XcrySDen Dankook Univ. Depart of Physics Solid State Physics Lab. Choi hye jin.
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Transcript of XcrySDen Dankook Univ. Depart of Physics Solid State Physics Lab. Choi hye jin.
![Page 1: XcrySDen Dankook Univ. Depart of Physics Solid State Physics Lab. Choi hye jin.](https://reader030.fdocuments.us/reader030/viewer/2022020921/5697bfc71a28abf838ca7878/html5/thumbnails/1.jpg)
XcrySDenXcrySDen
Dankook Univ.Dankook Univ.Depart of PhysicsDepart of Physics
Solid State Physics Lab.Solid State Physics Lab.Choi hye jin Choi hye jin
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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/
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XCrySDen workXCrySDen work
widget with periodic table of widget with periodic table of elements elements
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XCrySDen workXCrySDen work
displaying molecular and crystalline displaying molecular and crystalline structure in several different display structure in several different display modes modes
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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
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XCrySDen workXCrySDen work
AnimationsAnimations displaying contours and colorplanes displaying contours and colorplanes displaying isosurfaces: displaying isosurfaces:
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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
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XCrySDen’s Main WindowXCrySDen’s Main Window
Measure button
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XCrySDen as a molecular viewerXCrySDen as a molecular viewer
File->xcrysden examples ->2.xsfFile->xcrysden examples ->2.xsfRotateRotate
Left mouse click and hold
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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 !!!
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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
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Start XCrySDenStart XCrySDen
Background colorBackground color
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Menu - FileMenu - File
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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
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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
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Menu – Display, ModifyMenu – Display, Modify
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Measure Measure
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Atomic symbols/ FontsAtomic symbols/ Fonts
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Atomic symbols/FontsAtomic symbols/Fonts
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Atomic symbols/FontsAtomic symbols/Fonts
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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
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Coordinate system colorCoordinate system color
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Atomic radiusAtomic radius
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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.
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Force Settings Force Settings
Scale ft : linear , logarithmic, square root, cubic
exponential, exp(x*x)
the most linear
force size > magnititude : logarithmic
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Unicolor BondsUnicolor Bonds
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Crystal CellsCrystal Cells
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H-bondsH-bonds
Electron negative atoms : N O F
the minimum A-H---B bond angle to be still considered as the H-bond
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Cell modeCell mode
Primitive cell mode Primitive cell mode Conventional cell modeConventional cell mode
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Winger-Seitz Cell Winger-Seitz Cell SettingsSettings
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Winger-Seitz Cell Winger-Seitz Cell Settings Settings
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Molecular surfaceMolecular surface
EXPONENTIAL
GAUSSIAN
Constant GAUSSIAN
Constant EXPONENTIAL
Distance FUNCTION
R_a : covalent or van der Waals
Solid, wire, dot
Smooth, float
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Pseuodo density or Gap analysisPseuodo density : look alike the charge-
density plotsGap analysis : periodic structures distance Functiondistance Function function function Chabazite crystal: Chabazite crystal:
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Animation Animation
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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
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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
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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.
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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 .
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Tools / DatagridTools / Datagrid
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IsosurfaceIsosurface
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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.
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Fermi surface (.BXSF)Fermi surface (.BXSF)
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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
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Tools/k-path selectedTools/k-path selected
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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
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Tools/k-path selectedTools/k-path selected
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Tools/k-path selectedTools/k-path selected