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Molekel - August 2009 ACS meeting
 

Molekel - August 2009 ACS meeting

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Presentation of the Molekel visualization program given at the ACS national meeting in August 2009. Shows how Molekel can be used to visualize quantum chemistry data.

Presentation of the Molekel visualization program given at the ACS national meeting in August 2009. Shows how Molekel can be used to visualize quantum chemistry data.

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    Molekel - August 2009 ACS meeting Molekel - August 2009 ACS meeting Presentation Transcript

    • Molekel – a visualization tool for quantum chemistry data U. Varetto, M. G. Giuffreda, Y. Jang Molekel – ACS meeting – August 2009 Swiss National Supercomputing Centre (CSCS)
    • TOC
      • Molekel
      • Main features
      • Quantum chemistry
      • Future directions
      Molekel – ACS meeting – August 2009
    • Molekel – ACS meeting – August 2009
    • Molekel – history
      • Project started in the early nineties by Peter F. Flükiger at the university of Geneva on Silicon Graphics hardware
      • Further developed by Stefan Portmann
      • Development stopped around 2000 with version 4.3
      • CSCS restarted development at the end of 2005
      • Current version is 5.4 released August 2009
      Molekel – ACS meeting – August 2009
    • Molekel – new version Molekel – ACS meeting – August 2009
      • Free and open source (GPL)
      • Multiplatform (including Mac OS)
      • Support for modern Graphical User Interface and graphics hardware
      • Better file format support (e.g. multi-grid .t41 &molden files with any atom ordering)
    • Molekel – ACS meeting – August 2009
    • Features – general Molekel – ACS meeting – August 2009
      • Visualization of structure information (Ball & stick, CPK,…) with support for techniques such as point sprites and level of detail to display large data sets
      • Generation of common molecular surfaces
      • Animation of trajectories
      • Visualization of backbone, residues and tertiary structure
      • Computation of distances, angles, and other geometry parameters
    • Features – quantum chemistry Molekel – ACS meeting – August 2009
      • Visualization of electronic structure data from common file formats such as Gaussian, GAMESS, ADF, Molden:
        • Electron density (density matrix read or computed from molecular orbital coefficients)
        • Molecular orbitals
        • Electrostatic potentials
        • Dipole moments
        • Vibrational modes
        • IR, Raman spectra
    • Features Molekel – ACS meeting – August 2009 Electrostatic Potential (with MEP)
    • Features Molekel – ACS meeting – August 2009 Molecular orbitals (standard transparency)
    • Features Molekel – ACS meeting – August 2009 Molecular orbitals (correct transparency)
    • Features Molekel – ACS meeting – August 2009 Vibrational modes & spectra
    • Features Molekel – ACS meeting – August 2009 Plane probe for scalar field visualization
    • Features – advanced Molekel – ACS meeting – August 2009
      • Support for programmable graphics (shaders)
      • Shading programs can be loaded and applied to any visible object
    • Features – advanced Molekel – ACS meeting – August 2009
      • Correct transparency through multi-pass rendering
      • Edge smoothing (anti-aliasing)
      • High resolution rendering (>300 dpi)
    • Molekel – ACS meeting – August 2009
    • Quantum chemistry – formats Molekel – ACS meeting – August 2009
      • Supported file formats:
        • Gaussian log and cube
          • gfoldprint (currently) required
        • GAMESS
        • ADF t41
          • Multiple grids supported
        • Molden
    • Quantum chemistry – data Molekel – ACS meeting – August 2009
      • Supported types of data:
        • MO coefficients
        • Density matrix: computed from orbital coefficients or read from file
        • Electrostatic potentials
        • Dipole moments
        • Vibrational modes
        • IR, Raman spectra
    • How-to – summary Molekel – ACS meeting – August 2009
      • Generate Gaussian output
      • Visualize data:
        • Electron density
        • HOMO/LUMO
        • Frequencies and vibrational modes
      • Enhance graphics quality
      • Save high resolution images
    • How-to – data generation Molekel – ACS meeting – August 2009 $ RunGauss #P HF/6-31G** gfoldprint pop=full cube=Potential,Prop generated from turbomolecoords 0 1 H -3.562 1.219 0.000 H -5.673 -2.437 0.000 H -7.783 1.218 0.000 Cl -3.026 -1.528 0.000 Cl -8.319 -1.528 0.000 Cl -5.673 3.056 0.000 C -5.673 1.337 0.000 C -4.515 0.669 0.000 C -4.515 -0.668 0.000 C -5.673 -1.337 0.000 C -6.831 -0.668 0.000 C -6.831 0.668 0.000 Gaussian input Gaussian output (log)
    • How-to – visualization Molekel – ACS meeting – August 2009
      • Make sure the end of line separators are in the same format as the operating system you are running Molekel on; use unix2dos or dos2unix if required
      • Load file by selecting file name and format
    • How-to – visualization Molekel – ACS meeting – August 2009
      • Generate electron density (“Surfaces”->”Electron Density” )
      • Hint: use low resolution (i.e. large step size) and check the “real-time” update box while adjusting the bounding box: the surface will be quickly recomputed at each change of the bounding box parameters
    • How-to – visualization Molekel – ACS meeting – August 2009
      • Generate HOMO and LUMO orbitals ( “Surfaces”->”Electron Density” )
      • Use the “Transparency” and “Color” sections to assign different colors and adjust transparency
    • How-to – visualization Molekel – ACS meeting – August 2009
      • Visualize vibrational modes: set the per-molecule animation settings to “Vibration”
      • Use the “Vibration” tab in the “Animation Preferences” window to combine together multiple modes
      • Click on the “play” or “next frame” button to display the arrows (arrow length proportional to velocity)
    • How-to – visualization Molekel – ACS meeting – August 2009
      • Open “radiation spectrum” dialog from “Analysis” menu
      • Select radiation type, adjust diagram
      • Use “save” button to export diagram to pdf or postscript
    • How-to – enhance quality Molekel – ACS meeting – August 2009
      • Increase resolution of atom/bonds and surfaces
      • Assign shader programs to molecule and surfaces
      • Enhance image quality by enabling anti-aliasing and correct transparency (enabled by default)
    • How-to – export image Molekel – ACS meeting – August 2009
      • Save image: use the scaling factor in the save dialog to magnify the saved image as needed
      700 pixels 579 pixels 2100 pixels 1737 pixels
    • Molekel – ACS meeting – August 2009
    • Performance Molekel – ACS meeting – August 2009
      • Faster evaluation (>10x) of electron density, MEP and orbitals using the graphics card for computation
      • Old graphics cards supported: will scale according to the capability of the graphics card
    • Graphics quality Molekel – ACS meeting – August 2009
      • Enhanced quality and speed on modern graphics cards using the techniques presented in the paper “ Interactive Volume Rendering of Functional Representations in Quantum Chemistry”* by Y. Jang and U. Varetto
      * to appear in IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2009)
    • Usability Molekel – ACS meeting – August 2009
      • Save/restore workspace: all settings and generated surfaces will be saved
      • Easier access to vibrational modes through the workspace tree window
      • Ability to edit object names (e.g. replace “orbital 45” with “HOMO” or “sigma”).
      • Easy to use graphical user interface for working with the plane probe with proper controls for adjusting the range of the displayed scalar value
      • Ability to visually place the bounding box used for surface computation
    • Resources Molekel – ACS meeting – August 2009
      • Website: molekel.cscs.ch
      • FTP: ftp.cscs.ch/out/molekel
      • e-mail: [email_address]