View source for ZnO (Quantum ESPRESSO)

{{HPC-InitialSetupMsg}}
This example shows how to create Infrared and Raman spectra of solid ZnO-Wurtzite, which are computed using the following 3 steps:

* Perform Self Consistent Field (scf) calculation with {{C|pw.x}}
* Calculate the vibrational frequencies (normal modes/phonons) with {{C|ph.x}}
* Extract the phonon information from {{C|ph.x}} output using {{C|dynmat.x}}
* Parse the {{C|dynmat.x}} output section that contains the spectra data and plot it with gnuplot

= 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|flory}}/qe/ZnO examples/|cd examples/ZnO|ls|output=<pre>O.pw-mt_fhi.UPF  README  Zn.pw-mt_fhi.UPF  zno.dm.qei  zno.ph.qei  zno.scf.qei</pre>}}

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

{{Cmd|cp {{HPC-Samples-Dir|flory}}/torque-qe.sh .|ls|output=<pre>
O.pw-mt_fhi.UPF  Zn.pw-mt_fhi.UPF  zno.dm.qei  zno.scf.qei
README           torque-qe.sh      zno.ph.qei
</pre>}}

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

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

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 ZnO simulation (1 node, 16 processes per node, etc.) and all we have to change is the name of the job, the Quantum Espresso module, and the name of the input file.

= Running Quantum Espresso =

== Perform Self Consistent Field (scf) calculation ==

=== Modify Queue Submission Script ===

Changing the job name to {{C|ZnO-pw}} and the input file to {{C|zno.scf}} results in a submission script that looks like this:

{{FileBox|lang=bash|filename=torque-qe.sh|title=(edited for running {{C|pw.x}})|1=
#PBS -l walltime=10:00:00,nodes=1:ppn=16
##PBS -M EmailAddress
##PBS -m bae
#PBS -q default
#PBS -N ZnO-pw
#PBS -o myoutput.txt
#PBS -j oe

QE_CMD=pw.x

. $(which qe-config)

# The input file must have a '.qei' extension (e.g., mysimulation.qei).
INPUTFILE=zno.scf

doQE
}}

=== 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               ZnO-pw           user            00:00:35 R default  
</pre>}}

The job should take about 1 minute. Check the job status with {{C|qstat}} to see when it is finished; when the job is no longer listed it has finished.

== Calculate the vibrational frequencies (normal modes/phonons) ==

=== Modify Queue Submission Script ===

{{FileBox|lang=bash|filename=torque-qe.sh|title=(edited for running {{C|ph.x}})|1=
#PBS -l walltime=10:00:00,nodes=1:ppn=16
##PBS -M EmailAddress
##PBS -m bae
#PBS -q default
#PBS -N ZnO-ph
#PBS -o myoutput.txt
#PBS -j oe

QE_CMD=ph.x

. $(which qe-config)

# The input file must have a '.qei' extension (e.g., mysimulation.qei).
INPUTFILE=zno.ph

doQE
}}

=== 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               ZnO-ph           user            00:00:35 R default  
</pre>}}

The job should take about 5 minutes. Check the job status with {{C|qstat}} to see when it is finished; when the job is no longer listed it has finished.

== phonon information ==

=== Modify Queue Submission Script ===

{{FileBox|lang=bash|filename=torque-qe.sh|title=(edited for running {{C|dynmat.x}})|1=
#PBS -l walltime=10:00:00,nodes=1:ppn=16
##PBS -M EmailAddress
##PBS -m bae
#PBS -q default
#PBS -N ZnO-dynmat
#PBS -o myoutput.txt
#PBS -j oe

QE_CMD=dynmat.x

. $(which qe-config)

# The input file must have a '.qei' extension (e.g., mysimulation.qei).
INPUTFILE=zno.dm

doQE
}}

=== 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               ZnO-ph           user            00:00:35 R default  
</pre>}}

The job should take less than a minute. Check the job status with {{C|qstat}} to see when it is finished; when the job is no longer listed it has finished.