[QE-users] ph.x can not run
Timrov Iurii
iurii.timrov at epfl.ch
Thu Dec 19 10:10:48 CET 2019
Dear Shaofeng Wang,
You are trying to perform a phonon calculation with the +U correction for a large system containing 93 atoms and using only 12 cores. I think that the code crashes because you do not have enough RAM. Please note that using PHonon+U for such a large system will be very very tough. Probably a better solution is to use Phonopy on top of DFT+U with supercells.
HTH
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 wangshaofeng at iae.ac.cn <wangshaofeng at iae.ac.cn>
Sent: Thursday, December 19, 2019 9:04:06 AM
To: users
Subject: [QE-users] ph.x can not run
Dear expert,
I am calculating a dynamical matrix using ph.x. But it can not run. The error is shown as follow. Please give me some suggestion.
Thanks in advance.
Program PHONON v.6.4.1 starts on 19Dec2019 at 0:32: 7
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);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
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 12 processors
MPI processes distributed on 1 nodes
R & G space division: proc/nbgrp/npool/nimage = 12
Reading data from directory:
./tmp/mm.save/
IMPORTANT: XC functional enforced from input :
Exchange-correlation = PBE ( 1 4 3 4 0 0)
Any further DFT definition will be discarded
Please, verify this is what you really want
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 1012 1012 253 123568 123568 15453
Max 1013 1013 255 123573 123573 15454
Sum 12155 12155 3047 1482853 1482853 185445
Generating pointlists ...
new r_m : 0.7846 (alat units) 1.4827 (a.u.) for type 1
new r_m : 0.7645 (alat units) 1.4447 (a.u.) for type 2
new r_m : 0.3978 (alat units) 0.7518 (a.u.) for type 3
new r_m : 0.3978 (alat units) 0.7518 (a.u.) for type 4
new r_m : 0.6791 (alat units) 1.2833 (a.u.) for type 5
Phonon calculation with DFPT+U; please cite
A. Floris et al., Phys. Rev. B 84, 161102(R) (2011)
in publications or presentations arising from this work.
Calculation of q = 0.0000000 0.0000000 0.0000000
ir calculation for HAsO4 adsorbed on goethite 110 in mm
bravais-lattice index = 0
lattice parameter (alat) = 1.8897 a.u.
unit-cell volume = 15341.5236 (a.u.)^3
number of atoms/cell = 93
number of atomic types = 5
kinetic-energy cut-off = 80.0000 Ry
charge density cut-off = 320.0000 Ry
convergence threshold = 1.0E-14
beta = 0.7000
number of iterations used = 4
Exchange-correlation = PBE ( 1 4 3 4 0 0)
Hubbard parameters:
U ( 1) = 3.30000000
U ( 2) = 3.30000000
celldm(1)= 1.88973 celldm(2)= 0.00000 celldm(3)= 0.00000
celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 12.2147 0.0000 0.0000 )
a(2) = ( 0.0000 10.9482 0.0000 )
a(3) = ( 0.0000 0.0000 17.0000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 0.0819 0.0000 0.0000 )
b(2) = ( 0.0000 0.0913 0.0000 )
b(3) = ( 0.0000 0.0000 0.0588 )
Atoms inside the unit cell:
Cartesian axes
site n. atom mass positions (alat units)
1 H 1.0079 tau( 1) = ( 1.12234 8.47343 5.06647 )
2 H 1.0079 tau( 2) = ( 2.57322 4.33959 4.43826 )
3 H 1.0079 tau( 3) = ( 2.54507 7.97823 1.08413 )
4 H 1.0079 tau( 4) = ( 0.95358 1.24139 1.69003 )
5 H 1.0079 tau( 5) = ( 1.50731 10.59710 0.32301 )
6 H 1.0079 tau( 6) = ( 2.56223 3.22337 0.49951 )
7 H 1.0079 tau( 7) = ( 3.02013 5.97989 5.95020 )
8 H 1.0079 tau( 8) = ( 1.11657 0.87403 5.71145 )
9 H 1.0079 tau( 9) = ( 4.38886 8.47398 4.96420 )
10 H 1.0079 tau( 10) = ( 5.63348 4.31121 4.41727 )
11 H 1.0079 tau( 11) = ( 5.69880 8.18447 0.95789 )
12 H 1.0079 tau( 12) = ( 4.15616 1.23787 1.64230 )
13 H 1.0079 tau( 13) = ( 3.68335 -0.41718 0.21817 )
14 H 1.0079 tau( 14) = ( 5.64184 3.24716 0.45592 )
15 H 1.0079 tau( 15) = ( 4.10690 0.79699 5.64323 )
16 H 1.0079 tau( 16) = ( 6.43988 8.36404 5.50599 )
17 H 1.0079 tau( 17) = ( 8.66013 4.34551 4.49757 )
18 H 1.0079 tau( 18) = ( 8.85525 8.05569 1.22272 )
19 H 1.0079 tau( 19) = ( 7.26703 1.15835 1.76365 )
20 H 1.0079 tau( 20) = ( 6.63268 10.58622 0.51057 )
21 H 1.0079 tau( 21) = ( 8.75040 3.21518 0.52301 )
22 H 1.0079 tau( 22) = ( 9.72366 5.80098 5.56701 )
23 H 1.0079 tau( 23) = ( 7.10488 0.78989 5.70570 )
24 H 1.0079 tau( 24) = ( 10.23777 8.35790 5.27171 )
25 H 1.0079 tau( 25) = ( 11.76575 4.38250 4.47156 )
26 H 1.0079 tau( 26) = ( 11.62271 8.09061 1.18360 )
27 H 1.0079 tau( 27) = ( 10.18874 1.30508 1.76682 )
28 H 1.0079 tau( 28) = ( 8.94148 10.64086 0.75306 )
29 H 1.0079 tau( 29) = ( 11.71830 3.36945 0.45177 )
30 H 1.0079 tau( 30) = ( 0.53865 5.83961 5.50125 )
31 H 1.0079 tau( 31) = ( 10.24451 0.97374 5.83049 )
32 H 1.0079 tau( 32) = ( 7.76150 5.93123 6.61613 )
33 H 1.0079 tau( 33) = ( 10.58477 10.52031 0.29869 )
34 O 15.9994 tau( 34) = ( 1.07970 5.96897 2.69764 )
35 O 15.9994 tau( 35) = ( 1.08047 8.23500 4.13181 )
36 O 15.9994 tau( 36) = ( 2.57127 4.06456 0.97787 )
37 O 15.9994 tau( 37) = ( 2.41326 5.85133 5.17613 )
38 O 15.9994 tau( 38) = ( 2.59340 3.69364 3.66020 )
39 O 15.9994 tau( 39) = ( 2.58204 10.68168 3.32289 )
40 O 15.9994 tau( 40) = ( 2.56568 8.43746 1.93298 )
41 O 15.9994 tau( 41) = ( 0.76649 10.71240 0.93256 )
42 O 15.9994 tau( 42) = ( 1.09538 1.60609 5.08133 )
43 O 15.9994 tau( 43) = ( 1.02834 1.96111 2.39319 )
44 O 15.9994 tau( 44) = ( 4.09676 5.94986 2.63985 )
45 O 15.9994 tau( 45) = ( 4.11694 8.22747 4.05302 )
46 O 15.9994 tau( 46) = ( 5.65578 4.05676 0.98560 )
47 O 15.9994 tau( 47) = ( 5.63807 5.86834 5.01668 )
48 O 15.9994 tau( 48) = ( 5.63368 3.66565 3.65320 )
49 O 15.9994 tau( 49) = ( 5.63465 10.65243 3.40622 )
50 O 15.9994 tau( 50) = ( 5.66353 8.39987 1.89772 )
51 O 15.9994 tau( 51) = ( 4.34139 10.73471 0.89449 )
52 O 15.9994 tau( 52) = ( 4.10121 1.56122 5.04985 )
53 O 15.9994 tau( 53) = ( 4.11790 1.94898 2.35943 )
54 O 15.9994 tau( 54) = ( 7.21411 5.89705 2.66423 )
55 O 15.9994 tau( 55) = ( 7.13646 8.15204 4.11161 )
56 O 15.9994 tau( 56) = ( 8.72176 4.04364 1.02172 )
57 O 15.9994 tau( 57) = ( 8.78367 5.83656 5.29801 )
58 O 15.9994 tau( 58) = ( 8.67150 3.68995 3.73244 )
59 O 15.9994 tau( 59) = ( 8.72059 10.67245 3.55138 )
60 O 15.9994 tau( 60) = ( 8.80388 8.38018 2.12945 )
61 O 15.9994 tau( 61) = ( 7.43493 10.65255 1.05441 )
62 O 15.9994 tau( 62) = ( 7.13020 1.56820 5.13020 )
63 O 15.9994 tau( 63) = ( 7.20308 1.91500 2.43533 )
64 O 15.9994 tau( 64) = ( 10.20696 5.95565 2.79882 )
65 O 15.9994 tau( 65) = ( 10.23983 8.19229 4.32056 )
66 O 15.9994 tau( 66) = ( 11.72531 4.14105 1.03415 )
67 O 15.9994 tau( 67) = ( 11.81076 5.86418 5.20360 )
68 O 15.9994 tau( 68) = ( 11.76207 3.71350 3.70846 )
69 O 15.9994 tau( 69) = ( 11.74205 10.69418 3.46463 )
70 O 15.9994 tau( 70) = ( 11.68976 8.40735 2.09243 )
71 O 15.9994 tau( 71) = ( 9.94885 10.73384 0.99701 )
72 O 15.9994 tau( 72) = ( 10.23921 1.65723 5.14798 )
73 O 15.9994 tau( 73) = ( 10.21802 1.98128 2.48378 )
74 O 15.9994 tau( 74) = ( 7.07132 6.02056 7.35698 )
75 O 15.9994 tau( 75) = ( 4.18092 6.27139 7.40096 )
76 O 15.9994 tau( 76) = ( 5.78137 8.30347 6.29357 )
77 Fe 55.8450 tau( 77) = ( 1.04682 9.72347 2.62366 )
78 Fe1 55.8450 tau( 78) = ( 2.59389 1.58652 3.72700 )
79 Fe 55.8450 tau( 79) = ( 2.62040 6.85509 3.57379 )
80 Fe1 55.8450 tau( 80) = ( 1.06022 4.14433 2.31704 )
81 Fe 55.8450 tau( 81) = ( 4.12951 9.71811 2.57959 )
82 Fe1 55.8450 tau( 82) = ( 5.63719 1.56412 3.76487 )
83 Fe 55.8450 tau( 83) = ( 5.68508 6.88647 3.34371 )
84 Fe1 55.8450 tau( 84) = ( 4.11193 4.12217 2.28869 )
85 Fe 55.8450 tau( 85) = ( 7.18919 9.62711 2.81373 )
86 Fe1 55.8450 tau( 86) = ( 8.68351 1.60418 3.88113 )
87 Fe 55.8450 tau( 87) = ( 8.61599 6.87184 3.64706 )
88 Fe1 55.8450 tau( 88) = ( 7.17773 4.07472 2.31155 )
89 Fe 55.8450 tau( 89) = ( 10.22216 9.67442 2.93407 )
90 Fe1 55.8450 tau( 90) = ( 11.75990 1.62587 3.82921 )
91 Fe 55.8450 tau( 91) = ( 11.76012 6.83408 3.56016 )
92 Fe1 55.8450 tau( 92) = ( 10.21322 4.15058 2.37869 )
93 As 74.9216 tau( 93) = ( 5.59227 6.55758 6.60320 )
Computing dynamical matrix for
q = ( 0.0000000 0.0000000 0.0000000 )
2 Sym.Ops. (with q -> -q+G )
G cutoff = 28.9460 ( 123573 G-vectors) FFT grid: (135,120,192)
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 0.0000000), wk = 1.0000000
PseudoPot. # 1 for Fe read from file:
../pseudo/ncpp/Fe_00PBE_OP.ncpp
MD5 check sum: 7dd2af9bf891824878553aaa4b1a5245
Pseudo is Norm-conserving, Zval = 16.0
Generated by old ld1 code (numerical format)
Using radial grid of 1160 points, 2 beta functions with:
l(1) = 1
l(2) = 2
PseudoPot. # 2 for Fe read from file:
../pseudo/ncpp/Fe_00PBE_OP.ncpp
MD5 check sum: 7dd2af9bf891824878553aaa4b1a5245
Pseudo is Norm-conserving, Zval = 16.0
Generated by old ld1 code (numerical format)
Using radial grid of 1160 points, 2 beta functions with:
l(1) = 1
l(2) = 2
PseudoPot. # 3 for O read from file:
../pseudo/ncpp/O_00PBE_OP.ncpp
MD5 check sum: 2e5ae166b87ab36fb9ab3e3b2efbba94
Pseudo is Norm-conserving, Zval = 6.0
Generated by old ld1 code (numerical format)
Using radial grid of 1130 points, 1 beta functions with:
l(1) = 1
PseudoPot. # 4 for H read from file:
../pseudo/ncpp/H_00PBE_OP.ncpp
MD5 check sum: e8e81ce5ac2edd34d10201b0089f8ee4
Pseudo is Norm-conserving, Zval = 1.0
Generated by old ld1 code (numerical format)
Using radial grid of 1076 points, 0 beta functions with:
PseudoPot. # 5 for As read from file:
../pseudo/ncpp/As_ONCV_PBE-1.2.upf
MD5 check sum: f455bf46e89b39f2ebbcf20cc3d72839
Pseudo is Norm-conserving, Zval = 5.0
Generated using ONCVPSP code by D. R. Hamann
Using radial grid of 1358 points, 6 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 2
l(6) = 2
Mode symmetry, C_1 (1) point group:
k=gamma and q=gamma tricks are used
Atomic displacements:
There are 279 irreducible representations
Representation 1 1 modes - Calculated using asr
Representation 2 1 modes - Calculated using asr
Representation 3 1 modes - Calculated using asr
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
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Atomic wfc used for the DFT+U projector are NOT orthogonalized
Calculating the dnsbare matrix...
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[57415,1],2]
Exit code: 174
--------------------------------------------------------------------------
________________________________
Shaofeng Wang
Ph.D
Email: wangshaofeng at iae.ac.cn
Key Laboratory of Pollution Ecology and Environmental Engineering
Institute of Applied Ecology
Chinese Academy of Sciences
China
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