[Pw_forum] How to deal with the error (bad termination exit code: 9) in phonon calculation?

liyincumt at gmail.com liyincumt at gmail.com
Thu May 28 09:42:13 CEST 2015


Dear QE developers,
I am trying to calculate the IR spectrum of a compound. First, I run ‘relax’ calculation and got a successful convergence. After that, I started a phonon calculation. I always got the error (bad termination exit code: 9). What does this “9” mean? How could I deal with it? 
Thanks a lot in advance!

Below are my input files.
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
&CONTROL
                       title = 'data_7107445-arginine' ,
                 calculation = 'relax' ,
                      outdir = '/home/calc/pwscf_calc' ,
                      wfcdir = '/home/calc/pwscf_calc' ,
                  pseudo_dir = '/home/calc/espresso-5.1.1/pseudo/' ,
                      prefix = 'data_7107445-arginine' ,
               etot_conv_thr = 5.0d-7 ,
               forc_conv_thr = 5.0d-4 ,
 /
 &SYSTEM
                       ibrav = -12,
                   celldm(1) = 18.437112,
                   celldm(2) = 1.64229,
                   celldm(3) = 0.571978,
                   celldm(5) = -0.1391731,
                         nat = 52,
                        ntyp = 4,
                     ecutwfc = 60 ,
                     ecutrho = 600 ,
 /
 &ELECTRONS
                    conv_thr = 1.0d-8 ,
                 mixing_beta = 0.7 ,
             diagonalization = 'david' ,
 /
 &IONS
                ion_dynamics = 'bfgs' ,
 /
ATOMIC_SPECIES
    H    1.00794  H.pbe-rrkjus.UPF 
    C   12.01070  C.pbe-rrkjus.UPF 
    N   14.00670  N.pbe-rrkjus.UPF 
    O   15.99940  O.pbe-rrkjus.UPF 
ATOMIC_POSITIONS alat 
    O      0.006300000    0.868200000   -0.013020000    
    O      0.227050000    0.848140000    0.009000000    
    C      0.113660000    0.830180000    0.075430000    
    N     -0.033250000    0.760590000    0.333950000    
    H     -0.054180000    0.815120000    0.399610000    
    H     -0.037610000    0.717490000    0.457260000    
    H      0.174350000    0.773830000    0.406070000    
    C      0.106340000    0.762260000    0.263410000    
    H      0.213720000    0.684400000    0.060870000    
    H      0.164840000    0.638380000    0.288880000    
    C      0.137820000    0.678170000    0.157380000    
    H     -0.057580000    0.626040000    0.098650000    
    H     -0.031440000    0.691400000   -0.106990000    
    C      0.009770000    0.646120000   -0.002820000    
    C      0.050230000    0.574960000   -0.158890000    
    H      0.112570000    0.595930000   -0.268380000    
    H      0.097240000    0.531350000   -0.055010000    
    N     -0.075080000    0.540090000   -0.301670000    
    H     -0.166460000    0.552870000   -0.257220000    
    C     -0.064600000    0.493230000   -0.493500000    
    N      0.058320000    0.475550000   -0.553220000    
    H      0.142080000    0.497130000   -0.455420000    
    H      0.065820000    0.440830000   -0.695370000    
    N     -0.177240000    0.464120000   -0.625370000    
    H     -0.268580000    0.477200000   -0.581240000    
    H     -0.169570000    0.429410000   -0.767470000    
    O      0.463600000   -0.043890000    0.555130000    
    O      0.676180000   -0.009900000    0.529510000    
    C      0.549490000   -0.001970000    0.458450000    
    N      0.351640000    0.045210000    0.173950000    
    H      0.337800000   -0.009980000    0.098730000    
    H      0.317190000    0.088270000    0.055990000    
    H      0.551850000    0.048920000    0.119150000    
    C      0.499980000    0.058530000    0.254810000    
    H      0.616920000    0.152610000    0.434850000    
    H      0.513740000    0.185840000    0.206620000    
    C      0.523500000    0.147600000    0.345010000    
    H      0.326790000    0.177670000    0.413310000    
    H      0.412360000    0.124580000    0.626920000    
    C      0.417650000    0.169790000    0.510300000    
    C      0.461390000    0.250030000    0.645100000    
    H      0.550340000    0.241340000    0.747570000    
    H      0.470870000    0.294590000    0.528260000    
    N      0.356090000    0.273940000    0.797270000    
    H      0.266500000    0.245270000    0.778340000    
    C      0.384690000    0.331760000    0.966840000    
    N      0.285130000    0.362190000    1.078710000    
    H      0.189970000    0.342050000    1.036490000    
    H      0.306350000    0.404930000    1.204040000    
    N      0.512780000    0.359050000    1.024210000    
    H      0.586910000    0.336560000    0.941400000    
    H      0.533710000    0.401790000    1.149600000    
K_POINTS automatic 
  1 1 2   0 0 0
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
normal modes for 7107445-arginine
 &inputph
  recover=.true.,
  prefix='data_7107445-arginine',
  epsil=.true.,
  fildyn='dmat.arginine',
  tr2_ph=1.0d-14,
  amass(1)=1.00794,
  amass(2)=12.01070,
  amass(3)=14.00670,
  amass(4)=15.99940,
  outdir='/home/calc/pwscf_calc/relax/60-1,1,2'
 /
0.0   0.0 0.0

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
 
     Program PHONON v.5.1.1 starts on 27May2015 at 22:28:35 
 
     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org", 
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/quote
 
     Parallel version (MPI), running on     8 processors
     R & G space division:  proc/nbgrp/npool/nimage =       8
 
   Info: using nr1, nr2, nr3 values from input
 
   Info: using nr1s, nr2s, nr3s values from input
 
     IMPORTANT: XC functional enforced from input :
     Exchange-correlation      =  SLA  PW   PBE  PBE ( 1  4  3  4 0 0)
     Any further DFT definition will be discarded
     Please, verify this is what you really want
 
               file H.pbe-rrkjus.UPF: wavefunction(s)  1S renormalized
               file C.pbe-rrkjus.UPF: wavefunction(s)  2S 2P renormalized
               file N.pbe-rrkjus.UPF: wavefunction(s)  2S renormalized
               file O.pbe-rrkjus.UPF: wavefunction(s)  2S renormalized
 
     Parallelization info
     --------------------
     sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
     Min        3329    1334    359               180845    45718    6414
     Max        3330    1335    360               180846    45748    6415
     Sum       26635   10675   2875              1446763   365877   51319
 
        1 /   1 q-points for this run, from  1 to  1:
       N       xq(1)         xq(2)         xq(3) 
       1   0.000000000   0.000000000   0.000000000
 
 
     Calculation of q =    0.0000000   0.0000000   0.0000000
 
     Modes are read from file 
 
                                                                                
 
     bravais-lattice index     =            0
     lattice parameter (alat)  =      18.4371  a.u.
     unit-cell volume          =    5829.8936 (a.u.)^3
     number of atoms/cell      =           52
     number of atomic types    =            4
     kinetic-energy cut-off    =      60.0000  Ry
     charge density cut-off    =     600.0000  Ry
     convergence threshold     =      1.0E-14
     beta                      =       0.7000
     number of iterations used =            4
     Exchange-correlation      =  SLA  PW   PBE  PBE ( 1  4  3  4 0 0)
 
 
     celldm(1)=   18.43711  celldm(2)=    1.64229  celldm(3)=    0.57198
     celldm(4)=    0.00000  celldm(5)=   -0.13917  celldm(6)=    0.00000
 
     crystal axes: (cart. coord. in units of alat)
               a(1) = (  1.0000  0.0000  0.0000 )  
               a(2) = (  0.0000  1.6423  0.0000 )  
               a(3) = ( -0.0796  0.0000  0.5664 )  
 
     reciprocal axes: (cart. coord. in units 2 pi/alat)
               b(1) = (  1.0000 -0.0000  0.1405 )  
               b(2) = (  0.0000  0.6089 -0.0000 )  
               b(3) = (  0.0000  0.0000  1.7655 )  
 
 
     Atoms inside the unit cell: 
 
     Cartesian axes
 
     site n.  atom      mass           positions (alat units)
        1     O   15.9994   tau(    1) = (    0.04287    1.02352    0.03591  )
        2     O   15.9994   tau(    2) = (    0.27856    1.05748    0.00573  )
        3     C   12.0107   tau(    3) = (    0.16102    1.03854    0.02000  )
        4     N   14.0067   tau(    4) = (    0.05457    0.82952    0.35665  )
        5     H    1.0079   tau(    5) = (   -0.00189    0.91286    0.33083  )
        6     H    1.0079   tau(    6) = (    0.00065    0.74562    0.32691  )
        7     H    1.0079   tau(    7) = (    0.22939    0.93655    0.28911  )
        8     C   12.0107   tau(    8) = (    0.18689    0.83358    0.30020  )
        9     H    1.0079   tau(    9) = (    0.36491    0.74203    0.22337  )
       10     H    1.0079   tau(   10) = (    0.23478    0.61920    0.27987  )
       11     C   12.0107   tau(   11) = (    0.26340    0.72571    0.26497  )
       12     H    1.0079   tau(   12) = (    0.03404    0.67233    0.12429  )
       13     H    1.0079   tau(   13) = (   -0.10300    0.73456    0.01090  )
       14     C   12.0107   tau(   14) = (   -0.06702    0.65388    0.07991  )
       15     C   12.0107   tau(   15) = (    0.05150    0.42124   -0.24709  )
       16     H    1.0079   tau(   16) = (    0.09124    0.35650   -0.33122  )
       17     H    1.0079   tau(   17) = (    0.13766    0.48411   -0.20780  )
       18     N   14.0067   tau(   18) = (   -0.06851    0.49734   -0.28771  )
       19     H    1.0079   tau(   19) = (   -0.12054    0.53991   -0.20815  )
       20     C   12.0107   tau(   20) = (   -0.09106    0.56713   -0.41457  )
       21     N   14.0067   tau(   21) = (   -0.01786    0.51128   -0.53616  )
       22     H    1.0079   tau(   22) = (    0.05755    0.44783   -0.49849  )
       23     H    1.0079   tau(   23) = (    0.10080    0.35501   -0.72741  )
       24     N   14.0067   tau(   24) = (   -0.23277    0.60277   -0.42240  )
       25     H    1.0079   tau(   25) = (   -0.25076    0.68421   -0.48467  )
       26     H    1.0079   tau(   26) = (   -0.24173    0.43287   -0.77413  )
       27     O   15.9994   tau(   27) = (    0.52609   -0.28488    0.58151  )
       28     O   15.9994   tau(   28) = (    0.72555   -0.15086    0.58742  )
       29     C   12.0107   tau(   29) = (    0.62517   -0.21713    0.58504  )
       30     N   14.0067   tau(   30) = (    0.32728   -0.06159    0.17918  )
       31     H    1.0079   tau(   31) = (    0.34645   -0.11255    0.09048  )
       32     H    1.0079   tau(   32) = (    0.26066    0.01772    0.17120  )
       33     H    1.0079   tau(   33) = (    0.50332   -0.13930    0.26726  )
       34     C   12.0107   tau(   34) = (    0.43439   -0.05106    0.27073  )
       35     H    1.0079   tau(   35) = (    0.54463    0.03755    0.42925  )
       36     H    1.0079   tau(   36) = (    0.53394    0.14565    0.12552  )
       37     C   12.0107   tau(   37) = (    0.45797    0.05127    0.35995  )
       38     H    1.0079   tau(   38) = (    0.27460    0.16552    0.31922  )
       39     H    1.0079   tau(   39) = (    0.33822    0.17909    0.48792  )
       40     C   12.0107   tau(   40) = (    0.36989    0.17453    0.37961  )
       41     C   12.0107   tau(   41) = (    0.47102    0.25697    0.69533  )
       42     H    1.0079   tau(   42) = (    0.56644    0.27561    0.75107  )
       43     H    1.0079   tau(   43) = (    0.48884    0.29636    0.59223  )
       44     N   14.0067   tau(   44) = (    0.36387    0.33856    0.75831  )
       45     H    1.0079   tau(   45) = (    0.27272    0.32935    0.70843  )
       46     C   12.0107   tau(   46) = (    0.34708    0.31974    0.90639  )
       47     N   14.0067   tau(   47) = (    0.24889    0.42293    0.95192  )
       48     H    1.0079   tau(   48) = (    0.15195    0.39305    0.92814  )
       49     H    1.0079   tau(   49) = (    0.25195    0.43263    1.05592  )
       50     N   14.0067   tau(   50) = (    0.47462    0.35078    0.97182  )
       51     H    1.0079   tau(   51) = (    0.54212    0.27211    0.97899  )
       52     H    1.0079   tau(   52) = (    0.46558    0.52213    1.25380  )
 
     Computing dynamical matrix for 
                    q = (   0.0000000   0.0000000   0.0000000 )
 
      2 Sym.Ops. (with q -> -q+G )
 
 
     G cutoff = 5166.2724  ( 180846 G-vectors)     FFT grid: (144,240, 90)
     G cutoff = 2066.5090  (  45725 G-vectors)  smooth grid: ( 96,150, 54)
     number of k points=     2
                       cart. coord. in units 2pi/alat
        k(    1) = (   0.0000000   0.0000000   0.0000000), wk =   1.0000000
        k(    2) = (   0.0000000   0.0000000  -0.8827504), wk =   1.0000000
 
     PseudoPot. # 1 for H  read from file:
     /home/calc/espresso-5.1.1/pseudo/H.pbe-rrkjus.UPF
     MD5 check sum: 7cc9d459525c9a0585f487a71c3c9563
     Pseudo is Ultrasoft, Zval =  1.0
     Generated by new atomic code, or converted to UPF format
     Using radial grid of 1061 points,  2 beta functions with: 
                l(1) =   0
                l(2) =   0
     Q(r) pseudized with 0 coefficients 
 
 
     PseudoPot. # 2 for C  read from file:
     /home/calc/espresso-5.1.1/pseudo/C.pbe-rrkjus.UPF
     MD5 check sum: 00fb224312de0c5b6853bd333518df6f
     Pseudo is Ultrasoft, Zval =  4.0
     Generated by new atomic code, or converted to UPF format
     Using radial grid of  627 points,  4 beta functions with: 
                l(1) =   0
                l(2) =   0
                l(3) =   1
                l(4) =   1
     Q(r) pseudized with 0 coefficients 
 
 
     PseudoPot. # 3 for N  read from file:
     /home/calc/espresso-5.1.1/pseudo/N.pbe-rrkjus.UPF
     MD5 check sum: 0c3fbe5807a93f9ba59d5a7019aa238b
     Pseudo is Ultrasoft, Zval =  5.0
     Generated by new atomic code, or converted to UPF format
     Using radial grid of 1257 points,  4 beta functions with: 
                l(1) =   0
                l(2) =   0
                l(3) =   1
                l(4) =   1
     Q(r) pseudized with 0 coefficients 
 
 
     PseudoPot. # 4 for O  read from file:
     /home/calc/espresso-5.1.1/pseudo/O.pbe-rrkjus.UPF
     MD5 check sum: 390ba29e75625707450f3bd3f0eb6be9
     Pseudo is Ultrasoft, Zval =  6.0
     Generated by new atomic code, or converted to UPF format
     Using radial grid of 1269 points,  4 beta functions with: 
                l(1) =   0
                l(2) =   0
                l(3) =   1
                l(4) =   1
     Q(r) pseudized with 0 coefficients 
 
 
     Mode symmetry, C_1 (1)     point group:
 
 
     Electric field:
     Dielectric constant
     Born effective charges as d Force / d E
 
 
     Atomic displacements:
     There are 156 irreducible representations
 
     Representation     1      1 modes -A  To be done
 
     Representation     2      1 modes -A  To be done
 
     Representation     3      1 modes -A  To be done
 
     Representation     4      1 modes -A  To be done
 
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     Representation   134      1 modes -A  To be done
 
     Representation   135      1 modes -A  To be done
 
     Representation   136      1 modes -A  To be done
 
     Representation   137      1 modes -A  To be done
 
     Representation   138      1 modes -A  To be done
 
     Representation   139      1 modes -A  To be done
 
     Representation   140      1 modes -A  To be done
 
     Representation   141      1 modes -A  To be done
 
     Representation   142      1 modes -A  To be done
 
     Representation   143      1 modes -A  To be done
 
     Representation   144      1 modes -A  To be done
 
     Representation   145      1 modes -A  To be done
 
     Representation   146      1 modes -A  To be done
 
     Representation   147      1 modes -A  To be done
 
     Representation   148      1 modes -A  To be done
 
     Representation   149      1 modes -A  To be done
 
     Representation   150      1 modes -A  To be done
 
     Representation   151      1 modes -A  To be done
 
     Representation   152      1 modes -A  To be done
 
     Representation   153      1 modes -A  To be done
 
     Representation   154      1 modes -A  To be done
 
     Representation   155      1 modes -A  To be done
 
     Representation   156      1 modes -A  To be done
 
 
 
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions



Dr. Yin Li 
Department of Biophysics,Medical School, University of Pecs,
No.12 Szigeti Street, Pecs, H-7624, HUNGARY
Phone: +36-72-535271/36271
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