Miscellaneous changes 2 #112
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Also specify if species failed to converge
kinetics_job.execute()
to handle conformer energies better (they are often None from failed TS guesses)
Made check_species_xyz() a method Initialize self.final_xyz with None instead of '' Determine spin multiplicity from conformers if needed Allow xyz to be a list (in which case values are appended to self.conformers instead of self.initial_xyz)
it is now None instead of ''
Also, create an output directory if doesn't exist
Required when a species is defined with an xyz list, but legacy conformer generation is turned off.
Considering species defined with a list of xyz when generate_conformers is turned off
Codecov Report
@@ Coverage Diff @@
## master #112 +/- ##
==========================================
+ Coverage 40.36% 40.52% +0.15%
==========================================
Files 22 22
Lines 5393 5419 +26
Branches 1407 1415 +8
==========================================
+ Hits 2177 2196 +19
- Misses 2866 2870 +4
- Partials 350 353 +3
Continue to review full report at Codecov.
|
Codecov Report
@@ Coverage Diff @@
## master #112 +/- ##
=========================================
+ Coverage 40.36% 42.17% +1.8%
=========================================
Files 22 22
Lines 5393 5544 +151
Branches 1407 1494 +87
=========================================
+ Hits 2177 2338 +161
+ Misses 2866 2850 -16
- Partials 350 356 +6
Continue to review full report at Codecov.
|
Changed xyz argument to coord Added a helpful error message if line has a different element length than expected
Removed `conformers_paths`, they can be given via `xyz`
the folder contains other important files such as conformers. Instead, opening a file with 'w' permission is enough to overwrite it if it exists
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xyzcan now be a list)