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| xcrysden [2014/05/21 11:39] – daniel | xcrysden [2020/03/06 09:12] (current) – external edit 127.0.0.1 |
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| XCrySDen (http://www.xcrysden.org/) is a very useful program that runs in the **X**-windows environment and generates **Cry**stal **S**tructures and electron **Den**sities . 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. | XCrySDen (http://www.xcrysden.org/) is a very useful program that runs in the **X**-windows environment and generates **Cry**stal **S**tructures and electron **Den**sities . 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. |
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| | For more instructions on setting up XCrySDen to work with your machine (along with pictures), see {{:tutorial_fixed.pdf|Andrew Stickel's tutorial}}. |
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| ==== XCrySDen via the Wien2k interface ==== | ==== XCrySDen via the Wien2k interface ==== |
| 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.) | 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) | * Open a terminal to the physics server (should be an X-terminal) |
| * List the processes running under your userid using ' 'ps' ' | * List the processes running under your userid using ''ps -u ph575_nn'' |
| * Kill and process called ' 'w2web' ' | * 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. | * List the processes again to be certain they're dead, and check that you are **unable** to access Wien2k via your browser. |
| * Run ' 'w2web' ' | * 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 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. |
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| * From **Windows**, use a Unix emulator to access your account (see below for instructions on emulator installation). Once an Xterminal is open type: | * 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'' | ''ssh -X ph575_nn@wien-server.physics.oregonstate.edu xcrysden'' (Make sure that the x-window system is launched before trying to launch ''xterm''.) |
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| * From a **Mac**, use X11 to access your account (Applications/Utilities/X11). At the prompt, type | * From a **Mac**, use X11 to access your account (Applications/Utilities/X11). At the prompt, type |
| To get the Physics server XCrySDen GUI running on your PC: | To get the Physics server XCrySDen GUI running on your PC: |
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| - Start the program XWin Server. | * **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. | * 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. |
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| Once within the xterm shell we are ready to ssh over to the Physics server. If just the command: | Once within the xterm shell we are ready to ssh over to the Physics server. If just the command: |
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| * 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. | * 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 described in the "Bandstrucure" section above, but it allows you to save the k-path only in a **.kpf format, which Wien does not recognize**. | * 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 [[:wien#bandstructure|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 [[:wien#bandstructure|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. | * 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. |
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| ==== XCrySDen on your own machine ==== | ==== XCrySDen on your own machine ==== |
| You can download XCrySDen from http://www.xcrysden.org/. Some configuration of the software will be necessary. | You can download XCrySDen from http://www.xcrysden.org/. Some configuration of the software will be necessary. |
