[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
Representation 5 1 modes -A To be done
Representation 6 1 modes -A To be done
Representation 7 1 modes -A To be done
Representation 8 1 modes -A To be done
Representation 9 1 modes -A To be done
Representation 10 1 modes -A To be done
Representation 11 1 modes -A To be done
Representation 12 1 modes -A To be done
Representation 13 1 modes -A To be done
Representation 14 1 modes -A To be done
Representation 15 1 modes -A To be done
Representation 16 1 modes -A To be done
Representation 17 1 modes -A To be done
Representation 18 1 modes -A To be done
Representation 19 1 modes -A To be done
Representation 20 1 modes -A To be done
Representation 21 1 modes -A To be done
Representation 22 1 modes -A To be done
Representation 23 1 modes -A To be done
Representation 24 1 modes -A To be done
Representation 25 1 modes -A To be done
Representation 26 1 modes -A To be done
Representation 27 1 modes -A To be done
Representation 28 1 modes -A To be done
Representation 29 1 modes -A To be done
Representation 30 1 modes -A To be done
Representation 31 1 modes -A To be done
Representation 32 1 modes -A To be done
Representation 33 1 modes -A To be done
Representation 34 1 modes -A To be done
Representation 35 1 modes -A To be done
Representation 36 1 modes -A To be done
Representation 37 1 modes -A To be done
Representation 38 1 modes -A To be done
Representation 39 1 modes -A To be done
Representation 40 1 modes -A To be done
Representation 41 1 modes -A To be done
Representation 42 1 modes -A To be done
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Representation 44 1 modes -A To be done
Representation 45 1 modes -A To be done
Representation 46 1 modes -A To be done
Representation 47 1 modes -A To be done
Representation 48 1 modes -A To be done
Representation 49 1 modes -A To be done
Representation 50 1 modes -A To be done
Representation 51 1 modes -A To be done
Representation 52 1 modes -A To be done
Representation 53 1 modes -A To be done
Representation 54 1 modes -A To be done
Representation 55 1 modes -A To be done
Representation 56 1 modes -A To be done
Representation 57 1 modes -A To be done
Representation 58 1 modes -A To be done
Representation 59 1 modes -A To be done
Representation 60 1 modes -A To be done
Representation 61 1 modes -A To be done
Representation 62 1 modes -A To be done
Representation 63 1 modes -A To be done
Representation 64 1 modes -A To be done
Representation 65 1 modes -A To be done
Representation 66 1 modes -A To be done
Representation 67 1 modes -A To be done
Representation 68 1 modes -A To be done
Representation 69 1 modes -A To be done
Representation 70 1 modes -A To be done
Representation 71 1 modes -A To be done
Representation 72 1 modes -A To be done
Representation 73 1 modes -A To be done
Representation 74 1 modes -A To be done
Representation 75 1 modes -A To be done
Representation 76 1 modes -A To be done
Representation 77 1 modes -A To be done
Representation 78 1 modes -A To be done
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Representation 80 1 modes -A To be done
Representation 81 1 modes -A To be done
Representation 82 1 modes -A To be done
Representation 83 1 modes -A To be done
Representation 84 1 modes -A To be done
Representation 85 1 modes -A To be done
Representation 86 1 modes -A To be done
Representation 87 1 modes -A To be done
Representation 88 1 modes -A To be done
Representation 89 1 modes -A To be done
Representation 90 1 modes -A To be done
Representation 91 1 modes -A To be done
Representation 92 1 modes -A To be done
Representation 93 1 modes -A To be done
Representation 94 1 modes -A To be done
Representation 95 1 modes -A To be done
Representation 96 1 modes -A To be done
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Representation 98 1 modes -A To be done
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Representation 100 1 modes -A To be done
Representation 101 1 modes -A To be done
Representation 102 1 modes -A To be done
Representation 103 1 modes -A To be done
Representation 104 1 modes -A To be done
Representation 105 1 modes -A To be done
Representation 106 1 modes -A To be done
Representation 107 1 modes -A To be done
Representation 108 1 modes -A To be done
Representation 109 1 modes -A To be done
Representation 110 1 modes -A To be done
Representation 111 1 modes -A To be done
Representation 112 1 modes -A To be done
Representation 113 1 modes -A To be done
Representation 114 1 modes -A To be done
Representation 115 1 modes -A To be done
Representation 116 1 modes -A To be done
Representation 117 1 modes -A To be done
Representation 118 1 modes -A To be done
Representation 119 1 modes -A To be done
Representation 120 1 modes -A To be done
Representation 121 1 modes -A To be done
Representation 122 1 modes -A To be done
Representation 123 1 modes -A To be done
Representation 124 1 modes -A To be done
Representation 125 1 modes -A To be done
Representation 126 1 modes -A To be done
Representation 127 1 modes -A To be done
Representation 128 1 modes -A To be done
Representation 129 1 modes -A To be done
Representation 130 1 modes -A To be done
Representation 131 1 modes -A To be done
Representation 132 1 modes -A To be done
Representation 133 1 modes -A To be done
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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