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OpenChemistry / avogadrolibs

Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
https://two.avogadro.cc/
BSD 3-Clause "New" or "Revised" License
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building supercell adds atoms without bonds #655

Open mayoun opened 3 years ago

mayoun commented 3 years ago

Avogadro version: 1.94.0 Qt version 5.12.0 Desktop: MacOS Mojave 10.14.6

When using the Build Supercell menu item, no bonds are shown for the added atoms. The only bonds displayed are for atoms in the initial unit cell. The unit cell is defined by a CIF file downloaded from materials project.org. If Bond Atoms is selected, unphysical bonds may be added (at least with the default bonding parameters). e.g. for TiO2, the command adds Ti-Ti bonds. The Super Cell Builder in v. 1.2.0 works as expected.

welcome[bot] commented 3 years ago

Thanks for opening your first issue here! Please try to include example files and screenshots if possible. If you're looking for support, please post on our forum: https://discuss.avogadro.cc/

avo-bot commented 1 year ago

This issue has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/double-bonds-not-preserved-when-building-supercell/4426/2

avo-bot commented 1 month ago

This issue has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/custom-labeling-in-avogadro/6342/18