I am trying to model system with carbon & silicon atoms using tersoff potential. Is it possible to count the number of bonds between C & Silicon atoms in a particular geometric region?? If not, can i just measure the distance between adjacent atoms and count it as a bond if the distance is less than cutoff ? I am thinking that as the atoms move back & forth thru the simulation domain, the distance may change.
So, please let me know the best way to have a sense on no of bonds.