Neighbor Lists

Construction of neighbor lists and callback helpers bridging to the KIM-API.

KIM_API.@cast_as_kim_neigh_fptr — Macro
@cast_as_kim_neigh_fptr(func)

Macro to create a C function pointer for KIM-API neighbor list callbacks. This macro converts a Julia function into a C-compatible function pointer for use with KIM-API's neighbor list interface.

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KIM_API.NeighborListContainer — Type
NeighborListContainer

Container for neighbor list data with KIMNeighborList backend.

This mutable struct stores the neighbor list query function for efficient access during KIM-API callback queries. It includes the query function and temporary storage for index conversions.

Fields

  • neighbors::Vector{Vector{Int32}}: Pre-computed neighbors for each atom
  • temp_storage::Vector{Int32}: Reusable storage for current neighbor query

Notes

The temp_storage field is used to convert between Julia's 1-based indexing and KIM-API's 0-based indexing during callback execution, avoiding memory allocations in the hot path.

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KIM_API.create_kim_neighborlists — Method

Create neighbor lists for KIM-API using KIMNeighborList C++ backend. It uses the lower level API of KIMNeighborList to return all required information. Below is the copy pasted code from the KIMNeighborList package

TODO: Add the desired function in KIMNeighborLists, so that here it is blank call to the neighlist library?

Returns: (nlcontainer, allcoordinates, allspecies, contributing, atomindices)

  • nl_container: Neighbor list data for each cutoff
  • all_coordinates: Positions including ghost atoms
  • all_species: Species including ghost atoms
  • contributing: 1 for real atoms, 0 for ghosts
  • atom_indices: Original atom index for each position

The function creates neighbor lists for each cutoff using the KIMNeighborList backend and handles ghost atom generation for periodic boundary conditions.

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