#include <Coordinate.hh>

Inheritance diagram for CASM::xtal::Coordinate:

Detailed Description

Represents cartesian and fractional coordinates.

Definition at line 34 of file Coordinate.hh.

Public Types
typedef Eigen::Vector3d	vector_type

typedef vector_type::Index	size_type

Public Member Functions
	Coordinate (const Lattice &_home)
	Minimal constructor only takes a lattice. More...

	Coordinate (Eigen::Ref< const vector_type > const &_vec, const Lattice &_home, COORD_TYPE _mode)

	Coordinate (double _x, double _y, double _z, const Lattice &_home, COORD_TYPE _mode)

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

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

const vector_type &	const_frac () const
	user override to force 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 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...

const vector_type &	const_cart () const
	user override to force 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 double &	const_cart (size_type index) const
	const Access a component of the Cartesian coordinate vector More...

vector_type	as_vec (COORD_TYPE _mode) const

Coordinate &	operator+= (const Coordinate &RHS)
	Positive translation of this coordinate by RHS.cart() More...

Coordinate &	operator-= (const Coordinate &RHS)
	Negative translation of this coordinate by RHS.cart() 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) const

bool	compare (const Coordinate &RHS) const
	Returns true if this->min_dist(RHS)<this->lattice().tol() More...

bool	compare (const Coordinate &RHS, Coordinate &translation) 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

void	set_lattice (const Lattice &new_lat, COORD_TYPE mode)
	Change the home lattice of the coordinate, selecting one representation (either CART or FRAC) that remains invariant. More...

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

const Lattice &	lattice () 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, Eigen::IOFormat format=Eigen::IOFormat(7, 12)) const

void	print (std::ostream &stream, char term=0, Eigen::IOFormat format=Eigen::IOFormat(7, 12)) const

void	print_axis (std::ostream &stream, COORD_TYPE mode, char term=0, Eigen::IOFormat format=Eigen::IOFormat(7, 12)) 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...

Coordinate	min_translation (const Coordinate &neighbor) const
	Returns translation coordinate (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	min_dist2 (const Coordinate &neighbor, const Eigen::Ref< const Eigen::Matrix3d > &metric) const

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

Private Member Functions
void	_update_cart ()

void	_update_frac ()

void	_set_frac (const Eigen::Ref< const vector_type > &f)

void	_set_frac (size_type ind, double val)

void	_set_cart (const Eigen::Ref< const vector_type > &c)

void	_set_cart (size_type ind, double val)

Private Attributes
Lattice const *	m_home

vector_type	m_frac_coord

vector_type	m_cart_coord

Member Typedef Documentation

◆ size_type

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

Definition at line 37 of file Coordinate.hh.

◆ vector_type

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

Definition at line 36 of file Coordinate.hh.

Constructor & Destructor Documentation

◆ Coordinate() [1/3]

CASM::xtal::Coordinate::Coordinate ( const Lattice & _home )

inlineexplicit

Minimal constructor only takes a lattice.

Definition at line 47 of file Coordinate.hh.

◆ Coordinate() [2/3]

CASM::xtal::Coordinate::Coordinate	(	Eigen::Ref< const vector_type > const &	_vec,
		const Lattice &	_home,
		COORD_TYPE	_mode
	)

◆ Coordinate() [3/3]

CASM::xtal::Coordinate::Coordinate	(	double	_x,
		double	_y,
		double	_z,
		const Lattice &	_home,
		COORD_TYPE	_mode
	)

Definition at line 21 of file Coordinate.cc.

Member Function Documentation

◆ _set_cart() [1/2]

void CASM::xtal::Coordinate::_set_cart ( const Eigen::Ref< const vector_type > & c )

inlineprivate

Definition at line 264 of file Coordinate.hh.

◆ _set_cart() [2/2]

void CASM::xtal::Coordinate::_set_cart	(	size_type	ind,
		double	val
	)

inlineprivate

Definition at line 269 of file Coordinate.hh.

◆ _set_frac() [1/2]

void CASM::xtal::Coordinate::_set_frac ( const Eigen::Ref< const vector_type > & f )

inlineprivate

Definition at line 254 of file Coordinate.hh.

◆ _set_frac() [2/2]

void CASM::xtal::Coordinate::_set_frac	(	size_type	ind,
		double	val
	)

inlineprivate

Definition at line 259 of file Coordinate.hh.

◆ _update_cart()

void CASM::xtal::Coordinate::_update_cart ( )

inlineprivate

Definition at line 247 of file Coordinate.hh.

◆ _update_frac()

void CASM::xtal::Coordinate::_update_frac ( )

inlineprivate

Definition at line 249 of file Coordinate.hh.

◆ almost_equal()

bool CASM::xtal::Coordinate::almost_equal ( const Coordinate & RHS ) const

Definition at line 66 of file Coordinate.cc.

◆ as_vec()

vector_type CASM::xtal::Coordinate::as_vec ( COORD_TYPE _mode ) const

inline

Definition at line 103 of file Coordinate.hh.

◆ cart() [1/4]

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

inline

Set Cartesian coordinate vector and update fractional coordinate vector.

Definition at line 562 of file Coordinate.hh.

◆ cart() [2/4]

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

inline

const Access the Cartesian coordinate vector

Definition at line 87 of file Coordinate.hh.

◆ cart() [3/4]

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

inline

Set a component of the Cartesian coordinate vector.

Definition at line 567 of file Coordinate.hh.

◆ cart() [4/4]

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

inline

const Access a component of the Cartesian coordinate vector

Definition at line 96 of file Coordinate.hh.

◆ compare() [1/2]

bool CASM::xtal::Coordinate::compare ( const Coordinate & RHS ) const

Returns true if this->min_dist(RHS)<this->lattice().tol()

Definition at line 72 of file Coordinate.cc.

◆ compare() [2/2]

bool CASM::xtal::Coordinate::compare	(	const Coordinate &	RHS,
		Coordinate &	translation
	)		const

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

Parameters

translation such that *this = (RHS+translation)

Definition at line 78 of file Coordinate.cc.

◆ compare_type()

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

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

Definition at line 84 of file Coordinate.cc.

◆ const_cart() [1/2]

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

inline

user override to force const Access the Cartesian coordinate vector

Definition at line 90 of file Coordinate.hh.

◆ const_cart() [2/2]

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

inline

const Access a component of the Cartesian coordinate vector

Definition at line 99 of file Coordinate.hh.

◆ const_frac() [1/2]

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

inline

user override to force const Access the fractional coordinate vector

Definition at line 68 of file Coordinate.hh.

◆ const_frac() [2/2]

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

inline

user override to force const Access the fractional coordinate vector

Definition at line 78 of file Coordinate.hh.

◆ dist()

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

distance (in Angstr) of neighbor from *this

Definition at line 148 of file Coordinate.cc.

◆ frac() [1/4]

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

inline

Set the fractional coordinate vector.

Definition at line 550 of file Coordinate.hh.

◆ frac() [2/4]

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

inline

const Access the fractional coordinate vector

Definition at line 64 of file Coordinate.hh.

◆ frac() [3/4]

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

inline

Set a component of the fractional coordinate vector.

Definition at line 555 of file Coordinate.hh.

◆ frac() [4/4]

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

inline

const Access a component of the fractional coordinate vector

Definition at line 74 of file Coordinate.hh.

◆ home()

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

inline

Access the home lattice of the coordinate.

Definition at line 200 of file Coordinate.hh.

◆ is_lattice_shift()

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

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

Definition at line 311 of file Coordinate.cc.

◆ is_within()

bool CASM::xtal::Coordinate::is_within ( ) const

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

Definition at line 244 of file Coordinate.cc.

◆ lattice()

const Lattice& CASM::xtal::Coordinate::lattice ( ) const

inline

Access the home lattice of the coordinate.

Definition at line 206 of file Coordinate.hh.

◆ min_dist()

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

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 152 of file Coordinate.cc.

◆ min_dist2()

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

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

Definition at line 178 of file Coordinate.cc.

◆ min_translation()

Coordinate CASM::xtal::Coordinate::min_translation ( const Coordinate & neighbor ) const

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

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

Definition at line 156 of file Coordinate.cc.

◆ operator!=()

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

inline

Definition at line 125 of file Coordinate.hh.

◆ operator+=()

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

Positive translation of this coordinate by RHS.cart()

Definition at line 37 of file Coordinate.cc.

◆ operator-()

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

unary minus of this coordinate

Definition at line 54 of file Coordinate.cc.

◆ operator-=()

Coordinate & CASM::xtal::Coordinate::operator-= ( const Coordinate & RHS )

Negative translation of this coordinate by RHS.cart()

Definition at line 44 of file Coordinate.cc.

◆ operator==()

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

Definition at line 60 of file Coordinate.cc.

◆ print() [1/2]

void CASM::xtal::Coordinate::print	(	std::ostream &	stream,
		char	term = `0`,
		Eigen::IOFormat	format = `Eigen::IOFormat(7, 12)`
	)		const

Definition at line 102 of file Coordinate.cc.

◆ print() [2/2]

void CASM::xtal::Coordinate::print	(	std::ostream &	stream,
		COORD_TYPE	mode,
		char	term = `0`,
		Eigen::IOFormat	format = `Eigen::IOFormat(7, 12)`
	)		const

Definition at line 121 of file Coordinate.cc.

◆ print_axis()

void CASM::xtal::Coordinate::print_axis	(	std::ostream &	stream,
		COORD_TYPE	mode,
		char	term = `0`,
		Eigen::IOFormat	format = `Eigen::IOFormat(7, 12)`
	)		const

Print normalized vector.

Definition at line 135 of file Coordinate.cc.

◆ read()

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

Definition at line 88 of file Coordinate.cc.

◆ robust_min_dist()

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

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 168 of file Coordinate.cc.

◆ set_lattice()

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

Change the home lattice of the coordinate, selecting one representation (either CART or FRAC) that remains invariant.

Parameters

invariant_mode

invariant_mode == CART: Cartesian coordinates stay the same, and fractional coordinates are updated Ex: (my_coord.set_lattice(superlattice, CART); // this is how superlattices get filled.

invariant_mode == FRAC: Fractional coordinates stay the same, and Cartesian coordinates are updated Ex: you can apply a strain by changing the lattice and keepin FRAC invariant (my_coord.set_lattice(strained_lattice, FRAC); Ex: you can apply a rotation by changing the lattice and keeping FRAC invariant (my_coord.set_lattice(rotated_lattice, FRAC);

Definition at line 190 of file Coordinate.cc.

◆ voronoi_number() [1/2]

int CASM::xtal::Coordinate::voronoi_number ( ) const

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

Definition at line 259 of file Coordinate.cc.

◆ voronoi_number() [2/2]

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

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

Definition at line 265 of file Coordinate.cc.

◆ voronoi_within() [1/2]

bool CASM::xtal::Coordinate::voronoi_within ( )

Map coordinate into the voronoi cell using a lattice translation.

Definition at line 274 of file Coordinate.cc.

◆ voronoi_within() [2/2]

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

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 290 of file Coordinate.cc.

◆ within() [1/2]

bool CASM::xtal::Coordinate::within ( )

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

Definition at line 205 of file Coordinate.cc.

◆ within() [2/2]

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

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 223 of file Coordinate.cc.

Member Data Documentation

◆ m_cart_coord

vector_type CASM::xtal::Coordinate::m_cart_coord

private

Definition at line 281 of file Coordinate.hh.

◆ m_frac_coord

vector_type CASM::xtal::Coordinate::m_frac_coord

private

Definition at line 281 of file Coordinate.hh.

◆ m_home

Lattice const* CASM::xtal::Coordinate::m_home

private

Definition at line 279 of file Coordinate.hh.

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

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

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ size_type

◆ vector_type

Constructor & Destructor Documentation

◆ Coordinate() [1/3]

◆ Coordinate() [2/3]

◆ Coordinate() [3/3]

Member Function Documentation

◆ _set_cart() [1/2]

◆ _set_cart() [2/2]

◆ _set_frac() [1/2]

◆ _set_frac() [2/2]

◆ _update_cart()

◆ _update_frac()

◆ almost_equal()

◆ as_vec()

◆ cart() [1/4]

◆ cart() [2/4]

◆ cart() [3/4]

◆ cart() [4/4]

◆ compare() [1/2]

◆ compare() [2/2]

◆ compare_type()

◆ const_cart() [1/2]

◆ const_cart() [2/2]

◆ const_frac() [1/2]

◆ const_frac() [2/2]

◆ dist()

◆ frac() [1/4]

◆ frac() [2/4]

◆ frac() [3/4]

◆ frac() [4/4]

◆ home()

◆ is_lattice_shift()

◆ is_within()

◆ lattice()

◆ min_dist()

◆ min_dist2()

◆ min_translation()

◆ operator!=()

◆ operator+=()

◆ operator-()

◆ operator-=()

◆ operator==()

◆ print() [1/2]

◆ print() [2/2]

◆ print_axis()

◆ read()

◆ robust_min_dist()

◆ set_lattice()

◆ voronoi_number() [1/2]

◆ voronoi_number() [2/2]

◆ voronoi_within() [1/2]

◆ voronoi_within() [2/2]

◆ within() [1/2]

◆ within() [2/2]

Member Data Documentation

◆ m_cart_coord

◆ m_frac_coord

◆ m_home