The input file in2d.bd demonstrates how to run a 2d simulation
of particles undergoing overdamped brownian motion in both
translational and rotational degrees of freedom.
The input file in3d_virial_on.bd demonstrates how to run a
similar simulation but in 3d. In this case, the virial
contribution of the brownian dynamics (the sum
sum_i <r_i dot sqrt{2D_t}W>/(3*volume) where W is
a random variable with mean 0 and variance dt) is
calculated via the fix_modify command. For long
enough times, this will be equal to rho*D_t*gamma_t
(the ideal gas term in equilibrium systems).
To confirm rotational diffusion is working correctly,
run the above simulations with dump files on and
measure \sum_i<e_i(0) dot e_i(t)>, and one should
find that this decays as an exponential with
timescale 1/((d-1)*D_r).
Note that both of the simulations above are not long
enough to get good statistics on e.g. ideal gas
pressure, rotational diffusion, or translational diffusion.
