Detailed Description

Relates to Molecule.

Classes
class	CASM::xtal::AtomPosition
	An atomic species associated with a position in space. More...

class	CASM::xtal::Molecule
	Class representing a Molecule. More...

Functions
	CASM::xtal::AtomPosition::AtomPosition (double _pos1, double _pos2, double _pos3, std::string const &_species)
	Construct with x,y,z position coordinates and atom name. More...

	CASM::xtal::AtomPosition::AtomPosition (Eigen::Ref< const Eigen::Vector3d > const &_pos, std::string const &_species)
	Construct with vector position and atom name. More...

std::string const &	CASM::xtal::AtomPosition::name () const
	Const access of species name. More...

Eigen::Vector3d const &	CASM::xtal::AtomPosition::cart () const
	Const access of Cartesian position of atom. More...

bool	CASM::xtal::AtomPosition::time_reversal_active () const

std::map< std::string, SpeciesAttribute > const &	CASM::xtal::AtomPosition::attributes () const

void	CASM::xtal::AtomPosition::set_attributes (std::map< std::string, SpeciesAttribute > _attr)

bool	CASM::xtal::AtomPosition::identical (AtomPosition const &RHS, double _tol) const
	Comparison with tolerance (max allowed distance between LHS and RHS, in Angstr.) More...

bool	CASM::xtal::compare_type (AtomPosition const &A, AtomPosition const &B, double tol)

static Molecule	CASM::xtal::Molecule::make_atom (std::string const &atom_name)
	Return an atomic Molecule with specified name. More...

static Molecule	CASM::xtal::Molecule::make_unknown ()
	Return an atomic Molecule with specified name. More...

static Molecule	CASM::xtal::Molecule::make_vacancy ()
	Return a vacancy Molecule. More...

	CASM::xtal::Molecule::Molecule (std::string const &_name, std::vector< AtomPosition > _atoms={}, bool _divisible=false)
	Construct with designated name, a list of atoms, and whether molecule is chemically divisible. More...

Index	CASM::xtal::Molecule::size () const
	Number of atoms contained Molecule. More...

std::string const &	CASM::xtal::Molecule::name () const
	Designated name of Molecule (may be unrelated to constituent species) More...

std::vector< AtomPosition > const &	CASM::xtal::Molecule::atoms () const
	Const access of all contained AtomPositions. More...

AtomPosition const &	CASM::xtal::Molecule::atom (Index i) const
	returns i'th atom position More...

bool	CASM::xtal::Molecule::is_atomic () const
	True if Molecule is atom with no other attributes. More...

bool	CASM::xtal::Molecule::is_vacancy () const
	True if Molecule represents vacancy. More...

bool	CASM::xtal::Molecule::time_reversal_active () const
	True if Molecule contains attributes that are affected by time reversal. More...

std::map< std::string, SpeciesAttribute > const &	CASM::xtal::Molecule::attributes () const
	Returns dictionary of all constituent attributes of the Molecule Does not include attributes associated with individual atoms. More...

void	CASM::xtal::Molecule::set_attributes (std::map< std::string, SpeciesAttribute > _attr)
	Set all constitutent attributes of Molecule overwrites any existing attributes. More...

void	CASM::xtal::Molecule::set_atoms (std::vector< AtomPosition > _atoms)
	set all constituent atoms of Molecule overwrites any existing atoms More...

bool	CASM::xtal::Molecule::identical (Molecule const &RHS, double _tol) const
	Check equality of two molecules, within specified tolerance. Compares atoms, irrespective of order, and attributes (name is not checked) More...

bool	CASM::xtal::Molecule::contains (std::string const &atom_name) const
	Returns true of molecule contains atom of specified name. More...

bool	CASM::xtal::Molecule::is_divisible () const

bool	CASM::xtal::Molecule::is_indivisible () const

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

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

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

xtal::AtomPosition &	CASM::sym::apply (const xtal::SymOp &op, xtal::AtomPosition &mutating_atom_pos)

xtal::AtomPosition	CASM::sym::copy_apply (const xtal::SymOp &op, xtal::AtomPosition atom_pos)

template<typename ExternSymOp >
xtal::AtomPosition	CASM::sym::copy_apply (const ExternSymOp &op, xtal::AtomPosition atom_pos)

xtal::Molecule &	CASM::sym::apply (const xtal::SymOp &op, xtal::Molecule &mutating_mol)

xtal::Molecule	CASM::sym::copy_apply (const xtal::SymOp &op, xtal::Molecule mol)

template<typename ExternSymOp >
xtal::Molecule	CASM::sym::copy_apply (const ExternSymOp &op, xtal::Molecule mol)

Variables
std::string	CASM::xtal::AtomPosition::m_species
	Atomic species. More...

Eigen::Vector3d	CASM::xtal::AtomPosition::m_position
	Cartesian position; origin is centered at site. More...

std::map< std::string, SpeciesAttribute >	CASM::xtal::AtomPosition::m_attribute_map

std::string	CASM::xtal::Molecule::m_name

std::vector< AtomPosition >	CASM::xtal::Molecule::m_atoms

bool	CASM::xtal::Molecule::m_divisible

std::map< std::string, SpeciesAttribute >	CASM::xtal::Molecule::m_attribute_map

Function Documentation

◆ apply() [1/2]

xtal::AtomPosition & CASM::sym::apply	(	const xtal::SymOp &	op,
		xtal::AtomPosition &	mutating_atom_pos
	)

Definition at line 100 of file Molecule.cc.

◆ apply() [2/2]

xtal::Molecule & CASM::sym::apply	(	const xtal::SymOp &	op,
		xtal::Molecule &	mutating_mol
	)

Definition at line 122 of file Molecule.cc.

◆ atom()

AtomPosition const& CASM::xtal::Molecule::atom ( Index i ) const

inline

returns i'th atom position

Definition at line 123 of file Molecule.hh.

◆ AtomPosition() [1/2]

CASM::xtal::AtomPosition::AtomPosition	(	double	_pos1,
		double	_pos2,
		double	_pos3,
		std::string const &	_species
	)

inline

Construct with x,y,z position coordinates and atom name.

Definition at line 30 of file Molecule.hh.

◆ AtomPosition() [2/2]

CASM::xtal::AtomPosition::AtomPosition	(	Eigen::Ref< const Eigen::Vector3d > const &	_pos,
		std::string const &	_species
	)

inline

Construct with vector position and atom name.

Definition at line 35 of file Molecule.hh.

◆ atoms()

std::vector<AtomPosition> const& CASM::xtal::Molecule::atoms ( ) const

inline

Const access of all contained AtomPositions.

Definition at line 120 of file Molecule.hh.

◆ attributes() [1/2]

std::map<std::string, SpeciesAttribute> const& CASM::xtal::AtomPosition::attributes ( ) const

inline

Definition at line 52 of file Molecule.hh.

◆ attributes() [2/2]

std::map<std::string, SpeciesAttribute> const& CASM::xtal::Molecule::attributes ( ) const

inline

Returns dictionary of all constituent attributes of the Molecule Does not include attributes associated with individual atoms.

Definition at line 145 of file Molecule.hh.

◆ cart()

Eigen::Vector3d const& CASM::xtal::AtomPosition::cart ( ) const

inline

Const access of Cartesian position of atom.

Definition at line 43 of file Molecule.hh.

◆ compare_type()

bool CASM::xtal::compare_type	(	AtomPosition const &	A,
		AtomPosition const &	B,
		double	tol
	)

Definition at line 19 of file Molecule.cc.

◆ contains()

bool CASM::xtal::Molecule::contains ( std::string const & atom_name ) const

Returns true of molecule contains atom of specified name.

Definition at line 80 of file Molecule.cc.

◆ copy_apply() [1/4]

template<typename ExternSymOp >

xtal::AtomPosition CASM::sym::copy_apply	(	const ExternSymOp &	op,
		xtal::AtomPosition	atom_pos
	)

Definition at line 208 of file Molecule.hh.

◆ copy_apply() [2/4]

template<typename ExternSymOp >

xtal::Molecule CASM::sym::copy_apply	(	const ExternSymOp &	op,
		xtal::Molecule	mol
	)

Definition at line 218 of file Molecule.hh.

◆ copy_apply() [3/4]

xtal::AtomPosition CASM::sym::copy_apply	(	const xtal::SymOp &	op,
		xtal::AtomPosition	atom_pos
	)

Definition at line 107 of file Molecule.cc.

◆ copy_apply() [4/4]

xtal::Molecule CASM::sym::copy_apply	(	const xtal::SymOp &	op,
		xtal::Molecule	mol
	)

Definition at line 139 of file Molecule.cc.

◆ identical() [1/2]

bool CASM::xtal::AtomPosition::identical	(	AtomPosition const &	RHS,
		double	_tol
	)		const

Comparison with tolerance (max allowed distance between LHS and RHS, in Angstr.)

Definition at line 12 of file Molecule.cc.

◆ identical() [2/2]

bool CASM::xtal::Molecule::identical	(	Molecule const &	RHS,
		double	_tol
	)		const

Check equality of two molecules, within specified tolerance. Compares atoms, irrespective of order, and attributes (name is not checked)

Definition at line 52 of file Molecule.cc.

◆ is_atomic()

bool CASM::xtal::Molecule::is_atomic ( ) const

True if Molecule is atom with no other attributes.

Definition at line 36 of file Molecule.cc.

◆ is_divisible()

bool CASM::xtal::Molecule::is_divisible ( ) const

inline

Definition at line 169 of file Molecule.hh.

◆ is_indivisible()

bool CASM::xtal::Molecule::is_indivisible ( ) const

inline

Definition at line 171 of file Molecule.hh.

◆ is_molecule_name()

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

inline

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

Definition at line 192 of file Molecule.hh.

◆ is_vacancy() [1/2]

bool CASM::xtal::Molecule::is_vacancy ( ) const

True if Molecule represents vacancy.

Definition at line 47 of file Molecule.cc.

◆ is_vacancy() [2/2]

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

inline

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

Definition at line 187 of file Molecule.hh.

◆ make_atom()

Molecule CASM::xtal::Molecule::make_atom ( std::string const & atom_name )

static

Return an atomic Molecule with specified name.

Definition at line 86 of file Molecule.cc.

◆ make_unknown()

static Molecule CASM::xtal::Molecule::make_unknown ( )

inlinestatic

Return an atomic Molecule with specified name.

Definition at line 99 of file Molecule.hh.

◆ make_vacancy()

Molecule CASM::xtal::Molecule::make_vacancy ( )

static

Return a vacancy Molecule.

Definition at line 90 of file Molecule.cc.

◆ Molecule()

CASM::xtal::Molecule::Molecule	(	std::string const &	_name,
		std::vector< AtomPosition >	_atoms = `{}`,
		bool	_divisible = `false`
	)

inline

Construct with designated name, a list of atoms, and whether molecule is chemically divisible.

Definition at line 106 of file Molecule.hh.

◆ name() [1/2]

std::string const& CASM::xtal::AtomPosition::name ( ) const

inline

Const access of species name.

Definition at line 40 of file Molecule.hh.

◆ name() [2/2]

std::string const& CASM::xtal::Molecule::name ( ) const

inline

Designated name of Molecule (may be unrelated to constituent species)

Definition at line 117 of file Molecule.hh.

◆ operator==()

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

inline

Definition at line 181 of file Molecule.hh.

◆ set_atoms()

void CASM::xtal::Molecule::set_atoms ( std::vector< AtomPosition > _atoms )

inline

set all constituent atoms of Molecule overwrites any existing atoms

Definition at line 157 of file Molecule.hh.

◆ set_attributes() [1/2]

void CASM::xtal::AtomPosition::set_attributes ( std::map< std::string, SpeciesAttribute > _attr )

inline

Definition at line 56 of file Molecule.hh.

◆ set_attributes() [2/2]

void CASM::xtal::Molecule::set_attributes ( std::map< std::string, SpeciesAttribute > _attr )

inline

Set all constitutent attributes of Molecule overwrites any existing attributes.

Definition at line 151 of file Molecule.hh.

◆ size()

Index CASM::xtal::Molecule::size ( ) const

inline

Number of atoms contained Molecule.

Definition at line 113 of file Molecule.hh.

◆ time_reversal_active() [1/2]

bool CASM::xtal::AtomPosition::time_reversal_active ( ) const

inline

Definition at line 45 of file Molecule.hh.

◆ time_reversal_active() [2/2]

bool CASM::xtal::Molecule::time_reversal_active ( ) const

inline

True if Molecule contains attributes that are affected by time reversal.

Definition at line 133 of file Molecule.hh.

Variable Documentation

◆ m_atoms

std::vector<AtomPosition> CASM::xtal::Molecule::m_atoms

private

Definition at line 175 of file Molecule.hh.

◆ m_attribute_map [1/2]

std::map<std::string, SpeciesAttribute> CASM::xtal::AtomPosition::m_attribute_map

private

Definition at line 71 of file Molecule.hh.

◆ m_attribute_map [2/2]

std::map<std::string, SpeciesAttribute> CASM::xtal::Molecule::m_attribute_map

private

Definition at line 178 of file Molecule.hh.

◆ m_divisible

bool CASM::xtal::Molecule::m_divisible

private

Definition at line 176 of file Molecule.hh.

◆ m_name

std::string CASM::xtal::Molecule::m_name

private

Definition at line 174 of file Molecule.hh.

◆ m_position

Eigen::Vector3d CASM::xtal::AtomPosition::m_position

private

Cartesian position; origin is centered at site.

Definition at line 69 of file Molecule.hh.

◆ m_species

std::string CASM::xtal::AtomPosition::m_species

private

Atomic species.

Definition at line 66 of file Molecule.hh.

Detailed Description

Classes

Functions

Variables

Function Documentation

◆ apply() [1/2]

◆ apply() [2/2]

◆ atom()

◆ AtomPosition() [1/2]

◆ AtomPosition() [2/2]

◆ atoms()

◆ attributes() [1/2]

◆ attributes() [2/2]

◆ cart()

◆ compare_type()

◆ contains()

◆ copy_apply() [1/4]

◆ copy_apply() [2/4]

◆ copy_apply() [3/4]

◆ copy_apply() [4/4]

◆ identical() [1/2]

◆ identical() [2/2]

◆ is_atomic()

◆ is_divisible()

◆ is_indivisible()

◆ is_molecule_name()

◆ is_vacancy() [1/2]

◆ is_vacancy() [2/2]

◆ make_atom()

◆ make_unknown()

◆ make_vacancy()

◆ Molecule()

◆ name() [1/2]

◆ name() [2/2]

◆ operator==()

◆ set_atoms()

◆ set_attributes() [1/2]

◆ set_attributes() [2/2]

◆ size()

◆ time_reversal_active() [1/2]

◆ time_reversal_active() [2/2]

Variable Documentation

◆ m_atoms

◆ m_attribute_map [1/2]

◆ m_attribute_map [2/2]

◆ m_divisible

◆ m_name

◆ m_position

◆ m_species