xcrysden1

Usage

Overview

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.

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.

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.