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

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/

XCrySDen work widget with periodic table of elements

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

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

XCrySDen work Animations displaying contours and colorplanes displaying isosurfaces:

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

XCrySDen’s Main Window Measure button

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

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 !!!

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

Start XCrySDen Background color Background color

Menu - File

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

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

Menu – Display, Modify

Measure

Atomic symbols/ Fonts

Atomic symbols/Fonts

Atomic symbols/Fonts

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

Coordinate system color

Atomic radius

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.

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

Unicolor Bonds

Crystal Cells

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

Cell mode Primitive cell mode Conventional cell mode

Winger-Seitz Cell Settings

Winger-Seitz Cell Settings

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

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

Animation

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

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

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.

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 .

Tools / Datagrid

Isosurface

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.

Fermi surface (.BXSF)

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

Tools/k-path selected

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

Tools/k-path selected

Tools/k-path selected