Atoms getting lost

Hello,

I am shearing a triclinic box with P P P boundary condition but atoms are getting lost while shearing. I request you to give me a suggestion to correct this.

units metal
dimension 3
boundary p p p
atom_style atomic
read_restart restart.tensile_equi

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

pair_style eam/alloy
pair_coeff * * MoTaTiWZrCu.set Mo Ta W Ti Zr Cu

#Equilibration at required Temperature
fix 6 all nve
thermo 1000
thermo_style custom step temp press ke pe etotal vol density

equilibration restart

#dump 41 all custom 1000 dump.hea_equi id type x y z
#dump_modify 41 element Mo Ta W Ti Zr
#dump_modify 41 sort id
run 9000
unfix 6

print “equi done”

variable tmp equal “lx”
variable tmp_y equal “ly”
variable tmp_z equal “lz”
variable L0 equal {tmp} variable Ly0 equal {tmp_y}
variable Lz0 equal ${tmp_z}

print “Initial Length, L0: ${L0}”
compute csym all centro/atom bcc
variable a loop 3
label loop

fix 27 all npt temp 300 300 1 iso 0 0 1 drag 1
thermo 1000
thermo_style custom step temp press ke pe etotal vol density
run 50000
unfix 27

fix 27 all npt temp 300 300 1 iso 0 0 1 drag 1
thermo 1000
thermo_style custom step temp press ke pe etotal vol density
run 50000
unfix 27

fix 28 all nve
thermo 1000
thermo_style custom step temp press ke pe etotal vol density
run 50000
unfix 28

fix 29 all npt temp 300 300 1 y 0 0 1 z 0 0 1 drag 1
variable A equal 5.0
variable Tp equal 10.0
variable displace equal “v_A * sin(2PI * stepdt/v_Tp)”
variable rate equal “2PIv_A/v_Tp * cos(2PI * stepdt/v_Tp)”
fix 30 all deform 1 xy variable v_displace v_rate remap v

Output strain and stress info to file

# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]

# p2, p3, p4 are in MPa

variable strain equal “(lx - v_L0)/v_L0”
variable strain_y equal “(ly - v_Ly0)/v_Ly0”
variable strain_z equal “(lz - v_Lz0)/v_Lz0”

The general advice is to isolate each piece of the protocol (approximately, each “run” command) and find out which one crashed. After you are sure that you have an equilibrated system, look into whether the strain rate is excessive. With 20000 steps, it is all but certain that your simulation was much shorter than the time between your message to the mailing list and the first reply.

If you want more information, consider making your question more specific:

https://lammps.sandia.gov/guidelines.html

Giacomo