ZnO (Quantum ESPRESSO): Difference between revisions
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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: | This example shows how to create Infrared and Raman spectra of solid ZnO-Wurtzite, which are computed using the following 3 steps: | ||
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* 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 | * Parse the {{C|dynmat.x}} output section that contains the spectra data and plot it with gnuplot | ||
{{HPC-InitialSetupMsg}} | |||
= Prepare Example Directory = | = Prepare Example Directory = | ||
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== Perform Self Consistent Field (scf) calculation == | == Perform Self Consistent Field (scf) calculation == | ||
Quantum Espresso module to {{C|pw.c}} | |||
=== Modify Queue Submission Script === | === 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: | 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= | {{FileBox|lang=bash|filename=torque-qe.sh|title=(edited for running {{C|pw.x}})|1= | ||
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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. | 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 -lh|output=<pre> | |||
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 | |||
</pre>}} | |||
== Calculate the vibrational frequencies (normal modes/phonons) == | == Calculate the vibrational frequencies (normal modes/phonons) == | ||
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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. | 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> | |||
-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 | |||
</pre>}} | |||
== phonon information == | == phonon information == | ||
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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. | 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 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 | |||
</pre>}} | |||
== Spectra Data == | |||
{{FileBox|filename=zno.dm.out|title=(Section of file 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 | |||
}} | |||
Revision as of 15:08, 3 January 2017
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 pw.x
- Calculate the vibrational frequencies (normal modes/phonons) with ph.x
- Extract the phonon information from ph.x output using dynmat.x
- Parse the dynmat.x output section that contains the spectra data and plot it with gnuplot
Important
The initial setup must be completed before continuing.
The initial setup must be completed before continuing.
Prepare Example Directory
First, make sure we are at the root of our home directory
user $cdNow, make an example directory, and copy the ellipse example directory into it.
user $mkdir examplesuser $cp -r /home/bgo/shared/examples/qe/ZnO examples/user $cd examples/ZnOuser $lsO.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 ellipse example directory.
user $cp /home/bgo/shared/samples/torque-qe.sh .user $lsO.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
Perform Self Consistent Field (scf) calculation
Quantum Espresso module to pw.c
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.shuser $qstatJob 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 -lhtotal 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)
Modify Queue Submission Script
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
The job is now ready to be sent to the cluster.
user $qsub torque-lmp.shuser $qstatJob ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 14222.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
Modify Queue Submission Script
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.shuser $qstatJob ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 14222.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 -lhtotal 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(Section of file 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