Glossary

ACF

Autocorrelation function. A measure of the correlation of a signal with itself at different time lags.

Green–Kubo relation

A mathematical expression that relates transport coefficients to the time integral of the autocorrelation function of the corresponding flux or velocity.

LAMMPS

Large-scale atomic/molecular massively parallel simulator. A software package for simulating molecular dynamics. See https://www.lammps.org/

MD

Molecular dynamics. A computational method used to simulate the physical movements of atoms and molecules.

NpT

Isothermal-isobaric ensemble. A statistical ensemble that represents a system in thermal equilibrium with a heat bath at constant temperature (T), pressure (p), and number of particles (N).

NVE

Microcanonical ensemble. A statistical ensemble that represents a closed system with fixed energy (E), volume (V), and number of particles (N).

NVT

Canonical ensemble. A statistical ensemble that represents a system in thermal equilibrium with a heat bath at constant temperature (T), volume (V), and number of particles (N).

PSD

Power spectral density. A measure of the power of a signal as a function of frequency. The Fourier transform of the autocorrelation function.

Uncertainty

In STACIE, uncertainties are expressed as standard deviations of the mean of a result, except when noted otherwise. This practically corresponds to the standard deviation of the result over repeated (computational) experiments, also known as the standard error.

Wiener–Khinchin theorem

A mathematical theorem that relates the autocorrelation function of a stationary random process to its power spectral density (PSD) via the Fourier transform.