brucefan1983/GPUMD: GPUMD-v3.1.1

Fixed a bug related to MD simulations with the NEP potential: This bug exists in both GPUMD-v3.0 and GPUMD-v3.1. The bug is only for the gpumd executable, not for the nep executable. It occurs when one runs MD simulations with one or more directions being non-periodic and the box thickness in a non-periodic direction is less than twice of the force cutoff distance of the NEP potential. In this case, the code will wrongly treat the non-periodic directions as periodic and replicate the box in those directions. We have fixed this bug in the current release, GPUMD-v3.1.1. If one wants to use NEP3 as first released in GPUMD-v3.1, one should use GPUMD-v3.1.1 instead. If one wants to use NEP2 as finally released in GPUMD-v3.0 and wants to avoid this bug, one should make the non-periodic directions thick enough or fix the code as in this commit (https://github.com/brucefan1983/GPUMD/commit/f3334dd7113a81e0846ef92b763d59ef477e326b) In short, we strongly suggest using NEP3 and GPUMD-v3.1.1, because NEP3 can achieve significantly higher accuracy compared to NEP2