There is a function to break molecular bonds, but when the bonds are broken in Avogadro2, the positions of the atoms are swapped, causing errors when used as input files for calculations.
Additionally, while Avogadro1 can visualize the stabilization process during structural stabilization, Avogadro2 cannot, making it difficult to create molecular structures and taking a considerable amount of time.
When will this issue be fixed in Avogadro2?
I’m not sure I know what you mean by that? Do you mean the AutoOptimize feature in Avogadro 1?
I do not see this behavior. The only way the atoms would change is if you break a bond and the “adjust hydrogens” feature is on.
I have just checked with a nightly build and not only do the atom index not change, but there’s a specific unit test for this.
Can you explain what you’re seeing and what version you are using?
Thank you for your reply.
Returning to the previous question, do you plan to use dynamic structural optimization, like the functionality of the AutoOptimize feature in avogadro1, for avodadro2 as well?
Yes, of course, it’s on the Avogadro 2025 Roadmap
If you want to follow that particular issue, it’s Return of the auto-optimize tool · Issue #1420 · OpenChemistry/avogadrolibs · GitHub