Detailed Description

Relates to Molecule.

Classes
singleton	CASM::OccupantDoF< T >

class	CASM::Specie

class	CASM::AtomPosition

class	CASM::Molecule

Typedefs
typedef OccupantDoF< Molecule >	CASM::MoleculeOccupant

typedef std::array< bool, 3 >	CASM::AtomPosition::sd_type

Functions
bool	CASM::is_vacancy (const std::string &name)
	A vacancy is any Specie/Molecule with (name == "VA" \|\| name == "va" \|\| name == "Va") More...

	CASM::Specie::Specie ()

	CASM::Specie::Specie (std::string init_name)

bool	CASM::Specie::is_vacancy () const

bool	CASM::Specie::operator== (const Specie &RHS) const

jsonParser &	CASM::to_json (const Specie &specie, jsonParser &json)

void	CASM::from_json (Specie &specie, const jsonParser &json)

	CASM::AtomPosition::AtomPosition (const Lattice &init_lattice)

	CASM::AtomPosition::AtomPosition (double elem1, double elem2, double elem3, std::string sp_name, const Lattice &init_lattice, COORD_TYPE mode, sd_type _SD_flag=sd_type{{false, false, false}})

bool	CASM::AtomPosition::operator== (const AtomPosition &RHS) const

void	CASM::AtomPosition::print (std::ostream &stream, const Coordinate &trans, int spaces, bool SD_is_on=false) const

AtomPosition &	CASM::AtomPosition::apply_sym (const SymOp &op)

AtomPosition &	CASM::AtomPosition::apply_sym_no_trans (const SymOp &op)

jsonParser &	CASM::to_json (const AtomPosition &apos, jsonParser &json)

void	CASM::from_json (AtomPosition &apos, const jsonParser &json)

	CASM::Molecule::Molecule (const Lattice &init_home)

Lattice const *	CASM::Molecule::home () const

void	CASM::Molecule::get_center ()

void	CASM::Molecule::generate_point_group ()

bool	CASM::Molecule::is_vacancy () const

Molecule &	CASM::Molecule::apply_sym (const SymOp &op)

Molecule &	CASM::Molecule::apply_sym_no_trans (const SymOp &op)

void	CASM::Molecule::set_lattice (const Lattice &new_lat, COORD_TYPE invariant_mode)

Molecule	CASM::Molecule::get_union (const Molecule &RHS)

Molecule &	CASM::Molecule::operator*= (const SymOp &RHS)

Molecule &	CASM::Molecule::operator+= (const Coordinate &RHS)

bool	CASM::Molecule::operator== (const Molecule &RHS) const

bool	CASM::Molecule::contains (const std::string &name) const

void	CASM::Molecule::read (std::istream &stream)

void	CASM::Molecule::print (std::ostream &stream, const Coordinate &trans, int spaces, char delim, bool SD_is_on=false) const

jsonParser &	CASM::Molecule::to_json (jsonParser &json) const

void	CASM::Molecule::from_json (const jsonParser &json)

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

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

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

Molecule	CASM::make_atom (std::string atom_name, const Lattice &lat)
	Return an atomic Molecule with specified name and Lattice. More...

Molecule	CASM::make_vacancy (const Lattice &lat)
	Return an vacancy Molecule with specified Lattice. More...

bool	CASM::is_molecule_name (const Molecule &mol, std::string name)
	Return true if Molecule name matches 'name', including Va checks. More...

jsonParser &	CASM::to_json (const Molecule &mol, jsonParser &json)

void	CASM::from_json (Molecule &mol, const jsonParser &json)

Variables
std::string	CASM::Specie::name

double	CASM::Specie::mass

double	CASM::Specie::magmom

double	CASM::Specie::U

double	CASM::Specie::J

Specie	CASM::AtomPosition::specie

sd_type	CASM::AtomPosition::SD_flag

Lattice const *	CASM::Molecule::m_home

Array< SymOp >	CASM::Molecule::point_group

Coordinate	CASM::Molecule::center

std::string	CASM::Molecule::name

Typedef Documentation

typedef OccupantDoF<Molecule> CASM::MoleculeOccupant

Definition at line 22 of file Molecule.hh.

typedef std::array<bool, 3> CASM::AtomPosition::sd_type

Definition at line 58 of file Molecule.hh.

Function Documentation

AtomPosition & CASM::AtomPosition::apply_sym ( const SymOp & op )

Definition at line 79 of file Molecule.cc.

Molecule & CASM::Molecule::apply_sym ( const SymOp & op )

Applies symmetry operation to a Molecule

Parameters

SymOp &op

Definition at line 128 of file Molecule.cc.

AtomPosition & CASM::AtomPosition::apply_sym_no_trans ( const SymOp & op )

Definition at line 90 of file Molecule.cc.

Molecule & CASM::Molecule::apply_sym_no_trans ( const SymOp & op )

Applies symmetry operation to a Molecule without adding translation

Parameters

SymOp &op

Definition at line 148 of file Molecule.cc.

CASM::AtomPosition::AtomPosition ( const Lattice & init_lattice )

inlineexplicit

Definition at line 63 of file Molecule.hh.

CASM::AtomPosition::AtomPosition	(	double	elem1,
		double	elem2,
		double	elem3,
		std::string	sp_name,
		const Lattice &	init_lattice,
		COORD_TYPE	mode,
		sd_type	_SD_flag = `sd_type {{false, false, false}}`
	)

inline

Definition at line 64 of file Molecule.hh.

bool CASM::Molecule::contains ( const std::string & name ) const

Definition at line 207 of file Molecule.cc.

void CASM::from_json	(	Specie &	specie,
		const jsonParser &	json
	)

re-throw exceptions

Definition at line 20 of file Molecule.cc.

void CASM::from_json	(	AtomPosition &	apos,
		const jsonParser &	json
	)

re-throw exceptions

Definition at line 105 of file Molecule.cc.

void CASM::Molecule::from_json ( const jsonParser & json )

Read Molecule from json. Assumes current lattice.

re-throw exceptions

Definition at line 252 of file Molecule.cc.

void CASM::from_json	(	Molecule &	mol,
		const jsonParser &	json
	)

re-throw exceptions

Definition at line 307 of file Molecule.cc.

void CASM::Molecule::generate_point_group ( )

void CASM::Molecule::get_center ( )

Molecule CASM::Molecule::get_union ( const Molecule & RHS )

Lattice const* CASM::Molecule::home ( ) const

inline

Definition at line 116 of file Molecule.hh.

bool CASM::is_molecule_name	(	const Molecule &	mol,
		std::string	name
	)

Return true if Molecule name matches 'name', including Va checks.

Return true if Molecule name matches 'name', including Va name checks.

Equivalent to:

( (is_vacancy(mol.name) && is_vacancy(name)) || (mol.name == name) )

Definition at line 298 of file Molecule.cc.

bool CASM::is_vacancy ( const std::string & name )

inline

A vacancy is any Specie/Molecule with (name == "VA" || name == "va" || name == "Va")

Definition at line 27 of file Molecule.hh.

bool CASM::Specie::is_vacancy ( ) const

inline

Definition at line 38 of file Molecule.hh.

bool CASM::Molecule::is_vacancy ( ) const

inline

Definition at line 124 of file Molecule.hh.

Molecule CASM::make_atom	(	std::string	atom_name,
		const Lattice &	lat
	)

Return an atomic Molecule with specified name and Lattice.

Definition at line 279 of file Molecule.cc.

Molecule CASM::make_vacancy ( const Lattice & lat )

Return an vacancy Molecule with specified Lattice.

Definition at line 287 of file Molecule.cc.

CASM::Molecule::Molecule ( const Lattice & init_home )

inlineexplicit

Definition at line 114 of file Molecule.hh.

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

Molecule& CASM::Molecule::operator*= ( const SymOp & RHS )

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

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

Molecule& CASM::Molecule::operator+= ( const Coordinate & RHS )

bool CASM::Specie::operator== ( const Specie & RHS ) const

inline

Definition at line 43 of file Molecule.hh.

bool CASM::AtomPosition::operator== ( const AtomPosition & RHS ) const

Definition at line 42 of file Molecule.cc.

bool CASM::Molecule::operator== ( const Molecule & RHS ) const

Definition at line 183 of file Molecule.cc.

void CASM::AtomPosition::print	(	std::ostream &	stream,
		const Coordinate &	trans,
		int	spaces,
		bool	SD_is_on = `false`
	)		const

Definition at line 54 of file Molecule.cc.

void CASM::Molecule::print	(	std::ostream &	stream,
		const Coordinate &	trans,
		int	spaces,
		char	delim,
		bool	SD_is_on = `false`
	)		const

Definition at line 220 of file Molecule.cc.

void CASM::Molecule::read ( std::istream & stream )

void CASM::Molecule::set_lattice	(	const Lattice &	new_lat,
		COORD_TYPE	invariant_mode
	)

Definition at line 168 of file Molecule.cc.

CASM::Specie::Specie ( )

inline

Definition at line 35 of file Molecule.hh.

CASM::Specie::Specie ( std::string init_name )

inlineexplicit

Definition at line 36 of file Molecule.hh.

jsonParser & CASM::to_json	(	const Specie &	specie,
		jsonParser &	json
	)

Definition at line 10 of file Molecule.cc.

jsonParser & CASM::to_json	(	const AtomPosition &	apos,
		jsonParser &	json
	)

Definition at line 96 of file Molecule.cc.

jsonParser & CASM::Molecule::to_json ( jsonParser & json ) const

Write Molecule to json. Does not write lattice.

Definition at line 234 of file Molecule.cc.

jsonParser & CASM::to_json	(	const Molecule &	mol,
		jsonParser &	json
	)

Definition at line 302 of file Molecule.cc.

Variable Documentation

Coordinate CASM::Molecule::center

Definition at line 111 of file Molecule.hh.

double CASM::Specie::J

Definition at line 34 of file Molecule.hh.

Lattice const* CASM::Molecule::m_home

private

Definition at line 102 of file Molecule.hh.

double CASM::Specie::magmom

Definition at line 34 of file Molecule.hh.

double CASM::Specie::mass

Definition at line 34 of file Molecule.hh.

std::string CASM::Specie::name

Definition at line 33 of file Molecule.hh.

std::string CASM::Molecule::name

Definition at line 112 of file Molecule.hh.

Array<SymOp> CASM::Molecule::point_group

private

Definition at line 104 of file Molecule.hh.

sd_type CASM::AtomPosition::SD_flag

Definition at line 61 of file Molecule.hh.

Specie CASM::AtomPosition::specie

Definition at line 59 of file Molecule.hh.

double CASM::Specie::U

Definition at line 34 of file Molecule.hh.

Detailed Description

Classes

Typedefs

Functions

Variables

Typedef Documentation

Function Documentation

Variable Documentation