Molecular Dynamics of Simple Systems: Ab initio MD simulation of mono- and diatomic molecules

This MD-Simulation was made for the course Statistical Physics and Computer Simulation at ETH Zurich by Jonas Luther and Rafael Steiner.

The given task was to transform an MD simulation with a classical Lennard-Jones potential to an ab initio simulation.

We chose to use psi4 as the library to perform our ab initio calculations.

Current Status of the Project

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• This Project is still under construction and there will soon be coming more changes to the program. Keep an eye on the repository to stay updated.

Results

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• Classical MD-Simulation with 1000 Lennard-Jonesium potential over the time span of 1ps

• Ab-Initio Simulation of 48 Helium atoms over a time span of 50 fs

• Ab-Initio Simulation of 64 H2 molecules over a time span of 50 fs

• Ab-Initio Simulation of 27 Molecules H2/O2 mixture over a time span of 50 fs

How to run

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• install all the required dependencies:

  • C++ 17:
    • glm 0.9.9.9
  • Python 3.8:
    • matplotlib 3.3.4
    • numpy 1.19.2
    • psi4 1.4rc2.dev99+c4c438c
    • mendeleev 0.5.2

• create a folder called tmp at the root of the project

• build the project located at ./mdatom-main/CMakeLists.txt with CMake

• run the python script main.py in the ab_initio folder

• run mdatom with the file ./mdatom-main/input.txt as the argument

Additional features

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• In each frame of the simulation a PNG of the current state is created in the ./animation folder. These files can be converted into an MP4 output_name.mp4 with ffmpeg by running ffmpeg -r 10 -i frame%d.png output_name.mp4 in the ./animation`folder.