View source for Ellipsoidal particles in spherical solvent (LAMMPS)

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

* Time-step is halved.
* Run times increased to 1,000,000.
* Creates a movie.


=Prepare Example Directory=

First, make sure we are at the root of our home directory

{{Cmd|cd}}

Now, make an {{Path|example}} directory, and copy the ellipse example directory into it. 

{{Cmd|mkdir examples|cp -r {{HPC-Examples-Dir}}/lammps/ellipse examples/|cd examples/ellipse|ls|output=<pre>ellipse.gayberne.lmp</pre>}}

We also need a script to submit the job to the cluster. Lets start with the sample script in {{Path|{{HPC-Samples-Dir|flory}}}} by copying it to our new ellipse example directory.

{{Cmd|cp {{HPC-Samples-Dir|flory}}/torque-lmp.sh .|ls|output=<pre>
ellipse.gayberne.lmp  torque-lmp.sh
</pre>}}

The {{Path|torque-lmp.sh}} script should look something like this:

{{HPC-torque-lmp|lang=bash|title=(original)}}

=Modify Queue Submission Script=

The submission script we just copied has default settings that have to be modified for this simulation. Lucky, most of the defaults work for the ellipse simulation (1 node, 16 processes per node, etc.) and all we have to change is the name of the job and the lammps input file. Changing the job name to {{C|ellipse-lmp}} and the input file to {{C|ellipse.gayberne}} results in a submission script that looks like this:

{{FileBox|lang=bash|filename=torque-lmp.sh|title=(edited)|1=
#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
}}

=Submit Job=

The job is now ready to be sent to the cluster. 

{{Cmd|qsub torque-lmp.sh|qstat|output=<pre>
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
14222.flory               ellipse-lmp      user            00:00:35 R default  
</pre>}}

The job should take about 4 minutes. Check the job status with {{C|qstat}} to see when it is finished; when the job is no longer listed it has finished.

=Check Results=

When the job completes you should find the following files:

{{Cmd|ls -lh|output=<pre>
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
</pre>}}

General information about the job can be found in {{Path|myoutout.txt}}, if any errors occurred they should be listed in this file. A successful run will look like this:

{{Cmd|cat myoutput.txt|output=<pre>
-------------- lmp-config (BEGIN) --------------

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

PBS_JOBID        : 14222.flory.usm.edu
Working Directory: /home/user/examples/ellipse
MPI command      : /home/user/shared/gnu-openmpi/bin/mpirun
LAMMPS command   : /home/user/shared/gnu-openmpi/bin/lmp
LAMMPS script    : /home/user/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 ) --------------
</pre>}}

The results from the LAMMPS simulation can be found in {{Path|ellipse.gayberne.out}}, and {{Path|movie.mkv}} is the movie.

To watch the movie, copy it to your computer. It should be about 1 minute 23 seconds long. During the first half of movie the box is shrinking (NPT ensemble), but the movie is also zooming in, making it look like the particles are getting larger.
[[Category:LAMMPS Examples]]