Incorrect Dihedral Angles

[greghjones]

Avogadro version: 1.95.1

• Avogadrolibs: 1.95.1
• Qt: 5.12.10

Desktop version: (please complete the following information):

• OS: Windows 10
• Version: 19043.1237
• Compiler: Github Release

Describe the bug
When measuring dihedral angles, sometimes the wrong value is obtained.

To Reproduce
Steps to reproduce the behavior:

1. Open a molecule.
2. Select the measure tool.
3. Select four atoms forming a dihedral.
4. Read the output.

Expected behavior
Correct dihedral calculated (see attached test XYZ file).

Screenshots
image

Additional context
Formula in angletools.h at first glance appears to match the accompanying Stackoverflow citation (Python code). The cited Python code, the current formula from Wikipedia, and Avogadro 1.2.0 all yield a dihedral of -66.51 degrees, as opposed to the displayed -74.30 degrees in Avogadro 1.95.1. Attached are a test case (dihedral in question is C1 - C2 - C3 - C4), as well as a Jupyter notebook demonstrating formula agreement.

Given that the formula appears correct, I'm not quite sure where the disagreement is coming from.

dihedral.zip

[ghutchis]

Not sure why the method doesn't work either. At first, I thought it was an atom order thing, but .. much easier to just fall back to the standard method.

(I'm going to try to fix the Stackoverflow method as I finish up the force field framework.. definitely worth saving some time when doing molecular dynamics.)

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
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