#include <NeighborList.hh>

Detailed Description

SuperNeighborList, linear indices of neighboring sites and unit cells

The SuperNeighborList takes the ordering of unit cells neighboring the origin unit cell from the PrimNeighborList and uses it to construct lists of linear indices of neighboring unit cells and neighboring sites for each unit cell in a particular supercell.

Neighbor list index naming conventions:

"unitcell_index", a linear index given to all unit cell "within" a supercell. Convert between unitcell_index and xtal::UnitCell with xtal::UnitCellIndexConverter.
"site_index", a linear index given to all sites "within" a supercell. Convert between site_index and xtal::UnitCellCoord with xtal::UnitCellCoordIndexConverter.

Definition at line 177 of file NeighborList.hh.

Public Types
typedef Index	size_type

Public Member Functions
	SuperNeighborList (Eigen::Matrix3l const &transformation_matrix_to_super, PrimNeighborList const &prim_nlist)
	Constructor. More...

	SuperNeighborList (const xtal::Superlattice &prim_grid, const PrimNeighborList &prim_nlist)
	Constructor. More...

size_type	unitcell_index (size_type site_index) const
	Get unitcell_index from site_index. More...

size_type	sublat_index (size_type site_index) const
	Get sublattice index from site_index. More...

const std::vector< size_type > &	sites (size_type unitcell_index) const
	const Access the list of sites neighboring a particular unit cell More...

const std::vector< size_type > &	unitcells (size_type unitcell_index) const
	const Access the list of unitcells neighboring a particular unit cell More...

bool	overlaps () const
	Returns true if periodic images of the neighbor list overlap. More...

std::unique_ptr< SuperNeighborList >	clone () const
	Clone. More...

Private Attributes
size_type	m_prim_grid_size
	store prim grid size for site index -> unitcell index conversion unitcell_index = site_index % m_prim_grid_size More...

std::vector< std::vector< size_type > >	m_site
	m_site[unitcell_index][neighbor site index] More...

std::vector< std::vector< size_type > >	m_unitcell
	m_unitcell[unitcell_index][neighbor unitcell index] More...

Member Typedef Documentation

◆ size_type

typedef Index CASM::SuperNeighborList::size_type

Definition at line 179 of file NeighborList.hh.

Constructor & Destructor Documentation

◆ SuperNeighborList() [1/2]

CASM::SuperNeighborList::SuperNeighborList	(	Eigen::Matrix3l const &	transformation_matrix_to_super,
		PrimNeighborList const &	prim_nlist
	)

Constructor.

Parameters

transformation_matrix_to_super	The transformation matrix, T, from primitive lattice vectors to supercell lattice vectors: `supercell_lat_column_mat = T * prim_lat_column_mat`.
prim_nlist	A reference to a PrimNeighborList defining the neighborhood for the origin unit cell. It is only used in the constructor, any changes to the PrimNeighborList will not be reflected in this SuperNeighborList.

The canonical order of UnitCellCoord is obtained by lexicographically sorting [r, i, j, k, b], where r = (i,j,k).transpose() * W * (i,j,k).
The canonical order of UnitCell is obtained by lexicographically sorting [r, i, j, k]
The sublattice iterators enable restricting the neighbor list to only sites that have degrees of freedom

Definition at line 235 of file NeighborList.cc.

◆ SuperNeighborList() [2/2]

CASM::SuperNeighborList::SuperNeighborList	(	const xtal::Superlattice &	superlattice,
		const PrimNeighborList &	prim_nlist
	)

Constructor.

Parameters

superlattice	The superlattice this neighbor list pertains to, coupled with its primitive tiling unit
prim_nlist	A reference to a PrimNeighborList defining the neighborhood for the origin unit cell. It is only used in the constructor, any changes to the PrimNeighborList will not be reflected in this SuperNeighborList.

The canonical order of UnitCellCoord is obtained by lexicographically sorting [r, i, j, k, b], where r = (i,j,k).transpose() * W * (i,j,k).
The canonical order of UnitCell is obtained by lexicographically sorting [r, i, j, k]
The sublattice iterators enable restricting the neighbor list to only sites that have degrees of freedom

Definition at line 289 of file NeighborList.cc.

Member Function Documentation

◆ clone()

std::unique_ptr< SuperNeighborList > CASM::SuperNeighborList::clone ( ) const

Clone.

Definition at line 320 of file NeighborList.cc.

◆ overlaps()

bool CASM::SuperNeighborList::overlaps ( ) const

Returns true if periodic images of the neighbor list overlap.

If periodic images of the neighborhood overlap, Clexulator 'delta' values will be incorrect.

Definition at line 310 of file NeighborList.cc.

◆ sites()

const std::vector< SuperNeighborList::size_type > & CASM::SuperNeighborList::sites ( size_type unitcell_index ) const

const Access the list of sites neighboring a particular unit cell

const Access the list of sites neighboring a particular unitcell

Definition at line 295 of file NeighborList.cc.

◆ sublat_index()

size_type CASM::SuperNeighborList::sublat_index ( size_type site_index ) const

inline

Get sublattice index from site_index.

Definition at line 195 of file NeighborList.hh.

◆ unitcell_index()

size_type CASM::SuperNeighborList::unitcell_index ( size_type site_index ) const

inline

Get unitcell_index from site_index.

Definition at line 190 of file NeighborList.hh.

◆ unitcells()

const std::vector< SuperNeighborList::size_type > & CASM::SuperNeighborList::unitcells ( size_type unitcell_index ) const

const Access the list of unitcells neighboring a particular unit cell

const Access the list of unitcells neighboring a particular unitcell

Definition at line 301 of file NeighborList.cc.

Member Data Documentation

◆ m_prim_grid_size

size_type CASM::SuperNeighborList::m_prim_grid_size

private

store prim grid size for site index -> unitcell index conversion unitcell_index = site_index % m_prim_grid_size

Definition at line 215 of file NeighborList.hh.

◆ m_site

std::vector<std::vector<size_type> > CASM::SuperNeighborList::m_site

private

m_site[unitcell_index][neighbor site index]

Configuration sites are ordered in blocks corresponding to each sublattice, b. Neighbors are specific only to a unitcell, so the neighbor list for site index s and s
- n*scel.volume() are identical.
So m_site.size() == m_prim_grid_size

Definition at line 225 of file NeighborList.hh.

◆ m_unitcell

std::vector<std::vector<size_type> > CASM::SuperNeighborList::m_unitcell

private

m_unitcell[unitcell_index][neighbor unitcell index]

Definition at line 228 of file NeighborList.hh.

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

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

Detailed Description

Public Types

Public Member Functions

Private Attributes

Member Typedef Documentation

◆ size_type

Constructor & Destructor Documentation

◆ SuperNeighborList() [1/2]

◆ SuperNeighborList() [2/2]

Member Function Documentation

◆ clone()

◆ overlaps()

◆ sites()

◆ sublat_index()

◆ unitcell_index()

◆ unitcells()

Member Data Documentation

◆ m_prim_grid_size

◆ m_site

◆ m_unitcell