[lammps-users] questions

Please post to the LAMMPS mail list, not to me personally.

The LAMMPS doc page for viscosity states:

LAMMPS does not check, but you should not use this fix to swap
velocities of atoms that are in constrained molecules, e.g. via fix
shake or fix rigid. This is because application of the constraints
will alter the amount of transferred momentum. You should, however, be
able to use flexible molecules. See the Maginn paper for an example of
using this algorithm in a computation of alcohol molecule properties.

You are using fix shake in your script.