[lammps-users] Atom IDs must be consecutive for dump xyz

Hi everybody,

I am simulatinng carbon nanotubes growth on a Fe cluster. The C atoms are vaporized in an atmosphere of Ar and are created with a

fix 4 C deposit 2000 1 40000 36904 region comp_box near 3.5.

then they deposit on the cluster and give nanotubes or graphitic structures

The simulation starts and looks good for something like 5000000 timesteps, than it gives this error :

"Atom IDs must be consecutive for dump xyz", which according to the guide is self explanatory, but, honestly, I do not really understand what happens. If I restart the simulation with a minimize it works for other 1000000-2000000 time steps and then it gives the same error again.

Anybody, knows what this error can mean in this circumstance.

Thanks in advance

Alessio

The input file is the following

#Fe-Fe MEAM, Fe-C Tersoff, C-C AIREBO 1 0 + LJ Argon (case12b)

restart 100000 temp.restart
#units metal
#boundary p p p
#atom_style atomic

variable lC equal 30.0
variable Lbox equal 2.66667
variable Lhi equal 1.192
variable Lhs equal 1.475
variable Lci equal 12.4564
variable Lcs equal 15.4181
variable Ts equal 800.0
variable vTi equal -0.001
variable vTs equal 0.001

lattice sc \{lC\} region comp\_box block 0\.0 {Lbox} 0.0 \{Lbox\} 0\.0 {Lbox}
region hole block \{Lhi\} {Lhs} \{Lhi\} {Lhs} \{Lhi\} {Lhs}
#create_box 3 comp_box

# Ar atmpsphere
#create_atoms 3 region comp_box
#delete_atoms region hole
#mass 3 39.948
#group Ar type 3

# Vaporized Carbon
#mass 1 12.0111
#group C type 1

# Fe cluster
lattice bcc 2.87
region cluster block \{Lci\} {Lcs} \{Lci\} {Lcs} \{Lci\} {Lcs}
#create_atoms 2 region cluster
#mass 2 55.847
#group Fe type 2

#velocity all create ${Ts} 34680 dist gaussian

read_restart temp.restart.13400000

pair_style hybrid meam tersoff airebo 2.5 1 1 lj/cut 10.0
pair_coeff * * tersoff FeC.tersoff C Fe NULL
pair_coeff * * meam library.meam Fe Fe.meam NULL Fe NULL
pair_coeff 1 3 lj/cut 0.02495 3.7
pair_coeff 2 3 lj/cut 0.05160 3.7
pair_coeff 3 3 lj/cut 0.01030 3.4
pair_coeff * * airebo CH.airebo C NULL NULL

neighbor 2.0 bin
neigh_modify delay 0

compute myTemp all temp
compute_modify myTemp dynamic yes extra 0

minimize 0.0 0.0 1000 1000

fix 1 all langevin \{Ts\} {Ts} 5.66 54309
fix 2 all nve
fix_modify 1 temp myTemp
#fix 3 C deposit 10 1 2500 1294 region comp_box near 3.0 vx \{vTi\} {vTs} vy \{vTi\} {vTs} vz \{vTi\} {vTs}
fix 4 C deposit 2000 1 40000 36904 region comp_box near 3.5 vx \{vTi\} {vTs} vy \{vTi\} {vTs} vz \{vTi\} {vTs}
fix 5 Fe momentum 50 linear 1 1 1
thermo 2000
thermo_modify temp myTemp
thermo_style custom step c_myTemp temp press atoms
thermo_modify lost ignore flush yes

dump all all xyz 2000 dump5.xyz
timestep 0.0005
run 40000000

If you lose an atom, then your IDs won't be consecutive. Don't
use xyz output format if this is the case.

Steve