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You can find a list of various ways in LAMMPS to calculate viscosity in Section 6.21 of the manual. I also suggest looking in the literature to see how This directory has 5 scripts that compute the viscosity (eta) of a Lennard-Jones fluid using 5 different methods. See the discussion in Section 6.21 of the This directory has 4 scripts that compute the viscosity (eta) of a Lennard-Jones fluid using 4 different methods. See the discussion in Section 6.21 of the The fourth method is based on the Green-Kubo (GK) formula which relates the ensemble average of the auto-correlation of the stress/pressure tensor to eta. According to the Green–Kubo relation, the viscosity of a homogeneous fluid in The Large-scale Atomic/Molecular Massively Parallel Simulator, or LAMMPS,This project computes viscosity (eta) of a Lennard-Jones fluid using Green-Kubo method. Green-Kubo is an equilibrium method. System has around 800 atoms.