Local atomic coordination properties

Several properties related to the atomic bonds and angles between them can be computed using Atomes. The existence or the absence of a bond between two atoms \(i\) of species \(\alpha\) and \(j\) of species \(\beta\) is determined by the analysis of the partial \(g_{\alpha\beta}(r)\) and total \(g(r)\) radial distribution functions. Precisely Atomes will consider that a bond exists if the interatomic distance \(D_{ij}\) is smaller than both the cutoff given to describe the maximum distance for first neighbor atoms between the species \(\alpha\) and \(\beta\), \(Rcut_{\alpha\beta}\) (often the first minimum of \(g_{\alpha\beta}(r)\)), and the first minimum of the total radial distribution function, \(Rcut_{tot}\).
Atomes allows the user to specify both \(Rcut_{\alpha\beta}\) and \(Rcut_{tot}\) to choose an appropriate description of the atomic bonds in the system under study. When atomic bonds in a model are defined properly other structural characteristics can be evaluated, as follows:

• Average first coordination numbers
• Individual atomic neighbor analysis
• Proportion of tetrahedral links and units in the structure model
• Distribution of bond lengths for the first coordination spheres
• Angles distributions