The force field I use is the Reaxff, and after modeling with the Reaxff, the structural analysis including bond statistics, coordination number and Qn species analysis , so do I need to use fix bond/reaxff to get the bond information and then count?
And I’ve seen some papers calculate bonds by atomically pair radius cutoff valuesand analyze structures(also use Reaxff), so I’m wondering which method is correct.
Thank you very much!
What is “correct” is a matter of interpretation, since the difference between bonded and non-bonded is not a binary (i.e. yes or no) one, but something gradual. You can have partially bonded interactions, transition states and more. What method you should use is dependent on how you define what is a bonded state. So how would you define that?
If this is defined by “the distance between two atoms is smaller than the sum of the covalent radii”, then you use a geometric criterion, but if it is defined by “the bond order parameter is larger than X” (default for ReaxFF is 0.3) you use what fix reaxff/bonds computes.
In many cases, the results from those two definitions will be rather similar and the difference would be a hint as to how large an error any of these analysis approaches has.