0.8.1

This is a hotfix release primarily for Windows.

Changelog

New runtypes

• None

Other new features and improvements

• None

Bug fixes and refinements

• Path behaviour has been improved, which fixes the plugin on Windows

0.8.0

Changelog

New runtypes

CREST

• solvate – use the CREST QCG method to grow an explicit solvent shell up to a specified number of solvent molecules
• tautomerize – search for other tautomers of the molecule with the same overall charge

Other new features and improvements

• Partial charges are parsed if printed by xtb and are passed back to Avogadro after running the Energy, Optimization, and Opt + Freq commands
• Geometry objects can be used as arguments for options of a Calculation's command [easyxtb]
• Separate Get commands are provided to download xtb and CREST [plugin]
• The Run xtb command has been removed in favour of allowing extra command line options to be set in the config dialog [plugin]
• All general settings for xtb and CREST are now set in the same configuration dialog in Avogadro [plugin]
• Configuration options for method, solvation etc. now permeate across all xtb and CREST runtypes, including when easyxtb is used in a stand-alone fashion
• Specifying the paths to the program binaries in the plugin's config menu is now done using a file picker [plugin]
• Calculations are now run in a /calcs subdirectory of the easyxtb directory by default

Bug fixes and refinements

• Correct CLI flag now used to specify the number of threads for xtb

Development and documentation

• Plugin scripts are now kept tidily in their own subdirectory
• Tests of calculation results are now checked by differences between results rather than comparison of rounded values

0.7.0

Summary

This release sees no user-facing changes in the Avogadro plugin.

The key changes for this release are a couple of breaking API changes in easyxtb:

1. charge and spin are no longer properties of a Calculation object but are instead properties of a Geometry object.

As you can see, the name for the spin-related property has also changed from multiplicity to spin, and it now represents the number of unpaired electrons. This was done in order to align with the meaning of --uhf in xtb and make independent use of easyxtb more intuitive.

This also means that charge and multiplicity can no longer be passed as arguments to the various convenience calculation functions. On the other hand, charge and spin are now valid arguments for the various methods for Geometry creation, and can also be set as normal for instance properties.

2. To improve clarity, the calc module is now the calculate module, and the conf module is now called configuration

This is also partly to reduce common namespace clashes as for example it is often convenient to use calc as the name of a Calculation object.

Changelog

New runtypes

• None

Other new features and improvements

• Make charge and spin properties of a Geometry (#43)
• Rename the calc and conf modules to calculate and configuration respectively

Bug fixes and refinements

• None

Development and documentation

• Add tests for basic IO and calculations with default settings (#44)
• Update the easyxtb README to reflect the API changes

0.6.0

xtb and CREST are now both run in parallel! The benefit is particularly noticeable for conformer searches.

New runtypes

• None

Other new features and improvements

• Calculations now run in parallel for significant speed-up (#38)

Bug fixes and refinements

• The command to open the calculation directory now works properly on Windows (#34)

Development and documentation

• Added dev dependencies for testing and formatting (#35)

0.5.0

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)

As of this release, 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

• 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

0.4.0

What's Changed

• Added type hints and docstrings by @matterhorn103 in #6
• Fixes for Windows and internal restructuring by @matterhorn103 in #7
• Empty calculation directory instead of deleting it by @matterhorn103 in #9
• Add ability to set GFN method and optimization level by @matterhorn103 in #10
• Various bug fixes

Full Changelog: 0.3.1...0.4.0

0.3.1

• Hotfix for incorrect version formatting in plugin.json

0.3.0

• Allow user to set path to Open Babel binary manually
• Discovery of binaries is improved, standardized, and made a little more robust
• Fixed handling of directories (created if don't exist)
• Output stream is always UTF-8 (temporary fix for #2)
• Fix so that titleless menu no longer appears in menu bar
• Moved things around and standardized syntax/behaviour of run and calculation functions to ease interoperability with avo_crest (in development)