Identify Atomic Bonds using Hoppe's EconNN Method

Uses Effective Coordination Numbers (ECoN) and Mean Fictive Ionic Radii (MEFIR).

Usage

econ_nn(distances, atomic_coordinates, tol = 0.2, use_fictive_radius = FALSE)

Arguments

distances

A data.table of interatomic distances.

atomic_coordinates

A data.table of atomic coordinates used to map species to radii.

tol

A bond strength cutoff (default 0.2).

use_fictive_radius

Logical. If TRUE, calculates Hoppe's fictive ionic radius.

Value

A data.table of bonded pairs.

References

Hoppe, R. (1979). "Effective Coordination Numbers (ECoN) and Mean Fictive Ionic Radii (MEFIR)." Zeitschrift Für Kristallographie, 150(1–4), 23–52. doi:10.1524/zkri.1979.150.14.23

Shannon, R. D. (1976). "Revised Effective Ionic Radii and Systematic Studies of Interatomic Distances in Halides and Chalcogenides." Acta Crystallographica Section A, 32(5), 751–767. doi:10.1107/S0567739476001551

See also

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

Examples

dists <- data.table::data.table(Atom1 = c("Si1", "Si1"), Atom2 = c("O1", "O2"),
                                Distance = c(1.6, 2.0),
                                DeltaX = c(1, 0), DeltaY = c(0, 1), DeltaZ = c(0, 0))
ac <- data.table::data.table(Label = c("Si1", "O1", "O2"),
                             OxidationState = c(4, -2, -2))
econ_nn(dists, ac)
#>     Atom1  Atom2 Distance DeltaX DeltaY DeltaZ   Weight
#>    <char> <char>    <num>  <num>  <num>  <num>    <num>
#> 1:    Si1     O1      1.6      1      0      0 1.110372