Hello!
Welcome to the greatest (and funniest) tutorial in the pair potential + GAP model space. In this tutorial, we will create and use a LAMMPS-style pair potential alongside a Librascal-fitted Gaussian Approximation Potential (GAP) to run Path-Integral Molecular Dynamics (PIMD) simulations. The notebook will give a more complete introduction on what you will learn, but please be aware that I will not be explaining the basics of how to create a GAP potential and how to run PIMD simulations. The notebook will, however, contain all the code needed to build the models, as well as instructions on how to run LAMMPS/Quantum Espresso/i-PI from the command line. There will also be some helpful links in case your knowledge is lacking in certain areas. In case you don't want to go through the pain of compiling the aforementioned software, you can load some pre-computed files (found in this repository) in order to run the notebook independetly and in its entirety. I of course recommend that you run all the calculations yourself, but as the saying goes, you can take a horse to water, but you can't force it to drink.
If you have any questions regarding this tutorial, feel free to send me, Victor Principe, an email at [email protected].
If you just want everything to work and have conda installed, here's all you need to do:
conda env create -f environment.yml
conda activate ppp
jupyter notebook
Otherwise, see below for the necessary and optional packages for this tutorial.
In order to run the notebook, you must have an environment with some essential packages. Most of these can be installed using
pip install jupyter numpy pandas pickle ase matplotlib skcosmo chemiscope scipy scikit-learn tqdm
You will also need to install Librascal, which can be done using the code below
git clone https://github.com/lab-cosmo/librascal
cd librascal
pip install .
If you would like to gain the most out of this tutorial, you will also need to compile the following software. More information can be found at the links provided.
- LAMMPS - https://www.lammps.org/
- Quantum Espresso - https://www.quantum-espresso.org
- i-PI - http://ipi-code.org
Once you have installed the necessary packages (and the optional ones, if you so wish), you can clone this repository and open the Jupyter console by doing
git clone https://github.com/victorprincipe/pair_potentials
cd pair_potentials
jupyter notebook
Then you can just open the notebook and enjoy the tutorial!