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smutao / PyVibMS

A PyMOL plugin for visualizing vibrations in molecules and solids
https://sites.smu.edu/dedman/catco/publications/pdf/434.pdf
BSD 2-Clause "Simplified" License
36 stars 8 forks source link

Problem with gaussian .log files #2

Open dmaratanes opened 1 month ago

dmaratanes commented 1 month ago

Hi, I'm having some trouble when trying to open some .log files from a gaussian calculated transition state and trying to visualize the vibrations. It opens the structure but it doesn't recognise the vibrations and no vibration modes appear, also the lattice vectors origin shows as 0.0, 0.0, 0.0.

The messages that appear when opening the file are: line 2155, in loadxyz parse_g16(xyz_file_path)

line 706, in parse_g16 nvib,natom = count_atom(container) ^^^^^^^^^^^^^^^^^^^^^

line 169, in count_atom natom = f2[0] - f1[0] - 1 ~~^^^

IndexError: list index out of range

Do you have any idea what the problem might be and how to fix it? Thanks

smutao commented 1 month ago

Could you please share that gaussian output file? I can take a look into this. ^^

dmaratanes commented 3 weeks ago

Sure, it would be files similar to this one. Maybe it has something to do with the system having Ir atoms, because in other systems with no metals it worked fine for me example.log