Extras: Setting up the necessary software in a virtual machine

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NOTE: If you are an MSE404 student you do not need to follow the instructions given here. These instructions are only for people who wish to run their own copy of the software on their own machine. Doing is only recommended for more advanced users or people without access to the compute server. It will mean many files will not be at the location given in the lab documents so you will need to be able to modify the instructions correctly yourself.

A virtual machine allows you to run a complete operating system contained within an application regardless of what operating system you have. One package that allows you to do this is VMWare. VMWare is available free to Imperial College students via http://www.imperial.ac.uk/admin-services/ict/store/software/software-for-students/.

Once you have it installed this, I suggest getting an Xubuntu iso from https://xubuntu.org/getxubuntu, and using this to create a new virtual machine. You can go with all the default settings, and pick whatever username and password you like.

Once this is complete, it should reboot and prompt you for the password you set during install to log you in to your desktop. Then first ensure the system is fully up-to-date with

sudo apt-get update
sudo apt-get upgrade

You may also prefer to change the keyboard settings, since it defaults to a US layout. If you go to the settings menu and pick “Language Support” you can drag e.g. “English (United Kingdom)” to the top of the list and click the “Apply System-Wide” button. You may also want to go to the “Regional Formats” tab and select the UK option and apply system wide again. Then go to the Keyboard settings menu and the “Layout” tab. At the bottom, click the “Add” button and scroll down to UK English (there are several sub-options here that may be better if you have e.g. a Mac). You can delete the US layout once you have added the UK one.

Then you can simply install quantum espresso from the repositories, with

sudo apt-get install quantum-espresso

This will install a slightly older version of quantum espresso (which still has all the features needed for these labs but may output additional files, such as the wavefunction in a slightly different place than mentioned in the lab description), and will not however create some of the directories, and help files that we use in the examples. So some of the commands given in the lab documents will not work without modification by you by default. In particular, you should skip the various module commands as they will not be necessary for you.

If you have access to the server

One way around this, if you have access to the server, would be be to copy these directories to the same place on your virtual machine. You can do this by connecting to the college VPN and using the following commands, substituting your college username for USER in the second command (which will also prompt you for your college password):

sudo mkdir -p /opt/share
sudo rsync -auz USER@mt-studenty.mt.ic.ac.uk:/opt/share/quantum-espresso /opt/share
sudo mkdir /opt/Courses
sudo rsync -auvz USER@mt-studenty.mt.ic.ac.uk:/opt/Courses/MSE404 /opt/Courses

Then you should have everything necessary in place. I would suggest re-running the last command at the beginning of each lab session to ensure you have the latest version of the lab documents.

If you do not have access to the server

There are two directories present on the server that are referred to at various points in the lab documentation:

  1. /opt/share/quantum-espresso - We have placed the various documentation files (txt, html and pdf) that are provided with the quantum-espresso source package in a directory here. It can be quite useful to refer to the text files from the command line. However the same information can all be found in the documentation section of the quantum espresso website. In particular the page with links to the input data description.
  2. /opt/Courses/MSE404 - this lets students copy a directory for the lab containing the instructions and example files at the beginning of each lab session. You could clone the git repository https://gitlab.com/eamonnmurray/MaterialsModelling.git whereever you like and use this instead. If you are a student taking the course, I suggest pulling the repo at the beginning of each session as we make changes as the course proceeds each year.

For example, you could clone the repository to the same directory as on the server:

sudo mkdir -p /opt/Courses
sudo git clone https://gitlab.com/eamonnmurray/MaterialsModelling.git /opt/Courses/MSE404

This will create the folder /opt/Courses/MSE404 with all the material for all the labs. To update this ahead of a lab session you can do

cd /opt/Courses/MSE404
sudo git pull