Identify Atomic Bonds using CrystalNN

Port of Pymatgen's CrystalNN weighting logic. Includes Porosity, Electronegativity, and Distance penalties. Uses specific Decision Tree logic for radii (Shannon -> Covalent -> Atomic) per pymatgen's fallback logic.

Usage

crystal_nn(
  distances,
  atomic_coordinates,
  expanded_coords,
  unit_cell_metrics,
  cutoff_length = 7,
  x_diff_weight = 3,
  porosity_adjustment = TRUE,
  distance_cutoffs = c(0.5, 1)
)

Arguments

distances

Ignored.

atomic_coordinates

Primary atom set.

expanded_coords

Expanded supercell.

unit_cell_metrics

Cell parameters.

cutoff_length

Voronoi cutoff. Default 7.0 matches Pymatgen CrystalNN default.

x_diff_weight

Electronegativity weight (default 3.0).

porosity_adjustment

Logical (default TRUE).

distance_cutoffs

Vector c(0.5, 1.0).

Value

A data.table of bonded pairs.

References

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.

Pauling, L. (1960). The Nature of the Chemical Bond and the Structure of Molecules and Crystals: An Introduction to Modern Structural Chemistry. Cornell University Press.

Pan, H., Ganose, A. M., Horton, M., et al. (2021). "Benchmarking Coordination Number Prediction Algorithms on Inorganic Crystal Structures." Inorganic Chemistry, 60(3), 1590–1603. doi:10.1021/acs.inorgchem.0c02996

See also

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

Examples

# \donttest{
cif_path <- system.file("extdata", "1590946.cif", package = "crystract")
if (file.exists(cif_path)) {
  res <- analyze_single_cif(cif_path, bonding_algorithms = "crystal_nn")
  print(head(res$bonds_crystal_nn[[1]]))
}
#> Key: <Atom1, Atom2, Distance>
#>     Atom1         Atom2 Distance    DeltaX        DeltaY    DeltaZ Weight
#>    <char>        <char>    <num>     <num>         <num>     <num>  <num>
#> 1:  Si1_2   Sr1_1_0_0_0 3.163544 -0.819110  2.220446e-16  3.055662  1.000
#> 2:  Si1_2   Sr1_2_0_0_0 3.245310  3.235890  0.000000e+00 -0.247086  0.914
#> 3:  Si1_2 Sr1_4_0_-1_-1 3.184477  0.755852 -2.575000e+00 -1.714338  0.970
#> 4:  Si1_2  Sr1_4_0_0_-1 3.184477  0.755852  2.575000e+00 -1.714338  0.970
#> 5:  Si1_2  Sr2_1_0_0_-1 3.261366 -1.903417  0.000000e+00 -2.648304  0.908
#> 6:  Si1_2 Sr2_3_-1_-1_0 3.465249 -2.214841 -2.575000e+00  0.686880  0.729
#>    DistanceError
#>            <num>
#> 1:             0
#> 2:             0
#> 3:             0
#> 4:             0
#> 5:             0
#> 6:             0
# }