xcrysden - Online in the Cloud

PROGRAM:

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 supported, 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 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 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.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.

Use xcrysden online using onworks.net services