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deepmodeling / dpdata

A Python package for manipulating atomistic data of software in computational science
https://docs.deepmodeling.com/projects/dpdata/
GNU Lesser General Public License v3.0
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[BUG] Abnormal Box Definition after Conversion from ABACUS stru File to LAMMPS lmp File #739

Open YuanFeiyue20 opened 1 month ago

YuanFeiyue20 commented 1 month ago

Bug summary

I encountered a problem when converting an ABACUS structure file (stru) to a LAMMPS format (lmp) using dpdata. The resulting lmp file contains an invalid box definition, where zlo is greater than zhi. This causes abortion in the model_devi step in DP-Gen, which depends on LAMMPS to execute. I'm not sure if this is a bug. Thank you for your attention.

dpdata Version

dpdata v0.2.18

Input Files, Running Commands, Error Log, etc.

Input files: STRU, stru_to_lmp.py STRU.txt, stru_to_lmp.txt Running Command: python3 stru_to_lmp.py Output file: conf.lmp conf.txt Error Log(in DP-Gen): init.err init.txt

Problem Details zlo: -8.5312811800 zhi: 0.0000000000 This configuration is incorrect since zhi should always be greater than zlo.

Steps to Reproduce

  1. Use dpdata stru_to_lmp.txt to convert an ABACUS stru file STRU.txt to LAMMPS lmp format.
  2. Inspect the resulting lmp file for box definitions, which here actually refers to the z direction.

Further Information, Files, and Links

No response