Hello! I was confused about the ‘compute msd’. I used this command to get msd of particles but the value was too small to cooperate with the dump file I have output. Below is my code:
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reset_timestep 0
fix shear first addforce 0.082 0 0
dump final_one all custom 5 dump.finalone id type x y z fx fy fz vx vy vz omegax omegay omegaz
dump_modify final_one sort id
compute 1 all msd com yes
variable msdx equal c_1[1]
variable msdy equal c_1[2]
variable msd equal c_1[4]
variable istep equal step
fix 9 all print 5 "${istep} ${msdx} ${msdy} ${msd}" screen no file msd1.dat
run 200000000
undump final_one
unfix 9
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The question is in my dumpfile the displacement of particles is on the order of 1 while in MSD file the msd is just on the order of 1e-5
I guess it is because that the value of compute msd is between each step but I am not sure.
Any help will be appreciated! Thanks advance!