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avo_xtb

avo_xtb is a plugin for Avogadro 2 that provides an in-app interface to the xtb program for quick and accurate calculations, as well as the CREST program for extended functionality.

xtb is developed by the Grimme group in Bonn and carries out semi-empirical quantum mechanical calculations using the group's extended Tight-Binding methods, referred to as "GFNn-xTB".

These methods provide fast and reasonably accurate calculation of Geometries, Frequencies, and Non-covalent interactions for molecular systems with up to roughly 1000 atoms, with broad coverage of the periodic table up to Z = 86 (radon).

crest (Conformer–Rotamer Ensemble Sampling Tool) adds a variety of sampling procedures for several interesting applications including conformer searches, thermochemistry, and solvation.

easyxtb

The Avogadro plugin is itself only a layer on top of the easyxtb Python package, which is written and maintained as part of this project. easyxtb is published on the PyPI repository and can be used independently of the plugin from Python as an interface to xtb and crest.

For more details on using easyxtb via the Python API, see easyxtb/README.md.

Capabilities

This plugin currently provides functionality to run the following calculation types and view the results directly in Avogadro:

xtb

  • single point energies
  • geometry optimizations
  • vibrational frequencies
  • combined opt + freq with automatic restart for negative frequencies
  • molecular orbitals

CREST

  • conformer searches
  • protonation and deprotonation screening
  • explicit solvent shell generation

Run options

The following options for xtb and/or CREST can currently be configured in the plugin:

  • number of parallel threads to use for calculations
  • implicit solvation with the ALPB model
  • choice of GFN-xTB parameterization
  • optimization level In addition, the pluding provides the possibility to specify extra command line options to pass to xtb and CREST in free form.

Requirements

xtb

Currently, the plugin does not download the xtb binary automatically, and it is not bundled with Avogadro. Instead, it must be obtained separately. There are five options that will make xtb visible to the plugin:

  1. Use the "Get xtb..." function within Avogadro after installing this plugin and let the plugin take care of everything for you
  2. Install xtb with conda from conda-forge and use Avogadro with the conda environment, either by setting it in the Python settings or by starting Avogadro with the environment activated
  3. Manually download the xtb binary and put it into the system PATH
  4. Manually download xtb and place it, or a link to it, entirely within the plugin's binary directory <user data>/easyxtb/bin/ (see below for more information on where this is on your system)
  5. Manually download xtb and manually specify its location in the Configure... menu

CREST

While xtb is cross-platform, crest is distributed only for Linux/UNIX systems. As a result, Windows and macOS users of the plugin will not have the calculations that rely on CREST available to them in the Avogadro interface.

crest can be made visible to the plugin in the same ways as for xtb listed above. If it is not in $PATH, the crest binary, or a link to it, should be located at <user data>/easyxtb/bin/crest. The "Get xtb..." option within Avogadro will also download crest on supported operating systems (only Linux at time of writing).

Data location

The core package that provides the calculation framework uses a central location to run its calculations, store its configuration, and save its log file. This location is <user data>/easyxtb, where <user data> is OS-dependent:

  • Windows: $USER_HOME\AppData\Local\easyxtb
  • macOS: ~/Library/Application Support/easyxtb
  • Linux: ~/.local/share/easyxtb

Additionally, if the environment variable XDG_DATA_HOME is set its value will be respected and takes precedence over the above paths (on all OSes).

Normally calculations are run in a subfolder at this location, but this can be customized in the plugin's configuration dialog.

Disclaimer

xtb and crest are distributed by the Grimme group under the LGPL license v3. The authors of Avogadro and avo_xtb bear no responsibility for xtb or CREST or the contents of the respective repositories. Source code for the programs is available at the repositories linked above.

Cite

General reference to xtb and the implemented GFN methods:

  • C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, J. Seibert, S. Spicher, S. Grimme WIREs Comput. Mol. Sci., 2020, 11, e01493. DOI: 10.1002/wcms.1493

For GFN2-xTB (default method):

For CREST:

  • P. Pracht, S. Grimme, C. Bannwarth, F. Bohle, S. Ehlert, G. Feldmann, J. Gorges, M. Müller, T. Neudecker, C. Plett, S. Spicher, P. Steinbach, P. Wesołowski, F. Zeller, J. Chem. Phys., 2024, 160, 114110. DOI: 10.1063/5.0197592
  • P. Pracht, F. Bohle, S. Grimme, Phys. Chem. Chem. Phys., 2020, 22, 7169-7192. DOI: 10.1039/C9CP06869D

See the xtb and CREST GitHub repositories for other citations.