#include <SiteCluster.hh>

Inheritance diagram for CASM::SiteCluster:

Detailed Description

Definition at line 20 of file SiteCluster.hh.

Public Types
typedef Site	WhichCoordType

typedef Array< Site >	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 Site	value_type

typedef Index	size_type

typedef Site *	iterator

typedef const Site *	const_iterator

Public Member Functions
	SiteCluster (const Lattice &init_home)

SiteCluster &	permute (const Array< Index > &iperm)

SiteCluster &	permute (const Permutation &perm)

SiteCluster &	apply_sym (const SymOp &op)

SiteCluster &	apply_sym_no_trans (const SymOp &op)

void	push_back (const Site &new_site)

void	set_nlist_inds (const Array< Index > &new_indices)

ReturnArray< Index >	nlist_inds () const
	Easily collect the current nlist_inds of the cluster's sites. More...

const Array< Array< Index > > &	trans_nlists () const
	Access and assign trans_nlists. More...

const Array< Index > &	trans_nlist (Index i) const

void	add_trans_nlist (const Array< Index > &new_nlist)

void	generate_clust_basis (multivector< BasisSet const * >::X< 2 > const &local_args, std::vector< BasisSet const * > const &global_args, Index max_poly_order=-1)

void	decorate (const Array< int > decor)

ReturnArray< Array< int > >	get_decor_map () const

ReturnArray< Array< int > >	get_full_decor_map () const

ReturnArray< SiteCluster >	get_decorations (const Array< Array< int > > &dmap) const

ReturnArray< int >	get_occ_array (const Array< int > &bitstring) const
	Extracts bits in bitstring corresponding to the cluster and returns them as an array. More...

void	print_clust_basis (std::ostream &stream, Index begin_ind=0, int space=18, char delim=0, COORD_TYPE mode=COORD_DEFAULT) const

jsonParser &	to_json (jsonParser &json) const

void	from_json (const jsonParser &json)

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	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< Site > &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...

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< Site > 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 (const Site &test_elem) const

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

Index	find (const Site &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...

Index	find (const Site &test_elem) const

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< Site > &basis)
	Figure out which basis atoms in basis correspond to the points in cluster (*this) More...

void	collect_basis_info (const Array< Site > &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 Site &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	operator== (const Array< Site > &RHS) const

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)

Index	size () const

void	swap (Array< Site > &RHS)

Site &	at (Index ind)

const Site &	at (Index ind) const

const Site &	operator[] (Index ind) const

Site &	operator[] (Index ind)

Site &	back ()

const Site &	back () const

Siteconst *	begin () const

Site *	begin ()

Siteconst *	cbegin () const

Siteconst *	end () const

Site *	end ()

Siteconst *	cend () const

void	pop_back ()

void	remove (Index ind)

void	clear ()

void	resize (Index new_N)

void	resize (Index new_N, const Site &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 Site &	max () const

const Site &	min () const

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

Site	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< Site > &RHS) const

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

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

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

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

bool	all_in (const Array &superset) const

Index	coincidence (const Array &superset) const

Index	incidences (const Site &test_elem) const

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

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

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

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

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

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

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

Public Attributes
BasisSet	clust_basis

Protected Member Functions
SymGroup &	_clust_group ()

SymGroupRep::RemoteHandle &	_permute_rep ()

Private Attributes
Array< Array< Index > >	m_trans_nlist_inds

Member Typedef Documentation

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

inherited

Definition at line 76 of file Array.hh.

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

inherited

Definition at line 75 of file Array.hh.

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

inherited

Definition at line 74 of file Array.hh.

typedef Site CASM::Array< Site >::value_type

inherited

Definition at line 73 of file Array.hh.

typedef Site CASM::GenericCluster< Site >::WhichCoordType

inherited

Definition at line 37 of file Cluster.hh.

typedef Array<Site > CASM::Array< Site >::X1

inherited

Definition at line 63 of file Array.hh.

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

inherited

Definition at line 64 of file Array.hh.

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

inherited

Definition at line 65 of file Array.hh.

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

inherited

Definition at line 66 of file Array.hh.

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

inherited

Definition at line 67 of file Array.hh.

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

inherited

Definition at line 68 of file Array.hh.

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

inherited

Definition at line 69 of file Array.hh.

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

inherited

Definition at line 70 of file Array.hh.

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

inherited

Definition at line 71 of file Array.hh.

Constructor & Destructor Documentation

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

Definition at line 6 of file SiteCluster.cc.

Member Function Documentation

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

inlineprotectedinherited

Definition at line 193 of file Cluster.hh.

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

inlineprotectedinherited

Definition at line 197 of file Cluster.hh.

void CASM::SiteCluster::add_trans_nlist ( const Array< Index > & new_nlist )

Definition at line 55 of file SiteCluster.cc.

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

inherited

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

inherited

Map every point of cluster inside unit cell.

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

inlineinherited

Definition at line 284 of file Array.hh.

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

inherited

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

inherited

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

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

inherited

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

inherited

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

Definition at line 318 of file SiteCluster.cc.

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

Definition at line 289 of file SiteCluster.cc.

ReturnArray<Index> CASM::Array< Site >::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< Site >::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

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

inlineinherited

Definition at line 157 of file Array.hh.

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

inlineinherited

Definition at line 162 of file Array.hh.

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

inlineinherited

Definition at line 177 of file Array.hh.

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

inlineinherited

Definition at line 180 of file Array.hh.

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

inlineinherited

Definition at line 185 of file Array.hh.

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

inlineinherited

Definition at line 192 of file Array.hh.

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

inherited

gets max_length and min_length

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

inherited

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

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

inlineinherited

Definition at line 189 of file Array.hh.

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

inlineinherited

Definition at line 201 of file Array.hh.

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

inlineinherited

Definition at line 216 of file Array.hh.

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

inlineinherited

Definition at line 46 of file Cluster.hh.

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

inherited

Finds the Permutation corresponding to each element of clust_group.

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

inherited

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

inherited

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

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

inherited

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

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

inherited

is test_cluster a subcluster of (*this)

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

inlineinherited

Definition at line 281 of file Array.hh.

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

inherited

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

void CASM::SiteCluster::decorate ( const Array< int > decor )

inline

Definition at line 75 of file SiteCluster.hh.

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

inlineinherited

Definition at line 197 of file Array.hh.

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

inlineinherited

Definition at line 204 of file Array.hh.

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

inherited

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

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

inherited

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

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

inherited

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

re-throw exceptions

Definition at line 381 of file SiteCluster.cc.

void CASM::SiteCluster::generate_clust_basis	(	multivector< BasisSet const * >::X< 2 > const &	local_args,
		std::vector< BasisSet const * > const &	global_args,
		Index	max_poly_order = `-1`
	)

Definition at line 95 of file SiteCluster.cc.

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

inherited

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

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

inherited

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

ReturnArray< Array< int > > CASM::SiteCluster::get_decor_map ( ) const

Definition at line 154 of file SiteCluster.cc.

ReturnArray< SiteCluster > CASM::SiteCluster::get_decorations ( const Array< Array< int > > & dmap ) const

Definition at line 256 of file SiteCluster.cc.

ReturnArray< Array< int > > CASM::SiteCluster::get_full_decor_map ( ) const

Definition at line 205 of file SiteCluster.cc.

ReturnArray< int > CASM::SiteCluster::get_occ_array ( const Array< int > & bitstring ) const

Extracts bits in bitstring corresponding to the cluster and returns them as an array.

Definition at line 304 of file SiteCluster.cc.

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

inherited

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

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

inlineinherited

Definition at line 42 of file Cluster.hh.

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

inherited

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".

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

are two clusters identical, to within permutation and translation

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

inherited

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

bool CASM::Array< Site >::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

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

inherited

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

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

inherited

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

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

inherited

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)

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

inherited

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

inherited

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

inlineinherited

Definition at line 108 of file Cluster.hh.

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

inherited

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

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

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

inherited

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

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

inherited

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

inlineinherited

Definition at line 112 of file Cluster.hh.

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

inherited

ReturnArray< Index > CASM::SiteCluster::nlist_inds ( ) const

Easily collect the current nlist_inds of the cluster's sites.

Definition at line 18 of file SiteCluster.cc.

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

inlineinherited

Definition at line 260 of file Array.hh.

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

inherited

create translated cluster

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

inherited

in=place translation of a cluster

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

inherited

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

inherited

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

inlineinherited

Definition at line 265 of file Array.hh.

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

inherited

are two clusters identical, to within a permutation

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

inherited

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

inherited

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

inlineinherited

Definition at line 268 of file Array.hh.

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

inlineinherited

Definition at line 167 of file Array.hh.

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

inlineinherited

Definition at line 172 of file Array.hh.

SiteCluster & CASM::SiteCluster::permute ( const Array< Index > & iperm )

Definition at line 276 of file SiteCluster.cc.

SiteCluster & CASM::SiteCluster::permute ( const Permutation & perm )

Definition at line 284 of file SiteCluster.cc.

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

inlineinherited

Definition at line 50 of file Cluster.hh.

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

inlineinherited

Definition at line 212 of file Array.hh.

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

inlineinherited

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

Definition at line 120 of file Cluster.hh.

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

inherited

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

inherited

void CASM::SiteCluster::print_clust_basis	(	std::ostream &	stream,
		Index	begin_ind = `0`,
		int	space = `18`,
		char	delim = `0`,
		COORD_TYPE	mode = `COORD_DEFAULT`
	)		const

Print cluster with basis_index and nlist_index (from 0 to size()-1), followed by cluster basis functions Functions are labeled {i}, starting from i =

Parameters

begin_ind

Definition at line 325 of file SiteCluster.cc.

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

inherited

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

inherited

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

inherited

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

inherited

void CASM::SiteCluster::push_back ( const Site & new_site )

Definition at line 11 of file SiteCluster.cc.

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

inherited

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

inherited

Reads the cluster.

Reads the cluster in the specified mode

Parameters

stream	Input file stream
mode	Cartesian or fractional mode

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

static ReturnArray<Site > CASM::Array< Site >::sequence	(	const Site &	initial,
		const Site &	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<Site > CASM::Array< Site >::sequence	(	const Site &	initial,
		const Site &	increment,
		const Site &	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

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

inlineinherited

Definition at line 54 of file Cluster.hh.

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

inherited

void CASM::SiteCluster::set_nlist_inds ( const Array< Index > & new_indices )

Use this method (and only this method) to set the nlist ind of each site it automatically reassigns DoF IDs for the associated basis functions.

Definition at line 27 of file SiteCluster.cc.

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

inlineinherited

Definition at line 58 of file Cluster.hh.

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

inlineinherited

Definition at line 145 of file Array.hh.

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inlineinherited

Definition at line 231 of file Array.hh.

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

Definition at line 357 of file SiteCluster.cc.

const Array< Index > & CASM::SiteCluster::trans_nlist ( Index i ) const

Definition at line 49 of file SiteCluster.cc.

const Array< Array< Index > > & CASM::SiteCluster::trans_nlists ( ) const

Access and assign trans_nlists.

Definition at line 43 of file SiteCluster.cc.

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

inherited

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

inherited

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

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

inherited

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

Parameters

Coordinate trans contains translation used to map within

Member Data Documentation

BasisSet CASM::SiteCluster::clust_basis

Definition at line 22 of file SiteCluster.hh.

Array<Array<Index> > CASM::SiteCluster::m_trans_nlist_inds

private

Definition at line 64 of file SiteCluster.hh.

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

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clusterography/SiteCluster.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/clusterography/SiteCluster.cc

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation