[QE-users] bugs in running NEB in QE 6.8
Paolo Giannozzi
p.giannozzi at gmail.com
Sun Aug 29 20:04:43 CEST 2021
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 yznu.edu.cn>, jibiaoli at foxmail.com
> <jibiaoli at foxmail.com>, jibiao.li at hotmail.com <jibiao.li at hotmail.com>*
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
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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