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    Xcrysden PDF

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    Keerati Maneesai
    XCrySDen is a program for visualizing crystalline and molecular structures. It can visualize structures from files in XSF format as well as outputs from DFT codes like PWscf. Key features include rotating and zooming structures, measuring distances and angles, modifying display parameters, and constructing k-paths for band structure calculations. Isosurfaces and contours can also be generated to visualize charge densities and other properties calculated on 3D grids.

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    Xcrysden PDF

    Uploaded by

    Keerati Maneesai
    314 views18 pages
    XCrySDen is a program for visualizing crystalline and molecular structures. It can visualize structures from files in XSF format as well as outputs from DFT codes like PWscf. Key features include rotating and zooming structures, measuring distances and angles, modifying display parameters, and constructing k-paths for band structure calculations. Isosurfaces and contours can also be generated to visualize charge densities and other properties calculated on 3D grids.

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    XCrySDen is a program for visualizing crystalline and molecular structures. It can visualize structures from files in XSF format as well as outputs from DFT codes like PWscf. Key features include rotating and zooming structures, measuring distances and angles, modifying display parameters, and constructing k-paths for band structure calculations. Isosurfaces and contours can also be generated to visualize charge densities and other properties calculated on 3D grids.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    314 views18 pages

    Xcrysden PDF

    Uploaded by

    Keerati Maneesai
    XCrySDen is a program for visualizing crystalline and molecular structures. It can visualize structures from files in XSF format as well as outputs from DFT codes like PWscf. Key features include rotating and zooming structures, measuring distances and angles, modifying display parameters, and constructing k-paths for band structure calculations. Isosurfaces and contours can also be generated to visualize charge densities and other properties calculated on 3D grids.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 18

    XCRYSDEN

    a short tutorial

    Cagliari, September 2005

    Guido Fratesi
    (mostly based on Anton Kokalj's work)
    Copy me ...
    this tutorial can be downloaded from:

    http://[ESPRESSO-TUTORIAL-SITE]/tutorial_xcrysden.pdf
    Basic scheme ...

    prepare by PWgui

    pw.x < stdin > stdout


    analyze by XCrySDen
    perform SCF calculation: analyze by XCrySDen
    PWgui
    pw.x < stdin > stdout
    output: prefix.*
    calculate property:
    PWgui
    pp.x < stdin > stdout
    output: filplot
    filter (transform) the data:
    PWgui analyze by XCrySDen
    pp.x < stdin > stdout
    output: fileout
    About XCrySDen
    XCrySDen is a crystalline and molecular structure
    visualisation program

    XCrySDen = (X-window) Crystalline Structures and


    Densities

    is free software (GNU General Public License)


    WEB page: http://www.xcrysden.org/
    XCrySDen Installation

    Download latest XCRYSDEN's version to local-scratch area as:


    cd /scratch/$USER/**** ( **** == your directory )
    wget http://www.xcrysden.org/download/xc-latest-
    linuxPC-static.tar.gz
    (or open web page http://www.xcrysden.org)
    tar zxvf xc-latest-linuxPC-static.tar.gz
    XCrySDen Installation
    Minimal installation (binary package):
    define: XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH
    environmental variables
    create: XCRYSDEN_SCRATCH directory.
    execute: xcrysden

    But use instead: ./xcConfigure script

    BEWARE: set XCRYSDEN_SCRATCH to something like:


    /scratch/$USER/xcrys_tmp
    What xcConfigure does?
    (1) defines: XCRYSDEN_TOPDIR and XCRYSDEN_SCRATCH
    environmental variables (writes either into
    ~/.bashrc, ~/.profile or ~/.cshrc)
    (2) creates: XCRYSDEN_SCRATCH directory.
    (3) creates: $HOME/.xcrysden directory.
    $HOME/.xcrysden/custom-definitions file.
    $HOME/.xcrysden/Xcrysden_defaults file.

    (4) asks several questions and writes answers in


    $HOME/.xcrysden/custom-definitions file.
    XCrySDen Installation
    Do the following:
    cd XCrySDen-*bin-static/
    ./xcConfigure
    ( set XCRYSDEN_SCRATCH to /scratch/$USER/xcrys_tmp )

    for Csh: source ~/.cshrc; rehash


    (for Bash: source ~/.bashrc )
    then execute with: xcrysden
    XCRYSDEN as a molecular
    viewer
    select menu: File->XCrySDen Examples ...->XSF Files
    open file: 2.xsf
    learn how to:
    rotate, zoom, change display mode, ...
    measure distances, angles, dihedrals, ...
    modify various display parameters ...
    learn the menus:
    Display menu: toggles displays (on/off)
    Modify menu: changes the appearance of displayed
    items
    How to print (to file)
    select menu: File->Print

    in the Print to File windows specify the name of the file. The format
    is selected by a given extension. For example:
    file.png will save PNG file
    file.gif will save GIF file
    file.eps will save EPS file
    etc.
    XCRYSDEN's print is a screen-dump therefore before printing (to file):
    maximize XCRYSDEN's main window
    zoom the structure as much as possible
    increase the tessellation factor (Modify->Tessellation Factor) to
    approx. 40 to 50
    Lighting On/Off display-mode
    VERY IMPORTANT !!!
    two levels of display modes:
    Lighting-Off mode:
    very fast, but can display only atoms and bonds !!!
    Lighting-On mode:
    more fancy display with shades, not so fast, but displays all
    possible items !!!

    Message:
    !!!for isosurfaces and alike use Lighting-On mode !!!
    XCRYSDEN as a crystal-structure viewer
    select menu: File->XCrySDen Examples ...->XSF Files
    open file: ZnS.xsf
    learn how to:
    modify number of displayed cells (Modify->Number of Units Drawn)
    change the unit of repetition (Display->Unit of Repetition ...->)
    display Wigner-Seitz cell (Display->Wigner-Seitz Cells)
    display Brillouin zone (Tools->k-path Selection)

    remember!!!
    Display menu: toggles displays (on/off)
    Modify menu: changes the appearance of displayed items
    open file: fcc-410-1x1.xsf
    display at least 44 unit cells (Modify->Number of Units Drawn)

    try: Tools->Color Scheme; select: Slab colors


    Generic use of XCRYSDEN
    Q: I want to visualize the structure from
    XXX formated file with XCRYSDEN?
    A: Write an XXX2xsf filter and convert
    your file to XSF format:
    xxx2xsf < file.xxx > file.xsf
    xcrysden --xsf file.xsf

    XSF specification is available on:


    http://www.xcrysden.org/doc/XSF.html
    Animation and Visualization of Forces
    select menu: File->XCrySDen Examples ...->XSF Files
    open file: ANIM.axsf

    animate forward by pressing: [>>] button

    display forces: Display->Forces


    modify the display of forces: Modify->Force Settings
    try to create a movie: press the [Animated GIF/MPEG >>] button
    ( Note: requires the whirlgif and mpeg_encode programs to be
    defined in ~/.xcrysden/custom-definitions )
    XCRYSDEN & PWscf
    Visualization of structures from PW.X input file:
    xcrysden --pwi input.file
    Visualization of structures from PW.X output file:
    xcrysden --pwo output.file

    Try PWscf input/output files located in


    $XCRYSDEN_TOPDIR/examples/PWSCF_Files/

    Hint: try xcrysden --help


    XCRYSDEN & PWscf
    Q: How to construct a PWscf's k-path for band-
    structure calculation with XCRYSDEN ???
    A:
    select menu:
    Tools-->k-path Selection
    select a k-path by mouse-clicking
    save the file with .pwscf extension
    (BEWARE: .pwscf extension is mandatory to get the
    pw.x formatted k-list)
    Isosurfaces and Contours
    select menu: File->XCrySDen Examples ...->XSF Files
    open file: CO_lumo.axsf.gz (Note: xcrysden can open compressed files)

    select menu: Tools->Data Grid


    then: + press [OK]
    + specify isovalue = 0.1
    + select: Render +/ isosurface
    + press: [Submit]

    two isosurfaces are drawn; isovalue: 0.01 and +0.01

    Q: what is the unit of the isovalue?

    A: XCRYSDEN does not assume any unit (as specified in file)

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