Bramble: adaptive common neighbor analysis (CNA) for the recognition of surface topologies in nanoparticles

In heterogeneous catalysis, the active site is the specific region on the catalyst surface where the chemical reaction occurs. It plays a vital role in facilitating reactions by providing a unique arrangement of atoms and chemical properties to promote the conversion of reactants into products. Identifying these atomic motifs is crucial towards the atom-scale understanding of catalysis. Towards this aim, the common neighbor analysis (CNA) procedure acts as a powerful computational method used to analyze and classify atomic structures in materials. It involves examining the local environment of each atom to identify and quantify the types of atomic coordination and bonding, providing insights into the structural properties and behavior of materials at the atomic scale. Bramble is an efficient C++-based command-line tool to perform the CNA analysis. Uniquely, it is coupled to a pattern identification library for facile identification of the CNA fingerprints. Furthermore, for unknown fingerprint it offers the option to perform a similarity analysis based on the minimization of the Hilbert-Schmidt norm