changing DL_Poly units

[lexi-x]

Fixes #2393

Changes made in this Pull Request:

• Added unit conversion to DL_Poly
• ~~Removed forces from TRZ~~
• Updated test values for DL_Poly

As mentioned in #2393, this likely requires more work with test cases and code modifications regarding where the DL_Poly conversions are made, so any feedback is appreciated!

PR Checklist

• [x] Issue raised/referenced?
• [x] Tests updated/added?
• [ ] Documentation updated/added?
• [ ] package/CHANGELOG file updated?
• [ ] Is your name in package/AUTHORS? (If it is not, add it!)

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

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📚 Documentation preview 📚: https://mdanalysis--4983.org.readthedocs.build/en/4983/

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 93.41%. Comparing base (dcaa087) to head (a267752). Report is 20 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4983      +/-   ##
===========================================
- Coverage    93.42%   93.41%   -0.02%     
===========================================
  Files          177      189      +12     
  Lines        21859    22925    +1066     
  Branches      3078     3078              
===========================================
+ Hits         20422    21415     +993     
- Misses         986     1059      +73     
  Partials       451      451              

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[lexi-x]

Based on feedback about TRZ being dropped, I removed the parts regarding TRZ in the latest commit.

[orbeckst]

@cbouy and @talagayev could you please review and shepherd this PR? This is a GSOC applicant for one of your projects.

[lexi-x]

@orbeckst @cbouy Thank you for your recommendations! Sorry for the delayed response, I was caught up in making the proposal and another pull request. I made the changes you recommended and I wanted to make sure that my thought process was valid in implementing them before making commits.

1. After changing the DL_POLY force units to Da*Angstrom/ps, I added the conversion factor to units.py based on my understanding of the unit conversions:

forceUnit_factor = {
    "kJ/(mol*Angstrom)": 1.0,
    "kJ/(mol*A)": 1.0,
    "kJ/(mol*\u212b)": 1.0,
    "kJ/(mol*nm)": 10.0,
    "Newton": 1e13 / constants["N_Avogadro"],
    "N": 1e13 / constants["N_Avogadro"],
    "J/m": 1e13 / constants["N_Avogadro"],
    "kcal/(mol*Angstrom)": 1 / constants["calorie"],
    "Da*Angstrom/ps": 1000.0 / constants["N_Avogadro"] / 1e10 * 1e12
} 

2. Regarding making the same unit conversions for History Reader, when I originally added the conversion to both functions, the test cases returned results that were scaled by 10000 instead of 100, so I suspect it was making double conversions. Would this still be an issue when using native force units instead of direct conversion? Thank you!

[orbeckst]

@lexi-x if all conversions are done in the standard way then there shouldn't be any double conversions. Try it and make the tests pass.

[orbeckst]

Explain to us why what you're doing is correct — that's the best way to be sure that you're right and makes it easy for us to review.

[orbeckst]

@lexi-x do you have some time to complete the PR? Would be great to get it done.

[orbeckst]

@lexi-x do you think you'll continue on the PR?

[lexi-x]

@lexi-x do you think you'll continue on the PR?

Yes sorry, I have been a bit busy lately but I'm making the edits right now.

[lexi-x]

@lexi-x do you have some time to complete the PR? Would be great to get it done.

I added the unit conversions and modified the tests accordingly, let me know if anything needs to be changed. Thanks!