XcrySDen

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XcrySDen

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

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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/

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XCrySDen work

• widget with periodic table of elements

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XCrySDen work

• displaying molecular and crystalline structure in
  several different display modes

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XCrySDen work

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

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XCrySDen work

• Animations
• displaying contours and colorplanes
• displaying isosurfaces

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XCrySDen work

• Reciprocal-space analysis
• selecting a k-path inside the
• Brillouin-zone
• visualizing Fermi surfaces

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XCrySDens Main Window
Measure button
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XCrySDen as a molecular viewer

• File-gtxcrysden examples -gt2.xsf
• Rotate

Left mouse click and hold
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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 !!!

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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

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Start XCrySDen
Background color
Background color
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Menu - File
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Supported File Formats

• Molecular structure formats
• XYZ
• PDB
• Gaussian Z-Matrix file
• Gaussian output file

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Supported File Formats

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

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Menu Display, Modify
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Measure
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Atomic symbols/ Fonts
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Atomic symbols/Fonts
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Atomic symbols/Fonts
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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

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Coordinate system color
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Atomic radius
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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.

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Force Settings
Scale ft linear , logarithmic, square root,
cubic exponential, exp(xx)
the most linear force size
gt magnititude logarithmic
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Unicolor Bonds
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Crystal Cells
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H-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 mode

• Primitive cell mode
• Conventional cell mode

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Winger-Seitz Cell Settings
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Winger-Seitz Cell Settings
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Molecular 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 analysis
• Pseuodo density look alike the charge-
  density plots
• Gap analysis periodic structures
• distance Function function
• Chabazite crystal

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Animation
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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

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solely for CRYSTAL GUI

• (i) cutting a slab out of a crystal,
• (ii) generating a supercell,
• (iii) adding, removing and substituting atoms

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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.
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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 .
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Tools / Datagrid
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Isosurface
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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.
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Fermi surface (.BXSF)
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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
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Tools/k-path selected
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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
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Tools/k-path selected
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Tools/k-path selected