Hi Enia , it seems that I have encountered exactly the same problem with GYH123456, I tried with my own example does not work, it seems to be openbabel library problem, but I am not sure of the exact reason, please can you help us find the reason, thank you! bonds.reaxc.reac timesteps 0 to 10000000 read from "bonds.reaxc.reac" conversion of reaction time history to species concentrations... 100.00% ... species generated ... virtual reactions removed ... stoichiometric formulas generated and atom...