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Unexpected Tokenizing error when using parse_lammps_dumps #3719

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kimiaGF opened this issue Mar 27, 2024 · 0 comments
Open

Unexpected Tokenizing error when using parse_lammps_dumps #3719

kimiaGF opened this issue Mar 27, 2024 · 0 comments
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@kimiaGF
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kimiaGF commented Mar 27, 2024

Python version

Python 3.9.17

Pymatgen version

Pymatgen 2024.3.1

Operating system version

Linux HPC

Current behavior

When using pymatgen.io.lammps.outputs.parse_lammps_dumps function to read a dump output, it incorrectly puts out an error on some dump files:

ParserError: Error tokenizing data. C error: Expected 20 fields in line 62686, saw 21

Expected Behavior

Correct behavior of this function returns a list of LammpsDump objects corresponding to each snapshot in Lammps simulation.

Minimal example

snapshots = [d for d in parse_lammps_dumps(path_to_dump_file)]

Relevant files to reproduce this bug

files are too large to upload to github, so they are uploaded to google drive.

To replicate the error, use dump.data_shock_chunk_-30.0.
To replicate a successful run, use dump.data_shock_chunk_-5.0.

@kimiaGF kimiaGF added the bug label Mar 27, 2024
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