The

1. For each non-equivalent atom A its Voronoi-Dirichlet polyhedron (VDP, Fig. 1) is constructed, and only the atoms X that are direct

2. For each atom type two kinds of radii are determined: Slater's radius, rs, (it is a constant that is predetermined in the ToposPro parameters) and averaged

3. For each pair A-X the reference distance D(A-X) is determined, which is equal to the minimum of two sums: R

4. The D(A-X) values are modified to take into account the features of the structure. For this purpose, if A is a metal atom or both A and X are non-metals, all distances

5. If A is a metal and with the D(A-X) values obtained at the previous steps it does not form any valence bond, the corresponding D(A-X) value is increased up to the maximal distance value of the closest group of contacts. As a result the closest contacts A-X will be considered as valence (the metal atom cannot have zero coordination number).

6. If both A and X are metals and at least one of them is s or p metal then the valence contact between them can exist only if there no valence bonds between them and non-metal atoms, otherwise D(A-X) is specified to zero. This prevents

8. If there are several non-equivalent pairs (A, X) and, hence, several Di(A-X) values have been chosen at the previous steps, then the maximal D

9. All contacts A-X with

The

The

The

With these three algorithms the user can compute adjacency matrices in an automated mode, which is very important for the analysis of large amounts of crystal structures.