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deepmodeling / dpdata

Manipulating multiple atomic simulation data formats, including DeePMD-kit, VASP, LAMMPS, ABACUS, etc.
https://docs.deepmodeling.com/projects/dpdata/
GNU Lesser General Public License v3.0
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[BUG] Cell file read incorrectly for 'qe/cp/traj' format #517

Closed rashidrafeek closed 11 months ago

rashidrafeek commented 11 months ago

When reading a qe/cp/traj output, the cells read from the [prefix].cel file is read incorrectly. The cells written in the [prefix].cel file produced in a cp.x calculation is transposed as mentioned here. But while reading them they are not transposed by dpdata and thereby a transposed cell instead of the original cell is read by dpdata. I noticed this when I tried to use dpdata to read a trajectory I ran previously and used the to_ase_structure function of LabeledSystem to write it into a different format and visualized it. I think the test file which tests this functionality was not created by a quantum espresso cp.x calculation.

I have modified dpdata locally to fix this and have confirmed that transposing the cell gives the desired result by visualizing. I can submit a pull request fixing this if it is okay.

wanghan-iapcm commented 11 months ago

@rashidrafeek Thank you very much for reporting the bug. You are right the test file was synthetic data. Could you please help us checking if the #520 fixes the issue and if the test file looks like one that is generated by cp.x?

rashidrafeek commented 11 months ago

Yeah, I have tested the PR and it does fix this issue. And yes, the transposed test file in the PR is similar to the one produced by QE.