Atomistic Simulation Basics

2. Atomistic Simulation Basics#

2.1. Overview#

Questions

  • What are the main simulation methods and when should I use each?

  • How do composition, structure and properties relate to each other?

Objectives

  • Describe the composition-structure-property paradigm

  • Identify appropriate simulation methods for a given problem

  • Navigate the Materials Project database

Keypoints

  • Atomistic simulation connects microscopic structure to macroscopic properties

  • DFT, MLIPs and MD operate at different fidelity/cost trade-offs

  • The Materials Project provides DFT-computed properties for thousands of materials

2.2. Lecture Slides#

The slides for this tutorial are embedded below. 📥 Download slides (.pptx)  |  Open in full screen

2.2.1. Exercise: The Composition–Structure–Property Paradigm#

Fill in the table below with appropriate entries for three materials studied in this course. For each, identify (a) the composition, (b) the crystal structure, and (c) one key property relevant to quantum optics.

Material

Composition

Structure

Key property

Materials Project ID

Diamond

C

Diamond cubic, Fd3̄m

Host for the NV-centre single photon emitter

?

Hexagonal Boron Nitride

?

?

?

?

Gallium Nitride

?

?

?

?

After filling in the table, use the Materials Project website (https://materialsproject.org) to look up each material and check your answers. You will need to sign up for an account. Note the Materials Project IDs (mp-XXXX) in the table above.

2.2.2. Exercise: Exploring the Materials Project Database#

The coursework requires you to choose a host material for a point defect study.

Using the Materials Project, identify candidate materials that satisfy:

  • Bandgap > 3 eV (wide gap needed so defect levels lie in gap)

  • Contains light elements such as C, N, B, Si or O (small spin-orbit coupling for long coherence times)

  • Stable crystal structure (energy above the convex hull < 0.2 eV/atom); for more information on the convex hull see this video.

Write a short paragraph (3–4 sentences) justifying each choice for hosting a point defect single-photon emitter. Bring your suggestions to the next lab session for discussion.

2.2.3. Extension Task: Using the Materials Project Application Programming Interface (API)#

The previous task asks you to use the Materials Project website to filter materials by hand. This is fine for a handful of queries, but screening studies to identify materials with a particular property compare thousands of candidates — this requires interacting with the database programmatically through its API (Application Programming Interface). An API is simply a defined way for one program to ask questions of another. Instead of clicking through a website, your Python script sends a structured request (“give me all materials with bandgap > 3 eV containing N or O”) and gets back structured data (a list of materials with their properties) that you can analyse.

Use the Materials Project API and post-processing with Python to reproduce the search from the previous task. This will require you to import the Python library mp-api and specify your API key.

from mp_api.client import MPRester

with MPRester("YOUR_API_KEY") as mpr:
    # Put your query code here - see: https://docs.materialsproject.org/downloading-data/using-the-api/querying-data
    ```
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