#include <Cluster.hh>

Detailed Description

template<typename CoordType>
class CASM::BasicStructure< CoordType >

BasicStructure specifies the lattice and atomic basis of a crystal.

Definition at line 16 of file Cluster.hh.

Public Member Functions
	BasicStructure (const Lattice &init_lat)

	BasicStructure ()

	BasicStructure (const fs::path &filepath)

	BasicStructure (const BasicStructure &RHS)

virtual	~BasicStructure ()

template<typename CoordType2 >
Index	find (const CoordType2 &test_site, double tol=TOL) const

template<typename CoordType2 >
Index	find (const CoordType2 &test_site, const Coordinate &shift, double tol) const

const Lattice &	lattice () const

template<typename CoordType2 >
UnitCellCoord	get_unit_cell_coord (const CoordType2 &test_site, double tol=TOL) const

virtual BasicStructure &	operator= (const BasicStructure &RHS)

void	copy_attributes_from (const BasicStructure &RHS)

void	update ()

virtual void	reset ()

void	set_site_internals ()
	Associate each site with its basis index by setting its internal flags (asym_ind -> -1) More...

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

CoordType	get_site (const UnitCellCoord &ucc) const

void	set_lattice (const Lattice &lattice, COORD_TYPE mode)

void	set_basis (Array< CoordType > basis_in)
	Manually set the basis sites. More...

void	generate_factor_group (SymGroup &factor_group, double map_tol) const
	apply a symmetry operation to the current structure (may change lattice vectors and order of basis atoms) More...

void	generate_factor_group_slow (SymGroup &factor_group, double map_tol) const

void	fg_converge (double small_tol, double large_tol, double increment)

void	fg_converge (SymGroup &factor_group, double small_tol, double large_tol, double increment)

SymGroupRepID	generate_basis_permutation_representation (const MasterSymGroup &factor_group, bool verbose) const

void	symmetrize (const SymGroup &relaxed_factors)

void	symmetrize (const double &tolerance)

bool	is_primitive (double prim_tol=TOL) const

bool	is_primitive (BasicStructure &new_prim, double prim_tol=TOL) const

void	fill_supercell (const BasicStructure &prim, double map_tol=TOL)
	fill an empty structure with the basis of its corresponding primitive cell More...

BasicStructure	create_superstruc (const Lattice &scel_lat, double map_tol=TOL) const
	Shortcut routine to create a supercell structure and fill it with sites. More...

void	generate_flowertrees_safe (const SiteOrbitree &in_tree, Array< SiteOrbitree > &out_trees)
	Gets clusters of every size radiating from one site and saves them to a flowertree. A garland for each site is constructed. More...

void	generate_flowertrees (const SiteOrbitree &in_tree, Array< SiteOrbitree > &out_trees)

void	map_superstruc_to_prim (BasicStructure &prim, const SymGroup &point_group)
	Figures out which prim basis each superstructure basis corresponds to. More...

void	merge_sites (double maxdist)
	If atoms are too close together, average their distance and make them one. More...

void	add_vacuum_shift (BasicStructure &new_surface_struc, double vacuum_thickness, Eigen::Vector3d shift, COORD_TYPE mode) const
	Add vacuum and shift c vector. The vacuum is always added parallel to c, and the shift vector should also be parallel to the ab plane (x,y,0) More...

void	add_vacuum_shift (BasicStructure &new_surface_struc, double vacuum_thickness, Coordinate shift) const

void	add_vacuum (BasicStructure &new_surface_struc, double vacuum_thickness) const
	Adds vacuum layer on top of ab plane. 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...

const Lattice &	get_lattice () const
	Return a reference to the lattice. More...

virtual void	read (std::istream &stream)
	Print intpolated images in seperate directries. More...

void	print_xyz (std::ostream &stream) const
	Output other formats. More...

void	print_cif (std::ostream &stream) const

jsonParser &	to_json (jsonParser &json) const

void	from_json (const jsonParser &json)

Public Attributes
std::string	title
	User-specified name of this Structure. More...

Array< CoordType >	basis
	Lattice vectors that specifies periodicity of the crystal. More...

Protected Attributes
Lattice	m_lattice

bool	SD_flag
	Specifies whether selectice dynamics is on or of for DFT calculations. More...

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

Constructor & Destructor Documentation

template<typename CoordType>

CASM::BasicStructure< CoordType >::BasicStructure ( const Lattice & init_lat )

inline

Definition at line 52 of file BasicStructure.hh.

template<typename CoordType>

CASM::BasicStructure< CoordType >::BasicStructure ( )

inline

Definition at line 53 of file BasicStructure.hh.

template<typename CoordType >

CASM::BasicStructure< CoordType >::BasicStructure ( const fs::path & filepath )

Definition at line 16 of file BasicStructure_impl.hh.

template<typename CoordType >

CASM::BasicStructure< CoordType >::BasicStructure ( const BasicStructure< CoordType > & 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 30 of file BasicStructure_impl.hh.

template<typename CoordType>

virtual CASM::BasicStructure< CoordType >::~BasicStructure ( )

inlinevirtual

Definition at line 60 of file BasicStructure.hh.

Member Function Documentation

template<typename CoordType >

void CASM::BasicStructure< CoordType >::add_vacuum	(	BasicStructure< CoordType > &	new_surface_struc,
		double	vacuum_thickness
	)		const

Adds vacuum layer on top of ab plane.

Definition at line 886 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::add_vacuum_shift	(	BasicStructure< CoordType > &	new_surface_struc,
		double	vacuum_thickness,
		Eigen::Vector3d	shift,
		COORD_TYPE	mode
	)		const

Add vacuum and shift c vector. The vacuum is always added parallel to c, and the shift vector should also be parallel to the ab plane (x,y,0)

Call this on a structure to get new_surface_struc: the structure with a layer of vacuum added parallel to the ab plane. vacuum_thickness: thickness of vacuum layer (Angstroms) shift: shift vector from layer to layer, assumes FRAC unless specified. The shift vector should only have values relative to a and b vectors (eg x, y, 0). Default shift is zero.

Definition at line 850 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::add_vacuum_shift	(	BasicStructure< CoordType > &	new_surface_struc,
		double	vacuum_thickness,
		Coordinate	shift
	)		const

Definition at line 874 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::copy_attributes_from ( const BasicStructure< CoordType > & RHS )

Use this is the copy interface for things that derive from BasicStructure<> It should be overloaded in derived classes so that all important attributes besides lattice, basis, and title get copied

Definition at line 55 of file BasicStructure_impl.hh.

template<typename CoordType >

BasicStructure< CoordType > CASM::BasicStructure< CoordType >::create_superstruc	(	const Lattice &	scel_lat,
		double	map_tol = `TOL`
	)		const

Shortcut routine to create a supercell structure and fill it with sites.

Operates on the primitive structure and takes as an argument the supercell lattice. It then returns a new superstructure.

This is similar to the Lattice*Primitive routine which returns a new superstructure. Unlike the fill_supercell routine which takes the primitive structure, this WILL fill the sites.

Definition at line 365 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::fg_converge	(	double	small_tol,
		double	large_tol,
		double	increment
	)

Definition at line 230 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::fg_converge	(	SymGroup &	factor_group,
		double	small_tol,
		double	large_tol,
		double	increment
	)

Definition at line 238 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::fill_supercell	(	const BasicStructure< CoordType > &	prim,
		double	map_tol = `TOL`
	)

fill an empty structure with the basis of its corresponding primitive cell

It is NOT wise to use this function unless you have already initialized a superstructure with lattice vectors.

It is more wise to use the two methods that call this method: Either the overloaded * operator which does: SCEL_Lattice * Prim_Structrue = New_Superstructure — or — New_Superstructure=Prim_BasicStructure<CoordType>.create_superstruc(SCEL_Lattice);

Both of these will return NEW superstructures.

Definition at line 322 of file BasicStructure_impl.hh.

template<typename CoordType >

template<typename CoordType2 >

Index CASM::BasicStructure< CoordType >::find	(	const CoordType2 &	test_site,
		double	tol = `TOL`
	)		const

return basis index of site that matches test_coord, if it is in basis otherwise, returns basis.size()

Definition at line 613 of file BasicStructure_impl.hh.

template<typename CoordType >

template<typename CoordType2 >

Index CASM::BasicStructure< CoordType >::find	(	const CoordType2 &	test_site,
		const Coordinate &	shift,
		double	tol
	)		const

return basis index of site that matches test_site+shift, if it is in basis otherwise, returns basis.size()

Definition at line 625 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::from_json ( const jsonParser & json )

re-throw exceptions

Definition at line 1201 of file BasicStructure_impl.hh.

template<typename CoordType >

SymGroupRepID CASM::BasicStructure< CoordType >::generate_basis_permutation_representation	(	const MasterSymGroup &	factor_group,
		bool	verbose
	)		const

Definition at line 275 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::generate_factor_group	(	SymGroup &	factor_group,
		double	map_tol
	)		const

apply a symmetry operation to the current structure (may change lattice vectors and order of basis atoms)

Definition at line 188 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::generate_factor_group_slow	(	SymGroup &	factor_group,
		double	map_tol
	)		const

Definition at line 103 of file BasicStructure_impl.hh.

template<typename CoordType>

void CASM::BasicStructure< CoordType >::generate_flowertrees	(	const SiteOrbitree &	in_tree,
		Array< SiteOrbitree > &	out_trees
	)

template<typename CoordType>

void CASM::BasicStructure< CoordType >::generate_flowertrees_safe	(	const SiteOrbitree &	in_tree,
		Array< SiteOrbitree > &	out_trees
	)

Gets clusters of every size radiating from one site and saves them to a flowertree. A garland for each site is constructed.

template<typename CoordType>

const Lattice& CASM::BasicStructure< CoordType >::get_lattice ( ) const

inline

Return a reference to the lattice.

Definition at line 177 of file BasicStructure.hh.

template<typename CoordType >

CoordType CASM::BasicStructure< CoordType >::get_site ( const UnitCellCoord & ucc ) const

Definition at line 671 of file BasicStructure_impl.hh.

template<typename CoordType >

template<typename CoordType2 >

UnitCellCoord CASM::BasicStructure< CoordType >::get_unit_cell_coord	(	const CoordType2 &	bsite,
		double	tol = `TOL`
	)		const

Return the UnitCellCoord corresponding to test_site (i.e., finds the basis index and the lattice translation)

Using the lattice of (*this), this function will return a UnitCellCoord that corresponds to a site passed to it within a given tolerance. This function is useful for making a nearest neighbor table from sites that land outside of the primitive cell.

Definition at line 646 of file BasicStructure_impl.hh.

template<typename CoordType >

bool CASM::BasicStructure< CoordType >::is_primitive ( double prim_tol = TOL ) const

Returns true if the structure describes a crystal primitive cell i.e., no translation smaller than a lattice vector can map the structure onto itself

Determines if structure is primitive description of the crystal

Definition at line 379 of file BasicStructure_impl.hh.

template<typename CoordType >

bool CASM::BasicStructure< CoordType >::is_primitive	(	BasicStructure< CoordType > &	new_prim,
		double	prim_tol = `TOL`
	)		const

Returns true if the structure describes a crystal primitive cell and finds the primitive cell and stores it in 'new_prim'

Determines if structure is primitive description of the crystal If not, finds primitive cell and copies to new_prim

Definition at line 421 of file BasicStructure_impl.hh.

template<typename CoordType>

const Lattice& CASM::BasicStructure< CoordType >::lattice ( ) const

inline

Definition at line 74 of file BasicStructure.hh.

template<typename CoordType>

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

private

template<typename CoordType >

void CASM::BasicStructure< CoordType >::map_superstruc_to_prim	(	BasicStructure< CoordType > &	prim,
		const SymGroup &	point_group
	)

Figures out which prim basis each superstructure basis corresponds to.

Definition at line 550 of file BasicStructure_impl.hh.

template<typename CoordType >

Index CASM::BasicStructure< CoordType >::max_possible_vacancies ( ) const

Counts sites that allow vacancies.

Definition at line 897 of file BasicStructure_impl.hh.

template<typename CoordType>

void CASM::BasicStructure< CoordType >::merge_sites ( double maxdist )

If atoms are too close together, average their distance and make them one.

template<typename CoordType >

BasicStructure< CoordType > & CASM::BasicStructure< CoordType >::operator+= ( const Coordinate & shift )

Translates all atoms in cell.

Definition at line 1137 of file BasicStructure_impl.hh.

template<typename CoordType >

BasicStructure< CoordType > & CASM::BasicStructure< CoordType >::operator-= ( const Coordinate & shift )

Definition at line 1152 of file BasicStructure_impl.hh.

template<typename CoordType >

BasicStructure< CoordType > & CASM::BasicStructure< CoordType >::operator= ( const BasicStructure< CoordType > & RHS )

virtual

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

Definition at line 40 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::print_cif ( std::ostream & stream ) const

Definition at line 1076 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::print_xyz ( std::ostream & stream ) const

Output other formats.

Definition at line 1059 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::read ( std::istream & stream )

virtual

Print intpolated images in seperate directries.

Definition at line 912 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::reset ( )

virtual

Reimplemented in CASM::Structure.

Definition at line 72 of file BasicStructure_impl.hh.

template<typename CoordType>

void CASM::BasicStructure< CoordType >::set_basis ( Array< CoordType > basis_in )

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 704 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::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 685 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::set_site_internals ( )

Associate each site with its basis index by setting its internal flags (asym_ind -> -1)

Definition at line 536 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::symmetrize ( const SymGroup & relaxed_factors )

Goes to a specified site of the basis and makes a flower tree of pairs. It then stores the length and multiplicity of the pairs in a double array, giving you a strict nearest neighbor table. This version also fills up a SiteOrbitree in case you want to keep it. Blatantly copied from Anna's routine in old new CASM Goes to a specified site of the basis and makes a flower tree of pairs. It then stores the length and multiplicity of the pairs in a double array, giving you a strict nearest neighbor table. The bouquet used for this falls into the void. Given a symmetry group, the basis of the structure will have each operation applied to it. The resulting set of basis from performing these operations will be averaged out, yielding a new average basis that will replace the current one.

Definition at line 782 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::symmetrize ( const double & tolerance )

Same as the other symmetrize routine, except this one assumes that the symmetry group you mean to use is the factor group of your structure within a certain tolerance.

Notice that the tolerance is also used on your point group!!

Definition at line 831 of file BasicStructure_impl.hh.

template<typename CoordType >

jsonParser & CASM::BasicStructure< CoordType >::to_json ( jsonParser & json ) const

Definition at line 1182 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::update ( )

Definition at line 86 of file BasicStructure_impl.hh.

template<typename CoordType >

void CASM::BasicStructure< CoordType >::within ( )

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

Definition at line 93 of file BasicStructure_impl.hh.

Member Data Documentation

template<typename CoordType>

Array<CoordType> CASM::BasicStructure< CoordType >::basis

Lattice vectors that specifies periodicity of the crystal.

Definition at line 42 of file BasicStructure.hh.

template<typename CoordType>

Lattice CASM::BasicStructure< CoordType >::m_lattice

protected

Definition at line 32 of file BasicStructure.hh.

template<typename CoordType>

bool CASM::BasicStructure< CoordType >::SD_flag

protected

Specifies whether selectice dynamics is on or of for DFT calculations.

Definition at line 35 of file BasicStructure.hh.

template<typename CoordType>

std::string CASM::BasicStructure< CoordType >::title

User-specified name of this Structure.

Definition at line 39 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/clusterography/Cluster.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/crystallography/BasicStructure.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/crystallography/BasicStructure_impl.hh

Detailed Description

template<typename CoordType> class CASM::BasicStructure< CoordType >

Public Member Functions

Public Attributes

Protected Attributes

Private Member Functions

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<typename CoordType>
class CASM::BasicStructure< CoordType >