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

4. XCrySDen work
widget with periodic table of elements

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

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

7. XCrySDen work Animations displaying contours and colorplanes
displaying isosurfaces:

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

9. XCrySDen’s Main Window
Measure button

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

11. 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 !!!

12. 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

13. Start XCrySDen
Background color
Background color

14. Menu - File

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

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

17. Menu – Display, Modify

18. Measure

19. Atomic symbols/ Fonts

20. Atomic symbols/Fonts

21. Atomic symbols/Fonts

22. 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

23. Coordinate system color

24. Atomic radius

25. 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.

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

27. Unicolor Bonds

28. Crystal Cells

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

30. Cell mode
Primitive cell mode
Conventional cell mode

31. Winger-Seitz Cell Settings

32. Winger-Seitz Cell Settings

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

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

35. Animation

36. 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

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

38. 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.

39. 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 .

40. Tools / Datagrid

41. Isosurface

44. 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.

45. Fermi surface (.BXSF)

47. 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

48. Tools/k-path selected

49. 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

50. Tools/k-path selected

51. Tools/k-path selected