lammpstutorials / lammpstutorials.github.io

LAMMPS tutorials for both beginners and advanced users

LAMMPS tutorials

This is the repository of the LAMMPS tutorials webpage. All the LAMMPS input scripts and data files can be found in a separate repository named lammpstutorials-inputs.

The tutorials are compatible with the 2Aug2023 stable release of LAMMPS.

About LAMMPS tutorials

The LAMMPStutorials website is made of seven tutorials that are ordered by increasing difficulty. Lennard-Jones fluid is meant for absolute LAMMPS and molecular dynamics beginners, and the complexity of the simulation is progressively increased for Pulling on a carbon nanotube, Polymer in water, Nanosheared electrolyte, and Reactive silicon dioxide. Finally, Water adsorption in silica and Free energy calculation use some more advanced simulation methods that are commonly used when studying soft matter systems, respectively grand canonical Monte Carlo simulations and a free energy method named umbrella sampling.

Access the files

You can access all the files by cloning this repository with its submodules:

git clone https://github.com/lammpstutorials/lammpstutorials.github.io.git --recurse-submodule

Alternatively, you can download the inputs only:

git clone https://github.com/lammpstutorials/lammpstutorials.github.io.git

The Matplotlib Pyplot functions for the figures are shared here.

Template

The template from the first page has been adapted from HTML5 UP. The other pages use the Sphinx generator with the furo style.

About me & Contact

I am a computer physicist in soft matter and fluids at interfaces. You can find more information on my personal webpage.

See the contact page. You can report issues here on Github, or send me an email. Your feedback is always appreciated.

License and Acknowledgments

All the LAMMPS inputs/data/parameter files and Python scripts are released under the GNU general public license v3.0. Feel free to adapt and/or re-publish them.

This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101065060.

lammpstutorials.github.io's Issues

Outdated delete_atoms command

Issue raised by Alireza Nazarahari: delete_atoms atom command in tutorial 2 must be updated to :

delete_atoms random fraction 0.5 no all membrane 482793

Wrong pressure tuto 3

The system is equilibrated at 0 pressure, not 1 atm as said

Specify origine parameters

Specify clearly in each tutorial from where the parameters are taken from.

Suggestion: list lammps package dependencies

I'm walking through your tutorials on an Arch Linux machine and I have to rebuild lammps every time I discover a new package is needed after running the input. It's not that much of a deal but my machine is quite slow. I would suggest to list all packages needed by the full walkthrough and the specific packages needed by each tutorial before the introduction paragraph to let their independence unaffected.

If you don't have such handy list I will be happy to contribute once I get to the end.

As a side note, I love these tutorials, thanks!

Verify parameters SPC-F water model

• the density value looks funny, and sometimes the simulation crashes
• timestep too large for flexible water model ?

Implement kscape slab in the nanoelectrolyte tutorial