xcrysden(1)

💖 xcrysden — the crystalline & molecular structure visualizer 💖

okay bestie, pull up a chair, because we're about to talk about the xcrysden(1) manual page and honestly? it's a lot, but we're gonna get through it together. this is the page for XCrySDen, the program, and yes the name is also right there in the header of the page, no we're not gonna retype the whole header line, we're better than that. 💅

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✨ NAME ✨

xcrysden — crystalline and molecular structure visualizer 🦋

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✨ SYNOPSIS ✨

xcrysden [special-options]
xcrysden [special-options] format-options file|directory

like. two whole modes. iconic. 👑

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🌸 DESCRIPTION 🌸

okay so XCrySDen is a crystalline and molecular structure visualisation program, and its whole thing — its main character energy, if you will — is displaying isosurfaces and contours, which you can superimpose on crystalline structures and then interactively rotate and manipulate. that's the vibe. you look at it, you spin it, you're obsessed. ✨

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💅 SPECIAL OPTIONS 💅

these are the special ones, the pre-game, the getting-ready-with-me options.

• -h, --help — shows you the help message. like, "hey bestie here's how this works" 🫶
• -v, --version — shows you the program version info. the receipts. 📋
• -u id, --use id — loads XCrySDen embedded into a container window with window-ID=id. yes, it's a whole nesting situation, it ate.
• -r dim, --reducedim dim — reduces the periodic dimension of the XSF file to dim. ⚠️ must be specified before the --xsf option — like, order matters, it's giving strict. e.g. xcrysden -r 2 --xsf file.
• -c file, --custom file — loads custom-definitions from a specified file. the syntax is that of ~/.xcrysden/custom-definitions. 🎀
• -a file, --attributes file — loads attributes from file. the format of the attributes file is literally this:

ELEMENTCOLOR
atomic-number1   red1 blue1 green1
atomic-number2   red2 blue2 green2
...
ELEMENTRADIUS
atomic-number1   radius1
atomic-number2   radius2
...

• -l file, --lights file — loads lights parameters from XCrySDen's lights formatted file. 💡 lighting is everything, no cap.

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🦋 FORMAT OPTIONS 🦋

now the file-format buffet. pick your format, bestie, there's one for everybody. 🍓

• --xsf file — loads structure from XCrySDen's-Structure-File (XSF) formatted file. the classic. the blueprint. 🌟
• --animxsf file, --axsf file — loads structures from Animated-XCrySDen's-Structure-File (AXSF) formatted file. plural structures! it moves! 💃
• --bxsf file — loads bands from a BXSF (Band-XSF) file and visualizes the Fermi Surface. 🔥
• --xmol file, --xyz file — loads structure from an XYZ formatted file. simple, cute, does the job.
• --pdb file — loads structure from a PDB formatted file. 🧬
• --gzmat file — loads structure from a Gaussian Z-matrix. heads up: this one requires the Open-Babel program. not optional, it's a whole dependency.
• --gaussian_out file, --gxx_out file, --g98_out file — loads structure from a Gaussian output file. fair warning: only single point calculation and optimization run is supported so far. but for the optimization run you can render all the structures that were produced during the run, which is lowkey kind of a serve. ✨
• --cube file, --gXX_cube file, --g98_cube file — loads structure from a Gaussian cube file. ⚠️ the cube file should be produced with the Cube=Cards option. and only scalar cube files are supported — that means Cube=(Cards,Density) or Cube=(Cards,Orbitals) or Cube=(Cards,Potential). refer to the GAUSSIAN manual for the meaning of these keywords, because that lore is not in here. 📚
• --orca_out file — loads structure(s) from an Orca output file. heads up: only Geometry optimization outputs were tested so far. 🙈
• --crystal_inp file — loads structure from a CRYSTAL (http://http://www.crystal.unito.it/) input file.
• --crystal_f9 file — loads structure from CRYSTAL (http://http://www.crystal.unito.it/) fortran unit 9.
• --wien_struct filehead|file|directory — loads structure from a WIEN2k (http://www.wien2k.at/) struct-file, where:
  • filehead = name of struct file without the .struct extension,
  • file = filename,
  • directory = name of case directory.
• --wien_kpath directory|struct-file — reads the struct file and renders the first Brillouin zone with special k-points. 🎯 k-path can be selected interactively by mouse-clicking the special k-points. user must specify EMIN and EMAX energies and the total number of k-points along the path. ⚠️ that number is merely an estimation of the total number of k-points, since XCrySDen tries to get a very uniform sampling of k-points along the path — so don't specify the WIEN2k maximum allowed number of k-points, because XCrySDen might generate a few points more. 💀
• --wien_renderdensity directory — reads struct, output, and rho files and renders the crystalline structure plus the precomputed charge density. 🌈
• --wien_density direcory — either a 2D or 3D region for charge density calculation is interactively chosen by mouse-clicking. XCrySDen generates in5 file(s), calculates and renders charge density either as isolines/colorplanes (2D) or isosurfaces (3D). ✨ (and yes, the manual literally spells the argument direcory there — we keep it exactly as it is, periodt.)
• --wien_fermisurface directory — pops up a task window for Fermi surface creation. after several steps the Fermi surface is (hopefully) drawn as a 3D isosurface. the "(hopefully)" is doing a lot of emotional labor there and we respect it. 🙏
• --fhi_inpini file — loads structure from an FHI98MD inp.ini formatted file.
• --fhi_coord file — loads structure from an FHI98MD coord.out formatted file.
• --pwi, --pw_inp file — loads structure from a pw.x input file. pw.x is a pseudopotential planewave program of the Quantum-ESPRESSO distribution (http://www.quantum-espresso.org/). ☕
• --pwo, --pw_out file — loads structure from a pw.x output file. pw.x is a pseudopotential planewave program of the Quantum-ESPRESSO distribution (http://www.quantum-espresso.org/). ☕
• -s script, --script script — loads a script from a file containing a Tcl script. 💻
• --os script, --oldscript script — loads an old-formatted script (prior to xcrysden-1.6) from file. vintage. archival. nostalgic-core. 🎀
• --print filename — prints the displayed structure to a file and exits. super useful inside shell scripts if you want "automatic" printing. like, it does the thing and then dips. 👋

example:

xcrysden --xsf file.xsf --script state.xcrysden --print file.png

in this example, --xsf file.xsf loads the structure from the XSF file, --script state.xcrysden sets up a desired display (a script like this is typically created via the File-->Save Current State menu option), and --print file.png prints the displayed structure to a file and exits xcrysden. chef's kiss. 🤌

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🔍 SEE ALSO 🔍

for more info about XCrySDen, go look here:

http://www.xcrysden.org/

and further documentation is available at:

http://www.xcrysden.org/Documentation.html

go read, bestie, iykyk. 📖

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👑 COPYRIGHT 👑

Copyright (C) 1996--2019 Anton Kokalj

this program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. you should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

this program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. see the GNU General Public License for more details. 🫡 (no warranty bestie, we said what we said)

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and that's the whole page, you ate it, you understood it, you're literally a Unix girlie now. 💖✨ this has been the xcrysden(1) page from XCrySDen, dated August 7, 2019 — mwah, go visualize something pretty. 🎀🦋🌸