Third year simulation experiment/Files to download
This is the first section of the third year simulation experiment. You can return to the introduction page, Third year simulation experiment, or jump ahead to the next section, Introduction to molecular dynamics simulation.
All of the simulations that you run in this experiment are going to be performed on the Imperial High Performance Computing (HPC) systems. To do this, you must login to one of the HPC machines, add your simulation task to a queue of jobs waiting to run, and then wait for it to finish. For the small-scale simulations that we will perform in this experiment, the queue time should not be too long. However, you should expect to have to wait up to several hours for results to be available, particularly in the later stages!
In each section of the exercise, we have tried to provide a number of mathematical and/or research exercises that you should attempt while you are waiting for the simulations in that section to be completed. You can also use this time to write your report on the previous sections!
In this first section, we will teach you how to login to the HPC computers and submit an example simulation. While you wait for that example to complete, you can move on to the next section and read about the theory of molecular dynamics simulations
Logging into the HPC Portal
The simulations that you will perform in this experiment can in principle be performed on a desktop computer. However, these machines can only do a single simulation at a time, and are rather slow. Instead, we are going to run simulations on the college's supercomputer resources. This offers two large advantages. Firstly, even the longest simulations we will perform should take only a few hours. More importantly, you will be able to perform several simulations at the same time. In fact, to use the HPC service you must add your simulations to a queue of "jobs" that the supercomputer will perform. You can add as many jobs as you like to this queue, and simple come back to collect the results some time later.
To start, go to the HPC portal login page (as a reminder you must be on the college VPN or remote desktop). You can login with your normal college credentials. We first need to create a "project" with which your simulations will be associated. Click Projects in the menu on the left hand side, then type a name in the "Add Project" box and click Add. You are free to choose whichever name you like, but a sensible choice might be something such as "ThirdYearSimulationExpt".
Leave the HPC Portal webpage open for now — we will return to it shortly.
Getting the files for the experiment
You can download all of the files that you will need for this experiment from this address. This .zip archive contains a folder called ImperialChem-Year3SimExpt1415-master, which you should extract to a location of your choice. It contains a number of subfolders — one for each section of the experiment. Every subsequent page of this lab manual will begin with a line telling you which folder contains the necessary files, like this one:
THE FILES THAT YOU NEED FOR THIS SECTION ARE FOUND IN THE "Intro" SUBFOLDER.
Have a look in the "Intro" folder now. It contains a file called melt_crystal.in, which you should open with a text editor (like Notepad++ which you can find in Software Hub on your Desktop). This file is called an "input script", and it controls how the simulation software operates. We will perform all of our simulations with a software package called LAMMPS. Over the course of the experiment, you will learn what all of the commands in this file mean. The LAMMPS manual contains a lot of valuable information about each of the commands, if you don't understand one of them or want to look up what some parameter means you can look it up there. To make life easier, we put "further info" links in the wiki. For now, we are going to use this file to run a few trial simulations.
This is the first section of the third year simulation experiment. You can return to the introduction page, Third year simulation experiment, or jump ahead to the next section, Introduction to molecular dynamics simulation.
