[QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)

Wed Nov 13 11:13:09 CET 2019

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 <shlzhang at 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-bounces at lists.quantum-espresso.org> on behalf of
> Timrov Iurii <iurii.timrov at epfl.ch>
> *Reply-To: *Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org
> >
> *Date: *Tuesday, November 12, 2019 at 11:31 AM
> *To: *"users at lists.quantum-espresso.org" <users at 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-bounces at lists.quantum-espresso.org> on behalf of
> Shenli Zhang <shlzhang at uchicago.edu>
> *Sent:* Tuesday, November 12, 2019 5:57:47 PM
> *To:* users at 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
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-- 
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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