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This example shows how to create Infrared and Raman spectra of solid ZnO-Wurtzite, which are computed using the following 3 steps:
{{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}}
* Perform Self Consistent Field (SCF) calculation with {{C|pw.x}}
* Calculate the vibrational frequencies (normal modes/phonons) with {{C|ph.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}}
* 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




Line 19: Line 19:
{{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>}}
{{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.
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>
{{Cmd|cp {{HPC-Samples-Dir|flory}}/torque-qe.sh .|ls|output=<pre>
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= Running Quantum Espresso =
= Running Quantum Espresso =


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


Quantum Espresso module to {{C|pw.c}}
== Self Consistent Field (SCF) Calculation ==
 
For SCF calculations we need to use the {{C|pw.x}} Quantum Espresso module.


=== Modify Queue Submission Script ===
=== Modify Queue Submission Script ===
Line 92: Line 94:


== Calculate the vibrational frequencies (normal modes/phonons) ==
== Calculate the vibrational frequencies (normal modes/phonons) ==
No we use the {{C|ph.x}} module of Quantum Espresso to calculate the virtation frequencies of ZnO.


=== Modify Queue Submission Script ===
=== 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=
{{FileBox|lang=bash|filename=torque-qe.sh|title=(edited for running {{C|ph.x}})|1=
Line 116: Line 122:
=== Submit Job ===
=== Submit Job ===


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


{{Cmd|qsub torque-lmp.sh|qstat|output=<pre>
{{Cmd|qsub torque-lmp.sh|qstat|output=<pre>
Job ID                    Name            User            Time Use S Queue
Job ID                    Name            User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
------------------------- ---------------- --------------- -------- - -----
14222.flory              ZnO-ph          user            00:00:35 R default   
14223.flory              ZnO-ph          user            00:00:35 R default   
</pre>}}
</pre>}}


Line 148: Line 154:
</pre>}}
</pre>}}


== phonon information ==
== 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 ===
=== 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=
{{FileBox|lang=bash|filename=torque-qe.sh|title=(edited for running {{C|dynmat.x}})|1=
Line 178: Line 188:
Job ID                    Name            User            Time Use S Queue
Job ID                    Name            User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
------------------------- ---------------- --------------- -------- - -----
14222.flory              ZnO-ph          user            00:00:35 R default   
14224.flory              ZnO-ph          user            00:00:35 R default   
</pre>}}
</pre>}}


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== Spectra Data ==
== Spectra Data ==


{{FileBox|filename=zno.dm.out|title=(Partial file: Section containing table)|1=
{{FileBox|filename=zno.dm.out|title=(Partial file: section containing table)|1=
     IR activities are in (D/A)^2/amu units
     IR activities are in (D/A)^2/amu units
     Raman activities are in A^4/amu units
     Raman activities are in A^4/amu units

Revision as of 15:36, 3 January 2017

Warning
This page is a work in progress by bgo (talk | contribs). Treat its contents with caution.

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 pw.x
  • Calculate the vibrational frequencies (normal modes/phonons) with ph.x
  • Extract the phonon information from ph.x output using dynmat.x


Important
The initial setup must be completed before continuing.

Prepare Example Directory

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

user $cd

Now, make an example directory, and copy the ellipse example directory into it.

user $mkdir examples
user $cp -r /home/bgo/shared/examples/qe/ZnO examples/
user $cd examples/ZnO
user $ls
O.pw-mt_fhi.UPF  README  Zn.pw-mt_fhi.UPF  zno.dm.qei  zno.ph.qei  zno.scf.qei

We also need a script to submit the job to the cluster. Lets start with the Quantum Espresso sample script in /home/bgo/shared/samples by copying it to our new ZnO example directory.

user $cp /home/bgo/shared/samples/torque-qe.sh .
user $ls
O.pw-mt_fhi.UPF  Zn.pw-mt_fhi.UPF  zno.dm.qei  zno.scf.qei
README           torque-qe.sh      zno.ph.qei

The torque-qe.sh script should look something like this:

FILE torque-qe.sh(original)
#PBS -l walltime=10:00:00,nodes=1:ppn=16
##PBS -M EmailAddress
##PBS -m bae
#PBS -q default
#PBS -N Jobname
#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=mysimulation

doQE


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: pw.x, to perform a self consistent field calculation; ph.x, to calculate the vibrational frequencies; and dynmat.x, to extract the phonon information.

Self Consistent Field (SCF) Calculation

For SCF calculations we need to use the pw.x Quantum Espresso module.

Modify Queue Submission Script

Changing the job name to ZnO-pw, the Quantum Espresso module to pw.x, and the input file to zno.scf results in a submission script that looks like this:

FILE torque-qe.sh(edited for running pw.x)
#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.

user $qsub torque-lmp.sh
user $qstat
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
14222.flory               ZnO-pw           user            00:00:35 R default

The job should take about 1 minute. Check the job status with 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:

user $ls -lh
total 400K
-rw-r--r-- 1 user user 162K Jan  3 14:36 O.pw-mt_fhi.UPF
-rw-r--r-- 1 user user 2.1K Jan  3 14:36 README
-rw-r--r-- 1 user user 180K Jan  3 14:36 Zn.pw-mt_fhi.UPF
-rw------- 1 user user  14K Jan  3 14:37 myoutput.txt
drwxrwxr-x 3 user user 4.0K Jan  3 14:37 tmp
-rwxr-xr-x 1 user user  271 Jan  3 14:36 torque-qe.sh
-rw-r--r-- 1 user user  117 Jan  3 14:36 zno.dm.qei
-rw-r--r-- 1 user user  255 Jan  3 14:36 zno.ph.qei
-rw-rw-r-- 1 user user  13K Jan  3 14:37 zno.scf.out
-rw-r--r-- 1 user user  720 Jan  3 14:36 zno.scf.qei

Calculate the vibrational frequencies (normal modes/phonons)

No we use the ph.x module of Quantum Espresso to calculate the virtation frequencies of ZnO.

Modify Queue Submission Script

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

FILE torque-qe.sh(edited for running ph.x)
#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

Send the job to the cluster:

user $qsub torque-lmp.sh
user $qstat
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
14223.flory               ZnO-ph           user            00:00:35 R default

The job should take about 5 minutes. Check the job status with 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:

user $ls -lh
-rw-r--r-- 1 user user 162K Jan  3 14:37 O.pw-mt_fhi.UPF
-rw-r--r-- 1 user user 2.1K Jan  3 14:37 README
-rw-r--r-- 1 user user 180K Jan  3 14:37 Zn.pw-mt_fhi.UPF
-rw-rw-r-- 1 user user  13K Jan  3 14:43 dmat.zno
-rw-rw-r-- 1 user user 2.4M Jan  3 14:38 drho_e1
-rw-rw-r-- 1 user user 2.4M Jan  3 14:38 drho_e2
-rw-rw-r-- 1 user user 2.4M Jan  3 14:38 drho_e3
-rw------- 1 user user  33K Jan  3 14:43 myoutput.txt
drwxrwxr-x 4 user user 4.0K Jan  3 14:38 tmp
-rwxr-xr-x 1 user user  270 Jan  3 14:37 torque-qe.sh
-rw-r--r-- 1 user user  117 Jan  3 14:37 zno.dm.qei
-rw-rw-r-- 1 user user  32K Jan  3 14:43 zno.ph.out
-rw-r--r-- 1 user user  255 Jan  3 14:37 zno.ph.qei
-rw-rw-r-- 1 user user  13K Jan  3 14:37 zno.scf.out
-rw-r--r-- 1 user user  720 Jan  3 14:37 zno.scf.qei

Phonon Information

Now use the 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 ZnO-dynmat, the Quantum Espresso module to dynmat.x, and the input file to zno.dm results in a submission script that looks like this:

FILE torque-qe.sh(edited for running dynmat.x)
#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.

user $qsub torque-lmp.sh
user $qstat
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
14224.flory               ZnO-ph           user            00:00:35 R default

The job should take less than a minute. Check the job status with 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:

user $ls -lh
total 7.7M
-rw-r--r-- 1 user user 162K Jan  3 14:46 O.pw-mt_fhi.UPF
-rw-r--r-- 1 user user 2.1K Jan  3 14:46 README
-rw-r--r-- 1 user user 180K Jan  3 14:46 Zn.pw-mt_fhi.UPF
-rw-rw-r-- 1 user user  13K Jan  3 14:46 dmat.zno
-rw-rw-r-- 1 user user 2.4M Jan  3 14:46 drho_e1
-rw-rw-r-- 1 user user 2.4M Jan  3 14:46 drho_e2
-rw-rw-r-- 1 user user 2.4M Jan  3 14:46 drho_e3
-rw------- 1 user user 3.0K Jan  3 14:47 myoutput.txt
drwxrwxr-x 4 user user 4.0K Jan  3 14:46 tmp
-rwxr-xr-x 1 user user  278 Jan  3 14:47 torque-qe.sh
-rwxr-xr-x 1 user user  274 Jan  3 14:46 torque-qe.sh~
-rw-rw-r-- 1 user user 2.4K Jan  3 14:47 zno.dm.out
-rw-r--r-- 1 user user  117 Jan  3 14:46 zno.dm.qei
-rw-rw-r-- 1 user user  32K Jan  3 14:46 zno.ph.out
-rw-r--r-- 1 user user  255 Jan  3 14:46 zno.ph.qei
-rw-rw-r-- 1 user user  13K Jan  3 14:46 zno.scf.out
-rw-r--r-- 1 user user  720 Jan  3 14:46 zno.scf.qei
-rw-rw-r-- 1 user user 3.7K Jan  3 14:47 zno_raman.axsf
-rw-rw-r-- 1 user user 2.1K Jan  3 14:47 zno_raman.mold
-rw-rw-r-- 1 user user 4.6K Jan  3 14:47 zno_raman.out

Spectra Data

FILE zno.dm.out(Partial file: section containing table)
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
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