I would like to calculate the number of A-A, A-B, etc, bonds in a large supercell of solid solution, where A,B,… are different atomic species. Is it possible to do this directly in GULP? I have tried using the “bond” and “distance” keywords, which returned in the output file the message:
No bonds found for any atoms in the system
I see in the help file there is also the “connect” option - would I have to manually specify which atoms in the supercell are bonded to which neighbours; ie.
connect A1 A2
and so forth? Your help would be greatly appreciated.
What is called a bond or a distance is obviously subjective and depends on the criteria you specify. By default, GULP has a cutoff for distances of 2 Angstroms, but you can increase this using the “cutd” option to anything you want until you find the distances you are looking for. Similarly, the bond option depends on the covalent radii and a tolerance to define what are bonds or not (you also need a “mole” option or similar to trigger the bond calculation). If you don’t find any bonds it means either one of the molecule options isn’t being used, or the covalent radii for the element are too short and need to be increased using the “covalent” option.