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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 pro- gram, 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 be- fore --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 structures from Animated-XCrySDen's-Structure-File (AXSF) for- matted 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 pro- gram). --gaussian_out file --gxx_out file --g98_out file Load structure from Gaussian output file. Only single point calcu- lation and optimization run is supported so far. For the optimiza- tion run it is possible to render all the structures that were pro- duced 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 supported, that is, Cube=(Cards,Density) or Cube=(Cards,Orbitals) or Cube=(Cards,Potential). Refer to GAUSSIAN manual for the meaning of this keywords. --orca_out file Load structure(s) from Orca output file. Only Geometry optimization outputs were tested so far. --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 special k-points. User must specify EMIN and EMAX energies and to- tal number of k-points along the path. This number is merely an es- timation 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 struc- ture and precomputed charge density. --wien_density direcory Either 2D or 3D region for charge density calculation is interac- tively chosen by mouse-clicking. XCrySDen generates in5 file(s), calculates and renders charge density either as isolines/color- planes (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 formatted file. --fhi_coord file Load structure from FHI98MD coord.out formatted 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.quantum-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. --os script --oldscript script Load old-formatted script (prior to xcrysden-1.6) from file. --print filename Print the displayed structure to a file and exit. This is useful within the shell scripts to achieve "automatic" printing. Example: xcrysden --xsf file.xsf --script state.xcrysden --print file.png In this example "--xsf file.xsf" loads the structure from XSF file, "--script state.xcrysden" setups a desired display (such a script is typically created via File-->Save Current State menu option) and "--print file.png" prints the displayed structure to a file and ex- its xcrysden. 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--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 MER- CHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. XCrySDen August 7, 2019 xcrysden(1)
NAME | SYNOPSIS | DESCRIPTION | SPECIAL OPTIONS | FORMAT OPTIONS | SEE ALSO | COPYRIGHT
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