Update documentation to reflect additions in RMG-database

[kspieks]

This minor PR updates the documentation that tabulates which levels of theory are supported by Arkane. It reflects changes from a recent RMG-database PR, which expanded the supported AEC atom types for coupled cluster calculations with CCSD(T)-F12/cc-pVDZ-F12 and CCSD(T)-F12/cc-pVTZ-F12.

[codecov]

Codecov Report

Merging #2175 (85f7f48) into master (3e94343) will increase coverage by 1.51%.
The diff coverage is 100.00%.

❗ Current head 85f7f48 differs from pull request most recent head ab56ef6. Consider uploading reports for the commit ab56ef6 to get more accurate results

@@            Coverage Diff             @@
##           master    #2175      +/-   ##
==========================================
+ Coverage   47.87%   49.39%   +1.51%     
==========================================
  Files         102      102              
  Lines       27064    29761    +2697     
  Branches     6944     8402    +1458     
==========================================
+ Hits        12957    14700    +1743     
- Misses      12720    13468     +748     
- Partials     1387     1593     +206     

Impacted Files	Coverage Δ
arkane/encorr/bac.py	76.05% <100.00%> (+0.28%)	⬆️
rmgpy/molecule/filtration.py	86.48% <0.00%> (-1.85%)	⬇️
arkane/kinetics.py	12.24% <0.00%> (ø)
rmgpy/molecule/draw.py	53.09% <0.00%> (+0.17%)	⬆️
rmgpy/data/kinetics/library.py	42.32% <0.00%> (+0.79%)	⬆️
rmgpy/rmg/model.py	42.85% <0.00%> (+1.77%)	⬆️
rmgpy/rmg/main.py	25.09% <0.00%> (+2.57%)	⬆️
rmgpy/rmg/input.py	45.60% <0.00%> (+4.33%)	⬆️
rmgpy/qm/mopac.py	74.51% <0.00%> (+5.69%)	⬆️
rmgpy/data/solvation.py	65.59% <0.00%> (+8.66%)	⬆️
... and 1 more

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[kspieks]

This PR also fixes a bug with arkane/encorr/bac.py that prevented it from properly overwritting existing BAC values in RMG-database.

arkane/encorr/bacTest.py is supposed to test that the previous "LevelOfTheory(method='ccsd(t)f12',basis='ccpvtzf12',software='molpro')" entry can be overwritten by the dummy test values. However, since arkane/encorr/bac.py has a logic error while parsing input/quantum_corrections/data.py, it will accidentally overwrite the first instance of "LevelOfTheory(method='ccsd(t)f12',basis='ccpvtzf12',software='molpro')" , which happens to be the new "CompositeLevelOfTheory(freq=LevelOfTheory(method='wb97xd3',basis='def2tzvp',software='qchem'),energy=LevelOfTheory(method='ccsd(t)f12',basis='ccpvdzf12',software='molpro'))" entry for the new RMG-database PR instead. This ultimately causes the unit test to fail since it is expecting "LevelOfTheory(method='ccsd(t)f12',basis='ccpvtzf12',software='molpro')" to have been overwritten. Since that PR is the first to add composite LoT to RMG-database, it has found this bug :)

This PR fixes this error and updates bacTest.py to additionally test that CompositeLevelOfTheory entries are ignored when relevant and overwitten when desired.

@xiaoruiDong Note that the additional test causes this PR's tests to fail due to

arkane.exceptions.BondAdditivityCorrectionError: No BACs available for writing

which is expected since no composite LoT currently exists in RMG-database to overwrite. This unittest will not pass until the twin RMG-database PR is merged. However, the tests for that PR will not pass until this PR is merged. I've checked out the update_ccsdtf12 branch of RMG-database and update_model_chem_doc from RMG-Py and run make test test-unittests locally. These tests pass, so these twin PRs are compatible with each other. But one will need to be merged in first

[xiaoruiDong]

Thanks, @kspieks. I just finished my review. My laptop was dead last week, so the review was postponed... Sorry about that. I am fine with your implementations. I added another commit... Just find there is a 5-layer-if-else + a 2 layer for combined together near your modifications, which is not friendly for reviewing. So I refactored the codes and added a few comments. I restarted both the test for RMG-Py and RMG-test for your PRs, and I will let you know once it finishes. If all checks pass, please remove the temporary commits and rebase the branch. I will help you merge them afterward.

[xiaoruiDong]

@kspieks The only failure test is by Travis, which is okay. Feel free to check my modifications and let me know if you have more to add. Otherwise, please rebase the branches, remove the temporary Git Action commit, and @me to merge your twin PRs. Thanks!

[kspieks]

@xiaoruiDong Thanks for your review and hope your laptop is fine now. I appreciate you making that code section more clear :) It looks good to me so I rebased and removed the temporary git action commit on both this PR and the PR for RMG-database