To reproduce:

1. Clone this repository ans submodules, using git clone --recurse-submodules https://github.com/otavioon/clap_lammps.git
2. Build docker image, using build_docker.sh script
3. Copy your private SSH key to clap_config/private directory and rename it to key.pem. Also copy your public SSH key to clap_config/private directory and rename it to key.pub. Note that, the public key can be generated using ssh-keygen -y -f key.pem > key.pub. Besides that, the keypair_name in the clap_config/config/logins.yaml must be filled with your KEYPAIR_NAME (name of keypair at AWS).
4. Write you Access Key ID in the clap_config/private/ec2_access_key.pub file and the Secret access key to clap_config/private/ec2_access_key.pem file.
5. Execute run_jupyter.sh script to launch a jupyter-lab server.

The lammps_run.ipynb notebook run create clusters and run the experiments and save the LAMMPS results to a results directory.

The lammps_analyse.ipynb notebook analyse and generate graphs from the results.