Ellipsoidal particles in spherical solvent (LAMMPS)

Ellipse sample from LAMMPS packages

Ellipsoidal particles in spherical solvent, 2d system. The example used here is nearly identical to the version released with LAMMPS with the following exceptions:

• Time-step is halved.
• Run times increased to 1,000,000.
• Save a movie.

movie 1m23sec

1st half of movie the box is shrinking, but the movie is zooming in at same rate which is why it looks like the particles are getting larger.

{{HPC-Examples-Dir}}

Parameter unnamed not defined. For correct usage see template's documention.

/lammps/ellipse

FILE torque-lmp.sh(original)

#PBS -l walltime=10:00:00,mem=15gb,nodes=1:ppn=16
##PBS -M EmailAddress
##PBS -m bae
#PBS -q default
#PBS -N Jobname
#PBS -o myoutput.txt
#PBS -j oe

. $(which lmp-config)

# The LAMMPS input file must have a '.lmp' extension (e.g., mysimulation.lmp).
INPUTFILE=mysimulation

doLAMMPS

change name of job from to ellipse-lmp change INPUTFILE from mysimulation to ellipse.gayberne Should look like this:

FILE torque-lmp.sh(edited)

#PBS -l walltime=10:00:00,mem=15gb,nodes=1:ppn=16
##PBS -M EmailAddress
##PBS -m bae
#PBS -q default
#PBS -N ellipse-lmp
#PBS -o myoutput.txt
#PBS -j oe

. $(which lmp-config)

# The LAMMPS input file must have a '.lmp' extension (e.g., mysimulation.lmp).
INPUTFILE=ellipse.gayberne

doLAMMPS

user $qsub torque-lmp.sh

About 4 minutes later:

user $ls -lh

total 22M
-rw-r--r-- 1 user user 1.8K Dec 20 17:25 ellipse.gayberne.lmp
-rw-rw-r-- 1 user user 1.5M Dec 20 17:29 ellipse.gayberne.out
-rw-rw-r-- 1 user user  398 Dec 20 17:26 log.cite
-rw-rw-r-- 1 user user  20M Dec 20 17:29 movie.mkv
-rw------- 1 user user  730 Dec 20 17:29 myoutput.txt
-rwxr-xr-x 1 user user  293 Dec 20 16:14 torque-lmp.sh

user $cat myoutput.txt

-------------- lmp-config (BEGIN) --------------

Start time       : Tue Dec 20 17:25:51 EST 2016

PBS_JOBID        : 14222.flory.usm.edu
Working Directory: /home/user/sims/gnu-openmpi/examples/ellipse
MPI command      : /home/user/shared/gnu-openmpi/bin/mpirun
LAMMPS command   : /home/user/shared/gnu-openmpi/bin/lmp
LAMMPS script    : /home/user/sims/gnu-openmpi/examples/ellipse/ellipse.gayberne.lmp
Processes        : 16
Controlling Node : n005.cluster.com
Nodes            : n005.cluster.com (16)

Command: mpirun  lmp -in "ellipse.gayberne.lmp" -log "ellipse.gayberne.out" -screen "none"

Stop  time       : Tue Dec 20 17:29:39 EST 2016

Elapsed time     : 0 days 00h 03m 48s

-------------- lmp-config ( END ) --------------

copy movie.mkv to your computer and what the animation.