tblite_adjlist Module Reference

Implementation of a sparse neighbour map in compressed sparse row format. More...

Data Types
module	adjacency_list
	Neighbourlist in CSR format. More...

Functions/Subroutines
subroutine, public	new_adjacency_list (self, mol, trans, cutoff, complete)
	Create new neighbourlist for a given geometry and cutoff.

Detailed Description

Implementation of a sparse neighbour map in compressed sparse row format.

A symmetric neighbour map given in dense format like

	1	2	3	4	5	6
1		x		x	x
2	x		x		x	x
3		x		x		x
4	x		x		x	x
5	x	x		x
6		x	x	x

Is stored in two compressed array identifying the neighbouring atom nlat and its cell index nltr. Two index arrays inl for the offset and nnl for the number of entries map the atomic index to the row index.

inl   =  0,       3,          7,      10,         14,      17, 20
nnl   =  |  2 ->  |  3 ->     |  2 ->  |  3 ->     |  2 ->  |  |
nlat  =     2, 4, 5, 1, 3, 5, 6, 2, 4, 6, 1, 3, 5, 6, 1, 2, 4, 2, 3, 4
nltr  =     1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1

An alternative representation would be to store just the offsets in inl and additional beyond the last element the total number of neighbors. However, the indexing is from inl(i) to inl(i+1)-1 could be confusing, therefore two arrays are used for clarity.

Function/Subroutine Documentation

new_adjacency_list()

subroutine, public tblite_adjlist::new_adjacency_list	(	type(adjacency_list), intent(out)	self,
		type(structure_type), intent(in)	mol,
		real(wp), dimension(:, :), intent(in)	trans,
		real(wp), intent(in)	cutoff,
		logical, intent(in), optional	complete )

Create new neighbourlist for a given geometry and cutoff.

Parameters

[out]	self	Instance of the neighbourlist
[in]	mol	Molecular structure data
[in]	trans	Translation vectors for all images
[in]	cutoff	Realspace cutoff for neighbourlist generation
[in]	complete	Whether a complete or a symmetrical reduced map should be generated