[QE-users] Error in Calculating the d2ns_bare matrix in ph.x

Mohad Abbasnejad mohaddeseh.abbasnejad at gmail.com
Sat Oct 3 08:24:42 CEST 2020


Thank you Dear Timrov for your reply

I am using QE 6.4,  96 cores with 2 nods. This is my scf and ph input:


&control
 calculation='scf',
 verbosity = 'low',
 restart_mode = 'from_scratch',
 prefix = 'structure',
 tstress = .true.,
 tprnfor = .true.,
 forc_conv_thr = 1.0D-4,
    pseudo_dir ='./',
    outdir='./',
 nstep=3000,
 wf_collect=.true.
/

&SYSTEM
 ibrav=0,
 nat=16,
 ntyp=4,
 ecutwfc=54,
 ecutrho=540,
 occupations='smearing',
 degauss=0.002,
 smearing='mv',
 lda_plus_u=.true.,
 hubbard_u(1)=0.8,
 hubbard_u(2)=0.8,
 hubbard_u(3)=0.8,
 nspin=2, starting_magnetization(1)=-0.25 ,starting_magnetization(2)=0.5,
starting_magnetization(3)=-0.25,

/
&electrons
 diagonalization='cg',
 mixing_mode = 'plain',
 mixing_beta = 0.4,
 conv_thr =  1.0d-6,
 electron_maxstep=600
/
&IONS
 ion_dynamics  = 'bfgs',
/
&cell
 cell_dynamics = 'bfgs',
/

ATOMIC_SPECIES
 Ti1  47.867    Ti.pbe-sp-van_ak.UPF
 Ti2  47.867    Ti.pbe-sp-van_ak.UPF
 Ti3  47.867    Ti.pbe-sp-van_ak.UPF
 O   15.9994   O.pbe-van_ak.UPF

K_POINTS {automatic}
6 6 6 0 0 0

CELL_PARAMETERS (bohr)
  10.111134720  -4.796028450   0.354034142
  10.111109901   4.795974443   0.354015885
  -4.375766517  -0.000014854  14.056013806

ATOMIC_POSITIONS (crystal)
Ti3      0.741339363   0.966762327   0.108086076
Ti3      0.258660637   0.033237673   0.891913924
Ti1      0.033235159   0.258661350   0.391913045
Ti1      0.966764841   0.741338650   0.608086955
Ti2      0.500000000   0.500000000  -0.000000000
Ti2      0.500000000   0.500000000   0.500000000
O        0.859056256   0.497199239   0.608571821
O        0.140943744   0.502800761   0.391428179
O        0.502800036   0.140945565   0.891430700
O        0.497199964   0.859054435   0.108569300
O        0.294040535   0.896343128   0.451238915
O        0.705959465   0.103656872   0.548761085
O        0.103655829   0.705960410   1.048758989
O        0.896344171   0.294039590  -0.048758989
O        0.681593682   0.318406936   0.249999781
O        0.318406318   0.681593064   0.750000219


and phinput file as follow:

Electron-phonon coefficients for structure
 &inputph
  tr2_ph=1.0d-14,
  prefix = 'structure',
  outdir='./',
  fildyn='structure.dyn',
  alpha_mix(1)=0.1,
  trans=.true.,
  ldisp=.true.
  recover=.true.,
  nq1=2, nq2=2, nq3=2
 /

Best regards
Mohaddeseh



On Fri, Oct 2, 2020 at 11:27 AM Timrov Iurii <iurii.timrov at epfl.ch> wrote:

> Dear Mohaddeseh,
>
>
> Please check the posting guidelines:
>
> https://www.quantum-espresso.org/forum
>
>
> In particular, you should tell us which version of QE do you use, provide
> input and output files (e.g. via Google Drive), tell us how do you run the
> job (how many cores, how many k pools, etc.), which compilers and libraries
> do you use.
>
>
> But my guess is that your job crashes because you do not have enough RAM.
>
>
> 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-bounces at lists.quantum-espresso.org> on behalf of
> Mohad Abbasnejad <mohaddeseh.abbasnejad at gmail.com>
> *Sent:* Thursday, October 1, 2020 9:03:12 PM
> *To:* Quantum ESPRESSO users Forum
> *Subject:* [QE-users] Error in Calculating the d2ns_bare matrix in ph.x
>
> Hello QE users
> When I am trying to calculate the d2ns_bare matrix for LDA+U phonon
> calculation of my structure, I am faced with this error:
>
>      Calculating the d2ns_bare matrix. It might take a while!
>      k point #     1   out of   224
>      k point #     2   out of   224
>      k point #     3   out of   224
>      k point #     4   out of   224
>      k point #     5   out of   224
>      k point #     6   out of   224
>      k point #     7   out of   224
>      k point #     8   out of   224
>      k point #     9   out of   224
>      k point #    10   out of   224
>      k point #    11   out of   224
>      k point #    12   out of   224
>      k point #    13   out of   224
>      k point #    14   out of   224
>      k point #    15   out of   224
>      k point #    16   out of   224
>      k point #    17   out of   224
>      k point #    18   out of   224
>      k point #    19   out of   224
>      k point #    20   out of   224
>      k point #    21   out of   224
>      k point #    22   out of   224
>      k point #    23   out of   224
>      k point #    24   out of   224
>      k point #    25   out of   224
>      k point #    26   out of   224
>      k point #    27   out of   224
>      k point #    28   out of   224
>      k point #    29   out of   224
>      k point #    30   out of   224
>      k point #    31   out of   224
>      k point #    32   out of   224
>      k point #    33   out of   224
>      k point #    34   out of   224
>      k point #    35   out of   224
>      k point #    36   out of   224
>      k point #    37   out of   224
>      k point #    38   out of   224
>      k point #    39   out of   224
>      k point #    40   out of   224
>      k point #    41   out of   224
>      k point #    42   out of   224
>      k point #    43   out of   224
>      k point #    44   out of   224
>      k point #    45   out of   224
>      k point #    46   out of   224
>      k point #    47   out of   224
>      k point #    48   out of   224
>      k point #    49   out of   224
>      k point #    50   out of   224
>      k point #    51   out of   224
>      k point #    52   out of   224
>      k point #    53   out of   224
>      k point #    54   out of   224
>      k point #    55   out of   224
>      k point #    56   out of   224
>      k point #    57   out of   224
>      k point #    58   out of   224
>      k point #    59   out of   224
>      k point #    60   out of   224
>      k point #    61   out of   224
>      k point #    62   out of   224
>      k point #    63   out of   224
>      k point #    64   out of   224
>      k point #    65   out of   224
>      k point #    66   out of   224
>      k point #    67   out of   224
>      k point #    68   out of   224
>      k point #    69   out of   224
>      k point #    70   out of   224
>      k point #    71   out of   224
>      k point #    72   out of   224
>      k point #    73   out of   224
>      k point #    74   out of   224
>      k point #    75   out of   224
>      k point #    76   out of   224
>      k point #    77   out of   224
>      k point #    78   out of   224
>      k point #    79   out of   224
>      k point #    80   out of   224
>      k point #    81   out of   224
>      k point #    82   out of   224
>      k point #    83   out of   224
>      k point #    84   out of   224
>      k point #    85   out of   224
>      k point #    86   out of   224
>      k point #    87   out of   224
>      k point #    88   out of   224
>      k point #    89   out of   224
>      k point #    90   out of   224
> Application 2461263 exit codes: 174
> Application 2461263 exit signals: Killed
> Application 2461263 resources: utime ~48102s, stime ~486s, Rss ~326644,
> inblocks ~0, outblocks ~183880
>
> Any comments would be appreciated.
>
> Thank you in advance.
> Mohaddeseh
>
>
> --
> ---------------------------------------------------------
> Mohaddeseh Abbasnejad,
> Assistant Professor of Physics,
> Faculty of Physics,
> Shahid Bahonar University of Kerman,
> Kerman, Iran
> P.O. Box 76169-133
> Tel: +98 34 31322199
> Fax: +98 34 33257434
> Cellphone: +98 917 731 7514
> E-Mail:     mohaddeseh.abbasnejad at gmail.com
> Website:  academicstaff.uk.ac.ir/moabbasnejad
> ---------------------------------------------------------
>
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-- 
---------------------------------------------------------
Mohaddeseh Abbasnejad,
Assistant Professor of Physics,
Faculty of Physics,
Shahid Bahonar University of Kerman,
Kerman, Iran
P.O. Box 76169-133
Tel: +98 34 31322199
Fax: +98 34 33257434
Cellphone: +98 917 731 7514
E-Mail:     mohaddeseh.abbasnejad at gmail.com
Website:  academicstaff.uk.ac.ir/moabbasnejad
---------------------------------------------------------
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