LAMMPS Glossary

This glossary contains short definitions of the most common LAMMPS-specific words encountered when working with LAMMPS.

Compute

A compute is a command that calculates specific quantities during a simulation, such as energy, temperature, or pressure. The output(s) of a computes named cname can be accessed using \(\text{c}\_\text{cname}\).

Example: Here, the first compute named ke_per_atom returns a vector containing the kinetic energy ke for each atom, and the second compute named mean_ke returns the sum of the elements of the vector. The sum is then printed in the log file using thermo_style, alongside the simulation step:

compute ke_per_atom all ke/atom
compute mean_ke all reduce sum c_ke_per_atom
thermo_style custom step c_mean_ke

Dump file

The dump command writes particle coordinates, velocities, and other information to a file for post-mortem analysis or visualization.

Ensemble

An ensemble refers to a specific thermodynamic state or a collection of states that characterize a system of particles. Different ensembles represent systems with different degrees of separation from the surrounding environment, ranging from completely isolated systems (e.g. microcanonical ensemble) to open systems (e.g. grand canonical ensemble).

As an important side note, it is common for LAMMPS beginners to assume that their system is in the NVE ensemble (or NVT, or NPT), simply because the fix nve (or fix nvt, or fix npt) is used, but this is not necessarily the case. For instance, in Lennard-Jones fluid, the input contains the following commands:

fix mynve all nve
fix mylgv all langevin 1.0 1.0 0.1 1530917

Here, the fix nve is used to perform the time integration and update the position and velocity of the atoms every timestep, and the fix langevin applies the Langevin thermostat [12]. Due to the Langevin thermostat, the system does exchange energy with a background implicit solvent, and is therefore not in the NVE (microcanonical) ensemble, but rather in the NVT (canonical) ensemble with a constant number of particles (N), constant volume (V), and a temperature fluctuating around an equilibrium value (T).

Input script

The input script is a text file where users define simulation parameters, forces, constraints, and other settings using LAMMPS commands.

Fix

A fix is a command that performs specific tasks during a simulation, such as imposing constraints, applying forces, or modifying particle properties.

Force field

A force field is a mathematical model describing the potential energy and forces between atoms or particles in a molecular system. It includes the potential energy functions (e.g. Lennard-Jones potential) and the parameters (e.g. the Lennard-Jones coefficients \(\sigma_{ij}\) and \(\epsilon_{ij}\)).

Grand canonical ensemble

In the grand canonical ensemble, which is also called the macrocanonical ensemble, the chemical potential (\(\mu\)), volume (V), and temperature (T) of the system are kept constant. This ensemble is relevant for systems exchanging particles with the environment.

LAMMPS

LAMMPS is the acronym for Large-scale Atomic/Molecular Massively Parallel Simulator, it designs the open-source molecular simulation software.

Minimization

Energy minimization refers to the computational process of adjusting the atomic positions within a given system to reduce the forces on the atoms until they become negligible. Several minimization methods are implemented in LAMMPS, including the conjugate gradient [17] and the steepest descent [53], see the min style page for an exhaustive list.

Neighbor list

Neighbor list enumerates all pairs of atoms with a separation smaller than the cutoff distance.

NVE ensemble

In the NVE ensemble, which is also called the microcanonical ensemble, the number of particles (N), the volume (V), and the total energy (E) of the system are kept constant. This ensemble is relevant for systems that are fully isolated and experience no exchange of particles or heat in the environment.

NVT ensemble

In the NVT ensemble, which is also called the canonical ensemble, the number of particles (N), volume (V), and temperature (T) of the system are kept constant. This ensemble is relevant for systems in thermal contact with the environment.

NPT ensemble

In the NPT ensemble, which is also called the isothermal-isobaric ensemble, the number of particles (N), pressure (P), and temperature (T) are kept constant. This ensemble is relevant for systems in thermal and mechanical equilibrium with the environment.

Pair style

The pair_style command sets the potential interactions between pairs of atoms (e.g. Lennard-Jones, Coulomb, Morse).

Parallel

LAMMPS is designed for parallel computing, enabling simulations to be distributed across multiple processors or cores. Parallel execution in LAMMPS can be achieved using message-passing parallelism (MPI) or threads.

Restart file

A restart file allows users to continue simulations from a saved state.

Run

A run is a command that executes the simulation for a specified number of time steps.

Seed

Seeds are used to initialize random number generators. By setting the seed to a specific value, the user can ensure that the sequence of random numbers generated by the simulation will be reproducible, which is essential during debugging.

Serial

LAMMPS can be run in serial mode on a single processor or core. This is suitable for small-scale simulations or when parallel computing resources are not available.

Time step

The simulation progresses through discrete time steps.