LAMMPS crashing? Movie issue?

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1

Hi all

I am working with a sputtering script that has been having no issues thus far. I recently made my speed lower and box slightly smaller and now after 4900 steps I get a crash message along with the line:

Error while decoding stream #0:0: Invalid data found when processing input

This is a totally new error but based on some research I am thinking it may be from my dump movie command? I get the same error with other forcefields. Below is my input script.

I have tried a timestep of 0.25, and downloaded the June 2018 update of LAMMPS, neither worked. I spent a fair amount of time getting this script going so really hoping someone can help with this error.

Thanks for your help, input file below:

surface sputtering demo

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

dimension variables

box length in x and y

variable len index 8.0

height of layer

variable hgt index 10

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

#simulation set up
units real
atom_style full
boundary p p f
lattice fcc 4.05
region box block 0.0 {len} 0.0 {len} -1.0 24 units lattice

particle density in z-direction is inhomogeneous:

only do domain decomposition in x- and y-direction

processors * * 1

------------------------ regions and atom types ----------------------------

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 2 region layer
group substrate region layer

mass 1 15.99
mass 2 26.98

region fixed block INF INF INF INF 0.0 0.5
group fixed region fixed
group mobile subtract all fixed

reaxff force field

pair_style reax/c NULL checkqeq yes
pair_coeff * * AlCHO.ff O Al
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c

neigh_modify delay 0

#neighbor 0.3 bin
#neigh_modify every 2 delay 6 check yes

minimize 1.0e-5 1.0e-8 1000 10000

------------------------ equilibration----------------------------

reset_timestep 0
timestep 0.5

velocity mobile create 300 87287

use the temperature of the mobile layer atoms as reference

compute mtemp mobile temp

fix 2 mobile nve
fix 3 mobile langevin 200 200 25 982434
fix_modify 3 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 100

define region for inserting particles

region sphere sphere {len2} {len2} 26 ${len2} units lattice
region insert intersect 2 box sphere

define group of inserted particles

group insert region insert
group insert type 1

deposite particles regularly into insert volume

fix insert insert deposit 100 1 200 12345 region insert vz -0.021 -0.021
neigh_modify every 1 delay 0 check yes

group insert region insert
group insert type 1

time integrate inserted particles

fix 5 insert nve

remove thermostat on layer atoms

unfix 3

variable nlayer equal count(mobile)+count(fixed)
variable ninsert equal count(insert)
variable submass equal mass(substrate)

thermo_style custom step atoms v_nlayer v_ninsert v_submass temp etotal
thermo_modify temp mtemp

handling of atoms the get bounced back from surface or sputtered off the surface.

thermo_modify lost ignore
dump 3 all movie 50 movie.mpg type type axes yes 0.8 0.02 view 80 -30 zoom 1.5

timestep 0.5
run 40000

2

As a follow up, it seems to always crash after 4900 steps, but it is dependent on the geometry? For example, 6x6x8 angstrom substrate ran fine, but when it was changed to 6x6x10 it crashed? Yet 8x8x10 worked? I am really confused by this. Any help would be greatly appreciated!

3

Without the exact error message and the line it pointed to (all contained in LAMMPS screen output), it is difficult to comment.

4

Thanks Ray, what makes this one very odd to me is that I am not getting an error message, it just gets a windows screen that comes up and says lmp_serial has stopped working and asks me to close the program (basically it crashed). After I select close the program a red error line then shows up saying:

Error while decoding stream #0:0: Invalid data found when processing input

The error line may be because I select close the program and then it comes up (in the command prompt). When the box is 8 x 8 x 10 it runs through, 6 x 6 x 8 it runs. But if 6 x 6 x 10 it crashes. It very confusing because I am confident in finding errors if it pointed me to a line, but I am at a loss on this one. Someone had a similar error a while back, and Axel suggested it may be a dump movie issue? I cc’d you Axel as maybe you have a similar idea?

https://lammps.sandia.gov/threads/msg42909.html

Thans a lot, I know I post here a lot!

5

Why not just remove dump movie and try again? Then you’ll know for sure if it is dump movie causing the problem.

The key to debugging an input script is to simplify and minimize the input script.

6

Just ran again, a 6x6x10 simulation box with movie line commented out and it still crashed, but without the error line. Making me think the error line is just a product of not being able to make the video due to the crash. Still though, stuck on why the crash. Likely in the deposit command, but only after a certain number of steps? Below is the log file in case that provides more info. The script gets through equilibration, minimization, but during the deposit and sputter appears to have issues. But oddly only with certain sizes in the substrate.

LAMMPS (29 Jun 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (…/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task

surface sputtering demo

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

dimension variables

box length in x and y

variable len index 6

height of layer

variable hgt index 10

delta between insert area and box

variable len0 index 0.1

full length minus delta

variable len1 equal {len}-{len0}
variable len1 equal 6-${len0}
variable len1 equal 6-0.1

half length

variable len2 equal ${len}0.5
variable len2 equal 60.5

#simulation set up
units real
atom_style full
boundary p p f
lattice fcc 4.09
Lattice spacing in x,y,z = 4.09 4.09 4.09
region box block 0.0 {len} 0.0 {len} -1.0 24 units lattice
region box block 0.0 6 0.0 ${len} -1.0 24 units lattice
region box block 0.0 6 0.0 6 -1.0 24 units lattice

particle density in z-direction is inhomogeneous:

only do domain decomposition in x- and y-direction

processors * * 1

------------------------ regions and atom types ----------------------------

two atom types: surface and sputter atoms

create_box 2 box
Created orthogonal box = (0 0 -4.09) to (24.54 24.54 98.16)
1 by 1 by 1 MPI processor grid

region layer block 0.0 {len} 0.0 {len} 0.0 {hgt} region layer block 0.0 6 0.0 {len} 0.0 {hgt} region layer block 0.0 6 0.0 6 0.0 {hgt}
region layer block 0.0 6 0.0 6 0.0 10
create_atoms 2 region layer
Created 1512 atoms
Time spent = 0.00100017 secs
group substrate region layer
1512 atoms in group substrate

mass 1 15.99
mass 2 107.86

region fixed block INF INF INF INF 0.0 0.5
group fixed region fixed
144 atoms in group fixed
group mobile subtract all fixed
1368 atoms in group mobile

reaxff force field

pair_style reax/c NULL checkqeq yes
pair_coeff * * AgZnO.ff O Ag
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c

neigh_modify delay 0

#neighbor 0.3 bin
#neigh_modify every 2 delay 6 check yes

minimize 1.0e-5 1.0e-8 1000 10000
Neighbor list info …
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 146.9 | 146.9 | 146.9 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -102970.23 0 -102970.23 40396.112
23 0 -104105.32 0 -104105.32 12293.312
Loop time of 19.5811 on 1 procs for 23 steps with 1512 atoms

99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-102970.233341 -104105.06425 -104105.318027
Force two-norm initial, final = 169.498 3.69832
Force max component initial, final = 13.9972 0.186578
Final line search alpha, max atom move = 0.140946 0.0262975
Iterations, force evaluations = 23 37

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total

7

Thanks for your suggestions Ray. I was able to run it on a larger cluster computer, making me think it has some thing to do with the processing power of my computer.

Cheers

Liam