFSpace.cc.

make_symmetry_adapted_dof_space_v2()

DoFSpace CASM::make_symmetry_adapted_dof_space_v2	(	DoFSpace const &	dof_space,
		SupercellSymInfo const &	sym_info,
		std::vector< PermuteIterator > const &	group,
		bool	calc_wedges,
		std::optional< SymRepTools_v2::VectorSpaceSymReport > &	symmetry_report
	)

Make DoFSpace with symmetry adapated basis.

Definition at line 635 of file DoFSpace.cc.

make_translation_permutations()

std::vector<Permutation> CASM::make_translation_permutations	(	const Eigen::Matrix3l &	transformation_matrix,
		int	basis_sites_in_prim
	)

Definition at line 24 of file SupercellSymInfo.cc.

make_unique_configdof() [1/4]

std::unique_ptr< ConfigDoF > CASM::make_unique_configdof	(	Structure const &	prim,
		Index	volume
	)

Construct zero-valued std::unique_ptr<ConfigDoF>

Definition at line 23 of file ConfigDoFTools.cc.

make_unique_configdof() [2/4]

std::unique_ptr< ConfigDoF > CASM::make_unique_configdof	(	Structure const &	prim,
		Index	volume,
		double	tol
	)

Construct zero-valued std::unique_ptr<ConfigDoF>

Definition at line 31 of file ConfigDoFTools.cc.

make_unique_configdof() [3/4]

std::unique_ptr< ConfigDoF > CASM::make_unique_configdof

(

Supercell const &

supercell

)

Construct zero-valued std::unique_ptr<ConfigDoF>

Definition at line 49 of file ConfigDoFTools.cc.

make_unique_configdof() [4/4]

std::unique_ptr< ConfigDoF > CASM::make_unique_configdof	(	Supercell const &	supercell,
		double	tol
	)

Construct zero-valued std::unique_ptr<ConfigDoF>

Definition at line 54 of file ConfigDoFTools.cc.

make_unique_sym_group() [1/2]

template<typename PermuteIteratorContainer >

std::unique_ptr<SymGroup> CASM::make_unique_sym_group	(	const PermuteIteratorContainer &	container,
		const Lattice &	supercell_lattice
	)

Returns a std::unique_ptr<SymGroup> generated from a container of PermuteIterator.

Parameters

container

A container of PermuteIterator

• The result is sorted

Definition at line 213 of file PermuteIterator.hh.

make_unique_sym_group() [2/2]

template<typename PermuteIteratorIt >

std::unique_ptr< SymGroup > CASM::make_unique_sym_group	(	PermuteIteratorIt	begin,
		PermuteIteratorIt	end,
		const Lattice &	supercell_lattice
	)

Returns a SymGroup generated from a range of PermuteIterator.

Returns a std::unique_ptr<SymGroup> generated from a range of PermuteIterator.

Parameters

begin,end

A range of PermuteIterator

• The result is sorted
• The result uses the Supercell lattice for periodic comparisons

Definition at line 282 of file PermuteIterator.cc.

make_vectorxd_dictionary< Supercell >()

template<>

VectorXdAttributeDictionary< Supercell > CASM::make_vectorxd_dictionary< Supercell >

(

)

Definition at line 19 of file SupercellIO.cc.

make_vectorxi_dictionary< Configuration >()

template<>

VectorXiAttributeDictionary<Configuration> CASM::make_vectorxi_dictionary< Configuration >

(

)

Definition at line 43 of file ConfigIO.cc.

make_vectorxi_dictionary< Supercell >()

template<>

VectorXiAttributeDictionary< Supercell > CASM::make_vectorxi_dictionary< Supercell >

(

)

Definition at line 19 of file SupercellIO.cc.

max()

template<typename T >

T CASM::max	(	const T &	A,
		const T &	B
	)

Definition at line 95 of file CASM_math.hh.

max_length_cluster_filter()

ClusterFilterFunction CASM::max_length_cluster_filter

(

double

max_length

)

Accept clusters with max pair distance less than max_length.

Definition at line 498 of file ClusterSpecs.cc.

max_length_neighborhood()

CandidateSitesFunction CASM::max_length_neighborhood

(

double

max_length

)

Sites within max_length distance to any site in the origin unit cell {b, 0, 0, 0}

Definition at line 514 of file ClusterSpecs.cc.

min()

template<typename T >

T CASM::min	(	const T &	A,
		const T &	B
	)

Definition at line 88 of file CASM_math.hh.

mod()

int CASM::mod	(	int	a,
		int	b
	)

Definition at line 262 of file CASM_math.cc.

mol_site_compatibility()

std::vector< std::set< Index > > CASM::mol_site_compatibility	(	xtal::SimpleStructure const &	sstruc,
		Configuration const &	_config
	)

Determine which sites of a Configuration can host each molecule of a SimpleStructure result[i] is set of site indices in.

Parameters

_config	that can host molecule 'i' of
sstruc

Definition at line 96 of file SimpleStructureTools.cc.

monte_command()

int CASM::monte_command

(

const CommandArgs &

args

)

–help option

–help option

Definition at line 123 of file monte.cc.

montecarlo()

void CASM::montecarlo

(

const CommandArgs &

args

)

Definition at line 286 of file status.cc.

multiline_help()

template<typename T >

std::string CASM::multiline_help

(

)

Help message for reading a type T from input.

Definition at line 10 of file Help.hh.

multinomial_coeff() [1/2]

template<typename IntType >

IntType CASM::multinomial_coeff

(

const Array< IntType > &

exponents

)

Definition at line 53 of file CASM_Array_math.hh.

multinomial_coeff() [2/2]

template<typename IntType >

IntType CASM::multinomial_coeff	(	const Array< IntType > &	exponents,
		const Array< Index > &	sublist
	)

Definition at line 65 of file CASM_Array_math.hh.

name()

template<typename DataObject >

GenericDatumFormatter<std::string, DataObject> CASM::name

(

)

Definition at line 924 of file DataFormatterTools.hh.

nchoosek()

template<typename IntType >

IntType CASM::nchoosek	(	IntType	n,
		IntType	k
	)

Definition at line 207 of file CASM_math.hh.

nearest_rational_number()

void CASM::nearest_rational_number	(	double	val,
		long &	numerator,
		long &	denominator,
		double	tol = TOL
	)

Definition at line 165 of file CASM_math.cc.

new_dir()

bool CASM::new_dir	(	const DirectoryStructure &	dir,
		ClexDescription const &	desc
	)

Add directories for a particular cluster expansion

Create bset, calc_settings, ref, and eci directories for the cluster expansion desc.

Returns

bool, true if all directories exist afterwards

Definition at line 61 of file ClexDescription.cc.

null_composition_space()

Eigen::MatrixXd CASM::null_composition_space	(	const ParamComposition::AllowedOccupants &	_allowed_occs,
		double	tol
	)

Return the null composition space of a ParamComposition::AllowedOccupants.

Return the null composition space of a BasicStructure.

Parameters

_allowed_occs	A BasicStructure to find the standard composition space for (does not check if it is actually primitive).
tol	tolerance for checking rank (default 1e-14)

• Each column corresponds to an orthogonal vector in atom fraction space
• Each row corresponds to a Molecule, ordered as from BasicStructure::struc_molecule

Definition at line 633 of file CompositionConverter.cc.

null_log()

Log& CASM::null_log ( )

inline

Definition at line 438 of file Log.hh.

num_blocks()

Index CASM::num_blocks	(	SymGroupRep const &	_rep,
		const SymGroup &	head_group
	)

counts number of nonzero blocks in matrix representation of head_group as specified by _rep Reveals number of invariant subspaces (with respect to head_group) that comprise the vector space supporting _rep

Definition at line 402 of file SymRepTools.cc.

one_chemical_reference_from_json()

std::pair< Eigen::VectorXd, std::vector< ChemicalReferenceState > > CASM::one_chemical_reference_from_json	(	BasicStructure const &	prim,
		jsonParser const &	json
	)

Read chemical reference from one of 3 alternative forms.

This function returns a pair with only one element initialized. If alternative 1, then the vector is set. If alternative 2 or 3, then the Eigen::VectorXd is set.

Expected input form: 1)

[
  {"A": 3.4, "C": 2.0, "energy_per_species": 2.0},
  {"B": 2.0, "energy_per_species": 4.0},
  {"C": 1.0, "energy_per_species": 3.0}
]

2) Expects all species in prim, except vacancy:

{"A": X, "C": X, "D": X}

3) Expects one element for each species in prim, including 0.0 for vacancy:

[X, X, X, X]

Definition at line 177 of file ChemicalReference_json_io.cc.

operator!=() [1/2]

bool CASM::operator!= ( DoFSet const &  A, DoFSet const &  B  )

inline

Definition at line 320 of file DoFSet.hh.

operator!=() [2/2]

bool CASM::operator!= ( SymGroupRepID const &  a, SymGroupRepID const &  b  )

inline

Compares false if group_index() and rep_index() are equal.

Definition at line 88 of file SymGroupRepID.hh.

operator*() [1/3]

double CASM::operator*	(	const ECIContainer &	_eci,
		const Eigen::VectorXd &	_corr
	)

Evaluate property given an ECIContainer and correlations.

Definition at line 10 of file ECIContainer.cc.

operator*() [2/3]

double CASM::operator*	(	const ECIContainer &	_eci,
		double const *	_corr_begin
	)

Evaluate property given an ECIContainer and pointer to beginning of range of correlation.

Definition at line 21 of file ECIContainer.cc.

operator*() [3/3]

BasisSet CASM::operator*	(	const SymOp &	LHS,
		const BasisSet &	RHS
	)

Definition at line 1408 of file BasisSet.cc.

operator<() [1/2]

bool CASM::operator<	(	const ClexDescription &	A,
		const ClexDescription &	B
	)

Compare using name strings: A.name < B.name.

Definition at line 37 of file ClexDescription.cc.

operator<() [2/2]

bool CASM::operator< ( SymGroupRepID const &  a, SymGroupRepID const &  b  )

inline

Less-than comparison for use in STL containers (std::set, std::map, etc)

Definition at line 93 of file SymGroupRepID.hh.

operator<<() [1/19]

DataStream& CASM::operator<< ( DataStream &  _stream, const FormattedPrintable &  _formatted  )

inline

Definition at line 754 of file DataFormatter.hh.

operator<<() [2/19]

template<class T >

DataStream& CASM::operator<< ( DataStream &  _stream, const std::vector< T > &  vec  )

inline

Definition at line 316 of file DataStream.hh.

operator<<() [3/19]

DataStream& CASM::operator<< ( DataStream &  _stream, float  f  )

inline

Definition at line 303 of file DataStream.hh.

operator<<() [4/19]

DataStream& CASM::operator<< ( DataStream &  _stream, int  i  )

inline

Definition at line 299 of file DataStream.hh.

operator<<() [5/19]

DataStream& CASM::operator<< ( DataStream &  _stream, unsigned int  i  )

inline

Definition at line 307 of file DataStream.hh.

operator<<() [6/19]

DataStream& CASM::operator<< ( DataStream &  _stream, unsigned long  i  )

inline

Definition at line 311 of file DataStream.hh.

operator<<() [7/19]

template<typename T >

Log& CASM::operator<<	(	Log &	log,
		const T &	msg_details
	)

Definition at line 394 of file Log.hh.

operator<<() [8/19]

Log & CASM::operator<<	(	Log &	log,
		std::ostream &(*)(std::ostream &)	fptr
	)

Definition at line 270 of file Log.cc.

operator<<() [9/19]

std::ostream & CASM::operator<<	(	std::ostream &	out,
		const Permutation &	perm
	)

Definition at line 11 of file PermutationIO.cc.

operator<<() [10/19]

std::ostream & CASM::operator<<	(	std::ostream &	_stream,
		const FormatFlag &	flag
	)

Definition at line 9 of file FormatFlag.cc.

operator<<() [11/19]

std::ostream& CASM::operator<< ( std::ostream &  _stream, const FormattedPrintable &  _formatted  )

inline

Definition at line 747 of file DataFormatter.hh.

operator<<() [12/19]

std::ostream& CASM::operator<< ( std::ostream &  out, SymGroupRepID const &  _id  )

inline

Definition at line 102 of file SymGroupRepID.hh.

operator<<() [13/19]

std::ostream & CASM::operator<<	(	std::ostream &	sout,
		ClusterInvariants const &	invariants
	)

Print ClusterInvariants.

Definition at line 10 of file ClusterInvariants_stream_io.cc.

operator<<() [14/19]

std::ostream& CASM::operator<<	(	std::ostream &	sout,
		const BasicClexParamPack::EvalMode &	val
	)

Definition at line 201 of file BasicClexParamPack.hh.

operator<<() [15/19]

std::ostream& CASM::operator<<	(	std::ostream &	sout,
		const Configuration &	c
	)

Definition at line 1094 of file Configuration.cc.

operator<<() [16/19]

std::ostream& CASM::operator<< ( std::ostream &  sout, const DiffClexParamPack::EvalMode &  val  )

inline

Definition at line 672 of file DiffClexParamPack.hh.

operator<<() [17/19]

std::ostream & CASM::operator<<	(	std::ostream &	sout,
		const IntegralCluster &	clust
	)

Print IntegralCluster to stream, using default Printer<IntegralCluster>

Definition at line 10 of file IntegralCluster_stream_io.cc.

operator<<() [18/19]

std::ostream & CASM::operator<<	(	std::ostream &	sout,
		WithinScelClusterInvariants const &	invariants
	)

Print WithinScelClusterInvariants.

Definition at line 29 of file ClusterInvariants_stream_io.cc.

operator<<() [19/19]

template<typename CounterType >

std::ostream& CASM::operator<<	(	std::ostream &	stream,
		const MultiCounter< CounterType > &	counter
	)

Definition at line 183 of file MultiCounter.hh.

operator==() [1/2]

bool CASM::operator== ( DoFSet const &  A, DoFSet const &  B  )

inline

Definition at line 314 of file DoFSet.hh.

operator==() [2/2]

bool CASM::operator== ( SymGroupRepID const &  a, SymGroupRepID const &  b  )

inline

Compares true if group_index() and rep_index() are equal.

Definition at line 83 of file SymGroupRepID.hh.

operator>>() [1/3]

template<class T >

std::istream& CASM::operator>>	(	std::istream &	_in,
		std::vector< T > &	vec
	)

Definition at line 10 of file stream_io.hh.

operator>>() [2/3]

std::istream& CASM::operator>>	(	std::istream &	sin,
		BasicClexParamPack::EvalMode &	val
	)

Definition at line 207 of file BasicClexParamPack.hh.

operator>>() [3/3]

std::istream& CASM::operator>> ( std::istream &  sin, DiffClexParamPack::EvalMode &  val  )

inline

Definition at line 678 of file DiffClexParamPack.hh.

opt_test()

void CASM::opt_test

(

)

Definition at line 52 of file complete_tests.cpp.

opt_test2()

void CASM::opt_test2

(

)

Definition at line 79 of file complete_tests.cpp.

orbit_print_mode_help()

std::string CASM::orbit_print_mode_help

(

)

Definition at line 22 of file help.cc.

origin_neighborhood()

CandidateSitesFunction CASM::origin_neighborhood

(

)

Only sites in the origin unit cell {b, 0, 0, 0}.

Definition at line 508 of file ClusterSpecs.cc.

pad()

Eigen::MatrixXd CASM::pad ( const Eigen::MatrixXd &  M, int  n  )

inline

Construct a matrix consisting of blocks M and Identity(n,n)

M ->  [ M 0 ]
      [ 0 I ]

Definition at line 73 of file PCA.hh.

parse() [1/25]

void CASM::parse	(	InputParser< AxesCounterParams > &	parser,
		Index	dof_space_dimension
	)

Parse DoFSpace subspace from "axes" and normal coordinate grid counter from "min", "max", and "increment"

Definition at line 439 of file DoFSpace.cc.

parse() [2/25]

void CASM::parse	(	InputParser< BasisFunctionSpecs > &	parser,
		Structure const &	prim,
		ParsingDictionary< DoFType::Traits > const *	dof_dict
	)

Parse BasisFunctionSpecs from JSON & validate

Allowed JSON attributes: dofs: array of string (optional, default= all prim dof keys) An array of string of dof type names that should be used to construct basis functions. The default value is all DoF types included in the prim. global_max_poly_order: int (optional, default=-1) See orbit_branch_max_poly_order documentation. orbit_branch_max_poly_order: object (optional, default={}) By default, for a given cluster orbit, polynomials of order up to the cluster size are created. Higher order polynomials can be requested either on a per-orbit-branch or global basis. The most specific level specified is used. Orbit branches are specified using the string value of the cluster size as a key.

Example: "orbit_branch_max_poly_order": { "4": 7 // use maximum polynomial order == 7, for orbits of cluster size == 4 }, "global_max_poly_order": 3, // use max(3, cluster size), for all other orbits

param_pack_type: string (optional, default="default") Specifies the ParamPack type to use when writing the Clexulator. Options are "default" or "diff", which enables fadbad automatic differentiating. dof_specs: object (required for some dofs) Provides DoF-particular specifications for constructing basis functions. Not all DoF types require their own DoFSpecs. See documentation for a particular DoF type to determine if it is required.

For "occ": (required if occupation dof included) site_basis_functions: string or array (required) Must be one of:

• "chebychev": For basis functions generated about the random alloy.
• "occupation": For basis functions generated about the order alloy generated by the first occupant listed for every sublattice in the prim structure.

• An array specifying sublat compositions, for "composition" basis functions generated about an average composition speficified for each sublattice.

  Example sublattice composition specification, for a prim structure with four sublattices and two allowed occupants ("A" and "B") on each sublattice:

  [
    { // composition on sublattices 0 and 1, as listed
    in prim
      "sublat_indices": [0, 1],
      "composition": {"A": 0.25, "B": 0.75}
    },
    { // composition on sublattices 2 and 3, as listed
    in prim
      "sublat_indices": [2, 3],
      "composition": {"A": 0.75, "B": 0.25}
    }
  ]
  

  For "<flavor>magspin": (optional if "<flavor>magspin" dof included) max_poly_order: int (optional, default=-1) Specifies the maximum polynomial order for site basis functions.

Definition at line 86 of file BasisFunctionSpecs_json_io.cc.

parse() [3/25]

void CASM::parse	(	InputParser< ClexBasisSpecs > &	parser,
		std::shared_ptr< Structure const >	shared_prim,
		ParsingDictionary< DoFType::Traits > const *	dof_dict
	)

Parse ClexBasisSpecs from JSON & validate (bspecs.json input)

Expects:

{
  "basis_function_specs": <BasisFunctionSpecs JSON>,
  "cluster_specs": <ClusterSpecs JSON>
}

Note:

• For BasisFunctionSpecs JSON format, see src/casm/basis_set/io/json/BasisFunctionSpecs_json_io.cc
• For ClusterSpecs JSON format, see src/casm/clusterography/io/json/ClusterSpecs_json_io.cc

Definition at line 15 of file ClexBasisSpecs_json_io.cc.

parse() [4/25]

void CASM::parse	(	InputParser< ClusterSpecs > &	parser,
		const std::shared_ptr< const Structure > &	shared_prim
	)

Parse PeriodicMaxLengthClusterSpecs or LocalMaxLengthClusterSpecs from JSON & validate.

This overload is equivalent to: parse(parser, shared_prim, shared_prim->factor_group()).

Definition at line 327 of file ClusterSpecs_json_io.cc.

parse() [5/25]

void CASM::parse	(	InputParser< ClusterSpecs > &	parser,
		const std::shared_ptr< const Structure > &	shared_prim,
		const SymGroup &	super_group
	)

Parse ClusterSpecs from JSON & validate.

Parse any supported type of ClusterSpecs from JSON & validate with specified generating_group.

Parameters

parser	(InputParser<ClusterSpecs>) Holds resulting value and error or warning messages
shared_prim	(const std::shared_ptr<const Structure> &) Prim structure
super_group	(const SymGroup &) Used to generate orbits.
transformation_matrix_to_super	(Eigen::Matrix3l const *) Optional super lattice transformation matrix for contexts when "within_scel_max_length" is supported.

This is used by PrimClex to read any user's bspecs.json file. Update this if you want to add more recognized cluster specs.

Notes on the naming conventions:

• An "orbit" is the set of all equivalent objects under some generating symmetry group. It is a general term, and in different contexts within CASM could be used for orbits of clusters, orbits of functions, or orbits of other objects.
• There are infinitely many orbits of 2-point clusters, corresponding to 1st nearest neighbor, 2nd nearest neighbor, 3rd nearest neighbor, etc. clusters. The same applies to 3-point, 4-point, etc. clusters.
• The "orbit tree" of all clusters is made up of "orbit branches" where each "branch" of the "orbit tree" is made up of all clusters with the same number of sites. For example, the n=2 "orbit branch" consists of all orbits of 2-point clusters, the n=3 "orbit branch" consists of all orbits of 3-point clusters, etc.

Notes on cluster generation methods:

• Clusters are generated recursively, meaning 2-point clusters are generated by attempting to add sites to 1-point clusters, 3-point clusters are generated by attempting to add sites to 2-point clusters, etc. This means that some (n+1)-point clusters that would otherwise be included may not be if the (n+1)-point cluster max_length is greater than the n-point cluster max_length. (The max_length value does not matter for null and 1-point cluster orbits, so this applies to n >= 2).

Expected JSON format:

method: string (required)
    Specify which cluster orbit generating method will be used. One of:
    - "periodic_max_length": Clusters differing by a lattice translation
    are considered
      equivalent. Cluster generation is truncated by specifying the
      maximum distance between sites in a cluster for 2-point, 3-point,
      etc. clusters. The point clusters comprising the asymmetric unit
      of the prim structure are always included. This is the appropriate
      method for cluster expansions of crystal properties.
    - "local_max_length": Clusters differing by a lattice translation
    are considered
      distinct. Cluster generation is truncated by specifying for
      2-point, 3-point, etc. clusters the radius of sites from
      "phenomenal" cluster include, and the maximum distance between
      sites in a cluster. This is the appropriate method for cluster
      expansions of properties associated with the "phenomenal" cluster.
params: object (required)
    Specifies parameters for the method selected by `method`. Options
    depend on the `method` chosen:

    For method=="periodic_max_length":
        orbit_branch_specs: object (required)
            Cluster generation is truncated by specifying the maximum
            distance between sites in a cluster for each orbit branch
            (i.e. 2-point, 3-point, etc. clusters). The null (0-point)
            clusters are always included. The 1-point clusters
            comprising the asymmetric unit of the prim structure are
            always included if 2-point clusters or greater are included
            or if "1" is present (with any value).


            Example 1: Generate up to 3-point clusters.
            - null cluster orbit is always included
            - 1-point cluster orbits are included because 2-point
              cluster orbits are included
            - max_length value for point branch 3 is >= max_length
              value for branch 2

                "orbit_branch_specs": {
                    "2": { "max_length": 10.0 },
                    "3": { "max_length": 8.0 }
                }

            Example 2: Generate null cluster orbit only
            - null cluster orbit is always included
              ("orbit_branch_specs" itself need not be included)

                "orbit_branch_specs": {}

            Example 3: Generate null and 1-point cluster orbits only
            - null cluster orbit is always included
            - only the presence of "1" needed to included 1-point
              cluster orbits, the max_length value is not necessary for
              1-point clusters and ignored if present

                "orbit_branch_specs": {
                    "1": {}
                }

        orbit_specs: array (optional)
            An array of clusters which are used to generate and include
            orbits of clusters whether or not they meet the `max_length`
            truncation criteria. See the cluster input format below.

    For method=="local_max_length":
        phenomenal: object (required)
            The "phenomenal" cluster about which local clusters are
            generated. See the cluster input format below.
        generating_group: array of int (required)
            An array of symop indices into the prim structure factor
            group specifying the invariant group of the "phenomenal"
            cluster which should be used to for generating local cluster
            orbits. In some contexts, the relevant symmetry is lower
            than that determined from the phenomenal cluster sites
            alone.
        orbit_branch_specs: object (required)
            All sites within `cutoff_radius` distance of any site in the
            phenomenal cluster are considered candidates for inclusion
            in clusters of a particular orbit branch. Cluster generation
            is truncated by specifying the maximum distance between
            sites in a cluster for each orbit branch. The `max_length`
            parameter is not necessary for 1-point clusters and ignored
            if present.

            Example:
                "orbit_branch_specs": {
                    "1": { "cutoff_radius": 6.0 },
                    "2": { "max_length": 9.0, "cutoff_radius": 6.0 },
                    "3": { "max_length": 8.0, "cutoff_radius": 6.0 },
                    ...
                }

        orbit_specs: array (optional)
            An array of clusters which are used to generate and include
            orbits of clusters whether or not they meet the
            `cutoff_radius` or `max_length` truncation criteria. See the
            cluster input format below.

Cluster input format for "orbit_specs" and "phenomenal": object coordinate_mode: string (optional, default="Integral") Specifies the coordinate mode used to specify cluster sites. May be:

• "Integral": 4-index coordinate [b, i, j, k], where b=sublattice index, and i,j,k are lattice vector indices. Also accepts "INT", "INTEGRAL", "integral".
• "Cartesian": 3-index coordinate [x, y, z] giving the site in Cartesian coordinates. Also accepts "CART", "cartesian".
• "Direct" or "Fractional": 3-index coordinate [a, b, c], where a,b,c are multiplied by the lattice vectors to give the site coordinate in Cartesian coordinates. Also accepts "FRAC", "fractional", "direct". sites: array of arrays (required) An array of coordinates of sites in the cluster. prototype: this is an allowed alias for "sites" include_subclusters: boolean (optional, default=true) Whether all subclusters of the specified clusters should also be included. This is not relevant for "phenomenal" and ignored if present.

Example cluster, with "Direct" coordinates: { "coordinate_mode" : "Direct", "sites" : [ [ 0.000000000000, 0.000000000000, 0.000000000000 ], [ 1.000000000000, 0.000000000000, 0.000000000000 ], [ 2.000000000000, 0.000000000000, 0.000000000000 ], [ 3.000000000000, 0.000000000000, 0.000000000000 ]], "include_subclusters" : true }

Example cluster, with "Integral" coordinates: { "coordinate_mode" : "Integral", "sites" : [ [ 0, 0, 0, 0 ], [ 0, 1, 0, 0 ], [ 1, 0, 0, 0 ]], "include_subclusters" : true }

Definition at line 513 of file ClusterSpecs_json_io.cc.

parse() [6/25]

void CASM::parse	(	InputParser< ConfigEnumInput > &	parser,
		std::shared_ptr< Structure const > const &	shared_prim
	)

Read ConfigEnumInput from JSON.

Definition at line 42 of file ConfigEnumInput_json_io.cc.

parse() [7/25]

void CASM::parse	(	InputParser< ConfigEnumOptions > &	parser,
		std::string	method_name,
		PrimClex const &	primclex,
		DataFormatterDictionary< Configuration > const &	dict
	)

Definition at line 72 of file enumerate_configurations_json_io.cc.

parse() [8/25]

void CASM::parse	(	InputParser< ConfigEnumRandomLocalParams > &	parser,
		MTRand &	mtrand
	)

Definition at line 82 of file ConfigEnumRandomLocalInterface.cc.

parse() [9/25]

void CASM::parse	(	InputParser< ConfigEnumRandomOccupationsParams > &	parser,
		MTRand &	mtrand
	)

Definition at line 60 of file ConfigEnumRandomOccupationsInterface.cc.

parse() [10/25]

void CASM::parse	(	InputParser< ConfigEnumSiteDoFsParams > &	parser,
		ConfigEnumInput const &	initial_state,
		AxesCounterParams &	axes_params,
		bool	sym_axes_option,
		bool	exclude_homogeneous_modes
	)

Parse the ConfigEnumSiteDoFsParams JSON input.

Definition at line 304 of file ConfigEnumSiteDoFsInterface.cc.

parse() [11/25]

void CASM::parse	(	InputParser< ConfigEnumStrainParams > &	parser,
		ConfigEnumInput const &	initial_state,
		AxesCounterParams &	axes_params,
		bool	sym_axes_option
	)

Parse the ConfigEnumStrainParams (except parse "axes" instead of wedges) from JSON input

Parameters

parser	InputParser will contain ConfigEnumStrainParams if successful and error messages otherwise
axes	Eigen::MatriXd speciying a custom user subspace / normal mode axes if provied, otherwise set to Identity matrix of size dof_space_dimension x dof_space_dimension.
dof_space_dimension	DoF space dimension detected from initial enumeration states

Definition at line 316 of file ConfigEnumStrainInterface.cc.

parse() [12/25]

void CASM::parse	(	InputParser< DoF_impl::MagSpinDoFSpecs > &	parser,
		const Structure &	prim
	)

Specify max polynomial order for magspin site basis functions

Options:

{
  "max_poly_order": <int, optional, default=-1>
}

Definition at line 85 of file MagSpinDoFTraits.cc.

parse() [13/25]

void CASM::parse	(	InputParser< DoF_impl::OccupationDoFSpecs > &	parser,
		const Structure &	prim
	)

Reads site_basis_functions from bspecs JSON and validate

site_basis_functions: string or array (required if "occ" dof included)
    Must be one of "chebychev" or "occupation" or an array specifying sublat
    compositions. Example sublat composition specification:
       [
         {
           "sublat_indices": [0, 1],
           "composition": {"A": 0.25, "B": 0.75}
         },
         {
           "sublat_indices": [2, 3],
           "composition": {"A": 0.75, "B": 0.25}
         }
      ]

Definition at line 706 of file OccupationDoFTraits.cc.

parse() [14/25]

void CASM::parse	(	InputParser< DoFSpace > &	parser,
		std::shared_ptr< Structure const > const &	shared_prim
	)

Definition at line 135 of file DoFSpace.cc.

parse() [15/25]

void CASM::parse

(

InputParser< ECIContainer > &

parser

)

Make ECIContainer from JSON (eci.json file)

Make ECIContainer from JSON (eci.json file)

Format:

{
  "orbits":[  // "cluster_functions", prior to 1.0.X
    {
      "eci": <float>,
      "linear_orbit_index": <int>, // "linear_cluster_index", prior to 1.0.X
      ...
    },
    ...
  ],
  ...
}

Note:

• Prior to version 1.0.X, the "orbits" array was named "cluster_functions" and the "linear_orbit_index" was named "linear_cluster_index". For compatibility, that format is also accepted.

Definition at line 31 of file ECIContainer_json_io.cc.

parse() [16/25]

void CASM::parse	(	InputParser< EnumerateSupercellsOptions > &	parser,
		std::string	method_name,
		PrimClex const &	primclex,
		DataFormatterDictionary< Supercell > const &	dict
	)

Definition at line 41 of file enumerate_supercells_json_io.cc.

parse() [17/25]

void CASM::parse	(	InputParser< IntegralCluster > &	parser,
		Structure const &	prim
	)

Parse IntegralCluster from JSON.

Format:

{
  "coordinate_mode" : ("FRAC", "CART", "INT" (default)) (optional)
  "sites" : [
    [b, i, j, k],
    ...
  ]
}

• Also accepts "prototype" in place of "sites"

Definition at line 89 of file IntegralCluster_json_io.cc.

parse() [18/25]

void CASM::parse	(	InputParser< LocalMaxLengthClusterSpecs > &	parser,
		const std::shared_ptr< const Structure > &	shared_prim,
		const SymGroup &	super_group
	)

Parse LocalMaxLengthClusterSpecs from JSON.

Parse LocalMaxLengthClusterSpecs from JSON

Parameters

parser	InputParser stores resulting value, errors, and warnings
shared_prim	Prim structure
super_group	Super group for generating sub groups. When reading the generating_group from JSON, only members of this group will be retained.

Expects:

{
  "generating_group": [0, ...], // required, array of symop indices for
  generating group "phenomenal": { // IntegralCluster as JSON
    "coordinate_mode" : <COORD_TYPE>, // ("FRAC", "CART", "INT" (default))
    (optional) "sites" : [
      [b, i, j, k], // of type matching coordinate_mode
      ...
    ]
  },
  "orbit_branch_specs": { // required, start at "1"
    "1": {"max_length":<number>, "cutoff_radius":<number>},
    "2": {"max_length":<number>, "cutoff_radius":<number>},
    ...},
  "orbit_specs": [ // optional
     ... prototype local clusters...
  ]
}

Definition at line 280 of file ClusterSpecs_json_io.cc.

parse() [19/25]

void CASM::parse	(	InputParser< PeriodicMaxLengthClusterSpecs > &	parser,
		const std::shared_ptr< const Structure > &	shared_prim,
		const SymGroup &	super_group
	)

Parse PeriodicMaxLengthClusterSpecs from JSON.

Parse PeriodicMaxLengthClusterSpecs from JSON

Expects:

{
  "orbit_branch_specs": { // optional
    "2": {"max_length":<number>, "cutoff_radius":<number>},
    "3": {"max_length":<number>, "cutoff_radius":<number>},
    ...},
  "orbit_specs": [ // optional
     ... prototype periodic clusters...
  ]
}

Notes:

• The null cluster orbit ("0") is always included with max_length value 0.0 (the value itself does not matter).
• The point cluster orbit ("1") is included with max_length value 0.0 (the value itself does not matter), if "1" is present with any value, or if "2" or greater is included.

Definition at line 221 of file ClusterSpecs_json_io.cc.

parse() [20/25]

void CASM::parse

(

InputParser< std::nullptr_t > &

parser

)

Temporary – enables compilation of legacy code.

Definition at line 148 of file InputParser.cc.

parse() [21/25]

void CASM::parse	(	InputParser< std::vector< IntegralClusterOrbitGenerator >> &	parser,
		Structure const &	prim
	)

Parse custom orbit specs from JSON.

Parse vector of IntegralClusterOrbitGenerator ("orbit_specs") from JSON

Format:

[
  {
    "coordinate_mode" : ("FRAC", "CART", "INT" (default)) (optional)
    "sites" : [ // also accepts "prototype"
      [b, i, j, k],
      ...
    ],
    "include_subclusters": <bool, optional, default=true>
  },
  ...
]

• Also accepts "prototype" in place of "sites"

Definition at line 43 of file ClusterOrbits_json_io.cc.

parse() [22/25]

void CASM::parse	(	InputParser< std::vector< std::pair< std::string, ConfigEnumInput >>> &	parser,
		std::shared_ptr< Structure const >	shared_prim,
		PrimClex const *	primclex,
		DB::Database< Supercell > &	supercell_db,
		DB::Database< Configuration > &	configuration_db
	)

Parse JSON to construct initial states for enumeration (as std::map<std::string, ConfigEnumInput>)

parse() [23/25]

template<typename T >

void CASM::parse

(

InputParser< T > &

parser

)

Definition at line 286 of file InputParser_impl.hh.

parse() [24/25]

void CASM::parse

(

InputParser< xtal::ScelEnumProps > &

parser

)

Make a ScelEnumProps object from JSON input.

Definition at line 48 of file SuperlatticeEnumeratorIO.cc.

parse() [25/25]

void CASM::parse	(	InputParser< xtal::ScelEnumProps > &	parser,
		DB::Database< Supercell > &	supercell_db
	)

Make a ScelEnumProps object from JSON input and support "unit_cell"==supercell name

Make a ScelEnumProps object from JSON input

Notes:

• Default "min" == 1
• Default "dirs" == "abc"
• Default "unit_cell" == 3x3 identity matrix

Definition at line 78 of file ConfigEnumInput_json_io.cc.

parse_args()

void CASM::parse_args	(	Completer::OptionHandlerBase &	opt,
		std::string	args
	)

Take CLI args string, 'casm X ...', and use boost::program_options to parse into Options

Definition at line 48 of file CLIParse.cc.

parse_axes_counter_range()

void CASM::parse_axes_counter_range

(

InputParser< AxesCounterParams > &

parser

)

Parse "min", "max", and one of "increment" or "num"

Parameters

parser

AxesCounterParams parser

Examples of equivalent input for a grid in 2d space:

• { "min": 0., "max": 0.101, "increment": 0.01}
• { "min": 0., "max": 0.1, "num": 11}
• { "min": [0., 0.], "max": [0.101, 0.101], "increment": [0.1, 0.1]}
• { "min": [0., 0.], "max": [0.1, 0.1], "num": [11, 11]}

Notes:

• all range inputs must be consistently either scalar or array
• "min", "max", "increment" must be number or array of number
• "num" must be int or array of int, specifies number of values to count over (including min and max values, unless num==1, then exclude max)
• only "min" is optional, with default value scalar 0, or vector 0, depending on type of "max"
• only one of "increment", "num" may be present
• sets AxesCounterParams members scalar_input based on input

Definition at line 267 of file DoFSpace.cc.

parse_axes_from_array()

void CASM::parse_axes_from_array	(	InputParser< AxesCounterParams > &	parser,
		Index	dof_space_dimension
	)

Read "axes" from a row-vector JSON matrix, store in parser.value->axes as a column vector matrix

Definition at line 367 of file DoFSpace.cc.

parse_axes_from_object()

void CASM::parse_axes_from_object	(	InputParser< AxesCounterParams > &	parser,
		Index	dof_space_dimension
	)

Parse DoF space axes from a JSON object

Expected format: (this parses "axes" only)

Full space case: { "axes": { "q1": [q10, q11, q12, ...], /// note: starts with "q1", not "q0" "q2": [q20, q21, q22, ...], "q3": [q30, q31, q32, ...], ... }, "min": [q1min, q2min, q3min, ...], /// optional, default is zeros vector "max": [q1max, q2max, q3max, ...], /// required "increment": [q1inc, q2inc, q3inc, ...], /// required }

Subspace case:

• if some qi (i in range [1, dof_space_dimension]) are missing, then use the subspace specified by the axes that are provided
• if scalars, min, max, increment will be used along each dimension
• if arrays, min.size() / max.size() / increment.size() must equal axes.size()
• example: { "axes": { "q1": [q10, q11, q12, ...], "q2": [q20, q21, q22, ...], "q3": [q30, q31, q32, ...], "q5": [q50, q51, q52, ...], }, "min": [q1min, q2min, q3min, q5min], /// optional, default is zeros vector "max": [q1max, q2max, q3max, q5max], /// required "increment": [q1inc, q2inc, q3inc, q5inc], /// required }

notes:

• if total dof_space_dimension is double digit, then use "q01", "q02", ... etc.
• if total dof_space_dimension is triple digit, then use "q001", "q002", ... etc.

Definition at line 332 of file DoFSpace.cc.

parse_ConfigEnumInput_desc()

std::string CASM::parse_ConfigEnumInput_desc

(

)

A string describing the JSON format for parsing named ConfigEnumInput.

Definition at line 124 of file ConfigEnumInput_json_io.cc.

parse_dof_space_axes()

void CASM::parse_dof_space_axes	(	InputParser< AxesCounterParams > &	parser,
		Index	dof_space_dimension
	)

Parse DoF space "axes"

Accepts a JSON object of axes or a row vector matrix of axes. May be rank deficient.

Parameters

parser	JSON to be parsed
axes	Set to be column vector matrix of axes
dof_space_dimension	Full DoF space dimension. If no "axes" in the JSON, the default axes are identity matrix of size dof_space_dimension. Errors are inserted into parser if axes vectors are not of length equal to dof_space_dimension.

TODO: document "axes" here

Definition at line 416 of file DoFSpace.cc.

parse_label_template()

std::vector<std::string> CASM::parse_label_template

(

std::string const &

_template

)

Definition at line 10 of file FunctionVisitor.cc.

parse_verbosity()

int CASM::parse_verbosity	(	KwargsParser &	parser,
		int	default_verbosity = 10
	)

Parse Log "verbosity" level from JSON

Expected that parser.self.find("verbosity") returns iterator to:

{
   "verbosity": <int or string, default=10, range=[0,100], "none" = 0,
   "quiet"=5,
                 "standard"=10, "verbose"=20, "debug"=100>
}

Definition at line 123 of file InputParser.cc.

partition_distinct_values()

template<typename Derived >

ReturnArray<Index> CASM::partition_distinct_values	(	const Eigen::MatrixBase< Derived > &	value,
		double	tol = TOL
	)

Definition at line 100 of file CASM_Array_math.hh.

permute_cluster_site_indices()

std::set< Index > CASM::permute_cluster_site_indices	(	Permutation const &	inverse_permute,
		std::set< Index > const &	cluster_site_indices
	)

Rather than permute values, here we want to permute cluster site indices.

Rather than permute values, here we want to permute cluster site indices

Since, when permuting values, value[i] = value[permute[i]], or, site_index_before = permute[site_index_after], to permute site indices use inverse_permute = permute.inverse, and then site_index_after = inverse_permute[site_index_before]

Definition at line 46 of file SupercellClusterOrbits.cc.

permuted_direct_sum_rep()

SymGroupRep CASM::permuted_direct_sum_rep	(	const SymGroupRep &	permute_rep,
		const std::vector< SymGroupRep const * > &	sum_reps
	)

Given a permutation of positions, and a list of matrix representations (one per position), build a large matrix representation that has blocks specified by the smaller matrices in

Parameters

sum_reps	and whose positions within the large matrix correspond to the permutation from
permute_rep

Definition at line 1194 of file SymRepTools.cc.

perturb_command()

int CASM::perturb_command

(

const CommandArgs &

args

)

Definition at line 36 of file perturb.cc.

po_test()

void CASM::po_test

(

)

Definition at line 106 of file complete_tests.cpp.

pos_path() [1/3]

template<typename ConfigType >

std::string CASM::pos_path

(

const ConfigType &

config

)

Definition at line 206 of file Calculable.cc.

pos_path() [2/3]

template<typename ConfigType >

std::string CASM::pos_path	(	const ConfigType &	config,
		std::string	calctype = ""
	)

pos_path() [3/3]

std::string CASM::pos_path	(	const PrimClex &	primclex,
		const std::string &	configname
	)

Definition at line 237 of file Calculable.cc.

prec_help()

std::string CASM::prec_help	(	std::string	what,
		int	default_prec
	)

Definition at line 28 of file help.cc.

print_aligned_site_basis_funcs()

void CASM::print_aligned_site_basis_funcs	(	std::shared_ptr< const Structure >	prim_ptr,
		ClexBasis const &	clex_basis,
		Log &	out,
		Index	indent_space = 6,
		COORD_TYPE	mode = FRAC
	)

Print aligned site basis functions, as for 'casm bset –functions –align'.

Print occ site basis functions, and continuous site and global bases.

Definition at line 390 of file ProtoFuncsPrinter.cc.

print_basis_functions() [1/2]

void CASM::print_basis_functions	(	Log &	log,
		PrimClex const &	primclex,
		std::string	basis_set_name,
		bool	align,
		OrbitPrinterOptions	opt = OrbitPrinterOptions()
	)

Pretty-print basis functions – read clusters from existing clust.json file.

Definition at line 35 of file ClexBasis_stream_io.cc.

print_basis_functions() [2/2]

void CASM::print_basis_functions	(	Log &	log,
		std::shared_ptr< Structure const > const &	shared_prim,
		ClexBasisSpecs const &	basis_set_specs,
		bool	align,
		OrbitPrinterOptions	opt = OrbitPrinterOptions()
	)

Pretty-print basis functions – generate, then print.

Definition at line 25 of file ClexBasis_stream_io.cc.

print_clust() [1/2]

template<typename ClusterOrbitIterator >

void CASM::print_clust	(	ClusterOrbitIterator	begin,
		ClusterOrbitIterator	end,
		Log &	out,
		const OrbitPrinterOptions &	opt = OrbitPrinterOptions()
	)

Print IntegralCluster orbits.

Definition at line 291 of file OrbitPrinter_impl.hh.

print_clust() [2/2]

template<typename ClusterOrbitIterator , typename OrbitPrinter >

void CASM::print_clust	(	ClusterOrbitIterator	begin,
		ClusterOrbitIterator	end,
		Log &	out,
		OrbitPrinter	printer
	)

Print IntegralCluster orbits.

Parameters

begin,end	Range of Orbit<SymCompareType>
out	output stream
mode	Coordinate output mode
printer	A functor to control printing for the orbit

Printer is expected to have:

• std::string Printer::indent(); 

• void Printer::coord_type(Log& out); 

•  void Printer::operator()(const Orbit<SymCompareType>& orbit, Log&
  out, Index orbit_index, Index Norbits); 

Definition at line 222 of file OrbitPrinter_impl.hh.

print_clust_basis()

Index CASM::print_clust_basis	(	std::ostream &	stream,
		BasisSet	_clust_basis,
		IntegralCluster const &	_prototype,
		Index	func_ind = 0,
		int	space = 18,
		char	delim = '\n'
	)

Print cluster with basis_index and nlist_index (from 0 to size()-1), followed by cluster basis functions Functions are labeled \Phi_{i}, starting from i =

Parameters

begin_ind

Returns the number of functions that were printed

Definition at line 44 of file ClexBasis.cc.

print_coordinates()

template<typename OrbitPrinter , typename Element >

void CASM::print_coordinates	(	OrbitPrinter &	printer,
		const Element &	element,
		Log &	out
	)

Definition at line 15 of file OrbitPrinter_impl.hh.

print_dof_space()

template<typename PermuteIteratorIt >

void CASM::print_dof_space	(	Log &	log,
		DoFSpace const &	dof_space,
		std::string const &	identifier,
		ConfigEnumInput const &	input_state,
		PermuteIteratorIt	permute_begin,
		PermuteIteratorIt	permute_end,
		bool	sym_axes,
		bool	calc_wedges
	)

Print DoFSpace information.

Print DoFSpace information

Parameters

log	Log to print to
name	Enumeration state name
dof_space	DoFSpace to print information for.
sym_axes	If true, calculate and print symmetry-adapted axes. If false, print only the axis glossary
calc_wedges	If this and sym_axes are true, calculate and print SubWedge

Notes:

• If !sym_axes, only prints axis glossary
• If sym_axes==true, construct and print VectorSpaceSymReport
  • TODO: Currently this prints the VectorSpaceSymReport using the JSON method. Could be specialized for nicer formatting.

Definition at line 32 of file stream_io_impl.hh.

print_errors()

void CASM::print_errors	(	KwargsParser const &	parser,
		Log &	log,
		std::string	header = "Errors"
	)

Formatted print error messages, including all subparsers.

Definition at line 168 of file InputParser.cc.

print_initial_states()

template<typename NamedInitialStatesType >

void CASM::print_initial_states	(	Log &	log,
		NamedInitialStatesType const &	named_initial_states
	)

Definition at line 66 of file stream_io_impl.hh.

print_monte_desc()

void CASM::print_monte_desc	(	std::ostream &	sout,
		const po::options_description &	desc
	)

Definition at line 27 of file monte.cc.

print_monte_help()

void CASM::print_monte_help	(	std::ostream &	sout,
		const po::options_description &	desc
	)

Definition at line 22 of file monte.cc.

print_options()

void CASM::print_options	(	Log &	log,
		ConfigEnumOptions const &	options
	)

Definition at line 6 of file stream_io.cc.

print_poscar()

void CASM::print_poscar	(	Configuration const &	configuration,
		std::ostream &	sout
	)

Print Configuration as a VASP POSCAR

Note: This makes use of VaspIO::PrintPOSCAR, which can be used directly for additional formatting options.

Definition at line 9 of file Configuration_stream_io.cc.

print_proto_clust_funcs()

template<typename OrbitType >

void CASM::print_proto_clust_funcs	(	ClexBasis const &	_clex_basis,
		std::ostream &	out,
		BasicStructure const &	_prim,
		std::vector< OrbitType > const &	_tree
	)

print_runtime_lib_options_help()

void CASM::print_runtime_lib_options_help

(

std::ostream &

sout

)

Definition at line 8 of file LogRuntimeLibrary.cc.

print_site_basis_funcs()

void CASM::print_site_basis_funcs	(	std::shared_ptr< const Structure >	prim_ptr,
		ClexBasis const &	clex_basis,
		Log &	out,
		Index	indent_space = 6,
		COORD_TYPE	mode = FRAC
	)

Print site basis functions, as for 'casm bset –functions'.

Definition at line 37 of file ProtoFuncsPrinter.cc.

print_splash()

void CASM::print_splash

(

std::ostream &

out

)

Definition at line 37 of file casm_functions.cc.

print_sym_info()

void CASM::print_sym_info	(	Log &	log,
		const SymInfo &	info,
		SymInfoOptions	opt
	)

Print SymInfo.

Of the form:

Mirror Operation with plane Normal = 0.25 0.25 0.0

Definition at line 32 of file SymInfo_stream_io.cc.

print_tex_tabular_cluster_sites()

void CASM::print_tex_tabular_cluster_sites	(	Log &	out,
		IntegralCluster const &	cluster,
		xtal::BasicStructure const &	prim,
		COORD_TYPE	mode
	)

Print prototype cluster sites as a tex tabular.

Definition at line 126 of file ProtoFuncsPrinter.cc.

print_warnings()

void CASM::print_warnings	(	KwargsParser const &	parser,
		Log &	log,
		std::string	header = "Warnings"
	)

Formatted print warning messages, including all subparsers.

Definition at line 150 of file InputParser.cc.

property_test()

void CASM::property_test

(

)

Definition at line 200 of file complete_tests.cpp.

prototype_iterator()

template<typename OrbitIterator >

PrototypeIterator<OrbitIterator> CASM::prototype_iterator

(

OrbitIterator

orbit_it

)

Convert an Orbit iterator to a prototype iterator.

Definition at line 210 of file Orbit.hh.

ran0()

double CASM::ran0

(

int &

idum

)

Definition at line 16 of file CASM_math.cc.

rand_unique()

std::vector<int> CASM::rand_unique	(	int	n,
		int	c,
		MTRand &	mtrand
	)

Choose c random unique numbers in [0,n)

Definition at line 62 of file Log.cc.

read_chemical_reference()

ChemicalReference CASM::read_chemical_reference	(	fs::path	filename,
		BasicStructure const &	prim,
		double	tol
	)

Read chemical reference states from JSON file.

See documentation with jsonConstructor<ChemicalReference> for expected format.

re-throw exceptions

re-throw exceptions

Definition at line 14 of file ChemicalReference_file_io.cc.

read_clust() [1/2]

template<typename ClusterOutputIterator >

ClusterOutputIterator CASM::read_clust	(	ClusterOutputIterator	result,
		const jsonParser &	json,
		const Structure &	prim
	)

Read JSON containing IntegralCluster prototypes, as IntegralCluster.

Read JSON containing IntegralCluster prototypes, as Orbit<SymCompareType>

• Uses 'prim' to generate IntegralCluster from prototypes read from the JSON
• Ignores "prim" and "bspecs" info in the JSON

Definition at line 338 of file OrbitPrinter_impl.hh.

read_clust() [2/2]

template<typename ClusterOutputIterator , typename SymCompareType >

ClusterOutputIterator CASM::read_clust	(	ClusterOutputIterator	result,
		const jsonParser &	json,
		const Structure &	prim,
		const SymGroup &	generating_grp,
		const SymCompareType &	sym_compare
	)

Read JSON containing Orbit<SymCompareType> prototypes.

• Uses 'prim', 'generating_grp', and 'sym_compare' to generate orbits from prototypes read from the JSON
• Ignores "prim" and "bspecs" info in the JSON

Definition at line 318 of file OrbitPrinter_impl.hh.

read_composition_axes()

CompositionAxes CASM::read_composition_axes

(

fs::path

_filename

)

Definition at line 10 of file CompositionAxes_file_io.cc.

read_prim() [1/3]

xtal::BasicStructure CASM::read_prim	(	jsonParser const &	json,
		double	xtal_tol,
		ParsingDictionary< AnisoValTraits > const *	_aniso_val_dict = nullptr
	)

Read prim.json.

Definition at line 308 of file BasicStructureIO.cc.

read_prim() [2/3]

xtal::BasicStructure CASM::read_prim	(	fs::path	filename,
		double	xtal_tol,
		ParsingDictionary< AnisoValTraits > const *	_aniso_val_dict = nullptr
	)

Definition at line 259 of file BasicStructureIO.cc.

read_prim() [3/3]

BasicStructure CASM::read_prim

(

ProjectSettings const &

project_settings

)

Definition at line 35 of file PrimClex.cc.

read_shared_prim()

std::shared_ptr<Structure const> CASM::read_shared_prim

(

ProjectSettings const &

project_settings

)

Definition at line 40 of file PrimClex.cc.

recast()

std::string CASM::recast

(

ARG_TYPE

atype

)

Definition at line 12 of file complete_tests.cpp.

recurs_cp_files()

Index CASM::recurs_cp_files	(	const fs::path &	from_dir,
		const fs::path &	to_dir,
		bool	dry_run,
		Log &	log
	)

Copy files recursively, and returns a count of copied files.

Definition at line 94 of file DirectoryStructure.cc.

recurs_rm_files()

void CASM::recurs_rm_files	(	fs::path	p,
		bool	dry_run,
		Log &	log
	)

Remove files recursively.

Definition at line 42 of file DirectoryStructure.cc.

reduced_column_echelon()

template<typename Derived >

Derived::PlainObject CASM::reduced_column_echelon	(	Eigen::MatrixBase< Derived > const &	M,
		double	_tol
	)

Returns reduced_column_echelon form of M.

Parameters

_tol	is used to identify zero values.

Definition at line 78 of file CASM_Eigen_math.hh.

ref_command()

int CASM::ref_command

(

const CommandArgs &

args

)

–help option

–help option

Definition at line 177 of file ref.cc.

references_unset()

void CASM::references_unset

(

const CommandArgs &

args

)

Definition at line 182 of file status.cc.

relative_casmroot()

fs::path CASM::relative_casmroot

(

const fs::path &

cwd

)

return relative path to current or parent directory containing ".casm" directory if none found, return empty path

Definition at line 29 of file DirectoryStructure.cc.

report_and_throw_if_invalid()

template<typename ErrorType >

void CASM::report_and_throw_if_invalid	(	KwargsParser const &	parser,
		Log &	log,
		ErrorType	error
	)

Print errors and warnings, throwing as specified if any errors exist in parser (and subparsers)

Definition at line 266 of file InputParser_impl.hh.

require_all_input_have_the_same_number_of_selected_sites()

void CASM::require_all_input_have_the_same_number_of_selected_sites

(

InputParser< std::vector< std::pair< std::string, ConfigEnumInput >>> &

parser

)

Definition at line 355 of file ConfigEnumSiteDoFsInterface.cc.

require_valid_sub_configurations()

void CASM::require_valid_sub_configurations	(	ParentInputParser &	parser,
		DB::Selection< Configuration > const &	config_selection,
		Supercell const &	supercell
	)

Definition at line 96 of file SuperConfigEnumInterface.cc.

reset_properties() [1/2]

void CASM::reset_properties ( ConfigDoF &  _dof )

inline

Definition at line 215 of file ConfigDoF.hh.

reset_properties() [2/2]

template<typename ConfigType >

void CASM::reset_properties

(

ConfigType &

config

)

Definition at line 147 of file Calculable.cc.

round()

int CASM::round

(

double

val

)

Definition at line 10 of file CASM_math.cc.

run_api_command()

template<typename CommandType >

int CASM::run_api_command

(

const CommandArgs &

args

)

Standardizes how 'casm X' api commands are executed and implemented.

Definition at line 40 of file APICommand_impl.hh.

run_command()

int CASM::run_command

(

const CommandArgs &

args

)

Set command line options using boost program_options

–help option

Set command line options using boost program_options

–help option

Definition at line 40 of file run.cc.

select_cluster_sites()

template<typename Inserter >

Inserter CASM::select_cluster_sites	(	ConfigEnumInput const &	reference_config_enum_input,
		std::vector< PrimPeriodicIntegralClusterOrbit > const &	orbits,
		Inserter	result
	)

Create ConfigEnumInput with unique cluster sites selected, starting from "prim_periodic" orbits

Definition at line 15 of file ClusterSitesSelector_impl.hh.

sequence() [1/2]

template<typename T >

std::vector<T> CASM::sequence	(	T	first,
		T	inc,
		T	last
	)

Definition at line 20 of file algorithm.hh.

sequence() [2/2]

template<typename T >

std::vector<T> CASM::sequence	(	T	first,
		T	last
	)

Definition at line 9 of file algorithm.hh.

set_dof_value()

void CASM::set_dof_value	(	Configuration &	config,
		DoFSpace const &	dof_space,
		Eigen::VectorXd const &	normal_coordinate
	)

Set config DoF value from a coordinate in the DoFSpace basis.

Definition at line 317 of file DoFSpace.cc.

settings_command()

int CASM::settings_command

(

const CommandArgs &

args

)

Set command line options using boost program_options

Set command line options using boost program_options

Definition at line 283 of file settings.cc.

sgn()

template<typename T , typename std::enable_if< std::is_integral< T >::value, T >::type * = nullptr>

int CASM::sgn

(

T

val

)

Definition at line 180 of file CASM_math.hh.

simple_json() [1/2]

SimpleJSonSiteStructure<false> CASM::simple_json ( BasicStructure &  struc, const std::string &  prefix  )

inline

Definition at line 130 of file jsonStruc.hh.

simple_json() [2/2]

SimpleJSonSiteStructure<true> CASM::simple_json ( const BasicStructure &  struc, const std::string &  prefix  )

inline

Definition at line 125 of file jsonStruc.hh.

singleline_enum_help< DB::SELECTION_TYPE >()

template<>

std::string CASM::singleline_enum_help< DB::SELECTION_TYPE > ( )

inline

Definition at line 21 of file Selection.hh.

singleline_help()

template<typename T >

std::string CASM::singleline_help

(

)

Help message for reading a type T from input.

Definition at line 16 of file Help.hh.

site_indices_are_invariant()

bool CASM::site_indices_are_invariant	(	PermuteIterator const &	permute_it,
		std::set< Index > const &	site_indices
	)

Return true if the permutation does not mix given sites and other sites.

Return true if the permutation does not given sites and other sites.

Definition at line 323 of file PermuteIterator.cc.

special_irrep_directions() [1/2]

multivector< Eigen::VectorXcd >::X< 2 > CASM::special_irrep_directions	(	SymGroupRep const &	_rep,
		SymGroup const &	head_group,
		double	vec_compare_tol
	)

Assuming that _rep is an irrep of head_group, find high-symmetry directions throws if _rep is not an irrep.

Returns

Set of directions in the vector space on which '_rep' is defined, such that each direction is invariant to a unique subgroup of 'head_group' (i.e., no other direction in the space, except the negative of that direction, is invariant to that subgroup) result[i] is an orbit of symmetrically equivalent directions, result[i][j] is an individual direction. Direction vectors are normalized to unit length. The total set of all directions is guaranteed to span the space.

Parameters

vec_compare_tol

tolerance for elementwise floating-point comparisons of vectors

Returns array of orbits of high-symmetry directions in the vector space on which this representation is defined. This routine is different from special_total_directions in that it does not rely on the character tables to generate the special directions. The routine also adopts the faster method to generating the irreducible transformation matrix

Definition at line 488 of file SymRepTools.cc.

special_irrep_directions() [2/2]

multivector< Eigen::VectorXcd >::X< 2 > CASM::special_irrep_directions	(	SymGroupRep const &	_rep,
		SymGroup const &	head_group,
		Eigen::Ref< const Eigen::MatrixXcd > const &	_subspace,
		double	vec_compare_tol,
		bool	all_subgroups = false
	)

Assuming that _rep is an irrep of head_group, find high-symmetry directions throws if _rep is not an irrep.

Returns

Set of directions in the vector space on which '_rep' is defined, such that each direction is invariant to a unique subgroup of 'head_group' (i.e., no other direction in the space, except the negative of that direction, is invariant to that subgroup) result[i] is an orbit of symmetrically equivalent directions, result[i][j] is an individual direction. Direction vectors are normalized to unit length. The total set of all directions is guaranteed to span the space.

Parameters

_subspace	matrix such that _subspace.rows()==_rep.dim() and whose columns specify a subspace of underlying vector space
vec_compare_tol	tolerance for elementwise floating-point comparisons of vectors
all_subgroups	denotes whether all subgroups of head_group should be used for symmetry analysis (if true), or only cyclic subgroups (if false)

Returns array of orbits of high-symmetry directions in the vector space on which this representation is defined. This routine is different from special_total_directions in that it does not rely on the character tables to generate the special directions. The routine also adopts the faster method to generating the irreducible transformation matrix

Definition at line 503 of file SymRepTools.cc.

special_subspaces()

std::vector< std::vector< Eigen::MatrixXd > > CASM::special_subspaces	(	SymGroupRep const &	_rep,
		const SymGroup &	head_group
	)

finds high-symmetry subspaces within vector space supporting _rep, wrt symmetry of head_group High-symmetry subspaces are closed under the action of a nontrivial subgroup of head_group, without spanning the entire vector space supporting _rep

Returns

Set of matrices MxN matrices (M>N) in the vector space on which '_rep' is defined, such that the column space of the matrix is invariant (i.e., closed) under the action of a nontrivial subgroup of head_group result[i] is an orbit of special subspaces that are equivalent by symmetry result[i][j] contains the spanning vectors of a specific special subspace Columns of each subspace matrix are orthogonal and normalized to unit length

Definition at line 610 of file SymRepTools.cc.

special_total_directions()

multivector< Eigen::VectorXd >::X< 3 > CASM::special_total_directions	(	SymGroupRep const &	_rep,
		const SymGroup &	head_group
	)

finds high-symmetry directions within vector space supporting _rep, wrt symmetry of head_group

Returns

Set of directions in the vector space on which '_rep' is defined, such that each direction is invariant a subgroup of 'head_group'. These are constructed by finding irreps of _rep and then calling special_irrep_directions on each result[i] is the set of special directions belonging to the i'th irrep constituting _rep result[i][j] is an orbit of symmetrically equivalent directions, and result[i][j][k] is an individual direction. Direction vectors are normalized to unit length. The total set of all directions is guaranteed to span the space.

Definition at line 467 of file SymRepTools.cc.

split_formatter_expression()

void CASM::split_formatter_expression	(	const std::string &	input_expr,
		std::vector< std::string > &	tag_names,
		std::vector< std::string > &	sub_exprs
	)

Definition at line 63 of file DataFormatter.cc.

standard_composition_axes()

template<typename OutputIterator >

OutputIterator CASM::standard_composition_axes	(	ParamComposition::AllowedOccupants	_allowed_occs,
		OutputIterator	result
	)

Generate CompositionConverter specifying standard composition axes for a prim Structure.

Generate CompositionConverter specifying standard composition axes for a _allowed_occs ParamComposition::AllowedOccupants.

Definition at line 242 of file CompositionConverter.hh.

standard_ConfigEnumInput_help()

std::string CASM::standard_ConfigEnumInput_help

(

)

Definition at line 9 of file standard_ConfigEnumInput_help.cc.

standardize_prim()

std::tuple<std::string, std::string, BasicStructure> CASM::standardize_prim	(	BasicStructure const &	prim,
		bool	force
	)

Check if PRIM is primitive

Check that the PRIM is in reduced form:

Definition at line 40 of file init.cc.

status_command()

int CASM::status_command

(

const CommandArgs &

args

)

Set command line options using boost program_options

–help option

1) Check if a project exists

2) Composition axes

3) Configuration generation

4) Calculate configuration properties

5) Choose chemical reference

6) Generate basis functions:

7) Fit effective cluster interactions (ECI):

7) Monte Carlo

Set command line options using boost program_options

–help option

1) Check if a project exists

2) Composition axes

3) Configuration generation

4) Calculate configuration properties

5) Choose chemical reference

6) Generate basis functions:

7) Fit effective cluster interactions (ECI):

7) Monte Carlo

Definition at line 364 of file status.cc.

status_unitialized()

void CASM::status_unitialized

(

const CommandArgs &

args

)

Definition at line 14 of file status.cc.

subopt_test()

void CASM::subopt_test

(

)

Definition at line 43 of file complete_tests.cpp.

subset_permutation_rep()

SymGroupRep CASM::subset_permutation_rep	(	const SymGroupRep &	permute_rep,
		const std::vector< std::set< Index >> &	subsets
	)

Given a permutation representation that permutes indices, calculate a new permutation representation of lower or equal dimension that describes the permutation of ordered subsets of indices. The total number of indices contained in

Parameters

subsets	must be <= permute_rep.dim() and each Index in
subsets	must be unique an on the range [0,permute_rep.dim())

Definition at line 1141 of file SymRepTools.cc.

sum()

template<typename Container >

Container::value_type CASM::sum	(	const Container &	container,
		typename Container::value_type	init_val = 0
	)

Definition at line 131 of file algorithm.hh.

super_command()

int CASM::super_command

(

const CommandArgs &

args

)

Set command line options using boost program_options

–help option

enforce a minimum volume

enforce a minimum volume

Set command line options using boost program_options

–help option

enforce a minimum volume

enforce a minimum volume

Definition at line 129 of file super.cc.

supercells_ungenerated()

void CASM::supercells_ungenerated

(

const CommandArgs &

args

)

Definition at line 93 of file status.cc.

swap() [1/5]

void CASM::swap	(	ConfigDoF &	A,
		ConfigDoF &	B
	)

Definition at line 260 of file ConfigDoF.cc.

swap() [2/5]

template<typename IteratorType >

void CASM::swap	(	FilteredConfigIterator< IteratorType > &	a,
		FilteredConfigIterator< IteratorType > &	b
	)

Definitions.

Definition at line 104 of file FilteredConfigIterator.hh.

swap() [3/5]

template<typename IteratorType >

void CASM::swap	(	FilterIterator< IteratorType > &	a,
		FilterIterator< IteratorType > &	b
	)

Definitions.

Definition at line 70 of file FilterIterator.hh.

swap() [4/5]

template<bool IsConst>

void CASM::swap	(	jsonParserIterator< IsConst > &	a,
		jsonParserIterator< IsConst > &	b
	)

Definition at line 800 of file jsonParser.cc.

swap() [5/5]

void CASM::swap	(	PermuteIterator &	a,
		PermuteIterator &	b
	)

Definition at line 315 of file PermuteIterator.cc.

swap< false >()

template void CASM::swap< false >	(	jsonParserIterator< false > &	,
		jsonParserIterator< false > &
	)

swap< true >()

template void CASM::swap< true >	(	jsonParserIterator< true > &	,
		jsonParserIterator< true > &
	)

sym_line()

std::string CASM::sym_line	(	const xtal::Coordinate &	axis,
		const xtal::Coordinate &	point,
		SymInfoOptions	opt
	)

Use axis and invariant point to return line in '0, y, 0'-type notation.

Definition at line 172 of file SymInfo_stream_io.cc.

sym_plane() [1/2]

std::string CASM::sym_plane	(	const xtal::Coordinate &	axis,
		const xtal::Coordinate &	point,
		SymInfoOptions	opt
	)

Use axis and invariant point to return plane in 'x, y, 0'-type notation.

Definition at line 325 of file SymInfo_stream_io.cc.

sym_plane() [2/2]

std::string CASM::sym_plane	(	const xtal::Coordinate &	v1,
		const xtal::Coordinate &	v2,
		const xtal::Coordinate &	point,
		SymInfoOptions	opt
	)

Use two perpendicular vectors in plane and invariant point to return plane in 'x, y, 0'-type notation.

Definition at line 225 of file SymInfo_stream_io.cc.

symmetrize()

void CASM::symmetrize	(	PrimClex &	primclex,
		jsonParser const &	json_options,
		jsonParser const &	cli_options_as_json
	)

Adjust a structure's lattice and basis to increase factor group symmetry.

Definition at line 292 of file symmetrize.cc.

symmetrize_desc()

std::string CASM::symmetrize_desc

(

)

Describe the symmetrize method.

Definition at line 245 of file symmetrize.cc.

throw_if_invalid_dof_space()

void CASM::throw_if_invalid_dof_space	(	Configuration const &	config,
		DoFSpace const &	dof_space
	)

Throw if !is_valid_dof_space(config, dof_space)

Definition at line 272 of file DoFSpace.cc.

throw_if_no_basis_set_specs()

void CASM::throw_if_no_basis_set_specs	(	std::string	basis_set_name,
		DirectoryStructure const &	dir
	)

Definition at line 585 of file DirectoryStructure.cc.

throw_if_no_clexulator_src()

void CASM::throw_if_no_clexulator_src	(	std::string	project_name,
		std::string	basis_set_name,
		DirectoryStructure const &	dir
	)

Definition at line 599 of file DirectoryStructure.cc.

throw_if_no_root_dir()

void CASM::throw_if_no_root_dir

(

DirectoryStructure const &

dir

)

Definition at line 579 of file DirectoryStructure.cc.

to_brief_unicode()

std::string CASM::to_brief_unicode	(	const SymInfo &	info,
		SymInfoOptions	opt
	)

Print symmetry symbol to string.

Of the form:

m 0.25 0.25 0.0

Uses prime symbol for time reversal symmetry.

Definition at line 364 of file SymInfo_stream_io.cc.

to_configdof()

std::pair< ConfigDoF, std::set< std::string > > CASM::to_configdof	(	SimpleStructure const &	_child_struc,
		Supercell const &	_scel
	)

Initializes configdof of Supercell '_scel' corresponding to an idealized child structure (encoded by _child_struc) _child_struc is assumed to have been idealized via structure-mapping or to be the result of converting a configuration to a SimpleStructure. result.second gives list of properties that were utilized in the course of building the configdof.

Definition at line 260 of file ConfigMapping.cc.

to_json() [1/56]

jsonParser & CASM::to_json	(	ClexBasisSpecs const &	basis_set_specs,
		jsonParser &	json,
		Structure const &	prim,
		ParsingDictionary< DoFType::Traits > const *	dof_dict
	)

Write ClexBasisSpecs to JSON (bspecs.json output)

Example:

{
   "basis_function_specs": <BasisFunctionSpecs JSON>,
   "cluster_specs": <ClusterSpecs JSON>
}

Definition at line 30 of file ClexBasisSpecs_json_io.cc.

to_json() [2/56]

jsonParser & CASM::to_json	(	CompositionAxes const &	composition_axes,
		jsonParser &	json
	)

Write CompositionAxes to JSON.

Definition at line 38 of file CompositionAxes_json_io.cc.

to_json() [3/56]

jsonParser & CASM::to_json	(	ConfigEnumInput const &	config_enum_input,
		jsonParser &	json
	)

Output ConfigEnumInput to JSON.

Definition at line 20 of file ConfigEnumInput_json_io.cc.

to_json() [4/56]

jsonParser & CASM::to_json	(	ConfigMapping::Settings const &	_set,
		jsonParser &	_json
	)

Definition at line 11 of file ConfigMapping_json_io.cc.

to_json() [5/56]

jsonParser & CASM::to_json	(	Configuration const &	configuration,
		jsonParser &	json
	)

Insert Configuration to JSON.

Insert Configuration to JSON

Format:

{
  "supercell_name": <string>,
  "transformation_matrix_to_supercell": <3x3 array of integer>,
  "dof": <JSON object representation of ConfigDoF>
}

Note:

• "supercell_name": string The name of the supercell. If the supercell is in canonical form, the name has the format "SCELV_A_B_C_D_E_F", where V is the integer supercell volume (multiple of the primitive cell), and "A_B_C_D_E_F" are integer values of the hermite normal form of the "transformation_matrix_to_supercell". If the supercell is not in canonical form, the name has the format "SCELV_A_B_C_D_E_F.FG_INDEX", where FG_INDEX is the index in the prim factor group of an operation that transforms the canonical form to the particular supercell.
• "transformation_matrix_to_supercell": 3x3 array of integer The integer transformation matrix T such that S = P*T, where P is a 3x3 column vector matrix of the prim lattice vectors and S is a 3x3 column vector matrix of the supercell lattice vectors.
• "dof": JSON object representation of ConfigDoF See to_json(ConfigDoF const &configdof, jsonParser &json) for details.

Definition at line 85 of file Configuration_json_io.cc.

to_json() [6/56]

template<typename T , typename... Args>

jsonParser& CASM::to_json	(	const Array< T > &	value,
		jsonParser &	json,
		Args &&...	args
	)

Definition at line 19 of file json_io.hh.

to_json() [7/56]

jsonParser & CASM::to_json	(	const BasisFunctionSpecs &	basis_function_specs,
		jsonParser &	json,
		Structure const &	prim,
		ParsingDictionary< DoFType::Traits > const *	dof_dict
	)

Definition at line 136 of file BasisFunctionSpecs_json_io.cc.

to_json() [8/56]

jsonParser & CASM::to_json	(	const BasisSet &	bset,
		jsonParser &	json
	)

Definition at line 1395 of file BasisSet.cc.

to_json() [9/56]

jsonParser & CASM::to_json	(	const ChemicalReference &	ref,
		jsonParser &	json
	)

Write chemical reference.

Write ChemicalReference.

Example form:

{
  "chemical_reference" : {
    "global" : ...,
    "supercell": {
      "SCELX": ...,
      "SCELY": ...
    },
    "config": {
      "SCELX/I": ...,
      "SCELY/J": ...
    }
  }
}

Each individual reference is a vector,

[X, X, X, X]

giving the hyperplane of the reference (each element is the reference value for pure Configurations of a given Molecule).

Definition at line 104 of file ChemicalReference_json_io.cc.

to_json() [10/56]

jsonParser & CASM::to_json	(	const ChemicalReferenceState &	ref_state,
		jsonParser &	json
	)

Write ChemicalReferenceState to: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'.

Definition at line 12 of file ChemicalReference_json_io.cc.

to_json() [11/56]

jsonParser & CASM::to_json	(	const ClexDescription &	desc,
		jsonParser &	json
	)

Definition at line 41 of file ClexDescription.cc.

to_json() [12/56]

jsonParser & CASM::to_json	(	const ClusterSpecs &	cspecs,
		jsonParser &	json
	)

Write PeriodicMaxLengthClusterSpecs or LocalMaxLengthClusterSpecs to JSON.

Definition at line 591 of file ClusterSpecs_json_io.cc.

to_json() [13/56]

jsonParser & CASM::to_json	(	const Completer::EnumOption &	enum_opt,
		jsonParser &	json
	)

Convert casm enum CLI input to JSON.

Convert casm enum CLI input to JSON

All are optionally present, if present on command line

{
  "desc": <array of string, name of enumeration method to print the
  description>, "help": <bool, print/return help>, "method": <string, name
  of enumeration method>, "settings": <string, represents path to settings
  JSON file>, "input": <string, a JSON string>, "min": <int, min supercell
  volume to do enumerations>, "max": <int, max supercell volume to do
  enumerations>, "filter": <array of string, filter query/select expression,
  save configs if evaluates true>, "all": <bool, use all existing supercells
  for enumeration>, "verbosity": <string, to be read by
  Log::verbosity_level>, "scelnames": <array of string, list of supercell
  names, context dependent usage>, "confignames": <array of string, list of
  config names, context dependent usage>, "dry_run": <bool, print/return
  method results but do not save results>
}

Definition at line 30 of file EnumInterface.cc.

to_json() [14/56]

jsonParser & CASM::to_json	(	const Completer::SymOption &	sym_opt,
		jsonParser &	json
	)

Convert casm sym CLI input to JSON.

Convert casm sym CLI input to JSON

All are optionally present, if present on command line

{
  "desc": <array of string, name of enumeration method to print the
  description>, "help": <bool, print/return help>,
  "print_lattice_point_group": <bool, true to print lattice point group>,
  "print_factor_group": <bool, true to print factor group>,
  "print_crystal_point_group": <bool, true to print crystal point group>,
  "coordinate_mode": <string, coordinate type for printing>,
  "symmetrize": <string, path to POSCAR file to symmetrize>,
  "tol": <number, enforced tolerance for symmetrization>,
  "dof_space_analysis": <bool, true to run dof_space_analysis>,
  "settings": <string, represents path to settings JSON file>,
  "input": <string, a JSON string>,
  "scelnames": <array of string, list of supercell names, context dependent
  usage>, "confignames": <array of string, list of config names, context
  dependent usage>, "selection": <string, configuration selection
  name/path>, "dofs": <array of string, DoF types for dof_space_analysis>,
  "calc_wedge": <bool, true to calculate DoF space wedge>,
}

Definition at line 32 of file json_io.cc.

to_json() [15/56]

jsonParser & CASM::to_json	(	const CompositionConverter &	f,
		jsonParser &	json
	)

Serialize CompositionConverter to JSON.

Definition at line 9 of file CompositionConverter_json_io.cc.

to_json() [16/56]

jsonParser & CASM::to_json	(	const ConfigDoF &	configdof,
		jsonParser &	json
	)

Insert ConfigDoF to JSON

Format:

{
  "volume": <int>,
  "occ": <array of integer>,
  "global_dofs": {
    <dof_name>: {
      "values": <1d array of numbers, DoF values in standard basis>
    },
    ...
  },
  "local_dofs": {
    <dof_name>: {
      "values": <2d array of numbers, DoF values in standard basis>
    },
    ...
  }
}

Reminder about standard DoF basis vs prim DoF basis:

• Each type of DoF refers to an AnisoValTraits object which contains the "standard" DoF basis
• The prim BasicStructure holds xtal::SiteDoFSet (representing local DoF) and xtal::DoFSet (representing global DoF) which contain an AnisoValTraits object and a separate "prim" DoF basis containing a set of named basis vectors which are denoted relative to the standard basis, allowing the user to specify the DoFSet components, name them, and restrict DoF values to a particular subspace.
• Examples of standard DoF basis specified by AnisoValTraits:
  • "disp" -> (dx, dy, dz) -> displacement components relative to fixed laboratory frame
  • "strain" -> (e_xx, e_yy, e_zz, sqrt(2)*e_yz, sqrt(2)*e_xz, sqrt(2)*e_xy) -> tensor elements
• ConfigDoF objects in memory store DoF values as coordinates in the prim DoF basis
• ConfigDoF JSON representation stores DoF values as coordinates in the standard DoF basis

Note:

• "occ": The integer value for each site corresponding to which Molecule in the Site::occupant_dof vector is occupying that site.

  Example: supercell volume=3, prim basis size=2,

  "occ": [
      occ[1], // "occ" value on site sublattice 0, unit cell 0
      occ[2], // "occ" value on site sublattice 0, unit cell 1
      occ[3], // "occ" value on site sublattice 0, unit cell 2
      occ[4], // "occ" value on site sublattice 1, unit cell 0
      occ[5], // "occ" value on site sublattice 1, unit cell 1
      occ[6]  // "occ" value on site sublattice 1, unit cell 2
    ]
  

• "local_dofs": The local DoF values are represented as a matrix, with each row representing a site DoF value and each colum representing a component of the DoF value: number of cols = DoF dimension (i.e. 3 for "disp") number of rows = (Supercell volume as multiple of the prim) * (prim basis size).

  Example: "disp" values, supercell volume=3, prim basis size=2

  "local_dofs": {
    "disp": {
      "values": [
        [dx[1], dy[1], dz[1]], // "disp" values on site: sublattice
        0, unit cell 0 [dx[2], dy[2], dz[2]], // "disp" values on
        site: sublattice 0, unit cell 1 [dx[3], dy[3], dz[3]], //
        "disp" values on site: sublattice 0, unit cell 2 [dx[4],
        dy[4], dz[4]], // "disp" values on site: sublattice 1, unit
        cell 0 [dx[5], dy[5], dz[5]], // "disp" values on site:
        sublattice 1, unit cell 1 [dx[6], dy[6], dz[6]], // "disp"
        values on site: sublattice 1, unit cell 2
      ]
    }
  }
  

• "global_dofs": The global DoF values are represented as a vector of size equal to the dimension of the DoF (i.e. 6 for "GLstrain").

  Example: "GLstrain" values (any supercell volume and prim basis size)

  "global_dofs": {
    "GLstrain": {
      "values": [Exx, Eyy, Ezz, sqrt(2)Exz, sqrt(2)Eyz, sqrt(2)Exy]
    }
  }
  

Definition at line 123 of file ConfigDoF_json_io.cc.

to_json() [17/56]

void CASM::to_json	(	const DoF_impl::MagSpinDoFSpecs &	occ_specs,
		jsonParser &	json
	)

Specify max polynomial order for magspin site basis functions

Options:

{
  "max_poly_order": <int, optional, default=-1>
}

Definition at line 97 of file MagSpinDoFTraits.cc.

to_json() [18/56]

void CASM::to_json	(	const DoF_impl::OccupationDoFSpecs &	occupation_dof_specs,
		jsonParser &	json
	)

Definition at line 715 of file OccupationDoFTraits.cc.

to_json() [19/56]

jsonParser& CASM::to_json ( const FormattedPrintable &  _obj, jsonParser &  json  )

inline

Definition at line 742 of file DataFormatter.hh.

to_json() [20/56]

jsonParser & CASM::to_json	(	const Function *	func,
		jsonParser &	json
	)

Definition at line 423 of file BasisFunction.cc.

to_json() [21/56]

jsonParser & CASM::to_json	(	const HyperPlaneReference &	ref,
		jsonParser &	json
	)

Definition at line 55 of file ChemicalReference_json_io.cc.

to_json() [22/56]

jsonParser & CASM::to_json	(	const IntegralClusterOrbitGenerator &	orbit_generator,
		jsonParser &	json
	)

Write custom orbit specs to JSON.

Definition at line 18 of file ClusterOrbits_json_io.cc.

to_json() [23/56]

jsonParser & CASM::to_json	(	const LocalMaxLengthClusterSpecs &	cspecs,
		jsonParser &	json
	)

Write LocalMaxLengthClusterSpecs to JSON.

Definition at line 570 of file ClusterSpecs_json_io.cc.

to_json() [24/56]

jsonParser & CASM::to_json	(	const MappedProperties &	prop,
		jsonParser &	json
	)

Definition at line 51 of file MappedProperties.cc.

to_json() [25/56]

jsonParser & CASM::to_json	(	const OccupantFunction &	func,
		jsonParser &	json
	)

Definition at line 321 of file OccupantFunction.cc.

to_json() [26/56]

jsonParser & CASM::to_json	(	const OrbitPrinterOptions &	opt,
		jsonParser &	json
	)

Definition at line 18 of file OrbitPrinter.cc.

to_json() [27/56]

jsonParser & CASM::to_json	(	const PeriodicMaxLengthClusterSpecs &	cspecs,
		jsonParser &	json
	)

Write PeriodicMaxLengthClusterSpecs to JSON.

Definition at line 554 of file ClusterSpecs_json_io.cc.

to_json() [28/56]

jsonParser & CASM::to_json	(	const Permutation &	value,
		jsonParser &	json
	)

Definition at line 18 of file PermutationIO.cc.

to_json() [29/56]

jsonParser & CASM::to_json	(	const PermuteIterator &	clust,
		jsonParser &	json
	)

Definition at line 335 of file PermuteIterator.cc.

to_json() [30/56]

jsonParser & CASM::to_json	(	const ScoreMappedProperties &	score,
		jsonParser &	json
	)

Definition at line 153 of file MappedProperties.cc.

to_json() [31/56]

template<bool IsConst>

jsonParser& CASM::to_json	(	const SimpleJSonSiteStructure< IsConst > &	jstruc,
		jsonParser &	json
	)

Definition at line 120 of file jsonStruc.hh.

to_json() [32/56]

void CASM::to_json	(	const SymInfo &	info,
		jsonParser &	json
	)

Adds to existing JSON object.

type of symmetry, given by one of the allowed values of symmetry_type

type of symmetry, given by one of the allowed values of symmetry_type

Definition at line 38 of file SymInfo_json_io.cc.

to_json() [33/56]

jsonParser & CASM::to_json	(	const SymInfoOptions &	opt,
		jsonParser &	json
	)

Definition at line 13 of file SymInfo_json_io.cc.

to_json() [34/56]

jsonParser & CASM::to_json	(	const Variable &	var,
		jsonParser &	json
	)

Definition at line 448 of file Variable.cc.

to_json() [35/56]

jsonParser & CASM::to_json	(	const xtal::AtomPosition &	apos,
		jsonParser &	json,
		Eigen::Ref< const Eigen::Matrix3d > const &	cart2frac
	)

Print AtomPosition to json after applying affine transformation cart2frac*cart()+trans.

Definition at line 33 of file BasicStructureIO.cc.

to_json() [36/56]

jsonParser & CASM::to_json	(	const xtal::BasicStructure &	prim,
		jsonParser &	json,
		COORD_TYPE	mode,
		bool	include_va = false
	)

Definition at line 513 of file BasicStructureIO.cc.

to_json() [37/56]

jsonParser & CASM::to_json	(	const xtal::Lattice &	lat,
		jsonParser &	json
	)

Definition at line 9 of file LatticeIO.cc.

to_json() [38/56]

jsonParser & CASM::to_json	(	const xtal::Molecule &	mol,
		jsonParser &	json,
		Eigen::Ref< const Eigen::Matrix3d > const &	c2f_mat
	)

Definition at line 92 of file BasicStructureIO.cc.

to_json() [39/56]

jsonParser & CASM::to_json	(	const xtal::ScelEnumProps &	props,
		jsonParser &	json
	)

Definition at line 9 of file SuperlatticeEnumeratorIO.cc.

to_json() [40/56]

jsonParser & CASM::to_json	(	const xtal::Site &	value,
		jsonParser &	json,
		COORD_TYPE	coordtype
	)

Definition at line 156 of file BasicStructureIO.cc.

to_json() [41/56]

jsonParser & CASM::to_json	(	const xtal::UnitCellCoord &	ucc_val,
		jsonParser &	fill_json
	)

Print to json as [b, i, j, k].

Definition at line 7 of file UnitCellCoordIO.cc.

to_json() [42/56]

jsonParser & CASM::to_json	(	DoFSpace const &	dofspace,
		jsonParser &	json,
		std::optional< std::string > const &	identifier,
		std::optional< ConfigEnumInput > const &	input_state,
		std::optional< SymRepTools_v2::VectorSpaceSymReport > const &	sym_report
	)

Definition at line 84 of file DoFSpace.cc.

to_json() [43/56]

jsonParser & CASM::to_json	(	DoFSpace const &	dofspace,
		jsonParser &	json,
		std::optional< std::string > const &	identifier = std::nullopt,
		std::optional< ConfigEnumInput > const &	input_state = std::nullopt,
		std::optional< VectorSpaceSymReport > const &	sym_report = std::nullopt
	)

Definition at line 56 of file DoFSpace.cc.

to_json() [44/56]

jsonParser & CASM::to_json	(	const IntegralCluster &	clust,
		jsonParser &	json
	)

Write IntegralCluster to JSON object.

Format:

{
  "min_length" : number,
  "max_length" : number,
  "sites" : [
    [b, i, j, k],
    ...
  ]
}

Definition at line 31 of file IntegralCluster_json_io.cc.

to_json() [45/56]

template<typename T , typename... Args>

jsonParser& CASM::to_json	(	std::optional< T > const &	value,
		jsonParser &	json
	)

Definition at line 11 of file optional.hh.

to_json() [46/56]

jsonParser & CASM::to_json	(	SymGroupRepID const &	_id,
		jsonParser &	json
	)

Definition at line 14 of file SymGroupRepID.cc.

to_json() [47/56]

jsonParser & CASM::to_json	(	SymRepTools::IrrepInfo const &	irrep,
		jsonParser &	json
	)

Definition at line 10 of file SymRepTools.cc.

to_json() [48/56]

jsonParser & CASM::to_json	(	SymRepTools::SubWedge const &	wedge,
		jsonParser &	json
	)

Definition at line 46 of file SymRepTools.cc.

to_json() [49/56]

jsonParser & CASM::to_json	(	SymRepTools_v2::IrrepInfo const &	irrep,
		jsonParser &	json
	)

Definition at line 158 of file SymRepTools.cc.

to_json() [50/56]

jsonParser & CASM::to_json	(	SymRepTools_v2::SubWedge const &	wedge,
		jsonParser &	json
	)

Definition at line 194 of file SymRepTools.cc.

to_json() [51/56]

jsonParser & CASM::to_json	(	SymRepTools_v2::VectorSpaceSymReport const &	obj,
		jsonParser &	json
	)

Definition at line 206 of file SymRepTools.cc.

to_json() [52/56]

jsonParser & CASM::to_json	(	VectorSpaceSymReport const &	obj,
		jsonParser &	json
	)

Definition at line 58 of file SymRepTools.cc.

to_json() [53/56]

jsonParser & CASM::to_json	(	xtal::DoFSet const &	_dof,
		jsonParser &	json
	)

Definition at line 8 of file DoFSetIO.cc.

to_json() [54/56]

jsonParser & CASM::to_json	(	xtal::SimpleStructure const &	simple_structure,
		jsonParser &	json,
		std::set< std::string > const &	excluded_species,
		COORD_TYPE	coordinate_mode
	)

Output SimpleStructure to JSON.

Output SimpleStructure to JSON

Parameters

simple_structure	xtal::SimpleStructure to output to JSON
json	A JSON object, into which the xtal::SimpleStructure JSON will output. This function will overwrite existing attributes with the same name, but will not erase any other existing attributes.
excluded_species	Names of any molecular or atomic species that should not be included in the output
coordinate_mode	COORD_TYPE (FRAC or CART) for output coordinates

Note:

• This is the expected format for properties.calc.json

Expected output:

{
  "coord_mode": ("Cartesian" (default), or "Direct" depending on 'mode')
  "atom_type": [  // array of atom type names
    <atom type name>,
    <atom type name>,
    ...
  ],
  "mol_type": [ // array of molecule type names
    <molecule type name>,
    <molecule type name>,
    ...
  ],
  "lattice": [
     [<first lattice vector>],
     [<second lattice vector>],
     [<third lattice vector>]
  ],
  "global_dofs": { // corresponds to simple_struc.properties
     <property name>: {
       "value": [<property vector>]
     },
     ...
  }
  "atom_dofs": { // corresponds to simple_struc.atom_info.properties
     <property name>: {
       "value": [
         [<property vector for site 0>],
         [<property vector for site 1>],
         ...
       ]
     },
     ...
  },
  "mol_dofs": { // corresponds to simple_struc.mol_info.properties
     <property name>: {
       "value": [
         [<property vector for site 0>],
         [<property vector for site 1>],
         ...
     },
     ...
  },
  "atom_coords": [ // atom coordinates, according to "coord_mode"
     [<coordinate for site 0>],
     [<coordinate for site 1>],
     ...
  ],
  "mol_coords": [ // molecule coordinates, according to "coord_mode"
     [<coordinate for site 0>],
     [<coordinate for site 1>],
     ...
  ],
  ...
  }

Definition at line 325 of file SimpleStructureIO.cc.

to_json() [55/56]

jsonParser & CASM::to_json	(	xtal::SiteDoFSet const &	_dof,
		jsonParser &	json
	)

Definition at line 15 of file DoFSetIO.cc.

to_json() [56/56]

jsonParser & CASM::to_json	(	xtal::SpeciesAttribute const &	_attr,
		jsonParser &	json
	)

From SpeciesAttribute to json.

Definition at line 26 of file BasicStructureIO.cc.

to_sequential_string()

std::string CASM::to_sequential_string	(	Index	i,
		Index	max_i,
		char	prepend_char = '0'
	)

Definition at line 248 of file CASM_math.cc.

to_string() [1/6]

template<class Key , class T , class Compare >

std::string CASM::to_string	(	const std::map< T, Key, Compare > &	container,
		std::string	begin = "{",
		std::string	end = "}",
		std::string	delim = ", "
	)

Definition at line 56 of file string_io.hh.

to_string() [2/6]

template<typename T1 , typename T2 >

std::string CASM::to_string

(

const std::pair< T1, T2 > &

value

)

Definition at line 17 of file string_io.hh.

to_string() [3/6]

template<class T , class Compare >

std::string CASM::to_string	(	const std::set< T, Compare > &	container,
		std::string	begin = "[",
		std::string	end = "]",
		std::string	delim = ", "
	)

Definition at line 48 of file string_io.hh.

to_string() [4/6]

std::string CASM::to_string	(	const std::string &	s,
		std::string	begin = "\"",
		std::string	end = "\""
	)

Definition at line 11 of file string_io.hh.

to_string() [5/6]

template<class T >

std::string CASM::to_string	(	const std::vector< T > &	container,
		std::string	begin = "[",
		std::string	end = "]",
		std::string	delim = ", "
	)

Definition at line 41 of file string_io.hh.

to_string() [6/6]

std::string CASM::to_string	(	const SymInfo &	info,
		SymInfoOptions	opt
	)

Print SymInfo to string.

Print SymInfo.

Of the form:

Mirror Operation with plane Normal = 0.25 0.25 0.0

Definition at line 108 of file SymInfo_stream_io.cc.

transf_mat()

Eigen::Matrix3l CASM::transf_mat	(	const Lattice &	prim_lat,
		const Lattice &	super_lat,
		double	tol
	)

Make superlattice transformation matrix [deprecated].

Definition at line 462 of file Supercell.cc.

type_name()

template<typename T >

std::string CASM::type_name

(

)

Get type name as string, via type_name<T>()

• Thanks to: https://stackoverflow.com/a/20170989

Definition at line 19 of file TypeInfo.hh.

valid_index()

bool CASM::valid_index

(

Index

i

)

Definition at line 5 of file definitions.cc.

vector_space_sym_report() [1/2]

VectorSpaceSymReport CASM::vector_space_sym_report	(	DoFSpace const &	dof_space,
		SupercellSymInfo const &	sym_info,
		std::vector< PermuteIterator > const &	group,
		bool	calc_wedges
	)

Make VectorSpaceSymReport.

Make VectorSpaceSymReport

Parameters

dof_space	DoFSpace to make VectorSpaceSymReport for
sym_info	Supercell symmetry info
group	Group used for vector space symmetry report
calc_wedges	If true, calculate the irreducible wedges for the vector space. This may take a long time.

Definition at line 560 of file DoFSpace.cc.

vector_space_sym_report() [2/2]

VectorSpaceSymReport CASM::vector_space_sym_report	(	SymGroupRep const &	_rep,
		SymGroup const &	head_group,
		Eigen::Ref< const Eigen::MatrixXd > const &	_subspace,
		bool	calc_wedges = false
	)

Construct the VectorSpaceSymReport for.

Parameters

_rep	matrix representation of head_group, this defines group action on the underlying vector space
head_group	group for which the sym report is to be generated
_subspace	matrix such that _subspace.rows()==_rep.dim() and whose columns specify a subspace of underlying vector space
calc_wedges	if true, 'irreducible_wedge' of returned object is initialized, if false, 'irreducible_wedge' is empty

Definition at line 725 of file SymRepTools.cc.

vector_space_sym_report_v2() [1/2]

SymRepTools_v2::VectorSpaceSymReport CASM::vector_space_sym_report_v2	(	DoFSpace const &	dof_space,
		SupercellSymInfo const &	sym_info,
		std::vector< PermuteIterator > const &	group,
		bool	calc_wedges
	)

Make VectorSpaceSymReport.

Make VectorSpaceSymReport

Parameters

dof_space	DoFSpace to make VectorSpaceSymReport for
sym_info	Supercell symmetry info
group	Group used for vector space symmetry report
calc_wedges	If true, calculate the irreducible wedges for the vector space. This may take a long time.

Definition at line 585 of file DoFSpace.cc.

vector_space_sym_report_v2() [2/2]

SymRepTools_v2::VectorSpaceSymReport CASM::vector_space_sym_report_v2	(	SymGroupRep const &	rep,
		SymGroup const &	head_group,
		Eigen::MatrixXd const &	subspace,
		bool	calc_wedges
	)

Construct VectorSpaceSymReport, using CASM::SymGroupRep and CASM::SymGroup.

Construct the VectorSpaceSymReport

Parameters

_rep	Matrix representation of head_group, this defines group action on the underlying vector space
head_group	group for which the sym report is to be generated
_subspace	matrix such that _subspace.rows()==_rep.dim() and whose columns specify a subspace of underlying vector space
calc_wedges	if true, 'irreducible_wedge' of returned object is initialized, if false, 'irreducible_wedge' is empty

Definition at line 45 of file VectorSpaceSymReport.cc.

verbosity_help()

std::string CASM::verbosity_help

(

)

Definition at line 35 of file help.cc.

version()

const std::string & CASM::version

(

)

Definition at line 14 of file autoversion.cc.

viable_supercells()

template<typename OrbitType >

std::vector< Eigen::Matrix3i > CASM::viable_supercells	(	std::vector< OrbitType > &	local_orbits,
		const std::vector< Eigen::Matrix3i > &	transf_mat_options
	)

Return superlattice transf. matrices for which has_local_neighborhood_overlap is false.

Parameters

local_orbits	Vector of IntegralCluster orbits defining the local neighborhood
transf_mat_options	A vector of supercell transformation matrices

Definition at line 224 of file ClusterOrbits_impl.hh.

view_command()

int CASM::view_command

(

const CommandArgs &

args

)

–help option

–help option

Definition at line 46 of file view.cc.

which_unique_combination() [1/4]

Index CASM::which_unique_combination	(	const Array< Index > &	input,
		const Array< Array< Index > > &	unique
	)

Definition at line 38 of file CASM_Array_math.cc.

which_unique_combination() [2/4]

Index CASM::which_unique_combination	(	const Array< Index > &	input,
		const Array< Array< Index > > &	unique,
		const Array< Array< Index > > &	ind_equiv
	)

Definition at line 9 of file CASM_Array_math.cc.

which_unique_combination() [3/4]

Index CASM::which_unique_combination	(	const Array< Index > &	input,
		const Array< Index >::X2 &	unique
	)

which_unique_combination() [4/4]

Index CASM::which_unique_combination	(	const Array< Index > &	input,
		const Array< Index >::X2 &	unique,
		const Array< Index >::X2 &	ind_equiv
	)

write_basis_permutation_rep()

void CASM::write_basis_permutation_rep	(	SymGroup const &	grp,
		jsonParser &	group_rep_json,
		SymGroupRepID	symgrouprep_id
	)

Describes how integral site coordinates transform under application of symmetry.

Writes an array, with one element for each group element, containing:

• matrix
• sublattice_permute
• sublattice_shift

The ith factor group operation transforms a basis site:

(b, r_frac) -> (b', r_frac')

according to:

b' = sublattice_permute[b]
r_frac' = matrix * r_frac + sublattice_shift[b]`

where b is the basis index and r_frac is the integer unit cell coordinate of a site.

Definition at line 118 of file SymGroup_json_io.cc.

write_chemical_reference()

void CASM::write_chemical_reference	(	const ChemicalReference &	chem_ref,
		fs::path	filename
	)

Write chemical reference states to JSON file.

See documentation with to_json(ChemicalReference const&, jsonParser &) for JSON format.

Definition at line 37 of file ChemicalReference_file_io.cc.

write_clust() [1/3]

template<typename ClusterOrbitIterator >

jsonParser & CASM::write_clust	(	ClusterOrbitIterator	begin,
		ClusterOrbitIterator	end,
		jsonParser &	json,
		const OrbitPrinterOptions &	opt = OrbitPrinterOptions()
	)

Write Orbit<SymCompareType> to JSON.

Write Orbit<SymCompareType> to JSON, including 'bspecs'.

Definition at line 381 of file OrbitPrinter_impl.hh.

write_clust() [2/3]

template<typename ClusterOrbitIterator , typename Printer >

jsonParser & CASM::write_clust	(	ClusterOrbitIterator	begin,
		ClusterOrbitIterator	end,
		jsonParser &	json,
		Printer	printer
	)

Write Orbit<SymCompareType> to JSON.

Format:

{
  "orbits": [
    {
      "prototype" : {
        "min_length" : number,
        "max_length" : number,
        "sites" : (JSON array of UnitCellCoord)
      }
    },
    ... for each orbit ...
  ],
  "prim" : (JSON object, the contents of prim.json)
}

Definition at line 367 of file OrbitPrinter_impl.hh.

write_clust() [3/3]

template<typename ClusterOrbitIterator , typename Printer >

jsonParser & CASM::write_clust	(	ClusterOrbitIterator	begin,
		ClusterOrbitIterator	end,
		jsonParser &	json,
		Printer	printer,
		const jsonParser &	bspecs
	)

Write Orbit<SymCompareType> to JSON, including 'bspecs'.

Format:

{
  "orbits": [
    {
      "prototype" : {
        "min_length" : number,
        "max_length" : number,
        "sites" : (JSON array of UnitCellCoord)
      }
    },
    ... for each orbit ...
  ],
  "bspecs" : (JSON object, the contents of bspecs.json)
  "prim" : (JSON object, the contents of prim.json)
}

Definition at line 420 of file OrbitPrinter_impl.hh.

write_composition_axes()

void CASM::write_composition_axes	(	fs::path	_filename,
		CompositionAxes const &	composition_axes
	)

Write CompositionAxes to file.

Definition at line 23 of file CompositionAxes_file_io.cc.

write_config_json()

void CASM::write_config_json	(	Configuration const &	configuration,
		DirectoryStructure const &	dir
	)

Write configuration "config.json" file (DoF values in standard basis) to standard location

Definition at line 49 of file clex_io.cc.

write_lat()

void CASM::write_lat	(	Supercell const &	supercell,
		DirectoryStructure const &	dir
	)

Write supercell "LAT" file (supercell lattice vectors as column vectors) to standard location

Definition at line 22 of file clex_io.cc.

write_matrix_rep()

void CASM::write_matrix_rep	(	SymGroupRepHandle const &	grp,
		jsonParser &	json
	)

Definition at line 160 of file SymGroup_json_io.cc.

write_occ_permutation_rep()

void CASM::write_occ_permutation_rep	(	SymGroup const &	grp,
		jsonParser &	json,
		std::vector< SymGroupRepID >	occupant_symrep_IDs
	)

Writes a 3d array, where occ_permutation_rep[b][i] is the permutation array for occupant values on sublattice 'b', due to group operation grp[i], according to: occ(l) = occ_permutation_rep[b][i][occ(l)]. Occupation values are transformed on each site in this way before begin permuted among sites.

Definition at line 145 of file SymGroup_json_io.cc.

write_pos()

void CASM::write_pos	(	Configuration const &	configuration,
		DirectoryStructure const &	dir
	)

Write configuration "POS" file (VASP POSCAR) to standard location.

Definition at line 29 of file clex_io.cc.

write_prim() [1/2]

void CASM::write_prim	(	const xtal::BasicStructure &	prim,
		fs::path	filename,
		COORD_TYPE	mode,
		bool	include_va = false
	)

Write prim.json to file.

Definition at line 429 of file BasicStructureIO.cc.

write_prim() [2/2]

void CASM::write_prim	(	const xtal::BasicStructure &	prim,
		jsonParser &	json,
		COORD_TYPE	mode,
		bool	include_va = false
	)

Write prim.json as JSON.

Definition at line 442 of file BasicStructureIO.cc.

write_prim_symmetry()

void CASM::write_prim_symmetry	(	PrimClex &	primclex,
		jsonParser const &	json_options,
		jsonParser const &	cli_options_as_json
	)

Write/print prim symmetry.

Definition at line 147 of file write_prim_symmetry.cc.

write_prim_symmetry_desc()

std::string CASM::write_prim_symmetry_desc

(

)

Describe the default casm sym option.

Definition at line 104 of file write_prim_symmetry.cc.

write_prim_symmetry_impl()

void CASM::write_prim_symmetry_impl	(	Structure const &	prim,
		DirectoryStructure const &	dir,
		COORD_TYPE	coordtype,
		bool	brief,
		Log &	log,
		bool	print_lattice_point_group,
		bool	print_factor_group,
		bool	print_crystal_point_group
	)

Write/print prim symmetry

Notes:

• The default casm sym action writes the following symmetry files:
  • Lattice point group: <root>/symmetry/lattice_point_group.json
  • Crystal factor group: <root>/symmetry/factor_group.json
  • Crystal point group: <root>/symmetry/crystal_point_group.json
• Optionally, it also prints symmetry information to log:
  • Print lattice point group with print_lattice_point_group
  • Print crystal factor group with print_factor_group
  • Print crystal point group with print_crystal_point_group
  • Control coordinate printing mode (FRAC vs CART) with coordtype
• Use cases:
  • Use this method to print symmetry info to screen
  • Use this method to write symmetry files if they have been deleted
  • Use this method to write symmetry files if the crystallography tolerance in project settings is modified

Definition at line 40 of file write_prim_symmetry.cc.

write_site_basis_funcs()

void CASM::write_site_basis_funcs	(	std::shared_ptr< const Structure >	prim_ptr,
		ClexBasis const &	clex_basis,
		jsonParser &	json
	)

Definition at line 465 of file ProtoFuncsPrinter.cc.

write_structure_json()

void CASM::write_structure_json	(	Configuration const &	configuration,
		DirectoryStructure const &	dir
	)

Write configuration "structure.json" file (structure that results from appling DoF) to standard location

Definition at line 38 of file clex_io.cc.

write_symgroup()

void CASM::write_symgroup	(	SymGroup const &	grp,
		jsonParser &	json
	)

Definition at line 47 of file SymGroup_json_io.cc.

write_symop()

void CASM::write_symop	(	SymGroup const &	grp,
		Index	i,
		jsonParser &	j
	)

Definition at line 18 of file SymGroup_json_io.cc.

Variable Documentation

CART

const COORD_TYPE CASM::CART = COORD_TYPE::CART

Definition at line 9 of file enum.hh.

COORD_DEFAULT

const COORD_TYPE CASM::COORD_DEFAULT = COORD_TYPE::COORD_DEFAULT

Definition at line 11 of file enum.hh.

FRAC

const COORD_TYPE CASM::FRAC = COORD_TYPE::FRAC

Definition at line 8 of file enum.hh.

include_va_opt

const std::string CASM::include_va_opt = "include-va"

Definition at line 37 of file init.cc.

INTEGRAL

const COORD_TYPE CASM::INTEGRAL = COORD_TYPE::INTEGRAL

Definition at line 10 of file enum.hh.

KB

const double CASM::KB = 8.6173423E-05

Definition at line 33 of file definitions.hh.

LOCAL

const PERIODICITY_TYPE CASM::LOCAL = PERIODICITY_TYPE::LOCAL

Definition at line 21 of file enum.hh.

molecule_opt

const std::string CASM::molecule_opt = "as-molecules"

Definition at line 35 of file init.cc.

PERIODIC

const PERIODICITY_TYPE CASM::PERIODIC = PERIODICITY_TYPE::PERIODIC

Definition at line 20 of file enum.hh.

PERIODICITY_DEFAULT

const PERIODICITY_TYPE CASM::PERIODICITY_DEFAULT

Initial value:

=
    PERIODICITY_TYPE::PERIODICITY_DEFAULT

Definition at line 22 of file enum.hh.

PLANCK

const double CASM::PLANCK = 4.135667516E-15

Definition at line 36 of file definitions.hh.

PRIM

const CELL_TYPE CASM::PRIM = CELL_TYPE::PRIM

Definition at line 29 of file enum.hh.

relaxed_opt

const std::string CASM::relaxed_opt = "relaxed"

Definition at line 33 of file init.cc.

SCEL

const CELL_TYPE CASM::SCEL = CELL_TYPE::SCEL

Definition at line 30 of file enum.hh.

subproject_opt

const std::string CASM::subproject_opt = "sub"

Definition at line 29 of file init.cc.

TOL

const double CASM::TOL = 0.00001

Definition at line 30 of file definitions.hh.

write_prim_opt

const std::string CASM::write_prim_opt = "write-prim"

Definition at line 31 of file init.cc.