Control-LAMMPS

This repository contains a LAMMPS interface for feedback control of molecular dynamics.

Installation

The process was tested on a desktop computer with Linux OS (Ubuntu 22.04.3 LTS, jammy)

Dependencies

For correct installation, the recommended steps are:

1. Install Python 3 or newer
2. Install MPI4PY library for Python
3. Download and build latest version of LAMMPS
   • Building flags: DBUILD_SHARED_LIBS=yes -DPKG_MANYBODY=yes
     • The command:
       • cmake ../cmake -DBUILD_SHARED_LIBS=yes -DPKG_MANYBODY=yes
4. Install Python 3 virtual enviroment (required for correct link between python MPI4PY library and LAMMPS)
5. Install python wrapper for LAMMPS

Several other standard Python libraries are also required.

How to run the examples

Two examples are provided:

1. sim1_prepare_system.py
2. sim2_closed_loop_ctrl.py

The examples can be run direcly using python but for faster simulation, we recommend using mpirun

An example of running the example in parallel:

• mpirun -np $N /bin/python3 ./sim1_prepare_system.py

where N is number of CPU cores used for execution.

Visualization

A dataset of a simulation with PID control is available in ./sim_data/sim_data.rar. The data is compressed into a .rar to reduce the data size. You can then use script output_visualization.py to plot the .pkl data or VMD (https://www.ks.uiuc.edu/Research/vmd/) to visualize LAMMPS trajectory file .lammpstrj .