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