XCrysDen

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Xcrysden.png
XCrysDen is a crystalline and molecular structure visualization program. The name of the program stands for Crystalline Structures and Densities and X because it runs under the X-Window environment. It facilitates a display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It also possesses some tools for analysis of properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone for the band-structure plots, and visualization of Fermi surfaces.

XCrysDen can be used for representation of molecular-models in several display modes (wireframe, sticks, ball-and-sticks, spacefill, ...), display of forces acting on atoms, real time operations such as rotation, translation and zooming of displayed structure, animations, measurement of distances, angles, and dihedrals, contour-plane and isosurface representation of scalar fields, "arrows" representation of the vector field, setting various attributes, such as colors of atoms and bonds, radii of atoms, thicknesses of bonds and lines, sizes of points, balls and spacefills etc. With respect to crystal structures, XCrysDen can be used to switch between primitive and conventional cell settings, change the number of the displayed unit cells, that is, display smaller or larger portions of a crystal, display the crystal lattice, visualize the Wigner-Seitz cell and Brillouin-zone, k-path selection for band-structure calculations, visualization of Fermi surfaces etc.

XCrysDen can read molecular (or crystal) structure from a few standard file formats such as XYZ, PDB, and its own internal XSF format. XCrysDen can visualize chemical structures for the ab initio simulation software such as Quantum Espresso and ABINIT (e.g. using the Cut3D utility). There are several utilities such as xsfConvert (for TB-LMTO-ASA and VASP), Sies2xsf (for SIESTA), c2x (for CASTEP).

XCrysDen provides TCL based scripting environment.

Entrypoint Binaries

XCrysDen is deployed in an individual docker container on Kogence. XCrysDen container offer following Entrypoint Binaries:

  • xcrysden:
    • xcrysden with no Options/Arguments will start the interactive XCrysDen program. Click on Visualizer tab, once it is active, of your Kogence Model and you will see the XCrysDen's GUI interface.
    • xcrysden -s scriptFile or xcrysden --script scriptFile will execute the plotting instructions in the scriptFile script.
    • xcrysden --xsf myOrbialsData.xsf will load xsf data.
    • xcrysden --xsf myOrbialsData.xsf --script scriptFile --print myOrbitalsPrint.png will load xsf data, execute plotting instructions in the TCL script scriptFile and then print the final view in a png.
    • All command line options described here are supported on Kogence: http://www.xcrysden.org/doc/comlin.html.

Using XCrysDen on Kognece

In order to use XCrysDen in your Model, connect XCrysDen container to your Model through the Stack tab of your Model. Selecting an Entrypoint Binary on the Stack tab is optional. If you do not select an Entrypoint on the Stack tab of your model then all the Entrypoint Binaries defined for the container would be available in the environment of all programs, scripts and other containers connected to your Model. For example, issuing the command xcrysden -s scriptFile will invoke the XCrysDen Entrypoint Binary from any of your model scripts, containers or from CloudShell and will execute the plotting instructions in the scriptFile script. Alternatively, you can select xcrysden Entrypoint Binary on the Stack tab and provide file name of the command script in the Options/Arguments box.