#include <Molecule.hh>

Inheritance diagram for CASM::Molecule:

Detailed Description

Definition at line 100 of file Molecule.hh.

Public Types
typedef Array< AtomPosition >	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 AtomPosition	value_type

typedef Index	size_type

typedef AtomPosition *	iterator

typedef const AtomPosition *	const_iterator

Public Member Functions
	Molecule (const Lattice &init_home)

Lattice const *	home () const

void	get_center ()

void	generate_point_group ()

bool	is_vacancy () const

Molecule &	apply_sym (const SymOp &op)

Molecule &	apply_sym_no_trans (const SymOp &op)

void	set_lattice (const Lattice &new_lat, COORD_TYPE invariant_mode)

Molecule	get_union (const Molecule &RHS)

Molecule &	operator*= (const SymOp &RHS)

Molecule &	operator+= (const Coordinate &RHS)

bool	operator== (const Molecule &RHS) const

bool	contains (const std::string &name) const

void	read (std::istream &stream)

void	print (std::ostream &stream, const Coordinate &trans, int spaces, char delim, bool SD_is_on=false) const

jsonParser &	to_json (jsonParser &json) const

void	from_json (const jsonParser &json)

Index	size () const

void	swap (Array< AtomPosition > &RHS)

AtomPosition &	at (Index ind)

const AtomPosition &	at (Index ind) const

const AtomPosition &	operator[] (Index ind) const

AtomPosition &	operator[] (Index ind)

AtomPosition &	back ()

const AtomPosition &	back () const

AtomPositionconst *	begin () const

AtomPosition *	begin ()

AtomPositionconst *	cbegin () const

AtomPositionconst *	end () const

AtomPosition *	end ()

AtomPositionconst *	cend () const

void	push_back (const AtomPosition &toPush)

void	pop_back ()

void	remove (Index ind)

void	clear ()

void	resize (Index new_N)

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

const AtomPosition &	min () const

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

AtomPosition	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< AtomPosition > &RHS) const

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

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

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

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

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

bool	all_in (const Array &superset) const

Index	coincidence (const Array &superset) const

Index	incidences (const AtomPosition &test_elem) const

Index	find (const AtomPosition &test_elem) const

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

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

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

bool	contains (const AtomPosition &test_elem) const

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

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

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

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

Public Attributes
Coordinate	center

std::string	name

Private Attributes
Lattice const *	m_home

Array< SymOp >	point_group

Member Typedef Documentation

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

inherited

Definition at line 76 of file Array.hh.

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

inherited

Definition at line 75 of file Array.hh.

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

inherited

Definition at line 74 of file Array.hh.

typedef AtomPosition CASM::Array< AtomPosition >::value_type

inherited

Definition at line 73 of file Array.hh.

typedef Array<AtomPosition > CASM::Array< AtomPosition >::X1

inherited

Definition at line 63 of file Array.hh.

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

inherited

Definition at line 64 of file Array.hh.

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

inherited

Definition at line 65 of file Array.hh.

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

inherited

Definition at line 66 of file Array.hh.

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

inherited

Definition at line 67 of file Array.hh.

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

inherited

Definition at line 68 of file Array.hh.

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

inherited

Definition at line 69 of file Array.hh.

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

inherited

Definition at line 70 of file Array.hh.

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

inherited

Definition at line 71 of file Array.hh.

Member Function Documentation

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

inherited

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

inlineinherited

Definition at line 284 of file Array.hh.

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

inherited

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

inherited

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

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

inherited

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

inherited

ReturnArray<Index> CASM::Array< AtomPosition >::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< AtomPosition >::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

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

inlineinherited

Definition at line 157 of file Array.hh.

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

inlineinherited

Definition at line 162 of file Array.hh.

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

inlineinherited

Definition at line 177 of file Array.hh.

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

inlineinherited

Definition at line 180 of file Array.hh.

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

inlineinherited

Definition at line 185 of file Array.hh.

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

inlineinherited

Definition at line 192 of file Array.hh.

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

inlineinherited

Definition at line 189 of file Array.hh.

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

inlineinherited

Definition at line 201 of file Array.hh.

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

inlineinherited

Definition at line 216 of file Array.hh.

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

inherited

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

inlineinherited

Definition at line 281 of file Array.hh.

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

inlineinherited

Definition at line 197 of file Array.hh.

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

inlineinherited

Definition at line 204 of file Array.hh.

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

inherited

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

inherited

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

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

bool CASM::Array< AtomPosition >::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 AtomPosition & CASM::Array< AtomPosition >::max ( ) const

inherited

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

inherited

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

inherited

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

inlineinherited

Definition at line 260 of file Array.hh.

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

inherited

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

inlineinherited

Definition at line 265 of file Array.hh.

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

inherited

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

inherited

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

inlineinherited

Definition at line 268 of file Array.hh.

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

inlineinherited

Definition at line 167 of file Array.hh.

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

inlineinherited

Definition at line 172 of file Array.hh.

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

inherited

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

inlineinherited

Definition at line 212 of file Array.hh.

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

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

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

inlineinherited

Definition at line 145 of file Array.hh.

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inherited

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

inlineinherited

Definition at line 231 of file Array.hh.

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

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/crystallography/Molecule.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/crystallography/Molecule.cc

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Attributes

Member Typedef Documentation

Member Function Documentation