ND Hindered Rotor Improvements #1849
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mjohnson541
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Topic: Performance
Arkane
Status: Ready for Review
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Codecov Report
@@ Coverage Diff @@
## master #1849 +/- ##
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+ Coverage 44.22% 44.25% +0.02%
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Files 83 83
Lines 21547 21551 +4
Branches 5646 5648 +2
==========================================
+ Hits 9530 9537 +7
+ Misses 10946 10944 -2
+ Partials 1071 1070 -1
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Dec 13, 2019
rmgpy/statmech/ndTorsions.py
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| return self.rootD(*phis) * np.exp(-self.V(*phis) / (constants.R * T)) | ||
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| intg = inte.nquad(f, ranges=rngs)[0] | ||
| return (self.rootD(*phis)) * np.exp(-self.V(*phis) / (constants.R * T)) |
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remove redundant parentheses around self.rootD(*phis)?
I ran into issues related to negative predicted moments of inertia with this interpolant This commit replaces that interpolant (the 2D case) with the LinearNDInterpolator
The old scheme using nquad only worked fast because the value of the integral was below the absolute tolerance, and it wasn't very accurate after fixing the numerical issue nquad takes impractically long since the integration is over a fit to data points we don't even know the function well enough for an nquad calculation to make sense for this reason I've used simpsons rule for integration which is much faster and should be just as accurate we still fit and use function evaluations for convenience
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rmgpy/statmech/conformer.pyx
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| @@ -384,7 +384,8 @@ cdef class Conformer(RMGObject): | |||
| elif pivots[0] in top1 and pivots[1] in top1: | |||
| raise ValueError('Both pivot atoms included in top; you must specify only one pivot atom that belongs' | |||
| ' with the specified top.') | |||
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| elif 0 in top1: | |||
| raise ValueError('Top must be zero indexed.') | |||
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Should the message say "should be one-indexed" instead?
Maybe also print top1 to point the user to the problem source
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This was referenced Dec 16, 2019
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This has a number of numerical improvements for the calculation of ND classical and semiclassical hindered rotor partition functions. I've removed use of SmoothBivarateSpline interpolation as this resulted in some negative fitted internal reduced moment of inertia values and I've fixed issues with the integration routine.
Also includes miscellaneous Arkane improvements: lets Arkane deal with RateUncertainty objects, makes the semiclassicalND rotors example consistent with the other Toulene examples, and adds a error trigger in internal reduced moment of inertia calculations that prevents use of 0-indexed atom numbers that result in all kinds of weird outputs from the function.