I am simulating a system of polyoxometalate and water using LAMMPS 2022 on HPC cluster. The generated output is not printed in the output file after the minimization step(even the dump file is not generated), although the job keeps running on the cluster. I have attached the input script and the output file, which is generated.
polyoxo.in (1.1 KB)
job.38586.out (4.9 KB)
Your pressure after minimization is way too high, 350,000 atm! It looks like your density is high, though my math could be wrong. You should double check your units when making and importing the data file.
High density and pressure can cause fix npt (to appear?) to hang.
This could be due to atoms moving very fast and thus having positions so far away from the simulation box that the rewrapping algorithm will be stuck in a loop that does not converge. We changed the heuristics for that with LAMMPS version 22 Dec 2022. So you should re-run your simulation with either version 22 Dec 2022 or 8 Feb 2023 of LAMMPS. If the aforementioned problem exists (usually due to a bad geometry or bad force field, or bad simulation settings), LAMMPS will abort with an error instead of getting stuck “chasing” those fast moving atoms.
Thanks, Dr. Axel. Using 8 Feb 2023 version, it worked.