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Re: [lammps-users] Lost atoms in reax fix deposit
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Re: [lammps-users] Lost atoms in reax fix deposit


From: Ray Shan <rshan@...1795...>
Date: Tue, 3 Jul 2018 17:25:09 +0000

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

 

Ray

 

 

From: "Morrissey, Liam S." <lsm088@...7202...>
Date: Tuesday, July 3, 2018 at 10:14 AM
To: LAMMPS Mailing List <lammps-users@lists.sourceforge.net>
Subject: [lammps-users] 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