I ran the following code snippet in order to calculate MSD of two
hydrogen atoms that I placed manually in an FCC copper system.
units metal
dimension 3
boundary p p p
atom_style atomic
atom_modify map array sort 0 0
read_data Data25.R1
pair_style bop
pair_coeff * * CuH.bop.table Cu H
comm_modify cutoff 11.4
mass 1 63.5460
mass 2 1.00794
timestep 0.001
thermo 200000
fix 1 all nvt temp 600 600 0.1
fix 3 all momentum 1 linear 1 1 1
thermo_style custom step temp press vol enthalpy ke pe etotal lx ly lz density atoms
group Cu type 1
group H type 2
compute 2 H msd
fix 4 H ave/time 20000 5 100000 c_2 file H.txt mode vector
thermo_style custom step temp press vol enthalpy ke pe etotal lx ly lz density atoms
thermo_modify lost warn
dump 2 all atom 200000 copper_box_300K.lammpstrj
dump 3 all custom 200000 copper_box_300k_final.dump id type x y z vx vy vz
restart 100000 poly.restart
write_data Data.R2
write_restart copper_box_300k.restart
run 1000000 upto
These two following lines that I have used to compute MSD and
then to take time averages, are they correct?
compute 2 H msd
fix 4 H ave/time 20000 5 100000 c_2 file H.txt mode vector
If yes, in the text file that is generated as H.txt, how will the data be presented?
Also, in the built in LAMMPS example list, I found a folder called DIFFUSION.
I am copying and pasting a few lines in that code used for computing MSD and
eventually, the slope. For now, all I need help with is to find the MSD in every timestep
for Hydrogen atoms in my case.
compute msd all msd com yes
variable twopoint equal c_msd[4]/4/(stepdt+1.0e-6)
fix 9 all vector 10 c_msd[4]
variable fitslope equal slope(f_9)/4/(10dt)
thermo_style custom step temp c_msd[4] v_twopoint v_fitslope
1) So, how should I modify the codes in the example (given above) to
get just the MSD in every timestep?
2) c_msd[4] - what does the 4 within the bracket represent here?
Any help would be highly appreciated.