Error:lost atoms

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1

Dear Lammpsers,

I am permanently facing with the lost atoms error and I don’t know why.

I think there is something wrong with “lattice sq2” command actually. Since, I deactivated the "fix nvt "command and applied instead the "fix nve "command in order to check whether the initial crystal structure is correct or not and it did not work! So, I think that lattice comment have some problem. So, any helpful comment is highly appreciated.

Yours Sincerely,
Bahman

deposition simulation

#Phase 1 ------------------------------------------Simulation main setup----------------------------------
dimension 2
units metal
atom_style atomic
boundary p f p # in 2d models z shall be periodic
lattice sq2 2

#simulation box
region box block 0 105 0 105 -0.5 0.5 units box
create_box 3 box #2 is number of atoms

#particle
region particle cylinder z 52.5 52.5 20 -0.5 0.5 units box
create_atoms 1 region particle
group particle region particle
mass 1 63.546

#substrate
region substrate block 0 105 5 21 -0.5 0.5 units box
create_atoms 2 region substrate
group substrate region substrate
mass 2 63.546

#lower_substrate
region lower_substrate block 0 105 0 5 -0.5 0.5 units box
create_atoms 3 region lower_substrate
group lower_substrate region lower_substrate
mass 3 63.546

#–Phase 2----------------------------------------Lennard Jones Potential-----------------------------------------------

pair_style lj/cut 10
pair_coeff * * 3 2.3
neighbor 2.0 bin
neigh_modify delay 5
#neigh_modify delay 0 every 1 check yes

#----Phase 4-------------------------------------Initial Equilibration at 300K ----------------------------------------
reset_timestep 0
timestep 0.005 # Achtung! in metal unit time-step is by default 1 picoseconds scale

velocity all create 300 12345 mom yes rot no

fix 1 substrate setforce 0.0 0.0 0.0
fix 2 lower_substrate setforce 0.0 0.0 0.0
#fix 3 particle nvt temp 300.0 300.0 100.0
fix 3 particle nve
#thermo_modify lost ignore flush yes
thermo 100
dump 1 all xyz 100 dump.txt
run 3000
unfix 3

#----Phase 5---------------------------------------Particle Impact at the room temperature --------------------

velocity particle set 0 -5 0 # *100m/s

fix 4 particle nve
#fix 5 substrate temp/rescale 100 300.0 300.0 10.0 1.0

thermo 100

dump 2 all xyz 100 dump.txt
undump 2
run 8000

2

Dear Lammpsers,

I am permanently facing with the lost atoms error and I don't know why.

I think there is something wrong with "lattice sq2" command actually.

do you have any proof for that? why do you exclude the possibility of
having a bad input.
e.g. the lennard jones parameters look *very* suspicious. for metal
units, your epsilon seems very large.

axel.

3

if i run your input, it prints E_pair and total energy as "Inf" and
pressure as "-nan"

that means, that you have created atoms, that are directly on top of each other.

when i insert the command:
delete_atoms overlap 0.1 all all

there are 52 close contact atoms deleted.

that is not the whole story, but there is *definitely* something wrong
with the geometry that you create.

axel.

4

more things to try out in proving that your model parameters are garbage.

if you run a minimization before an MD, you should see, that your
atoms are moving away from each other. so either your choice of
epsilon/sigma is wrong or your choice of lattice parameter.

axel.