Issues with equilibrating a nanowire with non-periodic boundary conditions

Dear LAMMPS Community,

I have been following the LAMMPS tutorials and successfully conducted uniaxial tensile simulations for bulk systems using periodic boundary conditions in all directions (p p p). I am now attempting to simulate nanowires and have switched to p s s boundary conditions, using fix nvt at 300K.

However, I have noticed that the nanowire begins to warp unexpectedly during the simulation. I suspect that this might be due to boundary effects or improper thermostat application, but I would greatly appreciate any advice on potential causes and solutions.

Below is my LAMMPS script:

------------------------ INITIALIZATION ----------------------------

units metal
boundary p s s
atom_style atomic

----------------------- ATOM DEFINITION ----------------------------

lattice hcp 3.20
region whole block 0 100 0 100 0 100 units box
create_box 1 whole
region LLF cylinder x 50 50 20 INF INF units box
lattice hcp 3.20 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
create_atoms 1 region LLF

------------------------ FORCE FIELDS ------------------------------

pair_style eam/fs
pair_coeff * * Al-Mg.eam.fs Mg

------------------------- SETTINGS ---------------------------------

compute csym all centro/atom 12
compute 2 all stress/atom
compute mytemp all temp
compute 11 all reduce sum c_2[1]
compute 12 all reduce sum c_2[2]
compute 13 all reduce sum c_2[3]
compute 14 all reduce sum c_2[4]
compute 15 all reduce sum c_2[5]
compute 16 all reduce sum c_2[6]

neighbor 0.3 bin
neigh_modify delay 10
thermo 100
velocity all create 100.0 16723
thermo_style custom step temp etotal press pxx pyy pzz lx ly lz

shell mkdir dump
shell cd dump

#---------------Energy Equilibration--------------------------
reset_timestep 0
fix 1 all nvt 300 300 $(1000.0dt)
dump 1 all custom 10000 dump.equilibrate.
id type x y z

run 10000
unfix 1

Please see the Guidelines post about how to properly format quoted text. This forum uses some kind of markdown for text and thus some of your quoted input is not rendered correctly (e.g. comments become headlines). This makes it difficult to read. Can you read everything correctly??

What do you mean by “warp”?

On what basis?

Your choice of periodicity in x while defining a nanowire along the z axis seems unusual.