1 / 31

VIBE Calculations of Vibrational modes Using Siam Quantum

VIBE Calculations of Vibrational modes Using Siam Quantum . A full-feature presentation by Nanta Sophonrat Adviser: Dr.Teepanis Chachiyo. Computational Physics @ KKU Date : May 7,2010. Outlines. Introduction Theoretical Background Programming Results Discussion Conclusion.

sai
Download Presentation

VIBE Calculations of Vibrational modes Using Siam Quantum

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. VIBECalculations of Vibrational modes Using Siam Quantum A full-feature presentation by NantaSophonrat Adviser: Dr.TeepanisChachiyo Computational Physics @ KKU Date : May 7,2010

  2. Outlines • Introduction • Theoretical Background • Programming • Results • Discussion • Conclusion

  3. Introduction: Ab initio Quantum Chemistry program using Hartree-Fock method to determine energy and wave function of molecule Input: Structure file + basis set file Output : Ground state energy + wave function http://www.physics.kku.ac.th/sq/ http://www.physics.kku.ac.th/Computational_physics/?q=node/33

  4. Introduction: Vibrational modes IR Spectroscopy ?  What theory lies beneath these tools? What do we use to identify molecules? http://webbook.nist.gov/chemistry http://www.physics.kku.ac.th/raman/ Raman Spectroscopy

  5. Introduction • Normal mode OR Vibrational mode • a pattern of motion in which all parts of the system oscillate with the same frequency • The frequency is called • “Natural frequency” What about molecules? http://en.wikipedia.org/wiki/Normal_mode

  6. Theoretical background molecular system Coordinate mass particle A particle B cartesian coordinate coordinate @ equilibrium

  7. Theoretical Background • Lagrange equation Generalized coordinate Mass-Weighted Hessian Lagrangian Kinetic energy Taylor’s expansion @ equilibrium ( ) Potential energy

  8. Theoretical Background 3N equations Differential Equation Eigenvalue equations = angular freq. Ref: Lecture on molecular vibration, Dr.TeepanisChachiyo (http://www.physics.kku.ac.th/computational_physics/)

  9. VIBEProgramming Flowchart start read structure file (@ equilibrium) + basis file find Mass-Weighted Hessian Solve eigenvalue equation eigenvalue = eigenvector = write file to animate each mode end

  10. Programming find Mass-Weighted Hessian from Siam Quantum x y z • Using Finite Different method A B case case for VIBE

  11. Programming H = mass-weighted hessian C = eigenvector E = eigenvalue S = overlap matrix (in this case = identity) Solve eigenvalue equation • in the form HC = ESC • using LAPACK eigenvalue = eigenvector = In case , we let it equal to zero. angular frequency is natural frequency.

  12. Programming write file to animate each mode • reposition by eigenvector T= no. of frame=50 t = 0,1,..,T suitable coefficient optional

  13. Programming • VIBE : usage http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

  14. Result1 : H2O (9 normal modes) mode 1 mode 3 mode 5 Torsion modes Rotational modes

  15. Result1 : H2O (9 normal modes) mode 2 mode 4 mode 6 OH stretching mode

  16. Result1 : H2O (9 normal modes) • Significant mode mode 9 mode 7 mode 8 OH symmetric Stretching mode OH antisymmetric Stretching mode Bending mode

  17. Result2 : H2O2 (12 normal modes) mode 2 mode 3 mode 1 Torsion Rotation Torsion

  18. Result2 : H2O2 (12 normal modes) mode 5 mode 6 mode 4 OH stretch + Rotation OH stretch OH stretch

  19. Result2 : H2O2 (12 normal modes) mode 7 (321) mode 7(631) mode 8 OH stretching OH stretching OO stretch

  20. Result2 : H2O2 (12 normal modes) mode 9 mode 10 Antisymmetric bending Symmetric bending

  21. Result2 : H2O2 (12 normal modes) mode 11 mode 12 OH antisymmetric stretching OH symmetric stretching

  22. Result Comparing • Vibe VS Gaussian • Example : H2O + basis 321G Gaussian 03W Vibe

  23. Result Comparing • Vibe VS Experiment • Example : H2O Vibe

  24. Table1 H2O : Vibe VS Gaussian

  25. Table2 H2O : Vibe&Gaussian VS Experiment

  26. Table3 H2O2: Vibe VS Gaussian

  27. Result Comparing • Experimental data: H2O2

  28. Table4 H2O2: Vibe&Gaussian VS Experiment

  29. Discussion • Over estimate approximation • From table 2 and 4, we can see that all of the error is positive. That is Vibe results is larger than experimental value. • Since the results of Vibe are corresponded to those of Gaussian as seen in table 1and 3; we can conclude that error is not from our algorithm. • In the nut shell, the error is due to Hartree-Fock methods itself that it is not taking Coulomb correlations into account. (for more info. please see Thijsen,Computational Physics,2007)

  30. Conclusion • Vibe is a program created to calculate natural frequency and vibrational modes which can be visualized using VMD. We use two molecules to test the accuracy of Vibe: H2O and H2O2.The results are compared with experimental data and with the results from Gaussian. The error compared with Gaussian is in the range of 0.16 – 3.99% which is acceptable; while the error compared with experimental data is in the range of 1.91 – 31.58%. We note that the all of the frequencies obtained from Vibe and also from Gaussian are larger than those from experiment. This is due to the limit of Hartree-Fock method used to calculated Energy in Siam Quantum and Gaussian.

  31. QUESTIONS THE END THANK YOU

More Related