[QE-users] 回复： bugs in running NEB in QE 6.8
Jibiao Li
jibiaoli at foxmail.com
Mon Aug 30 02:40:51 CEST 2021
Sorry, Paolo, I just found its a problem of job submitting format. When I added 2>1&1 to the end of the command: mpirun -np 50 neb.x -inp ufu.neb.inp > ufu.neb.out, everything goes smoothly. Thank you for your time.
Jibiao Li
------------------ 原始邮件 ------------------
发件人: "Quantum ESPRESSO users Forum" <p.giannozzi at gmail.com>;
发送时间: 2021年8月30日(星期一) 凌晨2:04
收件人: "Quantum ESPRESSO users Forum"<users at lists.quantum-espresso.org>;
主题: Re: [QE-users] bugs in running NEB in QE 6.8
It works for me
Paolo
On Sat, Aug 28, 2021 at 8:45 AM Jibiao Li <jibiaoli at foxmail.com> wrote:
Dear QE developer,
Here I am reporting a bug in neb. It exits in QE6.8 and the developer version rather than the old versions. The problem is the output file stopped at the first iteration and did not get updated, though the calculations were still running. Moreover, the processes can not be killed by the command "kill" +PID. What's the way out?
(I am using the latest oneAPI environment for the FORTRAN compiler and parallel environment . )
... ...
string_method = neb
restart_mode = from_scratch
opt_scheme = broyden
num_of_images = 9
nstep_path = 198
CI_scheme = auto
first_last_opt = T
use_freezing = F
ds = 1.0000 a.u.
k_max = 0.7000 a.u.
k_min = 0.1000 a.u.
suggested k_max = 0.6169 a.u.
suggested k_min = 0.0881 a.u.
path_thr = 0.0500 eV / A
------------------------------ iteration 1 ------------------------------
tcpu = 0.6 self-consistency for image 1
ufu.neb.inp:
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode = 'from_scratch',
string_method = 'neb',
nstep_path = 198,
ds = 1.D0,
opt_scheme = 'broyden',
first_last_opt = .TRUE.,
num_of_images = 9,
k_max = 0.7D0,
k_min = 0.1D0,
CI_scheme = 'auto',
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
prefix = 'ufu',
outdir = './',
pseudo_dir = '/home/jibiaoli/pseudo/PAW' ,
/
&SYSTEM
ibrav = 6,
celldm(1) = 19.312063827,
celldm(3) = 2.4,
nat = 48,
ntyp = 3,
ecutwfc = 45 ,
ecutrho = 491 ,
input_dft = 'sla+pw+ggx+vdw1' ,
occupations = 'smearing' ,
degauss = 0.02D0 ,
smearing = 'methfessel-paxton' ,
/
&ELECTRONS
electron_maxstep = 299,
mixing_beta = 0.2D0 ,
diagonalization = 'david' ,
/
ATOMIC_SPECIES
O 15.99900 O.pbe-n-kjpaw_psl.1.0.0.UPF
H 1.00790 H.pbe-kjpaw_psl.1.0.0.UPF
Li 6.94100 Li.pbe-sl-kjpaw_psl.1.0.0.UPF
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS angstrom
H 1.7032500000 2.6019899930 8.7397927326
O 1.7032500000 3.4065000000 8.1600637482
H 1.7032500000 4.2110100070 8.7397927326
Li 0.0000945099 -0.0671745047 6.8706341140
Li 0.1189610012 3.4065000000 6.9025883303
Li 0.0000945099 6.8801745047 6.8706341140
Li 3.4064054901 -0.0671745047 6.8706341140
Li 3.2875389988 3.4065000000 6.9025883303
Li 3.4064054901 6.8801745047 6.8706341140
Li 6.8130000000 -0.0092361609 6.8724083106
Li 6.8130000000 3.4065000000 6.9029237449
Li 6.8130000000 6.8222361609 6.8724083106
Li 1.7032500000 1.6321265359 5.0173582231
Li 1.7032500000 5.1808734641 5.0173582231
Li 1.7032500000 8.5162500000 5.0640857671
Li 5.0786783791 1.7203557491 5.1167513492
Li 5.0786783791 5.0926442509 5.1167513492
Li 5.1162073197 8.5162500000 5.0650139710
Li 8.5473216209 1.7203557491 5.1167513492
Li 8.5473216209 5.0926442509 5.1167513492
Li 8.5097926803 8.5162500000 5.0650139710
Li 0.0000000000 0.0000000000 3.4065000000 0 0 0
Li 0.0000000000 3.4065000000 3.4065000000 0 0 0
Li 0.0000000000 6.8130000000 3.4065000000 0 0 0
Li 3.4065000000 0.0000000000 3.4065000000 0 0 0
Li 3.4065000000 3.4065000000 3.4065000000 0 0 0
Li 3.4065000000 6.8130000000 3.4065000000 0 0 0
Li 6.8130000000 0.0000000000 3.4065000000 0 0 0
Li 6.8130000000 3.4065000000 3.4065000000 0 0 0
Li 6.8130000000 6.8130000000 3.4065000000 0 0 0
Li 1.7032500000 1.7032500000 1.7032500000 0 0 0
Li 1.7032500000 5.1097500000 1.7032500000 0 0 0
Li 1.7032500000 8.5162500000 1.7032500000 0 0 0
Li 5.1097500000 1.7032500000 1.7032500000 0 0 0
Li 5.1097500000 5.1097500000 1.7032500000 0 0 0
Li 5.1097500000 8.5162500000 1.7032500000 0 0 0
Li 8.5162500000 1.7032500000 1.7032500000 0 0 0
Li 8.5162500000 5.1097500000 1.7032500000 0 0 0
Li 8.5162500000 8.5162500000 1.7032500000 0 0 0
Li 0.0000000000 0.0000000000 0.0000000000 0 0 0
Li 0.0000000000 3.4065000000 0.0000000000 0 0 0
Li 0.0000000000 6.8130000000 0.0000000000 0 0 0
Li 3.4065000000 0.0000000000 0.0000000000 0 0 0
Li 3.4065000000 3.4065000000 0.0000000000 0 0 0
Li 3.4065000000 6.8130000000 0.0000000000 0 0 0
Li 6.8130000000 0.0000000000 0.0000000000 0 0 0
Li 6.8130000000 3.4065000000 0.0000000000 0 0 0
Li 6.8130000000 6.8130000000 0.0000000000 0 0 0
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS angstrom
H 4.1880286210 4.2303611703 9.1648473150
O 3.4059936087 3.7135636395 8.8787627733
H 2.6243240118 4.2314069085 9.1636936586
Li 0.0015350623 0.0042154632 6.8580126560
Li -0.0798460756 3.4008324529 6.8242103879
Li 0.0020913327 6.8089091857 6.8876707504
Li 3.4065308337 -0.0630190645 6.8500462444
Li 3.4066274524 3.3070893499 7.0061364927
Li 3.4065037515 6.8846349854 6.8416610168
Li 6.8114362533 0.0042482546 6.8580497403
Li 6.8930292978 3.4007964966 6.8241014552
Li 6.8109262564 6.8088847720 6.8877383018
Li 1.7029437256 1.6988797250 5.0687235469
Li 1.7063000500 5.0983186318 5.1038437734
Li 1.6911399936 8.5090607992 5.0791124289
Li 5.1101414293 1.6988428867 5.0686918751
Li 5.1067369440 5.0983439681 5.1037686027
Li 5.1218619226 8.5090656953 5.0790587690
Li 8.5163339760 1.6872654558 5.0552704570
Li 8.5163314435 5.1307764554 5.0744493612
Li 8.5162568364 8.5108246112 5.0819676798
Li 0.0000000000 0.0000000000 3.4065000000 0 0 0
Li 0.0000000000 3.4065000000 3.4065000000 0 0 0
Li 0.0000000000 6.8130000000 3.4065000000 0 0 0
Li 3.4065000000 0.0000000000 3.4065000000 0 0 0
Li 3.4065000000 3.4065000000 3.4065000000 0 0 0
Li 3.4065000000 6.8130000000 3.4065000000 0 0 0
Li 6.8130000000 0.0000000000 3.4065000000 0 0 0
Li 6.8130000000 3.4065000000 3.4065000000 0 0 0
Li 6.8130000000 6.8130000000 3.4065000000 0 0 0
Li 1.7032500000 1.7032500000 1.7032500000 0 0 0
Li 1.7032500000 5.1097500000 1.7032500000 0 0 0
Li 1.7032500000 8.5162500000 1.7032500000 0 0 0
Li 5.1097500000 1.7032500000 1.7032500000 0 0 0
Li 5.1097500000 5.1097500000 1.7032500000 0 0 0
Li 5.1097500000 8.5162500000 1.7032500000 0 0 0
Li 8.5162500000 1.7032500000 1.7032500000 0 0 0
Li 8.5162500000 5.1097500000 1.7032500000 0 0 0
Li 8.5162500000 8.5162500000 1.7032500000 0 0 0
Li 0.0000000000 0.0000000000 0.0000000000 0 0 0
Li 0.0000000000 3.4065000000 0.0000000000 0 0 0
Li 0.0000000000 6.8130000000 0.0000000000 0 0 0
Li 3.4065000000 0.0000000000 0.0000000000 0 0 0
Li 3.4065000000 3.4065000000 0.0000000000 0 0 0
Li 3.4065000000 6.8130000000 0.0000000000 0 0 0
Li 6.8130000000 0.0000000000 0.0000000000 0 0 0
Li 6.8130000000 3.4065000000 0.0000000000 0 0 0
Li 6.8130000000 6.8130000000 0.0000000000 0 0 0
LAST_IMAGE
ATOMIC_POSITIONS angstrom
H 5.1097500000 4.2107968180 8.7400241937
O 5.1097500000 3.4065000000 8.1600376966
H 5.1097500000 2.6022031820 8.7400241937
Li 0.0000000000 -0.0092349236 6.8725299952
Li 0.0000000000 3.4065000000 6.9028611154
Li 0.0000000000 6.8222349236 6.8725299952
Li 3.4065972434 -0.0671808805 6.8707740388
Li 3.5253810253 3.4065000000 6.9027103228
Li 3.4065972434 6.8801808805 6.8707740388
Li 6.8129027566 -0.0671808805 6.8707740388
Li 6.6941189747 3.4065000000 6.9027103228
Li 6.8129027566 6.8801808805 6.8707740388
Li 1.7343390531 1.7204130087 5.1167734558
Li 1.7343390531 5.0925869913 5.1167734558
Li 1.6967519133 8.5162500000 5.0649404073
Li 5.1097500000 1.6320458311 5.0174213869
Li 5.1097500000 5.1809541689 5.0174213869
Li 5.1097500000 8.5162500000 5.0642051386
Li 8.4851609469 1.7204130087 5.1167734558
Li 8.4851609469 5.0925869913 5.1167734558
Li 8.5227480867 8.5162500000 5.0649404073
Li 0.0000000000 0.0000000000 3.4065000000 0 0 0
Li 0.0000000000 3.4065000000 3.4065000000 0 0 0
Li 0.0000000000 6.8130000000 3.4065000000 0 0 0
Li 3.4065000000 0.0000000000 3.4065000000 0 0 0
Li 3.4065000000 3.4065000000 3.4065000000 0 0 0
Li 3.4065000000 6.8130000000 3.4065000000 0 0 0
Li 6.8130000000 0.0000000000 3.4065000000 0 0 0
Li 6.8130000000 3.4065000000 3.4065000000 0 0 0
Li 6.8130000000 6.8130000000 3.4065000000 0 0 0
Li 1.7032500000 1.7032500000 1.7032500000 0 0 0
Li 1.7032500000 5.1097500000 1.7032500000 0 0 0
Li 1.7032500000 8.5162500000 1.7032500000 0 0 0
Li 5.1097500000 1.7032500000 1.7032500000 0 0 0
Li 5.1097500000 5.1097500000 1.7032500000 0 0 0
Li 5.1097500000 8.5162500000 1.7032500000 0 0 0
Li 8.5162500000 1.7032500000 1.7032500000 0 0 0
Li 8.5162500000 5.1097500000 1.7032500000 0 0 0
Li 8.5162500000 8.5162500000 1.7032500000 0 0 0
Li 0.0000000000 0.0000000000 0.0000000000 0 0 0
Li 0.0000000000 3.4065000000 0.0000000000 0 0 0
Li 0.0000000000 6.8130000000 0.0000000000 0 0 0
Li 3.4065000000 0.0000000000 0.0000000000 0 0 0
Li 3.4065000000 3.4065000000 0.0000000000 0 0 0
Li 3.4065000000 6.8130000000 0.0000000000 0 0 0
Li 6.8130000000 0.0000000000 0.0000000000 0 0 0
Li 6.8130000000 3.4065000000 0.0000000000 0 0 0
Li 6.8130000000 6.8130000000 0.0000000000 0 0 0
END_POSITIONS
K_POINTS automatic
4 4 1 0 0 0
END_ENGINE_INPUT
END
Dr. Jibiao Li,
Department of Material Science and Engineering
Yangtze Normal University
Juxian Dadao 16#, Fuling, Chongqing, China
Email: jibiaoli at yznu.edu.cn, jibiaoli at foxmail.com, jibiao.li at hotmail.com
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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