A new way of thinking about conformers

[alongd]

• Generate non-TS conformers bottom-up instead of top-down
• Use Gromacs with a fitted force field if desired (if species.force_field is set to 'fit')

[codecov]

Codecov Report

Merging #143 into master will increase coverage by 2.62%.
The diff coverage is 60.56%.

@@            Coverage Diff             @@
##           master     #143      +/-   ##
==========================================
+ Coverage   42.93%   45.56%   +2.62%     
==========================================
  Files          27       28       +1     
  Lines        6118     7223    +1105     
  Branches     1583     1882     +299     
==========================================
+ Hits         2627     3291     +664     
- Misses       3110     3462     +352     
- Partials      381      470      +89

Impacted Files	Coverage Δ
arc/job/submit.py	100% <ø> (ø)	⬆️
arc/settings.py	100% <ø> (ø)	⬆️
arc/ts/run_autotst.py	34.28% <0%> (ø)	⬆️
arc/species/__init__.py	100% <100%> (ø)	⬆️
arc/arc_exceptions.py	100% <100%> (ø)	⬆️
arc/parser.py	87.76% <100%> (ø)	⬆️
arc/scheduler.py	18.26% <18.38%> (-0.77%)	⬇️
arc/job/job.py	21.39% <25%> (+0.15%)	⬆️
arc/plotter.py	33.82% <30%> (+3.22%)	⬆️
arc/utils/scale.py	69.14% <43.75%> (-0.98%)	⬇️
... and 9 more

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[alongd]

Tasks:

• Minimize acpype as much as possible and add tests
• Conformers tests
• Todo flags
• Test conformers in speciesTests
• Use the Gaussian_SVPFit.out file in testing
• Report the most stable conformer
• Chirality translations
• load conformers yaml file into a species xyz
• Does it filter by dE threshold?
• Solve undeterministic symmetry

    File "/home/travis/build/ReactionMechanismGenerator/ARC/arc/species/conformersTest.py", line 808, in test_determine_torsion_symmetry
      for i in range(len(torsions))]), 19)
  AssertionError: 20 != 19```
  

• Add chiral adjastments to 'gromacs', or remove it... ?