Why was there all zero data output in the msd.out file when I ran PIMD with GPUMD, compared to a normal nvt_ber ensemble simulation?

GPUMD
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OK, this is because PIMD/RPMD/TRPMD does not support MSD (mean-square displacement) calculation. You can use compte_sdc (compute_sdc — GPUMD documentation) instead, which can calculate the VAC (velocity auto-correlation function) and the SDC (self-diffusion coefficient), and the results are physically equivalent to MSD.

As an aside, I noticed that you used PIMD in the second run (the production run) to calculate the MSD. This might not be what you intended to use. I think you need to change to use TRPMD (ensemble (PIMD) — GPUMD documentation). So you can write

ensemble trpmd 32

for the second run.

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Thanks for your reply , I will try your suggestion .