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henry bond length drift checks; speed up on rotation and translation #73

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merged 13 commits into from Sep 13, 2018

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SimonEnsemble
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  • in henry_coefficient, we now check for bond length drift and reset the molecule from a fresh copy if a little drift is observed; fail if drift is so severe that results thus far cannot be trusted
  • sped up rotate! and translate_to! with broadcast now that fractional coords are in a matrix
  • added a few more tests for rotate and translate to make sure bond length drift is not observed. H2S is a more rigorous test since it is nonlinear compared to CO2.

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coveralls commented Sep 12, 2018

Pull Request Test Coverage Report for Build 164

  • 13 of 13 (100.0%) changed or added relevant lines in 1 file are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage increased (+0.01%) to 87.397%

Totals Coverage Status
Change from base Build 153: 0.01%
Covered Lines: 742
Relevant Lines: 849

💛 - Coveralls

@SimonEnsemble SimonEnsemble assigned Surluson and unassigned Surluson Sep 12, 2018
@Surluson Surluson self-assigned this Sep 12, 2018
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Tests run and most everything looks good.
The docstring for bond_length_drift shows the default value for atol=1e-15 while the actual function has atol::Float64=1e-14.
And I do see some difference between atol's in the test, what's the reasoning behind that?

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@Surluson thanks, fixed doc string inconsistency. we just can't expect the atol to be so low after rotating. 1e-14 is still small enough. eventually we should use quaternions for rotations as I hear they are more numerically stable!

@SimonEnsemble SimonEnsemble merged commit 41671d2 into master Sep 13, 2018
@SimonEnsemble SimonEnsemble deleted the henry_fix branch September 13, 2018 01:35
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4 participants