Lost atoms in reax fix deposit

Hi,

Following the example deposit I have been modifying it for the deposition on oxygen on iron. However, when I run it says lost atom 306 to 305. I have done some error hunting and it appears when I comment out:

fix 2 addatoms nve
fix 3 mobile langevin 300 300 25 587283
fix 4 mobile nve

The script runs. However, I don’t know why this is the case. I fix mobile nve to essentially hold the bottom of the box rigid. I also fix add atoms nve. My parameters for langevin are temperature and then Tdamp which I took as 100x timestep.

Not sure if it is a LAMMPS error (unlikely) or something I am doing.

Entire script below:

sample surface deposition script for atoms

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

units real
dimension 3
boundary p p f
atom_style full
variable latparam equal 2.85

define lattice and large simulation box

lattice bcc {latparam} region box block 0 5 0 5 0 10 create_box 2 box lattice bcc {latparam} orient x 1 0 0 orient y 0 1 0 orient z 0 0 1

make substrate region

region substrate block 0 5 0 5 0 3
create_atoms 2 region substrate

mass 1 16.12
mass 2 55.85

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

pair_style reax/c NULL checkqeq yes
pair_coeff * * ffield.reax.Fe_O_C_H O Fe
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c

neigh_modify delay 0

#make a region called mobile that I think ultimately fixes the bottom portion of Z
group addatoms type 1
region mobile block 0 5 0 5 2 10
group mobile region mobile

compute due to extra atoms added

compute add addatoms temp
compute_modify add dynamic/dof yes extra/dof 0

nve on the addatoms and nve/langevin on mobile

fix 2 addatoms nve
fix 3 mobile langevin 300 300 25 587283
fix 4 mobile nve

#make the slab for insertion
region slab block 0 5 0 5 8 9

add the atoms, 10 atoms in total, 1 every 100 steps, no closer than 1 and -1z velocity

fix 5 addatoms deposit 10 1 100 12345 region slab near 1.0 vz -1 -1
fix 6 addatoms wall/reflect zhi EDGE

#out those thermo IDs, every 100 steps, and compute temptation
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add

#dump 1 all atom 50 dump.deposit.atom

dump 2 all image 50 image.*.jpg type type axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5

#dump 3 all movie 50 movie.mpg type type &

axes yes 0.8 0.02 view 80 -30

#dump_modify 3 pad 5

timestep 0.25

run 1000

What does “vz 1 -1” convert to in units of km/s?

Ray

Wow, very fast. I consulted some literature and put it to a typical atomic oxygen impact speed, which works out to be 0.074 Ang/fs or 7.4 km/s. The simulation runs, deposits 5 of the 10 atoms, and then says lost atoms, original 181 current 180. Does anything appear wrong with my nve/langevin sequence? Also, this is the line I changed:

fix 5 addatoms deposit 10 1 100 12345 region slab rate -.074
fix 6 addatoms wall/reflect zhi EDGE

I no longer use the key word near, but don’t think this would have an effect.

What is the purpose of changing “vz” to “rate”? The rate option moves the insertion volume in the z direction (3d) or y direction (2d). This enables particles to be inserted from a successively higher height over time.