sputter example doesn't show atom deposition


I visualized .xyz file, which I got from in.sputter example file in lammps package, using VMD.

The result shows only 7 frames, and I guess 7 frames are results of only minimal equilibration process, not sputtering. I was wondering if I am the only one who is getting this problem. Otherwise, is there any way I can get full animation that shows sputtering process as well? Below is the example input of sputtering.

Thank you,

Sungae Lee

surface sputtering demo

dimension variables

box length in x and y

variable len index 20.0

height of layer

variable hgt index 8.0

delta between insert area and box

variable len0 index 0.1

full length minus delta

variable len1 equal {len}-{len0}

half length

variable len2 equal ${len}*0.5

units lj

atom_style atomic

boundary p p f

lattice fcc 0.85

region box block 0.0 {len} 0.0 {len} -1.0 40.0 units lattice

particle density in z-direction is inhomogeneous:

only do domain decomposition in x- and y-direction

processors * * 1

two atom types: surface and sputter atoms

create_box 2 box

region layer block 0.0 {len} 0.0 {len} 0.0 ${hgt}

create_atoms 1 region layer

mass 1 1.0

mass 2 3.0

region fixed block INF INF INF INF 0.0 0.1

group fixed region fixed

group mobile subtract all fixed

pair_style lj/cut 2.5

pair_coeff 1 1 1.0 1.0

pair_coeff 2 2 0.5 1.2

neighbor 0.3 bin

neigh_modify every 2 delay 6 check yes

minimize 1.0e-5 1.0e-8 1000 10000

reset_timestep 0

velocity mobile create 0.4 87287

use the temperature of the mobile layer atoms as reference

compute mtemp mobile temp

fix 1 mobile nve

fix 2 mobile langevin 0.2 0.2 5.0 982434

fix_modify 2 temp mtemp

thermo 100

thermo_style custom step atoms temp etotal

thermo_modify temp mtemp

dump id all xyz 200 sputter.xyz

minimal equilibration

run 1000

define region for inserting particles

region sphere sphere {len2} {len2} 42.0 ${len2} units lattice

region insert intersect 2 box sphere

define group of inserted particles

group insert region insert

deposite particles regularly into insert volume

fix insert insert deposit 50 2 200 12345 region insert vz -8.0 -9.0 &

target {len2} {len2} ${hgt} units lattice

neigh_modify every 1 delay 0 check yes

time integrate inserted particles

fix 4 insert nve

remove thermostat on layer atoms

unfix 2

variable nlayer equal count(mobile)+count(fixed)

variable ninsert equal count(insert)

thermo_style custom step atoms v_nlayer v_ninsert temp etotal

thermo_modify temp mtemp

handling of atoms the get bounced back from surface

or sputtered off the surface.

thermo_modify lost ignore

run 15000

This is more of a vmd question than a lammps question.

Please look very carefully at what error messages you get on the vmd console. Vmd does not normally support reading the trajectories with a varying number of atoms. You need to apply one of several workarounds. For example use topotools.


I also don’t know what the in.sputter file is - I don’t
believe it is part of the LAMMPS distro. So you
may be better off contacting its authors.