#include <ClusterFunctions.hh>

Inheritance diagram for CASM::GenericOrbit< ClustType >:

Detailed Description

template<typename ClustType>
class CASM::GenericOrbit< ClustType >

GenericOrbit is the set of all clusters that are equivalent with respect to a SymGroup and have at least one point in the unit cell. If two clusters can be mapped onto each other by translation only one of them will be included in orbit (typically)

Definition at line 10 of file ClusterFunctions.hh.

Public Types
typedef Array< ClustType >	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 ClustType	value_type

typedef Index	size_type

typedef ClustType *	iterator

typedef const ClustType *	const_iterator

Public Member Functions
	GenericOrbit (const ClustType &init_prototype)

void	set_lattice (const Lattice &new_home, COORD_TYPE mode)
	calls set_lattice on prototype, and all equivalent clusters More...

void	get_equivalent (const SymGroup &sym_group, double tol)

GenericOrbit &	apply_sym (const SymOp &op)
	Apply symmetry to prototype and all the clusters in the orbit. More...

bool	contains (const ClustType &test_clust, double tol) const

bool	contains (const typename ClustType::WhichCoordType &test_site, double tol) const

Index	find (const ClustType &test_clust, double tol) const
	Same as contains, but returns index of equivalent cluster that maps onto test_clust. More...

Index	find (const ClustType &test_clust, Coordinate &trans, double tol) const

void	collect_basis_info (const Array< typename ClustType::WhichCoordType > &basis, const Coordinate &shift)
	calls collect_basis_info on all clusters in orbit More...

void	collect_basis_info (const Array< typename ClustType::WhichCoordType > &basis)
	calls collect_basis_info on all clusters in orbit, with respect to a translation More...

SymGroupRep const *	get_full_permutation_representation ()
	get permutation representation of every operation in equivalence_map to describe how operations permute site order More...

SymGroupRep const *	get_full_coord_representation ()

double	max_length () const
	return max_length of clusters in Orbit More...

double	min_length () const
	return min_length of clusters in Orbit More...

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

void	read (std::istream &stream, COORD_TYPE mode, const SymGroup &sym_group)
	reads in an Orbit More...

ReturnArray< std::string >	orbit_function_cpp_strings (const Array< FunctionVisitor * > &labelers)
	returns Array of std::string, each of which is More...

ReturnArray< std::string >	flower_function_cpp_strings (const Array< FunctionVisitor * > &labelers, Index nlist_index)
	nlist_index is the index into the nlist for the site the flower centers on More...

ReturnArray< std::string >	delta_occfunc_flower_function_cpp_strings (BasisSet site_basis, const Array< FunctionVisitor * > &labelers, Index nlist_index, Index b_index, Index f_index)

Index	get_index () const

void	set_index (Index ind) const

jsonParser &	to_json (jsonParser &json) const

void	from_json (const jsonParser &json)
	Assumes the prototype lattice is already set. More...

Index	size () const

void	swap (Array< ClustType > &RHS)

ClustType &	at (Index ind)

const ClustType &	at (Index ind) const

const ClustType &	operator[] (Index ind) const

ClustType &	operator[] (Index ind)

ClustType &	back ()

const ClustType &	back () const

ClustTypeconst *	begin () const

ClustType *	begin ()

ClustTypeconst *	cbegin () const

ClustTypeconst *	end () const

ClustType *	end ()

ClustTypeconst *	cend () const

void	push_back (const ClustType &toPush)

void	pop_back ()

void	remove (Index ind)

void	clear ()

void	resize (Index new_N)

void	resize (Index new_N, const ClustType &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 &	permute (const Array< Index > &perm_array)

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 ClustType &	max () const

const ClustType &	min () const

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

ClustType	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< ClustType > &RHS) const

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

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

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

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

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

bool	all_in (const Array &superset) const

Index	coincidence (const Array &superset) const

Index	incidences (const ClustType &test_elem) const

Index	find (const ClustType &test_elem) const

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

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

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

bool	contains (const ClustType &test_elem) const

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

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

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

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

Public Attributes
ClustType	prototype

Array< Array< SymOp > >	equivalence_map

Private Attributes
Index	index
	Linear index of this orbit, when many orbits are stored in a complicated structure (e.g., Orbitree) More...

Index	permute_rep_ID

Index	coord_rep_ID

Array< GenericOrbit * >	sub_cluster
	Pointers to all orbits whose clusters are subclusters of clusters in this orbit. More...

Member Typedef Documentation

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

inherited

Definition at line 76 of file Array.hh.

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

inherited

Definition at line 75 of file Array.hh.

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

inherited

Definition at line 74 of file Array.hh.

typedef ClustType CASM::Array< ClustType >::value_type

inherited

Definition at line 73 of file Array.hh.

typedef Array<ClustType > CASM::Array< ClustType >::X1

inherited

Definition at line 63 of file Array.hh.

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

inherited

Definition at line 64 of file Array.hh.

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

inherited

Definition at line 65 of file Array.hh.

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

inherited

Definition at line 66 of file Array.hh.

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

inherited

Definition at line 67 of file Array.hh.

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

inherited

Definition at line 68 of file Array.hh.

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

inherited

Definition at line 69 of file Array.hh.

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

inherited

Definition at line 70 of file Array.hh.

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

inherited

Definition at line 71 of file Array.hh.

Constructor & Destructor Documentation

template<typename ClustType>

CASM::GenericOrbit< ClustType >::GenericOrbit ( const ClustType & init_prototype )

inline

Definition at line 53 of file Orbit.hh.

Member Function Documentation

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

inherited

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

inlineinherited

Definition at line 284 of file Array.hh.

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

inherited

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

inherited

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

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

inherited

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

inherited

template<typename ClustType >

GenericOrbit< ClustType > & CASM::GenericOrbit< ClustType >::apply_sym ( const SymOp & op )

Apply symmetry to prototype and all the clusters in the orbit.

Definition at line 106 of file Orbit_impl.hh.

ReturnArray<Index> CASM::Array< ClustType >::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< ClustType >::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

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

inlineinherited

Definition at line 157 of file Array.hh.

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

inlineinherited

Definition at line 162 of file Array.hh.

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

inlineinherited

Definition at line 177 of file Array.hh.

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

inlineinherited

Definition at line 180 of file Array.hh.

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

inlineinherited

Definition at line 185 of file Array.hh.

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

inlineinherited

Definition at line 192 of file Array.hh.

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

inlineinherited

Definition at line 189 of file Array.hh.

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

inlineinherited

Definition at line 201 of file Array.hh.

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

inlineinherited

Definition at line 216 of file Array.hh.

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

inherited

template<typename ClustType >

void CASM::GenericOrbit< ClustType >::collect_basis_info	(	const Array< typename ClustType::WhichCoordType > &	basis,
		const Coordinate &	shift
	)

calls collect_basis_info on all clusters in orbit

Definition at line 188 of file Orbit_impl.hh.

template<typename ClustType >

void CASM::GenericOrbit< ClustType >::collect_basis_info ( const Array< typename ClustType::WhichCoordType > & basis )

calls collect_basis_info on all clusters in orbit, with respect to a translation

Definition at line 197 of file Orbit_impl.hh.

template<typename ClustType >

bool CASM::GenericOrbit< ClustType >::contains	(	const ClustType &	test_clust,
		double	tol
	)		const

go through all cluster in orbit array and see if test_clust is among them, to within a lattice translation only translates if the periodicity flag is on

Definition at line 124 of file Orbit_impl.hh.

template<typename ClustType >

bool CASM::GenericOrbit< ClustType >::contains	(	const typename ClustType::WhichCoordType &	test_site,
		double	tol
	)		const

check if test_site is contained in any of the equivalent clusters, to within a lattice translation only translates if the periodicity flag is on

Definition at line 140 of file Orbit_impl.hh.

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

inlineinherited

Definition at line 281 of file Array.hh.

template<typename ClustType >

ReturnArray< std::string > CASM::GenericOrbit< ClustType >::delta_occfunc_flower_function_cpp_strings	(	BasisSet	site_basis,
		const Array< FunctionVisitor * > &	labelers,
		Index	nlist_index,
		Index	b_index,
		Index	f_index
	)

b_index is the basis site index, f_index is the index of the configurational site basis function in Site::occupant_basis nlist_index is the index into the nlist for the site the flower centers on

b_index is the basis site index, f_index is the index of the configurational site basis function in Site::occupant_basis nlist_index is the index of the basis site in the neighbor list

Definition at line 364 of file Orbit_impl.hh.

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

inlineinherited

Definition at line 197 of file Array.hh.

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

inlineinherited

Definition at line 204 of file Array.hh.

template<typename ClustType >

Index CASM::GenericOrbit< ClustType >::find	(	const ClustType &	test_clust,
		double	tol
	)		const

Same as contains, but returns index of equivalent cluster that maps onto test_clust.

Definition at line 156 of file Orbit_impl.hh.

template<typename ClustType >

Index CASM::GenericOrbit< ClustType >::find	(	const ClustType &	test_clust,
		Coordinate &	trans,
		double	tol
	)		const

Same as contains, but returns index of equivalent cluster that maps onto test_clust translation that maps equivalent cluster onto test_clust is stored in 'trans'

Definition at line 172 of file Orbit_impl.hh.

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

inherited

template<typename ClustType >

ReturnArray< std::string > CASM::GenericOrbit< ClustType >::flower_function_cpp_strings	(	const Array< FunctionVisitor * > &	labelers,
		Index	nlist_index
	)

nlist_index is the index into the nlist for the site the flower centers on

nlist_index is the index of the basis site in the neighbor list

Definition at line 312 of file Orbit_impl.hh.

template<typename ClustType >

void CASM::GenericOrbit< ClustType >::from_json ( const jsonParser & json )

Assumes the prototype lattice is already set.

re-throw exceptions

Definition at line 458 of file Orbit_impl.hh.

template<typename ClustType >

void CASM::GenericOrbit< ClustType >::get_equivalent	(	const SymGroup &	sym_group,
		double	tol
	)

Take prototype cluster, find all of the equivalent clusters (fills orbit array) only translates if the periodicity flag is on Also, fill equivalence_map example: GenericOrbit<SiteCluster> my_orbit(my_cluster); //specifies prototype my_orbit.get_equivalent(my_point_group); //maps protype onto all its equivalents

Definition at line 34 of file Orbit_impl.hh.

template<typename ClustType>

SymGroupRep const* CASM::GenericOrbit< ClustType >::get_full_coord_representation ( )

get symmetry representation of every operation in equivalence_map to describe how operations map coordinates at site 'i' of prototype onto coordinates of site 'j' of equivalent cluster

template<typename ClustType>

SymGroupRep const* CASM::GenericOrbit< ClustType >::get_full_permutation_representation ( )

get permutation representation of every operation in equivalence_map to describe how operations permute site order

template<typename ClustType>

Index CASM::GenericOrbit< ClustType >::get_index ( ) const

inline

Definition at line 121 of file Orbit.hh.

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

inherited

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

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

bool CASM::Array< ClustType >::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

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

inherited

template<typename ClustType>

double CASM::GenericOrbit< ClustType >::max_length ( ) const

inline

return max_length of clusters in Orbit

Definition at line 96 of file Orbit.hh.

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

inherited

template<typename ClustType>

double CASM::GenericOrbit< ClustType >::min_length ( ) const

inline

return min_length of clusters in Orbit

Definition at line 100 of file Orbit.hh.

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

inherited

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

inlineinherited

Definition at line 260 of file Array.hh.

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

inherited

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

inlineinherited

Definition at line 265 of file Array.hh.

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

inherited

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

inherited

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

inlineinherited

Definition at line 268 of file Array.hh.

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

inlineinherited

Definition at line 167 of file Array.hh.

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

inlineinherited

Definition at line 172 of file Array.hh.

template<typename ClustType >

ReturnArray< std::string > CASM::GenericOrbit< ClustType >::orbit_function_cpp_strings ( const Array< FunctionVisitor * > & labelers )

returns Array of std::string, each of which is

Definition at line 278 of file Orbit_impl.hh.

Array& CASM::Array< ClustType >::permute ( const Array< Index > & perm_array )

inherited

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

inlineinherited

Definition at line 212 of file Array.hh.

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

inherited

void CASM::Array< ClustType >::push_back ( const ClustType & toPush )

inherited

template<typename ClustType>

void CASM::GenericOrbit< ClustType >::read	(	std::istream &	stream,
		int	num_sites,
		COORD_TYPE	mode
	)

template<typename ClustType >

void CASM::GenericOrbit< ClustType >::read	(	std::istream &	stream,
		COORD_TYPE	mode,
		const SymGroup &	sym_group
	)

reads in an Orbit

Reads the orbit in the specified mode.

Parameters

stream	Input file stream
mode	Cartesian or fractional mode

Definition at line 213 of file Orbit_impl.hh.

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

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

void CASM::GenericOrbit< ClustType >::set_index ( Index ind ) const

inline

Definition at line 126 of file Orbit.hh.

template<typename ClustType >

void CASM::GenericOrbit< ClustType >::set_lattice	(	const Lattice &	new_home,
		COORD_TYPE	mode
	)

calls set_lattice on prototype, and all equivalent clusters

Definition at line 12 of file Orbit_impl.hh.

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

inlineinherited

Definition at line 145 of file Array.hh.

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inlineinherited

Definition at line 231 of file Array.hh.

template<typename ClustType >

jsonParser & CASM::GenericOrbit< ClustType >::to_json ( jsonParser & json ) const

Definition at line 424 of file Orbit_impl.hh.

Member Data Documentation

template<typename ClustType>

Index CASM::GenericOrbit< ClustType >::coord_rep_ID

private

Definition at line 36 of file Orbit.hh.

template<typename ClustType>

Array< Array<SymOp> > CASM::GenericOrbit< ClustType >::equivalence_map

equivalence_map[i][j] is a symmetry operation that maps 'prototype' onto cluster 'i' 'j' indexes ALL the symmetry operations that perform this map

Definition at line 51 of file Orbit.hh.

template<typename ClustType>

Index CASM::GenericOrbit< ClustType >::index

mutableprivate

Linear index of this orbit, when many orbits are stored in a complicated structure (e.g., Orbitree)

Definition at line 35 of file Orbit.hh.

template<typename ClustType>

Index CASM::GenericOrbit< ClustType >::permute_rep_ID

private

Definition at line 36 of file Orbit.hh.

template<typename ClustType>

ClustType CASM::GenericOrbit< ClustType >::prototype

One example of the clusters contained in this orbit All clusters in the Orbit are equivalent to 'prototype' by symmetry

Definition at line 47 of file Orbit.hh.

template<typename ClustType>

Array<GenericOrbit *> CASM::GenericOrbit< ClustType >::sub_cluster

private

Pointers to all orbits whose clusters are subclusters of clusters in this orbit.

Definition at line 38 of file Orbit.hh.

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

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clusterography/ClusterFunctions.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clusterography/Orbit.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clusterography/Orbit_impl.hh

Detailed Description

template<typename ClustType> class CASM::GenericOrbit< ClustType >

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<typename ClustType>
class CASM::GenericOrbit< ClustType >