I’m confused, if your image is rendering broken bonds, what do you mean by “all six bonds break?” It looks like most atoms only have two broken bonds along a crack.
I don’t think it’s right to interact with each other as long as the bonds of one atom are broken，So I wonder if it would be nice to add something like biconncomp in the graph in matlab
How are atoms incorrectly interacting? With bond forces, pair forces? Is your concern that the implementation of the model you’re using (bpm/spring, bpm/rotational?) is incorrect, or are you requesting a new model be added? I’m not familiar with Matlab, so the analogy is unfortunately lost on me.
To get more helpful responses, I recommend reading the guidelines for posting. I’d like to help, but it’s hard to give good advice without a clear question and system details.