Avogadro 1.102 Release

Announcements
1

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and many feature enhancements. Thanks to many for suggestions, bug reports, and discussions.

Draft documentation can be found at https://two.avogadro.cc

You can download Linux, Windows, and Mac versions through: Release Avogadro 1.102.0 · OpenChemistry/avogadrolibs · GitHub

If you have comments or suggestions, please join us at https://discuss.avogadro.cc and as always, help and contributions in many forms are always welcome, particularly if you’d like to help with user documentation or website development.

:glowing_star: Highlights (tldr)

  • This release is intended as a final beta before a 2.0 stable release
  • Add the popular auto optimize tool
  • Updated charts, including spectra using the JKQtPlotter framework
  • Both macOS and Windows releases have migrated to the new Qt6 framework
    • Windows releases are now offered in the Microsoft Store as well as signed MSIX packages
  • Use pixi if available to install Python and plugins
  • A pile of bug fixes, updated language translations, and more

:sparkles: Features

  • Add an “add molecule” + icon in the molecule list @Daniel-Aguila (#2285)
  • Show frozen atoms or constrained bonds, atoms, torsions in the property views @ghutchis (#2279)
  • Add UI support for freezing X, Y, Z axis @ghutchis (#2276)
  • Update animation tool with start and end frames @ghutchis (#2058)
  • Use JKQtPlotter for charts (e.g. spectra) @ghutchis (#2220)
    • Easier to save plots to graphics, SVG, or PDF including a preview
  • Add wireframe style for surfaces @ghutchis (#2201)
  • Add support for UFF optimization with unit cells
  • Update the ORCA input generator with support for constraints and frozen XYZ atoms

:bug: Bug Fixes

  • Make isoValue in Molecular Orbital window consistent with Surfaces dialog @Kcorbyerd (#2312)
  • Fix selection of atoms in orthographic projection @ghutchis (#2294)
  • Disable split view to prevent crashing @ghutchis (#2298)
  • Fix several bugs with UFF angle gradients found with AutoOptimize (#2240)
  • Don’t reset the camera when switching molecules @ghutchis (#629)
  • Update the about dialog to handle light-dark themes @ghutchis (#624)
  • Fix File → Close behavior @Daniel-Aguila (#623)
  • Fix installation of Python with pixi, repeatedly ask @ghutchis (#2290)
  • Fix overly verbose MDL / SDF debug messages about M CHG, etc. @ghutchis (#2277)
  • Fix #1965 - don’t create the progress box until needed @ghutchis (#2274)
  • Fix crash with undo / redo from template tool @ghutchis (#2272)
  • Fix the missing “close” icon for the molecule model @ghutchis (#2273)
  • Fix possible crashes in cube generation due to mutex locking @ghutchis (#2267)
  • Don’t start the forcefield setup at launch @ghutchis (#2258)
  • Fix reading MO from Molden, including correct eV conversion @ghutchis (#2237)
  • Ignore the Mutex when deleting Cubes @ghutchis (#2233)
  • Read and write cube data and surfaces in cjson files @ghutchis (#2230)
  • Make sure to read Mulliken partial charges from fchk files @ghutchis (#2231)
  • fix(XYZ): fix parser of totalEnergy @e-kwsm (#2225)
  • Fix reading open-shell ORCA calculations @ghutchis (#2223)
  • Check SMILES and pop up a warning if there’s something wrong @ghutchis (#2206)

:rocket: Performance Improvements

  • Don’t start the forcefield setup at launch @ghutchis (#2258)

:toolbox: Maintenance

  • Fix incorrect usage of .empty method when .clear() was intended @ghutchis (#2295)
  • add Turbomole test and improve parser @e-kwsm (#2212)
  • Fix QtTesting record scripts and playback @ghutchis (#625)
  • Complete the AppxManifest @ghutchis (#615)
  • Adapt Flatpak manifest for VTK->JKQtPlotter transition @matterhorn103 (#609)
  • fix: explicitly include <cassert> @e-kwsm (#2288)
  • Compress PNG files with ImageOptim @ghutchis (#2286)
  • Add some very basic quantum IO unit tests @ghutchis (#2275)
  • Add calc unit tests @ghutchis (#2269)
  • Add a lot more unit cell tests @ghutchis (#2271)
  • Make sure to codesign all components before notarizing @ghutchis (#2259)
  • Add Qt6 packages for macOS and Windows @ghutchis (#2261, #2234)
  • refactor(lexicalCast)!: use std::optional for return value @e-kwsm (#2232)
  • build: update path to avogadrogenerators @e-kwsm (#2197)
  • fix(Variant): remove unused char member from union, and add missing template specialization for char @e-kwsm (#2216)
  • Use MACOS define instead of OSX (deprecated) @ghutchis (#2214)
  • Create OSSF security scorecard.yml @ghutchis (#2209)
  • Drop MMTF format test since it’s unsupported. @ghutchis (#2205)
  • Use vcpkg to install eigen3 libarchive libxml2 and zlib @ghutchis (#2203)
  • docs: fix -Wdocument @e-kwsm (#2198)
  • Try using Windows vcpkg to install Eigen for Python builds @ghutchis (#2202)
  • Fix minor warnings from render layout duplicate names

:books: Translations

  • Translations updates from Hosted Weblate @weblate
  • Automated translation updates @github-actions[bot]

Credits

Thanks to @Daniel-Aguila for their first contribution in this release!

Thanks to many contributors, including: @Daniel-Aguila, @NorwayFun, @andibing, @arifpedia, @dependabot[bot], @e-kwsm, @ghutchis, @Kcorbyerd, @maksim2005UKR, @matterhorn103, @milotype, @oersen, @tacitcoast, @weblate, David D, Eisuke Kawashima, Otto Myers, Remus-Gabriel Chelu, Weblate Translation Memory, dependabot[bot], github-actions[bot] and btbt_bt

2 Likes