It seems all the text in my response somehow did not go through.
Thank you for looking into this, Aidan. I did notice the non-numerical output before, but I was getting that only when I had 1 or 3 chains, and not when I had 2 chains. I had resolved the nan values by correcting geometry once before, so I was looking out for that. But since I create multiple chains by replicating the same initial structure (for the case with 1 or 2 chains), I did not expect it to be because of overlapping particles (if there was an error in 1 chain, it should have been there for 2 chains too).
When I tried it again just now with only 2 chains, I get numerical results at first (for energy, pressure and pair energy) and then a segmentation fault. The data file I used is attached. Other files are as before. I also checked the initial coordinates for all atoms, and they are all distinct, and within the box dimensions. Could you please try checking with this file as well? I am not sure but I am probably missing something very basic here.
Thanks again,
Ankit
pmmaReax.data (9.77 KB)