“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. It can run on most UNIX platforms, without any special hardware requirements.” - www.xcrysden.org

XCrySDen (http://www.xcrysden.org/) is a very useful program that runs in the X-windows environment and generates Crystal Structures and electron Densities . It allows you to view a crystal structure in real space and in reciprocal space. Within the context of Wien2K and W2Web, XCrySDen is a program which may be used to select k-paths for band structure dispersion plots. It may also be used interactively with Wien2K to generate Fermi surface images. It should be possible to get XCrySDen to interface completely within W2Web, but you have to be logged in with a X-terminal with the '-X' option at the same time. Without the Xterminal login, only selecting the k-path for bandstructure diagrams will work. Otherwise, it is necessary to manipulate some files manually and this is a bit tricky the first time. (See below). The XCrySDen website is very useful for quick instructions and for the Wien interface.

For more instructions on setting up XCrySDen to work with your machine (along with pictures), see Andrew Stickel's tutorial.

Wien2k interfaces with XCrySDen to graph crystal structures, generate k-paths, plot electron density and so on. For XCrySDen to run, you must be logged in to the wien-server via the xterm and xwinshell (Windows) or via X11 (Mac) while you are running Wien in the Browser. If, despite your being connected to the server via an xterm, Wien fails to call XCrysDen as you expect and gives a message X-Windows need to run XCrySDen, you must reset the the w2web interface. (Sometimes, the interaction between the two programs quits without warning.)

• Open a terminal to the physics server (should be an X-terminal)
• List the processes running under your userid using ps -u ph575_nn
• Kill all processes called w2web (by entering kill xxxx where xxxx is the number listed next to w2web).
• List the processes again to be certain they're dead, and check that you are unable to access Wien2k via your browser.
• Run w2web

You should be able to access Wien2k via the browser (log in again) and XCrySDen and Wien should be talking again provided the X-terminal is still open.

You can run XCrySDen on the Physics server by using the X Window System protocol.

• In a Linux environment, simply type

xcrysden

• From Windows, use a Unix emulator to access your account (see below for instructions on emulator installation). Once an Xterminal is open type:

ssh -X ph575_nn@wien-server.physics.oregonstate.edu xcrysden (Make sure that the x-window system is launched before trying to launch xterm.)

• From a Mac, use X11 to access your account (Applications/Utilities/X11). At the prompt, type

ssh ph575_nn@wien-server.physics.oregonstate.edu -X xcrysden

Spring 2014 – An update to Mountain Lion or Mavericks seems to cause xcrysden to break on MacOS systems. As of now there is no known way to make this work. (If you are able to get it working then please share!)

Cygwin is a UNIX emulation engine. Aside from the main engine, additional ‘packages’ must be downloaded and installed. Each package adds additional functionality to the emulation engine, all can be viewed and marked for download via the main Cygwin setup program.

Go to http://cygwin.com/install.html and get the setup.exe file (download link in the beginning text of the webpage).

Once you run the setup.exe file hit next> and then choose install from internet, next>. Select install for all users and choose a root directory for Cygwin (i.e. where you want it installed).

Next choose a download location for storing temporary files related to the setup (just go with default folder if you have no other preference). Select next>.

Choose Direct Connection next>.

Choose a website to download more needed files (specifically outlined below) from. The ftp ones seemed to be quicker than the http. Select next> and it should connect to the site and a select packages screen will appear.

All the packages which may ever be needed are listed alphabetically below. It is possible that the first package, cygwin, and the last one, xinit, are the only two needed for opening an X Windows terminal and running XCrySDen on the Jansen server, however the others are needed when running XCrySDen on your own machine. Since the file size of each package is pretty small it doesn't hurt to download them all in case they may be called upon by the program in some way.

• cygwin
• bash
• bc
• coreutils
• gawk
• grep
• gzip
• ImageMagick
• less
• mesa
• more
• opengl
• openssh
• tcltk
• X-start-menu-icons
• xterm
• xinit

Use the search box in the corner to locate these. The easiest thing is to have the select package screen in category view mode (button upper right to change view). Type in the search word for each package in the list above (e.g. cygwin). After the word All at the top of the file structure tree click on the word Default so that it changes to Install. This may download some unnecessary stuff but it is OK. For the bc package using the search bar brings up a bunch of stuff since those letters appear next to each other in a lot of the available Cygwin packages. The only thing needed is bc: The GNU numeric…. under the utils heading. Select next> and let it download and install any dependent files if needed (it will warn you if so).

You should be able to grab all the packages in one go, but if not continue to rerun the Cygwin setup.exe file with all the same initial root directory and download folder options until each has been installed.

After completing the above steps, you should have two new program folders available within the program start menu, these are Cygwin and Cygwin-X. The first contains one program Cygwin Bash Shell. This is a UNIX command line interface, which is needed if you want to get XCrySDen running on your own PC (see below). The second, Cygwin-X, contains a few programs. The two we are concerned with are XWin Server and xterm. Combined these programs allow a graphical user interface for a program running on the Jansen server (XCrySDen) to run on your PC.

To get the Physics server XCrySDen GUI running on your PC:

• Start the program XWin Server.
• A window for xterm may appear automatically upon starting the server program, but if not then manually click on the program xterm (Start>Programs>Cygwin-X>xterm) to start one.

Once within the xterm shell we are ready to ssh over to the Physics server. If just the command:

ssh -X ph575_nn@wien-server.physics.oregonstate.edu

is sent then you should be able to go back to the w2web interface in your web browser and the buttons under ElectronDensity and BandStructure will automatically send the commands to the Physics server to start XCrySDen. Alternatively you could start XCrySDen right away by typing

ssh -X ph575_nn@wien-server.physics.oregonstate.edu xcrysden

as stated above in the section ‘XCrySDen on the Physics server’ for Windows use

A note about speed: XCrySDen's speed depends on the speed of your internet connection. From campus, XCrySDen seems to stream very smoothly, but from off campus locations the interface can lag significantly.

• To look at your structure in real space, go to the File menu, Open WIEN2k Struct file. You'll get a list of your directories in Wien, and you select the one you're interested in, say TiC, then click OK. You'll get a list of the files in the TiC directory. Select the one called TiC.struct. Click OK. You'll be able to rotate the structure expand it and so on using the graphical interface.
• You can also look at the reciprocal space image from the Tools menu, by selecting Select k-path. This looks similar to what is described in the Wien bandstructure section, but it allows you to save the k-path only in a .kpf format, which Wien does not recognize. To get the approriate klist_band file into Wien to run the bandstructure, follow the instructions in the bandstructure section.
• To generate Fermi surfaces go to the File menu, select Open Wien2K, select Fermi Surface. This process runs a ‘W2Web’ type interface to walk through the necessary programs and generate the appropriate files.

You can download XCrySDen from http://www.xcrysden.org/. Some configuration of the software will be necessary.