XcrySDenXcrySDen

Dankook Univ.Dankook Univ.Depart of PhysicsDepart of Physics

Solid State Physics Lab.Solid State Physics Lab.Choi hye jin Choi hye jin

About XCrySDenAbout XCrySDen

XCrySDenXCrySDen is a is a crystallinecrystalline and and molecularmolecular str structure visualization programucture visualization program

XCrySDenXCrySDen = ( = (XX-window)-window)CryCrystalline stalline SStructures and tructures and DenDensitiessities

Is free software(GNU General Public liecense)Is free software(GNU General Public liecense) WEB page : http://www.xcrysden.org/WEB page : http://www.xcrysden.org/

XCrySDen workXCrySDen work

widget with periodic table of widget with periodic table of elements elements

XCrySDen workXCrySDen work

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

XCrySDen workXCrySDen work

displaying crystal and Wigner-Seitz displaying crystal and Wigner-Seitz cells cells

visualizing the forces as vectors visualizing the forces as vectors

XCrySDen workXCrySDen work

AnimationsAnimations displaying contours and colorplanes displaying contours and colorplanes displaying isosurfaces: displaying isosurfaces:

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

XCrySDen workXCrySDen work

XCrySDen’s Main WindowXCrySDen’s Main Window

Measure button

XCrySDen as a molecular viewerXCrySDen as a molecular viewer

File->xcrysden examples ->2.xsfFile->xcrysden examples ->2.xsfRotateRotate

Left mouse click and hold

LightingLighting Lighting-OnLighting-On mode yields fancy mode yields fancy graphics with shades. graphics with shades. Lighting-OffLighting-Off mode is very simple and fast, mode is very simple and fast,

but without shades.but without shades.

Lighting-OffLighting-Off mode can display mode can display onlyonly structure, crystal cages and nothing else !!!structure, crystal cages and nothing else !!!

Mouse HintMouse Hint

Rotation:Rotation: left mouse buttonleft mouse button Translation:Translation: middle mouse buttonmiddle mouse button (or both buttons for two-button mouse)(or both buttons for two-button mouse) Zoom (+):Zoom (+): Shift + Left mouse button a Shift + Left mouse button a

nd move the pointer up nd move the pointer up Zoom (-):Zoom (-): Shift + Left mouse button an Shift + Left mouse button an

d move the pointer down d move the pointer down Fullscreen mode:Fullscreen mode: double-click the left double-click the left

mouse button. mouse button. Pop-up menu:Pop-up menu: right mouse button right mouse button

Start XCrySDenStart XCrySDen

Background colorBackground color

Menu - FileMenu - File

Supported File FormatsSupported File Formats

Molecular structure formats:Molecular structure formats:

XYZXYZ

PDBPDB

Gaussian Z-Matrix fileGaussian Z-Matrix file

Gaussian output fileGaussian output file

Supported File FormatsSupported File Formats

Cystal structure formats:Cystal structure formats: XSFXSF((XXcrySDen crySDen SSturucture turucture FFile)ile) CRYSTAL files: input fileCRYSTAL files: input file unit 9unit 9 WIEN2k files WIEN2k files PWscf files : input file, output filePWscf files : input file, output file

Menu – Display, ModifyMenu – Display, Modify

Measure Measure

Atomic symbols/ FontsAtomic symbols/ Fonts

Atomic symbols/FontsAtomic symbols/Fonts

Atomic symbols/FontsAtomic symbols/Fonts

Atomic colorAtomic color

Update ColorUpdate Color updates the atomic color of updates the atomic color of

selected element selected element Defalut ColorDefalut Color

resets the atomic color of seresets the atomic color of selected element back to its dlected element back to its d

efault valueefault value Reset AllReset All

resets all atomic colors bacresets all atomic colors back to default values k to default values

Coordinate system colorCoordinate system color

Atomic radiusAtomic radius

Tessellation Factor Tessellation Factor

This factor determines the This factor determines the quality of the structure display quality of the structure display (balls, bonds, vectors).(balls, bonds, vectors). It has nothing to the with the qual It has nothing to the with the quality of an isosurface display. The greater the value of ity of an isosurface display. The greater the value of tesstessellation factorellation factor the better the quality of display. the better the quality of display.

Force Settings Force Settings

Scale ft : linear , logarithmic, square root, cubic

exponential, exp(x*x)

the most linear

force size > magnititude : logarithmic

Unicolor BondsUnicolor Bonds

Crystal CellsCrystal Cells

H-bondsH-bonds

Electron negative atoms : N O F

the minimum A-H---B bond angle to be still considered as the H-bond

Cell modeCell mode

Primitive cell mode Primitive cell mode Conventional cell modeConventional cell mode

Winger-Seitz Cell Winger-Seitz Cell SettingsSettings

Winger-Seitz Cell Winger-Seitz Cell Settings Settings

Molecular surfaceMolecular 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 analysisPseuodo density : look alike the charge-

density plotsGap analysis : periodic structures distance Functiondistance Function function function Chabazite crystal: Chabazite crystal:

Animation Animation

How to record a movie How to record a movie press the press the Start Start

Recording Recording Animated-GIF/MPEGAnimated-GIF/MPEG button; the button will button; the button will appear red-colored to appear red-colored to indicate the indicate the record record modemode is on is on

use the use the animationanimation buttons to animate the buttons to animate the structure forth and structure forth and back ... back ...

press the red press the red [Stop [Stop Recording and Recording and Save]Save] and specify the and specify the filename to save into filename to save into

solely for CRYSTAL GUI solely for CRYSTAL GUI (i) cutting a slab out of a (i) cutting a slab out of a

crystal,crystal, (ii) generating a supercel(ii) generating a supercel

l, l, (iii) adding, removing and (iii) adding, removing and

substituting atoms substituting atoms

solely for CRYSTAL GUIsolely for CRYSTAL GUI

(i) band widths, (i) band widths,

(ii) density-of-states, (ii) density-of-states,

(iii) band structure (one can sele(iii) band structure (one can select th k-path inside Brillouin zone ct th k-path inside Brillouin zone graphically), graphically),

(iv) electronic densities and elec(iv) electronic densities and electrostatic potentials as 2D contotrostatic potentials as 2D contours or 3D isosurfaces.urs or 3D isosurfaces.

Tool menuTool 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 / DatagridTools / Datagrid

IsosurfaceIsosurface

Creating the BXSF fileCreating the BXSF file

Visualize Fermi surfaceVisualize Fermi surface

Calculate Calculate eigenvalues eigenvalues in the in the irreducible wedge of Brillouin Zone(irreducible wedge of Brillouin Zone(IBZIBZ)) IBZ eigenvalues should generated IBZ eigenvalues should generated whole BZ, stored in proper formatwhole BZ, stored in proper format Band XSF = .BXSFBand XSF = .BXSF

WIEN : Xcrysden can automatically calculate the eigenvalues using the WIEN program, generated .BXSF file.

Fermi surface (.BXSF)Fermi surface (.BXSF)

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 modeDisplays the BZ and reciprocal unit cell in transparent –solid + wireframe mode

Displays Fermi surface in Brillouin zone

Tools/k-path selectedTools/k-path selected

Tools/k-path selectedTools/k-path selected

Bravais lattice typesGAMMA, X, W, K, L points for the fcc lattice

▪ primitive cubic ▪ fcc ▪ bcc ▪ primitive tetragonal ▪ body centered tetragonal ▪ primitive orthorhomobic

Tools/k-path selectedTools/k-path selected

Tools/k-path selectedTools/k-path selected