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Dated documentation for PairList structure #21

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mcsloy opened this issue Mar 10, 2022 · 0 comments
Open

Dated documentation for PairList structure #21

mcsloy opened this issue Mar 10, 2022 · 0 comments

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@mcsloy
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mcsloy commented Mar 10, 2022

The documentation provided for the PairList structure is outdated. It makes references to fields that no longer exist, such as r, and fails to mention others, such as s.

"""
`PairList` stores a neighbourlist as a list of pairs
```
PairList(X, cutoff, cell, pbc)
PairList(nlist::CellList)
```
where
* `X` : positions, either as 3 x N matrix or as `Vector{SVec}`
* `cutoff` : positive real value
* `cell` : 3 x 3 matrix, with rows denoting the cell vectors
* `pbc` : 3-tuple or array, storing periodicity information
### Kw-args:
* `int_type` : default is `Int`
* `store_first` : whether to store the array of first indices, default `true`
* `sorted` : whether to sort the `j` vector, default `false`
### PairList fields
`X, cutoff, i, j, r, R, first`, where
`(i[n], j[n])` denotes the indices of a neighbour pair, `r[n]` the distance
between those atoms, `R[n]` the vectorial distance, note this is identical to
`X[i[n]]-X[j[n]]` without periodic b.c.s, but with periodic boundary conditions
it is different. `first[m]` contains the index to the first `(i[n], j[n])` for
which `i[n] == first[m]`, i.e., `(j, first)` essentially defines a compressed
column storage of the adjacancy matrix.
"""
struct PairList{T <: Real, TI <: Integer}
X::Vector{SVec{T}}
C::SMat{T}
cutoff::T
i::Vector{TI}
j::Vector{TI}
S::Vector{SVec{TI}}
first::Vector{TI}
end

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