Greetings
I have been studying the input script for calculating diffusion coefficient given in the ‘DIFFUSE’ folder in ‘examples’. A part of the input script ‘in.msd.2d’ is mentioned here:
fix 1 all nve
fix 2 all langevin $t $t 0.1 498094
fix 3 all enforce2d
#equilibration run
thermo 1000
run 5000
unfix 2
#data gathering run
reset_timestep 0
#factor of 4 in 2 variables is for 2d
compute msd all msd com yes
variable twopoint equal c_msd[4]/4/(step * dt + 1.0e-6)
fix 9 all vector 10 c_msd[4]
variable fitslope equal slope(f_9)/4/(10*dt)
I have some questions form this part of script as follows:
- Why was the thermostat turned off before data gathering run?
- The c_msd[4] is divided by a factor of 4. I do not understand the reasoning behind it. What would be the case for 3d systems?