Purpose

An atoms object contains atomic numbers, all dynamical variables and connectivity information for all the atoms in the simulation cell. It is initialised like this:

where N is the number of atoms to allocate space for and lattice is a $3\times3$ matrix of lattice vectors given as column vectors.

Atoms also contains a Connection object, which stores distance information about the atom neghbours after calc_connect has been called. Rather than using a minimum image convention, all neighbours are stored up to a radius of cutoff, including images