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Table of Contents
OpenMX
OpenMX is open source software that calculates perform density functional theory (DFT) calculations for your class project. You will use it to calculate band structures in this course. OpenMX is installed on the computers in Weniger 412 and you can access from there or you can ssh in remotely from your own computer. Mitchell Senger has written a wonderful tutorial (link needed) to help you get started. After completing Mitchell's tutorial, you will have produced your first band structure calculation. Once you have completed one example, you'll can find additional information and tutorials on the OpenMX user manual on the OpenMX website.
For calculations for your own material, you will need the position of the atoms in your material. The Crystallography Open Database is one good place to look for crystallography information files (.cif files). A great way to visualize the information in a .cif file is to drag the .cif file into the browser-based OpenMX Viewer. Chrome is the recommended browser for OpenMX Viewer.
For you own calculations, you will need to choose an appropriate path through k-space. This Brillouin zone database is a useful resource. The wikipedia article about Brillouin zones is also helpful for visualizing your path.
Computers in Weniger 412
The computers in Weniger 412 were reconfigured over summer 2018 so that you now log in with your onid credentials. If you are in the computer room using the terminals, you may use any computer, and your results will be in your home directory regardless of which computer you use.
We will, however, assign you a particular computer and request that you use that machine when you log in remotely. This will prevent unintentional overload of the system.
Linux
There are about 24 terminals in Weniger 412, running Linux. The graphical interface is called Nautilus - it looks a bit like Windows. OpenMX runs in command line mode, though, so you will need some rudimentary unix knowledge. Mitchell's tutorial is helpful. (There are lots of UNIX tutorials on the web. Here are simple ones from Rubin Landau of OSU Physics http://www.physics.oregonstate.edu/~rubin/nacphy/UNIX/ and from the University of Surrey: http://www.ee.surrey.ac.uk/Teaching/Unix/).
Here are some very basic unix commands:
pwd | print working directory (tells where you currently are) |
ls | list files in the working (current) directory |
ls -l | list long form of files in the working directory |
cd TiC | change directory to the one named “TiC” |
cd .. | change directory to a level up from the current one |
rm myfile | remove the file named “myfile” from the the working directory. Remember there is no recycling bin, so be careful |
cp myfile /home/ph575_nn/TiC | copy myfile in the current directory to a directory called /home/ph575_nn/TiC. |
mkdir Docs | make a directory called Docs |
ps -u janet | list all processes being run by user janet (displays a number XXXX with each) |
kill XXXX | kill the process identified by the number XXXX (see below) |
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
ps -u ph575_nn ←- your account name here
and something like below will appear
27186 ? 00:00:02 w2web
to kill the job identified by the job number 27186 in the first column, enter the following into the terminal
kill 27186
