xcrysden(1) XCrySDen xcrysden(1)
NAME
xcrysden - crystalline and molecular structure visualizer
SYNOPSIS
xcrysden [special-options]
xcrysden [special-options] format-options file|directory
DESCRIPTION
XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be
superimposed on crystalline structures and interactively rotated and manipulated.
SPECIAL OPTIONS
-h
--help
Display help message.
-v
--version
Display program version information.
-u id
--use id
Load XCrySDen embedded into container window with window-ID=id.
-r dim
--reducedim dim
Reduce periodic dimension of XSF file to dim. Must be specified before --xsf option, e.g., xcrysden -r 2 --xsf file.
-c file
--custom file
Load custom-definitions from a specified file (the syntax is that of ~/.xcrysden/custom-definitions).
-a file
--attributes file
Load attributes from file. The format of the attributes file is the following:
ELEMENTCOLOR
atomic-number1 red1 blue1 green1
atomic-number2 red2 blue2 green2
...
ELEMENTRADIUS
atomic-number1 radius1
atomic-number2 radius2
...
-l file
--lights file
Load lights parameters from XCrySDen's lights formatted file.
FORMAT OPTIONS
--xsf file
Load structure from XCrySDen's-Structure-File (XSF) formatted file.
--animxsf file
--axsf file
Load structres from Animated-XCrySDen's-Structure-File (AXSF) formatted file.
--bxsf file
Load bands from BXSF (Band-XSF) file and visualize Fermi Surface.
--xmol file
--xyz file
Load structure from XYZ formatted file.
--pdb file
Load structure from PDB formatted file.
--gzmat file
Load structure from Gaussian Z-matrix (requires Open-Babel program).
--gaussian_out file
--gXX_out file
--g98_out file
Load structure from Gaussian output file. Only single point calculation and optimization run is supported so far. For the optimization
run it is possible to render all the structures that were produced during the run.
--cube file
--gXX_cube file
--g98_cube file
Load structure from Gaussian cube file. The cube file should be produced with the Cube=Cards option. Only scalar cube files are sup-
ported, that is, Cube=(Cards,Density) or Cube=(Cards,Orbitals) or Cube=(Cards,Potential). Refer to GAUSSIAN manual for the meaning of
this keywords.
--crystal_inp file
Load structure from CRYSTAL (http://http://www.crystal.unito.it/) input file.
--crystal_f9 file
Load structure from CRYSTAL (http://http://www.crystal.unito.it/) fortran unit 9.
--wien_struct filehead|file|directory
Load structure from WIEN2k (http://www.wien2k.at/) struct-file, where:
filehead = name of struct file without .struct extension,
file = filename,
directory = name of case directory.
--wien_kpath directory|struct-file
Read struct file and render first Brillouin zone with special k-points. K-path can be selected interactively by mouse-clicking the spe-
cial k-points. User must specify EMIN and EMAX energies and total number of k-points along the path. This number is merely an estima-
tion of total number of k-points, since XCrySDen tries to get very uniform sampling of k-points along the path (don't specify WIEN2k
maximum allowed number of k-points, since XCrySDen maight generate few points more).
--wien_renderdensity directory
Read struct, output, and rho files and renders crystalline structure and precomputed charge density.
--wien_density direcory
Either 2D or 3D region for charge density calculation is interactively chosen by mouse-clicking. XCrySDen generates in5 file(s), calcu-
lates and renders charge density either as isolines/colorplanes (2D) or isosurfaces (3D).
--wien_fermisurface directory
Pop-up a task window for Fermi surface creation. After several steps the Fermi surface is (hopefully) drawn as 3D isosurface.
--fhi_inpini file
Load structure from FHI98MD inp.ini formated file.
--fhi_coord file
Load structure from FHI98MD coord.out formated file.
--pwi
--pw_inp file
Load structure from pw.x input file. pw.x is a pseudopotential planewave program of the Quantum-ESPRESSO distribution (http://www.quan-
tum-espresso.org/).
--pwo
--pw_out file
Load structure from 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
Load script from file containing Tcl script.
SEE ALSO
Fore more information about XCrySDen, see:
http://www.xcrysden.org/.
Further documentation is available at:
http://www.xcrysden.org/Documentation.html.
COPYRIGHT
Copyright (C) 1996--2012 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 MER-
CHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
XCrySDen February 7, 2012 xcrysden(1)