HomeNewsAtomistic simulation tutorial release

Atomistic simulation tutorial release

To further promote materials development using atomistic simulation, we are releasing “Atomistic simulation tutorial”. The document and code are available below.


These are the table of contents at the time of release.

  • Chapter 1: Introduction
  • Chapter 2: Opt (Structural optimization)
  • Chapter 3: Energy
  • Chapter 4: Vibration, phonon
  • Chapter 5: Reaction path analysis
  • Chapter 6: Molecular Dynamics

We are going to update the contents to further cover wide range of the topics.


In recent years, words such as Sustainable Development Goals (SDGs) have become common, and activities aimed at making the world a better place in a sustainable manner are flourishing. In this context, there is a growing demand for the development of high-efficiency catalytic and battery materials for the utilization of renewable energy sources toward a carbon neutral society.

The development of new materials is in demand in a variety of fields, including the development of higher-performance semiconductors in line with the advancement of technologies such as the IoT, AI, and 5G.

By using simulation, it is possible to narrow down candidates from an exhaustive material space that has never been envisioned before, and to elucidate phenomena that are difficult to observe experimentally.

However, expertise skill is required to perform the simulation.

While there are many textbooks that can be used as references for learning chemistry and physics theory, different knowledge is needed to tackle the real business problem in practice. This tutorial focuses on such practical contents and aims to enable readers to actually run simulations.

PFCC offers Matlantis™, which provides an environment in which a variety of atomic simulations can be performed. The PFP used as the core technology of Matlantis is both fast and versatile. It is also ideal for learning purposes, such as running simulations of various atomic systems and trying them out by trial and error, which is why we were able to create this tutorial.

Please also refer following for the details of PFP (currently Japanese slides only)

To create the contents…

The author took care about following points

  • Easy to understand with as many illustrations as possible
    • Taking advantage of the online materials, we have made them as easy to read as possible by including many illustrations, and by drawing atoms in 3D so that they can be checked interactively.
  • Focuses on acquiring the knowledge necessary for practical use rather than a rigorous understanding of mathematical formulas
    • The tutorial is designed to be readable in a simple manner, focusing more on acquiring the knowledge necessary to perform simulations in practice.
    • For readers who want to understand the details, references and links are provided so that they can proceed with in-depth study.
  • Hands on tutorial
    • This is a hands-on tutorial. With both code and text, you can understand the simulation by actually running the simulation.
    • Note that the Matlantis license is required to run the code. However, you should be able to get a good understanding of what atomic simulations can do and how they are performed by just reading the document as well.


The number of people who specialize in simulation is still small compared to those who conduct experiments, even in large companies. We would be happy if we could contribute to further increasing the number of people who can conduct both experiments and calculations in the development of new materials in the future.

We also hope that in the future this material will be a useful reference for students studying computational chemistry at universities.

We have previously published matlantis-contrib, this tutorial can also be used to acquire the prior knowledge necessary to understand these calculation cases. We hope that this will accelerate new materials discovery using simulation.