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.

Published in: Technology, Education

Molekel - August 2009 ACS meeting

  1. 1. 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)
  2. 2. TOC <ul><li>Molekel </li></ul><ul><li>Main features </li></ul><ul><li>Quantum chemistry </li></ul><ul><li>Future directions </li></ul>Molekel – ACS meeting – August 2009
  3. 3. Molekel – ACS meeting – August 2009
  4. 4. Molekel – history <ul><li>Project started in the early nineties by Peter F. Flükiger at the university of Geneva on Silicon Graphics hardware </li></ul><ul><li>Further developed by Stefan Portmann </li></ul><ul><li>Development stopped around 2000 with version 4.3 </li></ul><ul><li>CSCS restarted development at the end of 2005 </li></ul><ul><li>Current version is 5.4 released August 2009 </li></ul>Molekel – ACS meeting – August 2009
  5. 5. Molekel – new version Molekel – ACS meeting – August 2009 <ul><li>Free and open source (GPL) </li></ul><ul><li>Multiplatform (including Mac OS) </li></ul><ul><li>Support for modern Graphical User Interface and graphics hardware </li></ul><ul><li>Better file format support (e.g. multi-grid .t41 &molden files with any atom ordering) </li></ul>
  6. 6. Molekel – ACS meeting – August 2009
  7. 7. Features – general Molekel – ACS meeting – August 2009 <ul><li>Visualization of structure information (Ball & stick, CPK,…) with support for techniques such as point sprites and level of detail to display large data sets </li></ul><ul><li>Generation of common molecular surfaces </li></ul><ul><li>Animation of trajectories </li></ul><ul><li>Visualization of backbone, residues and tertiary structure </li></ul><ul><li>Computation of distances, angles, and other geometry parameters </li></ul>
  8. 8. Features – quantum chemistry Molekel – ACS meeting – August 2009 <ul><li>Visualization of electronic structure data from common file formats such as Gaussian, GAMESS, ADF, Molden: </li></ul><ul><ul><li>Electron density (density matrix read or computed from molecular orbital coefficients) </li></ul></ul><ul><ul><li>Molecular orbitals </li></ul></ul><ul><ul><li>Electrostatic potentials </li></ul></ul><ul><ul><li>Dipole moments </li></ul></ul><ul><ul><li>Vibrational modes </li></ul></ul><ul><ul><li>IR, Raman spectra </li></ul></ul>
  9. 9. Features Molekel – ACS meeting – August 2009 Electrostatic Potential (with MEP)
  10. 10. Features Molekel – ACS meeting – August 2009 Molecular orbitals (standard transparency)
  11. 11. Features Molekel – ACS meeting – August 2009 Molecular orbitals (correct transparency)
  12. 12. Features Molekel – ACS meeting – August 2009 Vibrational modes & spectra
  13. 13. Features Molekel – ACS meeting – August 2009 Plane probe for scalar field visualization
  14. 14. Features – advanced Molekel – ACS meeting – August 2009 <ul><li>Support for programmable graphics (shaders) </li></ul><ul><li>Shading programs can be loaded and applied to any visible object </li></ul>
  15. 15. Features – advanced Molekel – ACS meeting – August 2009 <ul><li>Correct transparency through multi-pass rendering </li></ul><ul><li>Edge smoothing (anti-aliasing) </li></ul><ul><li>High resolution rendering (>300 dpi) </li></ul>
  16. 16. Molekel – ACS meeting – August 2009
  17. 17. Quantum chemistry – formats Molekel – ACS meeting – August 2009 <ul><li>Supported file formats: </li></ul><ul><ul><li>Gaussian log and cube </li></ul></ul><ul><ul><ul><li>gfoldprint (currently) required </li></ul></ul></ul><ul><ul><li>GAMESS </li></ul></ul><ul><ul><li>ADF t41 </li></ul></ul><ul><ul><ul><li>Multiple grids supported </li></ul></ul></ul><ul><ul><li>Molden </li></ul></ul>
  18. 18. Quantum chemistry – data Molekel – ACS meeting – August 2009 <ul><li>Supported types of data: </li></ul><ul><ul><li>MO coefficients </li></ul></ul><ul><ul><li>Density matrix: computed from orbital coefficients or read from file </li></ul></ul><ul><ul><li>Electrostatic potentials </li></ul></ul><ul><ul><li>Dipole moments </li></ul></ul><ul><ul><li>Vibrational modes </li></ul></ul><ul><ul><li>IR, Raman spectra </li></ul></ul>
  19. 19. How-to – summary Molekel – ACS meeting – August 2009 <ul><li>Generate Gaussian output </li></ul><ul><li>Visualize data: </li></ul><ul><ul><li>Electron density </li></ul></ul><ul><ul><li>HOMO/LUMO </li></ul></ul><ul><ul><li>Frequencies and vibrational modes </li></ul></ul><ul><li>Enhance graphics quality </li></ul><ul><li>Save high resolution images </li></ul>
  20. 20. 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)
  21. 21. How-to – visualization Molekel – ACS meeting – August 2009 <ul><li>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 </li></ul><ul><li>Load file by selecting file name and format </li></ul>
  22. 22. How-to – visualization Molekel – ACS meeting – August 2009 <ul><li>Generate electron density (“Surfaces”->”Electron Density” ) </li></ul><ul><li>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 </li></ul>
  23. 23. How-to – visualization Molekel – ACS meeting – August 2009 <ul><li>Generate HOMO and LUMO orbitals ( “Surfaces”->”Electron Density” ) </li></ul><ul><li>Use the “Transparency” and “Color” sections to assign different colors and adjust transparency </li></ul>
  24. 24. How-to – visualization Molekel – ACS meeting – August 2009 <ul><li>Visualize vibrational modes: set the per-molecule animation settings to “Vibration” </li></ul><ul><li>Use the “Vibration” tab in the “Animation Preferences” window to combine together multiple modes </li></ul><ul><li>Click on the “play” or “next frame” button to display the arrows (arrow length proportional to velocity) </li></ul>
  25. 25. How-to – visualization Molekel – ACS meeting – August 2009 <ul><li>Open “radiation spectrum” dialog from “Analysis” menu </li></ul><ul><li>Select radiation type, adjust diagram </li></ul><ul><li>Use “save” button to export diagram to pdf or postscript </li></ul>
  26. 26. How-to – enhance quality Molekel – ACS meeting – August 2009 <ul><li>Increase resolution of atom/bonds and surfaces </li></ul><ul><li>Assign shader programs to molecule and surfaces </li></ul><ul><li>Enhance image quality by enabling anti-aliasing and correct transparency (enabled by default) </li></ul>
  27. 27. How-to – export image Molekel – ACS meeting – August 2009 <ul><li>Save image: use the scaling factor in the save dialog to magnify the saved image as needed </li></ul>700 pixels 579 pixels 2100 pixels 1737 pixels
  28. 28. Molekel – ACS meeting – August 2009
  29. 29. Performance Molekel – ACS meeting – August 2009 <ul><li>Faster evaluation (>10x) of electron density, MEP and orbitals using the graphics card for computation </li></ul><ul><li>Old graphics cards supported: will scale according to the capability of the graphics card </li></ul>
  30. 30. Graphics quality Molekel – ACS meeting – August 2009 <ul><li>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 </li></ul>* to appear in IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2009)
  31. 31. Usability Molekel – ACS meeting – August 2009 <ul><li>Save/restore workspace: all settings and generated surfaces will be saved </li></ul><ul><li>Easier access to vibrational modes through the workspace tree window </li></ul><ul><li>Ability to edit object names (e.g. replace “orbital 45” with “HOMO” or “sigma”). </li></ul><ul><li>Easy to use graphical user interface for working with the plane probe with proper controls for adjusting the range of the displayed scalar value </li></ul><ul><li>Ability to visually place the bounding box used for surface computation </li></ul>
  32. 32. Resources Molekel – ACS meeting – August 2009 <ul><li>Website: molekel.cscs.ch </li></ul><ul><li>FTP: ftp.cscs.ch/out/molekel </li></ul><ul><li>e-mail: [email_address] </li></ul>

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