Dear Iurii and Paolo,
Thank you so much for all the advice! It works for me now. And I’ve tested a bit to see which factor matters: 1. I used Iurii’s input, it works well using QE 6.4.1, but would crash using QE 6.4 (not sure if this is because a compilation issue as I just used the module on the cluster) 2. I verified each different parameters using QE 6.4.1 (add/remove nbnd, change ecutwfc/ecutrho ratio, conv_thr and add ‘’ for outdir), and found ecutwfc/ecutrho is the reason for my previous crash. 3. I set the occupations to be “fixed” because I want to calculate dielectric constant, it seems the ph.x program will complain if I use “smearing”, even if it converges to an insulating state. Thank you! Shenli -- Shenli Zhang Postdoc Pritzker School of Molecular Engineering The University of Chicago 5640 South Ellis Avenue, Chicago, IL 60637 From: users <users-boun...@lists.quantum-espresso.org> on behalf of Timrov Iurii <iurii.tim...@epfl.ch> Reply-To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> Date: Wednesday, November 13, 2019 at 4:54 AM To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> Subject: Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1) Dear Shenli and Paolo, I changed a bit the input for PW and PH and it did not crash for me (only at the very end, for some reason). I used QE 6.4.1, 8 cores, ifort 15.0.2 20150121. The input and output files are here (available temporary): https://drive.google.com/open?id=1Z4fSndJZPcK_A5PVa3hMsft8IGqXWHZB For reference, I show here only the input files: &control calculation='scf', restart_mode='from_scratch', prefix='LCO' pseudo_dir = '/scratch/timrov/q-e-qe-6.4.1/pseudo/', outdir='/scratch/timrov/q-e-qe-6.4.1/tempdir/' / &system ibrav = -5, celldm(1) = 10.1352, celldm(4) = 0.47876847, nat = 10, ntyp = 3, ecutwfc = 40.0 ecutrho = 320.0 occupations='fixed' lda_plus_u = .true., lda_plus_u_kind = 0, U_projection_type = 'atomic', Hubbard_U(2) = 3.0 / &electrons conv_thr = 1.d-14 mixing_beta = 0.7 / ATOMIC_SPECIES La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF Co 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF O 16 O.pbe-n-kjpaw_psl.1.0.0.UPF ATOMIC_POSITIONS {crystal} O 0.312627155 0.750000000 0.187372845 O 0.750000000 0.187372845 0.312627155 O 0.187372845 0.312627155 0.750000000 O 0.687372845 0.250000000 0.812627155 O 0.812627155 0.687372845 0.250000000 O 0.250000000 0.812627155 0.687372845 Co 0.000000000 0.000000000 0.000000000 Co 0.500000000 0.500000000 0.500000000 La 0.250000000 0.250000000 0.250000000 La 0.750000000 0.750000000 0.750000000 K_POINTS {automatic} 4 4 4 0 0 0 phonons of LCO at Gamma &inputph prefix = 'LCO', outdir='/scratch/timrov/q-e-qe-6.4.1/tempdir/', tr2_ph = 1.0d-14, epsil = .true. fildyn='LCO.dynG', / 0.000000000000000 0.000000000000000 0.000000000000000 Shenli: Could you try please to use exactly the same inputs as me with QE 6.4.1 and see what happens? Paolo: I do not know what to say why you obtain NaN's... Do you use exactly the same input as Shenli? Greetings, Iurii -- Dr. Iurii Timrov Postdoctoral Researcher STI - IMX - THEOS and NCCR - MARVEL Swiss Federal Institute of Technology Lausanne (EPFL) CH-1015 Lausanne, Switzerland +41 21 69 34 881 http://people.epfl.ch/265334 ________________________________ From: users <users-boun...@lists.quantum-espresso.org> on behalf of Paolo Giannozzi <p.gianno...@gmail.com> Sent: Wednesday, November 13, 2019 11:13:09 AM To: Quantum ESPRESSO users Forum Subject: Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1) It doesn't segfaults for me but it produces NaN's. Note that: - SCF convergence with fixed occupancies is very bad. I started from the charge density and wavefunctions obtained with smearing. - outdir='rhomb_U3', between ' ' Paolo On Tue, Nov 12, 2019 at 10:52 PM Shenli Zhang <shlzh...@uchicago.edu<mailto:shlzh...@uchicago.edu>> wrote: Dear Iurii, Thank you so much for your reply. The output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred” is not in the output file of ph.x, but is in the output file generated by the slurm system, which is a job scheduler for the cluster I use. In the ph.x output, there is no error message, but the program just stopped in the line “Calculating the dnsorth_cart matrix…” I double checked the memory setting, it doesn’t seem to be the problem here. As I’ve increased the number of CPUs used to the point where I could actually run DFPT+U on an orthorhombic supercell of the same system. And thanks for the advice on the parameter settings. I reduced the ecutrho/ecutwfc here in order to do a quick test. I tried the ultrasoft pseudopotentials, and the error still persists. And yes my system is a nonmagnetic insulator and the scf calculation converged successfully. The reason I think this error is probably due to the unit cell shape is because I also created an orthorhombic supercell of the same system with the same parameter settings, and I could run the DFPT+U without any problem. Regards, Shenli -- Shenli Zhang Postdoc Pritzker School of Molecular Engineering The University of Chicago 5640 South Ellis Avenue, Chicago, IL 60637 From: users <users-boun...@lists.quantum-espresso.org<mailto:users-boun...@lists.quantum-espresso.org>> on behalf of Timrov Iurii <iurii.tim...@epfl.ch<mailto:iurii.tim...@epfl.ch>> Reply-To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org>> Date: Tuesday, November 12, 2019 at 11:31 AM To: "users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org>" <users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org>> Subject: Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1) Dear Shenli Zhang, > with an output error “forrtl: severe (174): SIGSEGV, segmentation fault > occurred” Was is printed in the output file of the PHonon calculation after the crash? Check if you have enough RAM to run DFPT+U, because it is heavy. Your input for a PW SCF calculation has some problem: - ecutrho/ecutwfc = 4 - this is true for norm-conserving pseudopotentials. But you are using PAW, for which the ratio should be 8 or more. Try to use DFPT+U with ultrasoft pseudopotentials (the ratio should be also 8 or more). - nbnd=50 - this is not needed: just remove it from the input file - occupations='fixed' : is your system a nonmagnetic insulator? Did your PW SCF calculation converged successfully? - conv_thr=1.0d-12 : I suggest to try conv_thr=1.0d-14 if you plan to compute phonons afterwards. HTH Regards, Iurii -- Dr. Iurii Timrov Postdoctoral Researcher STI - IMX - THEOS and NCCR - MARVEL Swiss Federal Institute of Technology Lausanne (EPFL) CH-1015 Lausanne, Switzerland +41 21 69 34 881 http://people.epfl.ch/265334 ________________________________ From: users <users-boun...@lists.quantum-espresso.org<mailto:users-boun...@lists.quantum-espresso.org>> on behalf of Shenli Zhang <shlzh...@uchicago.edu<mailto:shlzh...@uchicago.edu>> Sent: Tuesday, November 12, 2019 5:57:47 PM To: users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> Subject: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1) Dear all, I’m testing phonon calculations using ph.x with DFPT+U in QE 6.4 and QE 6.4.1, however the calculation always stops at the line “Calculating the dnsorth_cart matrix…” with an output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred” I ran my system without U successfully. And I also ran the LiCoO2 +U example successfully. The only difference I can think of between my input file and the example file is the unit cell shape, where my LaCoO3 system has a rhombohedral unit cell and the example LiCoO2 has an orthorhombic one. Could this be a problem or did I make some mistakes? Attached are the input files for my system LCO. Thank you! SCF calculation input: &control calculation='scf' prefix='LaCoO3p_relax' outdir=rhomb_U3 pseudo_dir = '/home/shlzhang/QE_simulation/LaCoO3/pseudo', / &system nbnd=50 ibrav=-5, celldm(1)=10.1352, celldm(4) =0.47876847, nat=10, ntyp= 3, ecutwfc =90, ecutrho =360, !for PAW ecutrho=4*ecutwfc, but need test occupations='fixed' !energy units in Ry lda_plus_u=.true. Hubbard_U(2)=3 / &electrons conv_thr=1.0d-12 / &ions / &cell !cell_dofree='shape' / ATOMIC_SPECIES La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF Co 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF O 16 O.pbe-n-kjpaw_psl.1.0.0.UPF ATOMIC_POSITIONS (crystal) O 0.312627155 0.750000000 0.187372845 O 0.750000000 0.187372845 0.312627155 O 0.187372845 0.312627155 0.750000000 O 0.687372845 0.250000000 0.812627155 O 0.812627155 0.687372845 0.250000000 O 0.250000000 0.812627155 0.687372845 Co -0.000000000 0.000000000 -0.000000000 Co 0.500000000 0.500000000 0.500000000 La 0.250000000 0.250000000 0.250000000 La 0.750000000 0.750000000 0.750000000 K_POINTS automatic 4 4 4 0 0 0 Phonon calculation input: phonons of bulk LaCoO3 at Gamma &inputph prefix='LaCoO3p_relax' outdir=rhomb_U3 fildyn='LaCoO3.dyn' max_seconds=82800 tr2_ph=1.0d-14 verbosity='debug' amass(1)=138.9055 amass(2)=58.9332 amass(3)=16 epsil=.true. trans=.true. / 0.00000000000 0.000000000000 0.000000000000000 -- Shenli Zhang Postdoc Pritzker School of Molecular Engineering The University of Chicago 5640 South Ellis Avenue, Chicago, IL 60637 _______________________________________________ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>) users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
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