CASM Namespace Reference

Detailed Description

Main CASM namespace.

What is being tested:

Cluster expansion class.

What is being used to test it:

Namespaces
	api_impl
	CASM_TMP
	Clexulator_impl
	ComparePTLeaf
	Completer
	ConfigIO
	Contains ConfigIO classes and functions.
	ConfigIO_impl
	ConfigMap_impl
	ConfigMapping
	ConfigSelection_impl
	Coordinate_impl
	DataStream_impl
	DoFIsEquivalent
	Namespace containing DoF comparison functors.
	HermiteCounter_impl
	Hull_impl
	HungarianMethod_impl
	Import_impl
	Monte
	multivector_impl
	normal_form_impl
	ref_impl
	SiteCluster_impl
	Update_impl
	VaspIO
	Functions and classes related to VASP input/output.

Classes
class	Args
class	Array
	Basic std::vector like container (deprecated) More...
class	ArraySizeLessThan
class	AtomFracMonteSampler
	Sampler for atom fraction. More...
class	AtomPosition
class	Base1DDatumFormatter
	Abstract base class for creating 1D DatumFormatter. More...
class	BaseCounter
	A Counter allows looping over many incrementing variables in one loop. More...
class	BaseDatumFormatter
	Abstract base class from which all other DatumFormatter<DataObject> classes inherit. More...
class	BaseValueFormatter
	Base class for creating scalar DatumFormatter. More...
class	BasicPolyPolyScalarProd
class	BasicStructure
	BasicStructure specifies the lattice and atomic basis of a crystal. More...
class	BasicVarVarScalarProd
class	BasisSet
class	ChemicalReference
struct	ChemicalReferencePrinter
	Structure to help print ChemicalReference. More...
struct	ChemicalReferenceState
	Stores the composition and energy in a single reference state. More...
class	Clex
	Data structure used for cluster expansions. More...
struct	ClexDescription
	Specifies a particular cluster expansion. More...
class	Clexulator
	Evaluates correlations. More...
class	ClustJsonHelper
struct	CommandArgs
	Data structure holding basic CASM command info. More...
struct	Comparisons
	Implements other comparisons in terms of '<'. More...
class	CompMonteSampler
	Sampler for parametric composition. More...
struct	CompositionAxes
class	CompositionConverter
	Convert between number of species per unit cell and parametric composition. More...
class	ConfigCompare
	Class for less than comparison of Configurations (with the same Supercell) More...
class	ConfigDoF
	A container class for the different degrees of freedom a Configuration might have. More...
class	ConfigDoFCompare
	Wrapper class for generic less than comparison of ConfigDoF. More...
class	ConfigDoFIsEquivalent
	Wrapper class for generic equality comparison of ConfigDoF. More...
class	ConfigEnumAllOccupations
	Enumerate over all possible occupations in a particular Supercell. More...
class	ConfigEnumEquivalents
	Enumerate all equivalent Configurations in a Supercell, as generated by Supercell factor group symmetry. More...
class	ConfigEnumInterpolation
class	ConfigEnumRandomOccupations
	Enumerate n random occupations in a particular Supercell. More...
class	ConfigEnumStrain
struct	ConfigInsertResult
	Holds results of Configuration::insert. More...
class	ConfigIsEquivalent
	Class for comparison of Configurations (with the same Supercell) More...
singleton	ConfigIterator
struct	ConfigMapCompare
class	ConfigMapper
singleton	ConfigSelection
class	ConfigSelectionIterator
class	Configuration
	A Configuration represents the values of all degrees of freedom in a Supercell. More...
class	ConstantReference
	Maps all Configurations to the same value. More...
class	ConstantValueFormatter
	Prints a string value specified at construction. A header string can also be passed. More...
struct	ContainerTraits
	Specialize container traits Expects: More...
struct	ContainerTraits< Eigen::VectorXd >
	Eigen::VectorXd container traits. More...
class	ContinuousDoF
class	COORD_MODE
	COORD_MODE specifies the current coordinate mode (Fractional or Cartesian) More...
class	Coordinate
	Represents cartesian and fractional coordinates. More...
class	CountDataStream
class	Counter
	A Counter allows looping over many incrementing variables in one loop. More...
class	CounterValueIterator
class	CounterValueIterator< MultiCounter< SubCounterType > >
struct	CovEvaluator
	Functor to help evaluate covariance. More...
singleton	DataFormatter
	Extract data from objects of 'DataObject' class. More...
class	DataFormatterDictionary
	Parsing dictionary for constructing a DataFormatter<DataObject> object. More...
class	DataFormatterOperator
	DataFormatters that operate on the results of other DataFormatters. More...
class	DataStream
class	DatumFormatterAlias
	Implements a DatumFormatter that is an alias for a combination of others. More...
class	DeltaProperties
class	DerivedID
struct	DictionaryConverter
struct	DictionaryConverter< DataObject, BaseDatumFormatter< DataObject > >
class	DirectoryStructure
	Specification of CASM project directory structure. More...
class	DiscreteDoF
class	DisplacementDoFEnvironment
class	DoF
class	DoFEnvironment
class	DoFManager
	DoFManager holds multiple DoFEnvironments, and provides a simple interface for adding and managing DoFs. More...
singleton	DynamicMatrix
class	ECIContainer
	A sparse container of ECI values and their corresponding orbit indices. More...
class	EnumEquivalents
	Enumerate over all equivalents. More...
class	EnumeratorBase
	Abstract base class for enumerators. More...
class	EnumeratorHandler
class	EnumInterface
	Template class to be specialized for each enumerator that may be accessed via the API. More...
class	EnumInterfaceBase
	Base class for generic use of enumerators that may be accessed through the API. More...
class	EnumIteratorBase
class	EquilibriumMonteSettings
class	FCC_ternary_Clexulator
class	FileEnumerator
	Lists all files in a CASM project, for use with 'casm files' command. More...
class	FillSupercell
class	FilteredConfigIterator
struct	FloatCompare
class	FormatFlag
class	FormattedPrintable
	Abstract base class to enable generic formatting. More...
class	Function
class	FunctionOperation
class	FunctionVisitor
class	Generic1DDatumFormatter
	A DatumFormatter that returns a 1D value of specified type, via functions that may be specified at runtime. More...
class	GenericCluster
singleton	GenericDatumFormatter
	A DatumFormatter that returns a value of specified type, via functions that may be specified at runtime. More...
class	GenericOrbit
class	GenericOrbitBranch
singleton	GenericOrbitree
class	GramSchmidt
class	GrandCanonical
class	GrandCanonicalConditions
class	GrandCanonicalEvent
	Data structure for storing information regarding a proposed grand canonical Monte Carlo event. More...
class	GrandCanonicalSettings
singleton	HallOfFame
	A container for storing best scoring objects. More...
class	HermiteCounter
class	HierarchyID
class	Hull
	Generate and inspect the convex hull generated from a selection of Configurations. More...
class	HyperPlaneReference
	Maps a Configuration to a scalar value via a hyperplane. More...
class	HyperPlaneReferenceBase
	Maps a Configuration to a scalar value via a hyperplane. More...
class	InnerProduct
class	InputEnumerator
	Generic input enumerator. More...
class	InputEnumeratorBase
	Base class for implementing specialized input enumerators. More...
class	InputEnumIterator
class	InputEnumIteratorBase
class	IsoCounter
	A IsoCounter allows looping over many incrementing variables in one loop. More...
struct	jsonConstructor
	Helper struct for constructing objects that need additional data. More...
struct	jsonConstructor< ChemicalReference >
	Read chemical reference from JSON. More...
struct	jsonConstructor< HyperPlaneReference >
struct	jsonConstructor< Monte::OccCandidate >
struct	jsonConstructor< Monte::OccSwap >
class	jsonParser
class	jsonParserIterator
class	LabeledMatrixXdDataStream
class	Lattice
class	LatticeEnumEquivalents
	Enumerate equivalent Lattics, given a SymGroup. More...
class	LatticeIsEquivalent
	Putting all the Lattice comparisons in one place. More...
class	LatticeMap
class	Log
class	Logging
class	MasterSymGroup
class	MatrixXdDataStream
class	MCData
	MCData stores observations of properties. More...
class	MCDataConvergence
	Checks if a range of observations have converged. More...
class	MCDataEquilibration
	Checks if a range of observations have equilibrated. More...
class	Molecule
class	MonteCarlo
	Interface base class for all types of Monte Carlo simulations (not meant to be used polymorphically) More...
class	MonteCarloDirectoryStructure
class	MonteCarloEnum
class	MonteCarloEnumCheck
class	MonteCarloEnumMetric
class	MonteCounter
	Track the number of passes, steps and samples taken in a Monte Carlo calculation. More...
class	MonteDriver
class	MonteSampler
	An abstract base class for sampling and storing data observations. More...
class	MonteSettings
	Settings for Monte Carlo calculations. More...
class	MultiCounter
struct	multivector
	Shortcut for multidimensional vector (std::vector< std::vector< ...) More...
class	NiggliRep
class	Norm
class	NormPerSpecies
class	NormPerUnitCell
class	OccFuncBasisIndexer
class	OccFuncLabeler
class	OccOccOperation
singleton	OccupantDoF
class	OccupantFunction
class	OccupationDoFEnvironment
class	OStringStreamLog
class	ParamComposition
class	PCA
	Principle component analysis. More...
class	PERIODICITY_MODE
class	Permutation
class	PermuteIterator
class	PolynomialFunction
class	PolyOccOperation
class	PolyPolyOperation
class	PolyTrie
class	PolyVarOperation
class	Popen
	Remember how to use popen. More...
class	PrimClex
	PrimClex is the top-level data structure for a CASM project. More...
class	PrimGrid
class	PrimNeighborList
	The PrimNeighborList gives the coordinates of UnitCell that are neighbors of the origin UnitCell. More...
class	ProjectBuilder
	Sets up directories and files for a new CASM project. More...
class	ProjectSettings
	Read/modify settings of an already existing CASM project. More...
class	Properties
class	PTIterator
class	PTLeaf
class	PTNode
class	QueryHandler
class	QueryMonteSampler
	Sampler for individual elements of a vector property. More...
struct	QueryTraits
struct	QueryTraits< Configuration >
class	RandomAccessEnumerator
	Generic random access enumerator. More...
class	RandomAccessEnumeratorBase
	Base class for implementing specialized random access enumerators. More...
class	RandomAccessEnumIterator
	The iterator type for RandomAccessEnumerator. More...
class	RandomAccessEnumIteratorBase
	RandomAccessEnumIterator implemenation. More...
class	ReturnArray
class	ReturnTensor
class	RuntimeLibrary
	Write, compile, load and use code at runtime. More...
class	SafeOfstream
	Write to a temporary file to ensure a good write, then rename. More...
struct	SamplerNameCompare
class	ScalarMonteSampler
	Sampler for a scalar property. More...
class	ScelEnumByNameT
	Enumerate over Supercell. More...
class	ScelEnumByPropsT
	Enumerate over Supercell. More...
class	ScelEnumEquivalents
	Enumerate equivalent Supercell. More...
class	ScelEnumProps
	Data structure for holding supercell enumeration properties. More...
singleton	ScelEnumT
	Enumerate over Supercell. More...
class	SimpleJSonSiteStructure
class	Site
class	SiteCluster
class	SiteExchanger
class	SiteFracMonteSampler
	Sampler for site fraction. More...
class	SiteMod
	Describes the modification of a variable on a basis site. More...
singleton	SparseTensor
class	Specie
class	StrainConverter
class	StrainDoFEnvironment
class	Structure
	Structure specifies the lattice and atomic basis of a crystal. More...
class	SubExpressionLabeler
class	Supercell
	Represents a supercell of the primitive parent crystal structure. More...
class	SupercellEnumerator
	A fake container of supercell matrices. More...
class	SupercellIterator
	Iterators used with SupercellEnumerator. More...
class	SuperConfigEnum
	Given a selection of Configurations, enumerate all tilings into some supercell. More...
class	SuperNeighborList
	The SuperNeighborList gives the linear indices of neighboring sites and unitcells in a particular Supercell. 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	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...
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	SymRepIndexCompare
class	Tensor
class	TensorBasis
class	test_Clexulator
class	TestEnum
	Enumerate over all possible occupations in a particular Supercell. More...
struct	traits
class	UnitCell
	Unit Cell Indices. More...
class	UnitCellCoord
	Unit Cell Coordinates. More...
class	ValEnumerator
class	ValEnumIterator
class	ValueDataStream
class	Variable
class	VariableLabeler
class	VarVarOperation
class	VectorDataStream
class	VectorMonteSampler
	Sampler for individual elements of a vector property. More...
class	ZrO_Clexulator

Typedefs
typedef ArgHandler::ARG_TYPE	ARG_TYPE
typedef std::function< int(const CommandArgs &)>	Command
typedef std::map< std::string, Command >	CommandMap
typedef ConfigSelection< true >	ConstConfigSelection
typedef unsigned int	uint
typedef unsigned long int	ulint
typedef long int	lint
typedef Eigen::MatrixXd::Index	EigenIndex
	For integer indexing: More...
typedef EigenIndex	Index
	For long integer indexing: More...
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	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...
typedef GenericOrbitree < SiteCluster >	SiteOrbitree
typedef Eigen::VectorXd	Correlation
typedef ScalarAttribute < Configuration >	Reference
typedef GenericOrbitree < HopCluster >	HopOrbitree
typedef ClustJsonHelper < SiteCluster >	SiteClusterJsonHelper
typedef ClustJsonHelper < SiteOrbit >	SiteOrbitJsonHelper
typedef ClustJsonHelper < SiteOrbitBranch >	SiteOrbitBranchJsonHelper
typedef ClustJsonHelper < SiteOrbitree >	SiteOrbitreeJsonHelper
typedef ClustJsonHelper< const SiteCluster >	ConstSiteClusterJsonHelper
typedef ClustJsonHelper< const SiteOrbit >	ConstSiteOrbitJsonHelper
typedef ClustJsonHelper< const SiteOrbitBranch >	ConstSiteOrbitBranchJsonHelper
typedef ClustJsonHelper< const SiteOrbitree >	ConstSiteOrbitreeJsonHelper
typedef GenericOrbit< SiteCluster >	SiteOrbit
typedef GenericOrbit< HopCluster >	HopOrbit
typedef GenericOrbitBranch < SiteCluster >	SiteOrbitBranch
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 ScelEnumT< false >	ScelEnum
typedef notstd::unique_cloneable_map < std::string, EnumInterfaceBase >	EnumeratorMap
	Used to hold a list of all enumerators that may be accessed via the API. More...
typedef OccupantDoF< Molecule >	MoleculeOccupant
typedef const MonteCarlo *	ConstMonteCarloPtr
	const pointer to const MonteCarlo More...
typedef SiteMod< int >	OccMod
	An OccMod describes the change in occupation variable on a site. More...
typedef Eigen::VectorXd	VectorXd
typedef Eigen::MatrixXd	MatrixXd
typedef Eigen::Matrix3d	Matrix3d

Enumerations
enum	COORD_TYPE { FRAC = 0, CART = 1, COORD_DEFAULT = 2 }
enum	PERIODICITY_TYPE { PERIODIC = 0, LOCAL = 1, PERIODICITY_DEFAULT = 2 }
enum	CELL_TYPE { PRIM = 0, SCEL = 1 }
enum	COMPLEX_OUTPUT_TYPE { REAL = 0, IMAG = 1, COMPLEX = 2 }
enum	CASMfileTypes { TYPEFILE, TYPEDIR, TYPEOTHER, IOERR }
enum	COMPOSITION_TYPE { PARAM_COMP = 0, NUMBER_ATOMS = 1 }
enum	STRAIN_METRIC {   GREEN_LAGRANGE = 0, BIOT = 1, HENCKY = 2, EULER_ALMANSI = 3,   DISP_GRAD = 4 }

Functions
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 ()
BasicStructure< Site >	read_prim (fs::path filename)
BasicStructure< Site >	read_prim (const jsonParser &json)
	Read prim.json. More...
void	write_prim (const BasicStructure< Site > &prim, fs::path filename, COORD_TYPE mode)
	Write prim.json to file. More...
void	write_prim (const BasicStructure< Site > &prim, jsonParser &json, COORD_TYPE mode)
	Write prim.json as JSON. More...
void	write_symop (const SymGroup &grp, Index i, jsonParser &j)
void	write_symgroup (const SymGroup &grp, jsonParser &json)
ChemicalReference	read_chemical_reference (fs::path filename, const Structure &prim, double tol)
	Read chemical reference states from JSON file. More...
ChemicalReference	read_chemical_reference (const jsonParser &json, const Structure &prim, double tol)
	Read chemical reference states from JSON. More...
void	write_chemical_reference (const ChemicalReference &chem_ref, fs::path filename)
void	write_chemical_reference (const ChemicalReference &chem_ref, jsonParser &json)
template<typename OutputIterator >
OutputIterator	read_composition_axes (OutputIterator result, const jsonParser &json)
	Read standard axes from JSON, and output to std::map<std::string, CompositionConverter> More...
void	write_basis (const SiteOrbitree &tree, const Structure &prim, jsonParser &json, double tol)
	Write summary of basis functions. More...
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...
PrimClex &	make_primclex_if_not (const CommandArgs &args, std::unique_ptr< PrimClex > &uniq_primclex, Log &status_log)
	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 args.log. More...
int	bset_command (const CommandArgs &args)
int	composition_command (const CommandArgs &args)
int	enum_command (const CommandArgs &args)
int	files_command (const CommandArgs &args)
int	format_command (const CommandArgs &args)
int	import_command (const CommandArgs &args)
int	init_command (const CommandArgs &args)
int	monte_command (const CommandArgs &args)
int	perturb_command (const CommandArgs &args)
int	query_command (const CommandArgs &args)
int	ref_command (const CommandArgs &args)
int	rm_command (const CommandArgs &args)
int	run_command (const CommandArgs &args)
int	select_command (const CommandArgs &args)
int	settings_command (const CommandArgs &args)
int	status_command (const CommandArgs &args)
int	super_command (const CommandArgs &args)
int	sym_command (const CommandArgs &args)
int	update_command (const CommandArgs &args)
int	version_command (const CommandArgs &args)
int	view_command (const CommandArgs &args)
template<typename EnumeratorMapInserter , typename RuntimeLibInserter >
std::pair < EnumeratorMapInserter, RuntimeLibInserter >	load_enumerator_plugins (const ProjectSettings &set, EnumeratorMapInserter enum_it, RuntimeLibInserter lib_it)
	Load enumerator plugins from a CASM project. More...
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)
jsonParser &	to_json (const ProjectSettings &set, jsonParser &json)
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...
jsonParser &	to_json (const Function *func, jsonParser &json)
jsonParser &	to_json (const BasisSet &bset, jsonParser &json)
void	from_json (BasisSet &bset, const jsonParser &json)
BasisSet	operator* (const SymOp &LHS, const BasisSet &RHS)
jsonParser &	to_json (const DoF *dof, jsonParser &json)
	creates jsonParser using polymorphism More...
void	from_json (DoF *dof, const jsonParser &json, const Lattice &lat)
jsonParser &	to_json (const OccupantDoF< int > &dof, jsonParser &json)
	overload for each template type to be used More...
void	from_json (OccupantDoF< int > &dof, const jsonParser &json)
jsonParser &	to_json (const OccupantDoF< Molecule > &dof, jsonParser &json)
void	from_json (OccupantDoF< Molecule > &dof, const jsonParser &json)
void	from_json (ContinuousDoF &dof, const jsonParser &json)
jsonParser &	to_json (const ContinuousDoF &dof, jsonParser &json)
jsonParser &	to_json (const OccupantFunction &func, jsonParser &json)
void	from_json (OccupantFunction &func, const jsonParser &json)
jsonParser &	to_json (const Variable &var, jsonParser &json)
void	from_json (Variable &var, const jsonParser &json)
template<class T >
std::istream &	operator>> (std::istream &_in, std::vector< T > &vec)
bool	valid_index (Index i)
std::istream &	operator>> (std::istream &sin, COORD_TYPE &coord)
void	print_splash (std::ostream &out)
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)
void	split_formatter_expression (const std::string &input_expr, std::vector< std::string > &tag_names, std::vector< std::string > &sub_exprs)
template<typename T >
bool	always_true (const T &)
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 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_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 >
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 >
VectorXdAttributeDictionary < DataObject >	make_vectorxd_dictionary ()
	Template to be specialized for constructing dictionaries for particular DataObject. More...
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 ENUM >
std::string	help ()
	Print help message describing recognized strings for allowed enum values. More...
template<typename ENUM >
void	invalid_enum_string (std::string val, std::ostream &serr)
	Throw invalid_argument error for unrecognized strings. More...
template<typename ENUM >
std::string	to_string (ENUM val)
	Return string representation of enum class. 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)
jsonParser &	to_json (const COORD_TYPE &value, jsonParser &json)
	Puts COORD_TYPE value (as string) More...
void	from_json (COORD_TYPE &value, const jsonParser &json)
jsonParser &	to_json (const PERIODICITY_TYPE &value, jsonParser &json)
	Puts PERIODICITY_TYPE value (as string) More...
void	from_json (PERIODICITY_TYPE &value, const jsonParser &json)
	Gets string value as PERIODICITY_TYPE. More...
jsonParser &	to_json (const CELL_TYPE &value, jsonParser &json)
	Puts CELL_TYPE value (as string) More...
void	from_json (CELL_TYPE &value, const jsonParser &json)
	Gets string value as CELL_TYPE. More...
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<>
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)
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...
boost::filesystem::path	find_diff (const jsonParser &A, const jsonParser &B, boost::filesystem::path diff=boost::filesystem::path())
	Return the location at which jsonParser 'A' != 'B' as a boost::filesystem::path. More...
boost::filesystem::path	find_diff (const jsonParser &A, const jsonParser &B, double tol, boost::filesystem::path diff=boost::filesystem::path())
	Return the location at which jsonParser !A.almost_equal(B, tol) as a boost::filesystem::path. More...
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 &	null_log ()
bool	operator< (const Clex &A, const Clex &B)
	Compare using descriptions: A.desc() < B.desc() More...
template<typename OutputIterator >
OutputIterator	standard_composition_axes (const Structure &prim, 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...
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...
Eigen::MatrixXd	end_members (const Structure &prim)
	Generate a column matrix containing all the possible molecular end members. More...
Eigen::MatrixXd	composition_space (const Structure &prim, double tol=1e-14)
	Return the composition space of a Structure. More...
Eigen::MatrixXd	null_composition_space (const Structure &prim, double tol=1e-14)
	Return the null composition space of a Structure. More...
jsonParser &	to_json (const ConfigDoF &value, jsonParser &json)
void	from_json (ConfigDoF &value, const jsonParser &json)
ConfigDoF &	apply (const PermuteIterator &it, ConfigDoF &dof)
void	swap (ConfigDoF &A, ConfigDoF &B)
Correlation	correlations (const ConfigDoF &configdof, const Supercell &scel, Clexulator &clexulator)
	Returns correlations using 'clexulator'. Supercell needs a correctly populated neighbor list. More...
Eigen::VectorXd	correlations_vec (const ConfigDoF &configdof, const Supercell &scel, Clexulator &clexulator)
	Returns correlations using 'clexulator'. Supercell needs a correctly populated neighbor list. More...
ReturnArray< int >	get_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::VectorXi	get_num_each_molecule_vec (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...
void	reset_properties (ConfigDoF &_dof)
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<typename ConfigType , typename PrimClexType >
void	swap (ConfigIterator< ConfigType, PrimClexType > &a, ConfigIterator< ConfigType, PrimClexType > &b)
template<bool IsConst>
std::ostream &	operator<< (std::ostream &_stream, const ConfigSelection< IsConst > &selection)
bool	get_selection (const Array< std::string > &criteria, const Configuration &config, bool is_selected)
Configuration &	apply (const PermuteIterator &it, Configuration &config)
Configuration	sub_configuration (Supercell &sub_scel, const Configuration &super_config, const UnitCell &origin)
	Returns the sub-configuration that fills a particular Supercell. More...
Configuration	make_configuration (PrimClex &primclex, std::string name)
	Make Configuration from name string. More...
Correlation	correlations (const Configuration &config, Clexulator &clexulator)
	Returns correlations using 'clexulator'. 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	relaxed_energy (const Configuration &config)
	Returns the relaxed energy, normalized per unit cell. More...
double	relaxed_energy_per_species (const Configuration &config)
	Returns the relaxed 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...
bool	is_calculated (const Configuration &config)
	Return true if all current properties have been been calculated for the configuration. More...
double	rms_force (const Configuration &_config)
	Root-mean-square forces of relaxed configurations, determined from DFT (eV/Angstr.) More...
double	basis_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::VectorXd	relaxed_mag_basis (const Configuration &_config)
	Returns the relaxed magnetic moment of each basis site. More...
Eigen::VectorXd	relaxed_mag (const Configuration &_config)
	Returns the relaxed magnetic moment for each molecule. 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 _config no symmetry transformation applied to _config will increase its lexicographic order More...
std::string	calc_status (const Configuration &_config)
	Status of calculation. More...
std::string	failure_type (const Configuration &_config)
bool	has_relaxed_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_basis_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)
bool	has_calc_status (const Configuration &_config)
bool	has_failure_type (const Configuration &_config)
std::ostream &	operator<< (std::ostream &sout, const Configuration &c)
void	reset_properties (Configuration &_config)
template<class U >
void	match_shape (Correlation &corr, const Array< Array< Array< U > > > &thing)
template<class ClustType >
void	match_shape (Correlation &corr, const GenericOrbitree< ClustType > &tree)
double	operator* (const ECIContainer &_eci, const Correlation &_corr)
	Evaluate property given an ECIContainer and Correlation. More...
double	operator* (const ECIContainer &_eci, double const *_corr_begin)
	Evaluate property given an ECIContainer and pointer to beginning of range of correlation. More...
ECIContainer	read_eci_out (const fs::path &filepath)
	Read eci.out file from specified path (deprecated) More...
ECIContainer	read_eci (const fs::path &filepath)
	Read eci.json file from specified path. More...
template<typename IteratorType >
void	swap (FilteredConfigIterator< IteratorType > &a, FilteredConfigIterator< IteratorType > &b)
	Definitions. More...
template<typename IteratorType >
FilteredConfigIterator < IteratorType >	filter_begin (const IteratorType &it, const IteratorType &it_end, const std::vector< std::string > &filter_expr, const DataFormatterDictionary< Configuration > &_dict)
template<typename IteratorType >
FilteredConfigIterator < IteratorType >	filter_end (const IteratorType &it_end)
SiteOrbitree	make_orbitree (Structure &prim, const jsonParser &json, double _tol)
	Make orbitree. For now specifically global. More...
void	print_clexulator (const Structure &prim, SiteOrbitree &tree, const PrimNeighborList &nlist, std::string class_name, std::ostream &stream, double xtal_tol)
	Print clexulator. More...
Supercell &	apply (const SymOp &op, Supercell &scel)
Supercell	copy_apply (const SymOp &op, const Supercell &scel)
std::string	generate_name (const Eigen::Matrix3i &transf_mat)
template<typename CoordType >
GenericCluster< CoordType >	operator* (const SymOp &LHS, const GenericCluster< CoordType > &RHS)
	create symmetry-transformed cluster More...
template<typename CoordType >
GenericCluster< CoordType >	operator+ (const GenericCluster< CoordType > &LHS, const Coordinate &RHS)
	create translated cluster More...
template<typename CoordType >
GenericCluster< CoordType >	operator- (const GenericCluster< CoordType > &LHS, const Coordinate &RHS)
	create translated cluster More...
template<typename CoordType >
bool	almost_equal (const GenericCluster< CoordType > &LHS, const GenericCluster< CoordType > &RHS, double tol)
template<typename T >
jsonParser &	to_json (const GenericCluster< T > &clust, jsonParser &json)
template<typename T >
void	from_json (GenericCluster< T > &clust, const jsonParser &json)
template<typename CoordType >
std::ostream &	operator<< (std::ostream &stream, const GenericCluster< CoordType > &cluster)
jsonParser &	to_json (const GenericOrbitBranch< SiteCluster > &branch, jsonParser &json)
void	from_json (GenericOrbitBranch< SiteCluster > &branch, const jsonParser &json)
	Assumes the pivot lattice is already set. More...
jsonParser &	to_json (const GenericOrbit< SiteCluster > &orbit, jsonParser &json)
void	from_json (GenericOrbit< SiteCluster > &orbit, const jsonParser &json)
	Assumes the prototype lattice is already set. More...
void	from_json (SiteClusterJsonHelper clust_helper, const jsonParser &json)
jsonParser &	to_json (const ConstSiteClusterJsonHelper &clust_helper, jsonParser &json)
jsonParser &	to_json (const ConstSiteOrbitJsonHelper &orbit_helper, jsonParser &json)
	Lean printing of Orbits (only the prototype gets printed; full orbit can later be reconstructed using struc.factor_group();. More...
void	from_json (SiteOrbitBranchJsonHelper branch_helper, const jsonParser &json)
jsonParser &	to_json (const ConstSiteOrbitBranchJsonHelper &branch_helper, jsonParser &json)
void	from_json (SiteOrbitreeJsonHelper tree_helper, const jsonParser &json)
jsonParser &	to_json (const ConstSiteOrbitreeJsonHelper &tree_helper, jsonParser &json)
template<typename ValueType >
ClustJsonHelper< ValueType >	jsonHelper (ValueType &_value, const Structure &_struc, double tol=TOL)
template<typename ClustType >
std::ostream &	operator<< (std::ostream &stream, const GenericOrbitree< ClustType > &orbitree)
template<typename ClustType >
void	from_json (GenericOrbitree< ClustType > &tree, const jsonParser &json)
	Assumes the prototype lattice is already set. More...
template<typename OutputIterator , typename TreeType , typename StrucType >
OutputIterator	orbit_neighborhood (OutputIterator result, const TreeType &tree, const StrucType &struc, Index nb, Index no, double tol)
	Iterate over all sites in an orbit and insert a UnitCellCoord. More...
template<typename OutputIterator , typename TreeType , typename StrucType >
OutputIterator	neighborhood (OutputIterator result, const TreeType &tree, const StrucType &struc, double tol)
	Iterate over all sites in an orbitree and insert a UnitCellCoord. More...
SiteCluster	operator* (const SymOp &LHS, const SiteCluster &RHS)
jsonParser &	to_json (const SiteCluster &clust, jsonParser &json)
void	from_json (SiteCluster &clust, const jsonParser &json)
template<typename T >
jsonParser &	to_json (const Array< T > &value, jsonParser &json)
template<typename T >
void	from_json (Array< T > &value, const jsonParser &json)
	This requires that 'T::T()' exists, if not, you must do this by hand. More...
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)
EnumeratorMap	make_enumerator_map ()
	Use to construct an EnumeratorMap. More...
jsonParser	make_enumerator_scel_enum_input (const jsonParser &_kwargs, const Completer::EnumOption &enum_opt)
	Standardizes parsing casm enum input options to make ScelEnum JSON input. More...
ScelEnumProps	make_enumerator_scel_enum_props (PrimClex &primclex, const jsonParser &_kwargs, const Completer::EnumOption &enum_opt)
	Standardizes parsing casm enum input options to make an ScelEnumProps. More...
std::unique_ptr < SupercellEnumerator< Lattice > >	make_enumerator_superlat_enum (PrimClex &primclex, const jsonParser &_kwargs, const Completer::EnumOption &enum_opt)
	Standardizes parsing casm enum input options to make an SupercellEnumerator<Lattice> More...
std::unique_ptr< ScelEnum >	make_enumerator_scel_enum (PrimClex &primclex, const jsonParser &_kwargs, const Completer::EnumOption &enum_opt)
	Standardizes parsing casm enum input options to make an ScelEnum. More...
std::vector< std::string >	make_enumerator_filter_expr (const jsonParser &_kwargs, const Completer::EnumOption &enum_opt)
	Standardizes parsing casm enum filter expressions. More...
template<typename ScelIterator , typename ConfigEnumConstructor >
int	insert_unique_canon_configs (std::string method, PrimClex &primclex, ScelIterator begin, ScelIterator end, ConfigEnumConstructor f, std::vector< std::string > filter_expr)
	Standardizes insertion from enumerators that construct unique primitive canonical configurations. More...
template<typename ScelIterator , typename ConfigEnumConstructor >
int	insert_configs (std::string method, PrimClex &primclex, ScelIterator begin, ScelIterator end, ConfigEnumConstructor f, std::vector< std::string > filter_expr, bool primitive_only)
	Standardizes insertion from enumerators that construct configurations. More...
template<typename LatticeIterator , typename ConfigEnumConstructor >
int	insert_configs_via_lattice_enum (std::string method, PrimClex &primclex, LatticeIterator begin, LatticeIterator end, ConfigEnumConstructor f, std::vector< std::string > filter_expr, bool primitive_only)
	Standardizes insertion from enumerators that construct configurations. More...
void	get_Hermitian (Eigen::MatrixXcd &original_mat, Eigen::MatrixXcd &hermitian_mat, Eigen::MatrixXcd &antihermitian_mat)
bool	is_Hermitian (Eigen::MatrixXcd &mat)
void	poly_fit (Eigen::VectorXcd &xvec, Eigen::VectorXcd &yvec, Eigen::VectorXcd &coeffs, int degree)
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_prod (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(std::ptr_fun(boost::math::iround < typename Derived::Scalar > )), const Derived >	iround (const Eigen::MatrixBase< Derived > &val)
	Round Eigen::MatrixXd to Eigen::MatrixXi. More...
template<typename Derived >
Eigen::CwiseUnaryOp< decltype(std::ptr_fun(boost::math::lround < 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...
std::vector< Eigen::Matrix3i >	_unimodular_matrices (bool positive, bool negative)
const std::vector < Eigen::Matrix3i > &	positive_unimodular_matrices ()
const std::vector < Eigen::Matrix3i > &	negative_unimodular_matrices ()
const std::vector < Eigen::Matrix3i > &	unimodular_matrices ()
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<typename CoordType >
BasicStructure< CoordType >	operator* (const SymOp &LHS, const BasicStructure< CoordType > &RHS)
template<typename CoordType >
BasicStructure< CoordType >	operator* (const Lattice &LHS, const BasicStructure< CoordType > &RHS)
template<typename CoordType >
BasicStructure< CoordType >	operator+ (const Coordinate &LHS, const BasicStructure< CoordType > &RHS)
template<typename CoordType >
BasicStructure< CoordType >	operator+ (const BasicStructure< CoordType > &LHS, const Coordinate &RHS)
template<typename CoordType >
jsonParser &	to_json (const BasicStructure< CoordType > &basic, jsonParser &json)
template<typename CoordType >
void	from_json (BasicStructure< CoordType > &basic, const jsonParser &json)
jsonParser &	to_json (const Coordinate &value, jsonParser &json)
void	from_json (Coordinate &value, const jsonParser &json)
Coordinate	operator* (const SymOp &LHS, const Coordinate &RHS)
Coordinate	operator+ (const Coordinate &LHS, const Coordinate &RHS)
Coordinate	operator- (const Coordinate &LHS, const Coordinate &RHS)
jsonParser &	to_json (const Lattice &lat, jsonParser &json)
void	from_json (Lattice &lat, const jsonParser &json)
double	volume (const Lattice &lat)
	Returns the volume of a Lattice. More...
Lattice &	apply (const SymOp &op, Lattice &lat)
	Apply SymOp to a Lattice. More...
Lattice	copy_apply (const SymOp &op, const Lattice &lat)
	Copy and apply SymOp to a Lattice. More...
Lattice	make_supercell (const Lattice &lat, const Eigen::Matrix3i &transf_mat)
	Returns a super Lattice. More...
std::pair< bool, Eigen::MatrixXi >	is_supercell (const Lattice &scel, const Lattice &unit, double tol)
	Check if scel is a supercell of unitcell unit and some integer transformation matrix T. More...
template<typename Object , typename OpIterator >
std::pair< OpIterator, Eigen::MatrixXi >	is_supercell (const Object &scel, const Object &unit, OpIterator begin, OpIterator end, double tol)
std::istream &	operator>> (std::istream &in, const Lattice &lattice_in)
Lattice	superdupercell (const Lattice &lat1, const Lattice &lat2)
	returns Lattice that is smallest possible supercell of both input Lattice More...
template<typename LatIterator , typename SymOpIterator >
Lattice	superdupercell (LatIterator begin, LatIterator end, SymOpIterator op_begin=SymOpIterator(), SymOpIterator op_end=SymOpIterator())
	returns Lattice that is smallest possible supercell of all input Lattice More...
Lattice	replace_vector (const Lattice &lat, const Eigen::Vector3d &new_vector, double tol)
Eigen::Matrix3d	cart2frac (const Eigen::Ref< const Eigen::Matrix3d > &cart_mat, const Lattice &lat)
	Returns 'frac_mat' which is transformation of 'cart_mat' if cart_vec_after = cart_mat*cart_vec then frac_vec_after = frac_mat*frac_vec where cart_vec = lat.lat_column_mat()*frac_vec and cart_vec_after = lat.lat_column_mat()*frac_vec_after. More...
Eigen::Matrix3d	frac2cart (const Eigen::Ref< const Eigen::Matrix3d > &frac_mat, const Lattice &lat)
	Returns 'cart_mat' which is transformation of 'frac_mat' if cart_vec_after = cart_mat*cart_vec then frac_vec_after = frac_mat*frac_vec where cart_vec = lat.lat_column_mat()*frac_vec and cart_vec_after = lat.lat_column_mat()*frac_vec_after. More...
bool	is_vacancy (const std::string &name)
	A vacancy is any Specie/Molecule with (name == "VA" || name == "va" || name == "Va") More...
jsonParser &	to_json (const Specie &specie, jsonParser &json)
void	from_json (Specie &specie, const jsonParser &json)
jsonParser &	to_json (const AtomPosition &apos, jsonParser &json)
void	from_json (AtomPosition &apos, const jsonParser &json)
Molecule	operator* (const SymOp &LHS, const Molecule &RHS)
Molecule	operator+ (const Coordinate &LHS, const Molecule &RHS)
Molecule	operator+ (const Molecule &LHS, const Coordinate &RHS)
Molecule	make_atom (std::string atom_name, const Lattice &lat)
	Return an atomic Molecule with specified name and Lattice. More...
Molecule	make_vacancy (const Lattice &lat)
	Return an vacancy Molecule with specified Lattice. More...
bool	is_molecule_name (const Molecule &mol, std::string name)
	Return true if Molecule name matches 'name', including Va checks. More...
jsonParser &	to_json (const Molecule &mol, jsonParser &json)
void	from_json (Molecule &mol, const jsonParser &json)
Eigen::Matrix3i	make_unit_cell (PrimClex &primclex, const jsonParser &json)
	Read unit cell transformation matrix from JSON input. More...
ScelEnumProps	make_scel_enum_props (PrimClex &primclex, const jsonParser &input)
	Make a ScelEnumProps object from JSON input. More...
template<typename UnitType >
Eigen::Matrix3i	enforce_min_volume (const UnitType &unit, const Eigen::Matrix3i &T, const SymGroup &point_grp, Index volume, bool fix_shape=false)
	Return a transformation matrix that ensures a supercell of at least some volume. More...
template<>
Eigen::Matrix3i	enforce_min_volume< Lattice > (const Lattice &unit, const Eigen::Matrix3i &T, const SymGroup &point_grp, Index volume, bool fix_shape)
Eigen::Matrix3i	canonical_hnf (const Eigen::Matrix3i &T, const SymGroup &effective_pg, const Lattice &ref_lattice)
	Return canonical hermite normal form of the supercell matrix, and op used to find it. More...
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 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 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 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 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 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...
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 Derived >
bool	almost_zero (const Eigen::MatrixBase< Derived > &val, double tol=TOL)
	Equivalent to almost_zero(double(val.norm()), 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...
bool	float_lexicographical_compare (const Eigen::VectorXd &A, const Eigen::VectorXd &B, 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)
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...
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)
Eigen::VectorXd	eigen_vector_from_string (const std::string &tstr, const int &size)
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...
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)
int	mod (int a, int b)
double	cuberoot (double number)
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 >
double	length (const Eigen::MatrixBase< Derived > &value)
template<typename Derived >
ReturnArray< Index >	partition_distinct_values (const Eigen::MatrixBase< Derived > &value, double tol=TOL)
double	hungarian_method (const Eigen::MatrixXd &cost_matrix, std::vector< Index > &optimal_assignments, const double _tol)
template<typename Derived >
Eigen::Matrix< int, Derived::RowsAtCompileTime, Derived::ColsAtCompileTime >	scale_to_int (const Eigen::MatrixBase< Derived > &val, double _tol=TOL)
	Take a vector of doubles, and multiply by some factor that turns it into a vector of integers (within a tolerance) More...
Eigen::MatrixXd	pad (const Eigen::MatrixXd &M, int n)
	Construct a matrix consisting of blocks M and Identity(n,n) More...
std::ostream &	operator<< (std::ostream &sout, const GrandCanonicalConditions &cond)
DataFormatter< ConstMonteCarloPtr >	make_results_formatter (const GrandCanonical &mc)
	Make a LTE results formatter. More...
DataFormatter< ConstMonteCarloPtr >	make_lte_results_formatter (const GrandCanonical &mc, const double &phi_LTE1, const std::string &configname)
	Make a results formatter. More...
jsonParser &	to_json (const GrandCanonicalConditions &conditions, jsonParser &json)
	Store GrandCanonicalConditions in JSON format. More...
void	from_json (GrandCanonicalConditions &conditions, const PrimClex &primclex, const jsonParser &json)
	Read GrandCanonicalConditions from JSON format. More...
GenericDatumFormatter< double, ConstMonteCarloPtr >	GrandCanonicalLTEFormatter (const double &phi_LTE1)
	Print single spin flip LTE. More...
void	write_lte_results (const MonteSettings &settings, const GrandCanonical &mc, const double &phi_LTE1, const std::string &configname, Log &_log)
	Will create new file or append to existing results file the results of the latest run. More...
template<typename RunType >
bool	monte_carlo_step (RunType &monte_run)
	Perform a single monte carlo step, return true if accepted. More...
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloMeanFormatter (std::string prop_name)
	Print mean property values: <prop_name> More...
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloPrecFormatter (std::string prop_name)
	Print calculated precision of property values: prec(<prop_name>) More...
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloCovFormatter (std::string prop_name1, std::string prop_name2)
	Print covariance: cov(prop_name1, prop_name2) More...
GenericDatumFormatter< bool, ConstMonteCarloPtr >	MonteCarloIsEquilibratedFormatter ()
	Print if equilibrated (not counting explicitly requested equilibration) More...
GenericDatumFormatter< bool, ConstMonteCarloPtr >	MonteCarloIsConvergedFormatter ()
	Print if converged. More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloTFormatter ()
	Print Temperature. More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloBetaFormatter ()
	Print Beta. More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloParamChemPotFormatter (const MonteType &mc, int index)
	Print param_chem_pot(x) More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloChemPotFormatter (const MonteType &mc, int index)
	Print chem_pot(N) More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloCompFormatter (const MonteType &mc, int index)
	Print comp(x) More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloCompNFormatter (const MonteType &mc, int index)
	Print comp_n(N) More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloHeatCapacityFormatter ()
	Print heat capacity, 'heat_capacity'. More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloSuscXFormatter (std::string comp_var_i, std::string comp_var_j)
	Print parametric susceptibility, 'susc_x(a,b)'. More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloSuscNFormatter (std::string species_i, std::string species_j)
	Print susceptibility, 'susc_n(A,B)'. More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloThermoChemSuscXFormatter (std::string comp_var_i)
	Print parametric thermo-chemical susceptibility, 'susc_x(S,a)'. More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloThermoChemSuscNFormatter (std::string species_i)
	Print thermo-chemical susceptibility, 'susc_n(S,A)'. More...
GenericDatumFormatter < MonteSampler::size_type, ConstMonteCarloPtr >	MonteCarloNEquilSamplesFormatter ()
	Print number of samples used for equilibration (not counting explicitly requested equilibration) More...
GenericDatumFormatter < MonteSampler::size_type, ConstMonteCarloPtr >	MonteCarloNAvgSamplesFormatter ()
	Print number of samples used in calculating means. More...
GenericDatumFormatter < MonteCounter::size_type, std::pair< ConstMonteCarloPtr, Index > >	MonteCarloPassFormatter ()
	Print Pass number of observation. More...
GenericDatumFormatter < MonteCounter::size_type, std::pair< ConstMonteCarloPtr, Index > >	MonteCarloStepFormatter ()
	Print Step number of observation. More...
GenericDatumFormatter< double, std::pair< ConstMonteCarloPtr, Index > >	MonteCarloObservationFormatter (std::string prop_name)
	Print value of observation. More...
GenericDatumFormatter< int, std::pair< ConstMonteCarloPtr, Index > >	MonteCarloOccFormatter (Index occ_index)
	Print value of a particular occupation variable. More...
DataFormatter< std::pair < ConstMonteCarloPtr, Index > >	make_observation_formatter (const MonteCarlo &mc)
	Make a observation formatter. More...
DataFormatter< std::pair < ConstMonteCarloPtr, Index > >	make_trajectory_formatter (const MonteCarlo &mc)
	Make a trajectory formatter. More...
template<typename MonteType >
void	write_results (const MonteSettings &settings, const MonteType &mc, Log &_log)
	Will create new file or append to existing file results of the latest run. More...
template<typename MonteType >
void	write_conditions_json (const MonteSettings &settings, const MonteType &mc, Index cond_index, Log &_log)
	Write conditions to conditions.cond_index directory. More...
void	write_observations (const MonteSettings &settings, const MonteCarlo &mc, Index cond_index, Log &_log)
	Will create (and possibly overwrite) new file with all observations from run with conditions.cond_index. More...
void	write_trajectory (const MonteSettings &settings, const MonteCarlo &mc, Index cond_index, Log &_log)
	Will create (and possibly overwrite) new file with all observations from run with conditions.cond_index. More...
void	write_POSCAR_initial (const MonteCarlo &mc, Index cond_index, Log &_log)
	For the initial state, write a POSCAR file. More...
void	write_POSCAR_final (const MonteCarlo &mc, Index cond_index, Log &_log)
	For the final state, write a POSCAR file. More...
void	write_POSCAR_trajectory (const MonteCarlo &mc, Index cond_index, Log &_log)
	For every snapshot taken, write a POSCAR file. More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloSiteFracFormatter (const MonteType &mc, int index)
	Print site_frac(x) for any class MonteType with valid 'Eigen::VectorXd MonteType::comp_n'. More...
template<typename MonteType >
GenericDatumFormatter< double, ConstMonteCarloPtr >	MonteCarloAtomFracFormatter (const MonteType &mc, int index)
	Print atom_frac(X) for any class MonteType with valid 'Eigen::VectorXd MonteType::comp_n'. More...
bool	operator== (const jsonParser &json, const MonteSettings &settings)
bool	operator!= (const jsonParser &json, const MonteSettings &settings)
jsonParser &	to_json (const SymGroup &group, jsonParser &json)
void	from_json (SymGroup &group, const jsonParser &json)
SymGroup	molecular_point_group (std::map< int, std::vector< Eigen::Vector3d > > coord_map)
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)
jsonParser &	to_json (const SymOp &sym, jsonParser &json)
void	from_json (SymOp &sym, const jsonParser &json)
std::string	include_path (const fs::path &dir)
std::string	link_path (const fs::path &dir)
const std::string &	version ()
void	write_prim_nlist (const Array< UnitCellCoord > &prim_nlist, const fs::path &nlistpath)
Array< UnitCellCoord >	read_prim_nlist (const fs::path &nlistpath)
void	display (std::ostream &sout, const CompositionAxes &opt)
template std::pair < enum_it_type, runtimelib_it_type >	load_enumerator_plugins (const ProjectSettings &set, enum_it_type enum_it, runtimelib_it_type lib_it)
bool	_has_existing_files (fs::path p)
fs::path	_calc_properties_path (const PrimClex &primclex, fs::path pos_path)
	Return path to properties.calc.json that will be imported checking a couple possible locations relative to pos_path. More...
void	_cp_files (const fs::path &pos_path, const Configuration &config, bool copy_additional_files, Log &log)
	Copy files in the same directory as properties.calc.json into the traning_data directory for a particular configuration. More...
void	_recurs_cp_files (const fs::path &from_dir, const fs::path &to_dir, Log &log)
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 MonteSettings &monte_settings, const CommandArgs &args, const Completer::MonteOption &monte_opt)
int	_run_Canonical (PrimClex &primclex, const MonteSettings &monte_settings, const CommandArgs &args, const Completer::MonteOption &monte_opt)
Eigen::Matrix3l	_default_nlist_weight_matrix (const Structure &prim, double tol)
	Default weight matrix for approximately spherical neighborhood in Cartesian coordinates. More...
std::set< int >	_default_nlist_sublat_indices (const Structure &prim)
	Default includes sublattices with >= 2 components. More...
void	query_help (const DataFormatterDictionary< Configuration > &_dict, std::ostream &_stream, std::vector< std::string > help_opt_vec)
int	_rm_configs (const CommandArgs &args, const Completer::RmOption &rm_opt)
int	_rm_scel (const CommandArgs &args, const Completer::RmOption &rm_opt)
template<typename ConfigIterType >
void	set_selection (const DataFormatterDictionary< Configuration > &dict, ConfigIterType begin, ConfigIterType end, const std::string &criteria, bool mk, Log &err_log)
template<typename ConfigIterType >
void	set_selection (const DataFormatterDictionary< Configuration > &dict, ConfigIterType begin, ConfigIterType end, const std::string &criteria, Log &err_log)
template<bool IsConst>
bool	write_selection (const DataFormatterDictionary< Configuration > &dict, const ConfigSelection< IsConst > &config_select, bool force, const fs::path &out_path, bool write_json, bool only_selected, Log &err_log)
void	select_help (const DataFormatterDictionary< Configuration > &_dict, std::ostream &_stream, std::vector< std::string > help_opt)
template<bool IsConst>
void	write_selection_stats (Index Ntot, const ConfigSelection< IsConst > &config_select, Log &log, bool only_selected)
template<bool IsConst>
void	write_master_selection_stats (Index Ntot, const ConfigSelection< IsConst > &config_select, Log &log)
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)
int	update_eci_format (fs::path root, const CommandArgs &args)
int	update_format (fs::path root, const CommandArgs &args)
void	print_details (const CommandArgs &args, const PrimClex &primclex)
std::string::const_iterator	end_of_literal (std::string::const_iterator it, std::string::const_iterator end_it)
template<>
ChemicalReferenceState	from_json (const jsonParser &json)
	Read ChemicalReferenceState from: '{"A" : X, "B" : X, ..., "energy_per_species" : X }'. More...
Eigen::MatrixXd	_composition_space (const Structure &prim, double tol)
	Non-orthogonal composition space. More...
template std::pair < config_dict_it_type, runtimelib_it_type >	load_query_plugins (const ProjectSettings &set, config_dict_it_type dict_it, runtimelib_it_type lib_it)
void	set_nlist_ind (const Structure &prim, SiteOrbitree &tree, const PrimNeighborList &nlist, double xtal_tol)
void	_generate_primitives (PrimClex &primclex, const Supercell &unit_cell, const jsonParser &kwargs, std::map< Configuration, std::string > &prim_subconfig)
void	_generate_equivalents (const PrimClex &primclex, Supercell &unit_cell, const std::map< Configuration, std::string > &prim_subconfig, std::vector< Configuration > &subconfig)
std::ostream &	operator<< (std::ostream &stream, const Coordinate &coord)
template Lattice	superdupercell< vec_lat_it, array_symop_cit > (vec_lat_it, vec_lat_it, array_symop_cit, array_symop_cit)
template std::pair < array_symop_cit, Eigen::MatrixXi >	is_supercell< Lattice, array_symop_cit > (const Lattice &, const Lattice &, array_symop_cit, array_symop_cit, double)
bool	standard_orientation_spatial_compare (const Eigen::Matrix3d &low_score_lat_mat, const Eigen::Matrix3d &high_score_lat_mat, double compare_tol)
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	_help ()
double	covariance (const Eigen::VectorXd &X, const Eigen::VectorXd &Y, double mean)
void	swap (PermuteIterator &a, PermuteIterator &b)
jsonParser &	to_json (const MasterSymGroup &sym, jsonParser &json)
void	from_json (MasterSymGroup &sym, const jsonParser &json)
void	confirm_lattice (const Lattice &known_niggli_form, const Eigen::Matrix3i &skewed_unimodular)
void	confirm_fcc_lattice (const Eigen::Matrix3i &skewed_unimodular)
void	confirm_bcc_lattice (const Eigen::Matrix3i &skewed_unimodular)
void	confirm_hexagonal_lattice (const Eigen::Matrix3i &skewed_unimodular)
void	confirm_cubic_lattice (const Eigen::Matrix3i &skewed_unimodular)
void	symmetric_testing ()
void	single_dimension_test ()
void	ZrO_supercell_enum_test ()
void	ZrO_supercell_enum_test2 ()
void	standard_orientation_compare_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...
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 (const Structure &prim, const jsonParser &json)
	Read chemical reference from one of 3 alternative forms. More...
void	from_json (ChemicalReference &ref, const jsonParser &json, const Structure &prim, double tol=1e-14)
	Read chemical reference from JSON. More...
template<typename T >
jsonParser &	to_json (const std::map< std::string, T > &map, jsonParser &json)
	Converts to a JSON object. More...
template<typename T >
void	from_json (std::map< std::string, T > &map, const jsonParser &json)
template<typename T >
jsonParser &	to_json (const std::vector< T > &vec, jsonParser &json)
	Converts to a JSON array. More...
template<typename T >
void	from_json (std::vector< T > &vec, const jsonParser &json)
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 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_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 >
void	from_json (Eigen::MatrixBase< Derived > &value, const CASM::jsonParser &json)
	Read Eigen Matrix/Vector from JSON. More...
ChemicalReference	auto_chemical_reference (const PrimClex &primclex, double lin_alg_tol)
	Automatically set ChemicalReference using calculated Configurations with 'extreme' compositions. 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< Site > &struc, const std::string &prefix)
SimpleJSonSiteStructure< false >	simple_json (BasicStructure< Site > &struc, const std::string &prefix)
Lattice	canonical_equivalent_lattice (const Lattice &in_lat, const SymGroup &point_grp, double compare_tol)
	Find the niggli, most standard oriented version of the given orbit (defined by the given SymGroup) of lattices. More...
Lattice	niggli (const Lattice &in_lat, double compare_tol, bool keep_handedness=false)
	Convert the given lattice into it's niggli reduced form, with the most standard orientation possilbe. More...
bool	is_niggli (const Eigen::Matrix3d &test_lat_mat, double compare_tol)
	Check whether the given lattice (represented as a matrix) is in niggli TYPE ?? reduced form (does not check for orientation) More...
bool	is_niggli (const Lattice &test_lat, double compare_tol)
	Check whether the given lattice is primitive (does not check for orientation) More...
Eigen::VectorXd	spatial_unroll (const Eigen::Matrix3d &lat_mat, double compare_tol)
	Generate a vector whose lexicographical value determines how well it's oriented in space. More...
bool	standard_orientation_spatial_compare (const Eigen::Matrix3d &low_score_lat_mat, Eigen::Matrix3d &high_score_lat_mat, double compare_tol)
	Compare the spatial orientation (ignoring matrix symmetry) and determine which one is oriented more standard. True if high is more standard. More...
bool	standard_orientation_compare (const Eigen::Matrix3d &low_score_lat_mat, const Eigen::Matrix3d &high_score_lat_mat, double compare_tol)
	Determine whether high_score has a more standard format than low_score. More...
jsonParser &	to_json (const Site &value, jsonParser &json)
void	from_json (Site &value, const jsonParser &json)
std::ostream &	operator<< (std::ostream &stream, const Site &site)
Site	operator* (const SymOp &LHS, const Site &RHS)
Site	operator+ (const Site &LHS, const Coordinate &RHS)
Site	operator+ (const Coordinate &LHS, const Site &RHS)
jsonParser &	to_json (const Structure &structure, jsonParser &json)
void	from_json (Structure &structure, const jsonParser &json)
Structure	operator* (const Lattice &LHS, const Structure &RHS)
Structure	operator+ (const Coordinate &LHS, const Structure &RHS)
Structure	operator+ (const Structure &LHS, const Coordinate &RHS)
Structure	operator+ (const Structure &LHS, const Structure &RHS)
Structure	operator+ (const Structure &LHS, const Lattice &RHS)
Structure	operator+ (const Lattice &LHS, const Structure &RHS)
std::vector< std::vector< Index > >	get_index_converter (const Structure &struc, std::vector< Molecule > mol_list)
	Helper Functions. More...
std::vector< std::vector< Index > >	get_index_converter (const Structure &struc, std::vector< std::string > mol_name_list)
std::vector< std::vector< Index > >	get_index_converter_inverse (const Structure &struc, std::vector< std::string > mol_name_list)
std::ostream &	operator<< (std::ostream &sout, const UnitCellCoord &site)
UnitCellCoord	operator+ (UnitCell frac, UnitCellCoord site)
	Add UnitCell to UnitCellCoord. More...
UnitCellCoord	operator+ (UnitCellCoord site, UnitCell frac)
	Add UnitCell to UnitCellCoord. More...
UnitCellCoord	operator- (UnitCellCoord site, UnitCell frac)
	Subtract UnitCell from UnitCellCoord. More...
bool	operator< (const UnitCellCoord &A, const UnitCellCoord &B)
	Compare UnitCellCoord. More...
bool	operator> (const UnitCellCoord &A, const UnitCellCoord &B)
	Compare UnitCellCoord. More...
bool	operator<= (const UnitCellCoord &A, const UnitCellCoord &B)
	Compare UnitCellCoord. More...
bool	operator>= (const UnitCellCoord &A, const UnitCellCoord &B)
	Compare UnitCellCoord. More...
bool	operator== (const UnitCellCoord &A, const UnitCellCoord &B)
	Compare UnitCellCoord. More...
bool	operator!= (const UnitCellCoord &A, const UnitCellCoord &B)
	Compare UnitCellCoord. More...
jsonParser &	to_json (const UnitCellCoord &ucc_val, jsonParser &fill_json)
	Print to json as [b, i, j, k]. More...
void	from_json (UnitCellCoord &fill_value, const jsonParser &read_json)
	Read from json [b, i, j, k]. More...
jsonParser &	to_json (const PermuteIterator &clust, jsonParser &json)
void	from_json (PermuteIterator &clust, const jsonParser &json)
template<typename BasisPermutable >
UnitCellCoord &	apply (const SymOp &op, UnitCellCoord &value, const BasisPermutable &obj)
	Apply symmetry to a UnitCellCoord. More...
UnitCellCoord &	apply (const SymBasisPermute &op, UnitCellCoord &value)
	Apply symmetry to a UnitCellCoord. More...
SymGroupRep	subset_permutation_rep (const SymGroupRep &permute_rep, const Array< Index >::X2 &subsets)
SymGroupRep	permuted_direct_sum_rep (const SymGroupRep &permute_rep, const Array< SymGroupRep const * > &sum_reps)
SymGroupRep	kron_rep (const SymGroupRep &LHS, const SymGroupRep &RHS)
jsonParser &	to_json (const SymGroupRep &rep, jsonParser &json)
void	from_json (SymGroupRep &rep, const jsonParser &json)
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)
jsonParser &	to_json (const SymMatrixXd &sym, jsonParser &json)
void	from_json (SymMatrixXd &sym, const jsonParser &json)
jsonParser &	to_json (const SymOpRepresentation *rep, jsonParser &json)
	creates jsonParser using polymorphism More...
void	from_json (SymOpRepresentation *rep, const jsonParser &json)
	This allocates a new object to 'rep'. More...
jsonParser &	to_json (const SymPermutation &sym, jsonParser &json)
void	from_json (SymPermutation &sym, const jsonParser &json)

Variables
const double	TOL = 0.00001
const double	KB = 8.6173423E-05
const double	PLANCK = 4.135667516E-15
enum	symmetry_type {   symmetry_type::identity_op, symmetry_type::mirror_op, symmetry_type::glide_op, symmetry_type::rotation_op,   symmetry_type::screw_op, symmetry_type::inversion_op, symmetry_type::rotoinversion_op, symmetry_type::invalid_op }
std::string	to_string (const SymInfo &info, COORD_TYPE mode)
	Print SymInfo to string. More...
std::string	description (const SymOp &op, const Lattice &lat, COORD_TYPE mode)
	Print SymInfo to string. More...
void	add_sym_info (const SymInfo &info, jsonParser &j)
	Add to existing JSON object. More...

Typedef Documentation

typedef ArgHandler::ARG_TYPE CASM::ARG_TYPE

Definition at line 10 of file complete_tests.cpp.

typedef ConfigSelection< true > CASM::ConstConfigSelection

Definition at line 23 of file ProjectSettings.hh.

typedef const MonteCarlo * CASM::ConstMonteCarloPtr

const pointer to const MonteCarlo

Definition at line 9 of file CanonicalIO.hh.

typedef ClustJsonHelper<const SiteCluster> CASM::ConstSiteClusterJsonHelper

Definition at line 44 of file jsonClust.hh.

typedef ClustJsonHelper<const SiteOrbitBranch> CASM::ConstSiteOrbitBranchJsonHelper

Definition at line 46 of file jsonClust.hh.

typedef ClustJsonHelper<const SiteOrbit> CASM::ConstSiteOrbitJsonHelper

Definition at line 45 of file jsonClust.hh.

typedef ClustJsonHelper<const SiteOrbitree> CASM::ConstSiteOrbitreeJsonHelper

Definition at line 47 of file jsonClust.hh.

typedef Eigen::VectorXd CASM::Correlation

Definition at line 9 of file Correlation.hh.

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

For integer indexing:

Definition at line 28 of file CASM_global_definitions.hh.

typedef GenericOrbit<HopCluster> CASM::HopOrbit

Definition at line 19 of file Orbit.hh.

typedef GenericOrbitree< HopCluster > CASM::HopOrbitree

Definition at line 14 of file ClusterFunctions.hh.

typedef EigenIndex CASM::Index

For long integer indexing:

Definition at line 54 of file CASM_global_definitions.hh.

typedef long int CASM::lint

Definition at line 25 of file CASM_global_definitions.hh.

typedef Eigen::Matrix3d CASM::Matrix3d

Definition at line 25 of file StrainConverter.hh.

typedef Eigen::MatrixXd CASM::MatrixXd

Definition at line 24 of file StrainConverter.hh.

typedef SiteMod<int> CASM::OccMod

An OccMod describes the change in occupation variable on a site.

Definition at line 68 of file DoFMod.hh.

typedef ScalarAttribute<Configuration> CASM::Reference

Definition at line 16 of file Reference.hh.

typedef ScelEnumT<false> CASM::ScelEnum

related

Definition at line 402 of file Enumerator.hh.

typedef ClustJsonHelper<SiteCluster> CASM::SiteClusterJsonHelper

Definition at line 39 of file jsonClust.hh.

typedef GenericOrbit<SiteCluster> CASM::SiteOrbit

Definition at line 16 of file Orbit.hh.

typedef GenericOrbitBranch<SiteCluster> CASM::SiteOrbitBranch

Definition at line 20 of file OrbitBranch.hh.

typedef ClustJsonHelper<SiteOrbitBranch> CASM::SiteOrbitBranchJsonHelper

Definition at line 41 of file jsonClust.hh.

typedef ClustJsonHelper<SiteOrbit> CASM::SiteOrbitJsonHelper

Definition at line 40 of file jsonClust.hh.

typedef GenericOrbitree< SiteCluster > CASM::SiteOrbitree

Definition at line 14 of file Clex.hh.

typedef ClustJsonHelper<SiteOrbitree> CASM::SiteOrbitreeJsonHelper

Definition at line 42 of file jsonClust.hh.

typedef unsigned int CASM::uint

Definition at line 23 of file CASM_global_definitions.hh.

typedef unsigned long int CASM::ulint

Definition at line 24 of file CASM_global_definitions.hh.

typedef Eigen::VectorXd CASM::VectorXd

Definition at line 21 of file StrainConverter.hh.

Enumeration Type Documentation

enum CASM::CASMfileTypes

Enumerator
TYPEFILE
TYPEDIR
TYPEOTHER
IOERR

Definition at line 68 of file CASM_global_definitions.hh.

enum CASM::CELL_TYPE

Enumerator
PRIM
SCEL

Definition at line 64 of file CASM_global_definitions.hh.

enum CASM::COMPLEX_OUTPUT_TYPE

Enumerator
REAL
IMAG
COMPLEX

Definition at line 66 of file CASM_global_definitions.hh.

enum CASM::COMPOSITION_TYPE

Enumerator
PARAM_COMP
NUMBER_ATOMS

Definition at line 15 of file ParamComposition.hh.

enum CASM::COORD_TYPE

Enumerator
FRAC
CART
COORD_DEFAULT

Definition at line 57 of file CASM_global_definitions.hh.

enum CASM::PERIODICITY_TYPE

Enumerator
PERIODIC
LOCAL
PERIODICITY_DEFAULT

Definition at line 62 of file CASM_global_definitions.hh.

enum CASM::STRAIN_METRIC

Enumerator
GREEN_LAGRANGE
BIOT
HENCKY
EULER_ALMANSI
DISP_GRAD

Definition at line 29 of file StrainConverter.hh.

Function Documentation

fs::path CASM::_calc_properties_path	(	const PrimClex &	primclex,
		fs::path	pos_path
	)

Return path to properties.calc.json that will be imported checking a couple possible locations relative to pos_path.

checks: 1) is a JSON file? is pos_path ends in ".json" or ".JSON", return pos_path 2) assume pos_path is /path/to/POS, checks for /path/to/calctype.current/properties.calc.json 3) assume pos_path is /path/to/POS, checks for /path/to/properties.calc.json else returns empty path

Definition at line 495 of file import.cc.

Eigen::MatrixXd CASM::_composition_space	(	const Structure &	prim,
		double	tol
	)

Non-orthogonal composition space.

Definition at line 649 of file CompositionConverter.cc.

void CASM::_cp_files	(	const fs::path &	pos_path,
		const Configuration &	config,
		bool	copy_additional_files,
		Log &	log
	)

Copy files in the same directory as properties.calc.json into the traning_data directory for a particular configuration.

• First: calc_props_path = _calc_properties_path(pos_path) to get properties.calc.json location
• If calc_props_path.empty(), return
• else if !copy_additional_files copy properties.calc.json file only and return
• else, recursively copy all files from calc_props_path.remove_filename() to the training data directory for the current calctype

Definition at line 534 of file import.cc.

std::set<int> CASM::_default_nlist_sublat_indices

(

const Structure &

prim

)

Default includes sublattices with >= 2 components.

Definition at line 24 of file ProjectSettings.cc.

Eigen::Matrix3l CASM::_default_nlist_weight_matrix	(	const Structure &	prim,
		double	tol
	)

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 19 of file ProjectSettings.cc.

template<typename MCType >

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

Definition at line 274 of file monte.cc.

template<typename MCType >

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

Definition at line 236 of file monte.cc.

void CASM::_generate_equivalents	(	const PrimClex &	primclex,
		Supercell &	unit_cell,
		const std::map< Configuration, std::string > &	prim_subconfig,
		std::vector< Configuration > &	subconfig
	)

sub-routine for EnumInterface<SuperConfigEnum>::run, generates equivalent configurations of all primitive configurations

Definition at line 130 of file SuperConfigEnum.cc.

void CASM::_generate_primitives	(	PrimClex &	primclex,
		const Supercell &	unit_cell,
		const jsonParser &	kwargs,
		std::map< Configuration, std::string > &	prim_subconfig
	)

sub-routine for EnumInterface<SuperConfigEnum>::run, generates primitive configurations from input

Definition at line 72 of file SuperConfigEnum.cc.

bool CASM::_has_existing_files

(

fs::path

p

)

Definition at line 479 of file import.cc.

std::string CASM::_help

(

)

Definition at line 8 of file GrandCanonicalSettings.cc.

template<typename MCType >

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

Definition at line 217 of file monte.cc.

void CASM::_recurs_cp_files	(	const fs::path &	from_dir,
		const fs::path &	to_dir,
		Log &	log
	)

Definition at line 556 of file import.cc.

int CASM::_rm_configs	(	const CommandArgs &	args,
		const Completer::RmOption &	rm_opt
	)

Definition at line 142 of file rm.cc.

int CASM::_rm_scel	(	const CommandArgs &	args,
		const Completer::RmOption &	rm_opt
	)

Definition at line 182 of file rm.cc.

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

Definition at line 409 of file monte.cc.

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

Definition at line 288 of file monte.cc.

template<typename MCType >

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

Definition at line 255 of file monte.cc.

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 69 of file CASM_math.hh.

template<typename CoordType >

bool CASM::almost_equal	(	const GenericCluster< CoordType > &	LHS,
		const GenericCluster< CoordType > &	RHS,
		double	tol
	)

Definition at line 888 of file Cluster_impl.hh.

template<typename T >

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

Definition at line 328 of file CASM_math.hh.

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 41 of file CASM_math.hh.

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 48 of file CASM_math.hh.

template<typename Derived >

bool CASM::almost_zero	(	const Eigen::MatrixBase< Derived > &	val,
		double	tol = TOL
	)

Equivalent to almost_zero(double(val.norm()), tol);.

Definition at line 61 of file CASM_math.hh.

template<typename T >

bool CASM::always_true

(

const T &

)

Definition at line 469 of file DataFormatter.hh.

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 77 of file CASM_global_definitions.hh.

template<typename BasisPermutable >

UnitCellCoord & CASM::apply	(	const SymOp &	op,
		UnitCellCoord &	value,
		const BasisPermutable &	obj
	)

Apply symmetry to a UnitCellCoord.

Parameters

op	The symmetry operation to apply
value	The UnitCellCoord being transformed
obj	The object that the UnitCellCoord coordinates refer to, typically a primitive Structure

• Requires BasisPermutable::basis_permutation_symrep_ID() to obtain the SymBasisPermute representation

Definition at line 142 of file SymBasisPermute.hh.

UnitCellCoord& CASM::apply ( const SymBasisPermute &  op, UnitCellCoord &  value  )

inline

Apply symmetry to a UnitCellCoord.

Definition at line 107 of file SymBasisPermute.hh.

ConfigDoF & CASM::apply	(	const PermuteIterator &	it,
		ConfigDoF &	dof
	)

Definition at line 175 of file ConfigDoF.cc.

void CASM::argtype_test

(

)

Definition at line 187 of file complete_tests.cpp.

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

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

Definition at line 225 of file ChemicalReference.cc.

void CASM::bset_uncalculated

(

const CommandArgs &

args

)

Definition at line 224 of file status.cc.

Lattice CASM::canonical_equivalent_lattice	(	const Lattice &	in_lat,
		const SymGroup &	point_grp,
		double	compare_tol
	)

Find the niggli, most standard oriented version of the given orbit (defined by the given SymGroup) of lattices.

Return a canonical Lattice by first converting the given Lattice into the standard Niggli form, followed by applying the point group of the Lattice so that the one oriented in the most standard manner is selected.

Definition at line 276 of file Niggli.cc.

Eigen::VectorXd CASM::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()

Definition at line 312 of file ConfigDoF.cc.

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 89 of file CASM_math.hh.

Eigen::MatrixXd CASM::composition_space	(	const Structure &	prim,
		double	tol
	)

Return the composition space of a Structure.

Parameters

prim	A Structure 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 Structure::get_struc_molecule

Definition at line 682 of file CompositionConverter.cc.

void CASM::composition_unselected

(

const CommandArgs &

args

)

Definition at line 78 of file status.cc.

void CASM::configs_uncalculated

(

const CommandArgs &

args

)

Definition at line 139 of file status.cc.

void CASM::configs_ungenerated

(

const CommandArgs &

args

)

Definition at line 111 of file status.cc.

void CASM::confirm_bcc_lattice

(

const Eigen::Matrix3i &

skewed_unimodular

)

Definition at line 44 of file Niggli_test.cpp.

void CASM::confirm_cubic_lattice

(

const Eigen::Matrix3i &

skewed_unimodular

)

Definition at line 58 of file Niggli_test.cpp.

void CASM::confirm_fcc_lattice

(

const Eigen::Matrix3i &

skewed_unimodular

)

Definition at line 37 of file Niggli_test.cpp.

void CASM::confirm_hexagonal_lattice

(

const Eigen::Matrix3i &

skewed_unimodular

)

Definition at line 51 of file Niggli_test.cpp.

void CASM::confirm_lattice	(	const Lattice &	known_niggli_form,
		const Eigen::Matrix3i &	skewed_unimodular
	)

Definition at line 15 of file Niggli_test.cpp.

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 66 of file algorithm.hh.

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 72 of file algorithm.hh.

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 78 of file algorithm.hh.

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 84 of file algorithm.hh.

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

Definition at line 84 of file CASM_global_definitions.hh.

Correlation CASM::correlations	(	const ConfigDoF &	configdof,
		const Supercell &	scel,
		Clexulator &	clexulator
	)

Returns correlations using 'clexulator'. Supercell needs a correctly populated neighbor list.

Definition at line 200 of file ConfigDoF.cc.

Eigen::VectorXd CASM::correlations_vec	(	const ConfigDoF &	configdof,
		const Supercell &	scel,
		Clexulator &	clexulator
	)

Returns correlations using 'clexulator'. Supercell needs a correctly populated neighbor list.

Definition at line 242 of file ConfigDoF.cc.

double CASM::covariance	(	const Eigen::VectorXd &	X,
		const Eigen::VectorXd &	Y,
		double	mean
	)

Definition at line 155 of file MCData.cc.

double CASM::cuberoot

(

double

number

)

Definition at line 292 of file CASM_math.cc.

template<typename T >

ReturnArray<T> CASM::cum_sum

(

const Array< T > &

arr

)

Definition at line 341 of file CASM_math.hh.

Log& CASM::default_err_log ( )

inline

Definition at line 206 of file Log.hh.

Log& CASM::default_log ( )

inline

Definition at line 201 of file Log.hh.

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

Definition at line 12 of file composition.cc.

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 545 of file CompositionConverter.cc.

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 561 of file CompositionConverter.cc.

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 501 of file CompositionConverter.cc.

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 577 of file CompositionConverter.cc.

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 42 of file CASM_math.cc.

void CASM::eci_uncalculated

(

const CommandArgs &

args

)

Definition at line 242 of file status.cc.

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

Definition at line 119 of file CASM_math.cc.

Eigen::MatrixXd CASM::end_members

(

const Structure &

prim

)

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

Parameters

prim	A Structure 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 Structure::get_struc_molecule, with units number Molecule / prim

Definition at line 640 of file CompositionConverter.cc.

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

Definition at line 9 of file DataFormatter.cc.

void CASM::engine_test

(

)

Definition at line 166 of file complete_tests.cpp.

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 214 of file CASM_math.hh.

template<typename IteratorType >

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

Definition at line 115 of file FilteredConfigIterator.hh.

template<typename IteratorType >

FilteredConfigIterator<IteratorType> CASM::filter_end

(

const IteratorType &

it_end

)

Definition at line 124 of file FilteredConfigIterator.hh.

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 10 of file algorithm.hh.

fs::path CASM::find_casmroot ( const fs::path &  cwd )

inline

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

Definition at line 24 of file DirectoryStructure.hh.

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 16 of file algorithm.hh.

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 22 of file algorithm.hh.

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 41 of file algorithm.hh.

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 47 of file algorithm.hh.

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 28 of file algorithm.hh.

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 53 of file algorithm.hh.

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 34 of file algorithm.hh.

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 59 of file algorithm.hh.

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 111 of file CASM_math.hh.

bool CASM::float_lexicographical_compare ( const Eigen::VectorXd &  A, const Eigen::VectorXd &  B, double  tol  )

inline

Floating point lexicographical comparison with tol.

Definition at line 117 of file CASM_math.hh.

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 130 of file CASM_math.hh.

template<typename DataObject >

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

(

)

Definition at line 362 of file DataFormatterTools.hh.

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

Gets string value as COORD_TYPE

If first letter is:

• 'c', 'C', 'k', or 'K' -> CART
• 'd', 'D', 'f', or 'F' -> FRAC
• else: COORD_DEFAULT

Definition at line 13 of file global.cc.

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

Gets string value as PERIODICITY_TYPE.

Definition at line 46 of file global.cc.

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

Gets string value as CELL_TYPE.

Definition at line 80 of file global.cc.

template<>

ChemicalReferenceState CASM::from_json

(

const jsonParser &

json

)

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

Definition at line 20 of file clex.cc.

void CASM::from_json	(	GenericOrbitBranch< SiteCluster > &	branch,
		const jsonParser &	json
	)

Assumes the pivot lattice is already set.

Assumes the prototype lattice is already set.

Definition at line 17 of file ClusterFunctions.cc.

void CASM::from_json	(	GenericOrbit< SiteCluster > &	orbit,
		const jsonParser &	json
	)

Assumes the prototype lattice is already set.

Definition at line 25 of file ClusterFunctions.cc.

void CASM::from_json	(	GrandCanonicalConditions &	conditions,
		const PrimClex &	primclex,
		const jsonParser &	json
	)

Read GrandCanonicalConditions from JSON format.

{
  "temperature" : number,
  "tol: number,
  "param_chem_pot" : {"a": number, "b": number, ...}
}

Definition at line 253 of file GrandCanonicalIO.cc.

void CASM::from_json	(	SymMatrixXd &	sym,
		const jsonParser &	json
	)

re-throw exceptions

re-throw exceptions

Definition at line 47 of file SymMatrixXd.cc.

void CASM::from_json	(	SiteClusterJsonHelper	clust_helper,
		const jsonParser &	json
	)

Definition at line 5 of file jsonClust.cc.

void CASM::from_json	(	SiteOrbitBranchJsonHelper	branch_helper,
		const jsonParser &	json
	)

Definition at line 45 of file jsonClust.cc.

void CASM::from_json	(	SiteOrbitreeJsonHelper	tree_helper,
		const jsonParser &	json
	)

Definition at line 88 of file jsonClust.cc.

void CASM::from_json	(	SymPermutation &	sym,
		const jsonParser &	json
	)

re-throw exceptions

re-throw exceptions

Definition at line 77 of file SymPermutation.cc.

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

re-throw exceptions

re-throw exceptions

Definition at line 419 of file SiteCluster.cc.

template<bool IsConst>

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

Definition at line 100 of file jsonStruc.hh.

void CASM::from_json	(	DoF *	dof,
		const jsonParser &	json,
		const Lattice &	lat
	)

This allocates a new object to 'dof'. It needs a Lattice in case it is a DiscreteDoF<Molecule>

This allocates a new object to 'dof'. It needs a Lattice in case it is a OccupantDoF<Molecule>

re-throw exceptions

re-throw exceptions

Definition at line 117 of file DoF.cc.

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

inline

Definition at line 110 of file SymGroupRepID.hh.

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

re-throw exceptions

re-throw exceptions

Definition at line 178 of file Permutation.cc.

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

inline

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

Definition at line 274 of file UnitCellCoord.hh.

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

Definition at line 491 of file Site.cc.

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

Definition at line 204 of file PermuteIterator.cc.

void CASM::from_json	(	SymOpRepresentation *	rep,
		const jsonParser &	json
	)

This allocates a new object to 'rep'.

re-throw exceptions

re-throw exceptions

Definition at line 99 of file SymOpRepresentation.cc.

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

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

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

Deserialize CompositionConverter from JSON.

re-throw exceptions

re-throw exceptions

Definition at line 602 of file CompositionConverter.cc.

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

Definition at line 167 of file ConfigDoF.cc.

void CASM::from_json	(	SymGroupRep &	rep,
		const jsonParser &	json
	)

Definition at line 1525 of file SymGroupRep.cc.

void CASM::from_json	(	Structure &	structure,
		const jsonParser &	json
	)

Definition at line 1269 of file Structure.cc.

template<typename ClustType >

void CASM::from_json	(	GenericOrbitree< ClustType > &	tree,
		const jsonParser &	json
	)

Assumes the prototype lattice is already set.

Definition at line 261 of file Orbitree.hh.

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

template<typename T >

void CASM::from_json	(	GenericCluster< T > &	clust,
		const jsonParser &	json
	)

Definition at line 309 of file Cluster.hh.

void CASM::from_json	(	OccupantDoF< int > &	dof,
		const jsonParser &	json
	)

re-throw exceptions

re-throw exceptions

Definition at line 29 of file DoF.cc.

void CASM::from_json	(	OccupantDoF< Molecule > &	dof,
		const jsonParser &	json
	)

re-throw exceptions

re-throw exceptions

Definition at line 62 of file DoF.cc.

void CASM::from_json	(	ContinuousDoF &	dof,
		const jsonParser &	json
	)

re-throw exceptions

re-throw exceptions

Definition at line 96 of file DoF.cc.

void CASM::from_json	(	MasterSymGroup &	sym,
		const jsonParser &	json
	)

re-throw exceptions

Definition at line 4634 of file SymGroup.cc.

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

Definition at line 144 of file CASM_math.cc.

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

Definition at line 153 of file CASM_math.cc.

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

Definition at line 172 of file CASM_math.cc.

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

Find greatest common factor.

Definition at line 92 of file CASM_math.cc.

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

Definition at line 137 of file complete_tests.cpp.

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

Helper Functions.

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 1297 of file Structure.cc.

std::vector< std::vector< Index > > CASM::get_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 1315 of file Structure.cc.

std::vector< std::vector< Index > > CASM::get_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].site_occupant().size()

Definition at line 1335 of file Structure.cc.

ReturnArray< int > CASM::get_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()

Definition at line 278 of file ConfigDoF.cc.

Eigen::VectorXi CASM::get_num_each_molecule_vec	(	const ConfigDoF &	configdof,
		const Supercell &	scel
	)

Returns num_each_molecule(molecule_type), where 'molecule_type' is ordered as Structure::get_struc_molecule()

Definition at line 295 of file ConfigDoF.cc.

ReturnArray< Array< int > > CASM::get_prime_factors

(

int

target

)

Definition at line 413 of file CASM_math.cc.

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::GrandCanonicalLTEFormatter

(

const double &

phi_LTE1

)

Print single spin flip LTE.

Definition at line 270 of file GrandCanonicalIO.cc.

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

Definition at line 444 of file CASM_math.cc.

std::string CASM::include_path

(

const fs::path &

dir

)

Definition at line 386 of file RuntimeLibrary.cc.

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

Definition at line 224 of file CASM_math.cc.

bool CASM::is_niggli	(	const Eigen::Matrix3d &	test_lat_mat,
		double	compare_tol
	)

Check whether the given lattice (represented as a matrix) is in niggli TYPE ?? reduced form (does not check for orientation)

Definition at line 218 of file Niggli.cc.

bool CASM::is_niggli	(	const Lattice &	test_lat,
		double	compare_tol
	)

Check whether the given lattice is primitive (does not check for orientation)

Definition at line 225 of file Niggli.cc.

template std::pair<array_symop_cit, Eigen::MatrixXi> CASM::is_supercell< Lattice, array_symop_cit >	(	const Lattice &	,
		const Lattice &	,
		array_symop_cit	,
		array_symop_cit	,
		double
	)

template<typename ValueType >

ClustJsonHelper<ValueType> CASM::jsonHelper	(	ValueType &	_value,
		const Structure &	_struc,
		double	tol = TOL
	)

Definition at line 62 of file jsonClust.hh.

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

Definition at line 1462 of file SymGroupRep.cc.

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

Find least common multiple.

Definition at line 114 of file CASM_math.cc.

int CASM::lcm

(

const Array< int > &

series

)

Find least common multiple.

Definition at line 402 of file CASM_math.cc.

template<typename Derived >

double CASM::length

(

const Eigen::MatrixBase< Derived > &

value

)

Definition at line 354 of file CASM_math.hh.

std::string CASM::link_path

(

const fs::path &

dir

)

Definition at line 393 of file RuntimeLibrary.cc.

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

template<typename EnumeratorMapInserter , typename RuntimeLibInserter >

std::pair< EnumeratorMapInserter, RuntimeLibInserter > CASM::load_enumerator_plugins	(	const ProjectSettings &	set,
		EnumeratorMapInserter	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 EnumeratorMap 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 31 of file EnumeratorHandler_impl.hh.

template std::pair<config_dict_it_type, runtimelib_it_type> CASM::load_query_plugins	(	const ProjectSettings &	set,
		config_dict_it_type	dict_it,
		runtimelib_it_type	lib_it
	)

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 100 of file QueryHandler_impl.hh.

template<typename DataObject >

DataFormatterDictionary< DataObject > CASM::make_attribute_dictionary

(

)

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

Dictionary of all Attribute.

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

Definition at line 1192 of file DataFormatterTools.hh.

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 711 of file DataFormatter.hh.

DataFormatter< ConstMonteCarloPtr > CASM::make_lte_results_formatter	(	const GrandCanonical &	mc,
		const double &	phi_LTE1,
		const std::string &	configname
	)

Make a results formatter.

Make a LTE results formatter.

Output data is:

• T
• phi_LTE
• Beta
• configname
• gs_potential_energy
• gs_formation_energy
• param_chem_pot(a) ...
• gs_comp(a) ...
• gs_comp_n(a) ...

For JSON format is:

{ "key0":[...], "key1":[...], ... }

Definition at line 156 of file GrandCanonicalIO.cc.

DataFormatter< std::pair< ConstMonteCarloPtr, Index > > CASM::make_observation_formatter

(

const MonteCarlo &

mc

)

Make a observation formatter.

For csv:

# Pass Step X1 X2 ...

For JSON:

{"Pass/Step":[...], "X":[...], ...}

Definition at line 177 of file MonteIO.cc.

template<typename DataObject >

DataFormatterDictionary< DataObject > CASM::make_operator_dictionary

(

)

Dictionary of all DatumFormatterOperator.

Definition at line 449 of file DataFormatterTools.hh.

DataFormatter< ConstMonteCarloPtr > CASM::make_results_formatter

(

const GrandCanonical &

mc

)

Make a LTE results formatter.

Make a results formatter.

Output data is:

• N_equil_samples
• N_avg_samples
• T
• Beta
• <potential_energy>, prec(<potential_energy>)
• <formation_energy>, prec(<formation_energy>)
• param_chem_pot(a) ...
• <comp(a)> prec(<comp(a)>) ...
• <comp_n(a)> prec(<comp_n(a)>) ...
• (other properties: correlations, atom_frac, site_frac, etc.)
• heat_capacity
• susc_x(a,a), ...
• susc_x(S,a), ...
• susc_n(A,A), ...
• susc_n(S,A), ...

For JSON format is:

{ "key0":[...], "key1":[...], ... }

Definition at line 34 of file GrandCanonicalIO.cc.

DataFormatter< std::pair< ConstMonteCarloPtr, Index > > CASM::make_trajectory_formatter

(

const MonteCarlo &

mc

)

Make a trajectory formatter.

For csv:

Pass Step occ(0) occ(1) ...

For JSON:

{"Pass" : [...], "Step":[...], "occ":[[...]]}

Definition at line 200 of file MonteIO.cc.

template<class U >

void CASM::match_shape	(	Correlation &	corr,
		const Array< Array< Array< U > > > &	thing
	)

Definition at line 12 of file Correlation.hh.

template<class ClustType >

void CASM::match_shape	(	Correlation &	corr,
		const GenericOrbitree< ClustType > &	tree
	)

Definition at line 26 of file Correlation.hh.

template<typename T >

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

Definition at line 32 of file CASM_math.hh.

template<typename T >

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

Definition at line 25 of file CASM_math.hh.

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

Definition at line 280 of file CASM_math.cc.

template<typename RunType >

bool CASM::monte_carlo_step

(

RunType &

monte_run

)

Perform a single monte carlo step, return true if accepted.

Definition at line 521 of file MonteDriver.hh.

void CASM::montecarlo

(

const CommandArgs &

args

)

Definition at line 280 of file status.cc.

template<typename MonteType >

GenericDatumFormatter<double, ConstMonteCarloPtr> CASM::MonteCarloAtomFracFormatter	(	const MonteType &	mc,
		int	index
	)

Print atom_frac(X) for any class MonteType with valid 'Eigen::VectorXd MonteType::comp_n'.

Definition at line 89 of file MonteIO_impl.hh.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloBetaFormatter

(

)

Print Beta.

Print Beta for any class MonteType with valid 'double MonteType::conditions().beta()'.

Definition at line 22 of file MonteIO_impl.hh.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloChemPotFormatter	(	const MonteType &	mc,
		int	index
	)

Print chem_pot(N)

Print chem_pot(N) for any class MonteType with valid 'double MonteType::conditions().chem_pot(index)'.

Definition at line 43 of file MonteIO_impl.hh.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloCompFormatter	(	const MonteType &	mc,
		int	index
	)

Print comp(x)

Print comp(x) for any class MonteType with valid 'double MonteType::conditions().param_composition()(index)'.

Definition at line 54 of file MonteIO_impl.hh.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloCompNFormatter	(	const MonteType &	mc,
		int	index
	)

Print comp_n(N)

Print comp(x) for any class MonteType with valid 'double MonteType::conditions().mol_composition()(index)'.

Definition at line 65 of file MonteIO_impl.hh.

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloCovFormatter	(	std::string	prop_name1,
		std::string	prop_name2
	)

Print covariance: cov(prop_name1, prop_name2)

Definition at line 69 of file MonteIO.cc.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloHeatCapacityFormatter

(

)

Print heat capacity, 'heat_capacity'.

• Heat capacity (per unit cell) = cov(potential_energy, potential_energy)*N/(k*T*T)

Definition at line 107 of file MonteIO_impl.hh.

GenericDatumFormatter< bool, ConstMonteCarloPtr > CASM::MonteCarloIsConvergedFormatter

(

)

Print if converged.

Definition at line 93 of file MonteIO.cc.

GenericDatumFormatter< bool, ConstMonteCarloPtr > CASM::MonteCarloIsEquilibratedFormatter

(

)

Print if equilibrated (not counting explicitly requested equilibration)

Definition at line 83 of file MonteIO.cc.

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloMeanFormatter

(

std::string

prop_name

)

Print mean property values: <prop_name>

Definition at line 10 of file MonteIO.cc.

GenericDatumFormatter< MonteSampler::size_type, ConstMonteCarloPtr > CASM::MonteCarloNAvgSamplesFormatter

(

)

Print number of samples used in calculating means.

Definition at line 113 of file MonteIO.cc.

GenericDatumFormatter< MonteSampler::size_type, ConstMonteCarloPtr > CASM::MonteCarloNEquilSamplesFormatter

(

)

Print number of samples used for equilibration (not counting explicitly requested equilibration)

Definition at line 103 of file MonteIO.cc.

GenericDatumFormatter< double, std::pair< ConstMonteCarloPtr, Index > > CASM::MonteCarloObservationFormatter

(

std::string

prop_name

)

Print value of observation.

Definition at line 143 of file MonteIO.cc.

GenericDatumFormatter< int, std::pair< ConstMonteCarloPtr, Index > > CASM::MonteCarloOccFormatter

(

Index

occ_index

)

Print value of a particular occupation variable.

Definition at line 154 of file MonteIO.cc.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloParamChemPotFormatter	(	const MonteType &	mc,
		int	index
	)

Print param_chem_pot(x)

Print param_chem_pot(x) for any class MonteType with valid 'double MonteType::conditions().param_chem_pot()(index)'.

Definition at line 32 of file MonteIO_impl.hh.

GenericDatumFormatter< MonteCounter::size_type, std::pair< ConstMonteCarloPtr, Index > > CASM::MonteCarloPassFormatter

(

)

Print Pass number of observation.

Definition at line 123 of file MonteIO.cc.

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloPrecFormatter

(

std::string

prop_name

)

Print calculated precision of property values: prec(<prop_name>)

Definition at line 26 of file MonteIO.cc.

template<typename MonteType >

GenericDatumFormatter<double, ConstMonteCarloPtr> CASM::MonteCarloSiteFracFormatter	(	const MonteType &	mc,
		int	index
	)

Print site_frac(x) for any class MonteType with valid 'Eigen::VectorXd MonteType::comp_n'.

Definition at line 76 of file MonteIO_impl.hh.

GenericDatumFormatter< MonteCounter::size_type, std::pair< ConstMonteCarloPtr, Index > > CASM::MonteCarloStepFormatter

(

)

Print Step number of observation.

Definition at line 133 of file MonteIO.cc.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloSuscNFormatter	(	std::string	species_i,
		std::string	species_j
	)

Print susceptibility, 'susc_n(A,B)'.

Print parametric susceptibility, 'susc_x(a,b)'.

• species_i: First species "A", "B", "C", ...
• species_j: Second species "A", "B", "C", ...

• Heat capacity (per unit cell) = cov(x_i, x_j)*N/(k*T)

Definition at line 162 of file MonteIO_impl.hh.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloSuscXFormatter	(	std::string	comp_var_i,
		std::string	comp_var_j
	)

Print parametric susceptibility, 'susc_x(a,b)'.

• comp_var_i: First parametric composition variable "a", "b", "c", ...
• comp_var_j: Second parametric composition variable "a", "b", "c", ...

• Heat capacity (per unit cell) = cov(x_i, x_j)*N/(k*T)

Definition at line 133 of file MonteIO_impl.hh.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloTFormatter

(

)

Print Temperature.

Print Temperature for any class MonteType with valid 'double MonteType::conditions().temperature()'.

Definition at line 12 of file MonteIO_impl.hh.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloThermoChemSuscNFormatter

(

std::string

species_i

)

Print thermo-chemical susceptibility, 'susc_n(S,A)'.

Definition at line 215 of file MonteIO_impl.hh.

template<typename MonteType >

GenericDatumFormatter< double, ConstMonteCarloPtr > CASM::MonteCarloThermoChemSuscXFormatter

(

std::string

comp_var_i

)

Print parametric thermo-chemical susceptibility, 'susc_x(S,a)'.

• species_i: First species "A", "B", "C", ...

• thermo-chemical susceptibility (per unit cell) = cov(potential_energy, x_i)*N/(k*T)

Definition at line 191 of file MonteIO_impl.hh.

template<typename IntType >

IntType CASM::multinomial_coeff

(

const Array< IntType > &

exponents

)

Definition at line 306 of file CASM_math.hh.

template<typename IntType >

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

Definition at line 318 of file CASM_math.hh.

template<typename IntType >

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

Definition at line 148 of file CASM_math.hh.

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

Definition at line 188 of file CASM_math.cc.

template<typename OutputIterator , typename TreeType , typename StrucType >

OutputIterator CASM::neighborhood	(	OutputIterator	result,
		const TreeType &	tree,
		const StrucType &	struc,
		double	tol
	)

Iterate over all sites in an orbitree and insert a UnitCellCoord.

Parameters

result	an OutputIterator for UnitCellCoord
tree	the Orbitree to iterate over
struc	the structure that UnitCellCoord are referenced to
tol	tolerance for mapping Coordinate to UnitCellCoord

Returns

the resulting OutputIterator

This simply outputs all UnitCellCoord for clusters that include the origin UnitCell, without any standard order. It can be used to create a set of UnitCellCoord for input to expand a PrimNeighborList.

Definition at line 314 of file Orbitree.hh.

Lattice CASM::niggli	(	const Lattice &	in_lat,
		double	compare_tol,
		bool	keep_handedness
	)

Convert the given lattice into it's niggli reduced form, with the most standard orientation possilbe.

Converts a given Lattice into a new Lattice that satisfies the Niggli criteria. Because there are several representations of the Lattice that satisfy these conditions, the one with the most standard orientation will be returned.

The returned Niggli cell will be right handed regardless of the inputted lattice, unless keep_handedness is set to true.

Definition at line 240 of file Niggli.cc.

Eigen::MatrixXd CASM::null_composition_space	(	const Structure &	prim,
		double	tol
	)

Return the null composition space of a Structure.

Parameters

prim	A Structure 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 Structure::get_struc_molecule

Definition at line 697 of file CompositionConverter.cc.

Log& CASM::null_log ( )

inline

Definition at line 211 of file Log.hh.

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

inline

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

Definition at line 91 of file SymGroupRepID.hh.

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

inline

Compare UnitCellCoord.

Definition at line 257 of file UnitCellCoord.hh.

bool CASM::operator!= ( const jsonParser &  json, const MonteSettings &  settings  )

inline

Definition at line 209 of file MonteSettings.hh.

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

Evaluate property given an ECIContainer and Correlation.

Definition at line 6 of file ECIContainer.cc.

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 16 of file ECIContainer.cc.

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

Definition at line 352 of file SiteCluster.cc.

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

Definition at line 520 of file Site.cc.

template<typename CoordType >

GenericCluster< CoordType > CASM::operator*	(	const SymOp &	LHS,
		const GenericCluster< CoordType > &	RHS
	)

create symmetry-transformed cluster

Definition at line 869 of file Cluster_impl.hh.

Structure CASM::operator*	(	const Lattice &	LHS,
		const Structure &	RHS
	)

Definition at line 1281 of file Structure.cc.

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

Definition at line 1154 of file BasisSet.cc.

UnitCellCoord CASM::operator+ ( UnitCell  frac, UnitCellCoord  site  )

inline

Add UnitCell to UnitCellCoord.

Definition at line 203 of file UnitCellCoord.hh.

UnitCellCoord CASM::operator+ ( UnitCellCoord  site, UnitCell  frac  )

inline

Add UnitCell to UnitCellCoord.

Definition at line 208 of file UnitCellCoord.hh.

Site CASM::operator+	(	const Site &	LHS,
		const Coordinate &	RHS
	)

Definition at line 526 of file Site.cc.

Site CASM::operator+	(	const Coordinate &	LHS,
		const Site &	RHS
	)

Definition at line 532 of file Site.cc.

template<typename CoordType >

GenericCluster< CoordType > CASM::operator+	(	const GenericCluster< CoordType > &	LHS,
		const Coordinate &	RHS
	)

create translated cluster

Definition at line 875 of file Cluster_impl.hh.

Structure CASM::operator+	(	const Coordinate &	LHS,
		const Structure &	RHS
	)

Structure CASM::operator+	(	const Structure &	LHS,
		const Coordinate &	RHS
	)

Structure CASM::operator+	(	const Structure &	LHS,
		const Structure &	RHS
	)

Structure CASM::operator+	(	const Structure &	LHS,
		const Lattice &	RHS
	)

Structure CASM::operator+	(	const Lattice &	LHS,
		const Structure &	RHS
	)

UnitCellCoord CASM::operator- ( UnitCellCoord  site, UnitCell  frac  )

inline

Subtract UnitCell from UnitCellCoord.

Definition at line 213 of file UnitCellCoord.hh.

template<typename CoordType >

GenericCluster< CoordType > CASM::operator-	(	const GenericCluster< CoordType > &	LHS,
		const Coordinate &	RHS
	)

create translated cluster

Definition at line 882 of file Cluster_impl.hh.

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 97 of file SymGroupRepID.hh.

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

inline

Compare UnitCellCoord.

Definition at line 218 of file UnitCellCoord.hh.

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

Definition at line 9 of file FormatFlag.cc.

std::ostream& CASM::operator<< ( std::ostream &  sout, const UnitCellCoord &  site  )

inline

Definition at line 89 of file UnitCellCoord.hh.

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

inline

Definition at line 115 of file SymGroupRepID.hh.

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

Definition at line 165 of file Permutation.cc.

std::ostream & CASM::operator<<	(	std::ostream &	sout,
		const GrandCanonicalConditions &	cond
	)

Definition at line 171 of file GrandCanonicalConditions.cc.

std::ostream & CASM::operator<<	(	std::ostream &	stream,
		const Site &	site
	)

Definition at line 417 of file Site.cc.

template<typename T >

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

Definition at line 191 of file Log.hh.

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

Definition at line 115 of file Log.cc.

template<typename CounterType >

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

Definition at line 214 of file MultiCounter.hh.

template<typename ClustType >

std::ostream & CASM::operator<<	(	std::ostream &	stream,
		const GenericOrbitree< ClustType > &	orbitree
	)

Allows for printing using the << operator.

Definition at line 1553 of file Orbitree_impl.hh.

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

inline

Definition at line 345 of file DataStream.hh.

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

inline

Definition at line 350 of file DataStream.hh.

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

inline

Definition at line 355 of file DataStream.hh.

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

inline

Definition at line 360 of file DataStream.hh.

template<class T >

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

inline

Definition at line 366 of file DataStream.hh.

std::ostream& CASM::operator<<	(	std::ostream &	stream,
		const Coordinate &	coord
	)

Definition at line 441 of file Coordinate.cc.

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

inline

Definition at line 728 of file DataFormatter.hh.

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

inline

Definition at line 734 of file DataFormatter.hh.

template<typename CoordType >

std::ostream& CASM::operator<<	(	std::ostream &	stream,
		const GenericCluster< CoordType > &	cluster
	)

Allows for printing using the << operator.

Definition at line 861 of file Cluster_impl.hh.

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

inline

Compare UnitCellCoord.

Definition at line 240 of file UnitCellCoord.hh.

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

inline

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

Definition at line 85 of file SymGroupRepID.hh.

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

inline

Compare UnitCellCoord.

Definition at line 249 of file UnitCellCoord.hh.

bool CASM::operator== ( const jsonParser &  json, const MonteSettings &  settings  )

inline

Definition at line 205 of file MonteSettings.hh.

bool CASM::operator> ( const UnitCellCoord &  A, const UnitCellCoord &  B  )

inline

Compare UnitCellCoord.

Definition at line 235 of file UnitCellCoord.hh.

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

inline

Compare UnitCellCoord.

Definition at line 245 of file UnitCellCoord.hh.

template<class T >

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

Definition at line 40 of file CASM_global_definitions.hh.

std::istream & CASM::operator>>	(	std::istream &	sin,
		COORD_TYPE &	coord
	)

Definition at line 9 of file CASM_global_definitions.cc.

void CASM::opt_test

(

)

Definition at line 52 of file complete_tests.cpp.

void CASM::opt_test2

(

)

Definition at line 79 of file complete_tests.cpp.

template<typename OutputIterator , typename TreeType , typename StrucType >

OutputIterator CASM::orbit_neighborhood	(	OutputIterator	result,
		const TreeType &	tree,
		const StrucType &	struc,
		Index	nb,
		Index	no,
		double	tol
	)

Iterate over all sites in an orbit and insert a UnitCellCoord.

Parameters

result	an OutputIterator for UnitCellCoord
tree	the Orbitree to iterate over
struc	the structure that UnitCellCoord are referenced to
tol	tolerance for mapping Coordinate to UnitCellCoord

Returns

the resulting OutputIterator

This simply outputs all UnitCellCoord for clusters that include the origin UnitCell, without any standard order. It can be used to create a set of UnitCellCoord for input to expand a PrimNeighborList.

Definition at line 279 of file Orbitree.hh.

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 88 of file PCA.hh.

template<typename Derived >

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

Definition at line 361 of file CASM_math.hh.

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

Definition at line 1414 of file SymGroupRep.cc.

void CASM::po_test

(

)

Definition at line 106 of file complete_tests.cpp.

void CASM::print_details	(	const CommandArgs &	args,
		const PrimClex &	primclex
	)

Definition at line 359 of file status.cc.

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

Definition at line 21 of file monte.cc.

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

Definition at line 16 of file monte.cc.

void CASM::print_splash

(

std::ostream &

out

)

Definition at line 24 of file CASM_global_definitions.cc.

void CASM::property_test

(

)

Definition at line 200 of file complete_tests.cpp.

void CASM::query_help	(	const DataFormatterDictionary< Configuration > &	_dict,
		std::ostream &	_stream,
		std::vector< std::string >	help_opt_vec
	)

Definition at line 10 of file query.cc.

double CASM::ran0

(

int &

idum

)

Definition at line 12 of file CASM_math.cc.

ECIContainer CASM::read_eci

(

const fs::path &

filepath

)

Read eci.json file from specified path.

Format:

{
  "site_functions":[
    {
      "asym_unit": X,
      "sublat_indices: [2, 3],
      "phi_b_0": {"Va":0.0, "O":1.0},
      "phi_b_1": {"Va":0.0, "O":1.0},
       ...
    },
    ...
  ],
  "cluster_functions":[
    {
      "eci": X.XXXXX,
      "prototype_function": "\phi_b_i(s_j)...",
      "orbit": [branch_index, orbit_index],
      "linear_function_index": I,
      "mult": X,
      "prototype": [
        [b, i, j, k],
        ...
      ]
    },
    ...
  ]
}

Definition at line 115 of file ECIContainer.cc.

ECIContainer CASM::read_eci_out

(

const fs::path &

filepath

)

Read eci.out file from specified path (deprecated)

I'm sure the format of eci.out is going to do nothing but change, so keep an eye on this one. The current format is:

Num clusters
Num structures
rms value
WCV structures
WCV score
some other rms value
#Header for ECI (we use these)   ECI/mult (ignore)   Cluster number (this is the index)
value                            value               value
value                            value               value
.
.
.
value                            value               value

Definition at line 48 of file ECIContainer.cc.

Array<UnitCellCoord> CASM::read_prim_nlist

(

const fs::path &

nlistpath

)

Definition at line 425 of file AppIO.cc.

std::string CASM::recast

(

ARG_TYPE

atype

)

Definition at line 12 of file complete_tests.cpp.

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

Remove files recursively.

Definition at line 7 of file DirectoryStructure.cc.

void CASM::references_unset

(

const CommandArgs &

args

)

Definition at line 190 of file status.cc.

fs::path CASM::relative_casmroot ( const fs::path &  cwd )

inline

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

Definition at line 39 of file DirectoryStructure.hh.

void CASM::reset_properties ( ConfigDoF &  _dof )

inline

Definition at line 202 of file ConfigDoF.hh.

int CASM::round

(

double

val

)

Definition at line 6 of file CASM_math.cc.

template<typename Derived >

Eigen::Matrix<int, Derived::RowsAtCompileTime, Derived::ColsAtCompileTime> CASM::scale_to_int	(	const Eigen::MatrixBase< Derived > &	val,
		double	_tol = TOL
	)

Take a vector of doubles, and multiply by some factor that turns it into a vector of integers (within a tolerance)

Definition at line 416 of file CASM_math.hh.

void CASM::select_help	(	const DataFormatterDictionary< Configuration > &	_dict,
		std::ostream &	_stream,
		std::vector< std::string >	help_opt
	)

Definition at line 92 of file select.cc.

void CASM::set_nlist_ind	(	const Structure &	prim,
		SiteOrbitree &	tree,
		const PrimNeighborList &	nlist,
		double	xtal_tol
	)

Definition at line 1143 of file PrimClex.cc.

template<typename ConfigIterType >

void CASM::set_selection	(	const DataFormatterDictionary< Configuration > &	dict,
		ConfigIterType	begin,
		ConfigIterType	end,
		const std::string &	criteria,
		bool	mk,
		Log &	err_log
	)

Definition at line 11 of file select.cc.

template<typename ConfigIterType >

void CASM::set_selection	(	const DataFormatterDictionary< Configuration > &	dict,
		ConfigIterType	begin,
		ConfigIterType	end,
		const std::string &	criteria,
		Log &	err_log
	)

Definition at line 45 of file select.cc.

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

int CASM::sgn

(

T

val

)

Definition at line 125 of file CASM_math.hh.

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

inline

Definition at line 110 of file jsonStruc.hh.

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

inline

Definition at line 115 of file jsonStruc.hh.

void CASM::single_dimension_test

(

)

Definition at line 88 of file Niggli_test.cpp.

Eigen::VectorXd CASM::spatial_unroll	(	const Eigen::Matrix3d &	lat_mat,
		double	compare_tol
	)

Generate a vector whose lexicographical value determines how well it's oriented in space.

Generates a vector of values from a Lattice column matrix, whose lexicographical value determines how standard it's orientation is.

First entry is the number of non-negative entries in the matrix. Next entries are the diagonal values. Next entries are the negative of the absolute value of the off diagonal entries. Finally, the signs of the off diagonal entries.

Maximizing the lexicographical value will favor matrices that are diagonal if possible, followed by a preference for upper triangular matrices. Off diagonal entries are minimized.

Definition at line 319 of file Niggli.cc.

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 22 of file DataFormatter.cc.

template<typename OutputIterator >

OutputIterator CASM::standard_composition_axes	(	const Structure &	prim,
		OutputIterator	result
	)

Generate CompositionConverter specifying standard composition axes for a prim Structure.

Definition at line 234 of file CompositionConverter.hh.

bool CASM::standard_orientation_compare	(	const Eigen::Matrix3d &	low_score_lat_mat,
		const Eigen::Matrix3d &	high_score_lat_mat,
		double	compare_tol
	)

Determine whether high_score has a more standard format than low_score.

Compares two lattice column matrices to each other and determines which one has a more standard orientation based on whether said matrices are (bi)symmetric and how aligned the vectors are along the Cartesian directions.

A bisymmetric matrix will always have better standard orientation than one that is simply symmetric. In turn, a symmetric matrix will always have a better standard orientation than on that is not. The criteria with lowest impact is the orientation of the lattice vectors in space, as defined in standard_orientation_spatial_compare

The routine returns "low_score_mat<high_score_mat", which is true if high_score_mat has a more standard orientation.

Definition at line 391 of file Niggli.cc.

void CASM::standard_orientation_compare_test

(

)

Definition at line 193 of file Niggli_test.cpp.

bool CASM::standard_orientation_spatial_compare	(	const Eigen::Matrix3d &	low_score_lat_mat,
		Eigen::Matrix3d &	high_score_lat_mat,
		double	compare_tol
	)

Compare the spatial orientation (ignoring matrix symmetry) and determine which one is oriented more standard. True if high is more standard.

bool CASM::standard_orientation_spatial_compare	(	const Eigen::Matrix3d &	low_score_lat_mat,
		const Eigen::Matrix3d &	high_score_lat_mat,
		double	compare_tol
	)

Given two lattice column matrices, determine which one of them is oriented in a more standard manner in space relative to the Cartesian coordinates.

The routine returns "low_score_lat_mat<high_score_lat_mat", which is true if high_score_lat_mat has a more standard spatial orientation.

Definition at line 370 of file Niggli.cc.

void CASM::status_unitialized

(

const CommandArgs &

args

)

Definition at line 10 of file status.cc.

void CASM::subopt_test

(

)

Definition at line 43 of file complete_tests.cpp.

SymGroupRep CASM::subset_permutation_rep	(	const SymGroupRep &	permute_rep,
		const Array< Index >::X2 &	subsets
	)

Definition at line 1369 of file SymGroupRep.cc.

void CASM::supercells_ungenerated

(

const CommandArgs &

args

)

Definition at line 94 of file status.cc.

template Lattice CASM::superdupercell< vec_lat_it, array_symop_cit >	(	vec_lat_it	,
		vec_lat_it	,
		array_symop_cit	,
		array_symop_cit
	)

template<typename ConfigType , typename PrimClexType >

void CASM::swap	(	ConfigIterator< ConfigType, PrimClexType > &	a,
		ConfigIterator< ConfigType, PrimClexType > &	b
	)

Definition at line 195 of file ConfigIterator.hh.

template<typename IteratorType >

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

Definitions.

Definition at line 106 of file FilteredConfigIterator.hh.

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

Definition at line 195 of file ConfigDoF.cc.

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

Definition at line 192 of file PermuteIterator.cc.

void CASM::symmetric_testing

(

)

Definition at line 66 of file Niggli_test.cpp.

jsonParser & CASM::to_json	(	const COORD_TYPE &	value,
		jsonParser &	json
	)

Puts COORD_TYPE value (as string)

Definition at line 33 of file global.cc.

jsonParser & CASM::to_json	(	const PERIODICITY_TYPE &	value,
		jsonParser &	json
	)

Puts PERIODICITY_TYPE value (as string)

Definition at line 67 of file global.cc.

jsonParser & CASM::to_json	(	const CELL_TYPE &	value,
		jsonParser &	json
	)

Puts CELL_TYPE value (as string)

Definition at line 98 of file global.cc.

jsonParser & CASM::to_json	(	const GenericOrbitBranch< SiteCluster > &	branch,
		jsonParser &	json
	)

Definition at line 12 of file ClusterFunctions.cc.

jsonParser & CASM::to_json	(	const GenericOrbit< SiteCluster > &	orbit,
		jsonParser &	json
	)

Definition at line 21 of file ClusterFunctions.cc.

jsonParser & CASM::to_json	(	const GrandCanonicalConditions &	conditions,
		jsonParser &	json
	)

Store GrandCanonicalConditions in JSON format.

{
  "temperature" : number,
  "tol: number,
  "param_chem_pot" : {"a": number, "b": number, ...}
}

Definition at line 230 of file GrandCanonicalIO.cc.

jsonParser & CASM::to_json	(	const SymMatrixXd &	sym,
		jsonParser &	json
	)

Definition at line 41 of file SymMatrixXd.cc.

jsonParser & CASM::to_json	(	const ConstSiteClusterJsonHelper &	clust_helper,
		jsonParser &	json
	)

Definition at line 19 of file jsonClust.cc.

jsonParser & CASM::to_json	(	const ConstSiteOrbitJsonHelper &	orbit_helper,
		jsonParser &	json
	)

Lean printing of Orbits (only the prototype gets printed; full orbit can later be reconstructed using struc.factor_group();.

Definition at line 34 of file jsonClust.cc.

jsonParser & CASM::to_json	(	const ConstSiteOrbitBranchJsonHelper &	branch_helper,
		jsonParser &	json
	)

Definition at line 72 of file jsonClust.cc.

jsonParser & CASM::to_json	(	const ConstSiteOrbitreeJsonHelper &	tree_helper,
		jsonParser &	json
	)

Definition at line 107 of file jsonClust.cc.

jsonParser & CASM::to_json	(	const SymPermutation &	sym,
		jsonParser &	json
	)

Definition at line 71 of file SymPermutation.cc.

jsonParser & CASM::to_json	(	const SiteCluster &	clust,
		jsonParser &	json
	)

Definition at line 416 of file SiteCluster.cc.

jsonParser & CASM::to_json	(	const DoF *	dof,
		jsonParser &	json
	)

creates jsonParser using polymorphism

Definition at line 110 of file DoF.cc.

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

inline

Definition at line 103 of file SymGroupRepID.hh.

template<bool IsConst>

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

Definition at line 105 of file jsonStruc.hh.

jsonParser & CASM::to_json	(	const Permutation &	value,
		jsonParser &	json
	)

Definition at line 172 of file Permutation.cc.

jsonParser & CASM::to_json ( const UnitCellCoord &  ucc_val, jsonParser &  fill_json  )

inline

Print to json as [b, i, j, k].

Definition at line 263 of file UnitCellCoord.hh.

jsonParser & CASM::to_json	(	const Site &	value,
		jsonParser &	json
	)

Definition at line 487 of file Site.cc.

jsonParser & CASM::to_json	(	const PermuteIterator &	clust,
		jsonParser &	json
	)

Definition at line 200 of file PermuteIterator.cc.

jsonParser & CASM::to_json	(	const SymOpRepresentation *	rep,
		jsonParser &	json
	)

creates jsonParser using polymorphism

Definition at line 92 of file SymOpRepresentation.cc.

jsonParser & CASM::to_json	(	const OccupantFunction &	func,
		jsonParser &	json
	)

Definition at line 349 of file OccupantFunction.cc.

jsonParser & CASM::to_json	(	const Variable &	var,
		jsonParser &	json
	)

Definition at line 450 of file Variable.cc.

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

Serialize CompositionConverter to JSON.

Definition at line 586 of file CompositionConverter.cc.

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

Definition at line 161 of file ConfigDoF.cc.

jsonParser & CASM::to_json	(	const SymGroupRep &	rep,
		jsonParser &	json
	)

Definition at line 1519 of file SymGroupRep.cc.

jsonParser & CASM::to_json	(	const Structure &	structure,
		jsonParser &	json
	)

Definition at line 1265 of file Structure.cc.

jsonParser & CASM::to_json	(	const Function *	func,
		jsonParser &	json
	)

Definition at line 385 of file BasisFunction.cc.

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

Definition at line 1141 of file BasisSet.cc.

template<typename T >

jsonParser& CASM::to_json	(	const GenericCluster< T > &	clust,
		jsonParser &	json
	)

Definition at line 304 of file Cluster.hh.

jsonParser & CASM::to_json	(	const OccupantDoF< int > &	dof,
		jsonParser &	json
	)

overload for each template type to be used

Definition at line 25 of file DoF.cc.

jsonParser & CASM::to_json	(	const OccupantDoF< Molecule > &	dof,
		jsonParser &	json
	)

Definition at line 56 of file DoF.cc.

jsonParser & CASM::to_json	(	const ContinuousDoF &	dof,
		jsonParser &	json
	)

Definition at line 92 of file DoF.cc.

jsonParser& CASM::to_json ( const FormattedPrintable &  _obj, jsonParser &  json  )

inline

Definition at line 723 of file DataFormatter.hh.

jsonParser& CASM::to_json	(	const MasterSymGroup &	sym,
		jsonParser &	json
	)

Definition at line 4630 of file SymGroup.cc.

int CASM::update_eci_format	(	fs::path	root,
		const CommandArgs &	args
	)

Definition at line 291 of file status.cc.

int CASM::update_format	(	fs::path	root,
		const CommandArgs &	args
	)

Definition at line 339 of file status.cc.

bool CASM::valid_index

(

Index

i

)

Definition at line 5 of file CASM_global_definitions.cc.

const std::string & CASM::version

(

)

Definition at line 14 of file autoversion.cc.

Index CASM::which_unique_combination	(	const Array< Index > &	input,
		const Array< Index >::X2 &	unique,
		const Array< Index >::X2 &	ind_equiv
	)

Index CASM::which_unique_combination	(	const Array< Index > &	input,
		const Array< Index >::X2 &	unique
	)

Index CASM::which_unique_combination	(	const Array< Index > &	input,
		const Array< Array< Index > > &	unique,
		const Array< Array< Index > > &	ind_equiv
	)

Definition at line 346 of file CASM_math.cc.

Index CASM::which_unique_combination	(	const Array< Index > &	input,
		const Array< Array< Index > > &	unique
	)

Definition at line 376 of file CASM_math.cc.

template<typename MonteType >

void CASM::write_conditions_json	(	const MonteSettings &	settings,
		const MonteType &	mc,
		Index	cond_index,
		Log &	_log
	)

Write conditions to conditions.cond_index directory.

Definition at line 290 of file MonteIO_impl.hh.

void CASM::write_lte_results	(	const MonteSettings &	settings,
		const GrandCanonical &	mc,
		const double &	phi_LTE1,
		const std::string &	configname,
		Log &	_log
	)

Will create new file or append to existing results file the results of the latest run.

Definition at line 278 of file GrandCanonicalIO.cc.

template<bool IsConst>

void CASM::write_master_selection_stats	(	Index	Ntot,
		const ConfigSelection< IsConst > &	config_select,
		Log &	log
	)

Definition at line 156 of file select.cc.

void CASM::write_observations	(	const MonteSettings &	settings,
		const MonteCarlo &	mc,
		Index	cond_index,
		Log &	_log
	)

Will create (and possibly overwrite) new file with all observations from run with conditions.cond_index.

Definition at line 213 of file MonteIO.cc.

void CASM::write_POSCAR_final	(	const MonteCarlo &	mc,
		Index	cond_index,
		Log &	_log
	)

For the final state, write a POSCAR file.

The current naming convention is 'POSCAR.final'

Definition at line 399 of file MonteIO.cc.

void CASM::write_POSCAR_initial	(	const MonteCarlo &	mc,
		Index	cond_index,
		Log &	_log
	)

For the initial state, write a POSCAR file.

The current naming convention is 'POSCAR.initial'

Definition at line 372 of file MonteIO.cc.

void CASM::write_POSCAR_trajectory	(	const MonteCarlo &	mc,
		Index	cond_index,
		Log &	_log
	)

For every snapshot taken, write a POSCAR file.

The current naming convention is 'POSCAR.sample' POSCAR title comment is printed with "Sample: # Pass: # Step: #"

Definition at line 427 of file MonteIO.cc.

void CASM::write_prim_nlist	(	const Array< UnitCellCoord > &	prim_nlist,
		const fs::path &	nlistpath
	)

Definition at line 413 of file AppIO.cc.

template<typename MonteType >

void CASM::write_results	(	const MonteSettings &	settings,
		const MonteType &	mc,
		Log &	_log
	)

Will create new file or append to existing file results of the latest run.

Will create new file or append to existing results file the results of the latest run.

Definition at line 238 of file MonteIO_impl.hh.

template<bool IsConst>

bool CASM::write_selection	(	const DataFormatterDictionary< Configuration > &	dict,
		const ConfigSelection< IsConst > &	config_select,
		bool	force,
		const fs::path &	out_path,
		bool	write_json,
		bool	only_selected,
		Log &	err_log
	)

Definition at line 69 of file select.cc.

template<bool IsConst>

void CASM::write_selection_stats	(	Index	Ntot,
		const ConfigSelection< IsConst > &	config_select,
		Log &	log,
		bool	only_selected
	)

Definition at line 145 of file select.cc.

void CASM::write_trajectory	(	const MonteSettings &	settings,
		const MonteCarlo &	mc,
		Index	cond_index,
		Log &	_log
	)

Will create (and possibly overwrite) new file with all observations from run with conditions.cond_index.

• Also writes "occupation_key" file giving occupant index -> species for each prim basis site

For csv:

site_index occ_index_0 occ_index_1 ...
0          Ni          Al
1          Ni          -
...

For JSON:

[["A", "B"],["A" "C"], ... ]

Definition at line 269 of file MonteIO.cc.

void CASM::ZrO_supercell_enum_test

(

)

Definition at line 120 of file Niggli_test.cpp.

void CASM::ZrO_supercell_enum_test2

(

)

Definition at line 152 of file Niggli_test.cpp.

Variable Documentation

const double CASM::KB = 8.6173423E-05

Definition at line 34 of file CASM_global_definitions.hh.

const double CASM::PLANCK = 4.135667516E-15

Definition at line 37 of file CASM_global_definitions.hh.

const double CASM::TOL = 0.00001

Definition at line 31 of file CASM_global_definitions.hh.