Avogadro 2 Files

🌟 Highlights (tldr)

• This release is intended to fix key problems with 1.100 on Windows (missing Open Babel) as well as on macOS 26 "Tahoe" (save dialogs)
• Should more easily find Python installs on Windows
• Added support for constraints for geometry optimizations
• Added an internal UFF implementation
• Tweaked the edit tool to adjust bond lengths when the bond order or element change via click
• A pile of bug fixes, updated language translations, and more

✨ Features

• Support for a WebMO plugin @ghutchis (#2172)
• Add a copy-as-xyz command @ghutchis (#2150)
• Add constraints to property tables \& save with CJSON @ghutchis (#2118)
• Add constraints for geometry optimization @ghutchis (#2096)
• Switch template tool to use updated SVG images @ghutchis (#2075)
• Improve cp2kinput @e-kwsm (#2067)
• If a cube exists (e.g., read from a file), create a default mesh @ghutchis (#2053)
• Update the molecule UI list to include richtext formulas @ghutchis (#2028)
• Add an internal implementation of UFF @ghutchis (#1963)
• When click-to-edit bond order also adjust the bond length @ghutchis (#2012)
• When clicking to change an element, tweak the bond length too @ghutchis (#2011)
• Add more options to the GAMESS input file generator @JorgeG94 (#1986)
• Rename "Meshes" interface text to "Surfaces" @ghutchis (#2009)
• Fix reading Chemeleon exyz files with no quotes around the Lattice @ghutchis (#2001)
• Add support for "allxyz" from Orca - trajectory files @ghutchis (#1995)
• Rename Analysis menu to imperative Analyze to match others @matterhorn103 (#1978)
• Add mode numbers to Vibrational Modes table @jcerezochem (#1952)
• Recognize *.tmol as turbomole @e-kwsm (#2185)
• Recognize CONTCAR and *.vasp as VASP geometry files @e-kwsm (#2152)
• Switch molecule list to enable rich-text formulas

🐛 Bug Fixes

• Reject files with invalid cell matrix @e-kwsm (#2191)
• Try to fix extraction on Windows using tar.gz instead of zip @ghutchis (#2193)
• Tweaks to support field names from Psi4 fchk @ghutchis (#2186)
• Fix generic "archive warn" messages for the download window @ghutchis (#2183)
• Fix possible crashes reading PDB files with few residues @ghutchis (#2182)
• Add additional search paths for Python on Windows @ghutchis (#2179)
• Fix [#2176] parsing files with ¹¹⁸Og and ¹¹⁹Uue @e-kwsm (#2177)
• Fix cml xmlns URI @e-kwsm (#2156)
• Fix nullptr dereference @e-kwsm (#2135)
• fix(templatetool): do not localize functional groups @e-kwsm (#2169)
• Export mol/sdf with proper header @ghutchis (#2133)
• fix(Unit Cell Editor): reject modification of cell and fractional matrices if singular @e-kwsm (#2094)
• chore(input): reduce singleStep @e-kwsm (#2093)
• Fix UFF analytical gradients @ghutchis (#2088)
• Fix some crashes exposed with fuzz testing @ghutchis (#2086)
• fix(wrapFractional): fix comparison @e-kwsm (#2080)
• Fix a bug when changing the bond order atoms wouldn't move properly @ghutchis (#2072)
• Fix crash on Linux when deleting non-hydrogen atoms @ghutchis (#2070)
• fix(cjson): fix properties parsing @e-kwsm (#2068)
• Make sure to save label options for atoms, bonds and residues @ghutchis (#2052)
• Fix bug with manual rotations around axes @ghutchis (#2016)
• Fix reading Gaussian cube - make sure to set origin correctly @ghutchis (#2000)
• Fix bug with Rename Elements window @pillose (#1989)
• Make sure to cancel "Insert SMILES" @ghutchis (#1969)
• Fix dark theme - make sure to use default text and document-close icons @ghutchis (#1967)
• Make sure to delete bonds even when "adjust hydrogens" is off @ghutchis (#1966)
• Make sure Gaussian fchk orbitals are read with eV energies @ghutchis (#1958)
• Harden file readers (from fuzz tests) @ghutchis (#1950)
• Fix minor warning about "undef" layer caused by QTAIM changes @ghutchis (#2023)
• Fix bug with fog not starting with the correct background color
• Add support for detecting theme change events - update tool icons
• When multiple files are dropped, make sure to queue them for reading
• Make sure to get the correct preferred language on Mac
• Ensure the display type list is sorted

🧰 Maintenance

• Update/correct/improve Linux metainfo, including release notes @matterhorn103
• Initial support for an isApplicable scene plugin method @ghutchis (#2029)
• refactor: use string literals @e-kwsm (#2141)
• Fix typos @e-kwsm (#2122)
• Add missing spaces, and remove trailing newlines and spaces before tabs @e-kwsm (#2101)
• style: remove redundant inline specifiers @e-kwsm (#2099)
• refactor: use std::clamp (C++17) @e-kwsm (#2100)
• Style: run clang-format @e-kwsm (#2065)
• Fixed [Build] link address @todbadrakh (#2031)
• refactor(FindOpenBabel3): improvement @e-kwsm (#2024)
• Re-enable CJSON conformer unit test @ghutchis (#2192)
• build(VTK): support VTK 9 @e-kwsm (#2161)
• fix(QtOpenGL): honor QT_VERSION @e-kwsm (#2154)
• refactor: avoid strncmp @e-kwsm (#2142)
• refactor: use hypot @e-kwsm (#2131)
• refactor: use std::exchange (C++14) @e-kwsm (#2130)
• Switch to using subdirectories in avogadrodata @ghutchis (#2085)
• fix override specification @e-kwsm (#2079)
• fix: fix test suite names @e-kwsm (#2078)
• chore: remove ENABLE_TRANSLATIONS that is no longer used @e-kwsm (#2077)
• Compress SVG icons using svgcleaner @ghutchis (#2074)
• Update GitHub builds with latest Windows and Qt versions @ghutchis (#2063)
• Fix ODR violations, move enums into class scope @PPN-SD (#2059)
• Bundle libssl and libcrypto with AppImage @matterhorn103 (#2061)
• Use system eigen when building for Linux (inc. AppImage) @ghutchis (#2054)
• Resolve compiler warnings: member initialisation, variable shadowing, fallthrough, and unused variables @rrsathe (#2038)
• Enable musl linux Python wheels @ghutchis (#2047)
• Update cibuildwheel @ghutchis (#2010)
• build: remove unused Qt5LinguistTools @e-kwsm (#2041)
• test: enable spacegrouptest only if USE_SPGLIB is true @e-kwsm (#2030)
• Update find_dependency calls for Qt6 @ghutchis (#2026)
• build: bump cmake_minimum_required @e-kwsm (#2022)
• Migrate QTAIM and Symmetry to Qt6 @ghutchis (#1998)
• Set USE_MMTF to OFF by default @matterhorn103 (#2005)
• build: replace FindPythonInterp with FindPython3 @e-kwsm (#1976)
• Update CJSON to use new .contains() syntax @ghutchis (#1947)

📚 Translations

• Automated translation updates @github-actions[bot]
• i18n: resolve conflict with weblate @e-kwsm (#2097)
• style(i18n): add --check=ellipsis-unicode for gettext and use unicode ellipsis @e-kwsm (#1977)

Credits

Thanks to many contributors, including: @CubeXtreme, @DGC0LS13, @JorgeG94, @Maetnicio, @NorwayFun, @PPN-SD, @Ricky-Tigg, @SantosSi, @TamilNeram, @Yeims20, @andibing, @dependabot[bot], @e-kwsm, @ghutchis, @jcerezochem, @jeannemfavret, @kuyoeku, @matterhorn103, @milotype, @nbehrnd, @pillose, @rrsathe, @snapper764, @stokito, @tacitcoast, @todbadrakh, @weblate, Alexandre R Soares, Eisuke Kawashima, Eric Remy, Hēphaïstos, LibreTranslate, Remus-Gabriel Chelu, Weblate Translation Memory, dependabot[bot], github-actions[bot], gmkeebiy, nicejammer, Илья Рябов and Максим Горпиніч