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Filter Ghost Distances Using Atomic Radii

filter_ghost_distances.Rd

Cleans a distance table by removing physically implausible distances. It uses a table of atomic radii to establish a plausible bond length range for each atom pair. Any calculated distance falling outside this range (defined by a margin) is considered a "ghost" distance and is removed. This is particularly useful for cleaning data from disordered crystal structures.

Usage

filter_ghost_distances(
  distances,
  atomic_coordinates,
  margin = 0.1,
  radii_type = "covalent"
)

Arguments

distances

A data.table of interatomic distances, typically from calculate_distances. Must contain Atom1, Atom2, and Distance.

atomic_coordinates

A data.table of asymmetric atoms from extract_atomic_coordinates. Used to link atom labels to element types.

margin

A numeric value (default 0.1) specifying the tolerance. A distance d between atoms with radii r1 and r2 is kept if (r1+r2)*(1-margin) <= d <= (r1+r2)*(1+margin).

radii_type

A character string specifying the type of radius to use for the calculation (e.g., "covalent", "ionic"). This value must correspond to an entry in the Type column of the active radii table. Defaults to "covalent". The radii table can be customized for the session using set_radii_data().

Value

A list containing two data.tables:

kept

The distances considered physically plausible.

removed

The "ghost" distances that were filtered out, with columns explaining the reason for removal.

See also

Other post-processing: calculate_weighted_average_network_distance(), set_radii_data()

Examples

# Create minimal dummy data for demonstration
distances <- data.table::data.table(
  Atom1 = c("Si1_1_0_0", "O1_1_0_0"),
  Atom2 = c("O1_1_0_0", "Si1_1_0_0"),
  Distance = c(1.6, 0.5) # 0.5 is implausibly short
)

atomic_coords <- data.table::data.table(
  Label = c("Si1", "O1")
)

# Run the filter
result <- filter_ghost_distances(distances, atomic_coords, margin = 0.1)

print(result$kept)
#> Empty data.table (0 rows and 3 cols): Atom1,Atom2,Distance
print(result$removed)
#>        Atom1     Atom2 Distance expected_dist lower_bound upper_bound
#>       <char>    <char>    <num>         <num>       <num>       <num>
#> 1: Si1_1_0_0  O1_1_0_0      1.6          1.83       1.647       2.013
#> 2:  O1_1_0_0 Si1_1_0_0      0.5          1.83       1.647       2.013
#>                   Reason
#>                   <char>
#> 1: Distance is TOO SHORT
#> 2: Distance is TOO SHORT