Self diffusion coefficient

Hello everyone!

I want to calculate self diffusion for helium (3d).
I used msd example and tried to change it for 3d. But the results are not correct…

Could you please tell what command I should add/change?


variable x equal 10
variable y equal 10
variable z equal 10

variable t equal 273.0
variable V equal vol
variable rc equal 7.325
variable pr equal 1.0
variable dt equal 4.0

units real
dimension 3
boundary p p p
atom_style atomic

lattice fcc 34.5
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box

pair_style lj/cut ${rc}
pair_coeff * * 0.02144 2.588

mass * 4.0026
velocity all create $t 97287 #mom yes rot yes dist gaussian

fix 1 all npt temp $t t 40 iso {pr} ${pr} 400
fix 2 all langevin $t $t 40 498094

thermo 1000
run 50000

unfix 2

reset_timestep 0

compute msd all msd com yes
variable twopoint equal c_msd[4]/9/(step*dt+1e-6)
fix 9 all vector 1 c_msd[4]
variable fitslope equal slope(f_9)/9/(dt)

thermo_style custom step temp press c_msd[4] v_twopoint v_fitslope

thermo 1000
run 3000000

Please first explain which changes you made and why.