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Check isomorphism for conformers #84

Merged
merged 6 commits into from
Mar 7, 2019
Merged

Check isomorphism for conformers #84

merged 6 commits into from
Mar 7, 2019

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alongd
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@alongd alongd commented Mar 7, 2019

Rank conformers by energy, check that the most stable one is isomorphic to the 2D graph representation of the species, if available. If not isomorphic, search for other conformers and report the energy difference.

Also improved arguments in Gaussian jobs

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codecov bot commented Mar 7, 2019

Codecov Report

Merging #84 into master will decrease coverage by 0.11%.
The diff coverage is 22.78%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #84      +/-   ##
==========================================
- Coverage    41.1%   40.99%   -0.12%     
==========================================
  Files          22       22              
  Lines        4885     4923      +38     
  Branches     1263     1274      +11     
==========================================
+ Hits         2008     2018      +10     
- Misses       2556     2576      +20     
- Partials      321      329       +8
Impacted Files Coverage Δ
arc/settings.py 100% <ø> (ø) ⬆️
arc/job/job.py 21.68% <0%> (-0.27%) ⬇️
arc/species/species.py 60.06% <12.5%> (-0.16%) ⬇️
arc/scheduler.py 18.48% <30.35%> (+0.39%) ⬆️
arc/reaction.py 42.35% <0%> (ø) ⬆️

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@alongd alongd force-pushed the conformer_isomorphism branch from fff78a4 to 5df4d37 Compare March 7, 2019 17:44
alongd added 6 commits March 7, 2019 13:40
also relocated TSGuesses to a different method,
determine_most_likely_ts_conformer(), soon to be further expanded
Use G16 defaults, no matter which version of gaussian is actually
running.
Improved accuracy of integrals (orbital electron dendity), SCF points in
the optimization, and the optimization grid.
@alongd alongd force-pushed the conformer_isomorphism branch from 5df4d37 to 8fcb78f Compare March 7, 2019 18:40
@alongd alongd merged commit 51c1aca into master Mar 7, 2019
@alongd alongd deleted the conformer_isomorphism branch March 7, 2019 19:40
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