NeighbourList

class pylimer_tools_cpp.NeighbourList(self: pylimer_tools_cpp.NeighbourList, atoms: list[pylimer_tools_cpp.Atom], box: pylimer_tools_cpp.Box, cutoff: float)

Bases: pybind11_object

Gives access to somewhat fast queries on the neighbourhood of atoms.

This class provides efficient spatial queries for finding atoms within a specified distance of each other.

Instantiate a new neighbour list.

Parameters:

• atoms – Vector of atoms to include in the neighbour list

• box – The simulation box

• cutoff – Maximum distance for neighbour searches

Methods Summary

get_atoms_close_to(self, atom[, ...])	List all atoms that are close to a given one.
remove_atom(self, atom[, debug_hint])	Remove an atom from this neighbour list.

Methods Documentation

get_atoms_close_to(self: pylimer_tools_cpp.NeighbourList, atom: pylimer_tools_cpp.Atom, upper_cutoff: float = 1.0, lower_cutoff: float = 0.0, unwrapped: bool = False, expect_self: bool = False) → list[pylimer_tools_cpp.Atom]

List all atoms that are close to a given one.

It is possible to request it within a new cutoff, though the underlying neighbour list will not be regenerated. For performance reasons, it is recommended to initialize a new NeighbourList if you require a different cutoff, depending on your use case.

You can use a negative value for the upper_cutoff to use the cutoff used for filling the neighbour list buckets.

Parameters:

• atom – The reference atom

• upper_cutoff – Maximum distance for neighbours

• lower_cutoff – Minimum distance for neighbours

• unwrapped – Whether to use unwrapped coordinates

• expect_self – Whether to expect the atom itself in results

Returns:

List of neighbouring atoms

remove_atom(self: pylimer_tools_cpp.NeighbourList, atom: pylimer_tools_cpp.Atom, debug_hint: str = '') → None

Remove an atom from this neighbour list. It will not show up when querying for neighbours, but its neighbours cannot be queried either.

Parameters:

• atom – The atom to remove

• debug_hint – Optional debug information