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| wien [2014/05/21 11:28] – daniel | wien [2020/03/06 09:12] (current) – external edit 127.0.0.1 |
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| | In previous years, we used Wien 2k rather than OpenMX to do the class DFT project. This old page is available because some of the FAQ are relevant, and there is some info about XCrysDen and unix that may be useful. |
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| ====== WIEN 2k Basic Instructions for PH575 students ====== | ====== WIEN 2k Basic Instructions for PH575 students ====== |
| Wien 2k is a commercial program that calculates dispersion relations, density of states, partial density of states, and other properties of crystalline solids. The program is named Wien 2k (pronounced "VEEN-2-kay") because it was developed by physicists in Vienna, Austria ("Vienna" is the English version of the German "Wien"), and the most recent modification of the program was in the year 2000. More information about the program is at the developers' website http://www.wien2k.at. | Wien 2k is a commercial program that calculates dispersion relations, density of states, partial density of states, and other properties of crystalline solids. The program is named Wien 2k (pronounced "VEEN-2-kay") because it was developed by physicists in Vienna, Austria ("Vienna" is the English version of the German "Wien"), and the most recent modification of the program was in the year 2000. More information about the program is at the developers' website http://www.wien2k.at. |
| * Also see {{:tutorial_fixed.pdf|Andrew Stickel's tutorial}}, which covers more details on setting up Wien on windows machines. He is a former student who really got into the program and many of the sub programs. | * Also see {{:tutorial_fixed.pdf|Andrew Stickel's tutorial}}, which covers more details on setting up Wien on windows machines. He is a former student who really got into the program and many of the sub programs. |
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| Prof. Guenter Schneider and I are also working to implement a more user-friendly interface using //flair//, the DFT code Dr. Schneider has written, and //gem//, a Python-based graphical interface. If you wish to be a guinea-pig for the flair/gem option, let me know **Flair/gem option not in 2014**. | Prof. Guenter Schneider and I are also working to implement a more user-friendly interface using //flair//, the DFT code Dr. Schneider has written, and //gem//, a Python-based graphical interface. |
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| ===== Computer Accounts ===== | ===== Computer Accounts ===== |
| * If you get a prompt asking for a username and password, then is likely your configuration got lost somewhere. Enter the same ph575_nn for user and same password as shell (for convenience). If it asks for a port number, enter the 100nn number. Hostname should be wien-server.physics.oregonstate.edu. Hit y for master node if it asks about it. | * If you get a prompt asking for a username and password, then is likely your configuration got lost somewhere. Enter the same ph575_nn for user and same password as shell (for convenience). If it asks for a port number, enter the 100nn number. Hostname should be wien-server.physics.oregonstate.edu. Hit y for master node if it asks about it. |
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| * You may omit the ''-X'' in the ssh command above if you simply want to manage files or run ''w2web''. However, if you want to run XCrySDen (see below: [[#XCrySDen]]), which needs the X-Window environment, you need the ''-X''. | * You may omit the ''-X'' in the ssh command above if you simply want to manage files or run ''w2web''. However, if you want to run XCrySDen (see page: [[:xcrysden|XCrySDen]]), which needs the X-Window environment, you need the ''-X''. **Notice that it is a uppercase letter ''X'', which is a different flag from a lowercase ''x''.** |
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| ===== View Structure ===== | ===== View Structure ===== |
| You can view the structure you've created with the ''view structure'' command, but ONLY if you have an X-terminal open to your wien-server account to allow you to run the graphics on the wien-server (see below under XCrysDen). | You can view the structure you've created with the ''view structure'' command, but ONLY if you have an X-terminal open to your wien-server account to allow you to run the graphics on the wien-server (see [[:xcrysden|XCrysDen]]). |
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| ===== Initialize ===== | ===== Initialize ===== |
| - If you run the ''Bandstructure'' program (see below), then decide to run the DoS program again, you may get an error (the reason is that the bandstructure & DoS programs use a different type of k-mesh or k-grid, and they overwrite each other). The fix is to run ''lapw1'' from the ''Execution/single prog'' menu. | - If you run the ''Bandstructure'' program (see below), then decide to run the DoS program again, you may get an error (the reason is that the bandstructure & DoS programs use a different type of k-mesh or k-grid, and they overwrite each other). The fix is to run ''lapw1'' from the ''Execution/single prog'' menu. |
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| ===== Bandstructure (or dispersion relation or spaghetti diagram) ===== | ===== Bandstructure ===== |
| Under ''Tasks''. | (Also known as dispersion relation or spaghetti diagram.) Under ''Tasks''. |
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| Follow instructions; they are quite straightforward. | Follow instructions; they are quite straightforward. |
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| - "Bandstructure" requires a different set of k-values than was used to generate the density of states. For DoS, Wien uses a k-mesh stored in ''case.klist''. For the bandstructure program, Wien generates a different k-mesh stored in a file called ''case.klist_band''. Wien has prestored k-paths for fcc, bcc, hcp and cubic lattices, but if you want different paths, or have a lattice of different symmetry, you may need to use the program "XCrySDen" to generate the k-points for this part. | - "Bandstructure" requires a different set of k-values than was used to generate the density of states. For DoS, Wien uses a k-mesh stored in ''case.klist''. For the bandstructure program, Wien generates a different k-mesh stored in a file called ''case.klist_band''. Wien has prestored k-paths for fcc, bcc, hcp and cubic lattices, but if you want different paths, or have a lattice of different symmetry, you may need to use the program [[:xcrysden|XCrySDen]] to generate the k-points for this part. |
| - If you get a message from Wien2k that ' 'X-windows is needed to run X-CrySDen' ' and it seems XCrySDen is not going to run, you must reset the ' 'w2web' ' as described in [[#XCrySDen via the Wien2k interface]] below. | - If you get a message from Wien2k that ''X-windows is needed to run X-CrySDen'' and it seems XCrySDen is not going to run, you must reset the ''w2web'' as described in [[xcrysden#XCrySDen via the Wien2k interface]]. |
| - To use XCrySDen to generate a ''case.klist_band'' file: If you have an X-terminal open, XCrySDen should open up if you select ''Generate k-mesh using XCrySDen'' on the Bandstructure menu. You should see the Brillouin zone, with high-symmetry points labeled as dots on the boundary. You can rotate the structure with the mouse. Click on the special points (they appear on the right when you select them and some will be labeled). Click 'OK' when you have the path you want. Then enter total number of k-points along the path. 50 is a good number to start with. Now save the file as ''xcrysden.klist''. Go back into Wien2k and under Task >> Bandstructure, and choose ''from xcrysden'' from the menu. When prompted to overwrite the case.klist_band file, click "yes". | - To use XCrySDen to generate a ''case.klist_band'' file: If you have an X-terminal open, XCrySDen should open up if you select ''Generate k-mesh using XCrySDen'' on the Bandstructure menu. You should see the Brillouin zone, with high-symmetry points labeled as dots on the boundary. You can rotate the structure with the mouse. Click on the special points (they appear on the right when you select them and some will be labeled). Click 'OK' when you have the path you want. Then enter total number of k-points along the path. 50 is a good number to start with. Now save the file as ''xcrysden.klist''. Go back into Wien2k and under Task >> Bandstructure, and choose ''from xcrysden'' from the menu. When prompted to overwrite the case.klist_band file, click "yes". |
| - If clicking ''Generate k-mesh using XCrySDen'' does not bring up XCrySDen, log in to the Wien2k server with an X-terminal (see "Access Wien 2k via the web" above). Go into the directory in which you are running your simulation. For example, if you are doing silicon in the WIEN2k/Si/ directory, enter 'cd WIEN2k/Si/'. Next, enter 'xcrysden' in the terminal. Once xcrysden opens, go to File -> Open Wien2k ... -> Select k-path. It will ask you to choose the case directory. It should be the default one you went into in the beginning. You should see the Brillouin zone, with high-symmetry points labeled as dots on the boundary. You can rotate the structure with the mouse. Click on the special points (they appear on the right when you select them and some will be labeled). Click 'OK' when you have the path you want. Then enter total number of k-points along the path. 50 is a good number to start with. Now save the file as ''xcrysden.klist''. Go back into Wien2k and under Task >> Bandstructure, and choose ''from xcrysden'' from the menu. When prompted to overwrite the case.klist_band file, click "yes". Now you can continue as normal. | - If clicking ''Generate k-mesh using XCrySDen'' does not bring up XCrySDen, log in to the Wien2k server with an X-terminal (see [[#Access Wien 2k via the web]] above). Go into the directory in which you are running your simulation. For example, if you are doing silicon in the WIEN2k/Si/ directory, enter 'cd WIEN2k/Si/'. Next, enter 'xcrysden' in the terminal. Once xcrysden opens, go to File -> Open Wien2k ... -> Select k-path. It will ask you to choose the case directory. It should be the default one you went into in the beginning. You should see the Brillouin zone, with high-symmetry points labeled as dots on the boundary. You can rotate the structure with the mouse. Click on the special points (they appear on the right when you select them and some will be labeled). Click 'OK' when you have the path you want. Then enter total number of k-points along the path. 50 is a good number to start with. Now save the file as ''xcrysden.klist''. Go back into Wien2k and under Task >> Bandstructure, and choose ''from xcrysden'' from the menu. When prompted to overwrite the case.klist_band file, click "yes". Now you can continue as normal. |
| - After you have run the spaghetti program, Wien may no longer rerun the DoS program because it now has the wrong k-mesh. You should to rerun ''lapw1'' in the ''single prog'' menu. This should fix the problem. (Seems not to be a problem in the current version of Wien). | - After you have run the spaghetti program, Wien may no longer rerun the DoS program because it now has the wrong k-mesh. You should to rerun ''lapw1'' in the ''single prog'' menu. This should fix the problem. (Seems not to be a problem in the current version of Wien). |
| - You must enter the **correct Fermi energy** for the spaghetti plot to be generated. There is a step where you must edit the ''case.insp'' file. The Fermi energy is listed in the file header, and you need to enter this number in the file itself where you see the "xxxx". e.g. You see in header the line | - You must enter the **correct Fermi energy** for the spaghetti plot to be generated. There is a step where you must edit the ''case.insp'' file. The Fermi energy is listed in the file header, and you need to enter this number in the file itself where you see the "xxxx". e.g. You see in header the line |
| **UNIX or Linux Users**: You don't need this section! | **UNIX or Linux Users**: You don't need this section! |
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| **Mac Users**: Newer Macs have Unix as part of their operating system. Run the ''Terminal'' program, which is in Applications/Utilities folder. If you want to run any program that needs the X-Window environment (e.g. XCrySDen below), you must run X11, found in Applications/Utilities or you can download it for free from Apple. | **Mac Users**: Newer Macs have Unix as part of their operating system. Run the ''Terminal'' program, which is in Applications/Utilities folder. If you want to run any program that needs the X-Window environment (such as [[:xcrysden|XCrySDen]]), you must run X11, found in Applications/Utilities or you can download it for free from Apple. |
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| **PC Users**: Windows users can use either Cygwin-X or Putty. Cygwin-X can be downloaded at http://www.cygwin.com/install.html and putty.exe can be downloaded at http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html. Cygwin-X and putty work with all versions of Windows. If you want to run XCrySDen with Wien2K, you have to use Cygwin-X. Cygwin-X installation is given below in "How to get XCrySDen running on the Jansen server with Windows (via Cygwin-X)" section. Be sure to load the package that has the ssh command. In the program menu, go to Cygwin-X -> Xwin Server. This should open up a "X-Terminal" program. Now look above to see how to run w2web or below to run XCrySDen. | **PC Users**: Windows users can use either Cygwin-X or Putty. Cygwin-X can be downloaded at http://www.cygwin.com/install.html and putty.exe can be downloaded at http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html. Cygwin-X and putty work with all versions of Windows. If you want to run XCrySDen with Wien2K, you have to use Cygwin-X. Cygwin-X installation is given in the [[:xcrysden|XCrySDen]] page. Be sure to load the package that has the ssh command. In the program menu, go to Cygwin-X -> Xwin Server. This should open up a "X-Terminal" program. |
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| If you are just running "w2web" it is recommended that you use Putty. It is simple and quick. If you are in Wngr 304, you will have to install Putty on your own account. It cannot be installed for all users at once. The file putty.exe takes only a few seconds to download. Next run putty.exe and a window labeled "PuTTY Configuration" should appear. In the bar that says "Host Name (or IP address)", enter "ph575_nn@wien-server.physics.oregonstate.edu" Below this bar is an option SSH that is already checked and that is why you do not have to enter it. | If you are just running ''w2web'' it is recommended that you use Putty. It is simple and quick. If you are in Wngr 304, you will have to install Putty on your own account. It cannot be installed for all users at once. The file putty.exe takes only a few seconds to download. Next run putty.exe and a window labeled "PuTTY Configuration" should appear. In the bar that says "Host Name (or IP address)", enter ''ph575_nn@wien-server.physics.oregonstate.edu'' Below this bar is an option SSH that is already checked and that is why you do not have to enter it. |
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| **All users**: | **All users**: |
| |''cd ..''| **c**hange **d**irectory to a level up from the current one| | |''cd ..''| **c**hange **d**irectory to a level up from the current one| |
| |''rm myfile''|**r**e**m**ove the file named "myfile" from the the working directory. Remember there is no recycling bin, so be careful| | |''rm myfile''|**r**e**m**ove the file named "myfile" from the the working directory. Remember there is no recycling bin, so be careful| |
| |''cp myfile /home/ph575_nn/TiC'' | **c**o**p**y ' 'myfile' ' in the current directory to a directory called ''/home/ph575_nn/TiC''. | | |''cp myfile /home/ph575_nn/TiC'' | **c**o**p**y ''myfile'' in the current directory to a directory called ''/home/ph575_nn/TiC''. | |
| |''mkdir Docs'' | **m**a**k**e a **dir**ectory called ''Docs'' | | |''mkdir Docs'' | **m**a**k**e a **dir**ectory called ''Docs'' | |
| |''ps -u janet'' | list all **p**roces**s**es being run by **u**ser **janet** (displays a number XXXX with each) | | |''ps -u janet'' | list all **p**roces**s**es being run by **u**ser **janet** (displays a number XXXX with each) | |
| If you need to kill a Wien2K job from the terminal environment (remember you can also "kill the process" using the bomb icon that you see from the Web portal), first enter the following in a terminal | If you need to kill a Wien2K job from the terminal environment (remember you can also "kill the process" using the bomb icon that you see from the Web portal), first enter the following in a terminal |
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| ''ps -ef | grep w2web | grep ph575_nn'' <-- your account name here | ''ps -u ph575_nn'' <-- your account name here |
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| and something like below will appear | and something like below will appear |
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| '' | ''27186 ? 00:00:02 w2web'' |
| ph575_01 4202 1 0 Mar26 ? 00:00:00 /usr/bin/perl /home/henri/WIEN2K/SRC_w2web/bin/w2web'' | |
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| ''ph575_01 10365 10334 0 11:50 pts/4 00:00:00 grep w2web'' | |
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| to kill the job identified by the job number 4202 in the second column, enter the following into the terminal | |
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| ''kill 4202'' | to kill the job identified by the job number 27186 in the first column, enter the following into the terminal |
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| Note that you do not have to kill job number 10365, since this is searching for a job called ''w2web'' and it has nothing to do with w2web. | ''kill 27186'' |
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