#include <Supercell.hh>

Inheritance diagram for CASM::Supercell:

Detailed Description

Represents a supercell of the primitive parent crystal structure.

Definition at line 49 of file Supercell.hh.

Public Types
using	permute_const_iterator = SupercellSymInfo::permute_const_iterator

typedef Base::MostDerived	MostDerived

Public Member Functions
	Supercell (const Supercell &RHS)

	Supercell (std::shared_ptr< Structure const > const &_shared_prim, const Lattice &superlattice)

	Supercell (std::shared_ptr< Structure const > const &_shared_prim, Eigen::Matrix3l const &superlattice_matrix)

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

	Supercell (const PrimClex *_prim, const Eigen::Ref< const Eigen::Matrix3l > &superlattice_matrix)

	~Supercell ()

Index	sublat (Index linear_index) const
	Return the sublattice index for a linear index. More...

Index	linear_index (const Coordinate &coord, double tol=TOL) const
	Given a Coordinate and tolerance, return linear index into Configuration. More...

Index	linear_index (const UnitCellCoord &bijk) const
	Return the linear index corresponding to integral coordinates. More...

Coordinate	coord (Index linear_index) const
	Return the linear index corresponding to integral coordinates. More...

UnitCellCoord	uccoord (Index linear_index) const
	Return the integral coordinates corresponding to a linear index. More...

Eigen::VectorXi	max_allowed_occupation () const
	returns maximum allowed occupation bitstring – used for initializing enumeration counters More...

const Structure &	prim () const

std::shared_ptr< Structure const > const &	shared_prim () const

double	crystallography_tol () const

bool	has_primclex () const
	Use while transitioning Supercell to no longer need a `PrimClex const *` More...

void	set_primclex (PrimClex const *primclex_ptr) const
	Use while transitioning Supercell to no longer need a `PrimClex const *` More...

const PrimClex &	primclex () const
	Use while transitioning Supercell to no longer need a `PrimClex const *` More...

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

Index	basis_size () const

Index	num_sites () const

SymGroupRep const &	permutation_symrep () const

Eigen::Matrix3l	transf_mat () const

const Lattice &	lattice () const
	The super lattice. More...

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

const SymGroup &	factor_group () const

const SupercellSymInfo &	sym_info () const

bool	operator< (const Supercell &B) const

std::pair< DB::DatabaseIterator< Supercell >, bool >	insert () const
	Insert the canonical form of this into the database. More...

std::string	name () const

std::string	alias () const
	Return "alias" if object stored in database and alias exists, return empty string otherwise. More...

bool	operator> (const MostDerived &B) const

bool	operator<= (const MostDerived &B) const

bool	operator>= (const MostDerived &B) const

bool	operator== (const MostDerived &B) const

bool	operator!= (const MostDerived &B) const

Protected Member Functions
void	clear_name () const
	Unset "name", if object is modified. More...

void	regenerate_name () const
	Regenerate "name". More...

void	set_name (std::string _name) const
	Set "name", explicity. More...

bool	eq_impl (const MostDerived &B) const

bool	ne_impl (const MostDerived &B) const

Private Member Functions
bool	eq_impl (const Supercell &B) const

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

Private Attributes
friend	Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > >

PrimClex const *	m_primclex

std::shared_ptr< Structure const >	m_shared_prim

SupercellSymInfo	m_sym_info

notstd::cloneable_ptr< SuperNeighborList >	m_nlist
	SuperNeighborList, mutable for lazy construction. More...

Index	m_nlist_size_at_construction

std::string	m_name

Member Typedef Documentation

◆ MostDerived

typedef Base::MostDerived CASM::DB::Named< Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > > >::MostDerived

inherited

Definition at line 25 of file Named.hh.

◆ permute_const_iterator

using CASM::Supercell::permute_const_iterator = SupercellSymInfo::permute_const_iterator

Definition at line 53 of file Supercell.hh.

Constructor & Destructor Documentation

◆ Supercell() [1/5]

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

Definition at line 36 of file Supercell.cc.

◆ Supercell() [2/5]

CASM::Supercell::Supercell	(	std::shared_ptr< Structure const > const &	_shared_prim,
		const Lattice &	superlattice
	)

Definition at line 52 of file Supercell.cc.

◆ Supercell() [3/5]

CASM::Supercell::Supercell	(	std::shared_ptr< Structure const > const &	_shared_prim,
		Eigen::Matrix3l const &	superlattice_matrix
	)

Definition at line 42 of file Supercell.cc.

◆ Supercell() [4/5]

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

Definition at line 87 of file Supercell.cc.

◆ Supercell() [5/5]

CASM::Supercell::Supercell	(	const PrimClex *	_prim,
		const Eigen::Ref< const Eigen::Matrix3l > &	superlattice_matrix
	)

Definition at line 77 of file Supercell.cc.

◆ ~Supercell()

CASM::Supercell::~Supercell ( )

Definition at line 111 of file Supercell.cc.

Member Function Documentation

◆ alias()

std::string CASM::DB::Named< Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > > >::alias

inherited

Return "alias" if object stored in database and alias exists, return empty string otherwise.

Definition at line 34 of file Named_impl.hh.

◆ basis_size()

Index CASM::Supercell::basis_size ( ) const

Definition at line 231 of file Supercell.cc.

◆ clear_name()

void CASM::DB::Named< Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > > >::clear_name

protectedinherited

Unset "name", if object is modified.

Definition at line 38 of file Named_impl.hh.

◆ coord()

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

Return the linear index corresponding to integral coordinates.

Return the coordinate corresponding to linear index in the supercell.

Definition at line 199 of file Supercell.cc.

◆ crystallography_tol()

double CASM::Supercell::crystallography_tol ( ) const

Definition at line 119 of file Supercell.cc.

◆ eq_impl() [1/2]

template<typename Base >

bool notstd::Comparisons< Base >::eq_impl ( const MostDerived & B ) const

inlineprotectedinherited

Definition at line 40 of file Comparisons.hh.

◆ eq_impl() [2/2]

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

private

Definition at line 289 of file Supercell.cc.

◆ factor_group()

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

Definition at line 260 of file Supercell.cc.

◆ generate_name_impl()

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

private

Return supercell name.

For supercells that are equivalent to the canonical supercell:

EQUIV_SCEL_NAME = $CANON_SCELNAME = SCELV_A_B_C_D_E_F
where 'V' is supercell volume (number of unit cells), and 'A-F' are the six non-zero elements of the hermite normal form of the supercell transformation matrix (T00*T11*T22, T00, T11, T22, T12, T02, T01)
CANON_SCEL is found in the supercell database (or constructed using the HNF for the tranformation matrix and then making the lattice canonical) For supercells that are not equivalent to the canonical supercell:
NONEQUIV_SCEL_NAME = $CANON_SCELNAME.$FG_INDEX
The CANON_SCEL is constructed, then the FG_INDEX-th prim factor_group operation is applied

Definition at line 317 of file Supercell.cc.

◆ has_primclex()

bool CASM::Supercell::has_primclex ( ) const

Use while transitioning Supercell to no longer need a PrimClex const *

Note:

Prefer not to access PrimClex via Supercell. In future, PrimClex access via Supercell will be removed completely.

Definition at line 127 of file Supercell.cc.

◆ insert()

std::pair< DB::DatabaseIterator< Supercell >, bool > CASM::Supercell::insert ( ) const

Insert the canonical form of this into the database.

Insert the canonical form of this into the database [deprecated].

Note: prefer using make_canonical_and_insert Note: does not commit the change in the database

Definition at line 283 of file Supercell.cc.

◆ lattice()

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

The super lattice.

Definition at line 239 of file Supercell.cc.

◆ linear_index() [1/2]

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

Given a Coordinate and tolerance, return linear index into Configuration.

This may be slow, first converts Coordinate -> UnitCellCoord, then gets linear_index from UnitCellCoord

Implementation:

Coordinate tcoord(coord);
tcoord.within();
return linear_index(UnitCellCoord(prim(), coord, tol));

Definition at line 183 of file Supercell.cc.

◆ linear_index() [2/2]

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

Return the linear index corresponding to integral coordinates.

Linear indices are grouped by sublattice, then ordered as determined by xtal::OrderedLatticePointGenerator.

Definition at line 193 of file Supercell.cc.

◆ max_allowed_occupation()

Eigen::VectorXi CASM::Supercell::max_allowed_occupation ( ) const

returns maximum allowed occupation bitstring – used for initializing enumeration counters

Definition at line 213 of file Supercell.cc.

◆ name()

std::string CASM::DB::Named< Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > > >::name

inherited

Definition at line 30 of file Named_impl.hh.

◆ ne_impl()

template<typename Base >

bool notstd::Comparisons< Base >::ne_impl ( const MostDerived & B ) const

inlineprotectedinherited

Definition at line 44 of file Comparisons.hh.

◆ nlist()

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

Returns the SuperNeighborList.

Requires that the prim_nlist has been set by one of:

constructing Supercell with a PrimClex const *
using set_primclex to set a PrimClex const *

At each access, the underlying PrimNeighborList will be checked and if it has been expanded then the SuperNeighborList will be extended also. References obtained from this function will be out of date if the underlying PrimNeighborList has been expanded, so it is prudent to only access the SuperNeighborList for immediate use.

Definition at line 244 of file Supercell.cc.

◆ num_sites()

Index CASM::Supercell::num_sites ( ) const

Definition at line 233 of file Supercell.cc.

◆ operator!=()

template<typename Base >

bool notstd::Comparisons< Base >::operator!= ( const MostDerived & B ) const

inlineinherited

Definition at line 37 of file Comparisons.hh.

◆ operator<()

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

Definition at line 267 of file Supercell.cc.

◆ operator<=()

template<typename Base >

bool notstd::Comparisons< Base >::operator<= ( const MostDerived & B ) const

inlineinherited

Definition at line 31 of file Comparisons.hh.

◆ operator==()

template<typename Base >

bool notstd::Comparisons< Base >::operator== ( const MostDerived & B ) const

inlineinherited

Definition at line 35 of file Comparisons.hh.

◆ operator>()

template<typename Base >

bool notstd::Comparisons< Base >::operator> ( const MostDerived & B ) const

inlineinherited

Definition at line 29 of file Comparisons.hh.

◆ operator>=()

template<typename Base >

bool notstd::Comparisons< Base >::operator>= ( const MostDerived & B ) const

inlineinherited

Definition at line 33 of file Comparisons.hh.

◆ permutation_symrep()

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

◆ prim()

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

Definition at line 113 of file Supercell.cc.

◆ primclex()

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

Use while transitioning Supercell to no longer need a PrimClex const *

Note:

Prefer not to access PrimClex via Supercell. In future, PrimClex access via Supercell will be removed completely.

Definition at line 150 of file Supercell.cc.

◆ regenerate_name()

void CASM::DB::Named< Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > > >::regenerate_name

protectedinherited

Regenerate "name".

Definition at line 41 of file Named_impl.hh.

◆ set_name()

void CASM::DB::Named< Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > > >::set_name ( std::string _name ) const

protectedinherited

Set "name", explicity.

Set "name", explicity modified.

Definition at line 44 of file Named_impl.hh.

◆ set_primclex()

void CASM::Supercell::set_primclex ( PrimClex const * _primclex ) const

Use while transitioning Supercell to no longer need a PrimClex const *

Note:

Prefer not to access PrimClex via Supercell. In future, PrimClex access via Supercell will be removed completely.

Definition at line 136 of file Supercell.cc.

◆ shared_prim()

std::shared_ptr< Structure const > const & CASM::Supercell::shared_prim ( ) const

Definition at line 115 of file Supercell.cc.

◆ sublat()

Index CASM::Supercell::sublat ( Index linear_index ) const

Return the sublattice index for a linear index.

Linear indices are grouped by sublattice, then ordered as determined by xtal::OrderedLatticePointGenerator. This function is equivalent to:

linear_index / volume();

CASM::Supercell::volume

Index volume() const

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

Definition: Supercell.cc:227

Definition at line 165 of file Supercell.cc.

◆ sym_info()

const SupercellSymInfo & CASM::Supercell::sym_info ( ) const

Definition at line 265 of file Supercell.cc.

◆ transf_mat()

Eigen::Matrix3l CASM::Supercell::transf_mat ( ) const

Definition at line 235 of file Supercell.cc.

◆ uccoord()

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

Return the integral coordinates corresponding to a linear index.

Linear indices are grouped by sublattice, then ordered as determined by xtal::OrderedLatticePointGenerator.

Definition at line 209 of file Supercell.cc.

◆ volume()

Index CASM::Supercell::volume ( ) const

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

Definition at line 227 of file Supercell.cc.

Member Data Documentation

◆ Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > >

friend CASM::Supercell::Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > >

private

Definition at line 148 of file Supercell.hh.

◆ m_name

std::string CASM::DB::Named< Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > > >::m_name

mutableprivateinherited

Definition at line 47 of file Named.hh.

◆ m_nlist

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

mutableprivate

SuperNeighborList, mutable for lazy construction.

Definition at line 173 of file Supercell.hh.

◆ m_nlist_size_at_construction

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 178 of file Supercell.hh.

◆ m_primclex

PrimClex const* CASM::Supercell::m_primclex

mutableprivate

Definition at line 166 of file Supercell.hh.

◆ m_shared_prim

std::shared_ptr<Structure const> CASM::Supercell::m_shared_prim

private

Definition at line 168 of file Supercell.hh.

◆ m_sym_info

SupercellSymInfo CASM::Supercell::m_sym_info

private

Definition at line 170 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

Detailed Description

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ MostDerived

◆ permute_const_iterator

Constructor & Destructor Documentation

◆ Supercell() [1/5]

◆ Supercell() [2/5]

◆ Supercell() [3/5]

◆ Supercell() [4/5]

◆ Supercell() [5/5]

◆ ~Supercell()

Member Function Documentation

◆ alias()

◆ basis_size()

◆ clear_name()

◆ coord()

◆ crystallography_tol()

◆ eq_impl() [1/2]

◆ eq_impl() [2/2]

◆ factor_group()

◆ generate_name_impl()

◆ has_primclex()

◆ insert()

◆ lattice()

◆ linear_index() [1/2]

◆ linear_index() [2/2]

◆ max_allowed_occupation()

◆ name()

◆ ne_impl()

◆ nlist()

◆ num_sites()

◆ operator!=()

◆ operator<()

◆ operator<=()

◆ operator==()

◆ operator>()

◆ operator>=()

◆ permutation_symrep()

◆ prim()

◆ primclex()

◆ regenerate_name()

◆ set_name()

◆ set_primclex()

◆ shared_prim()

◆ sublat()

◆ sym_info()

◆ transf_mat()

◆ uccoord()

◆ volume()

Member Data Documentation

◆ Comparisons< SupercellCanonicalForm< CRTPBase< Supercell > > >

◆ m_name

◆ m_nlist

◆ m_nlist_size_at_construction

◆ m_primclex

◆ m_shared_prim

◆ m_sym_info