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XCrySDen - Crystalline and Molecular Structure Visualization Program

XCrySDen is a free software program for visualizing crystalline and molecular structures. It can display structures in different modes, visualize forces as vectors, and perform reciprocal-space analysis. With XCrySDen, you can easily visualize and analyze crystal and molecular structures.

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XCrySDen - Crystalline and Molecular Structure Visualization Program

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  1. XcrySDen Dankook Univ. Depart of Physics Solid State Physics Lab. Choi hye jin

  2. About XCrySDen • XCrySDen is a crystalline and molecular structure visualization program • XCrySDen = (X-window)Crystalline Structures and Densities • Is free software(GNU General Public liecense) • WEB page : http://www.xcrysden.org/

  3. XCrySDen work • widget with periodic table of elements

  4. XCrySDen work • displaying molecular and crystalline structure in several different display modes

  5. XCrySDen work • displaying crystal and Wigner-Seitz cells • visualizing the forces as vectors

  6. XCrySDen work • Animations • displaying contours and colorplanes • displaying isosurfaces:

  7. XCrySDen work • Reciprocal-space analysis: • selecting a k-path inside the Brillouin-zone • visualizing Fermi surfaces

  8. XCrySDen’s Main Window Measure button

  9. XCrySDen as a molecular viewer File->xcrysden examples ->2.xsf Rotate Left mouse click and hold

  10. Lighting • Lighting-On mode yields fancy graphics with shades. • Lighting-Off mode is very simple and fast, but without shades. • Lighting-Off mode can display only structure, crystal cages and nothing else !!!

  11. Mouse Hint • Rotation:left mouse button • Translation:middle mouse button (or both buttons for two-button mouse) • Zoom (+): Shift + Left mouse button and move the pointer up • Zoom (-): Shift + Left mouse button and move the pointer down • Fullscreen mode: double-click the left mouse button. • Pop-up menu: right mouse button

  12. Start XCrySDen Background color Background color

  13. Menu - File

  14. Supported File Formats • Molecular structure formats: XYZ PDB Gaussian Z-Matrix file Gaussian output file

  15. Supported File Formats • Cystal structure formats: XSF(XcrySDen Sturucture File) CRYSTAL files: input file unit 9 WIEN2k files PWscf files : input file, output file

  16. Menu – Display, Modify

  17. Measure

  18. Atomic symbols/ Fonts

  19. Atomic symbols/Fonts

  20. Atomic symbols/Fonts

  21. Atomic color • Update Color updates the atomic color of selected element • Defalut Color resets the atomic color of selected element back to its default value • Reset All resets all atomic colors back to default values

  22. Coordinate system color

  23. Atomic radius

  24. Tessellation Factor • This factor determines the quality of the structure display (balls, bonds, vectors). It has nothing to the with the quality of an isosurface display. The greater the value of tessellation factor the better the quality of display.

  25. Force Settings Scale ft : linear , logarithmic, square root, cubic exponential, exp(x*x) the most linear force size > magnititude : logarithmic

  26. Unicolor Bonds

  27. Crystal Cells

  28. H-bonds Electron negative atoms : N O F the minimum A-H---B bond angle to be still considered as the H-bond

  29. Cell mode • Primitive cell mode • Conventional cell mode

  30. Winger-Seitz Cell Settings

  31. Winger-Seitz Cell Settings

  32. Molecular surface EXPONENTIAL GAUSSIAN Constant GAUSSIAN Constant EXPONENTIAL Distance FUNCTION R_a : covalent or van der Waals Solid, wire, dot Smooth, float

  33. Pseuodo density or Gap analysis Pseuodo density : look alike the charge- density plots Gap analysis : periodic structures distance Function function Chabazite crystal:

  34. Animation

  35. How to record a movie • press the Start Recording Animated-GIF/MPEG button; the button will appear red-colored to indicate the record mode is on • use the animation buttons to animate the structure forth and back ... • press the red [Stop Recording and Save] and specify the filename to save into

  36. solely for CRYSTAL GUI • (i) cutting a slab out of a crystal, • (ii) generating a supercell, • (iii) adding, removing and substituting atoms

  37. solely for CRYSTAL GUI (i) band widths, (ii) density-of-states, (iii) band structure (one can select th k-path inside Brillouin zone graphically), (iv) electronic densities and electrostatic potentials as 2D contours or 3D isosurfaces.

  38. Tool menu If a DATAGRID section (2D or 3D) is present in loaded XSF (XCrySDen Structure File) then this menu-item is active. Via this option user will be able to render 3D isosurfaces and/or 2D isolines and colorplanes .

  39. Tools / Datagrid

  40. Isosurface

  41. Creating the BXSF file • Visualize Fermi surface Calculate eigenvalues in the irreducible wedge of Brillouin Zone(IBZ) IBZ eigenvalues should generated whole BZ, stored in proper format Band XSF = .BXSF WIEN : Xcrysden can automatically calculate the eigenvalues using the WIEN program, generated .BXSF file.

  42. Fermi surface (.BXSF)

  43. Displays Fermi surface in Brillouin zone Display Fermi surface in reciprocal unit cell Toggles the cropping of Fermi surface to BZ Toggles the display of the BZ and reciprocal unit cell frames Displays the BZ and reciprocal unit cell in wireframe mode Displays the BZ and reciprocal unit cell in transparent –solid mode Displays the BZ and reciprocal unit cell in transparent –solid + wireframe mode

  44. Tools/k-path selected

  45. Tools/k-path selected Bravais lattice types GAMMA, X, W, K, L points for the fcc lattice ▪ primitive cubic ▪ fcc ▪ bcc ▪ primitive tetragonal ▪ body centered tetragonal ▪ primitive orthorhomobic

  46. Tools/k-path selected

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