#include <Clex.hh>

Inheritance diagram for CASM::GenericOrbitree< ClustType >:

Detailed Description

template<typename ClustType>
singleton CASM::GenericOrbitree< ClustType >

Definition at line 13 of file Clex.hh.

Public Types
typedef Array < GenericOrbitBranch < 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 GenericOrbitBranch < ClustType >	value_type

typedef Index	size_type

typedef GenericOrbitBranch < ClustType > *	iterator

typedef const GenericOrbitBranch< ClustType > *	const_iterator

Public Member Functions
	GenericOrbitree (const Lattice &t_lat, double _tol)

	GenericOrbitree (const GenericOrbitree< ClustType > &starttree)

double	tol () const
	Access orbitree tolerance. More...

GenericOrbit< ClustType > &	orbit (Index np, Index no)
	Access orbits using 2-D indexing. More...

const GenericOrbit< ClustType > &	orbit (Index np, Index no) const

const ClustType &	prototype (Index np, Index no) const
	Access prototype of orbit (np, no) More...

ClustType &	prototype (Index np, Index no)

const ClustType &	equiv (Index np, Index no, Index ne) const
	Access equivalent cluster 'ne' of orbit (np, no) More...

ClustType &	equiv (Index np, Index no, Index ne)

Index	size (Index np) const
	Number of orbits in OrbitBranch 'np'. More...

Index	size (Index np, Index no) const
	Number of equivalent clusters in Orbit (np, no) More...

Index	basis_set_size () const
	Count number of basis functions at each orbit and sum result. More...

const jsonParser &	bspecs () const

void	set_bspecs (const jsonParser &_bspecs)

void	resize (Index NP)
	Initialize NP orbitbranches in the Orbitree. Any existing orbits get deleted. More...

void	push_back (const GenericOrbit< ClustType > &new_orbit)

void	push_back (const GenericOrbitBranch< ClustType > &new_branch)
	push_back new OrbitBranch. Verifies that new branch uses this->lattice as home lattice More...

void	set_lattice (const Lattice &new_lat, COORD_TYPE mode)
	sets lattice=new_lat and also updates all OrbitBranches, Orbits, and Clusters More...

void	get_index () const
	Populates 'index', 'index_to_row' and 'index_to_column' Arrays. More...

void	sort ()
	Calls 'sort()' on each OrbitBranch to sort Orbits by lengthscale. More...

void	sort (Index np)
	Calls 'sort()' on the np OrbitBranch. More...

void	collect_basis_info (const Structure &struc)

void	get_s2s_vec ()
	Call get_s2s_vec on all clusters in orbitree. More...

void	generate_clust_bases (std::vector< BasisSet const * > const &global_args, Index max_poly_order=-1)
	get clust_basis for all equivalent clusters More...

void	generate_clust_bases (Index max_poly_order=-1)

Index	find (const ClustType &test_clust) const
	If cluster/orbit exists in current orbitree, return its linear index; else, return number of orbits in orbitree. More...

Index	find (const GenericOrbit< ClustType > &test_orbit) const

Index	find (const ClustType &test_clust, Index nb) const

bool	contains (const ClustType &test_clust)
	If cluster exists in current orbitree, return true. More...

bool	contains (const GenericOrbit< ClustType > &test_orbit)
	If orbit exists in current orbitree, return true. More...

void	generate_orbitree (const Structure &prim, bool verbose=false)

void	generate_orbitree_TB (const Structure &prim)

void	generate_orbitree (const Structure &prim, const int maxClust)

void	generate_orbitree_neighbour (const Structure &prim, const Array< int > maxNeighbour)

void	generate_decorated_orbitree (const GenericOrbitree< ClustType > &in_tree, const SymGroup &symgroup, PERIODICITY_TYPE ptype, bool full_decor=false)

void	generate_hop_orbitree (const GenericOrbitree< SiteCluster > &in_tree, const Structure &prim)

void	generate_orbitree_from_proto_file (std::string filename, const SymGroup &sym_group, PERIODICITY_TYPE ptype)

void	generate_in_cell (const Structure &prim, const Lattice &cell, int num_images=0)

void	get_clusters_by_site (const GenericOrbitree< ClustType > &in_tree, GenericOrbitree< ClustType > &out_tree, int num_sites)

void	get_hierarchy () const

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

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

void	read_CSPECS (std::istream &stream)

void	print (std::ostream &stream) const

void	write_full_clust (std::string file) const

void	write_proto_clust (std::string file) const

void	write_full_decorated_clust (std::string file) const

void	write_proto_decorated_clust (std::string file) const

void	print_full_clust (std::ostream &out) const

void	print_full_basis_info (std::ostream &out) const

void	print_proto_clust (std::ostream &out) const

void	print_proto_clust_funcs (std::ostream &out) const

void	print_full_decorated_clust (std::ostream &out) const

void	print_proto_decorated_clust (std::ostream &out) const

void	write_eci_in (std::string filename) const

void	print_eci_in (std::ostream &out) const

void	get_dynamical_matrix (MatrixXcd &dmat, const Coordinate &k, Index bands_per_site)

void	apply_sym (const SymOp &op)

template<class PhenomType >
void	generate_local_orbitree (const Structure &prim, const PhenomType &tmp_phenom_clust, bool include_phenom_clust_sites)
	Constructs a local orbitree about a Phenom Cluster, given a Structure. More...

void	trans_and_expand (const Array< Coordinate > &prim_grid, bool override=0)

GenericOrbitree< ClustType > &	operator= (const GenericOrbitree< ClustType > &RHS)

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

void	read_orbitree_from_json (const std::string &json_file_name, const SymGroup &sym_group, const Structure &ref_struc)

bool	read_custom_clusters_from_json (const jsonParser &json, const Structure &struc, const SymGroup &sym_group, bool verbose=false)
	Add more orbits to Orbitree based on JSON input. More...

void	add_subclusters (const ClustType &big_clust, const Structure &prim, bool verbose=false)
	Adding in subclusters of a specific cluster into *this Orbitree. More...

const GenericOrbitBranch < ClustType > &	asym_unit () const

Index	size () const

void	swap (Array< GenericOrbitBranch< ClustType > > &RHS)

GenericOrbitBranch< ClustType > &	at (Index ind)

const GenericOrbitBranch < ClustType > &	at (Index ind) const

const GenericOrbitBranch < ClustType > &	operator[] (Index ind) const

GenericOrbitBranch< ClustType > &	operator[] (Index ind)

GenericOrbitBranch< ClustType > &	back ()

const GenericOrbitBranch < ClustType > &	back () const

GenericOrbitBranch< ClustType > const *	begin () const

GenericOrbitBranch< ClustType > *	begin ()

GenericOrbitBranch< ClustType > const *	cbegin () const

GenericOrbitBranch< ClustType > const *	end () const

GenericOrbitBranch< ClustType > *	end ()

GenericOrbitBranch< ClustType > const *	cend () const

void	pop_back ()

void	remove (Index ind)

void	clear ()

void	resize (Index new_N, const GenericOrbitBranch< ClustType > &fill_val)

void	reserve (Index new_max)

void	sort (const CompareType &comp)

void	sort (Array< Index > &ind_order)

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 GenericOrbitBranch < ClustType > &	max () const

const GenericOrbitBranch < ClustType > &	min () const

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

GenericOrbitBranch< 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< GenericOrbitBranch< ClustType > > &RHS) const

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

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

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

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

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

bool	all_in (const Array &superset) const

Index	coincidence (const Array &superset) const

Index	incidences (const GenericOrbitBranch< ClustType > &test_elem) const

Index	find (const GenericOrbitBranch< ClustType > &test_elem) const

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

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

Index	almost_reverse_find (const GenericOrbitBranch< 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 GenericOrbitBranch< ClustType > &test_elem) const

bool	almost_contains (const GenericOrbitBranch< 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 < GenericOrbitBranch < ClustType > >	sequence (const GenericOrbitBranch< ClustType > &initial, const GenericOrbitBranch< ClustType > &final)
	Returns an array with the sequence (initial, ++initial, ..., final), inclusive. More...

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

Public Attributes
Lattice	lattice

double	m_tol

Index	max_num_sites

Index	min_num_components

Array< double >	max_length

double	min_length

Array< int >	num_clusts
	we don't use num_clusts yet. It might be a better way to specify how many clusters to enumerate More...

Array< int >	index_to_row

Array< int >	index_to_column

Array< Array< int > >	index

Index	Norbits

Array< Array< int > >	subcluster

Private Member Functions
void	_generate_asym_unit (const Structure &prim)

void	_populate_site_bases ()

const GenericOrbitBranch < ClustType > &	_asym_unit () const

Private Attributes
GenericOrbitBranch< ClustType >	m_asym_unit

Array< Array< Index > >	m_b2asym

jsonParser	m_bspecs

Member Typedef Documentation

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

inherited

Definition at line 76 of file Array.hh.

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

inherited

Definition at line 75 of file Array.hh.

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

inherited

Definition at line 74 of file Array.hh.

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

inherited

Definition at line 73 of file Array.hh.

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

inherited

Definition at line 63 of file Array.hh.

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

inherited

Definition at line 64 of file Array.hh.

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

inherited

Definition at line 65 of file Array.hh.

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

inherited

Definition at line 66 of file Array.hh.

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

inherited

Definition at line 67 of file Array.hh.

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

inherited

Definition at line 68 of file Array.hh.

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

inherited

Definition at line 69 of file Array.hh.

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

inherited

Definition at line 70 of file Array.hh.

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

inherited

Definition at line 71 of file Array.hh.

Constructor & Destructor Documentation

template<typename ClustType>

CASM::GenericOrbitree< ClustType >::GenericOrbitree	(	const Lattice &	t_lat,
		double	_tol
	)

inline

phenom_clust is the 'phenomenal cluster' around which local clusters are obtained When generating a local orbitree, the symmetry properties of phenom_cluster are used BP- Now phenom_clust is only a temporary object in generate_local_orbitree()

Definition at line 77 of file Orbitree.hh.

template<typename ClustType >

CASM::GenericOrbitree< ClustType >::GenericOrbitree ( const GenericOrbitree< ClustType > & starttree )

Definition at line 10 of file Orbitree_impl.hh.

Member Function Documentation

template<typename ClustType>

const GenericOrbitBranch<ClustType>& CASM::GenericOrbitree< ClustType >::_asym_unit ( ) const

inlineprivate

Definition at line 234 of file Orbitree.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::_generate_asym_unit ( const Structure & prim )

private

Definition at line 2528 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::_populate_site_bases ( )

private

Definition at line 2554 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::add_subclusters	(	const ClustType &	big_clust,
		const Structure &	prim,
		bool	verbose = `false`
	)

Adding in subclusters of a specific cluster into *this Orbitree.

Definition at line 2407 of file Orbitree_impl.hh.

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

inherited

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

inlineinherited

Definition at line 284 of file Array.hh.

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

inherited

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

inherited

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

inherited

template<typename ClustType >

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

Definition at line 2112 of file Orbitree_impl.hh.

ReturnArray<Index> CASM::Array< GenericOrbitBranch< 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< GenericOrbitBranch< 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

template<typename ClustType>

const GenericOrbitBranch<ClustType>& CASM::GenericOrbitree< ClustType >::asym_unit ( ) const

inline

Definition at line 227 of file Orbitree.hh.

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

inlineinherited

Definition at line 157 of file Array.hh.

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

inlineinherited

Definition at line 162 of file Array.hh.

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

inlineinherited

Definition at line 177 of file Array.hh.

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

inlineinherited

Definition at line 180 of file Array.hh.

template<typename ClustType >

Index CASM::GenericOrbitree< ClustType >::basis_set_size ( ) const

Count number of basis functions at each orbit and sum result.

Definition at line 104 of file Orbitree_impl.hh.

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

inlineinherited

Definition at line 185 of file Array.hh.

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

inlineinherited

Definition at line 192 of file Array.hh.

template<typename ClustType>

const jsonParser& CASM::GenericOrbitree< ClustType >::bspecs ( ) const

inline

Definition at line 104 of file Orbitree.hh.

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

inlineinherited

Definition at line 189 of file Array.hh.

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

inlineinherited

Definition at line 201 of file Array.hh.

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

inlineinherited

Definition at line 216 of file Array.hh.

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

inherited

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::collect_basis_info ( const Structure & struc )

Set basis_ind() of each site of each cluster in GenericOrbitree<ClustType> using the order of basis sites in 'struc'

Definition at line 223 of file Orbitree_impl.hh.

template<typename ClustType >

bool CASM::GenericOrbitree< ClustType >::contains ( const ClustType & test_clust )

If cluster exists in current orbitree, return true.

Definition at line 300 of file Orbitree_impl.hh.

template<typename ClustType>

bool CASM::GenericOrbitree< ClustType >::contains ( const GenericOrbit< ClustType > & test_orbit )

If orbit exists in current orbitree, return true.

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

inlineinherited

Definition at line 281 of file Array.hh.

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

inlineinherited

Definition at line 197 of file Array.hh.

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

inlineinherited

Definition at line 204 of file Array.hh.

template<typename ClustType >

const ClustType & CASM::GenericOrbitree< ClustType >::equiv	(	Index	np,
		Index	no,
		Index	ne
	)		const

Access equivalent cluster 'ne' of orbit (np, no)

Definition at line 75 of file Orbitree_impl.hh.

template<typename ClustType >

ClustType & CASM::GenericOrbitree< ClustType >::equiv	(	Index	np,
		Index	no,
		Index	ne
	)

Definition at line 82 of file Orbitree_impl.hh.

template<typename ClustType >

Index CASM::GenericOrbitree< ClustType >::find ( const ClustType & test_clust ) const

If cluster/orbit exists in current orbitree, return its linear index; else, return number of orbits in orbitree.

Definition at line 233 of file Orbitree_impl.hh.

template<typename ClustType >

Index CASM::GenericOrbitree< ClustType >::find ( const GenericOrbit< ClustType > & test_orbit ) const

Definition at line 275 of file Orbitree_impl.hh.

template<typename ClustType >

Index CASM::GenericOrbitree< ClustType >::find	(	const ClustType &	test_clust,
		Index	nb
	)		const

Definition at line 260 of file Orbitree_impl.hh.

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

inherited

template<typename ClustType >

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

Assumes the pivot lattice is already set.

re-throw exceptions

Definition at line 2469 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::generate_clust_bases	(	std::vector< BasisSet const * > const &	global_args,
		Index	max_poly_order = `-1`
	)

get clust_basis for all equivalent clusters

Definition at line 190 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::generate_clust_bases ( Index max_poly_order = -1 )

Definition at line 183 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::generate_decorated_orbitree	(	const GenericOrbitree< ClustType > &	in_tree,
		const SymGroup &	symgroup,
		PERIODICITY_TYPE	ptype,
		bool	full_decor = `false`
	)

Definition at line 879 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::generate_hop_orbitree	(	const GenericOrbitree< SiteCluster > &	in_tree,
		const Structure &	prim
	)

Definition at line 953 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::generate_in_cell	(	const Structure &	prim,
		const Lattice &	cell,
		int	num_images = `0`
	)

Definition at line 1246 of file Orbitree_impl.hh.

template<typename ClustType >

template<class PhenomType >

void CASM::GenericOrbitree< ClustType >::generate_local_orbitree	(	const Structure &	prim,
		const PhenomType &	tmp_phenom_clust,
		bool	include_phenom_clust_sites
	)

Constructs a local orbitree about a Phenom Cluster, given a Structure.

First finds the point clusters, then pair clusters, then triplets, etc.
If 'include_phenom_clust_sites' is true, then clusters include sites in the phenom_clust, else they are not.
Sets the Orbitrees 'phenom_clust' to 'tmp_phenom_clust'

make an orbitree of local clusters around the cluster 'clust' in the structure 'prim' must set GenericOrbitree<ClustType>::max_num_sites and GenericOrbitree<ClustType>::max_length prior to calling GenericOrbitree<ClustType>::generate_local_orbitree

Definition at line 1880 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::generate_orbitree	(	const Structure &	prim,
		bool	verbose = `false`
	)

Definition at line 355 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::generate_orbitree	(	const Structure &	prim,
		const int	maxClust
	)

Definition at line 497 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::generate_orbitree_from_proto_file	(	std::string	filename,
		const SymGroup &	sym_group,
		PERIODICITY_TYPE	ptype
	)

Not sure how to treat this

Definition at line 1127 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::generate_orbitree_neighbour	(	const Structure &	prim,
		const Array< int >	maxNeighbour
	)

Definition at line 684 of file Orbitree_impl.hh.

template<typename ClustType>

void CASM::GenericOrbitree< ClustType >::generate_orbitree_TB ( const Structure & prim )

template<typename ClustType>

void CASM::GenericOrbitree< ClustType >::get_clusters_by_site	(	const GenericOrbitree< ClustType > &	in_tree,
		GenericOrbitree< ClustType > &	out_tree,
		int	num_sites
	)

template<typename ClustType>

void CASM::GenericOrbitree< ClustType >::get_dynamical_matrix	(	MatrixXcd &	dmat,
		const Coordinate &	k,
		Index	bands_per_site
	)

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::get_hierarchy ( ) const

Definition at line 1350 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::get_index ( ) const

Populates 'index', 'index_to_row' and 'index_to_column' Arrays.

Definition at line 312 of file Orbitree_impl.hh.

template<typename ClustType>

void CASM::GenericOrbitree< ClustType >::get_s2s_vec ( )

Call get_s2s_vec on all clusters in orbitree.

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

inherited

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

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inlineinherited

Definition at line 260 of file Array.hh.

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

inherited

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

inlineinherited

Definition at line 265 of file Array.hh.

template<typename ClustType >

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

Definition at line 1516 of file Orbitree_impl.hh.

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

inherited

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

inherited

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

inlineinherited

Definition at line 268 of file Array.hh.

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

inlineinherited

Definition at line 167 of file Array.hh.

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

inlineinherited

Definition at line 172 of file Array.hh.

template<typename ClustType >

GenericOrbit< ClustType > & CASM::GenericOrbitree< ClustType >::orbit	(	Index	np,
		Index	no
	)

Access orbits using 2-D indexing.

Definition at line 54 of file Orbitree_impl.hh.

template<typename ClustType >

const GenericOrbit< ClustType > & CASM::GenericOrbitree< ClustType >::orbit	(	Index	np,
		Index	no
	)		const

Definition at line 47 of file Orbitree_impl.hh.

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

inherited

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

inlineinherited

Definition at line 212 of file Array.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::print ( std::ostream & stream ) const

Definition at line 1485 of file Orbitree_impl.hh.

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

inherited

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::print_eci_in ( std::ostream & out ) const

Definition at line 2133 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::print_full_basis_info ( std::ostream & out ) const

Definition at line 1666 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::print_full_clust ( std::ostream & out ) const

Definition at line 1630 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::print_full_decorated_clust ( std::ostream & out ) const

Definition at line 1798 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::print_proto_clust ( std::ostream & out ) const

Definition at line 1701 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::print_proto_clust_funcs ( std::ostream & out ) const

Definition at line 1738 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::print_proto_decorated_clust ( std::ostream & out ) const

Definition at line 1832 of file Orbitree_impl.hh.

template<typename ClustType >

const ClustType & CASM::GenericOrbitree< ClustType >::prototype	(	Index	np,
		Index	no
	)		const

Access prototype of orbit (np, no)

Definition at line 61 of file Orbitree_impl.hh.

template<typename ClustType >

ClustType & CASM::GenericOrbitree< ClustType >::prototype	(	Index	np,
		Index	no
	)

Definition at line 68 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::push_back ( const GenericOrbit< ClustType > & new_orbit )

push_back a new orbit. If orbit has clusters of N sites, it will be placed in lowest-index OrbitBranch that contains N-clusters. If none is found, a new OrbitBranch is added

Definition at line 134 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::push_back ( const GenericOrbitBranch< ClustType > & new_branch )

push_back new OrbitBranch. Verifies that new branch uses this->lattice as home lattice

Definition at line 124 of file Orbitree_impl.hh.

template<typename ClustType>

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

template<typename ClustType>

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

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::read_CSPECS ( std::istream & stream )

Definition at line 1410 of file Orbitree_impl.hh.

template<typename ClustType >

bool CASM::GenericOrbitree< ClustType >::read_custom_clusters_from_json	(	const jsonParser &	json,
		const Structure &	struc,
		const SymGroup &	sym_group,
		bool	verbose = `false`
	)

Add more orbits to Orbitree based on JSON input.

Expected JSON format:

{
  “orbits” : [
   { "coordinate_mode" : “Direct”,   // could be “Fractional”, “Direct”, or “Cartesian”, future “UnitCellCoordinate”
     "prototype" : [
       [ 0.000000000000, 0.000000000000, 0.000000000000 ],
       [ 1.000000000000, 0.000000000000, 0.000000000000 ],
       [ 2.000000000000, 0.000000000000, 0.000000000000 ],
       [ 3.000000000000, 0.000000000000, 0.000000000000 ]
     ],
     “include_subclusters” : true  (Default true if not specified)
   },
   ... more orbit specs ...
}

Definition at line 2278 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::read_orbitree_from_json	(	const std::string &	json_file_name,
		const SymGroup &	sym_group,
		const Structure &	ref_struc
	)

Definition at line 2228 of file Orbitree_impl.hh.

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

inherited

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

inherited

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::resize ( Index NP )

Initialize NP orbitbranches in the Orbitree. Any existing orbits get deleted.

Definition at line 117 of file Orbitree_impl.hh.

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

inherited

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

inherited

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

static ReturnArray<GenericOrbitBranch< ClustType > > CASM::Array< GenericOrbitBranch< ClustType > >::sequence	(	const GenericOrbitBranch< ClustType > &	initial,
		const GenericOrbitBranch< 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<GenericOrbitBranch< ClustType > > CASM::Array< GenericOrbitBranch< ClustType > >::sequence	(	const GenericOrbitBranch< ClustType > &	initial,
		const GenericOrbitBranch< ClustType > &	increment,
		const GenericOrbitBranch< 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::GenericOrbitree< ClustType >::set_bspecs ( const jsonParser & _bspecs )

inline

Definition at line 108 of file Orbitree.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::set_lattice	(	const Lattice &	new_lat,
		COORD_TYPE	mode
	)

sets lattice=new_lat and also updates all OrbitBranches, Orbits, and Clusters

Definition at line 150 of file Orbitree_impl.hh.

template<typename ClustType >

Index CASM::GenericOrbitree< ClustType >::size ( Index np ) const

Number of orbits in OrbitBranch 'np'.

Definition at line 89 of file Orbitree_impl.hh.

template<typename ClustType >

Index CASM::GenericOrbitree< ClustType >::size	(	Index	np,
		Index	no
	)		const

Number of equivalent clusters in Orbit (np, no)

Definition at line 96 of file Orbitree_impl.hh.

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

inlineinherited

Definition at line 145 of file Array.hh.

template<typename ClustType >

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

Calls 'sort()' on each OrbitBranch to sort Orbits by lengthscale.

Definition at line 165 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::sort ( Index np )

Calls 'sort()' on the np OrbitBranch.

Definition at line 176 of file Orbitree_impl.hh.

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inlineinherited

Definition at line 231 of file Array.hh.

template<typename ClustType >

double CASM::GenericOrbitree< ClustType >::tol ( ) const

Access orbitree tolerance.

Definition at line 40 of file Orbitree_impl.hh.

template<typename ClustType>

void CASM::GenericOrbitree< ClustType >::trans_and_expand	(	const Array< Coordinate > &	prim_grid,
		bool	override = `0`
	)

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::write_eci_in ( std::string filename ) const

Definition at line 2123 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::write_full_clust ( std::string file ) const

Definition at line 1562 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::write_full_decorated_clust ( std::string file ) const

Definition at line 1596 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::write_proto_clust ( std::string file ) const

Definition at line 1579 of file Orbitree_impl.hh.

template<typename ClustType >

void CASM::GenericOrbitree< ClustType >::write_proto_decorated_clust ( std::string file ) const

Definition at line 1614 of file Orbitree_impl.hh.

Member Data Documentation

template<typename ClustType>

Array< Array<int> > CASM::GenericOrbitree< ClustType >::index

mutable

Definition at line 63 of file Orbitree.hh.

template<typename ClustType>

Array<int> CASM::GenericOrbitree< ClustType >::index_to_column

mutable

Definition at line 62 of file Orbitree.hh.

template<typename ClustType>

Array<int> CASM::GenericOrbitree< ClustType >::index_to_row

mutable

Arrays to map 2-D orbit indices onto a single index for my_orbitree[i][j], there is a unique index k=index[i][j] 'i' can be found using index_to_row[k] 'j' can be found using index_to_column[k]

Definition at line 62 of file Orbitree.hh.

template<typename ClustType>

Lattice CASM::GenericOrbitree< ClustType >::lattice

Definition at line 42 of file Orbitree.hh.

template<typename ClustType>

GenericOrbitBranch<ClustType> CASM::GenericOrbitree< ClustType >::m_asym_unit

private

Definition at line 239 of file Orbitree.hh.

template<typename ClustType>

Array<Array<Index> > CASM::GenericOrbitree< ClustType >::m_b2asym

private

Definition at line 243 of file Orbitree.hh.

template<typename ClustType>

jsonParser CASM::GenericOrbitree< ClustType >::m_bspecs

private

Definition at line 246 of file Orbitree.hh.

template<typename ClustType>

double CASM::GenericOrbitree< ClustType >::m_tol

Definition at line 44 of file Orbitree.hh.

template<typename ClustType>

Array<double> CASM::GenericOrbitree< ClustType >::max_length

Maximum allowed between any two points in a cluster of Orbitree[i] (e.g., max_length[i] is the max length allowed for a cluster in the 'i' OrbitBranch)

Definition at line 51 of file Orbitree.hh.

template<typename ClustType>

Index CASM::GenericOrbitree< ClustType >::max_num_sites

Definition at line 47 of file Orbitree.hh.

template<typename ClustType>

double CASM::GenericOrbitree< ClustType >::min_length

minimum length allowed between any two points in a cluster if negative, N-clusters with repeated points are allowed

Definition at line 54 of file Orbitree.hh.

template<typename ClustType>

Index CASM::GenericOrbitree< ClustType >::min_num_components

Definition at line 47 of file Orbitree.hh.

template<typename ClustType>

Index CASM::GenericOrbitree< ClustType >::Norbits

mutable

Definition at line 64 of file Orbitree.hh.

template<typename ClustType>

Array<int> CASM::GenericOrbitree< ClustType >::num_clusts

we don't use num_clusts yet. It might be a better way to specify how many clusters to enumerate

Definition at line 56 of file Orbitree.hh.

template<typename ClustType>

Array< Array<int> > CASM::GenericOrbitree< ClustType >::subcluster

mutable

For each orbit 'k', lists all orbits that contain subclusters of the clusters in orbit 'k' (given by their linear index)

Definition at line 68 of file Orbitree.hh.

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

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clex/Clex.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clusterography/Orbitree.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clusterography/Orbitree_impl.hh

Detailed Description

template<typename ClustType> singleton CASM::GenericOrbitree< ClustType >

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<typename ClustType>
singleton CASM::GenericOrbitree< ClustType >