Losing atoms while minimizing a substrate using the REAXFF potential.

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1

Hi lammps users,
I am trying to minimize a substrate with 1315 atoms. I am not using any min_style. Could somebody please tell me why am losing atoms while minimizing. Could this be because of the neighbor list or the time step for which each MD run is made. I am using the REAXFF potential and the units are real.

Please find my lammps input script below and the config file with the coordinates attached. Would really appreciate any input with regards to this problem am facing.

Input Script:

units real
atom_style charge
dimension 3
boundary p p f

read_data ConfigFile.txt

pair_style reax
pair_coeff * * ffield.reax 6 3
group fixed id <> 1 288
group rescale id <> 289 576
group moving id <> 289 1315
group top id <> 577 1315
timestep 1.0
neighbor 0.5 bin

neigh_modify every 1 delay 0 check yes

fix 3 moving setforce NULL NULL NULL

dump Velocities all custom 1 dumpminimization.txt id type x y z vx vy vz

dump Coords all xyz 1 minimizedvmdcoords.xyz

thermo_style custom step temp press pe etotal

thermo 1

minimize 1.0e-4 1.0e-6 100 1000

Regards,
Saketh.
University of Toledo.

ConfigFile.txt (91.9 KB)

2

Hi lammps users,
I am trying to minimize a substrate with 1315 atoms. I am not using any
min_style. Could somebody please tell me why am losing atoms while
minimizing. Could this be because of the neighbor list or the time step for
which each MD run is made. I am using the REAXFF potential and the units are
real.

Please find my lammps input script below and the config file with the
coordinates attached. Would really appreciate any input with regards to this
problem am facing.

hard to say since you didn't say which reax parameter set you are using
and the one shipped with LAMMPS that has the same name doesn't work.

it is unlikely that neighbor listing is the problem,
but perhaps you are cutting your box boundaries too
close at the bottom.

also, your fix 3 is pointless as it does nothing(!),
but shouldn't there be a fix using setforce 0.0 0.0 0.0
to keep the bottom layer atoms in place?

axel.

3

Your z boundary is "f" whcih means that if an atom
moves outside the box during minimization you will
lose it. Visualize your system and you will probably
see that happen.

Steve