#include <Cluster.hh>

Inheritance diagram for CASM::GenericCluster< CoordType >:

Detailed Description

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

A cluster is a group of points (CoordType) in the crystal A CoordType is any type that derives from Coordinate

Definition at line 22 of file Cluster.hh.

Public Types
typedef CoordType	WhichCoordType

typedef Array< CoordType >	X1

typedef Array< X1 >	X2

typedef Array< X2 >	X3

typedef Array< X3 >	X4

typedef Array< X4 >	X5

typedef Array< X5 >	X6

typedef Array< X6 >	X7

typedef Array< X7 >	X8

typedef Array< X8 >	X9

typedef CoordType	value_type

typedef Index	size_type

typedef CoordType *	iterator

typedef const CoordType *	const_iterator

Public Member Functions
	GenericCluster (const Lattice &init_home)

const Lattice &	home () const

const SymGroup &	clust_group () const

const SymGroupRep::RemoteHandle &	permute_rep () const

void	set_clust_group (const Array< SymOp > &new_group)

void	set_permute_rep (SymGroupRepID perm_rep_ID)

void	set_lattice (const Lattice &new_home, COORD_TYPE mode)

void	push_back (const CoordType &new_coord)

void	within (Index pivot_ind=0)
	Translate entire cluster so that point at(pivot_ind) is inside unit cell. More...

void	within (Index pivot_ind, Coordinate &trans)
	Translate entire cluster so that point at(pivot_ind) is inside unit cell. More...

void	all_within ()
	Map every point of cluster inside unit cell. More...

void	update_data_members (const BasicStructure< CoordType > &ref_struc)

*bool	image_check (const Lattice &cell, int nV=0) const
	Checks to see if cluster is "compact" relative to (Lattice cell) in other words, period images of the cluster points are farther away than the points themselves. Returns true if cluster is not "compact". More...

GenericCluster &	permute (const Array< Index > &perm)
	permute sites of the cluster, and everything that depends on the site order More...

GenericCluster &	permute (const Permutation &perm)

GenericCluster &	apply_sym (const SymOp &op)
	apply symmetry to all points of the cluster More...

GenericCluster &	apply_sym_no_trans (const SymOp &op)
	apply symmetry to all points of the cluster without translation More...

void	generate_clust_group (const SymGroup &super_group, std::vector< Permutation > *perm_array_ptr=nullptr, double tol=TOL)
	Finds the sub_group of super_group that is the point group of the cluster. More...

std::vector< Permutation >	clust_group_permutations (double tol) const
	Finds the Permutation corresponding to each element of clust_group. More...

void	calc_properties ()
	gets max_length and min_length More...

void	calc_properties (GenericCluster< CoordType > phenom_clust)
	calculate min/max lengths relative the phenom_clust & this cluster More...

double	max_length () const

double	min_length () const

Coordinate	geometric_center () const
	Returns the geometric center of "mass" of a cluster (treats all sites as having equal mass) More...

void	prepare_prototype ()
	Performs preparatory steps on prototype before doing Orbit::get_equivalent() More...

bool	contains (const GenericCluster &test_cluster) const
	is test_cluster a subcluster of (*this) More...

bool	contains_periodic (const CoordType &test_coord, double tol) const
	Like Array<CoordType>::contains(), but takes periodicity mode into account. More...

Index	find (const CoordType &test_elem, double tol) const
	is test_cluster a subcluster of (*this), and how do the indices map points of test_cluster More...

bool	find (const GenericCluster &test_cluster, Array< Index > &index, double tol) const
	is test_cluster a subcluster of (this), and how do the indices map 'index' is populated with the indices of (this) that correspond to the points of test_cluster More...

bool	map_onto_subcluster (const GenericCluster &pivot, double tol=TOL)

bool	map_onto_subcluster (const GenericCluster &pivot, int num_maps, double tol=TOL)

void	collect_basis_info (const Array< CoordType > &basis)
	Figure out which basis atoms in basis correspond to the points in cluster (*this) More...

void	collect_basis_info (const Array< CoordType > &basis, const Coordinate &shift)

void	read (std::istream &stream, int num_sites, COORD_TYPE mode, bool SD_is_on)

void	read (std::istream &stream, COORD_TYPE mode)
	Reads the cluster. More...

void	print (std::ostream &stream, char delim= '\n', COORD_TYPE mode=COORD_DEFAULT) const

void	print_shifted (std::ostream &stream, const Coordinate &shift, char delim= '\n', COORD_TYPE mode=COORD_DEFAULT) const

void	print_sites (std::ostream &stream, int space, char delim= '\n', COORD_TYPE mode=COORD_DEFAULT) const

void	print_basis_info (std::ostream &stream, int space, char delim= '\n', COORD_TYPE mode=COORD_DEFAULT) const

void	print_decorated_sites (std::ostream &stream, int space, char delim= '\n', COORD_TYPE mode=COORD_DEFAULT) const

void	merge (const GenericCluster &RHS)
	adds unique points of 'RHS' to (*this) More...

void	merge (const CoordType &RHS)
	Adds new point to cluster, but only if it is unique. More...

GenericCluster &	operator+= (const Coordinate &RHS)
	in=place translation of a cluster More...

GenericCluster &	operator-= (const Coordinate &RHS)

GenericCluster	operator+ (const GenericCluster &RHS)
	create translated cluster More...

bool	operator== (const GenericCluster &RHS) const
	are two clusters identical, to within a permutation More...

bool	is_equivalent (const GenericCluster &test_clust) const
	are two clusters identical, to within permutation and translation More...

bool	is_equivalent (const GenericCluster &test_clust, Coordinate &trans) const
	are two clusters identical, to within permutation and translation translation that maps clusters is stored in 'trans' More...

bool	map_onto (const GenericCluster &test_clust, double tol)
	if is_equivalent(test_clust) is true, return true and map (*this) onto test_clust More...

bool	map_onto (const GenericCluster &test_clust, Coordinate &trans, double tol)

jsonParser &	to_json (jsonParser &json) const
	Write GenericCluster to json. Does not write lattice. More...

void	from_json (const jsonParser &json)

Index	size () const

void	swap (Array< CoordType > &RHS)

CoordType &	at (Index ind)

const CoordType &	at (Index ind) const

const CoordType &	operator[] (Index ind) const

CoordType &	operator[] (Index ind)

CoordType &	back ()

const CoordType &	back () const

CoordTypeconst *	begin () const

CoordType *	begin ()

CoordTypeconst *	cbegin () const

CoordTypeconst *	end () const

CoordType *	end ()

CoordTypeconst *	cend () const

void	pop_back ()

void	remove (Index ind)

void	clear ()

void	resize (Index new_N)

void	resize (Index new_N, const CoordType &fill_val)

void	reserve (Index new_max)

void	sort (const CompareType &comp)

void	sort (Array< Index > &ind_order)

void	sort ()

Array &	append (const Array &new_tail)

Array &	append_unique (const Array &new_tail)

void	swap_elem (Index i, Index j)

Array &	ipermute (const Array< Index > &perm_array)

bool	next_permute ()

ReturnArray< Index >	as_perm_inverse () const

ReturnArray< Index >	as_perm_transform_by (const Array< Index > &trans_perm) const

const CoordType &	max () const

const CoordType &	min () const

ReturnArray< CoordType >	sub_array (Index ind_begin, Index ind_end) const

CoordType	sum () const

bool	is_ascending () const

bool	is_descending () const

bool	is_constant () const

bool	is_permute () const

bool	has_fixed_points () const
	Checks whether any values are equal to their index – only valid for Array<Index> More...

bool	operator== (const Array< CoordType > &RHS) const

bool	operator!= (const Array< CoordType > &RHS) const

bool	operator< (const Array< CoordType > &RHS) const

bool	operator> (const Array< CoordType > &RHS) const

bool	operator<= (const Array< CoordType > &RHS) const

bool	operator>= (const Array< CoordType > &RHS) const

bool	all_in (const Array &superset) const

Index	coincidence (const Array &superset) const

Index	incidences (const CoordType &test_elem) const

Index	find (const CoordType &test_elem) const

Index	reverse_find (const CoordType &test_elem) const
	Same as find, but starts from the last element of the Array. More...

Index	almost_find (const CoordType &test_elem, double tol_val=TOL) const

Index	almost_reverse_find (const CoordType &test_elem, double tol_val=TOL) const
	Same as almost_find, but start from the last element of the Array. More...

bool	contains (const CoordType &test_elem) const

bool	almost_contains (const CoordType &test_elem, double tol_val=TOL) const

void	print_column (std::ostream &stream, const std::string &indent="") const

Static Public Member Functions
static ReturnArray< CoordType >	sequence (const CoordType &initial, const CoordType &final)
	Returns an array with the sequence (initial, ++initial, ..., final), inclusive. More...

static ReturnArray< CoordType >	sequence (const CoordType &initial, const CoordType &increment, const CoordType &final)

Protected Member Functions
SymGroup &	_clust_group ()

SymGroupRep::RemoteHandle &	_permute_rep ()

Private Attributes
Lattice const *	m_lat_ptr

double	m_min_length

double	m_max_length

SymGroup	m_clust_group

SymGroupRep::RemoteHandle	m_permute_rep

Member Typedef Documentation

typedef const CoordType * CASM::Array< CoordType >::const_iterator

inherited

Definition at line 76 of file Array.hh.

typedef CoordType * CASM::Array< CoordType >::iterator

inherited

Definition at line 75 of file Array.hh.

typedef Index CASM::Array< CoordType >::size_type

inherited

Definition at line 74 of file Array.hh.

typedef CoordType CASM::Array< CoordType >::value_type

inherited

Definition at line 73 of file Array.hh.

template<typename CoordType>

typedef CoordType CASM::GenericCluster< CoordType >::WhichCoordType

Definition at line 37 of file Cluster.hh.

typedef Array<CoordType > CASM::Array< CoordType >::X1

inherited

Definition at line 63 of file Array.hh.

typedef Array<X1> CASM::Array< CoordType >::X2

inherited

Definition at line 64 of file Array.hh.

typedef Array<X2> CASM::Array< CoordType >::X3

inherited

Definition at line 65 of file Array.hh.

typedef Array<X3> CASM::Array< CoordType >::X4

inherited

Definition at line 66 of file Array.hh.

typedef Array<X4> CASM::Array< CoordType >::X5

inherited

Definition at line 67 of file Array.hh.

typedef Array<X5> CASM::Array< CoordType >::X6

inherited

Definition at line 68 of file Array.hh.

typedef Array<X6> CASM::Array< CoordType >::X7

inherited

Definition at line 69 of file Array.hh.

typedef Array<X7> CASM::Array< CoordType >::X8

inherited

Definition at line 70 of file Array.hh.

typedef Array<X8> CASM::Array< CoordType >::X9

inherited

Definition at line 71 of file Array.hh.

Constructor & Destructor Documentation

template<typename CoordType >

CASM::GenericCluster< CoordType >::GenericCluster ( const Lattice & init_home )

Definition at line 9 of file Cluster_impl.hh.

Member Function Documentation

template<typename CoordType>

SymGroup& CASM::GenericCluster< CoordType >::_clust_group ( )

inlineprotected

Definition at line 193 of file Cluster.hh.

template<typename CoordType>

SymGroupRep::RemoteHandle& CASM::GenericCluster< CoordType >::_permute_rep ( )

inlineprotected

Definition at line 197 of file Cluster.hh.

bool CASM::Array< CoordType >::all_in ( const Array< CoordType > & superset ) const

inherited

template<typename CoordType >

void CASM::GenericCluster< CoordType >::all_within ( )

Map every point of cluster inside unit cell.

Definition at line 183 of file Cluster_impl.hh.

bool CASM::Array< CoordType >::almost_contains	(	const CoordType &	test_elem,
		double	tol_val = `TOL`
	)		const

inlineinherited

Definition at line 284 of file Array.hh.

Index CASM::Array< CoordType >::almost_find	(	const CoordType &	test_elem,
		double	tol_val = `TOL`
	)		const

inherited

Index CASM::Array< CoordType >::almost_reverse_find	(	const CoordType &	test_elem,
		double	tol_val = `TOL`
	)		const

inherited

Same as almost_find, but start from the last element of the Array.

Array& CASM::Array< CoordType >::append ( const Array< CoordType > & new_tail )

inherited

Array& CASM::Array< CoordType >::append_unique ( const Array< CoordType > & new_tail )

inherited

template<typename CoordType >

GenericCluster< CoordType > & CASM::GenericCluster< CoordType >::apply_sym ( const SymOp & op )

apply symmetry to all points of the cluster

Definition at line 74 of file Cluster_impl.hh.

template<typename CoordType >

GenericCluster< CoordType > & CASM::GenericCluster< CoordType >::apply_sym_no_trans ( const SymOp & op )

apply symmetry to all points of the cluster without translation

Definition at line 85 of file Cluster_impl.hh.

ReturnArray<Index> CASM::Array< CoordType >::as_perm_inverse ( ) const

inherited

Construct permutation that undoes the permutation performed by 'this' Inverse operation is calculated the same, regardless of permutation convention

ReturnArray<Index> CASM::Array< CoordType >::as_perm_transform_by ( const Array< Index > & trans_perm ) const

inherited

Given N distinct objects labeled from 0 to N-1, a permutation 'P_permute' that physically permutes the objects (with labels) in terms of their labels, and a permutation 'L_permute' that permutes their labels only, rewrite 'P_permute' in terms of the relabeling induced by 'L_permute' Rearrange 'this' permutation to form an equivalent permutation for any list that has already been permuted by trans_perm. Does not (nearly certain of this) depend on permutation convention

CoordType & CASM::Array< CoordType >::at ( Index ind )

inlineinherited

Definition at line 157 of file Array.hh.

const CoordType & CASM::Array< CoordType >::at ( Index ind ) const

inlineinherited

Definition at line 162 of file Array.hh.

CoordType & CASM::Array< CoordType >::back ( )

inlineinherited

Definition at line 177 of file Array.hh.

const CoordType & CASM::Array< CoordType >::back ( ) const

inlineinherited

Definition at line 180 of file Array.hh.

CoordType const* CASM::Array< CoordType >::begin ( ) const

inlineinherited

Definition at line 185 of file Array.hh.

CoordType * CASM::Array< CoordType >::begin ( )

inlineinherited

Definition at line 192 of file Array.hh.

template<typename CoordType >

void CASM::GenericCluster< CoordType >::calc_properties ( )

gets max_length and min_length

Definition at line 681 of file Cluster_impl.hh.

template<typename CoordType>

void CASM::GenericCluster< CoordType >::calc_properties ( GenericCluster< CoordType > phenom_clust )

calculate min/max lengths relative the phenom_clust & this cluster

sets max_length based on lengths between sites in the cluster or lengths between sites in the cluster and the phenom_clust
only set min_length based on lengths between sites in the cluster

Definition at line 717 of file Cluster_impl.hh.

CoordType const* CASM::Array< CoordType >::cbegin ( ) const

inlineinherited

Definition at line 189 of file Array.hh.

CoordType const* CASM::Array< CoordType >::cend ( ) const

inlineinherited

Definition at line 201 of file Array.hh.

void CASM::Array< CoordType >::clear ( )

inlineinherited

Definition at line 216 of file Array.hh.

template<typename CoordType>

const SymGroup& CASM::GenericCluster< CoordType >::clust_group ( ) const

inline

Definition at line 46 of file Cluster.hh.

template<typename _CoordType >

std::vector< Permutation > CASM::GenericCluster< _CoordType >::clust_group_permutations ( double tol ) const

Finds the Permutation corresponding to each element of clust_group.

Definition at line 124 of file Cluster_impl.hh.

Index CASM::Array< CoordType >::coincidence ( const Array< CoordType > & superset ) const

inherited

template<typename CoordType>

void CASM::GenericCluster< CoordType >::collect_basis_info ( const Array< CoordType > & basis )

Figure out which basis atoms in basis correspond to the points in cluster (*this)

Definition at line 431 of file Cluster_impl.hh.

template<typename CoordType>

void CASM::GenericCluster< CoordType >::collect_basis_info	(	const Array< CoordType > &	basis,
		const Coordinate &	shift
	)

Figure out which basis atoms in basis correspond to the points in cluster (*this) when cluster is translated by 'shift'

Definition at line 411 of file Cluster_impl.hh.

template<typename CoordType >

bool CASM::GenericCluster< CoordType >::contains ( const GenericCluster< CoordType > & test_cluster ) const

is test_cluster a subcluster of (*this)

Definition at line 235 of file Cluster_impl.hh.

bool CASM::Array< CoordType >::contains ( const CoordType & test_elem ) const

inlineinherited

Definition at line 281 of file Array.hh.

template<typename CoordType>

bool CASM::GenericCluster< CoordType >::contains_periodic	(	const CoordType &	test_coord,
		double	tol
	)		const

Like Array<CoordType>::contains(), but takes periodicity mode into account.

Definition at line 251 of file Cluster_impl.hh.

CoordType const* CASM::Array< CoordType >::end ( ) const

inlineinherited

Definition at line 197 of file Array.hh.

CoordType * CASM::Array< CoordType >::end ( )

inlineinherited

Definition at line 204 of file Array.hh.

template<typename CoordType>

Index CASM::GenericCluster< CoordType >::find	(	const CoordType &	test_elem,
		double	tol
	)		const

is test_cluster a subcluster of (*this), and how do the indices map points of test_cluster

Definition at line 262 of file Cluster_impl.hh.

template<typename CoordType>

bool CASM::GenericCluster< CoordType >::find	(	const GenericCluster< CoordType > &	test_cluster,
		Array< Index > &	index,
		double	tol
	)		const

is test_cluster a subcluster of (*this), and how do the indices map 'index' is populated with the indices of (*this) that correspond to the points of test_cluster

Definition at line 276 of file Cluster_impl.hh.

Index CASM::Array< CoordType >::find ( const CoordType & test_elem ) const

inherited

template<typename CoordType >

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

re-throw exceptions

Definition at line 258 of file Cluster.hh.

template<typename _CoordType >

void CASM::GenericCluster< _CoordType >::generate_clust_group	(	const SymGroup &	super_group,
		std::vector< Permutation > *	perm_array_ptr = `nullptr`,
		double	tol = `TOL`
	)

Finds the sub_group of super_group that is the point group of the cluster.

Definition at line 100 of file Cluster_impl.hh.

template<typename CoordType >

Coordinate CASM::GenericCluster< CoordType >::geometric_center ( ) const

Returns the geometric center of "mass" of a cluster (treats all sites as having equal mass)

Definition at line 220 of file Cluster_impl.hh.

bool CASM::Array< CoordType >::has_fixed_points ( ) const

inherited

Checks whether any values are equal to their index – only valid for Array<Index>

template<typename CoordType>

const Lattice& CASM::GenericCluster< CoordType >::home ( ) const

inline

Definition at line 42 of file Cluster.hh.

template<typename CoordType >

bool CASM::GenericCluster< CoordType >::image_check	(	const Lattice &	cell,
		int	nV = `0`
	)		const

Checks to see if cluster is "compact" relative to (Lattice cell) in other words, period images of the cluster points are farther away than the points themselves. Returns true if cluster is not "compact".

Definition at line 201 of file Cluster_impl.hh.

Index CASM::Array< CoordType >::incidences ( const CoordType & test_elem ) const

inherited

Array& CASM::Array< CoordType >::ipermute ( const Array< Index > & perm_array )

inherited

bool CASM::Array< CoordType >::is_ascending ( ) const

inherited

bool CASM::Array< CoordType >::is_constant ( ) const

inherited

bool CASM::Array< CoordType >::is_descending ( ) const

inherited

template<typename CoordType >

bool CASM::GenericCluster< CoordType >::is_equivalent ( const GenericCluster< CoordType > & test_clust ) const

are two clusters identical, to within permutation and translation

Definition at line 591 of file Cluster_impl.hh.

template<typename CoordType >

bool CASM::GenericCluster< CoordType >::is_equivalent	(	const GenericCluster< CoordType > &	test_clust,
		Coordinate &	trans
	)		const

are two clusters identical, to within permutation and translation translation that maps clusters is stored in 'trans'

Definition at line 608 of file Cluster_impl.hh.

bool CASM::Array< CoordType >::is_permute ( ) const

inherited

Checks that Array contains values from 0 to perm_array.size()-1 and that no value is repeated does not depend on definition of permutation convention

template<typename CoordType >

bool CASM::GenericCluster< CoordType >::map_onto	(	const GenericCluster< CoordType > &	test_clust,
		double	tol
	)

if is_equivalent(test_clust) is true, return true and map (*this) onto test_clust

Definition at line 629 of file Cluster_impl.hh.

template<typename CoordType >

bool CASM::GenericCluster< CoordType >::map_onto	(	const GenericCluster< CoordType > &	test_clust,
		Coordinate &	trans,
		double	tol
	)

if is_equivalent(test_clust) is true, return true and map (*this) onto test_clust translation that maps clusters is stored in 'trans'

Definition at line 654 of file Cluster_impl.hh.

template<typename CoordType >

bool CASM::GenericCluster< CoordType >::map_onto_subcluster	(	const GenericCluster< CoordType > &	pivot,
		double	tol = `TOL`
	)

if pivot is a sub_cluster, return true and translate (*this) by a lattice translation so that the points of 'pivot' are coincident with subcluster points in (*this)

Definition at line 299 of file Cluster_impl.hh.

template<typename CoordType >

bool CASM::GenericCluster< CoordType >::map_onto_subcluster	(	const GenericCluster< CoordType > &	pivot,
		int	num_maps,
		double	tol = `TOL`
	)

Definition at line 355 of file Cluster_impl.hh.

const CoordType & CASM::Array< CoordType >::max ( ) const

inherited

template<typename CoordType>

double CASM::GenericCluster< CoordType >::max_length ( ) const

inline

Definition at line 108 of file Cluster.hh.

template<typename CoordType >

void CASM::GenericCluster< CoordType >::merge ( const GenericCluster< CoordType > & RHS )

adds unique points of 'RHS' to (*this)

Merge adds the unique points of RHS onto the current cluster.

Definition at line 540 of file Cluster_impl.hh.

template<typename CoordType>

void CASM::GenericCluster< CoordType >::merge ( const CoordType & RHS )

Adds new point to cluster, but only if it is unique.

const CoordType & CASM::Array< CoordType >::min ( ) const

inherited

template<typename CoordType>

double CASM::GenericCluster< CoordType >::min_length ( ) const

inline

Definition at line 112 of file Cluster.hh.

bool CASM::Array< CoordType >::next_permute ( )

inherited

bool CASM::Array< CoordType >::operator!= ( const Array< CoordType > & RHS ) const

inlineinherited

Definition at line 260 of file Array.hh.

template<typename CoordType>

GenericCluster CASM::GenericCluster< CoordType >::operator+ ( const GenericCluster< CoordType > & RHS )

create translated cluster

template<typename CoordType >

GenericCluster< CoordType > & CASM::GenericCluster< CoordType >::operator+= ( const Coordinate & RHS )

in=place translation of a cluster

Definition at line 552 of file Cluster_impl.hh.

template<typename CoordType >

GenericCluster< CoordType > & CASM::GenericCluster< CoordType >::operator-= ( const Coordinate & RHS )

Definition at line 561 of file Cluster_impl.hh.

bool CASM::Array< CoordType >::operator< ( const Array< CoordType > & RHS ) const

inherited

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

inlineinherited

Definition at line 265 of file Array.hh.

template<typename CoordType >

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

are two clusters identical, to within a permutation

Definition at line 570 of file Cluster_impl.hh.

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

inherited

bool CASM::Array< CoordType >::operator> ( const Array< CoordType > & RHS ) const

inherited

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

inlineinherited

Definition at line 268 of file Array.hh.

const CoordType & CASM::Array< CoordType >::operator[] ( Index ind ) const

inlineinherited

Definition at line 167 of file Array.hh.

CoordType & CASM::Array< CoordType >::operator[] ( Index ind )

inlineinherited

Definition at line 172 of file Array.hh.

template<typename CoordType >

GenericCluster< CoordType > & CASM::GenericCluster< CoordType >::permute ( const Array< Index > & perm )

permute sites of the cluster, and everything that depends on the site order

Definition at line 55 of file Cluster_impl.hh.

template<typename CoordType >

GenericCluster< CoordType > & CASM::GenericCluster< CoordType >::permute ( const Permutation & perm )

Definition at line 68 of file Cluster_impl.hh.

template<typename CoordType>

const SymGroupRep::RemoteHandle& CASM::GenericCluster< CoordType >::permute_rep ( ) const

inline

Definition at line 50 of file Cluster.hh.

void CASM::Array< CoordType >::pop_back ( )

inlineinherited

Definition at line 212 of file Array.hh.

template<typename CoordType>

void CASM::GenericCluster< CoordType >::prepare_prototype ( )

inline

Performs preparatory steps on prototype before doing Orbit::get_equivalent()

Definition at line 120 of file Cluster.hh.

template<typename CoordType >

void CASM::GenericCluster< CoordType >::print	(	std::ostream &	stream,
		char	delim = `'\n'`,
		COORD_TYPE	mode = `COORD_DEFAULT`
	)		const

Definition at line 756 of file Cluster_impl.hh.

template<typename CoordType >

void CASM::GenericCluster< CoordType >::print_basis_info	(	std::ostream &	stream,
		int	space,
		char	delim = `'\n'`,
		COORD_TYPE	mode = `COORD_DEFAULT`
	)		const

Definition at line 817 of file Cluster_impl.hh.

void CASM::Array< CoordType >::print_column	(	std::ostream &	stream,
		const std::string &	indent = `""`
	)		const

inherited

template<typename CoordType >

void CASM::GenericCluster< CoordType >::print_decorated_sites	(	std::ostream &	stream,
		int	space,
		char	delim = `'\n'`,
		COORD_TYPE	mode = `COORD_DEFAULT`
	)		const

Definition at line 838 of file Cluster_impl.hh.

template<typename CoordType >

void CASM::GenericCluster< CoordType >::print_shifted	(	std::ostream &	stream,
		const Coordinate &	shift,
		char	delim = `'\n'`,
		COORD_TYPE	mode = `COORD_DEFAULT`
	)		const

Definition at line 776 of file Cluster_impl.hh.

template<typename CoordType >

void CASM::GenericCluster< CoordType >::print_sites	(	std::ostream &	stream,
		int	space,
		char	delim = `'\n'`,
		COORD_TYPE	mode = `COORD_DEFAULT`
	)		const

Definition at line 797 of file Cluster_impl.hh.

template<typename CoordType>

void CASM::GenericCluster< CoordType >::push_back ( const CoordType & new_coord )

Definition at line 523 of file Cluster_impl.hh.

template<typename CoordType>

void CASM::GenericCluster< CoordType >::read	(	std::istream &	stream,
		int	num_sites,
		COORD_TYPE	mode,
		bool	SD_is_on
	)

template<typename CoordType >

void CASM::GenericCluster< CoordType >::read	(	std::istream &	stream,
		COORD_TYPE	mode
	)

Reads the cluster.

Reads the cluster in the specified mode

Parameters

stream	Input file stream
mode	Cartesian or fractional mode

Definition at line 457 of file Cluster_impl.hh.

void CASM::Array< CoordType >::remove ( Index ind )

inherited

void CASM::Array< CoordType >::reserve ( Index new_max )

inherited

void CASM::Array< CoordType >::resize ( Index new_N )

inherited

void CASM::Array< CoordType >::resize	(	Index	new_N,
		const CoordType &	fill_val
	)

inherited

Index CASM::Array< CoordType >::reverse_find ( const CoordType & test_elem ) const

inherited

Same as find, but starts from the last element of the Array.

static ReturnArray<CoordType > CASM::Array< CoordType >::sequence	(	const CoordType &	initial,
		const CoordType &	final
	)

staticinherited

Returns an array with the sequence (initial, ++initial, ..., final), inclusive.

Returns an array with the sequence (initial, ++initial, ..., final), inclusive requires that operator<() and operator++() are defined on type T

static ReturnArray<CoordType > CASM::Array< CoordType >::sequence	(	const CoordType &	initial,
		const CoordType &	increment,
		const CoordType &	final
	)

staticinherited

Returns an array with the sequence (initial, initial+increment, ..., final?), inclusive if final is in the sequence requires that operator<() and operator+=() are defined on type T

Returns an array with the sequence (initial, initial+increment, ..., final?), inclusive if final is in the sequence

template<typename CoordType>

void CASM::GenericCluster< CoordType >::set_clust_group ( const Array< SymOp > & new_group )

inline

Definition at line 54 of file Cluster.hh.

template<typename CoordType >

void CASM::GenericCluster< CoordType >::set_lattice	(	const Lattice &	new_home,
		COORD_TYPE	mode
	)

Definition at line 21 of file Cluster_impl.hh.

template<typename CoordType>

void CASM::GenericCluster< CoordType >::set_permute_rep ( SymGroupRepID perm_rep_ID )

inline

Definition at line 58 of file Cluster.hh.

Index CASM::Array< CoordType >::size ( ) const

inlineinherited

Definition at line 145 of file Array.hh.

void CASM::Array< CoordType >::sort ( const CompareType & comp )

inherited

void CASM::Array< CoordType >::sort ( Array< Index > & ind_order )

inherited

void CASM::Array< CoordType >::sort ( )

inherited

ReturnArray<CoordType > CASM::Array< CoordType >::sub_array	(	Index	ind_begin,
		Index	ind_end
	)		const

inherited

CoordType CASM::Array< CoordType >::sum ( ) const

inherited

void CASM::Array< CoordType >::swap ( Array< CoordType > & RHS )

inherited

void CASM::Array< CoordType >::swap_elem	(	Index	i,
		Index	j
	)

inlineinherited

Definition at line 231 of file Array.hh.

template<typename CoordType >

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

Write GenericCluster to json. Does not write lattice.

Definition at line 227 of file Cluster.hh.

template<typename CoordType>

void CASM::GenericCluster< CoordType >::update_data_members ( const BasicStructure< CoordType > & ref_struc )

Definition at line 33 of file Cluster_impl.hh.

template<typename CoordType >

void CASM::GenericCluster< CoordType >::within ( Index pivot_ind = 0 )

Translate entire cluster so that point at(pivot_ind) is inside unit cell.

Definition at line 139 of file Cluster_impl.hh.

template<typename CoordType >

void CASM::GenericCluster< CoordType >::within	(	Index	pivot_ind,
		Coordinate &	trans
	)

Translate entire cluster so that point at(pivot_ind) is inside unit cell.

Parameters

Coordinate trans contains translation used to map within

Definition at line 161 of file Cluster_impl.hh.

Member Data Documentation

template<typename CoordType>

SymGroup CASM::GenericCluster< CoordType >::m_clust_group

private

Definition at line 204 of file Cluster.hh.

template<typename CoordType>

Lattice const* CASM::GenericCluster< CoordType >::m_lat_ptr

private

Definition at line 202 of file Cluster.hh.

template<typename CoordType>

double CASM::GenericCluster< CoordType >::m_max_length

private

Definition at line 203 of file Cluster.hh.

template<typename CoordType>

double CASM::GenericCluster< CoordType >::m_min_length

private

Definition at line 203 of file Cluster.hh.

template<typename CoordType>

SymGroupRep::RemoteHandle CASM::GenericCluster< CoordType >::m_permute_rep

private

Definition at line 205 of file Cluster.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/clusterography/Cluster_impl.hh

Detailed Description

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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