Dear LAMMPS users,
I am using hybrid command in LAMMPS . I would like to calculate He msd vs time in Ni.I am using 1 atom of He randomly place in 4000 atoms of FCC Ni. My problem is as I increase temperature my MSD going down and is not linear as shown in the attachment. Can you please advise me on my input script?
log 600.out
units metal
boundary p p p
atom_style atomic
lattice fcc 3.52
region box block 0 10.0 0 10.0 0 10.0
create_box 2 box
create_atoms 1 box
create_atoms 2 random 1 878567 box
pair_style hybrid eam beck 8.0 morse 10.0
pair_coeff 1 1 eam nimib
pair_coeff 2 2 beck 399.6438 0.867636 0.675 4.390 0.0003746 2.96
pair_coeff 1 2 morse 0.0029 1.287 4.1
mass 1 58.6934
mass 2 4.002
group Ni type 1
group he type 2
fix 1 all nve
timestep 0.001
thermo 1000
thermo_style custom step pe lx ly lz press pxx pyy pzz
min_style cg
minimize 1e-30 1e-30 100000 100000
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.1
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms vol etotal
thermo 100000
minimize 1.0e-30 1.0e-30 100000 1000000
unfix 1
velocity all create 1000 12345 mom yes rot no
fix 1 all npt temp 1000 1000 1 iso 0 0 1 drag 1
Set thermo output
timestep 0.001
thermo 10000
thermo_style custom step lx ly lz press pxx pyy pzz pe temp
Run for at least 10 picosecond (assuming 1 fs timestep)
run 500000
unfix 1
reset_timestep 0
fix 1 all nve
timestep 0.001
Set thermo output
thermo 100000
compute msd he msd
compute 2 Ni msd
variable twopoint equal c_msd[4]/6/(step*dt+1.0e-6)
fix 9 all vector 100000 c_msd[4]
variable fitslope equal slope(f_9)/6/(100000*dt)
thermo_style custom step temp c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_2[4] v_twopoint v_fitslope
dump 3 all custom 1000 1000.dump id type x y z
dump_modify 3 every 1000000
fix 6 all recenter INIT INIT INIT
run 20000000
unfix 1
unfix 9
unfix 6
Thank You
Ravi