Ubuntu Manpage: xcrysden - crystalline and molecular structure visualizer

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.

COPYRIGHT