I’m happy to announce a new version of the xtb plugin for Avogadro 2!
I would love to hear any feedback and reports of bugs that crop up, feel free to post them in this thread!
This release sees a complete overhaul of the plugin’s code. Rather than just being a collection of individual scripts, the plugin now has a robust and flexible common backend. As well as improving reliablity, this should make adding new runtypes much quicker and easier going forward.
Two key changes should also help getting the plugin set up: it no longer uses Open Babel for anything, which was one of the main causes of issues, and the plugin now writes a log file, which should help with support.
The main infrastructure for setting up and running calculations, and parsing their results, is now contained within an internal Python package, dubbed easyxtb. For anyone interested, easyxtb is as of now also available on PyPI, and can be used independently of the avo_xtb plugin as a simple API for the xtb and CREST packages.
As before, the plugin provides commands to run the following common calculation types and view the results directly and immediately in Avogadro 2:
- Single point energy
- Geometry optimization
- Vibrational frequencies
- Opt + Freq
- Molecular orbitals
- Conformer search (requires CREST)
In addition, the plugin now has capabilities for:
New runtypes
- Protonation and deprotonation screening, to add or remove a proton at the most likely position (requires CREST)
Other new features and improvements
- Opt + Freq will now continue reoptimizing until there are no negative frequencies remaining
- Logging of the plugin’s processes for easier diagnosis of issues
- An “About avo_xtb” to easily view the versions of the plugin, backend, xtb, and CREST, and locations to the xtb and CREST binaries
Bug fixes and refinements
- Removal of Open Babel dependency
- xtb 6.7, CREST 3.0
- Python minimum and target version is now 3.10
What is xtb and why do I want it?
Avogadro offers a handy built-in Force Field Framework for fast optimization of structures. This uses Molecular Mechanics techniques, which are extremely fast, but don’t take into account the quantum chemical nature of molecules, so they are not very accurate and for systems with interesting bonding (including hydrogen bonds) they tend to give the wrong results. Ferrocene is a prime example.
If you have lots (>1000) atoms, molecular mechanics is your only realistic choice, but for small molecules so-called “semi-empirical” quantum mechanical methods can give much better results while still being very fast. With the plugin you can get qualitatively accurate geometries, vibrations, and orbitals in only a few seconds!
xtb is a program developed by the Grimme group in Bonn that carries out semi-empirical quantum mechanical calculations using the group’s extended Tight-Binding methods, referred to as “GFNn-xTB".
These methods have been very popular amongst the chemistry community. While numerical results are not as accurate as the methods computational chemists typically use like DFT, xtb is still extremely helpful for getting a quick but broadly correct picture of things, making it well suited for educational purposes or as a preliminary step before more accurate calculations.
How to get the new version
The updated plugin will soon be available from the plugin manager in the Avogadro interface.
Alternatively, get it from the GitHub repository.
