Sometimes I imagine an LLM model trained on the #LAMMPS forum and mailing-list basically answering most #moleculardynamics related questions with:
* You should (re)read the manual.
* There are not enough information to conclude about your results.
* What do you expect in the first place?
* Garbage in, garbage out.
* As Axel Kohlmeyer said here...
* Talk to your advisor.
* This is expected and documented behavior.
In think that in this case it would actually be helpful.
A major update has been made to the LAMMPS tutorials website, reflecting the changes from the recently submitted publication!
Check it out:
https://lammpstutorials.github.io/index.html
#LAMMPS #Simulation #Tutorials #ComputationalScience #OpenSource
#Research #Science @simongravelle
Thats not all, an eighth tutorial on the REACTER protocol is now available.
LAMMPS tutorials is now available as an article! https://arxiv.org/abs/2503.14020
Written in collaboration with Jake and Axel (LAMMPS devs), it is a considerable improvement compared to the previous version available online.
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While molecular simulations thus become accessible to a larger audience, the `black box' nature of such software packages and wide array of options and features can make it challenging to use them correctly, particularly for beginners in the topic of MD simulations. LAMMPS is one such versatile molecular simulation code, designed for modeling particle-based systems across a broad range of materials science and computational chemistry applications, including atomistic, coarse-grained, mesoscale, grid-free continuum, and discrete element models. LAMMPS is capable of efficiently running simulations of varying sizes from small desktop computers to large-scale supercomputing environments. Its flexibility and extensibility make it ideal for complex and extensive simulations of atomic and molecular systems, and beyond. This article introduces a suite of tutorials designed to make learning LAMMPS more accessible to new users. The first four tutorials cover the basics of running molecular simulations in LAMMPS with systems of varying complexities. The second four tutorials address more advanced molecular simulation techniques, specifically the use of a reactive force field, grand canonical Monte Carlo, enhanced sampling, and the REACTER protocol. In addition, we introduce LAMMPS-GUI, an enhanced cross-platform graphical text editor specifically designed for use with LAMMPS and able to run LAMMPS directly on the edited input. LAMMPS-GUI is used as the primary tool in the tutorials to edit inputs, run LAMMPS, extract data, and visualize the simulated systems.
I am shamefully copying this post from Linkedin but if you happen to know any candidate, do not hesitate to reach:
It's on. To my #ComputationalChemistry network, I am calling on you. 🙇
The PM2E team in the CIMAP laboratory (www.cimap.ensicaen.fr) is looking for a #PhD hashtag#candidate. The goal of the project is to understand key parameters in #semiconductor defects stability and physics (both vacancies and color centers, see for example: https://doi.org/10.1016/j.nimb.2022.12.025) through the use of
#DFT and #MolecularModeling. The end goals of the project is concerned with application for #QuantumComputing through the making of stable #qubit. Collaboration and communication with experimentalists will be part of the project.
If you're interested in #MolecularDynamics, #MonteCarlo simulations, or DFT and quantum calculations, we are waiting for you. We are using codes such as #Lammps and #QuantumEspresso. We are looking for a candidate finishing or already having a master degree (or equivalent diploma) with training in #physics/ #MaterialsScience / #TheoreticalChemistry. Any experience in programming using #Python, #C and the #Linux environment would be considered a plus.
The position is located in Alençon (Orne) between Caen and Le Mans. Founding is assured for relevant candidates.
Link to the offer (in french, you can ask for an english version): https://www.abg.asso.fr/en/candidatOffres/show/id_offre/127985/job/simulation-atomistique-de-defauts-crees-par-irradiation-dans-les-semiconducteurs
Je remet ici l'information:
L'équipe PM2E d'Alençon est à la recherche d'un #stagiaire en #physique #numerique ou #chimie théorique pour travailler sur la simulation de la stabilité de défauts dans des #semi_conducteurs . L’objectif est de reproduire des simulations avec un modèle à 2 températures dans #lammps et de les compléter avec des simulations quantiques (avec Quantum Espresso).
https://cimap.ensicaen.fr/wp-content/uploads/2024/12/Sujets-de-stage-M2-VH.pdf
Le sujet pourrait déboucher sur une proposition de #thèse (financement quasiment sûr).
Does anyone know how to run LAMMPS? I'm trying to do a simulation of sodium chloride saline diffusion, and i can't figure out the parameters for a 2D simulation.
I keep losing water molecules!
#LAMMPS
J'ai fait une petite simulations rigolote pour vérifier numériquement un vieux truc que j'ai trouvé dans un article de Boltzmann. Si on met une particule dans un plan avec deux ressorts qui ont des constantes de forces k1 et k2, la trajectoire est périodique si k1/k2 est un nombre rationnel: https://youtu.be/keGGbb2uiB8
Évidemment si c'est pas un nombre rationnel (genre pi), c'est pas périodique: https://youtu.be/Tty0jFWKkv8
Voilà, c'est tout pour moi.
Molecular dynamics and multiscale modelling for sustainability
DAIMON Team - CNR-ISMN
Full time researcher in #moleculardynamics and #multiscalemodelling for sustainable materials @CNR-ISMN Bologna, Italy #Gromacs #LAMMPS
See the full job description on jobRxiv: https://jobrxiv.org/job/daimon-team-cnr-ismn-27778-molecular-dynamics-and-multiscale-modelling-for-su...
https://jobrxiv.org/job/daimon-team-cnr-ismn-27778-molecular-dynamics-and-multiscale-modelling-for-sustainability/?feed_id=69895
Just gave a new look and some updates to the lammpstutorials GCMC tutorial : https://lammpstutorials.github.io
This tutorial is meant for people wanting to perform constant pressure/chemical potential adsorption simulations. #lammps #moleculardynamics #simulations
G. Clavier
LAMMPS tutorials
Alex 🔧🔮🌎🪿
Enthalpiste
jobRxiv
Simon Gravelle