Dear Lammps users,
I am trying to study the effect of stress on hydrogen atom in Zr. I am doing it in 3 steps . minimizing structure , calculating MSD at const volume , deforming it and then calculating MSD at constant volume by using the following script. But I cannot see any movement of hydrogens after deformation of Zirconium?.Can you tell if I made any mistake in script?
units metal
boundary p p p
atom_style atomic
pair_style meam
lattice hcp 3.232
region box block 0 10 0 10 0 10
create_box 2 box
create_atoms 1 box
create_atoms 2 random 10 878567 box
group zr type 1
group hydrogen type 2
pair_coeff * * meamf ZrN Hz ZrH2.meam ZrN Hz
neighbor 2 bin
neigh_modify delay 10 check yes
mass 1 91.224
mass 2 1.0079
fix 1 all nve/limit 0.1
minimize 1.00e-30 1.00e-30 100000 1000000
unfix 1
velocity all create 800.0 4928459 rot yes dist gaussian
fix 1 all nvt temp 800.0 800.0 100.0
fix 2 all temp/rescale 1 800.0 800.0 0.05 1.0
compute 1 hydrogen msd
compute 2 zr msd
thermo 1000
thermo_style custom step etotal ke temp pe press vol c_1[1] c_1[2] c_1[3] c_1[4] c_2[1] c_2[2] c_2[3] c_2[4]
run 4000000
unfix 1
unfix 2
thermo_style custom step lx ly lz press pxx pyy pzz pe temp
run 1
Store final cell length for strain calculations
variable tmp equal “lx”
variable L0 equal {tmp}
print "Initial Length, L0: {L0}"