  Successful scientific applications of large-scale molecular dynamics often
rely on automated methods for identifying the local crystalline structure of
condensed phases. Many existing methods for structural identification, such as
Common Neighbour Analysis, rely on interatomic distances (or thresholds
thereof) to classify atomic structure. As a consequence they are sensitive to
strain and thermal displacements, and preprocessing such as quenching or
temporal averaging of the atomic positions is necessary to provide reliable
identifications. We propose a new method, Polyhedral Template Matching (PTM),
which classifies structures according to the topology of the local atomic
environment, without any ambiguity in the classification, and with greater
reliability than e.g. Common Neighbour Analysis in the presence of thermal
fluctuations. We demonstrate that the method can reliably be used to identify
structures even in simulations near the melting point, and that it can identify
the most common ordered alloy structures as well. In addition, the method makes
it easy to identify the local lattice orientation in polycrystalline samples,
and to calculate the local strain tensor. An implementation is made available
under a Free and Open Source Software license.
