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 in Virtual Machines (VM). Before the beginning of your lab session, you should have received an invitation email to register/connect to the VM.

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. Each simulation should take a few minutes. 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 Virtual Machines 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

Connecting to the Virtual Machine

You will be using a Microsoft Azure Lab Virtual Machine (VM) to access the software needed for the lab.

1. You will receive an invitation email, before your session starts, with the subject Register for Lab - IC_Chemistry_UK_LS.

2. Follow the link to 'Register for the lab' in the email which will direct you to the Azure Lab Services page.

3. On the web page, you should see a box corresponding to the VM shared with you. In the bottom left, slide the toggle from left to right to start the VM (It may take some time to start running).

4. Once running, at the bottom right of the box, click the computer-style icon next to the three vertical dots.

A file with the extension rdp will be downloaded: IC_Chemistry_UK_LS.rdp. Follow the instructions for your operating service below to use the file:

Windows

a. Navigate to where the file has downloaded and double click on the file to open.

Linux

a. Open a terminal window and through the terminal, go to the location where the file has downloaded.

b. Type the command:

 remmina IC_Chemistry_UK_LS.rdp

to run the file.

Mac

a. Download and install the Microsoft Remote Desktop app for Mac OS.

b. Open the Microsoft Remote Desktop app

c. On the top toolbar bar, click on the cog icon and then select Import from RDP file..

d. Navigate and select the downloaded rdp file.

e. There should now be an 'IC_Chemistry_UK_LS' PC showing, double click on this to initialise.

5. You should be asked to Accept Certificate?, select Yes.

6. You will be asked to Enter authentication credentials:

a. Change the username into "chemistry" by removing "~/".

b. Enter the password provided in the invitation email to 'Register for the Lab'.

The VM should now launch and you will be taken to a Windows desktop where you should be able to see the LAMMPS icon on the desktop. Double click this to launch.

If you have any problems with accessing the VM then let a demonstrator know.

How to run lammps

Once connected to the Microsoft Azure Window virtual machine, click on Lammps-shell (bottom left icon) to open a special lammps terminal,
then click on the yellow folder as indicated by the arrow and drag-and-drop it in the terminal after "cd "

To run, type:

         source melt_crystal.in

Remember to open a new Lammps-shell for each calculation

In your windows folder, edit the input file with Notepad or Code

VMD is available as an icon on the desktop (and anaconda is installed).

Getting the files for the experiment

You can download all of the files that you will need for this experiment from this address or from this address . You should copy the folder ImperialChem-Year3SimExpt2122-master 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++ or VSCode which you can find on Software Hub. VSCode is also on the Virtual Machines). 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.