Monte Carlo simulation of Argon

So let’s run out first simulation with Lumol. The easiest system to simulate is a Lennard-Jones fluid, which is a good model for noble gas fluids. Here we will simulate super-critical argon using the Metropolis Monte Carlo algorithm.

For this simulation, you will need the following files:

  • the initial configuration argon.xyz
  • the input file argon.toml

You can download both files here.

After extracting the archive, you can run the simulation with lumol argon.toml. The simulation should complete in a few seconds and produce two files: energy.dat and trajectory.xyz.

Input file anatomy

The input file is written using the TOML syntax, you can learn more about this syntax here. The file starts with a header declaring the version of the input file syntax used, here the version 1:

[input]
version = 1

Then, we declare which system that we want to simulate in the systems array. We define this system using an XYZ file for which we also have to provide the unit cell size.

[[systems]]
file = "argon.xyz"
cell = 21.65

We also need to define the interaction potential between the atoms in the system, which we’ll do in the potential.pairs section. Here, we are using a Lennard-Jones potential with a cutoff distance of 10 Angstrom for all Argron (Ar) pairs.

[[systems.potentials.pairs]]
atoms = ["Ar", "Ar"]
cutoff = "10 A"
lj = {sigma = "3.4 A", epsilon = "1.0 kJ/mol"}

Next, we define how we want to simulate our system. For this brief tutorial simulating 100000 steps should be enough. We also specify some output: the energy is written to energy.dat every 100 steps, and the trajectory is written to trajectory.xyz also every 100 steps.

[[simulations]]
nsteps = 100000
outputs = [
    {type = "Energy", file = "energy.dat", frequency = 100},
    {type = "Trajectory", file = "trajectory.xyz", frequency = 100}
]

Finally, we define how to propagate the system from one step to another. We are using a Monte Carlo simulation in this tutorial. We need to specify the temperature (set to 500 K) and the set of moves that we want to perform to change the systems. The only Monte Carlo move in this example is a translation for which we set the maximum amplitude (the furthest a particle can be translated in a single move) to 1 Angstrom.

[simulations.propagator]
type = "MonteCarlo"
temperature = "500 K"
moves = [
    {type = "Translate", delta = "1 A"},
]

Wrapping all this together, here is the complete input file:

[input]
version = 1

[[systems]]
file = "argon.xyz"
cell = 21.65

[[systems.potentials.pairs]]
atoms = ["Ar", "Ar"]
cutoff = "10 A"
lj = {sigma = "3.4 A", epsilon = "1.0 kJ/mol"}

[[simulations]]
nsteps = 100000
outputs = [
    {type = "Energy", file = "energy.dat", frequency = 100},
    {type = "Trajectory", file = "trajectory.xyz", frequency = 100}
]

[simulations.propagator]
type = "MonteCarlo"
temperature = "500 K"
moves = [
    {type = "Translate", delta = "1 A"},
]

As mentioned above, you can start the simulation using

lumol argon.toml

So now we know how to run a simulation of a Lennard-Jones fluid. How about we add electrostatic interactions in the next example?

Hello Sodium Chloride!