#include <BasicStructure.hh>

Detailed Description

BasicStructure specifies the lattice and atomic basis of a crystal.

Definition at line 32 of file BasicStructure.hh.

Public Member Functions
	BasicStructure (const Lattice &init_lat)

	BasicStructure ()

	BasicStructure (const BasicStructure &RHS)

	~BasicStructure ()

const Lattice &	lattice () const

const std::vector< Site > &	basis () const

std::vector< Site > &	set_basis ()

const std::string &	title () const

DoFSet const &	global_dof (std::string const &dof_type) const

std::map< DoFKey, DoFSet > const &	global_dofs () const

BasicStructure &	operator= (const BasicStructure &RHS)

void	within ()
	Translate all basis sites so that they are inside the unit cell. More...

void	set_lattice (const Lattice &lattice, COORD_TYPE mode)

void	set_title (std::string const &_title)
	Set the title of the structure. More...

void	set_global_dofs (std::map< DoFKey, DoFSet > const &new_dof_map)
	Manually set the global DoFs. More...

void	set_global_dofs (std::vector< DoFSet > const &new_dof_vec)
	Manually set the global DoFs. More...

void	set_basis (std::vector< Site > const &_basis, COORD_TYPE mode=CART)
	Manually set the basis sites. More...

void	push_back (Site const &_site, COORD_TYPE mode=CART)
	Manually set the basis sites. More...

bool	is_time_reversal_active () const
	Returns true if structure has attributes affected by time reversal. More...

BasicStructure &	operator+= (const Coordinate &shift)
	Translates all atoms in cell. More...

BasicStructure &	operator-= (const Coordinate &shift)

Index	max_possible_vacancies () const
	Counts sites that allow vacancies. More...

void	print_xyz (std::ostream &stream, bool frac=false) const
	Output other formats. More...

Static Public Member Functions
static BasicStructure	from_poscar_stream (std::istream &poscar_stream, double tol=TOL)

Protected Attributes
Lattice	m_lattice

std::string	m_title
	User-specified name of this Structure. More...

std::vector< Site >	m_basis
	Lattice vectors that specifies periodicity of the crystal. More...

std::map< DoFKey, DoFSet >	m_global_dof_map
	continuous global degrees of freedom More...

Private Member Functions
void	main_print (std::ostream &stream, COORD_TYPE mode, bool version5, int option) const

void	read (std::istream &stream, double tol=TOL)

Constructor & Destructor Documentation

◆ BasicStructure() [1/3]

CASM::xtal::BasicStructure::BasicStructure ( const Lattice & init_lat )

inline

Definition at line 55 of file BasicStructure.hh.

◆ BasicStructure() [2/3]

CASM::xtal::BasicStructure::BasicStructure ( )

inline

Definition at line 56 of file BasicStructure.hh.

◆ BasicStructure() [3/3]

CASM::xtal::BasicStructure::BasicStructure ( const BasicStructure & RHS )

Have to explicitly define the copy constructor so that sites in the new structure do not depend on the lattice of 'RHS'

Definition at line 27 of file BasicStructure.cc.

◆ ~BasicStructure()

CASM::xtal::BasicStructure::~BasicStructure ( )

inline

Definition at line 65 of file BasicStructure.hh.

Member Function Documentation

◆ basis()

const std::vector<Site>& CASM::xtal::BasicStructure::basis ( ) const

inline

Definition at line 71 of file BasicStructure.hh.

◆ from_poscar_stream()

BasicStructure CASM::xtal::BasicStructure::from_poscar_stream	(	std::istream &	poscar_stream,
		double	tol = `TOL`
	)

static

Definition at line 18 of file BasicStructure.cc.

◆ global_dof()

DoFSet const & CASM::xtal::BasicStructure::global_dof ( std::string const & dof_type ) const

Definition at line 53 of file BasicStructure.cc.

◆ global_dofs()

std::map<DoFKey, DoFSet> const& CASM::xtal::BasicStructure::global_dofs ( ) const

inline

Definition at line 79 of file BasicStructure.hh.

◆ is_time_reversal_active()

bool CASM::xtal::BasicStructure::is_time_reversal_active ( ) const

Returns true if structure has attributes affected by time reversal.

Definition at line 323 of file BasicStructure.cc.

◆ lattice()

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

inline

Definition at line 69 of file BasicStructure.hh.

◆ main_print()

void CASM::xtal::BasicStructure::main_print	(	std::ostream &	stream,
		COORD_TYPE	mode,
		bool	version5,
		int	option
	)		const

private

◆ max_possible_vacancies()

Index CASM::xtal::BasicStructure::max_possible_vacancies ( ) const

Counts sites that allow vacancies.

Definition at line 108 of file BasicStructure.cc.

◆ operator+=()

BasicStructure & CASM::xtal::BasicStructure::operator+= ( const Coordinate & shift )

Translates all atoms in cell.

Definition at line 292 of file BasicStructure.cc.

◆ operator-=()

BasicStructure & CASM::xtal::BasicStructure::operator-= ( const Coordinate & shift )

Definition at line 302 of file BasicStructure.cc.

◆ operator=()

BasicStructure & CASM::xtal::BasicStructure::operator= ( const BasicStructure & RHS )

Have to explicitly define the assignment operator so that sites in this structure do not depend on the lattice of 'RHS'

Definition at line 39 of file BasicStructure.cc.

◆ print_xyz()

void CASM::xtal::BasicStructure::print_xyz	(	std::ostream &	stream,
		bool	frac = `false`
	)		const

Output other formats.

Definition at line 269 of file BasicStructure.cc.

◆ push_back()

void CASM::xtal::BasicStructure::push_back	(	Site const &	_site,
		COORD_TYPE	mode = `CART`
	)

Manually set the basis sites.

Definition at line 101 of file BasicStructure.cc.

◆ read()

void CASM::xtal::BasicStructure::read	(	std::istream &	stream,
		double	tol = `TOL`
	)

private

Definition at line 121 of file BasicStructure.cc.

◆ set_basis() [1/2]

std::vector<Site>& CASM::xtal::BasicStructure::set_basis ( )

inline

Definition at line 73 of file BasicStructure.hh.

◆ set_basis() [2/2]

void CASM::xtal::BasicStructure::set_basis	(	std::vector< Site > const &	_basis,
		COORD_TYPE	mode = `CART`
	)

Manually set the basis sites.

Allows for the basis elements of a basic structure to be manually set, e.g. as in jsonParser.cc.

Definition at line 94 of file BasicStructure.cc.

◆ set_global_dofs() [1/2]

void CASM::xtal::BasicStructure::set_global_dofs ( std::map< DoFKey, DoFSet > const & new_dof_map )

inline

Manually set the global DoFs.

Definition at line 101 of file BasicStructure.hh.

◆ set_global_dofs() [2/2]

void CASM::xtal::BasicStructure::set_global_dofs ( std::vector< DoFSet > const & new_dof_vec )

inline

Manually set the global DoFs.

Definition at line 106 of file BasicStructure.hh.

◆ set_lattice()

void CASM::xtal::BasicStructure::set_lattice	(	const Lattice &	lattice,
		COORD_TYPE	mode
	)

change the lattice and update site coordinates. Argument 'mode' specifies which mode is preserved e.g.: struc.set_lattice(new_lat, CART) calculates all Cartesian coordinates, invalidates the FRAC coordinates, and changes the lattice

Definition at line 74 of file BasicStructure.cc.

◆ set_title()

void CASM::xtal::BasicStructure::set_title ( std::string const & _title )

Set the title of the structure.

Definition at line 84 of file BasicStructure.cc.

◆ title()

const std::string& CASM::xtal::BasicStructure::title ( ) const

inline

Definition at line 75 of file BasicStructure.hh.

◆ within()

void CASM::xtal::BasicStructure::within ( )

Translate all basis sites so that they are inside the unit cell.

Definition at line 65 of file BasicStructure.cc.

Member Data Documentation

◆ m_basis

std::vector<Site> CASM::xtal::BasicStructure::m_basis

protected

Lattice vectors that specifies periodicity of the crystal.

Definition at line 40 of file BasicStructure.hh.

◆ m_global_dof_map

std::map<DoFKey, DoFSet> CASM::xtal::BasicStructure::m_global_dof_map

protected

continuous global degrees of freedom

Definition at line 43 of file BasicStructure.hh.

◆ m_lattice

Lattice CASM::xtal::BasicStructure::m_lattice

protected

Definition at line 34 of file BasicStructure.hh.

◆ m_title

std::string CASM::xtal::BasicStructure::m_title

protected

User-specified name of this Structure.

Definition at line 37 of file BasicStructure.hh.

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

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

Detailed Description

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Constructor & Destructor Documentation

◆ BasicStructure() [1/3]

◆ BasicStructure() [2/3]

◆ BasicStructure() [3/3]

◆ ~BasicStructure()

Member Function Documentation

◆ basis()

◆ from_poscar_stream()

◆ global_dof()

◆ global_dofs()

◆ is_time_reversal_active()

◆ lattice()

◆ main_print()

◆ max_possible_vacancies()

◆ operator+=()

◆ operator-=()

◆ operator=()

◆ print_xyz()

◆ push_back()

◆ read()

◆ set_basis() [1/2]

◆ set_basis() [2/2]

◆ set_global_dofs() [1/2]

◆ set_global_dofs() [2/2]

◆ set_lattice()

◆ set_title()

◆ title()

◆ within()

Member Data Documentation

◆ m_basis

◆ m_global_dof_map

◆ m_lattice

◆ m_title