I met a problem for the usage of bond_harmonic. I wrote my own fix command to add specific atoms during simulation, by calling create_atom() in atom_vec.cpp. Additionally, my model also contains a pre-defined bond lists. I found that after adding several tens of atoms, the bond list seems to have problem. In the visualization, some bonds appeared on the newly-added atoms and some old bonds just disappear, which is not correct.
I guess this behavior is because my code make the bond list (might be static in memory) broken? But after I read the source code I still cannot locate the reason. I was wondering if someone with experience can let me know how the bond list works (what is the data structure and are they dynamic during simulation). Thank you so much!