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

SimonEnsemble / PorousMaterials.jl

Julia package towards classical molecular modeling of nanoporous materials

GNU General Public License v3.0

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

Closed SimonEnsemble closed 5 years ago

SimonEnsemble commented 5 years ago

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.

coveralls commented 5 years ago

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

💛 - Coveralls

SimonEnsemble commented 5 years ago

@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!