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Avogadro Changelog

What's new in Avogadro 2 0.7.2

Feb 17, 2014
  • Interface:
  • Fixed a bug in setting/retrieving user specified path to the Python interpreter
  • Commands / Extensions:
  • Fixed bugs related to adding/removing programs in the MoleQueue submission dialog
  • Prevent jobs from being submitted without programs in the selected MoleQueue queue

New in Avogadro 1.1.1 (Dec 13, 2013)

  • Interface:
  • Rudimentary support for retinal display Macs
  • Tools:
  • Support for manual adjustment of the view
  • Commands / Extensions:
  • DNA/RNA builder
  • Simple LAMMPS input generator for water
  • PSI4 input generator added
  • Fixed QTAIM to work on Windows
  • Rendering / Display:
  • Updated gl2ps snapshot

New in Avogadro 0.7.0 (Dec 3, 2013)

  • INTERFACE:
  • Prompt to save on changes to the molecule
  • Display the current version of the application in the window title
  • Basic support for periodic structures/crystals
  • RPC interface for remote control/interaction
  • Job submission using MoleQueue
  • Search for similar molecules in MongoChem
  • TOOLS:
  • Measurement tool
  • Bond-centric tool
  • Text rendering
  • COMMANDS / EXTENSIONS:
  • A new Crystallography extension provides functionality for dealing with crystal structures
  • Improved Cartesian editor:
  • Allows copy/paste from a variety of computational chemistry packages
  • Python-based input generators for several packages:
  • GAMESS-UK
  • APBS
  • Gaussian
  • MolPro
  • MOPAC
  • NWChem
  • Q-Chem
  • Terachem
  • Ported support for Bader's Atoms-In-Molecule analysis, using QTAIM, contributed by Prof. Eric Brown, of Loyola University, Chicago
  • Interface to NIH chemical structure resolver, search for chemicals by name
  • Use Open Babel for file conversion, structure optimization, etc in a separate process
  • Paste chemical descriptors in to the interface
  • RENDERING / DISPLAY:
  • Specialized scene graph with support for impostor-based sphere rendering. Support for several standard visualization types:
  • Ball and stick
  • Licorice
  • Van der Waals (with or without ambient occlusion)
  • Triangle meshes, typically displaying isosurfaces

New in Avogadro 1.1.0 (Sep 13, 2012)

  • A new Crystallography extension provides significantly improved functionality for dealing with crystal structures, including:
  • Perception of space groups
  • Adjusting coordinates by "symmetrizing" them
  • Fractional coordinate editing
  • Scaling unit cells by volume
  • Reducing to a primitive unit cell
  • Viewing along Miller planes
  • Generating surfaces and slabs with arbitrary Miller planes
  • A new crystal library, ("Import -> Crystal") including over 480 files across 20 types of crystals:
  • All elements
  • Common oxides, sulfides, III-V semiconductors, etc
  • Most common structure types
  • New builder options:
  • Invert chirality
  • Nanotube builder based on TubeGen
  • Enlarged fragment library (over 380 fragments, 76% increase!)
  • New Orbital window:
  • Allows easy selection of particular orbitals (by number or energy) for surface rendering
  • Display of orbital energies (where supported)
  • DIsplay of orbital symmetries (where supported)
  • Improved orbital/surface support:
  • Support for GAMESS-US and GAMESS-UK formats
  • Support for the Molden file format
  • OpenQube project
  • Improved Cartesian editor:
  • Allows copy/paste from a variety of computational chemistry packages
  • New computational chemistry interfaces including:
  • ABINIT, contributed by Prof. Matthieu Verstraete
  • Dalton
  • GAMESS-UK, contributed by Jens Thomas
  • Terachem

New in Avogadro 1.0.3 (Apr 25, 2011)

  • Fixed building of translations on Linux and Mac OS X.

New in Avogadro 1.0.2 (Apr 23, 2011)

  • Updated install rules for minimal Windows package. No Python/extended dependencies.

New in Avogadro 1.0.1 (Nov 22, 2010)

  • Fixed crashes and highlighting in Properties extension
  • Fixed crashes with network extensions when using Qt 4.5.2+
  • Fixed crash on exit if forcefields are missing
  • 3D structures are now downloaded when using Network Fetch
  • Fixed crash in Project Tree Editor
  • Fixed open and save on Windows if non-latin symbols occur in path
  • Fixed saving/loading of last used bond order when drawing
  • Fixed improper behavior of PluginListView (plugin info didn't change on keyboard movements)
  • New supplementary files:
  • New avopkg tool for management of 3rd party plugins
  • File avogadro.prf for integration with QMake build system for 3rd party extension developers
  • Man pages for Unix platforms

New in Avogadro 1.0.0 (Oct 23, 2009)

  • General:
  • The code currently expects to be editing 3D molecule files, ideally with one molecule per file.
  • This means:
  • Avogadro cannot currently read or edit compressed (.gz) multi-molecule files. Uncompressed files, or single-molecule .gz files are fine.
  • Saving to a 2D format will not necessarily produce correct 2D stereochemistry.
  • Tools / Building:
  • Several future builder features are not yet implemented, including:
  • Crystal structure builder
  • Carbon Nanotube builder
  • Z-matrix editor (early version committed - needs more work)
  • Interface:
  • Export graphics will only save the current resolution in the window in bitmap form.

New in Avogadro 0.9.8 (Sep 24, 2009)

  • General:
  • Updated user interface and icons.
  • Introduced a menu option to reset display types.
  • Updated translations, fixed encoding issues that affected some translations on Windows.
  • Avogadro will now run correctly from the build directory on the Mac too.
  • Fixes to display type labels.
  • Improved recent file list handling.
  • Fixes to dipole moment reading and display.
  • Fixes to file saving, marking of modified windows.
  • More bugs found and fixed.
  • Rendering:
  • Speed and efficiency enhancements for single colored meshes.
  • Tools:
  • Various draw tool bugs fixed.
  • Aesthetic fixes to the autorotate slider -- easier to see central position.
  • Extensions:
  • New Chemical Identifier Resolver extension -- type in a chemical name and search http://cactus.nci.nih.gov/chemical/structure for structures.

New in Avogadro 0.9.7 (Jul 18, 2009)

  • Enabled detached 3D views - multiple views of the molecule simultaneously.
  • Updated icons and user interface reorganization.
  • Inline display type configuration buttons, improved model-view classes.
  • Updated translations.
  • More bugs found and fixed.

New in Avogadro 0.9.5 (Jun 3, 2009)

  • General
  • More build system improvements - external plugins can easily be built against libavogadro on Linux and Mac.
  • Includes a standard Mac "app bundle" -- completely relocatable disk image
  • Added a check for updated versions of Avogadro on the network (e.g., when 0.9.6 or 1.0 is released)
  • Includes improved translations and localization, including localized numbers everywhere and a full translation in Indonesian
  • More bugs found and fixed.
  • Interface
  • Updated interface allows more screen space for drawing / viewing
  • Tools moved to a new toolbar
  • Tool and Display Settings appear on demand
  • Updated keyboard shortcuts for switching tools
  • Keyboard shortcuts for switching elements in the Draw tool: type the element symbol (e.g., Fe for iron)
  • Visual cues can now be disabled for the navigation tool
  • Moved "insert fragment" to Build menu
  • Rendering
  • Significantly improved protein "Cartoon" display type
  • Added a custom color option
  • Display of forces from geometry optimization is fixed (was broken in previous 0.9 releases)
  • Extensions
  • Added "Insert Peptide" builder for oligopeptides.
  • Added visualization of NMR spectra.
  • Atom, bond, angle, and torsion property tables now allow editing. This means you can now set a bond length, angle or dihedral exactly.
  • Allow sorting of property tables for each column.
  • Improved vibration plugin, fixing many bugs, and smoothing the animation.
  • Added syntax highlighting for GAMESS-US.
  • Now can run local Gaussian 03 jobs.

New in Avogadro 0.9.4 (May 4, 2009)

  • Interface
  • Export of generated cubes now possible again.
  • 2D cleanup code improvements for 2D molecule files.
  • Rendering
  • Calculation of cubes for output from MolPro added.
  • Extensions
  • Improvements to the plotting support of IR spectra.
  • New NWChem input file dialog.
  • New MolPro input file dialog.
  • Improvements and optimization of the super cell builder.

New in Avogadro 0.9.3 (Apr 2, 2009)

  • General:
  • Avogadro now finds all plugins relative to the binary location.
  • Windows build should now be fully relocatable.
  • Improvements to the desktop file and icon in Linux with association of various file types.
  • Patched FindPythonLibs.cmake - should fix issues on non-Debian Linux distros.
  • More bugs found and fixed.
  • Interface:
  • More dialog parenting issues corrected.
  • Rendering:
  • Animation of molecular vibrations.
  • Unit cell rendering can be turned off.
  • Colored meshes now handle transparency correctly.
  • Improvements to mesh handling in the orbital display.
  • Extensions:
  • Animation of vibrations.
  • Plotting support added, IR spectra plotted in the vibration extension.
  • Improvements to the super cell builder.
  • Surfaces extension bug fixes and improvements.

New in Avogadro 0.9.2 (Mar 2, 2009)

  • General:
  • Tool and extension parenting issues fixed, application shutdown is now much smoother.
  • Forcefields on Windows should now work with any shortcut/run directory.
  • Work to make Avogadro find plugins relative to the binary - relocatable install directory.
  • Versioned configuration, old configurations will be discarded.
  • Bump in the plugin version due to API changes in our plugins.
  • Desktop file and icon in Linux with association of various file types we support.
  • More bugs found and fixed.
  • Interface:
  • Combined configuration / preferences dialog added.
  • Rendering:
  • New cartoon rendering engine with some inital support for ribbons.
  • Unit cell rendering can be turned off.
  • Quick rendering setting now correctly reported.
  • POV-Ray colored mesh rendering bug fixed.
  • Extensions:
  • New super cell builder that supports building super cells with improved bonding.
  • Surfaces extension bug fix for electron density calculations.
  • New MOPAC plugin that supports direct execution of MOPAC.
  • New vibrations extension for molecular vibration visualization.

New in Avogadro 0.9.1 (Feb 17, 2009)

  • General:
  • New CPack based NSIS installer for Windows.
  • Manifest issues of the 0.9.0 Windows installer resolved.
  • Several bugs causing crashes of Avogadro were resolved.
  • Interface:
  • Combined configuration / preferences dialog added.
  • Rendering:
  • Ball and stick display type now supports transparency.
  • Re-enabled "Force" rendering, particularly for display of calculated vibrations
  • Rendering of computed vibrations from Gaussian, Q-Chem, MOPAC, and GAMESS-US using Open Babel

New in Avogadro 0.8.1 (Jun 10, 2008)

  • Orbitals are cleared with the rest of the molecule.
  • Orbitals engine can now display the size of the cube being rendered.
  • AutoOpt tool now displays the energy as it optimizes.
  • Quick render functions added to sphere engine and surface display types.
  • Large speed improvement to the surface rendering.
  • The manipulate tool now works much faster than before.
  • Several bug fixes for the "Insert Fragment..." dialog. Insert smiles available again.
  • More robust adjust hydrogens feature, still not perfect.
  • Improved unit cell dialog.
  • Conformer energies are now displayed.
  • Python extension now searches for system wide scripts too.
  • Gaussian input deck generator now uses extender for preview.
  • Gaussian input deck generator now supports z-matrix output.
  • GAMESS input deck dialog reduced in vertical size to accommodate smaller resolutions.
  • Export of graphics dialog improved.
  • Add engines now adds the engine selected (previous bug caused random engine to be added with name selected).
  • Plugin version bumped to 1.1, will prevent stale plugin files from being loaded.
  • Fixed several possible crashes and added additional checks to improve stability.

New in Avogadro 0.8.0 (May 20, 2008)

  • Axis rendering from the origin, to indicate the exact frame of reference.
  • Improved surface and orbital rendering.
  • Clipping planes for van der Waals surfaces.
  • Improved performance of "quick rendering" during user interaction.
  • Improved POV-Ray export.
  • New "alignment" tool, which currently allows picking two atoms to align to the X, Y or Z axes for a constant frame of reference.
  • New fragment library, to draw in arbitrary fragments. Includes a base library, as well as an unlimited number of user directories.
  • Improved selection tool to be more intuitive.
  • Added initial support for basic Gaussian calculations.
  • Added support for generating molecular orbitals from a Gaussian formatted checkpoint (*.fchk files).
  • Support for multiple Gaussian cubes in one file (e.g., multiple molecular orbitals).
  • Fixed bugs for weighted-rotor searching and other molecular mechanics in combination with Open Babel.
  • Improved molecular mechanics speed via Open Babel.
  • Removed tabs for rendering configuration and primitives
  • Allows drag-and-drop of files to the viewer window to open.
  • Added file format filters for open and save dialogs.
  • Improved save dialogs on Linux.
  • Improved look of "property" editors, including Cartesian coordinates.
  • A variety of additional interface cleanups and improvements.
  • Embedded Python interpreter.
  • Initial support for animations and GROMACS trajectories (*.xtc files).
  • Prevents possible over-writing of files if errors occur during saving.
  • Fixed several possible crashes and added additional "defensive programming."
  • Many, many bug fixes and small enhancements.

New in Avogadro 0.6.1 (Mar 14, 2008)

  • Fixed issue with losing the OpenGL context when switching views/virtual desktops.
  • Protein ribbon engine now includes the last two points.
  • Fixed rendering of selected atoms/bonds for the ball and stick engine.
  • Second light source was added to the default OpenGL view enhancing surface rendering.
  • Render cache invalidation more fine grained. Improved rendering performance on bigger molecules.
  • Cursor types now changed depending upon actions in the select/rotate tool.
  • Eye candy now solid which improves rendering performance.
  • If a window is moved off screen it will be placed in a viewable area on the Mac.
  • Many, many more enhancements and bug fixes.

New in Avogadro 0.6.0 (Mar 1, 2008)

  • Cloning render engines allowing parts of the molecule to be displayed using different styles etc.
  • Protein ribbon engine to display secondary structure.
  • Ring engine to highlight ring structures in molecules.
  • Polyhedron engine highlighting metallic centers in molecules for example.
  • Configurable color maps such as user specified colors.
  • Added an isosurface generator using the marching cubes algorithm.
  • New molecular orbitals engine that can display molecular orbitals and other surfaces from cube files.
  • New Van der Waals surface engine generates a VdW surface with optional ESP coloring.
  • An improved periodic table for drawing and editing.
  • Selection menu
  • Add, remove, clear, invert selection.
  • Select by residue, chain, molecule (i.e., click on one atom, select a whole group or molecule).
  • Select by element, residue name, solvent.
  • Selections using SMARTS.
  • Menu reorganization.
  • Persistent window/tool settings.
  • stacked widgets giving more space to the OpenGL window displaying the molecule.
  • Improved force field options, including calculating the energy, and conformational searching.
  • Geometry optimization is threaded with a progress dialog.
  • Improved speed of geometry optimization with Open Babel 2.2 builds.
  • Initial support for internationalization and translation.
  • Partial translations for French, German and British English.
  • Many, many more enhancements and bug fixes.