table of contents
| 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 structures 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 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 total number of k-points along the path. This number is merely an estimation 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), calculates 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 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 exits 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 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
| August 7, 2019 | XCrySDen |