atomicrex Namespace Reference

This file collects the definition of classes that define various simple crystal structures. More...

Classes
class	ABOPotential
	This class defines the ABOP potential format. More...
class	AtomCoordinatesDOF
	This DOF manages the atomic positions in a structure. More...
class	AtomicStructure
	Base class for maintaining structures. More...
class	AtomVectorProperty
class	B1LatticeStructure
	This class defines a sodium chloride lattice (NaCl, B1). More...
class	B2LatticeStructure
	This class defines a cesiumchloride lattice (CsCl, B2). More...
class	B3LatticeStructure
	This class defines a zincblende lattice (ZnS, B3). More...
class	B4LatticeStructure
	This class defines a wurtzite lattice structure (B4). More...
class	BCCLatticeStructure
	This class defines a body-centered cubic (BCC) lattice. More...
class	betaSnLatticeStructure
	This class defines a beta-tin lattice. More...
class	BhLatticeStructure
	This class defines a tungsten carbide (Bh) lattice structure. More...
class	BinaryCubicLatticeStructure
	Base class for cubic lattice structures with two atom types (binary). More...
class	BinaryHexaRhomboTetraLatticeStructure
	Base class for hexagonal, rhombohedral, and tetragonal lattice structures with two atom types (binary). More...
class	C15LatticeStructure
	This class defines a C15 lattice structure (e.g., Cu2Mg, Fe2Y). More...
class	C1LatticeStructure
	This class defines a fluorite lattice (CaF2, C1). More...
class	CDIPairInteraction
class	CDIPotential
class	CoupledFitProperty
class	CubicSpline
class	D2dLatticeStructure
	This class defines a D2d lattice structure (e.g. CaCu5). More...
class	D8aLatticeStructure
	This class defines a D8a lattice structure (e.g., Mn23Th6, Fe23Y6). More...
class	DegreeOfFreedom
	Base class for all degrees of freedom a potential or a structure may have. More...
class	DerivedProperty
class	DHCPLatticeStructure
	This class defines a double hexagonal close-packed lattice (DHCP, 4H). More...
class	DIALatticeStructure
	This class defines diamond lattice. More...
class	DimerStructure
	This class defines a dimer. More...
class	EAMPotential
	This class defines general embedded atom method (EAM) potentials. More...
class	FCCLatticeStructure
	This class defines a face-centered cubic (FCC) lattice. More...
class	FitGroup
class	FitJob
class	FitObject
class	FitProperty
class	FunctionBase
	Base class for all one-dimensional functions that can be fitted. More...
class	FunctionConstant
class	FunctionExpA
class	FunctionExpB
class	FunctionExpGaussian
class	FunctionInverseArgument
class	FunctionMorseA
class	FunctionMorseB
class	FunctionMorseC
class	FunctionPoly
class	FunctionProduct
class	FunctionSpline
class	FunctionSum
class	GridCubicSpline
class	HCPLatticeStructure
	This class defines a hexagonal close-packed lattice (HCP, 2H). More...
class	L10LatticeStructure
	This class defines a L10 lattice structure (e.g., NiAl, CuAu). More...
class	L12LatticeStructure
	This class defines a L12 lattice structure (e.g., Ni3Al, Cu3Au). More...
class	LBFGSMinimizer
class	LennardJonesPotential
	This class defines a Lennard-Jones potential. More...
class	Matrix_3
	A 3x3 matrix. More...
class	MEAMPotential
	This class defines general modified embedded atom method (MEAM) potentials. More...
class	Minimizer
	Abstract base class for minimization algorithms. More...
class	MsgLogger
class	NeighborList
struct	NeighborListEntry
class	Ni17Th2LatticeStructure
	This class defines a Ni17Th2 lattice structure (e.g. Ni17Th2, alpha-Fe17Y2). More...
class	NloptMinimizer
class	NumericalDerivative
class	NumericalGradientEvaluator
class	NumericalIntegration
class	OMGLatticeStructure
	This class defines a omega-lattice structure. More...
class	PairInteraction
class	PairPotential
class	ParsedFunction
struct	PerAtomAndInteractionInfo
struct	PerAtomAndTypeInfo
class	Point_3
	A point in 3d space. More...
class	PointDefectStructure
	This class defines point defects (vacancies, interstitials, substitutionals) in a super-cell. More...
class	Potential
	Base class for potential. More...
class	ScalarDOF
	A simple scalar degree of freedom that consists of a single value. More...
class	ScalarFitProperty
class	SCLatticeStructure
	This class defines a simple cubic lattice. More...
class	SpaMinimizer
class	SplitBregmanMinimizer
class	SuperCellStructure
	This class defines a N x N x N supercell structure. More...
class	TabulatedEAMPotential
class	TabulatedMEAMPotential
class	TersoffPotential
	This class defines the Tersoff potential format. More...
class	Th2Zn17LatticeStructure
	This class defines a Th2Zn17 lattice structure (e.g. Th2Zn17, beta-Fe17Y2). More...
class	UnaryCubicLatticeStructure
	Base class for cubic lattice structures with one atom type (unary). More...
class	UnaryHexaRhomboTetraLatticeStructure
	Base class for hexagonal, rhombohedral, and tetragonal lattice structures with one atom type (unary). More...
class	UserStructure
class	Vector_3
	A vector with three components. More...

Typedefs
using	FPString = std::string
	The default string type used throughout the code:
typedef double	FloatType

Enumerations
enum	LoggerVerbosity {   none, minimum, medium, maximum,   debug }
	Levels of program output verbosity.

Functions
double	obj_wrapper (const std::vector< double > &x, std::vector< double > &g, void *data)
int	sign (double x)
	Our signum function.
FPString	makePathRelative (const FPString &path, const FPString &relative_to)
FPString	makePathRelative (const FPString &path)
template<typename T >
T	square (const T &f)
	Computes the square of a number.
template<typename T >
Matrix_3< T >	operator- (const Matrix_3< T > &a, const Matrix_3< T > &b)
	Subtracts a 3x3 matrix from a 3x3 Matrix.
std::ostream &	separatorLine (std::ostream &stream)
	This stream manipulator function outputs a separator line to the output stream.

Detailed Description

This file collects the definition of classes that define various simple crystal structures.

This file defines the SuperCellStructure class.

This is the Python interface module for atomicrex. It primarily provides
convenient access to the atomicrex job object and the atomic structures
associated with it.

Function Documentation

makePathRelative() [1/2]

FPString atomicrex::makePathRelative ( const FPString &  path, const FPString &  relative_to  )

inline

Given an absolute input path 'path', and an absolute base path 'relative_to', returns a relative path that points to the same file/directory as 'path'.

makePathRelative() [2/2]

FPString atomicrex::makePathRelative ( const FPString &  path )

inline

Given an absolute input path 'path', returns a path relative to the current working directory that points to the same file/directory as 'path'.