Hello lammps-users,
May I know why my simulation loses atoms out of the simulation box? I am trying to grow graphene on top of copper. Does it because of the thermostat that I use in the simulation? Provided is the code I use in the simulation. Thank you. I will accept in all kindness your comments and suggestions for me to be able to simulate properly the growth of graphene on top of copper. Thank you very much.
###Initialization
units metal
dimension 3
boundary p p f
atom_style atomic
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region bigbox block 0.0 6.0 0.0 6.0 0.0 2.0 units lattice
create_box 2 bigbox ##copperRegion
region copperRegion block 0.0 6.0 0.0 6.0 0.0 1.75 units lattice
create_atoms 2 region copperRegion units lattice
##create_atoms 2 region copperRegion units lattice
region copperMobile block 0.0 6.0 0.0 6.0 0.3 1.75 units lattice
region forNVT block 0.0 6.0 0.0 6.0 1.75 2.0 units lattice
##group forNVT region bigbox
group copGroup region copperMobile
group copRegion region copperRegion
group carbonDeposit type 1
##group NVTfix subtract forNVT copRegion
group NVTfix region forNVT
mass 1 12.0107
mass 2 63.546
###Settings
pair_style hybrid/overlay eam lj/cut 2.5 airebo 3.0
##pair_style hybrid/overlay eam/alloy airebo 3.0 1 0 lj/cut 2.5
##pair_coeff * * eam/alloy Cu01.eam.alloy Cu NULL
##pair_coeff * * airebo CH.airebo NULL C
##pair_coeff 1 2 lj/cut 0.001 3.274
pair_coeff * * airebo CH.airebo C NULL
pair_coeff 2 2 eam Cu_u3.eam
pair_coeff 1 2 lj/cut 0.001 3.274
neighbor 2.0 bin
neigh_modify every 2 delay 6 check yes ##delay 0
compute add carbonDeposit temp
compute_modify add dynamic/dof yes extra/dof 0
fix 1 NVTfix nvt temp 1000.0 1000.0 10.0 ###apply thermostat
fix 2 copGroup langevin 1000.0 1000.0 10.0 699483 ##NVT except for the substrate
fix 3 copGroup nve
fix 4 carbonDeposit deposit 64 1 10 92345 region copperMobile units lattice ##near 1.0 vz -1.0 -1.0
fix 5 carbonDeposit wall/reflect zhi EDGE
thermo_style custom step time atoms temp press pe ke etotal epair
thermo_modify lost warn flush yes
thermo 100
dump ddump all atom 10 dump.one
###Run a simulation
timestep 0.001 ###picoseconds timestep 0.001 picoseconds
run 10000