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Identify Atomic Bonds using the Minimum Distance Method

minimum_distance.Rd

Identifies bonded atoms by finding the nearest neighbor distance (d_min) for each central atom and defining a cutoff distance (d_cut) as d_cut = (1 + delta) * d_min.

Usage

minimum_distance(distances, delta = 0.1)

Arguments

distances

A data.table of interatomic distances from calculate_distances.

delta

The relative tolerance parameter (default 0.1).

Value

A data.table of bonded pairs.

See also

Other bonding algorithms: brunner_nn_reciprocal(), crystal_nn(), econ_nn(), voronoi_nn()

Examples

dists <- data.table::data.table(Atom1 = c("A", "A"), Atom2 = c("B", "C"),
                                Distance = c(1.5, 2.5),
                                DeltaX = c(1, 0), DeltaY = c(0, 1), DeltaZ = c(0, 0))
minimum_distance(dists, delta = 0.1)
#>     Atom1  Atom2 Distance DeltaX DeltaY DeltaZ Weight
#>    <char> <char>    <num>  <num>  <num>  <num>  <num>
#> 1:      A      B      1.5      1      0      0      1