Fix kinetics fitting with Tmin & Tmax in Arakne #1672
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Codecov Report
@@ Coverage Diff @@
## master #1672 +/- ##
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- Coverage 41.88% 41.86% -0.02%
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Files 176 176
Lines 29368 29368
Branches 6059 6059
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- Hits 12301 12296 -5
- Misses 16188 16192 +4
- Partials 879 880 +1
Continue to review full report at Codecov.
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Codecov Report
@@ Coverage Diff @@
## master #1672 +/- ##
==========================================
+ Coverage 41.87% 41.88% +0.01%
==========================================
Files 176 176
Lines 29369 29369
Branches 6059 6059
==========================================
+ Hits 12297 12302 +5
+ Misses 16192 16188 -4
+ Partials 880 879 -1
Continue to review full report at Codecov.
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arkane/kinetics.py
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| else: | ||
| self.Tmin = None | ||
| self.Tmin = (298, 'K') |
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Could you simplify these assignments into:
self.Tmin = Tmin if Tmin is not None else (298, 'K')?
Same for Tmax?
We could also simplify Tcount:
self.Tcount = Tcount if Tcount > 3. else 50
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Good idea. I just added that.
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Previously, there were two spots where a list of temperatures was created for fitting high pressure kinetics in Arkane. One fit using inverse temperature spacing and the other one fit with linear temperature spacing. See #1671 This commit moves the location for creating a listing of temperatures to the __init__ method, so there is only one spot where temperatures are initialized. The default min and max in `generateKinetics` was moved into the __init__ method. Three unittests were written for obtaining the proper temperatures in the __init__ method. `generateKinetics` previously accepted an arguement Tlist, which is already an attribute of KineticsJob, creating redundancy. The Tlist argument was removed and self.Tlist was used in this method instead, simplifying the code. Calls to quantity.Quantity in the __init__ method were unnecessary before setting them with quantity.Temperature, so the __init__ code was simplified by setting attributes with (value, 'K') instead. Documentation was updated to better describe the three methods of specifying temperature when calling `kinetics` in Arkane
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Motivation or Problem
Previously, there were two spots where a list of temperatures
was created for fitting high pressure kinetics in Arkane.
One fit using inverse temperature spacing and the other one fit
with linear temperature spacing. See #1671
Description of Changes
This PR consolidates creating a listing of temperatures
to the init method, so there is only one spot where temperatures
are initialized. The default min and max in
generateKineticswasmoved into the init method. Three unittests were written for
obtaining the proper temperatures in the init method.
generateKineticspreviously accepted an arguement Tlist, whichis already an attribute of KineticsJob, creating redundancy.
The Tlist argument was removed and self.Tlist was used
in this method instead, simplifying the code.
Calls to quantity.Quantity in the init method were unnecessary
before setting them with quantity.Temperature, so the init
code was simplified by setting attributes with (value, 'K') instead.
Documentation was updated to better describe the three methods
of specifying temperatures when calling
kineticsin ArkaneTesting
did
make testand ran the kinetics examples in RMG. also didmake htmlto check for errors in the documentation.Reviewer Tips
Read over code to make sure it makes sense.