ZnO (Quantum ESPRESSO)
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
Initial Setup
We need to complete the initial setup tutorial first, to be sure that the GNU Compiler Collection, and Open MPI will be used for our simulations.
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 ZnO 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 ZnO 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:
torque-qe.sh#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.
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:
- zno.scf.qei
- zno.ph.qei
- zno.dm.qei
All three have a 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 pw.x; ph for ph.x; and dm for dynmat.x.
Pseudopotentials
Quantum ESPRESSO requires a pseudopotential for each atom in the system to be studied, for this example (ZnO) they are:
- O.pw-mt_fhi.UPF
- Zn.pw-mt_fhi.UPF
These files were downloaded from the Quantum ESPRESSO pseudopotentials repository.
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:
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_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.
user $qsub torque-qe.shuser $qstatJob ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 14589.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 -ltotal 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
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, myoutput.txt should look similar to this:
myoutput.txt-------------- 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 ph.x module of Quantum ESPRESSO to calculate the vibrational 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:
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_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:
user $qsub torque-qe.shuser $qstatJob ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 14590.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 -lhtotal 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
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 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 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:
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_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.
user $qsub torque-qe.shuser $qstatJob ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 14592.flory ZnO-dynmat 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 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
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 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
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