Difference between revisions of "To Do for 1.1"

Revision as of 09:52, 22 February 2010

The upcoming development series 1.1.x will be a series of unstable/beta releases, leading up to the 1.2.0 release. This process will be similar to the 0.9.x releases which lead up to the stable 1.0.x series.

Specific Plans

The Avogadro 1.1.x releases and 1.2 will rely on the current Open Babel 2.3.x releases (i.e., the current SVN trunk). Snapshots of Open Babel will be made to coincide with our releases.

General Ideas

• New draw tool for templates/fragments (e.g., click to add a benzene ring)

Open Babel Needs

• Reading multiple geometries and energies from QM codes (e.g., transition state searches, reaction paths, geometry optimizations, relaxed scans).
• Reading orbital energies
• Support for reading orbital coefficients (both restricted and unrestricted spin orbitals)

Geoff Hutchison

• Enhancing the "project tree" to highlight multiple molecular fragments independently
• Automatic structure -> name (including searching for multiple molecular fragments)
• Support in Open Babel for orbital energies -- and orbital energy diagrams in Avogadro
• Work on periodic force field calculations in Open Babel

Konstantin Tokarev

• Engines
  • Display arbitrary axes (done)
  • Add font and color settings to labels (in progress)
  • Element settings dialog: setup custom colors/sizes/labels for atoms of different elements
  • Arbitrary planes

• Tools
  • Angle between planes (?)

• Extensions
  • Spectra
    • Refactor spectra extension and improve UI (in progress)
    • Add suppport for Raman spectra (done)
    • Show intensities for widened peaks
    • New type of spectra scaling: different scale factors for different intervals
    • Automatic fit of PlotWidget limits to loaded data
  • Properties
    • Make properties dialogs more usable (in progress)
  • Vibrations
    • Moved vibration list to dock (done)
    • Vibration animation export (?)
• Add filtering to properties dialogs and vibrations list
• New dock for geometry optimization and relaxed scan results
• Embed image into OpenOffice.org via pipe (?)

Tim Vandermeersch

• Packmol extension
  • You always need to specify the number of molecules for a given volume
    • Estimating this would be nice... (i.e. find some correlation)
    • (Automatic, time constraint iteration might be nice to find ideal number of atoms)
    • To few molecules = pseudo vacuum conditions, just not enough molecules
    • To many molecules = increased pressure + packmol takes to long to converge
  • A wizard with some default systems
    • Protein (or molecule) + solvent + counter ions (make it smart so counter ions are correctly added to make the system charge neutral. Required for Ewald, PME, ...)
    • (Protein) + Lipid bilayer + solvent
    • Micelle/double layered/...?
    • Molecule at interface... (find best fitting plane for molecule -> determine correct rotation)
  • Allow user to browse for files that contain the used structures
    • Use QDesktopServices to obtain temporarily location so it doesn't matter if the files are not in the same dir
    • Convert the files so they all have the same format (e.g. pdb, required for packmol)
  • Text editor for experts with syntax highlighting
    • Simple parser for this text to give #atoms/volume hints
    • If there is time left: A simple 3D widget with a preview of all described volumes in wireframe might be nice to identify problems early
• Gromacs extension
  • Generate input files
  • There is a new libdrf to read in trajectories
  • Some overlap with Packmol: solvation + counter ions...
  • In progress but code currently not accessible (broken mainboard)
• Both these extensions would benefit from better performance for large systems (Marcus? ;) )