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Update Voronota-LT, add alternative modes to Voronoi analysis. #456

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merged 1 commit into from
Oct 7, 2024

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kliment-olechnovic
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@kliment-olechnovic kliment-olechnovic commented Oct 4, 2024

Version 0.9.4 of Voronota-LT has an improved API and a new ability to update the tessellation without fully rebuilding it when possible.

The Voronoi analysis class now has adjustable running mode. The class implementation makes use of the "pImpl" idiom.

Examples collection now contains "voronota" directory with polymer-based and peptide based multichain simulation configuration files and the corresponding output logs.

Description

Please see the commit title and its extended description.
All changes concern the Voronoi analysis class.
Relevant examples were added to test the introduced modifications.
clang-format was applied to the modified faunus source code (analysis.h and voronota.cpp).
Code style naming conventions were followed.

No new tests failed because of the new modifications.
However, some tests failed before any modifications were introduced (on a fresh fork, mostly because the system that the tests were executed on had no 'python' and 'jupyter' commands):
4 - chargemove (Failed)
6 - penalty (Failed)
7 - multipole (Failed)
8 - virial (Failed)
19 - smartmc (Failed)
20 - speciation (Failed)
21 - speciation_group (Failed)
28 - phosphate (Failed)
33 - bulk-replay (Failed)

Version 0.9.4 of Voronota-LT has an improved API and a new ability
to update the tessellation without fully rebuilding it when possible.

The Voronoi analysis class now has adjustable running mode.
The class implementation makes use of the "pImpl" idiom.

Examples collection now contains "voronota" directory with
polymer-based and peptide based multichain simulation
configuration files and the corresponding output logs.
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@IVinterbladh IVinterbladh left a comment

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Looks good, nicely commented and structured!

@IVinterbladh IVinterbladh merged commit cae83c2 into mlund:master Oct 7, 2024
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2 participants