[QE-users] Phonon calculations with different parallelization
Dear All, My Phonon calculations provide different frequency values for different parallelization on the cluster especially for the total number of processors used. Is it possible or I am doing something very wrong? As vibrational frequency is gauge invariat how it can be possible? Thanks, Chirantan ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Phonon calculation does not converge
Hello Lorenzo Paulatto and Nicola Marzari, I performed relax and scf both with the prescribed cutoff as discussed in the previous mail and now I am running phonon. I am trying to increase the 'nmix_ph' to 16 as I have more memory available in the server, but the error says, 'Error in routine phq_readin (1): Wrong nmix_ph'. I checked online where 'https://lists.quantum-espresso.org/pipermail/users/2015-October/033664.html' Prof. Paolo Giannozzi said to keep it below 5, but in 2015. So what is going on? Please help, I never included nmix_ph before, but using more memory and speeding up the phonon calculation will help me a lot. Regards, Chirantan From: users on behalf of Lorenzo Paulatto Sent: Tuesday, January 23, 2024 10:02 AM To: users@lists.quantum-espresso.org Subject: Re: [QE-users] Phonon calculation does not converge The calculation is not only not converging, it is actually diverging. Changing alpha_mix and increasing nmix_ph can help, but it may also indicate something wrong with the calculation. I.e. a metal treated as semiconductor, or a ghost in the pseudopotential (which may be likely if you use norm-conservig cutoff with an ultrasoft dataset) hth On 1/23/24 08:47, Chirantan Pramanik wrote: Hello All, I was running Phonon for a few systems of carbonate minerals for a long time. Recently I used SSSP pseudopotential for PBE and faced a problem like the one pasted below. Optimization and SCF calculations are properly done. But phonon calculation is not converging. Please help. I think changing alpha_mix can be useful, but for my stable and optimized system, it should converge easily. section from ph.x output: iter # 97 total cpu time : 1799.1 secs av.it.: 84.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 1.595E+08 iter # 98 total cpu time : 1822.7 secs av.it.: 92.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 3.870E+10 iter # 99 total cpu time : 1846.5 secs av.it.: 92.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 4.585E+10 iter # 100 total cpu time : 1869.3 secs av.it.: 88.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 5.897E+09 End of self-consistent calculation No convergence has been achieved Please help in this regard. Thanks and Regards, Chirantan Chirantan Pramanik Postdoctoral Researcher Dept. of Earth and Planetary Sciences Weizmann Institute of Science Rehovot, Israel ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu>) users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users -- Dr. Lorenzo Paulatto IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université phone: +33 (0)1 442 79822 / skype: paulatz http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/ 23-24/423 B115, 4 place Jussieu 75252 Paris CX 05 ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Issues with vc-relax for a slab
If vc-relax is applicable for surface optimization then increasing
electron_maxstep should help. I needed electron_maxstep even around 2000 for
some calculations. But did you previously optimise surface using vc-relax?
Chirantan Pramanik
Postdoctoral fellow,
EPS, Weizmann Institute of Science
Israel
From: users on behalf of Anupriya
Nyayban
Sent: Friday, January 26, 2024 12:44:35 PM
To: users@lists.quantum-espresso.org
Subject: Re: [QE-users] Issues with vc-relax for a slab
Dear users and experts,
I have considered a (311) plane of 2 layers of ZnFe2O4 structure. The attached
input file is for the vc-relax calculation.
calculation='vc-relax'
restart_mode='from_scratch',
prefix='zn'
pseudo_dir = '.'
outdir='tmp'
verbosity='high'
etot_conv_thr = 1.0D-5
forc_conv_thr = 1.0D-4
/
ibrav = 0
A = 21.62370
nat = 112
ntyp = 3
ecutwfc = 30.0,
ecutrho = 240.0,
occupations = 'smearing',
smearing = 'mv',
degauss = 0.02,
vdw_corr = 'DFT-D3'
/
conv_thr = 1.d-9
mixing_beta = 0.3
electron_maxstep = 300
startingpot = "atomic"
startingwfc = "atomic+random"
/
ion_dynamics = "bfgs"
/
cell_dynamics = "bfgs"
press_conv_thr = 5.0e-01
/
CELL_PARAMETERS {alat}
1.000 0.000 0.000
0.29977738132 0.331662474918549 0.000
0.000 0.000 2.019068156482969
ATOMIC_SPECIES
Zn 65.38000 Zn_ONCV_PBE-1.0.upf
Fe 55.84500 Fe_ONCV_PBE-1.0.upf
O 15.99900 O_ONCV_PBE-1.0.upf
ATOMIC_POSITIONS {crystal}
Zn 0.8636360 0.9545450 0.4757970
Zn 0.8636360 0.4545450 0.4757970
Zn 0.3636360 0.4545450 0.4757970
Zn 0.3636360 0.9545450 0.4757970
Zn 0.5454540 0.1818190 0.4876030
Zn 0.0454550 0.1818180 0.4876030
Zn 0.0454550 0.6818180 0.4876030
Zn 0.5454550 0.6818180 0.4876020
Zn 0.5909090 0.8636360 0.5230200
Zn 0.5909090 0.3636360 0.5230200
Zn 0.0909090 0.3636360 0.5230200
Zn 0.0909090 0.8636360 0.5230200
Zn 0.2727270 0.0909090 0.5348250
Zn 0.7727270 0.0909090 0.5348260
Zn 0.7727270 0.5909090 0.5348260
Zn 0.2727270 0.5909090 0.5348250
Fe 0.9545460 0.0681820 0.4817000
Fe 0.7045450 0.3181820 0.4817000
Fe 0.2045460 0.5681820 0.4817000
Fe 0.5909090 0.8636360 0.4580880
Fe 0.2045460 0.8181810 0.4817000
Fe 0.7045450 0.5681820 0.4817000
Fe 0.5909090 0.3636360 0.4580880
Fe 0.9545450 0.5681820 0.4817000
Fe 0.7045460 0.8181820 0.4817000
Fe 0.2045450 0.0681820 0.4817000
Fe 0.2045450 0.3181820 0.4817000
Fe 0.7045460 0.0681810 0.4817000
Fe 0.4545450 0.0681820 0.4817000
Fe 0.0909090 0.8636370 0.4580880
Fe 0.0909090 0.3636360 0.4580880
Fe 0.4545450 0.5681820 0.4817000
Fe 0.6818180 0.9772720 0.5289220
Fe 0.4318180 0.2272730 0.5289220
Fe 0.9318180 0.4772730 0.5289230
Fe 0.3181820 0.7727270 0.5053110
Fe 0.9318180 0.7272720 0.5289230
Fe 0.4318180 0.4772730 0.5289220
Fe 0.3181820 0.2727270 0.5053110
Fe 0.6818180 0.4772730 0.5289230
Fe 0.4318180 0.7272730 0.5289230
Fe 0.9318180 0.9772730 0.5289230
Fe 0.9318180 0.2272730 0.5289230
Fe 0.4318180 0.9772720 0.5289230
Fe 0.1818180 0.9772730 0.5289230
Fe 0.8181820 0.7727280 0.5053110
Fe 0.8181820 0.2727270 0.5053110
Fe 0.1818180 0.4772730 0.5289230
O 0.0212080 0.3515410 0.4687100
O 0.6424390 0.0363410 0.4939000
O 0.2696900 0.8454660 0.4718660
O 0.5212080 0.5848340 0.4687110
O 0.5212080 0.0848340 0.4687100
O 0.0212080
Re: [QE-users] Phonon calculation does not converge
I am using SSSP Precision (version 1.3.0). Thank you for the details, I was using cutoff_wfc= 60 but the table says 75 Ry for O which is the highest among all the atoms in my system. I am rerunning the relax calculations. I chose 60 for O checking the corresponding convergence tests for O.pbe-n-kjpaw_psl.0.3.1.UPF but now I notice that the O pseudopotential file is O.pbe-n-kjpaw_psl.0.1.UPF (which seems not tested in the link: https://www.materialscloud.org/discover/sssp/plot/precision/O). Are they the same? Also, SSSP precision pseudopotential files are different types across the elements. For example, O and C are paw, Ca is ussp. I was curious about the combinations for any material as I was using BURAI previously which would notify if the types of pseudopotentials are different. Thanks, Chirantan Pramanik From: users on behalf of Nicola Marzari via users Sent: Tuesday, January 23, 2024 10:09 AM To: Quantum ESPRESSO users Forum Subject: Re: [QE-users] Phonon calculation does not converge Out of curiosity, wouldn’t a low cutoff (not that one should use it) miss a ghost state (that is very localized)? In passing, sssp pseudos are tested re not having ghosts, and have default suggested cutoffs. Just make sure you use the latest version 1.3 Nicola Sent from a tiny keyboard... Contact info: http://theossrv1.epfl.ch/Main/Contact On 23 Jan 2024, at 09:02, Lorenzo Paulatto wrote: The calculation is not only not converging, it is actually diverging. Changing alpha_mix and increasing nmix_ph can help, but it may also indicate something wrong with the calculation. I.e. a metal treated as semiconductor, or a ghost in the pseudopotential (which may be likely if you use norm-conservig cutoff with an ultrasoft dataset) hth On 1/23/24 08:47, Chirantan Pramanik wrote: Hello All, I was running Phonon for a few systems of carbonate minerals for a long time. Recently I used SSSP pseudopotential for PBE and faced a problem like the one pasted below. Optimization and SCF calculations are properly done. But phonon calculation is not converging. Please help. I think changing alpha_mix can be useful, but for my stable and optimized system, it should converge easily. section from ph.x output: iter # 97 total cpu time : 1799.1 secs av.it.: 84.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 1.595E+08 iter # 98 total cpu time : 1822.7 secs av.it.: 92.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 3.870E+10 iter # 99 total cpu time : 1846.5 secs av.it.: 92.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 4.585E+10 iter # 100 total cpu time : 1869.3 secs av.it.: 88.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 5.897E+09 End of self-consistent calculation No convergence has been achieved Please help in this regard. Thanks and Regards, Chirantan Chirantan Pramanik Postdoctoral Researcher Dept. of Earth and Planetary Sciences Weizmann Institute of Science Rehovot, Israel ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu<http://www.max-centre.eu>) users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users -- Dr. Lorenzo Paulatto IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université phone: +33 (0)1 442 79822 / skype: paulatz http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/ 23-24/423 B115, 4 place Jussieu 75252 Paris CX 05 ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Phonon calculation does not converge
Hello All, I was running Phonon for a few systems of carbonate minerals for a long time. Recently I used SSSP pseudopotential for PBE and faced a problem like the one pasted below. Optimization and SCF calculations are properly done. But phonon calculation is not converging. Please help. I think changing alpha_mix can be useful, but for my stable and optimized system, it should converge easily. section from ph.x output: iter # 97 total cpu time : 1799.1 secs av.it.: 84.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 1.595E+08 iter # 98 total cpu time : 1822.7 secs av.it.: 92.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 3.870E+10 iter # 99 total cpu time : 1846.5 secs av.it.: 92.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 4.585E+10 iter # 100 total cpu time : 1869.3 secs av.it.: 88.0 thresh= 1.000E-02 alpha_mix = 0.700 |ddv_scf|^2 = 5.897E+09 End of self-consistent calculation No convergence has been achieved Please help in this regard. Thanks and Regards, Chirantan Chirantan Pramanik Postdoctoral Researcher Dept. of Earth and Planetary Sciences Weizmann Institute of Science Rehovot, Israel ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Can not perform multiple optimization calculations
Hi All, I am using QE for 1.5 years and calculating phonon frequencies for isotopic molecules. I am using a server in my Institute and I am running jobs in parallel with mpi enabled through qsub using PBS job scripts. The problem is when I run multiple optimization jobs for pw.x only one of them completes and others stop in between at random places without finishing. This problem does not occur in phonon calculation jobs in ph.x code. Please help me to understand the problem. My cluster admin told me that two jobs are interfering but why this is occurring only with optimization jobs? one pbs script is attached below. #!/bin/bash #PBS -N opt #PBS -l select=4:ncpus=24:mem=120GB #PBS -q long #PBS -S /bin/bash #PBS -V mpirun -np 96 '/home/pramanik/qe-6.7/bin/pw.x' /work/pramanik/c332pbesolvc.out Thanks, Chirantan Chirantan Pramanik Postdoctoral Researcher Dept. of Earth and Planetary Sciences Weizmann Institute of Science Rehovot, Israel ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
