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The instructions on this page show how to run a simple LAMMPS molecular dynamics example using an E4S base container from DockerHub.

Step 1: Docker Image

Download E4S base image ecpe4s/e4s-spack-cpu.

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This image includes Spack and MPI, making it a strong starting point for installing LAMMPS.

Step 2: Run Container

Start an interactive container session.

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Mount your working directory so your input script and outputs persist on your host machine.

Step 3: Install and Load LAMMPS

Use Spack to install and load LAMMPS.

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Spack resolves dependencies and prepares your environment for running the executable.

Step 4: Create Input File

Create a simple LAMMPS input script.

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Use cat > in.lj to create the script, then run it in the next step.

Step 5: Run Example

Execute the LAMMPS simulation with mpirun.

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The sample runs a short Lennard-Jones simulation and prints thermodynamic output.

What You Learn

Understand the end-to-end workflow.

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Container setup, Spack install/load, script creation, and simulation execution.

Getting Started with LAMMPS Using the E4S Base Container

(Docker Desktop on macOS or Linux)

This short guide walks you through a complete LAMMPS beginner workflow.

1. Download the E4S Base Image

Pull the E4S base container:

docker pull ecpe4s/e4s-spack-cpu:latest

Optional check:

docker images ecpe4s/e4s-spack-cpu

2. Run the Container in Interactive Mode

Create a working directory:

mkdir -p ~/lammps-quickstart
cd ~/lammps-quickstart

Start an interactive shell inside the container:

docker run -it --rm \
  --entrypoint bash \
  -v "$PWD:/work" \
  -w /work \
  ecpe4s/e4s-spack-cpu:latest

You are now inside the container.

3. Install and Load LAMMPS with Spack

Inside the container, load MPI:

spack load mpich

Install LAMMPS (this can take several minutes):

spack install lammps +mpi ^mpich

Load LAMMPS:

spack load lammps +mpi ^mpich

Confirm loaded packages:

spack find --loaded

Locate the LAMMPS executable:

LAMMPS_EXE=$(command -v lmp || command -v lmp_mpi)
echo "$LAMMPS_EXE"

4. Create a Simple LAMMPS Input File

Create a file named in.lj.

You can do this with an editor, or directly in the terminal using:

cat > in.lj

Then paste the following input and press Ctrl-D to save:

units           lj
atom_style      atomic
boundary        p p p

lattice         fcc 0.8442
region          box block 0 4 0 4 0 4
create_box      1 box
create_atoms    1 box
mass            1 1.0

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0 2.5

neighbor        0.3 bin
neigh_modify    every 1 delay 0 check yes

velocity        all create 1.0 87287
fix             1 all nve

timestep        0.005
thermo          10
run             100

5. Run the Example

Run the simulation on one MPI rank:

mpirun -n 1 "$LAMMPS_EXE" -in in.lj

Expected output includes thermodynamic columns such as Step, Temp, TotEng, and Press.

What You Learned

  • How to use an E4S base container for a reproducible LAMMPS environment
  • How to install and load LAMMPS with Spack
  • How to run a simple molecular dynamics input script

Next, you can try larger systems, more timesteps, and multiple MPI ranks.