flokno
commented
8 months ago Dear @tingguangli , when you run
tdep_parse_output --helpYou see
Usage: tdep_parse_output [OPTIONS] FILES...
Parse DFT force/stress calculations via ase.io.read
╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * files FILES... [default: None] [required] │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --timestep FLOAT [default: 1.0] │
│ --temperature FLOAT [default: None] │
│ --discard-start INTEGER [default: 0] │
│ --ignore-forces --no-ignore-forces [default: no-ignore-forces] │
│ --format TEXT [default: None] │
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy it or customize the installation. │
│ --help Show this message and exit. │
╰──i.e., you can add the timestep via --timestep (in fs).
tingguangli
When I use atomic_distribution in TDEP to get the MSD plot based on an AIMD calculation in vasp, I feel like it only reads the NSW in VASP INCAR file but not the actual time step. (like if I choose time step 2fs and NSW = 30, it will be the same plot for I choose NSW =30 but time step = 1 fs in VASP.) I am wondering is that becasue that the way TDEP read the VASP file wrongly. I used the vasp tools: https://github.com/tdep-developers/tdep-tutorials/tree/main/00_preparation/parsing/VASP for parsing vasprun.xml to TDEP input file format.