[QE-users] NEB calculation no symmetry found
Offermans Willem
willem.offermans at vito.be
Wed Feb 13 09:50:53 CET 2019
Dear Quantum Espresso friends,
I made a mistake in my previous e-mail.
The atom coordinates are not in Angstrom but in Bohr.
I have corrected this in my calculations, but still no symmetry found.
$ grep "ymmetr" pd_?/PW.out
pd_1/PW.out: No symmetry found
pd_2/PW.out: No symmetry found
pd_3/PW.out: No symmetry found
pd_4/PW.out: No symmetry found
pd_5/PW.out: No symmetry found
pd_6/PW.out: No symmetry found
pd_7/PW.out: No symmetry found
So the question remains. What is the reason that the symmetry cannot be detected?
As an extra check I have made a scf calculation on the last image.
$ grep "Sym. Ops." pd.out
2 Sym. Ops., with inversion, found ( 1 have fractional translation)
So pw.x can find the symmetry whereas neb.x cannot!
I’m very happy to send the input files, if someone needs them.
Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,
Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073
Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>
[cid:982BA063-B96A-4A1B-89AB-5A01CA9FC70D at vito.local]
On 12 Feb 2019, at 17:13, Offermans Willem <willem.offermans at vito.be<mailto:willem.offermans at vito.be>> wrote:
Dear Quantum Espresso friends,
I’m running a NEB calculation with 7 images.
I’m pretty sure that all my images have S2-symmetry (inversion centre + identity).
Though, if I look into the output files, I find:
grep "ymmetr" pd_?/PW.out
pd_1/PW.out: No symmetry found
pd_2/PW.out: No symmetry found
pd_2/PW.out: No symmetry found
pd_2/PW.out: No symmetry found
pd_2/PW.out: No symmetry found
pd_2/PW.out: No symmetry found
pd_2/PW.out: No symmetry found
pd_3/PW.out: No symmetry found
pd_3/PW.out: No symmetry found
pd_3/PW.out: No symmetry found
pd_3/PW.out: No symmetry found
pd_3/PW.out: No symmetry found
pd_3/PW.out: No symmetry found
pd_4/PW.out: No symmetry found
pd_4/PW.out: No symmetry found
pd_4/PW.out: No symmetry found
pd_4/PW.out: No symmetry found
pd_4/PW.out: No symmetry found
pd_4/PW.out: No symmetry found
pd_5/PW.out: No symmetry found
pd_5/PW.out: No symmetry found
pd_5/PW.out: No symmetry found
pd_5/PW.out: No symmetry found
pd_5/PW.out: No symmetry found
pd_5/PW.out: No symmetry found
pd_6/PW.out: No symmetry found
pd_6/PW.out: No symmetry found
pd_6/PW.out: No symmetry found
pd_6/PW.out: No symmetry found
pd_6/PW.out: No symmetry found
pd_6/PW.out: No symmetry found
pd_7/PW.out: No symmetry found
How is this possible?
I will add my input file below:
<snip>
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode = 'from_scratch'
string_method = 'neb',
nstep_path = 20,
ds = 2.D0,
opt_scheme = "broyden",
num_of_images = 7,
k_max = 0.3D0,
k_min = 0.2D0,
CI_scheme = "auto",
path_thr = 0.1D0,
first_last_opt = .false.
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
prefix = "pd"
outdir = "./NEB/",
pseudo_dir = "./",
restart_mode = 'from_scratch'
/
&SYSTEM
ecutwfc = 30
ecutrho = 120
use_all_frac = .true.
occupations = 'smearing'
degauss = 0.0001
ntyp = 2
nat = 22
ibrav = 0
/
&ELECTRONS
electron_maxstep = 400
conv_thr = 0.0001
mixing_beta = 0.3
/
&IONS
/
&CELL
/
ATOMIC_SPECIES
Pd 106.42 Pd.pbe-n-kjpaw_psl.0.2.2.UPF
O 15.999 O.pbe-n-kjpaw_psl.0.1.UPF
K_POINTS automatic
3 3 1 0 0 0
CELL_PARAMETERS angstrom
5.57800000000000 0.00000000000000 0.00000000000000
2.78900000000000 4.83068970230960 0.00000000000000
0.00000000000000 0.00000000000000 18.21767171365942
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS angstrom
Pd -0.01490994696280 -0.00861835697216 2.38110417937417
Pd 1.49613843381522 -0.00868501784470 2.37969044908998
Pd 0.74057531627402 1.30007876757352 2.37968785899117
Pd 2.22039519051022 1.28200464831010 2.43670134163577
Pd 0.74441518517331 0.42984635397301 3.62786391133110
Pd 2.22112400683407 0.42455255944903 3.61110281545226
Pd 1.47818848230179 1.71125385043500 3.61102345584068
Pd 2.96366339120505 1.71104966346595 3.61273375980160
Pd 1.47860823477315 0.85375616486628 4.83651108827726
Pd 2.95553735935819 0.85419557524731 4.82714929410673
Pd 2.21743446250864 2.13242109861785 4.82705369055552
Pd 3.69436358709369 2.13286050899887 4.81769189638499
Pd 2.20930843066178 1.27556701039921 6.04146922486065
Pd 3.69478333956505 1.27536282343016 6.04317952882158
Pd 2.95184781503275 2.56206411441613 6.04310016921001
Pd 4.42855663669352 2.55677031989216 6.02633907333116
Pd 2.95257663135661 1.70461202555506 7.21750164302649
Pd 4.43239650559280 1.68653790629165 7.27451512567109
Pd 3.67683338805162 2.99530169170986 7.27451253557227
Pd 5.18788176882963 2.99523503083732 7.27309880528808
O 0.74168416891108 0.42824462511755 1.77480220957131
O 4.43128765295575 2.55837204874761 7.87940077509094
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS angstrom
Pd 0.04023436386900 0.02288014855855 2.36464252923658
Pd 1.53271250490005 -0.00026197908883 2.39592133819472
Pd 0.76638515079264 1.32694706092622 2.39587321327115
Pd 2.24037915977502 1.29313874845863 2.42972384375755
Pd 0.75362759780251 0.43513575118311 3.62124529528041
Pd 2.23406050229889 0.43119791923338 3.61297395825268
Pd 1.49045921606111 1.71897121506454 3.61295018394033
Pd 2.96826980221421 1.71370905943549 3.61761897854504
Pd 1.48161205644027 0.85589401255010 4.83295035441641
Pd 2.95594623945377 0.85376250201812 4.82740510741815
Pd 2.21702558241306 2.13285417184704 4.82679787724411
Pd 3.69135976542656 2.13072266131506 4.82125263024584
Pd 2.20470201965262 1.27290761442968 6.03658400611720
Pd 3.68251260580573 1.26764545880063 6.04125280072194
Pd 2.93891131956794 2.55541875463179 6.04122902640959
Pd 4.41934422406432 2.55148092268205 6.03295768938183
Pd 2.93259266209181 1.69347792540653 7.22447914090469
Pd 4.40658667107419 1.65966961293894 7.25832977139111
Pd 3.64025931696677 2.98687865295400 7.25828164646754
Pd 5.13273745799784 2.96373652530661 7.28956045542567
O 0.84791000737715 0.48920629774724 1.76363838886783
O 4.32506181448969 2.49741037611793 7.89056459579442
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS angstrom
Pd 0.02546206653436 0.01437352399892 2.38524314057437
Pd 1.50427315887314 -0.01267879881569 2.40456410718953
Pd 0.74141031132652 1.30832673443525 2.40423534189436
Pd 2.22266980374675 1.28262373923901 2.42487917196399
Pd 0.74688871233551 0.43129616521648 3.62891974577109
Pd 2.22576647249297 0.42640629648024 3.62422001969190
Pd 1.48222657336274 1.71406948188701 3.62404047991757
Pd 2.96284776820994 1.71040589790329 3.61204247034872
Pd 1.48418267010516 0.85800129438488 4.83271004673676
Pd 2.95630962520977 0.85419340128256 4.82765404743212
Pd 2.21666219665706 2.13242327258260 4.82654893723014
Pd 3.68878915176167 2.12861537948027 4.82149293792549
Pd 2.21012405365689 1.27621077596187 6.04216051431352
Pd 3.69074524850409 1.27254719197816 6.03016250474468
Pd 2.94720534937386 2.56021037738493 6.02998296497037
Pd 4.42608310953133 2.55532050864868 6.02528323889115
Pd 2.95030201812008 1.70399293462616 7.22932381269825
Pd 4.43156151054031 1.67828993942992 7.24996764276790
Pd 3.66869866299369 2.99929547268087 7.24963887747272
Pd 5.14750975533247 2.97224314986625 7.26895984408788
O 0.96618931141895 0.55710985678959 1.72479571109891
O 4.20678251044789 2.42950681707558 7.92940727356334
Pd -0.00050687656600 -0.00089720178027 2.40847340569703
Pd 1.47759887955505 -0.02357072253100 2.40467229638546
Pd 0.71881751707614 1.29048151565404 2.40444536371054
Pd 2.20540922124980 1.27265370734188 2.41369266028974
Pd 0.74111740306375 0.42783715695144 3.62837008403613
Pd 2.21739255357954 0.42397368270196 3.62882616089867
Pd 1.47630806035116 1.70753738015574 3.62840361035015
Pd 2.95575395196702 1.70618745727064 3.60257256328033
Pd 1.48395820418100 0.85706141211691 4.83441908980237
Pd 2.95560840175695 0.85485239310772 4.82753896408998
Pd 2.21736342010988 2.13176428075744 4.82666402057228
Pd 3.68901361768583 2.12955526174825 4.81978389485989
Pd 2.21721786989981 1.28042921659452 6.05163042138192
Pd 3.69666376151568 1.27907929370942 6.02579937431210
Pd 2.95557926828729 2.56264299116320 6.02537682376360
Pd 4.43185441880309 2.55877951691372 6.02583290062611
Pd 2.96756260061703 1.71396296652328 7.24051032437250
Pd 4.45415430479069 1.69613515821112 7.24975762095173
Pd 3.69537294231177 3.01018739639618 7.24953068827679
Pd 5.17347869843282 2.98751387564544 7.24572957896522
O 1.08502746808268 0.62579486305652 1.70388077612506
O 4.08794435378415 2.36082181080866 7.95032220853719
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS angstrom
Pd -0.02292559897995 -0.01382503959689 2.42173725051719
Pd 1.44895161488471 -0.04535527300462 2.40537971650900
Pd 0.68561117203061 1.27671835155637 2.40519829813990
Pd 2.17335770514861 1.25424349043561 2.38326132451485
Pd 0.73550322830860 0.42471243433628 3.62751696323895
Pd 2.21119871384517 0.42245426273987 3.62611680620115
Pd 1.47156617268427 1.70322017807330 3.62593725644819
Pd 2.94966539040879 1.70269004865517 3.59624280792181
Pd 1.48273051218476 0.85673133808466 4.82949766961002
Pd 2.95472362542175 0.85658326043619 4.82737187715954
Pd 2.21824819644508 2.13003341342898 4.82683110750271
Pd 3.69024130968206 2.12988533578049 4.82470531505224
Pd 2.22330643145804 1.28392662521000 6.05796017674044
Pd 3.70140564918256 1.28339649579186 6.02826572821406
Pd 2.96177310802166 2.56416241112529 6.02808617846113
Pd 4.43746859355823 2.56190423952888 6.02668602142328
Pd 2.99961411671822 1.73237318342955 7.27094166014739
Pd 4.48736064983622 1.70989832230880 7.24900468652237
Pd 3.72402020698212 3.03197194686979 7.24882326815325
Pd 5.19589742084678 3.00044171346206 7.23246573414506
O 1.23065540266270 0.70992813933571 1.72985837151787
O 3.94231641920413 2.27668853452946 7.92434461314438
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS angstrom
Pd -0.04708572926312 -0.02768014028907 2.43210746998474
Pd 1.42504610870905 -0.06031797315813 2.40211645877545
Pd 0.66063493983647 1.26361001970355 2.40197490632270
Pd 2.16379533818910 1.24878034367971 2.37716519987558
Pd 0.72620755379283 0.41923049418829 3.63014685505194
Pd 2.20328083642238 0.41808462516606 3.62992051909970
Pd 1.46391876891542 1.69852717321030 3.62984167234477
Pd 2.94200441257508 1.69830883456801 3.59739558990992
Pd 1.48388875132037 0.85702482966625 4.82654770134495
Pd 2.95412729976020 0.85696405624197 4.82714322094116
Pd 2.21884452210663 2.12965261762319 4.82705976372109
Pd 3.68908307054646 2.12959184419890 4.82765528331731
Pd 2.23096740929175 1.28830783929715 6.05680739475232
Pd 3.70905305295142 1.28808950065486 6.02436131231749
Pd 2.96969098544445 2.56853204869911 6.02428246556257
Pd 4.44676426807400 2.56738617967688 6.02405612961031
Pd 3.00917648367773 1.73783633018545 7.27703778478666
Pd 4.51233688203037 1.72300665416161 7.25222807833956
Pd 3.74792571315778 3.04693464702331 7.25208652588680
Pd 5.22005755112995 3.01429681415424 7.22209551467752
O 1.37458930167646 0.79314870586476 1.78357309465173
O 3.79838252019037 2.19346796800041 7.87062989001052
LAST_IMAGE
ATOMIC_POSITIONS angstrom
Pd -0.00330510761759 -0.00126294851365 2.44006418317495
Pd 1.47432747396174 -0.02526652696133 2.38681480875857
Pd 0.71917195715365 1.28851993336488 2.38818124169618
Pd 2.23558221293615 1.28943518715903 2.38343842319349
Pd 0.73690934164695 0.42592671499404 3.62742729476899
Pd 2.21282401863750 0.42746968541657 3.63097519826187
Pd 1.47564636723945 1.70413298880555 3.63079725336742
Pd 2.95323117119125 1.70601366841878 3.57807641022279
Pd 1.47967414176301 0.85413529581195 4.83110144304972
Pd 2.95360354792685 0.85735144254421 4.82753643335944
Pd 2.21936827393998 2.12926523132095 4.82666655130282
Pd 3.69329768010382 2.13248137805321 4.82310154161253
Pd 2.21974065067558 1.28060300544639 6.07612657443946
Pd 3.69732545462739 1.28248368505961 6.02340573129483
Pd 2.96014780322933 2.55914698844859 6.02322778640040
Pd 4.43606248021987 2.56068995887112 6.02677568989325
Pd 2.93738960893068 1.69718148670613 7.27076456146874
Pd 4.45379986471318 1.69809674050028 7.26602174296609
Pd 3.69864434790507 3.01188320082649 7.26738817590368
Pd 5.17627692948442 2.98787962237882 7.21413880148731
O 1.47627247303936 0.85143436484018 1.78962553611488
O 3.69669934882747 2.13518230902499 7.86457744854738
END_POSITIONS
END_ENGINE_INPUT
END
EOF
Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,
Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073
Willem.Offermans at Vito.be<mailto:Willem.Offermans at Vito.be>
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