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layout carpentry venue address country language latlng humandate humantime startdate enddate instructor helper email collaborative_notes eventbrite root
lesson
swc
UK
English
Rui Apóstolo
.

Description

This lesson is an introduction to molecular dynamics (MD) simulations using the LAMMPS package. It will cover the following topics:

  • Molecular dynamics simulation fundamentals.
  • Creating a LAMMPS input file.
  • Using force-fields and creating independant LAMMPS topology (data) files.
  • Computing and averaging physical properties during simulation.
  • Other software related to LAMMPS input creation, data post-processing, and visualization.

For this lesson, we expect attendees to be familiar with HPC environments. We will not be covering the differences between HPC and regular computing environments. This lesson is aimed at anyone who:

  • has experience using bash (or any other shell).
  • has an interest in running simulations using LAMMPS.

General Information

{% comment %} LOCATION

This block displays the address and links to maps showing directions if the latitude and longitude of the workshop have been set. You can use https://itouchmap.com/latlong.html to find the lat/long of an address. {% endcomment %} {% if page.latlng %}

Where: {{page.address}}. Get directions with OpenStreetMap or Google Maps.

{% endif %}

{% comment %} DATE

This block displays the date and links to Google Calendar. {% endcomment %} {% if page.humandate %}

When: {{page.humandate}}. {% include workshop_calendar.html %}

{% endif %}

{% comment %} SPECIAL REQUIREMENTS

Modify the block below if there are any special requirements. {% endcomment %}

Requirements: Participants must have a working laptop or desktop computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have access to a terminal (Max and Linux users should have a terminal installed by default; Windows users should get either MobaXterm or, if they are already familiar with it, Windows Subsystems for Linux (WSL). They are also required to abide by the ARCHER2 Training Code of Conduct.

{% comment %} ACCESSIBILITY

Modify the block below if there are any barriers to accessibility or special instructions. {% endcomment %}

Accessibility: We are committed to making this workshop accessible to everybody.

Materials will be provided in advance of the lesson. If we can help making learning easier for you (e.g. sign-language interpreters) please get in touch (using contact details below) and we will attempt to provide them.

{% comment %} CONTACT EMAIL ADDRESS

Display the contact email address set in the configuration file. {% endcomment %}

Contact: Please email {% if page.email %} {% for email in page.email %} {% if forloop.last and page.email.size > 1 %} or {% else %} {% unless forloop.first %} , {% endunless %} {% endif %} {{email}} {% endfor %} {% else %} to-be-announced {% endif %} for more information.

Prerequisites

You should have used remote HPC facilities before. In particular, you should be happy with connecting using SSH, know what a batch scheduling system is and be familiar with using the Linux command line. You should also be happy editing plain text files in a remote terminal (or, alternatively, editing them on your local system and copying them to the remote HPC system using scp). {: .prereq}

{% include links.md %}