#include <Site.hh>

Inheritance diagram for CASM::Site:

Detailed Description

Definition at line 16 of file Site.hh.

Public Types
typedef Eigen::Vector3d	vector_type

typedef vector_type::Index	size_type

Public Member Functions
	Site (const Lattice &init_home)

	Site (const Coordinate &init_pos, const std::string &occ_name)

	Site (const Coordinate &init_pos, std::initializer_list< Molecule > site_occ)
	Construct site with initial position and the allowed Molecule. More...

const MoleculeOccupant &	site_occupant () const

const Array< ContinuousDoF > &	displacement () const

void	update_data_members (const Site &_ref_site)

bool	is_vacant () const
	Checks if current occupant is a vacancy. More...

Index	nlist_ind () const
	access m_nlist_ind More...

std::string	occ_name () const
	Name of current occupant (name of molecule, but for single atom, molecule name is species name) More...

const Molecule &	occ () const

bool	compare (const Coordinate &test_coord, double compare_tol=TOL) const

bool	compare (const Site &test_site, double compare_tol=TOL) const

bool	compare (const Site &test_site, const Coordinate &shift, double compare_tol=TOL) const

bool	compare_type (const Site &test_site) const

bool	operator== (const Site &test_site) const

bool	almost_equal (const Site &test_site, double tol) const

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

bool	contains (const std::string &name, int &index) const

void	set_lattice (const Lattice &new_lat, COORD_TYPE mode)

void	set_site_occupant (const MoleculeOccupant &new_dof)

void	set_occ_value (int new_val)

void	set_occ (const Molecule &new_occ)

Array< std::string >	allowed_occupants () const

void	set_basis_ind (Index)
	set basis_ind of site and its occupant functions More...

void	set_nlist_ind (Index)
	set m_nlist_ind of Site and its DoFs More...

Site &	apply_sym (const SymOp &op)

Site &	apply_sym_no_trans (const SymOp &op)

void	read (std::istream &stream, bool SD_is_on=false)

void	read (std::istream &stream, std::string &elem, bool SD_is_on)

void	print (std::ostream &stream) const

void	print_occ (std::ostream &stream) const

void	print_mol (std::ostream &stream, int spaces, char delim, bool SD_is_on=false) const

Site &	operator+= (const Coordinate &translation)

Site &	operator-= (const Coordinate &translation)

jsonParser &	to_json (jsonParser &json) const

void	from_json (const jsonParser &json)

Coordinate_impl::FracCoordinate	frac ()
	Set the fractional coordinate vector. More...

const vector_type &	frac () const
	const Access the fractional coordinate vector More...

Coordinate_impl::FracCoordinateComponent	frac (size_type index)
	Set a component of the fractional coordinate vector. More...

const double &	frac (size_type index) const
	const Access a component of the fractional coordinate vector More...

const vector_type &	const_frac () const
	user override to force const Access the fractional coordinate vector More...

const double &	const_frac (size_type index) const
	user override to force const Access the fractional coordinate vector More...

Coordinate_impl::CartCoordinate	cart ()
	Set Cartesian coordinate vector and update fractional coordinate vector. More...

const vector_type &	cart () const
	const Access the Cartesian coordinate vector More...

Coordinate_impl::CartCoordinateComponent	cart (size_type index)
	Set a component of the Cartesian coordinate vector. More...

const double &	cart (size_type index) const
	const Access a component of the Cartesian coordinate vector More...

const vector_type &	const_cart () const
	user override to force const Access the Cartesian coordinate vector More...

const double &	const_cart (size_type index) const
	const Access a component of the Cartesian coordinate vector More...

Coordinate	operator- () const
	unary minus of this coordinate More...

bool	operator== (const Coordinate &RHS) const

bool	operator!= (const Coordinate &RHS) const

bool	almost_equal (const Coordinate &RHS, double tol) const

bool	compare (const Coordinate &RHS, Coordinate &translation, double tol=TOL) const

bool	compare_type (const Coordinate &RHS) const
	Return true – Exists to allow duck-typing with Site. More...

bool	within ()

bool	within (Coordinate &translation)

bool	is_within () const
	Checks to see if coordinate is in the unit cell, but does not translate it. More...

int	voronoi_number () const

int	voronoi_number (const Lattice &cell) const

bool	voronoi_within ()
	Map coordinate into the voronoi cell using a lattice translation. More...

bool	voronoi_within (Coordinate &translation)

bool	is_lattice_shift (double tol=TOL) const
	Checks to see if coordinate is at a lattice translation with respect to the origin. More...

Index	basis_ind () const
	Access basis Index. More...

const Lattice &	home () const
	Access the home lattice of the coordinate. More...

void	read (std::istream &stream, COORD_TYPE mode)

void	print (std::ostream &stream, COORD_TYPE mode, char term=0, int prec=7, int pad=5) const

void	print (std::ostream &stream, char term=0, int prec=7, int pad=5) const

void	print_axis (std::ostream &stream, COORD_TYPE mode, char term=0, int prec=7, int pad=5) const
	Print normalized vector. More...

double	dist (const Coordinate &neighbor) const
	distance (in Angstr) of neighbor from *this More...

double	min_dist (const Coordinate &neighbor) const
	Returns distance (in Angstr) to nearest periodic image of neighbor. More...

double	min_dist (const Coordinate &neighbor, Coordinate &translation) const
	Returns distance (in Angstr) to nearest periodic image of neighbor. More...

double	robust_min_dist (const Coordinate &neighbor) const
	Returns distance (in Angstr) to nearest periodic image of neighbor. More...

double	robust_min_dist (const Coordinate &neighbor, Coordinate &translation) const
	Returns distance (in Angstr) to nearest periodic image of neighbor. More...

double	min_dist2 (const Coordinate &neighbor, const Eigen::Ref< const Eigen::Matrix3d > &metric) const
	Finds same shift as min_dist but returns shift(CART).transpose()metricshift(CART) More...

Static Public Member Functions
static Coordinate	origin (const Lattice &_home)
	construct a coordinate describing origin of _home lattice More...

Private Member Functions
bool	_compare_type_no_ID (const Site &test_site) const

Index	_type_ID () const

Static Private Member Functions
static Array< Site > &	_type_prototypes ()

Private Attributes
Index	m_nlist_ind

Index	m_type_ID

Array< ContinuousDoF >	m_displacement

MoleculeOccupant	m_site_occupant

Member Typedef Documentation

typedef vector_type::Index CASM::Coordinate::size_type

inherited

Definition at line 37 of file Coordinate.hh.

typedef Eigen::Vector3d CASM::Coordinate::vector_type

inherited

Definition at line 36 of file Coordinate.hh.

Constructor & Destructor Documentation

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

explicit

Definition at line 10 of file Site.cc.

CASM::Site::Site	(	const Coordinate &	init_pos,
		const std::string &	occ_name
	)

Definition at line 17 of file Site.cc.

CASM::Site::Site	(	const Coordinate &	init_pos,
		std::initializer_list< Molecule >	site_occ
	)

Construct site with initial position and the allowed Molecule.

Definition at line 33 of file Site.cc.

Member Function Documentation

bool CASM::Site::_compare_type_no_ID ( const Site & test_site ) const

private

Definition at line 497 of file Site.cc.

Index CASM::Site::_type_ID ( ) const

private

Definition at line 504 of file Site.cc.

static Array<Site>& CASM::Site::_type_prototypes ( )

inlinestaticprivate

Definition at line 101 of file Site.hh.

Array< std::string > CASM::Site::allowed_occupants ( ) const

Definition at line 212 of file Site.cc.

bool CASM::Site::almost_equal	(	const Site &	test_site,
		double	tol
	)		const

Definition at line 175 of file Site.cc.

bool CASM::Coordinate::almost_equal	(	const Coordinate &	RHS,
		double	tol
	)		const

inherited

Definition at line 66 of file Coordinate.cc.

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

Definition at line 73 of file Site.cc.

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

Definition at line 88 of file Site.cc.

Index CASM::Coordinate::basis_ind ( ) const

inlineinherited

Access basis Index.

Definition at line 190 of file Coordinate.hh.

Coordinate_impl::CartCoordinate CASM::Coordinate::cart ( )

inlineinherited

Set Cartesian coordinate vector and update fractional coordinate vector.

Definition at line 593 of file Coordinate.hh.

const vector_type& CASM::Coordinate::cart ( ) const

inlineinherited

const Access the Cartesian coordinate vector

Definition at line 87 of file Coordinate.hh.

Coordinate_impl::CartCoordinateComponent CASM::Coordinate::cart ( Coordinate::size_type index )

inlineinherited

Set a component of the Cartesian coordinate vector.

Definition at line 599 of file Coordinate.hh.

const double& CASM::Coordinate::cart ( size_type index ) const

inlineinherited

const Access a component of the Cartesian coordinate vector

Definition at line 100 of file Coordinate.hh.

bool CASM::Site::compare	(	const Coordinate &	test_coord,
		double	compare_tol = `TOL`
	)		const

Definition at line 125 of file Site.cc.

bool CASM::Site::compare	(	const Site &	test_site,
		double	compare_tol = `TOL`
	)		const

Definition at line 135 of file Site.cc.

bool CASM::Site::compare	(	const Site &	test_site,
		const Coordinate &	shift,
		double	compare_tol = `TOL`
	)		const

Definition at line 146 of file Site.cc.

bool CASM::Coordinate::compare	(	const Coordinate &	RHS,
		Coordinate &	translation,
		double	tol = `TOL`
	)		const

inherited

Returns true if this->min_dist(RHS)<tol if true, calculates

Parameters

translation such that *this = (RHS+translation)

Definition at line 80 of file Coordinate.cc.

bool CASM::Site::compare_type ( const Site & test_site ) const

Definition at line 158 of file Site.cc.

bool CASM::Coordinate::compare_type ( const Coordinate & RHS ) const

inherited

Return true – Exists to allow duck-typing with Site.

Definition at line 86 of file Coordinate.cc.

const vector_type& CASM::Coordinate::const_cart ( ) const

inlineinherited

user override to force const Access the Cartesian coordinate vector

Definition at line 92 of file Coordinate.hh.

const double& CASM::Coordinate::const_cart ( size_type index ) const

inlineinherited

const Access a component of the Cartesian coordinate vector

Definition at line 105 of file Coordinate.hh.

const vector_type& CASM::Coordinate::const_frac ( ) const

inlineinherited

user override to force const Access the fractional coordinate vector

Definition at line 66 of file Coordinate.hh.

const double& CASM::Coordinate::const_frac ( size_type index ) const

inlineinherited

user override to force const Access the fractional coordinate vector

Definition at line 79 of file Coordinate.hh.

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

Definition at line 181 of file Site.cc.

bool CASM::Site::contains	(	const std::string &	name,
		int &	index
	)		const

Definition at line 191 of file Site.cc.

const Array<ContinuousDoF>& CASM::Site::displacement ( ) const

inline

Definition at line 28 of file Site.hh.

double CASM::Coordinate::dist ( const Coordinate & neighbor ) const

inherited

distance (in Angstr) of neighbor from *this

Definition at line 146 of file Coordinate.cc.

Coordinate_impl::FracCoordinate CASM::Coordinate::frac ( )

inlineinherited

Set the fractional coordinate vector.

Definition at line 581 of file Coordinate.hh.

const vector_type& CASM::Coordinate::frac ( ) const

inlineinherited

const Access the fractional coordinate vector

Definition at line 61 of file Coordinate.hh.

Coordinate_impl::FracCoordinateComponent CASM::Coordinate::frac ( Coordinate::size_type index )

inlineinherited

Set a component of the fractional coordinate vector.

Definition at line 587 of file Coordinate.hh.

const double& CASM::Coordinate::frac ( size_type index ) const

inlineinherited

const Access a component of the fractional coordinate vector

Definition at line 74 of file Coordinate.hh.

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

re-throw exceptions

Definition at line 458 of file Site.cc.

const Lattice& CASM::Coordinate::home ( ) const

inlineinherited

Access the home lattice of the coordinate.

Definition at line 195 of file Coordinate.hh.

bool CASM::Coordinate::is_lattice_shift ( double tol = TOL ) const

inherited

Checks to see if coordinate is at a lattice translation with respect to the origin.

Definition at line 367 of file Coordinate.cc.

bool CASM::Site::is_vacant ( ) const

Checks if current occupant is a vacancy.

Definition at line 41 of file Site.cc.

bool CASM::Coordinate::is_within ( ) const

inherited

Checks to see if coordinate is in the unit cell, but does not translate it.

Definition at line 301 of file Coordinate.cc.

double CASM::Coordinate::min_dist ( const Coordinate & neighbor ) const

inherited

Returns distance (in Angstr) to nearest periodic image of neighbor.

Is unsafe if min_dist is comparable to half a lattice vector in length

Definition at line 155 of file Coordinate.cc.

double CASM::Coordinate::min_dist	(	const Coordinate &	neighbor,
		Coordinate &	translation
	)		const

inherited

Returns distance (in Angstr) to nearest periodic image of neighbor.

This version calculates the translation such that (neighbor+translation) is the periodic nearest period image of neighbor

Definition at line 169 of file Coordinate.cc.

double CASM::Coordinate::min_dist2	(	const Coordinate &	neighbor,
		const Eigen::Ref< const Eigen::Matrix3d > &	metric
	)		const

inherited

Finds same shift as min_dist but returns shift(CART).transpose()*metric*shift(CART)

Definition at line 205 of file Coordinate.cc.

Index CASM::Site::nlist_ind ( ) const

access m_nlist_ind

Definition at line 48 of file Site.cc.

const Molecule & CASM::Site::occ ( ) const

Const reference to occupying molecule. ***WARNING*** only use if you are certain the occupant has been set. If you only need to know occupant name or whether site is vacant, use Site::is_vacant() or Site::occ_name() instead

Definition at line 63 of file Site.cc.

std::string CASM::Site::occ_name ( ) const

Name of current occupant (name of molecule, but for single atom, molecule name is species name)

Definition at line 54 of file Site.cc.

bool CASM::Coordinate::operator!= ( const Coordinate & RHS ) const

inlineinherited

Definition at line 120 of file Coordinate.hh.

Site & CASM::Site::operator+= ( const Coordinate & translation )

Definition at line 103 of file Site.cc.

Coordinate CASM::Coordinate::operator- ( ) const

inherited

unary minus of this coordinate

Definition at line 53 of file Coordinate.cc.

Site & CASM::Site::operator-= ( const Coordinate & translation )

Definition at line 114 of file Site.cc.

bool CASM::Site::operator== ( const Site & test_site ) const

Definition at line 169 of file Site.cc.

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

inherited

Definition at line 59 of file Coordinate.cc.

void CASM::Site::print ( std::ostream & stream ) const

Print coordinate of site with name of all possible occupying molecule

Definition at line 379 of file Site.cc.

void CASM::Coordinate::print	(	std::ostream &	stream,
		COORD_TYPE	mode,
		char	term = `0`,
		int	prec = `7`,
		int	pad = `5`
	)		const

inherited

Definition at line 112 of file Coordinate.cc.

void CASM::Coordinate::print	(	std::ostream &	stream,
		char	term = `0`,
		int	prec = `7`,
		int	pad = `5`
	)		const

inherited

Definition at line 107 of file Coordinate.cc.

void CASM::Coordinate::print_axis	(	std::ostream &	stream,
		COORD_TYPE	mode,
		char	term = `0`,
		int	prec = `7`,
		int	pad = `5`
	)		const

inherited

Print normalized vector.

Definition at line 129 of file Coordinate.cc.

void CASM::Site::print_mol	(	std::ostream &	stream,
		int	spaces,
		char	delim,
		bool	SD_is_on = `false`
	)		const

Print each AtomPosition in current molecule, with name of occupying atom

Definition at line 410 of file Site.cc.

void CASM::Site::print_occ ( std::ostream & stream ) const

Print coordinate of site with name of occupying molecule

Definition at line 394 of file Site.cc.

void CASM::Site::read	(	std::istream &	stream,
		bool	SD_is_on = `false`
	)

Definition at line 243 of file Site.cc.

void CASM::Site::read	(	std::istream &	stream,
		std::string &	elem,
		bool	SD_is_on
	)

Definition at line 334 of file Site.cc.

void CASM::Coordinate::read	(	std::istream &	stream,
		COORD_TYPE	mode
	)

inherited

Definition at line 92 of file Coordinate.cc.

double CASM::Coordinate::robust_min_dist ( const Coordinate & neighbor ) const

inherited

Returns distance (in Angstr) to nearest periodic image of neighbor.

It is safe in all cases, because it uses the lattice Wigner-Seitz cell to determine the nearest image, but this makes it slower than min_dist

Definition at line 179 of file Coordinate.cc.

double CASM::Coordinate::robust_min_dist	(	const Coordinate &	neighbor,
		Coordinate &	translation
	)		const

inherited

Returns distance (in Angstr) to nearest periodic image of neighbor.

This version calculates the translation such that (neighbor+translation) is the periodic nearest period image of neighbor It is safe in all cases, because it uses the lattice Wigner-Seitz cell to determine the nearest image, but this makes it slower than min_dist

Definition at line 190 of file Coordinate.cc.

void CASM::Site::set_basis_ind ( Index new_ind )

set basis_ind of site and its occupant functions

Definition at line 222 of file Site.cc.

void CASM::Site::set_lattice	(	const Lattice &	new_lat,
		COORD_TYPE	mode
	)

Definition at line 202 of file Site.cc.

void CASM::Site::set_nlist_ind ( Index new_ind )

set m_nlist_ind of Site and its DoFs

Definition at line 228 of file Site.cc.

void CASM::Site::set_occ ( const Molecule & new_occ )

inline

Definition at line 70 of file Site.hh.

void CASM::Site::set_occ_value ( int new_val )

inline

Definition at line 66 of file Site.hh.

void CASM::Site::set_site_occupant ( const MoleculeOccupant & new_dof )

inline

Definition at line 61 of file Site.hh.

const MoleculeOccupant& CASM::Site::site_occupant ( ) const

inline

Definition at line 24 of file Site.hh.

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

Definition at line 439 of file Site.cc.

void CASM::Site::update_data_members ( const Site & _ref_site )

Definition at line 424 of file Site.cc.

int CASM::Coordinate::voronoi_number ( ) const

inherited

Number of periodic images of this coordinate that are on voronoi cell boundary of its home lattice

Definition at line 317 of file Coordinate.cc.

int CASM::Coordinate::voronoi_number ( const Lattice & cell ) const

inherited

Number of periodic images of this coordinate that are on voronoi cell boundary of 'cell'

Definition at line 325 of file Coordinate.cc.

bool CASM::Coordinate::voronoi_within ( )

inherited

Map coordinate into the voronoi cell using a lattice translation.

Definition at line 333 of file Coordinate.cc.

bool CASM::Coordinate::voronoi_within ( Coordinate & translation )

inherited

Same as voronoi_within(), but lattice translation is stored in Coordinate translation such that coord_after = coord_before + translation returns true if *this was already within the voronoi cell

Definition at line 348 of file Coordinate.cc.

bool CASM::Coordinate::within ( )

inherited

Map coordinate into the unit cell using a lattice translation returns true if *this was already within the unit cell

Definition at line 261 of file Coordinate.cc.

bool CASM::Coordinate::within ( Coordinate & translation )

inherited

Same as within(), but lattice translation is stored in Coordinate translation, such that coord_after = coord_before + translation returns true if *this was already within the unit cell

Definition at line 280 of file Coordinate.cc.

Member Data Documentation

Array<ContinuousDoF> CASM::Site::m_displacement

private

Definition at line 112 of file Site.hh.

Index CASM::Site::m_nlist_ind

private

Definition at line 107 of file Site.hh.

MoleculeOccupant CASM::Site::m_site_occupant

private

Definition at line 117 of file Site.hh.

Index CASM::Site::m_type_ID

mutableprivate

Definition at line 108 of file Site.hh.

The documentation for this class was generated from the following files:

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/crystallography/Site.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/crystallography/Site.cc

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation