LAMMPS

Large-scale Atomic/Molecular Massively Parallel Simulator

Introduction to LAMMPS

Developed by Sandia National Laboratories, LAMMPS is an open-source software package designed for molecular dynamics simulations. It implements multi-machine parallel computing using MPI and provides empirical potential functions for atoms in the periodic table. LAMMPS is adept at simulating real systems, such as metals or water, with results consistent with experimental data. Learn more about LAMMPS, also here its LAMMPS GitHub.

Key Features of LAMMPS

• Versatile Simulations: Capable of simulating liquid, solid, and gaseous states, and a variety of system types including all-atom, polymer, biological, metallic, granular, and coarse-grained models.
• Optimization Algorithms: Employs well-established algorithms for efficient simulation of particles in different states.
• Diverse Model Potentials: Offers a range of model potential functions for systems like polymer chains.
• Multi-Scale Simulation Capability: Suitable for atomic, mesoscopic, and continuous scale matter systems.
• Advanced Material Modeling: LAMMPS is a classical molecular dynamics code with a focus on material modeling.

Particle and Model Types

LAMMPS supports a wide array of particle types and models, including:

• Atoms and coarse-grained particles
• United-atom and all-atom polymers, organic molecules, proteins, and DNA
• Metals, granular materials, and coarse-grained mesoscale models
• Various finite-size particle models

Services and Applications

LAMMPS can be used for:

• Hyperdynamics molecular dynamics
• Parallel replica dynamics
• Temperature accelerated dynamics
• Material modeling
• Properties calculation under thermal, mechanical, and chemical conditions

Computational Performance

• Runs efficiently on single processors and in parallel
• Utilizes message passing techniques and spatial decomposition
• Accelerated performance on CPU, GPU, and Intel Xeon Phis

Tags for LAMMPS

1. Molecular Dynamics Simulation
2. Material Modeling
3. Parallel Computing
4. Multi-Scale Systems
5. Particle Simulation

Explore LAMMPS Documentation

How to Run LAMMPS:

This example demonstrates how to run a simple case with LAMMPS. We utilize an example provided on GitHub, from which you'll need to download the zip file amoeba.zip. Additionally, you should create (or download) the run_script.sh file that prepares and runs the simulation inputs.

Steps to Execute on Our Platform

1. Upload Files: Click on the folder icon next to the Volume line and upload both amoeba.zip and run_script.sh to the working directory (/data) of your project.
2. Set Project Directory: Make sure the Project Directory is set to /data (or the mounted volume to entered!).
   1. if you want to change the Project Directory, make sure to apply the changes in the run_script.sh accordingly.
3. Configure Run Script: In the Run Script field, enter run_script.sh as the input.
4. Create the Project: Click on Create to prepare your project environment.
5. Run the Container: Go to the project tab and start the container to run the script.