Identify Atomic Bonds using Voronoi Tessellation

Performs 3D Voronoi analysis on the supercell.

Usage

voronoi_nn(
  atomic_coordinates,
  expanded_coords,
  unit_cell_metrics,
  cutoff = 13,
  tol = 0
)

Arguments

atomic_coordinates

A data.table of the primary (asymmetric) atom set.

expanded_coords

A data.table of atoms in the expanded supercell.

unit_cell_metrics

A data.table with cell parameters.

cutoff

Distance cutoff (default 13.0).

tol

Tolerance for solid angle weights (default 0).

Value

A data.table of bonded pairs.

References

O'Keeffe, M. (1979). "A Proposed Rigorous Definition of Coordination Number." Acta Crystallographica Section A, 35(5), 772–775. doi:10.1107/S0567739479001765

Aurenhammer, F., Klein, R., & Lee, D.-T. (2013). Voronoi Diagrams and Delaunay Triangulations. World Scientific Publishing Company.

See also

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

Examples

# \donttest{
cif_path <- system.file("extdata", "1590946.cif", package = "crystract")
if (file.exists(cif_path)) {
  res <- analyze_single_cif(cif_path, bonding_algorithms = "voronoi")
  print(head(res$bonds_voronoi[[1]]))
}
#> Key: <Atom1, Atom2, Distance>
#>     Atom1         Atom2 Distance  SolidAngle       Area    DeltaX        DeltaY
#>    <char>        <char>    <num>       <num>      <num>     <num>         <num>
#> 1:  Si1_2  Si1_1_-1_0_0 4.932659 0.004328448 0.02851541 -4.055000  2.220446e-16
#> 2:  Si1_2   Si1_1_0_0_0 4.932659 0.004328448 0.02851541  4.055000  2.220446e-16
#> 3:  Si1_2   Sr1_1_0_0_0 3.163544 1.687714706 6.98543858 -0.819110  2.220446e-16
#> 4:  Si1_2  Sr1_2_-1_0_0 4.880369 0.051103880 0.31256672 -4.874110  0.000000e+00
#> 5:  Si1_2   Sr1_2_0_0_0 3.245310 1.546340541 6.41452789  3.235890  0.000000e+00
#> 6:  Si1_2 Sr1_4_0_-1_-1 3.184477 1.609248649 6.54596788  0.755852 -2.575000e+00
#>       DeltaZ    MaxSA     Weight DistanceError
#>        <num>    <num>      <num>         <num>
#> 1:  2.808576 1.687715 0.00256468             0
#> 2:  2.808576 1.687715 0.00256468             0
#> 3:  3.055662 1.687715 1.00000000             0
#> 4: -0.247086 1.687715 0.03027993             0
#> 5: -0.247086 1.687715 0.91623337             0
#> 6: -1.714338 1.687715 0.95350751             0
# }