Avogadro v1.1.0

Avogadro 1.1.0 was released on September 12, 2012.

What’s New

This release marks the first of a new set of development “beta” releases of Avogadro, for adventurous users and programmers. It’s stable enough for day-to-day use–we use it ourselves. That said, we expect there are bugs, missing features, and we do not yet recommend it for Linux distributions to package, since the programming interfaces may still change before 1.2.0 is released.

Most importantly, we seek community feedback as to needed features, bug reports, and anything else. Thanks!

The following list includes some of the changes since [Avogadro 1.0.3](Avogadro 1.0.3 “wikilink”).

Interface

• Support for “growing” molecules by inserting a fragment in place of a selected hydrogen atom

• Searches PubChem for an IUPAC name using the “Molecular Properties” command

• Custom atomic colors, atomic radii, and atom and bond labels.

Tools

• Support for adding centers of mass and centers of geometry using the selection tool

Commands / Extensions

• 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

• Support for Bader’s Atoms-In-Molecule analysis, using QTAIM, contributed by Prof. Eric Brown, of Loyola University, Chicago

Rendering / Display

• New orthographic display

• New color plugins:

  • Color by SMARTS – match a given Daylight SMARTS pattern

Known Issues & Limitations

None at this time.