Teaching Materials Science using the (d3-)force

Georgios Varnavides

An interactive narrative teaching materials science concepts with molecular-dynamics simulations, (ab-)using the d3-force module.

Project Components

The project consists of two parts

• Development of an extension to d3-force module, called d3-force-md, to include:
  • True velocity-verlet integration (force averaging, with finite time-step)
  • Updated forceLink force to ensure energy-conservation
  • Implementation of two new forces, common in molecular dynamics simulations
• Interactive narrative using d3-force-md to teach Materials Science concepts
  • Aimed at undergraduate students

Project Deliverables

* d3-force-md Module

The module source code is hosted in its own repository. Forked from the d3-force repository, the main contributions can be found in the following files: src/simulation.js, src/link.js, src/lennardJonesPotential.js, src/centralPotential.js.

Installation

The module is published on NPM, and can be installed using npm install d3-force-md. Alternatively, it can also be used as a standalone library. AMD, CommonJS, and vanilla environments are supported. In vanilla, a d3 global is exported:

<script src="https://d3js.org/d3-dispatch.v2.min.js"></script>
<script src="https://d3js.org/d3-quadtree.v2.min.js"></script>
<script src="https://d3js.org/d3-timer.v2.min.js"></script>
<script src="https://unpkg.com/d3-force-md"></script>
<script>

var simulation = d3.forceSimulation(nodes);

</script>

Documentation

In addition to the full documentation found in the module repository, a trimmed version highlighting the changes introduced to the API can be found in this notebook. A comparison with the d3-force module can also be found in this notebook.

* Interactive Narrative

The interactive narrative, deployed as an Observable notebook, uses the d3-force-md module to introduce a variety of Materials Science concepts such as:

• Lattice dynamics

• Physical origin of surface energy

• Dislocations during materials deformation

• An interactive simulation playground

* Project Video

The 1-minute video teaser can be found here.

* Project Paper

The paper describing the project in more detail can be found here.