[QE-users] Inconsistency of atomic species in neb.x calculations
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Wed Nov 13 13:39:34 CET 2019
Dear Marko
If I remember well (but I could be wrong) neb.x expects that atom 1 in
the first image is the same atom 1 in the last image, atom 2 is atom
2, etc.
HTH
Giuseppe
Mladenovic Marko <marko.mladenovic at epfl.ch> ha scritto:
> Hello everyone,
>
>
> I am investigating the ionic diffusion in halide perovskites by
> performing neb.x calculations. In some cases, I get the error "
>
> inconsistency of atomic species". Input file for one of the examples
> that gives this error is given below. I understand that the error
> suggest that there is something is wrong with the coordinates,
> however, I cannot see any problem with them. Has anyone else
> encountered this kind of issue?
>
> Thank you!
>
> Marko Mladenovic, PhD
> Postdoctoral researcher
> École polytechnique fédérale de Lausanne
> SB - ISIC - LCBC
> web: https://people.epfl.ch/marko.mladenovic
>
>
> BEGIN
> BEGIN_PATH_INPUT
> &PATH
> restart_mode = 'from_scratch'
> string_method = 'neb',
> nstep_path = 500,
> ds = 2.D0,
> opt_scheme = "broyden",
> num_of_images = 3,
> ! k_max = 0.3D0,
> ! k_min = 0.2D0,
> CI_scheme = "auto",
> path_thr = 0.1D0,
> first_last_opt=.true.
> /
> END_PATH_INPUT
> BEGIN_ENGINE_INPUT
> &CONTROL
> ! prefix = "pwscf"
> ! outdir = "/tmp",
> pseudo_dir = "/scratch/mladenov/PPQE/",
> /
> &SYSTEM
> ibrav = 0,
> ! celldm(1) = 1.D0,
> nat = 95,
> ntyp = 5,
> ecutwfc = 40.0D0,
> ecutrho = 280.0D0,
> occupations = "smearing",
> degauss = 0.05D0,
> tot_charge=1
> /
> &ELECTRONS
> conv_thr = 1.D-8,
> mixing_beta = 0.3D0,
> /
> &IONS
> pot_extrapolation = "second_order",
> wfc_extrapolation = "second_order",
> /
> ATOMIC_SPECIES
> Pb 207.2 Pb.pbesol-dn-rrkjus_psl.0.2.2.UPF
> Br 126.90447 Br.pbesol-n-rrkjus_psl.0.2.UPF
> C 12.0107 C.pbesol-n-rrkjus_psl.0.1.UPF
> N 14.0067 N.pbesol-n-rrkjus_psl.0.1.UPF
> H 1.00794 H.pbesol-rrkjus_psl.0.1.UPF
> BEGIN_POSITIONS
> FIRST_IMAGE
> ATOMIC_POSITIONS {angstrom}
> Pb 2.95893 2.95983 3.09277
> Br 3.28187 -0.07743 2.78260
> Br 0.02242 2.80350 3.14248
> N -0.30045 0.80458 0.16245
> H -0.64683 1.37235 -0.64167
> H 0.46452 1.36374 0.59580
> H -1.07168 0.70009 0.86517
> C 0.19677 -0.51160 -0.29605
> H 0.56789 -1.07782 0.56904
> H 1.01268 -0.35602 -1.01613
> H -0.62500 -1.05666 -0.78008
> Pb 3.17620 3.14976 8.97932
> Br 2.86384 2.81160 6.02077
> Br 3.49913 0.11250 8.66915
> Br 0.23969 2.99344 9.02903
> N -0.08318 0.99452 6.04900
> H -0.42956 1.56229 5.24487
> H 0.68179 1.55368 6.48234
> H -0.85442 0.89003 6.75172
> C 0.41403 -0.32166 5.59050
> H 0.78515 -0.88788 6.45559
> H 1.22995 -0.16608 4.87042
> H -0.40773 -0.86672 5.10647
> Pb 2.76768 8.92015 3.28271
> Br 2.45532 8.58198 0.32415
> Br 3.09061 5.88289 2.97254
> Br -0.16884 8.76382 3.33242
> N -0.49170 6.76490 0.35239
> H -0.83808 7.33268 -0.45174
> H 0.27327 7.32407 0.78573
> H -1.26294 6.66041 1.05511
> C 0.00551 5.44873 -0.10612
> H 0.37663 4.88250 0.75897
> H 0.82143 5.60430 -0.82619
> H -0.81625 4.90366 -0.59014
> Pb 2.98494 9.11009 9.16926
> Br 2.67259 8.77192 6.21070
> Br 3.30788 6.07283 8.85909
> Br 0.04843 8.95376 9.21897
> N -0.27443 6.95484 6.23894
> H -0.62081 7.52261 5.43481
> H 0.49053 7.51400 6.67228
> H -1.04567 6.85035 6.94166
> C 0.22278 5.63867 5.78043
> H 0.59390 5.07244 6.64552
> H 1.03870 5.79424 5.06035
> H -0.59898 5.09360 5.29641
> Pb 8.86536 2.76857 3.31004
> Br 8.55300 2.43041 0.35148
> Br 9.18829 -0.26869 2.99987
> Br 5.92884 2.61224 3.35975
> N 5.60598 0.61332 0.37972
> H 5.25960 1.18110 -0.42441
> H 6.37094 1.17249 0.81306
> H 4.83474 0.50883 1.08244
> C 6.10319 -0.70285 -0.07879
> H 6.47431 -1.26908 0.78630
> H 6.91911 -0.54727 -0.79886
> H 5.28143 -1.24792 -0.56281
> Pb 9.08262 2.95851 9.19659
> Br 8.77027 2.62034 6.23803
> Br 9.40556 -0.07875 8.88642
> Br 6.14611 2.80218 9.24630
> N 5.82325 0.80326 6.26627
> H 5.47687 1.37103 5.46214
> H 6.58821 1.36243 6.69961
> H 5.05201 0.69877 6.96899
> C 6.32046 -0.51291 5.80776
> H 6.69158 -1.07914 6.67285
> H 7.13638 -0.35734 5.08768
> H 5.49870 -1.05798 5.32374
> Pb 8.67410 8.72890 3.49998
> Br 8.36175 8.39073 0.54142
> Br 8.99704 5.69164 3.18981
> Br 5.73759 8.57257 3.54969
> N 5.41472 6.57365 0.56966
> H 5.06835 7.14142 -0.23447
> H 6.17969 7.13281 1.00300
> H 4.64349 6.46916 1.27238
> C 5.91194 5.25747 0.11115
> H 6.28306 4.69125 0.97624
> H 6.72786 5.41305 -0.60893
> H 5.09017 4.71241 -0.37287
> Pb 8.89137 8.91883 9.38653
> Br 8.57901 8.58067 6.42797
> Br 9.21430 5.88157 9.07636
> Br 5.95486 8.76251 9.43623
> N 5.63199 6.76359 6.45621
> H 5.28561 7.33136 5.65208
> H 6.39696 7.32275 6.88955
> H 4.86075 6.65910 7.15893
> C 6.12921 5.44741 5.99770
> H 6.50032 4.88118 6.86279
> H 6.94512 5.60299 5.27762
> H 5.30744 4.90235 5.51367
> LAST_IMAGE
> ATOMIC_POSITIONS {angstrom}
> Pb 2.95893 2.95983 3.09277
> Br 2.64658 2.62166 0.13422
> Br 3.28187 -0.07743 2.78260
> Br 0.02242 2.80350 3.14248
> N -0.30045 0.80458 0.16245
> H -0.64683 1.37235 -0.64167
> H 0.46452 1.36374 0.59580
> H -1.07168 0.70009 0.86517
> C 0.19677 -0.51160 -0.29605
> H 0.56789 -1.07782 0.56904
> H 1.01268 -0.35602 -1.01613
> H -0.62500 -1.05666 -0.78008
> Pb 3.17620 3.14976 8.97932
> Br 2.86384 2.81160 6.02077
> Br 3.49913 0.11250 8.66915
> Br 0.23969 2.99344 9.02903
> N -0.08318 0.99452 6.04900
> H -0.42956 1.56229 5.24487
> H 0.68179 1.55368 6.48234
> H -0.85442 0.89003 6.75172
> C 0.41403 -0.32166 5.59050
> H 0.78515 -0.88788 6.45559
> H 1.22995 -0.16608 4.87042
> H -0.40773 -0.86672 5.10647
> Pb 2.76768 8.92015 3.28271
> Br 2.45532 8.58198 0.32415
> Br 3.09061 5.88289 2.97254
> Br -0.16884 8.76382 3.33242
> N -0.49170 6.76490 0.35239
> H -0.83808 7.33268 -0.45174
> H 0.27327 7.32407 0.78573
> H -1.26294 6.66041 1.05511
> C 0.00551 5.44873 -0.10612
> H 0.37663 4.88250 0.75897
> H 0.82143 5.60430 -0.82619
> H -0.81625 4.90366 -0.59014
> Pb 2.98494 9.11009 9.16926
> Br 2.67259 8.77192 6.21070
> Br 3.30788 6.07283 8.85909
> Br 0.04843 8.95376 9.21897
> N -0.27443 6.95484 6.23894
> H -0.62081 7.52261 5.43481
> H 0.49053 7.51400 6.67228
> H -1.04567 6.85035 6.94166
> C 0.22278 5.63867 5.78043
> H 0.59390 5.07244 6.64552
> H 1.03870 5.79424 5.06035
> H -0.59898 5.09360 5.29641
> Pb 8.86536 2.76857 3.31004
> Br 9.18829 -0.26869 2.99987
> Br 5.92884 2.61224 3.35975
> N 5.60598 0.61332 0.37972
> H 5.25960 1.18110 -0.42441
> H 6.37094 1.17249 0.81306
> H 4.83474 0.50883 1.08244
> C 6.10319 -0.70285 -0.07879
> H 6.47431 -1.26908 0.78630
> H 6.91911 -0.54727 -0.79886
> H 5.28143 -1.24792 -0.56281
> Pb 9.08262 2.95851 9.19659
> Br 8.77027 2.62034 6.23803
> Br 9.40556 -0.07875 8.88642
> Br 6.14611 2.80218 9.24630
> N 5.82325 0.80326 6.26627
> H 5.47687 1.37103 5.46214
> H 6.58821 1.36243 6.69961
> H 5.05201 0.69877 6.96899
> C 6.32046 -0.51291 5.80776
> H 6.69158 -1.07914 6.67285
> H 7.13638 -0.35734 5.08768
> H 5.49870 -1.05798 5.32374
> Pb 8.67410 8.72890 3.49998
> Br 8.36175 8.39073 0.54142
> Br 8.99704 5.69164 3.18981
> Br 5.73759 8.57257 3.54969
> N 5.41472 6.57365 0.56966
> H 5.06835 7.14142 -0.23447
> H 6.17969 7.13281 1.00300
> H 4.64349 6.46916 1.27238
> C 5.91194 5.25747 0.11115
> H 6.28306 4.69125 0.97624
> H 6.72786 5.41305 -0.60893
> H 5.09017 4.71241 -0.37287
> Pb 8.89137 8.91883 9.38653
> Br 8.57901 8.58067 6.42797
> Br 9.21430 5.88157 9.07636
> Br 5.95486 8.76251 9.43623
> N 5.63199 6.76359 6.45621
> H 5.28561 7.33136 5.65208
> H 6.39696 7.32275 6.88955
> H 4.86075 6.65910 7.15893
> C 6.12921 5.44741 5.99770
> H 6.50032 4.88118 6.86279
> H 6.94512 5.60299 5.27762
> H 5.30744 4.90235 5.51367
> END_POSITIONS
> K_POINTS { automatic }
> 2 2 2 0 0 0
> CELL_PARAMETERS (angstrom)
> 11.81285 -0.38251 0.43454
> -0.38251 11.92065 0.37988
> 0.43454 0.37988 11.77310
> END_ENGINE_INPUT
> END
>
>
>
>
>
> <https://people.epfl.ch/marko.mladenovic>
GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
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