LAMMPS: Example

Here, we demonstrate the non-interactive usage of the LAMMPS image recipe.

Running LAMMPS Non-interactively

First, let’s create a temporary folder, temp in your home directory and cd to it

mkdir ~/temp && cd ~/temp

Use your favorite text editor to create a new input file. Let’s call it in.lj and copy-paste the following code block into it and then, save it.

# 1) Initialization
units lj
dimension 3
atom_style atomic
pair_style lj/cut 2.5
boundary p p p

# 2) System definition
region simulation_box block -20 20 -20 20 -20 20
create_box 2 simulation_box
create_atoms 1 random 1500 341341 simulation_box
create_atoms 2 random 100 127569 simulation_box

# 3) Simulation settings
mass 1 1
mass 2 1
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 0.5 3.0

# 4) Visualization
thermo 10

# 5) Run
minimize 1.0e-4 1.0e-6 1000 10000

This input file is borrowed from LAMMPS Tutorial page and intends to run a molecular dynamics simulation of a Lennard-Jones binary fluid consisting of neutral dots with Langevin thermostat within the NVT ensemble.

At this stage, the content of your directory should look like the following

temp
└── in.lj

Let’s copy the docker run command from the catalog, paste it into a terminal and edit it to look like the following command line

docker run --rm -w /home -v $(pwd):/home molssi/lammps-mamba141:latest /bin/bash -c "lmp_serial -in in.lj"

then press Enter. If nothing goes wrong, you should see a long list of lines ending in

Nlocal:           1600 ave        1600 max        1600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            756 ave         756 max         756 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           2178 ave        2178 max        2178 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2178
Ave neighs/atom = 1.36125
Neighbor list builds = 141
Dangerous builds = 1
Total wall time: 0:00:00

Note

The same Docker image recipe can also be used with Apptainer (Singularity) to obtain the same result via the following command

apptainer exec docker://molssi/lammps-mamba141:latest lmp_serial -in in.lj

Note that Apptainer binds /home/$USER, /tmp and current working directory ($PWD) from the host system to the running container by default. For further details see the Apptainer documentation.

By default, LAMMPS generates a log.lammps file with the auto-generated output upon finishing the job execution.

Note

You can store the generated output in a separate output file by passing the -l <output_name> to the execution command as follows

docker run --rm -w /home -v $(pwd):/home molssi/lammps-mamba141:latest /bin/bash -c /bin/bash -c "lmp_serial -in in.lj -l log.out"

or

apptainer exec docker://molssi/lammps-mamba141:latest lmp_serial -in in.lj -l log.out