#include <Supercell.hh>

Inheritance diagram for CASM::Supercell:

Detailed Description

Represents a supercell of the primitive parent crystal structure.

Definition at line 37 of file Supercell.hh.

Public Types
typedef boost::container::stable_vector < Configuration >	ConfigList

typedef ConfigIterator < Configuration, PrimClex >	config_iterator

typedef ConfigIterator< const Configuration, const PrimClex >	config_const_iterator

typedef PermuteIterator	permute_const_iterator

Public Member Functions
	Supercell (const Supercell &RHS)

	Supercell (PrimClex *_prim, const Lattice &superlattice)

	Supercell (PrimClex *_prim, const Eigen::Ref< const Eigen::Matrix3i > &superlattice_matrix)

Index	get_linear_index (const Site &site, double tol=TOL) const

Index	get_linear_index (const Coordinate &coord, double tol=TOL) const

Index	find (const UnitCellCoord &bijk) const

Coordinate	coord (const UnitCellCoord &bijk) const

Coordinate	coord (Index linear_ind) const

ReturnArray< int >	max_allowed_occupation () const

Configuration	configuration (const BasicStructure< Site > &structure_to_config, double tol=TOL)

Structure	superstructure () const

Structure	superstructure (const Configuration &config) const

Structure	superstructure (Index config_index) const
	Returns a structure corresponding to the specified configuration. More...

Eigen::MatrixXd	real_coordinates () const

Eigen::MatrixXd	recip_coordinates () const

PrimClex &	get_primclex () const

const PrimGrid &	prim_grid () const

const Structure &	get_prim () const

Index	volume () const
	Return number of primitive cells that fit inside of *this. More...

Index	basis_size () const

Index	num_sites () const

UnitCellCoord	uccoord (Index i) const

const Eigen::MatrixXcd &	fourier_matrix () const

const Eigen::MatrixXcd &	phase_factor () const

const Eigen::MatrixXd &	k_mesh () const

SymGroupRepID	permutation_symrep_ID () const

SymGroupRep const &	permutation_symrep () const

Index	get_b (Index i) const

const Eigen::Matrix3i &	get_transf_mat () const

const Lattice &	get_real_super_lattice () const

const Lattice &	get_recip_prim_lattice () const

const SuperNeighborList &	nlist () const
	Returns the SuperNeighborList. More...

ConfigList &	get_config_list ()

const ConfigList &	get_config_list () const

const Configuration &	get_config (Index i) const

Configuration &	get_config (Index i)

config_iterator	config_begin ()

config_iterator	config_end ()

config_const_iterator	config_cbegin () const

config_const_iterator	config_cend () const

Index	get_id () const

std::string	get_name () const
	Return supercell name. More...

const SymGroup &	factor_group () const

const Permutation &	factor_group_permute (Index i) const

const Permutation &	translation_permute (Index i) const

const Array< Permutation > &	translation_permute () const

permute_const_iterator	translate_begin () const
	Begin iterator over pure translational permutations. More...

permute_const_iterator	translate_end () const
	End iterator over pure translational permutations. More...

permute_const_iterator	permute_begin () const

permute_const_iterator	permute_end () const

permute_const_iterator	permute_it (Index fg_index, Index trans_index) const

fs::path	get_path () const
	Return path to supercell directory. More...

Index	amount_selected () const
	Count how many configs are selected in *this. More...

bool	is_canonical () const

SymOp	to_canonical () const

SymOp	from_canonical () const

Supercell &	canonical_form () const

bool	is_equivalent (const Supercell &B) const

bool	operator< (const Supercell &B) const

void	set_id (Index id)

void	generate_factor_group () const

void	generate_permutations () const

void	generate_reference_config_props (Index config_index)
	Calculate reference properties for a configuration (must have reference states in appropriate directories) More...

void	generate_all_reference_config_props ()
	Calculate reference properties for each configuration in *this (see above) More...

void	generate_delta_config_props (Index config_index)
	Calculate delta properties for a configuration (must have read in calculated and reference properties) More...

void	generate_all_delta_config_props ()
	Calculate delta properties for each configuration in *this (see above) More...

void	generate_fourier_matrix ()
	Structure Factor. More...

void	generate_fourier_matrix (const Eigen::MatrixXd &real_coordinates, const Eigen::MatrixXd &recip_coordinates)

Array< bool >	is_commensurate_kpoint (const Eigen::MatrixXd &recip_coordinates, double tol=TOL)

void	populate_structure_factor ()

void	populate_structure_factor (const Index &config_index)

void	enumerate_perturb_configurations (const std::string &background, fs::path CSPECS, double tol=TOL, bool verbose=false, bool print=false)

void	enumerate_perturb_configurations (Configuration background_config, fs::path CSPECS, double tol=TOL, bool verbose=false, bool print=false)

void	enumerate_perturb_configurations (const Structure &background, fs::path CSPECS, double tol=TOL, bool verbose=false, bool print=false)

void	enumerate_perturb_configurations (Configuration background_config, const SiteOrbitree &background_tree, Array< Array< Array< Index > > > &config_index, Array< Array< Array< permute_const_iterator > > > &config_symop_index, jsonParser &jsonsrc, double tol=TOL)

bool	contains_config (const Configuration &config) const

bool	contains_config (const Configuration &config, Index &index) const

bool	add_config (const Configuration &config)

bool	add_config (const Configuration &config, Index &index, Supercell::permute_const_iterator &permute_it)

bool	add_canon_config (const Configuration &config, Index &index)

std::pair < config_const_iterator, bool >	insert_config (const Configuration &config)
	Insert a configuration that may be non-canonical. More...

std::pair < config_const_iterator, bool >	insert_canon_config (const Configuration &config)
	Insert a configuration that is known to be canonical. More...

config_const_iterator	find (const Configuration &config) const

void	read_config_list (const jsonParser &json)

template<typename ConfigIterType >
void	add_unique_canon_configs (ConfigIterType it_begin, ConfigIterType it_end)

template<typename ConfigIterType >
void	add_configs (ConfigIterType it_begin, ConfigIterType it_end)

void	read_relaxed_structure (Index configNum, const Lattice &home_lattice)

void	read_relaxed_structure (Index configNum)

void	read_clex_relaxations (const Lattice &home_lattice)

bool	is_supercell_of (const Structure &structure) const

bool	is_supercell_of (const Structure &structure, Eigen::Matrix3d &multimat) const

ReturnArray< int >	vacant () const

void	print_bijk (std::ostream &stream)

void	print_sublat_to_comp (std::ostream &stream)
	Old CASM style corr.in output for all the configurations in *this supercell. More...

void	print_PERTURB_json (std::ofstream &file, const Configuration &background_config, const Array< Array< Array< Index > > > &perturb_config_index, const Array< Array< Array< permute_const_iterator > > > &perturb_config_symop_index, bool print_config_name) const

jsonParser &	write_config_list (jsonParser &json)
	Call Configuration::write out every configuration in supercell. More...

void	printUCC (std::ostream &stream, COORD_TYPE mode, UnitCellCoord ucc, char term=0, int prec=7, int pad=5) const

bool	operator> (const Supercell &B) const

bool	operator<= (const Supercell &B) const

bool	operator>= (const Supercell &B) const

bool	operator== (const Supercell &B) const

bool	operator!= (const Supercell &B) const

Protected Member Functions
const Supercell &	derived () const

bool	_ne (const Supercell &B) const

Private Member Functions
void	generate_fourier_matrix (const Eigen::MatrixXd &real_coordinates, const Eigen::MatrixXd &recip_coordinates, const bool &override)

void	generate_phase_factor (const Eigen::MatrixXd &shift_vectors, const Array< bool > &is_commensurate, const bool &override)

bool	_eq (const Supercell &B) const

void	_add_canon_config (const Configuration &config)

void	_generate_name () const

Private Attributes
PrimClex *	primclex

Lattice	real_super_lattice

Lattice	recip_prim_lattice

PrimGrid	m_prim_grid

PrimGrid	recip_grid

SymGroupRepID	m_perm_symrep_ID

SymGroup	m_factor_group

std::string	m_name
	unique name of the supercell based on hermite normal form (see _generate_name() ) More...

Eigen::MatrixXcd	m_fourier_matrix

Eigen::MatrixXcd	m_phase_factor

Eigen::MatrixXd	m_k_mesh

notstd::cloneable_ptr < SuperNeighborList >	m_nlist
	More...

Index	m_nlist_size_at_construction

Supercell *	m_canonical
	Store a pointer to the canonical equivalent Supercell. More...

ConfigList	config_list

std::map< const Configuration *, Index, ConfigMapCompare >	m_config_map

Eigen::Matrix3i	transf_mat

double	scaling

Index	m_id
	index into PrimClex::supercell_list More...

friend	Comparisons< Supercell >

Member Typedef Documentation

typedef ConfigIterator<const Configuration, const PrimClex> CASM::Supercell::config_const_iterator

Definition at line 45 of file Supercell.hh.

typedef ConfigIterator<Configuration, PrimClex> CASM::Supercell::config_iterator

Definition at line 44 of file Supercell.hh.

typedef boost::container::stable_vector<Configuration> CASM::Supercell::ConfigList

Definition at line 41 of file Supercell.hh.

typedef PermuteIterator CASM::Supercell::permute_const_iterator

Definition at line 48 of file Supercell.hh.

Constructor & Destructor Documentation

CASM::Supercell::Supercell ( const Supercell & RHS )

Definition at line 694 of file Supercell.cc.

CASM::Supercell::Supercell	(	PrimClex *	_prim,
		const Lattice &	superlattice
	)

Definition at line 725 of file Supercell.cc.

CASM::Supercell::Supercell	(	PrimClex *	_prim,
		const Eigen::Ref< const Eigen::Matrix3i > &	superlattice_matrix
	)

Definition at line 711 of file Supercell.cc.

Member Function Documentation

void CASM::Supercell::_add_canon_config ( const Configuration & canon_config )

private

Adds to config_list, assuming 'canon_config' is in canonical form and not already there

Definition at line 638 of file Supercell.cc.

bool CASM::Supercell::_eq ( const Supercell & B ) const

private

Definition at line 1258 of file Supercell.cc.

void CASM::Supercell::_generate_name ( ) const

private

Definition at line 858 of file Supercell.cc.

bool CASM::Comparisons< Supercell >::_ne ( const Supercell & B ) const

inlineprotectedinherited

Definition at line 56 of file Comparisons.hh.

bool CASM::Supercell::add_canon_config	(	const Configuration &	canon_config,
		Index &	index
	)

Assumes 'canon_config' is in canonical form, adds to config_list if not already there. Location in config_list is stored in 'index'.

Definition at line 590 of file Supercell.cc.

bool CASM::Supercell::add_config ( const Configuration & config )

Converts 'config' to canonical form, then adds to config_list if not already present. Location in config_list is stored in 'index'. Permutation that resulted in canonical form is stored in 'permute_it'. Return 'true' if new config, 'false' otherwise.

Might want to rewrite without using new canon_config for memory/speed issues.

Definition at line 568 of file Supercell.cc.

bool CASM::Supercell::add_config	(	const Configuration &	config,
		Index &	index,
		Supercell::permute_const_iterator &	permute_it
	)

Definition at line 574 of file Supercell.cc.

Index CASM::Supercell::amount_selected ( ) const

Count how many configs are selected in *this.

Definition at line 874 of file Supercell.cc.

Index CASM::Supercell::basis_size ( ) const

inline

Definition at line 216 of file Supercell.hh.

Supercell & CASM::Supercell::canonical_form ( ) const

Definition at line 910 of file Supercell.cc.

Supercell::config_iterator CASM::Supercell::config_begin ( )

Definition at line 100 of file Supercell.cc.

Supercell::config_const_iterator CASM::Supercell::config_cbegin ( ) const

Definition at line 109 of file Supercell.cc.

Supercell::config_const_iterator CASM::Supercell::config_cend ( ) const

Definition at line 113 of file Supercell.cc.

Supercell::config_iterator CASM::Supercell::config_end ( )

Definition at line 104 of file Supercell.cc.

Configuration CASM::Supercell::configuration	(	const BasicStructure< Site > &	structure_to_config,
		double	tol = `TOL`
	)

Generate a Configuration from a Structure

Generally expected the user will first call Supercell::is_supercell_of(const Structure &structure, Matrix3<double> multimat)
tested OK for perfect prim coordinates, not yet tested with relaxed coordinates using 'tol'

Definition at line 955 of file Supercell.cc.

bool CASM::Supercell::contains_config ( const Configuration & config ) const

Checks if the Configuration 'config' is contained in Supercell::config_list. Only checks Configuration::occupation for equivalence. Does not check for symmetrically equivalent Configurations, so put your 'config' in canonical form first.

Definition at line 522 of file Supercell.cc.

bool CASM::Supercell::contains_config	(	const Configuration &	config,
		Index &	index
	)		const

Checks if the Configuration 'config' is contained in Supercell::config_list. Only checks Configuration::configdof for equivalence. Does not check for symmetrically equivalent Configurations, so put your 'config' in canonical form first.

If equivalent found, 'index' contains it's index into config_list, else 'index' = config_list.size().

Definition at line 538 of file Supercell.cc.

Coordinate CASM::Supercell::coord ( const UnitCellCoord & bijk ) const

Definition at line 45 of file Supercell.cc.

Coordinate CASM::Supercell::coord ( Index linear_ind ) const

Definition at line 53 of file Supercell.cc.

const Supercell & CASM::Comparisons< Supercell >::derived ( ) const

inlineprotectedinherited

Definition at line 48 of file Comparisons.hh.

void CASM::Supercell::enumerate_perturb_configurations	(	const std::string &	background,
		fs::path	CSPECS,
		double	tol = `TOL`,
		bool	verbose = `false`,
		bool	print = `false`
	)

enumerate_perturb_configurations, using filename of 'background' structure

Definition at line 211 of file Supercell.cc.

void CASM::Supercell::enumerate_perturb_configurations	(	Configuration	background_config,
		fs::path	CSPECS,
		double	tol = `TOL`,
		bool	verbose = `false`,
		bool	print = `false`
	)

enumerate_perturb_configurations, using 'config' Configuration and 'CSPECS' to generate the 'background_config' and 'background_tree'. The factor group of the decorated config is used to generate the orbitree

Definition at line 225 of file Supercell.cc.

void CASM::Supercell::enumerate_perturb_configurations	(	const Structure &	background,
		fs::path	CSPECS,
		double	tol = `TOL`,
		bool	verbose = `false`,
		bool	print = `false`
	)

enumerate_perturb_configurations, using 'background' Structure and 'CSPECS' to generate the 'background_config' and 'background_tree'.

Definition at line 383 of file Supercell.cc.

void CASM::Supercell::enumerate_perturb_configurations	(	Configuration	background_config,
		const SiteOrbitree &	background_tree,
		Array< Array< Array< Index > > > &	config_index,
		Array< Array< Array< permute_const_iterator > > > &	config_symop_index,
		jsonParser &	jsonsrc,
		double	tol = `TOL`
	)

Enumerate configurations that are perturbations of a 'background_config'. The 'perturbed' configurations differ from the 'background' structure by clusters in the 'background_tree'. 'tol' provides a tolerance for mapping the clusters to Configuration sites.

Enumerated configurations are added to 'Supercell::config_list' if they do not already exist there, using the 'permute_group' to check for equivalents.

Array< Array< Array<int> > > config_indices contains the mapping of [branch][orbit][decor] to config_list index Array< Array< Array<int> > > config_symop contains the index of the symop which mapped the config to canonical form

jsonsrc is a jsonParser (object type) describing the source of the enumerate configurations

Definition at line 407 of file Supercell.cc.

const SymGroup & CASM::Supercell::factor_group ( ) const

Definition at line 132 of file Supercell.cc.

const Permutation & CASM::Supercell::factor_group_permute ( Index i ) const

Definition at line 141 of file Supercell.cc.

Index CASM::Supercell::find ( const UnitCellCoord & bijk ) const

Definition at line 39 of file Supercell.cc.

Supercell::config_const_iterator CASM::Supercell::find ( const Configuration & config ) const

Definition at line 549 of file Supercell.cc.

const Eigen::MatrixXcd& CASM::Supercell::fourier_matrix ( ) const

inline

Definition at line 229 of file Supercell.hh.

SymOp CASM::Supercell::from_canonical ( ) const

Definition at line 902 of file Supercell.cc.

void CASM::Supercell::generate_all_delta_config_props ( )

Calculate delta properties for each configuration in *this (see above)

void CASM::Supercell::generate_all_reference_config_props ( )

Calculate reference properties for each configuration in *this (see above)

void CASM::Supercell::generate_delta_config_props ( Index config_index )

Calculate delta properties for a configuration (must have read in calculated and reference properties)

void CASM::Supercell::generate_factor_group ( ) const

Definition at line 821 of file Supercell.cc.

void CASM::Supercell::generate_fourier_matrix	(	const Eigen::MatrixXd &	real_coordinates,
		const Eigen::MatrixXd &	recip_coordinates,
		const bool &	override
	)

private

Structure factor calculation routines -> Use only the public versions of these functions The calculations, and math is explained as comments above m_fourier_matrix and m_phase_factor

Definition at line 1176 of file Supercell.cc.

void CASM::Supercell::generate_fourier_matrix ( )

Structure Factor.

Definition at line 1168 of file Supercell.cc.

void CASM::Supercell::generate_fourier_matrix	(	const Eigen::MatrixXd &	real_coordinates,
		const Eigen::MatrixXd &	recip_coordinates
	)

Definition at line 1172 of file Supercell.cc.

void CASM::Supercell::generate_permutations ( ) const

Definition at line 829 of file Supercell.cc.

void CASM::Supercell::generate_phase_factor	(	const Eigen::MatrixXd &	shift_vectors,
		const Array< bool > &	is_commensurate,
		const bool &	override
	)

private

Definition at line 1210 of file Supercell.cc.

void CASM::Supercell::generate_reference_config_props ( Index config_index )

Calculate reference properties for a configuration (must have reference states in appropriate directories)

Index CASM::Supercell::get_b ( Index i ) const

inline

Definition at line 259 of file Supercell.hh.

const Configuration& CASM::Supercell::get_config ( Index i ) const

inline

Definition at line 287 of file Supercell.hh.

Configuration& CASM::Supercell::get_config ( Index i )

inline

Definition at line 291 of file Supercell.hh.

ConfigList& CASM::Supercell::get_config_list ( )

inline

Definition at line 279 of file Supercell.hh.

const ConfigList& CASM::Supercell::get_config_list ( ) const

inline

Definition at line 283 of file Supercell.hh.

Index CASM::Supercell::get_id ( ) const

inline

Definition at line 303 of file Supercell.hh.

Index CASM::Supercell::get_linear_index	(	const Site &	site,
		double	tol = `TOL`
	)		const

Definition at line 18 of file Supercell.cc.

Index CASM::Supercell::get_linear_index	(	const Coordinate &	coord,
		double	tol = `TOL`
	)		const

Definition at line 30 of file Supercell.cc.

std::string CASM::Supercell::get_name ( ) const

Return supercell name.

If lattice is the canonical equivalent, then return 'SCELV_A_B_C_D_E_F'
Else, return 'SCELV_A_B_C_D_E_F.$FG_INDEX', where $FG_INDEX is the index of the first symmetry operation in the primitive structure's factor group such that the lattice is equivalent to apply(fg_op, canonical equivalent)

Definition at line 123 of file Supercell.cc.

fs::path CASM::Supercell::get_path ( ) const

Return path to supercell directory.

Definition at line 865 of file Supercell.cc.

const Structure & CASM::Supercell::get_prim ( ) const

Definition at line 74 of file Supercell.cc.

PrimClex& CASM::Supercell::get_primclex ( ) const

inline

Definition at line 201 of file Supercell.hh.

const Lattice& CASM::Supercell::get_real_super_lattice ( ) const

inline

Definition at line 267 of file Supercell.hh.

const Lattice& CASM::Supercell::get_recip_prim_lattice ( ) const

inline

Definition at line 271 of file Supercell.hh.

const Eigen::Matrix3i& CASM::Supercell::get_transf_mat ( ) const

inline

Definition at line 263 of file Supercell.hh.

std::pair< Supercell::config_const_iterator, bool > CASM::Supercell::insert_canon_config ( const Configuration & config )

Insert a configuration that is known to be canonical.

Definition at line 619 of file Supercell.cc.

std::pair< Supercell::config_const_iterator, bool > CASM::Supercell::insert_config ( const Configuration & config )

Insert a configuration that may be non-canonical.

Definition at line 611 of file Supercell.cc.

bool CASM::Supercell::is_canonical ( ) const

Definition at line 886 of file Supercell.cc.

Array< bool > CASM::Supercell::is_commensurate_kpoint	(	const Eigen::MatrixXd &	recip_coordinates,
		double	tol = `TOL`
	)

Definition at line 1153 of file Supercell.cc.

bool CASM::Supercell::is_equivalent ( const Supercell & B ) const

bool CASM::Supercell::is_supercell_of ( const Structure & structure ) const

Check if a Structure fits in this Supercell

Checks that 'structure'.lattice is supercell of 'real_super_lattice'
Does NOT check basis sites

Definition at line 924 of file Supercell.cc.

bool CASM::Supercell::is_supercell_of	(	const Structure &	structure,
		Eigen::Matrix3d &	mat
	)		const

Check if a Structure fits in this Supercell

Checks that 'structure'.lattice is supercell of 'real_super_lattice'
Does NOT check basis sites

Definition at line 935 of file Supercell.cc.

const Eigen::MatrixXd& CASM::Supercell::k_mesh ( ) const

inline

Definition at line 237 of file Supercell.hh.

ReturnArray< int > CASM::Supercell::max_allowed_occupation ( ) const

Definition at line 61 of file Supercell.cc.

const SuperNeighborList & CASM::Supercell::nlist ( ) const

Returns the SuperNeighborList.

Definition at line 79 of file Supercell.cc.

Index CASM::Supercell::num_sites ( ) const

inline

Definition at line 220 of file Supercell.hh.

bool CASM::Comparisons< Supercell >::operator!= ( const Supercell & B ) const

inlineinherited

Definition at line 41 of file Comparisons.hh.

bool CASM::Supercell::operator< ( const Supercell & B ) const

Definition at line 1246 of file Supercell.cc.

bool CASM::Comparisons< Supercell >::operator<= ( const Supercell & B ) const

inlineinherited

Definition at line 29 of file Comparisons.hh.

bool CASM::Comparisons< Supercell >::operator== ( const Supercell & B ) const

inlineinherited

Definition at line 37 of file Comparisons.hh.

bool CASM::Comparisons< Supercell >::operator> ( const Supercell & B ) const

inlineinherited

Definition at line 25 of file Comparisons.hh.

bool CASM::Comparisons< Supercell >::operator>= ( const Supercell & B ) const

inlineinherited

Definition at line 33 of file Comparisons.hh.

SymGroupRep const& CASM::Supercell::permutation_symrep ( ) const

inline

Definition at line 255 of file Supercell.hh.

SymGroupRepID CASM::Supercell::permutation_symrep_ID ( ) const

inline

Definition at line 249 of file Supercell.hh.

Supercell::permute_const_iterator CASM::Supercell::permute_begin ( ) const

Definition at line 179 of file Supercell.cc.

Supercell::permute_const_iterator CASM::Supercell::permute_end ( ) const

Definition at line 185 of file Supercell.cc.

Supercell::permute_const_iterator CASM::Supercell::permute_it	(	Index	fg_index,
		Index	trans_index
	)		const

Definition at line 191 of file Supercell.cc.

const Eigen::MatrixXcd& CASM::Supercell::phase_factor ( ) const

inline

Definition at line 233 of file Supercell.hh.

void CASM::Supercell::populate_structure_factor ( )

Definition at line 1228 of file Supercell.cc.

void CASM::Supercell::populate_structure_factor ( const Index & config_index )

Definition at line 1238 of file Supercell.cc.

const PrimGrid& CASM::Supercell::prim_grid ( ) const

inline

Definition at line 205 of file Supercell.hh.

void CASM::Supercell::print_bijk ( std::ostream & stream )

Definition at line 200 of file Supercell.cc.

void CASM::Supercell::print_PERTURB_json	(	std::ofstream &	file,
		const Configuration &	background_config,
		const Array< Array< Array< Index > > > &	perturb_config_index,
		const Array< Array< Array< permute_const_iterator > > > &	perturb_config_symop_index,
		bool	print_config_name
	)		const

Print the PERTURB file for perturbations enumerated around a Configuration

If 'print_config_name' == true, print config using Configuration::name() If 'print_config_name' == false, print config using config_index

Definition at line 775 of file Supercell.cc.

void CASM::Supercell::print_sublat_to_comp ( std::ostream & stream )

Old CASM style corr.in output for all the configurations in *this supercell.

void CASM::Supercell::printUCC	(	std::ostream &	stream,
		COORD_TYPE	mode,
		UnitCellCoord	ucc,
		char	term = `0`,
		int	prec = `7`,
		int	pad = `5`
	)		const

void CASM::Supercell::read_clex_relaxations ( const Lattice & home_lattice )

void CASM::Supercell::read_config_list ( const jsonParser & json )

Definition at line 654 of file Supercell.cc.

void CASM::Supercell::read_relaxed_structure	(	Index	configNum,
		const Lattice &	home_lattice
	)

void CASM::Supercell::read_relaxed_structure ( Index configNum )

Eigen::MatrixXd CASM::Supercell::real_coordinates ( ) const

Initialize a nx3 vector of real space coords, corresponding to the real space grid points

Definition at line 1122 of file Supercell.cc.

Eigen::MatrixXd CASM::Supercell::recip_coordinates ( ) const

Initialize a nx3 vector of kpoints that we are interested in by using kpoints that are listed in recip_grid. We will only generate k-points in the IBZ, so always call voronoi_within on the coordinate

Definition at line 1139 of file Supercell.cc.

void CASM::Supercell::set_id ( Index id )

inline

Definition at line 355 of file Supercell.hh.

Structure CASM::Supercell::superstructure ( ) const

Returns a Structure equivalent to the Supercell

basis sites are ordered to agree with Supercell::config_index_to_bijk
occupation set to prim default, not curr_state

Definition at line 1037 of file Supercell.cc.

Structure CASM::Supercell::superstructure ( const Configuration & config ) const

Returns a Structure equivalent to the Supercell

basis sites are ordered to agree with Supercell::config_index_to_bijk
occupation set to config
prim set to (*primclex).prim

Definition at line 1068 of file Supercell.cc.

Structure CASM::Supercell::superstructure ( Index config_index ) const

Returns a structure corresponding to the specified configuration.

This is a safer version that takes an Index instead of an actual Configuration. It might be better to have the version that takes a Configuration private, that way you can't pass it anything that's incompatible.

Definition at line 1090 of file Supercell.cc.

SymOp CASM::Supercell::to_canonical ( ) const

Definition at line 894 of file Supercell.cc.

Supercell::permute_const_iterator CASM::Supercell::translate_begin ( ) const

Begin iterator over pure translational permutations.

Begin iterator over translation permutations.

Definition at line 161 of file Supercell.cc.

Supercell::permute_const_iterator CASM::Supercell::translate_end ( ) const

End iterator over pure translational permutations.

End iterator over translation permutations.

Definition at line 168 of file Supercell.cc.

const Permutation & CASM::Supercell::translation_permute ( Index i ) const

Definition at line 147 of file Supercell.cc.

const Array< Permutation > & CASM::Supercell::translation_permute ( ) const

Definition at line 154 of file Supercell.cc.

UnitCellCoord CASM::Supercell::uccoord ( Index i ) const

inline

Definition at line 224 of file Supercell.hh.

ReturnArray< int > CASM::Supercell::vacant ( ) const

Returns an Array<int> consistent with Configuration::occupation that is all vacancies. A site which can not contain a vacancy is set to -1.

Definition at line 1105 of file Supercell.cc.

Index CASM::Supercell::volume ( ) const

inline

Return number of primitive cells that fit inside of *this.

Definition at line 212 of file Supercell.hh.

jsonParser & CASM::Supercell::write_config_list ( jsonParser & json )

Call Configuration::write out every configuration in supercell.

Run through every selected Configuration in *this and call write() on it. This will update all the JSON files and also rewrite POS, DoF etc. Meant for when you calculated some properties (e.g. formation energies or correlations) and want it outputted, but didn't generate any new configurations.

Definition at line 758 of file Supercell.cc.

Member Data Documentation

friend CASM::Supercell::Comparisons< Supercell >

private

Definition at line 447 of file Supercell.hh.

ConfigList CASM::Supercell::config_list

private

Definition at line 146 of file Supercell.hh.

Supercell* CASM::Supercell::m_canonical

mutableprivate

Store a pointer to the canonical equivalent Supercell.

Definition at line 143 of file Supercell.hh.

std::map<const Configuration *, Index, ConfigMapCompare> CASM::Supercell::m_config_map

private

Definition at line 149 of file Supercell.hh.

SymGroup CASM::Supercell::m_factor_group

mutableprivate

Definition at line 85 of file Supercell.hh.

Eigen::MatrixXcd CASM::Supercell::m_fourier_matrix

private

Definition at line 100 of file Supercell.hh.

Index CASM::Supercell::m_id

private

index into PrimClex::supercell_list

Definition at line 156 of file Supercell.hh.

Eigen::MatrixXd CASM::Supercell::m_k_mesh

private

Calculating the structure factor: vectors you need : Eigen::VectorXd intensities //this needs to be as long //as the number of sites in the supercell Calculations (these are done in Configuration): intensities.segment<volume()>(i*volume()) * fourier_matrix = Q.column(i) Q is arranged as: [Q1(k1) Q2(k1) ... Qn(k1)] [Q1(k2) Q2(k2) ... Qn(k2)] ... [Q1(kn) Q2(kn) ... Qn(kn)] Structure factors are then calculated as S: S = Q * m_phase_factor S is arranged as: [S(k1) S(k2) ... S(kn)] In the code: Q is called sublat_sf k-point mesh for the Fourier Transform An Eigen::MatrixXd that should be nx3 each row is a coordinate in reciprocal space

Definition at line 127 of file Supercell.hh.

std::string CASM::Supercell::m_name

mutableprivate

unique name of the supercell based on hermite normal form (see _generate_name() )

Definition at line 88 of file Supercell.hh.

notstd::cloneable_ptr<SuperNeighborList> CASM::Supercell::m_nlist

mutableprivate

SuperNeighborList, mutable for lazy construction

Definition at line 136 of file Supercell.hh.

Index CASM::Supercell::m_nlist_size_at_construction

mutableprivate

Store size of PrimNeighborList at time of construction of SuperNeighborList to enable checking if SuperNeighborList should be re-constructed

Definition at line 140 of file Supercell.hh.

SymGroupRepID CASM::Supercell::m_perm_symrep_ID

mutableprivate

Definition at line 72 of file Supercell.hh.

Eigen::MatrixXcd CASM::Supercell::m_phase_factor

private

The phase factor matrix is arranged as: [exp(-i k1 tau1) exp(-i k2 tau1) ... exp(-i kn tau1)] [exp(-i k1 tau2) exp(-i k2 tau2) ... exp(-i kn tau2)] ... [exp(-i k1 taun) exp(-i k2 taun) ... exp(-i kn taun)] tau_{i} is the shift vector for the ith basis atom

Definition at line 108 of file Supercell.hh.

PrimGrid CASM::Supercell::m_prim_grid

private

Definition at line 60 of file Supercell.hh.

PrimClex* CASM::Supercell::primclex

private

Definition at line 52 of file Supercell.hh.

Lattice CASM::Supercell::real_super_lattice

private

Definition at line 55 of file Supercell.hh.

PrimGrid CASM::Supercell::recip_grid

private

Definition at line 63 of file Supercell.hh.

Lattice CASM::Supercell::recip_prim_lattice

private

Definition at line 58 of file Supercell.hh.

double CASM::Supercell::scaling

private

Definition at line 153 of file Supercell.hh.

Eigen::Matrix3i CASM::Supercell::transf_mat

private

Definition at line 151 of file Supercell.hh.

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

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/clex/Supercell.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/clex/Supercell.cc

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