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Improve error/warning messages concerning energy barriers in Arkane #1575

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merged 4 commits into from
Jun 13, 2019

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alongd
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@alongd alongd commented Apr 9, 2019

Added a warning if a reaction barrier is too high in Arkane.
Also enhanced a related error message in tunnelling.
Minor: corrected reciprocal T axis units in Arkane plots (1000/K is strange, should be either 1/K or K^-1)

@alongd alongd requested a review from goldmanm April 9, 2019 18:09
@alongd alongd force-pushed the arkane_energies branch from bcc2ec0 to 20adfba Compare April 9, 2019 18:10
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alongd commented Apr 9, 2019

Addresses #1574

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codecov bot commented Apr 9, 2019

Codecov Report

Merging #1575 into master will not change coverage.
The diff coverage is n/a.

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@@          Coverage Diff           @@
##           master   #1575   +/-   ##
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  Coverage    41.5%   41.5%           
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  Files         176     176           
  Lines       29306   29306           
  Branches     6033    6033           
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  Hits        12163   12163           
  Misses      16292   16292           
  Partials      851     851

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The 1000/K axis is a pretty common convention to get the axis numbers into a more readily readable range, numbers in the ones or tenths digit instead of being in the thousandths digit and a bunch of leading zeros. The 1000/K axis is strangely artificial though and even though it makes the results more readable, it does not make them any more intelligible.

Might I suggest instead adding a second axis, either in K or C? Something like what this link describes doing in Origin. Then you can keep either 1000/K or 1/K on the primary axis to keep the linearity of the Arrhenius plot, but the secondary axis makes it more easily understood which is probably your goal.

http://blog.originlab.com/graphing/display-celsius-as-top-axis-in-arrhenius-plot

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alongd commented Apr 10, 2019

Thanks for the suggestion, I agree it looks better to have a dual T axis.
I'll clarify that my original comment was just for the axis units (should be 1/K and not 1000/K as we currently have), I did not mean to change the axis scaling (we'll keep the primary axis at 1000/T, not 1/T).
Again, thanks for the helpful comment, I'll try to implement it!

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Oh I see! Yeah, having the units be 1000/K makes it ambiguous if the transform has already been done or done twice. Weird minor error. Carry on!

@alongd alongd mentioned this pull request Apr 30, 2019
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alongd commented Apr 30, 2019

@goldmanm, could you take a look?

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alongd commented May 16, 2019

@goldmanm, could you take a look at this PR?

alongd added 4 commits June 13, 2019 10:22
`1000/K` is strange, should be either `1/K` or `K^-1`
arbitrarily chose 500 kJ/mol. Usually if this is triggered than the
barrier is even much higher.
Added the barrier heights to the error message
@alongd alongd force-pushed the arkane_energies branch from c81617a to 3921d0c Compare June 13, 2019 14:23
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alongd commented Jun 13, 2019

@goldmanm, could you take a look at this PR?

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@alongd, I don't know how I missed the messages before. Looking at it now.

@goldmanm goldmanm merged commit 9da9be0 into master Jun 13, 2019
@goldmanm goldmanm deleted the arkane_energies branch June 13, 2019 18:56
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3 participants