QtNEMD - A friendly python front-end for non-equilibrium molecular dynamics

QtNEMD is a python application which provides a friendly graphical front-end in Qt for molecular dynamics calculations using software for developed by the Bernhardt group at the University of Queensland.

This project is currently a work in progress, bug reports and feature requests welcome.

Installation

Prerequisites

You'll need the following software packages installed on your computer:

1. Python 3
2. The pip python package manager (usually bundled with your python distribution)
3. Python virtual environment manager venv
4. make (the software has been tested on Gnu Make, but other dialects may work)
5. The g++ compiler
6. CMake
7. Qt5

Automatic installation

There is an install.sh script in the top-level directory which should automatically install all dependencies (provided you've already installed the pre-requisites). This script as been tested in Linux (Fedora/CentOS and Ubuntu) and Windows Subsystem for Linux (running Ubuntu). It does not currently work on MacOS on Apple Silicon (e.g. the M1), as PyQT5 has not (yet) been ported to this platform. To run it, do:

bash ./install.sh

This will download all python dependencies and will download and build LAMMPS. LAMMPS is a very large codebase, so this step may take some time on slow internet connections.

Manual installation

This software depends on the following python modules:

1. numpy
2. PyQt5 graphical user interface library
3. pyqtgraph

These packages can be automatically installed by pip via the following command:

pip install -r requirements.txt

You'll also need to install the LAMMPS molecular dynamics software and compile it with its Python interface. Follow the instructions in the LAMMPS documentation

Running QtNEMD

Run the code by doing:

chmod +x main.py
./main.py

Again, this code has been tested on Fedora and Ubuntu Linux and Windows Subsystem for Linux. It does not currently work on MacOS on Apple Silicon (e.g. the M1).