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cryos / avogadro

Avogadro 1 is not under active development, the repository was archived in September 2021. Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
http://avogadro.cc/
GNU General Public License v2.0
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Issue with auto-opt tool #960

Closed phys1csb1tch closed 2 years ago

phys1csb1tch commented 2 years ago

For some reason when auto optimizing molecules that form a triangle in the geometry the field tempts to tie the two TM together. This has happened before for Cu2Rh2 molecules (and my advisor had to run the optimization in his version of Avogadro, that worked correctly) and now is happening with this Cu3Ru3. Sb knows how to fix it? Image 1 optimizes to image 2 IMG_20210816_180356_1 IMG_20210816_181733

ghutchis commented 2 years ago

I don't think I can recommend the Avogadro optimizer for a task like this. I'd highly suggest the free, open source XTB program, which runs approximate quantum calculations on XYZ format files (like your edit) https://xtb-docs.readthedocs.io/en/latest/contents.html

If you have questions, I'd recommend using the new forum https://discuss.avogadro.cc/