View source for ZnO (Quantum ESPRESSO)

{{WIP|author=bgo}}
This example shows how to create Infrared and Raman spectra of solid ZnO-Wurtzite, which are computed using the following three 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}}

= Initial Setup =

We need to complete the [[Initial Setup|initial setup tutorial]] first, to be sure that the [//gcc.gnu.org GNU Compiler Collection], and [//www.open-mpi.org Open MPI] will be used for our simulations.

{{HPC-InitialSetupMsg}}

= 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 {{Path|ZnO}} 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 ZnO 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}}

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 =

To calculate the Infrared and Raman spectra we will use three modules of Quantum ESPRESSO: {{C|pw.x}}, to perform a self consistent field calculation; {{C|ph.x}}, to calculate the vibrational frequencies; and {{C|dynmat.x}}, to extract the phonon information. 

== Input Files ==

Each module of Quantum ESPRESSO requires their own input file, along with pseudopotentials that describe each atom.

=== Modules ===

The input files, one for each module, in this example are:

* {{C|zno.scf.qei}}
* {{C|zno.ph.qei}}
* {{C|zno.dm.qei}}

All three have a {{C|qei}} filename extension (which stands for ''Quantum ESPRESSO Inputfile''), and is required for the queue submission script to properly identify the input file. There is no requirement for the rest of the filename, however it is traditional to start it with the name of the material being studied (ZnO, in this example) followed by an abbreviation for the Quantum ESPRESSO module used: scf, or pw for {{C|pw.x}}; ph for {{C|ph.x}}; and dm for {{C|dynmat.x}}. 

=== Pseudopotentials ===

Quantum ESPRESSO requires a pseudopotential for each atom in the system to be studied, for this example (ZnO) they are:

* {{C|O.pw-mt_fhi.UPF}}
* {{C|Zn.pw-mt_fhi.UPF}}

These files were downloaded from the Quantum ESPRESSO [http://www.quantum-espresso.org/pseudopotentials  pseudopotentials repository].

== Self Consistent Field (SCF) Calculation ==

For SCF calculations we need to use the {{C|pw.x}} Quantum ESPRESSO module.

=== Modify Queue Submission Script ===

Changing the job name to {{C|ZnO-pw}}, the Quantum ESPRESSO module to {{C|pw.x}}, 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_MODULE=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-qe.sh|qstat|output=<pre>
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
14589.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.

=== Check Results ===

When the job completes you should find the following files:

{{Cmd|ls -l|output=<pre>
total 392
-rw-r--r-- 1 user user 165332 Jan  4 11:15 O.pw-mt_fhi.UPF
-rw-r--r-- 1 user user   2113 Jan  4 11:15 README
-rw-r--r-- 1 user user 183650 Jan  4 11:15 Zn.pw-mt_fhi.UPF
-rw------- 1 user user    670 Jan  4 11:16 myoutput.txt
drwxrwxr-x 3 user user   4096 Jan  4 11:16 tmp
-rwxr-xr-x 1 user user    271 Jan  4 11:16 torque-qe.sh
-rw-r--r-- 1 user user    117 Jan  4 11:15 zno.dm.qei
-rw-r--r-- 1 user user    255 Jan  4 11:15 zno.ph.qei
-rw-rw-r-- 1 user user  12941 Jan  4 11:16 zno.scf.out
-rw-r--r-- 1 user user    720 Jan  4 11:15 zno.scf.qei
</pre>}}

The three new items created are described here:

; myoutput.txt
* A summary of the simulation.
* If any problem occurs trying to run the simulation, this should be the first place to look for errors.
; tmp
* A directory containing intermediate calculations which are utilized by other Quantum ESPRESSO modules.
; zno.scf.out
* The results of the SCF calculation.
* Should be the second place to look for errors on unsuccessful runs.

For a successful run, {{Path|myoutput.txt}} should look similar to this:

{{FileBox|filename=myoutput.txt|1=
-------------- qe-config (BEGIN) --------------

Start time       : Wed Jan  4 11:16:33 EST 2017

PBS_JOBID        : 14589.flory.usm.edu
Working Directory: /home/user/examples/ZnO
MPI command      : /home/bgo/shared/gnu-openmpi/bin/mpirun
QE module        : /home/bgo/shared/gnu-openmpi/bin/pw.x
QE script        : /home/user/examples/ZnO/zno.scf.qei
Processes        : 16
Controlling Node : n008.cluster.com
Nodes            : n008.cluster.com (16)

Command: mpirun  pw.x -inp "zno.scf.qei" > "zno.scf.out"

Stop  time       : Wed Jan  4 11:16:38 EST 2017

Elapsed time     : 0 days 00h 00m 05s

-------------- qe-config ( END ) --------------
}}

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

Now we use the {{C|ph.x}} module of Quantum ESPRESSO to calculate the vibrational frequencies of ZnO.

=== Modify Queue Submission Script ===

Changing the job name to {{C|ZnO-ph}}, the Quantum ESPRESSO module to {{C|ph.x}}, and the input file to {{C|zno.ph}} results in a submission script that looks like this:

{{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_MODULE=ph.x

. $(which qe-config)

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

doQE
}}

=== Submit Job ===

Send the job to the cluster: 

{{Cmd|qsub torque-qe.sh|qstat|output=<pre>
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
14590.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.

=== Check Results ===

When the job completes you should find the following files:

{{Cmd|ls -lh|output=<pre>
total 7.7M
-rw-r--r-- 1 user user 162K Jan  4 11:20 O.pw-mt_fhi.UPF
-rw-r--r-- 1 user user 2.1K Jan  4 11:20 README
-rw-r--r-- 1 user user 180K Jan  4 11:20 Zn.pw-mt_fhi.UPF
-rw-rw-r-- 1 user user  13K Jan  4 11:26 dmat.zno
-rw-rw-r-- 1 user user 2.4M Jan  4 11:21 drho_e1
-rw-rw-r-- 1 user user 2.4M Jan  4 11:21 drho_e2
-rw-rw-r-- 1 user user 2.4M Jan  4 11:21 drho_e3
-rw------- 1 user user  667 Jan  4 11:26 myoutput.txt
drwxrwxr-x 4 user user 4.0K Jan  4 11:21 tmp
-rwxr-xr-x 1 user user  270 Jan  4 11:21 torque-qe.sh
-rw-r--r-- 1 user user  117 Jan  4 11:20 zno.dm.qei
-rw-rw-r-- 1 user user  32K Jan  4 11:26 zno.ph.out
-rw-r--r-- 1 user user  255 Jan  4 11:20 zno.ph.qei
-rw-rw-r-- 1 user user  13K Jan  4 11:20 zno.scf.out
-rw-r--r-- 1 user user  720 Jan  4 11:20 zno.scf.qei
</pre>}}

The new items created are described here:

; drho_e1, drho_e2, and drho_e3
* Dynamical matrix and Charge density responses.
* For more details on these files, see the manual [http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PH.html here].
; myoutput.txt
* This file was created from the previous run, but has been overwritten by this run.
* A summary of the simulation.
* If any problem occurs trying to run the simulation, this should be the first place to look for errors.
; zno.ph.out
* The results of the phonon calculation.
* Should be the second place to look for errors on unsuccessful runs.

== Phonon Information ==

Now use the {{C|dynmat.x}} Quantum ESPRESSO module to extract the Infrared and Raman spectra data from the results of the previous two jobs.

=== Modify Queue Submission Script ===

Changing the job name to {{C|ZnO-dynmat}}, the Quantum ESPRESSO module to {{C|dynmat.x}}, and the input file to {{C|zno.dm}} results in a submission script that looks like this:

{{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_MODULE=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-qe.sh|qstat|output=<pre>
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
14592.flory               ZnO-dynmat       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.

=== Check Results ===

When the job completes you should find the following files:

{{Cmd|ls -lh|output=<pre>
total 7.7M
-rw-r--r-- 1 user user 162K Jan  4 11:27 O.pw-mt_fhi.UPF
-rw-r--r-- 1 user user 2.1K Jan  4 11:27 README
-rw-r--r-- 1 user user 180K Jan  4 11:27 Zn.pw-mt_fhi.UPF
-rw-rw-r-- 1 user user  13K Jan  4 11:27 dmat.zno
-rw-rw-r-- 1 user user 2.4M Jan  4 11:27 drho_e1
-rw-rw-r-- 1 user user 2.4M Jan  4 11:27 drho_e2
-rw-rw-r-- 1 user user 2.4M Jan  4 11:27 drho_e3
-rw------- 1 user user  675 Jan  4 11:28 myoutput.txt
drwxrwxr-x 4 user user 4.0K Jan  4 11:27 tmp
-rwxr-xr-x 1 user user  278 Jan  4 11:43 torque-qe.sh
-rw-rw-r-- 1 user user 2.4K Jan  4 11:28 zno.dm.out
-rw-r--r-- 1 user user  117 Jan  4 11:27 zno.dm.qei
-rw-rw-r-- 1 user user  32K Jan  4 11:27 zno.ph.out
-rw-r--r-- 1 user user  255 Jan  4 11:27 zno.ph.qei
-rw-rw-r-- 1 user user  13K Jan  4 11:27 zno.scf.out
-rw-r--r-- 1 user user  720 Jan  4 11:27 zno.scf.qei
-rw-rw-r-- 1 user user 3.7K Jan  4 11:28 zno_raman.axsf
-rw-rw-r-- 1 user user 2.1K Jan  4 11:28 zno_raman.mold
-rw-rw-r-- 1 user user 4.6K Jan  4 11:28 zno_raman.out
</pre>}}

The new items created are described here:

; zno_raman.axsf, zno_raman.mold, zno_raman.out
* Phonon frequencies and normalized phonon displacements.
* For more details on these files, see the manual [http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_DYNMAT.html here].
; myoutput.txt
* This file was created from a previous run, but has been overwritten by this run.
* A summary of the simulation.
* If any problem occurs trying to run the simulation, this should be the first place to look for errors.
; zno.dm.out
* The results of the phonon calculation.
* Should be the second place to look for errors on unsuccessful runs.

== Spectra Data ==

{{FileBox|filename=zno.dm.out|title=(Partial file: section containing table)|1=
     IR activities are in (D/A)^2/amu units
     Raman activities are in A^4/amu units
     multiply Raman by 0.000650 for Clausius-Mossotti correction

# mode   [cm-1]    [THz]      IR          Raman   depol.fact
    1     -0.00   -0.0000    0.0000      5406.9725    0.7500
    2     -0.00   -0.0000    0.0000      5757.6500    0.7500
    3     -0.00   -0.0000    0.0000      5688.7322    0.7499
    4     -0.00   -0.0000    0.0000       171.9037    0.4691
    5      0.00    0.0000    0.0000       554.2156    0.5434
    6      0.00    0.0000    0.0000      2358.3724    0.7367
    7    105.98    3.1773    0.1227      1281.9877    0.7500
    8    124.94    3.7456    0.0000      4603.4623    0.7500
    9    287.20    8.6100   13.4004      3428.9212    0.7500
   10    391.76   11.7446   71.1599     37311.9784    0.1040
   11    407.14   12.2057  101.4467      9438.8013    0.7500
   12    532.61   15.9672    6.1669       385.1588    0.7500
}}
[[Category:Quantum ESPRESSO Examples]]