Fix _get_dipole_info for DDEC6 ChargemolAnalysis and add test case

[JonathanSchmidt1]

Summary

Major changes:

• fix 1: _get_dipole_info was previously getting the y and z component and the magnitude instead of x,y and z. The only test case was 0,0,0 so it was never noticed.

Previously the dipole was only checked for the spin unpolarized structure with no dipoles (I added some extra spaces to make it more readable what is dipole and what is dipole_magn):

atom number,   atomic symbol,      x,           y,           z,     _ net_charge,     dipole_x,   dipole_y,     dipole_z, dipole_mag, Qxy, Qxz, Qyz,Q(x^2-y^2), Q(3z^2 - R^2), three eigenvalues of traceless quadrupole moment tensor
     1                     Na     0.000000     0.000000     0.000000     0.843200     0.000000     0.000000    -0.000000     0.000000    -0.000003    -0.000003    -0.000003     0.000000     0.000000    -0.000000     0.000000     0.000000
     2                     Cl     2.829447     2.829447     2.829447    -0.843200    -0.000000    -0.000000    -0.000000    0.000000    -0.000020    -0.000020    -0.000020    -0.000000    -0.000000    -0.000041     0.000020     0.000020

New test case for dipole:

atom number, atomic symbol,     x,          y,            z,          net_charge,  dipole_x,     dipole_y,   dipole_z,    dipole_mag, Qxy, Qxz, Qyz,Q(x^2-y^2), Q(3z^2 - R^2), three eigenvalues of traceless quadrupole moment tensor
          1              O      0.000000    -0.000000     0.319088     0.482714    -0.000000     0.000000    -0.127251     _0.127251_    -0.000000    -0.000000    -0.000000     0.040943    -0.162587    -0.050728     0.003219     0.047509
          2              O      0.000000     1.135186    -0.159544     0.258643     0.000000    -0.027857    -0.010944     _0.029929_     0.000000     0.000000    -0.096730    -0.074725    -0.273919    -0.128456     0.008578     0.119878
          3              O      0.000000    -1.135186    -0.159544     0.258643     0.000000     0.027857    -0.010944     _0.029929_    -0.000000     0.000000     0.096730    -0.074725    -0.273919    -0.128456     0.008578     0.119878

output of previous function:
[[0.0, -0.127251, 0.127251], [-0.027857, -0.010944, 0.029929], [0.027857, -0.010944, 0.029929]]
new output:
[[-0.0, 0.0, -0.127251], [0.0, -0.027857, -0.010944], [0.0, 0.027857, -0.010944]]

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.

Only thing left to do is that someone else confirms that it's correct now.

[coderabbitai]

Walkthrough

The update involves adjusting the index range for parsing dipole information in chargemol_caller.py of pymatgen and adding a new test assertion in test_chargemol_caller.py to validate the parsed data.

Changes

File Path	Change Summary
.../chargemol_caller.py	Adjusted index range for dipole information parsing from [7:10] to [6:9].
.../test_chargemol_caller.py	Added assertion for ca.dipoles in test_parse_chargemol2.

Possibly related issues

• Issue Incorrect Parsing of OSZICAR with VASP 6.3.2 #3699: While this issue focuses on parsing OSZICAR files, the essence of ensuring accurate data extraction aligns with the recent change's goal of improving precision in parsing within pymatgen.

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Recent Review Details

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Commits

Files that changed from the base of the PR and between 6376b61 and 6b0030f.

Files selected for processing (1)

• pymatgen/command_line/chargemol_caller.py (4 hunks)

Files skipped from review as they are similar to previous changes (1)

• pymatgen/command_line/chargemol_caller.py

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[janosh]

thanks a lot for fixing and adding a test! 👍