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<p>Yes, that was the problem! I swapped the rows so that there is the same ordering of atom types in both the initial and the final image and it works!</p>
<p><br>
</p>
<p>Thanks a lot,</p>
<p>Marko<br>
</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of Giuseppe Mattioli <giuseppe.mattioli@ism.cnr.it><br>
<b>Sent:</b> Wednesday, November 13, 2019 1:39:34 PM<br>
<b>To:</b> Quantum ESPRESSO users Forum<br>
<b>Subject:</b> Re: [QE-users] Inconsistency of atomic species in neb.x calculations</font>
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Dear Marko<br>
If I remember well (but I could be wrong) neb.x expects that atom 1 in <br>
the first image is the same atom 1 in the last image, atom 2 is atom <br>
2, etc.<br>
HTH<br>
Giuseppe<br>
<br>
Mladenovic Marko <marko.mladenovic@epfl.ch> ha scritto:<br>
<br>
> Hello everyone,<br>
><br>
><br>
> I am investigating the ionic diffusion in halide perovskites by <br>
> performing neb.x calculations. In some cases, I get the error "<br>
><br>
> inconsistency of atomic species". Input file for one of the examples <br>
> that gives this error is given below. I understand that the error <br>
> suggest that there is something is wrong with the coordinates, <br>
> however, I cannot see any problem with them. Has anyone else <br>
> encountered this kind of issue?<br>
><br>
> Thank you!<br>
><br>
> Marko Mladenovic, PhD<br>
> Postdoctoral researcher<br>
> École polytechnique fédérale de Lausanne<br>
> SB - ISIC - LCBC<br>
> web: <a href="https://people.epfl.ch/marko.mladenovic">https://people.epfl.ch/marko.mladenovic</a><br>
><br>
><br>
> BEGIN<br>
> BEGIN_PATH_INPUT<br>
> &PATH<br>
> restart_mode = 'from_scratch'<br>
> string_method = 'neb',<br>
> nstep_path = 500,<br>
> ds = 2.D0,<br>
> opt_scheme = "broyden",<br>
> num_of_images = 3,<br>
> ! k_max = 0.3D0,<br>
> ! k_min = 0.2D0,<br>
> CI_scheme = "auto",<br>
> path_thr = 0.1D0,<br>
> first_last_opt=.true.<br>
> /<br>
> END_PATH_INPUT<br>
> BEGIN_ENGINE_INPUT<br>
> &CONTROL<br>
> ! prefix = "pwscf"<br>
> ! outdir = "/tmp",<br>
> pseudo_dir = "/scratch/mladenov/PPQE/",<br>
> /<br>
> &SYSTEM<br>
> ibrav = 0,<br>
> ! celldm(1) = 1.D0,<br>
> nat = 95,<br>
> ntyp = 5,<br>
> ecutwfc = 40.0D0,<br>
> ecutrho = 280.0D0,<br>
> occupations = "smearing",<br>
> degauss = 0.05D0,<br>
> tot_charge=1<br>
> /<br>
> &ELECTRONS<br>
> conv_thr = 1.D-8,<br>
> mixing_beta = 0.3D0,<br>
> /<br>
> &IONS<br>
> pot_extrapolation = "second_order",<br>
> wfc_extrapolation = "second_order",<br>
> /<br>
> ATOMIC_SPECIES<br>
> Pb 207.2 Pb.pbesol-dn-rrkjus_psl.0.2.2.UPF<br>
> Br 126.90447 Br.pbesol-n-rrkjus_psl.0.2.UPF<br>
> C 12.0107 C.pbesol-n-rrkjus_psl.0.1.UPF<br>
> N 14.0067 N.pbesol-n-rrkjus_psl.0.1.UPF<br>
> H 1.00794 H.pbesol-rrkjus_psl.0.1.UPF<br>
> BEGIN_POSITIONS<br>
> FIRST_IMAGE<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pb 2.95893 2.95983 3.09277<br>
> Br 3.28187 -0.07743 2.78260<br>
> Br 0.02242 2.80350 3.14248<br>
> N -0.30045 0.80458 0.16245<br>
> H -0.64683 1.37235 -0.64167<br>
> H 0.46452 1.36374 0.59580<br>
> H -1.07168 0.70009 0.86517<br>
> C 0.19677 -0.51160 -0.29605<br>
> H 0.56789 -1.07782 0.56904<br>
> H 1.01268 -0.35602 -1.01613<br>
> H -0.62500 -1.05666 -0.78008<br>
> Pb 3.17620 3.14976 8.97932<br>
> Br 2.86384 2.81160 6.02077<br>
> Br 3.49913 0.11250 8.66915<br>
> Br 0.23969 2.99344 9.02903<br>
> N -0.08318 0.99452 6.04900<br>
> H -0.42956 1.56229 5.24487<br>
> H 0.68179 1.55368 6.48234<br>
> H -0.85442 0.89003 6.75172<br>
> C 0.41403 -0.32166 5.59050<br>
> H 0.78515 -0.88788 6.45559<br>
> H 1.22995 -0.16608 4.87042<br>
> H -0.40773 -0.86672 5.10647<br>
> Pb 2.76768 8.92015 3.28271<br>
> Br 2.45532 8.58198 0.32415<br>
> Br 3.09061 5.88289 2.97254<br>
> Br -0.16884 8.76382 3.33242<br>
> N -0.49170 6.76490 0.35239<br>
> H -0.83808 7.33268 -0.45174<br>
> H 0.27327 7.32407 0.78573<br>
> H -1.26294 6.66041 1.05511<br>
> C 0.00551 5.44873 -0.10612<br>
> H 0.37663 4.88250 0.75897<br>
> H 0.82143 5.60430 -0.82619<br>
> H -0.81625 4.90366 -0.59014<br>
> Pb 2.98494 9.11009 9.16926<br>
> Br 2.67259 8.77192 6.21070<br>
> Br 3.30788 6.07283 8.85909<br>
> Br 0.04843 8.95376 9.21897<br>
> N -0.27443 6.95484 6.23894<br>
> H -0.62081 7.52261 5.43481<br>
> H 0.49053 7.51400 6.67228<br>
> H -1.04567 6.85035 6.94166<br>
> C 0.22278 5.63867 5.78043<br>
> H 0.59390 5.07244 6.64552<br>
> H 1.03870 5.79424 5.06035<br>
> H -0.59898 5.09360 5.29641<br>
> Pb 8.86536 2.76857 3.31004<br>
> Br 8.55300 2.43041 0.35148<br>
> Br 9.18829 -0.26869 2.99987<br>
> Br 5.92884 2.61224 3.35975<br>
> N 5.60598 0.61332 0.37972<br>
> H 5.25960 1.18110 -0.42441<br>
> H 6.37094 1.17249 0.81306<br>
> H 4.83474 0.50883 1.08244<br>
> C 6.10319 -0.70285 -0.07879<br>
> H 6.47431 -1.26908 0.78630<br>
> H 6.91911 -0.54727 -0.79886<br>
> H 5.28143 -1.24792 -0.56281<br>
> Pb 9.08262 2.95851 9.19659<br>
> Br 8.77027 2.62034 6.23803<br>
> Br 9.40556 -0.07875 8.88642<br>
> Br 6.14611 2.80218 9.24630<br>
> N 5.82325 0.80326 6.26627<br>
> H 5.47687 1.37103 5.46214<br>
> H 6.58821 1.36243 6.69961<br>
> H 5.05201 0.69877 6.96899<br>
> C 6.32046 -0.51291 5.80776<br>
> H 6.69158 -1.07914 6.67285<br>
> H 7.13638 -0.35734 5.08768<br>
> H 5.49870 -1.05798 5.32374<br>
> Pb 8.67410 8.72890 3.49998<br>
> Br 8.36175 8.39073 0.54142<br>
> Br 8.99704 5.69164 3.18981<br>
> Br 5.73759 8.57257 3.54969<br>
> N 5.41472 6.57365 0.56966<br>
> H 5.06835 7.14142 -0.23447<br>
> H 6.17969 7.13281 1.00300<br>
> H 4.64349 6.46916 1.27238<br>
> C 5.91194 5.25747 0.11115<br>
> H 6.28306 4.69125 0.97624<br>
> H 6.72786 5.41305 -0.60893<br>
> H 5.09017 4.71241 -0.37287<br>
> Pb 8.89137 8.91883 9.38653<br>
> Br 8.57901 8.58067 6.42797<br>
> Br 9.21430 5.88157 9.07636<br>
> Br 5.95486 8.76251 9.43623<br>
> N 5.63199 6.76359 6.45621<br>
> H 5.28561 7.33136 5.65208<br>
> H 6.39696 7.32275 6.88955<br>
> H 4.86075 6.65910 7.15893<br>
> C 6.12921 5.44741 5.99770<br>
> H 6.50032 4.88118 6.86279<br>
> H 6.94512 5.60299 5.27762<br>
> H 5.30744 4.90235 5.51367<br>
> LAST_IMAGE<br>
> ATOMIC_POSITIONS {angstrom}<br>
> Pb 2.95893 2.95983 3.09277<br>
> Br 2.64658 2.62166 0.13422<br>
> Br 3.28187 -0.07743 2.78260<br>
> Br 0.02242 2.80350 3.14248<br>
> N -0.30045 0.80458 0.16245<br>
> H -0.64683 1.37235 -0.64167<br>
> H 0.46452 1.36374 0.59580<br>
> H -1.07168 0.70009 0.86517<br>
> C 0.19677 -0.51160 -0.29605<br>
> H 0.56789 -1.07782 0.56904<br>
> H 1.01268 -0.35602 -1.01613<br>
> H -0.62500 -1.05666 -0.78008<br>
> Pb 3.17620 3.14976 8.97932<br>
> Br 2.86384 2.81160 6.02077<br>
> Br 3.49913 0.11250 8.66915<br>
> Br 0.23969 2.99344 9.02903<br>
> N -0.08318 0.99452 6.04900<br>
> H -0.42956 1.56229 5.24487<br>
> H 0.68179 1.55368 6.48234<br>
> H -0.85442 0.89003 6.75172<br>
> C 0.41403 -0.32166 5.59050<br>
> H 0.78515 -0.88788 6.45559<br>
> H 1.22995 -0.16608 4.87042<br>
> H -0.40773 -0.86672 5.10647<br>
> Pb 2.76768 8.92015 3.28271<br>
> Br 2.45532 8.58198 0.32415<br>
> Br 3.09061 5.88289 2.97254<br>
> Br -0.16884 8.76382 3.33242<br>
> N -0.49170 6.76490 0.35239<br>
> H -0.83808 7.33268 -0.45174<br>
> H 0.27327 7.32407 0.78573<br>
> H -1.26294 6.66041 1.05511<br>
> C 0.00551 5.44873 -0.10612<br>
> H 0.37663 4.88250 0.75897<br>
> H 0.82143 5.60430 -0.82619<br>
> H -0.81625 4.90366 -0.59014<br>
> Pb 2.98494 9.11009 9.16926<br>
> Br 2.67259 8.77192 6.21070<br>
> Br 3.30788 6.07283 8.85909<br>
> Br 0.04843 8.95376 9.21897<br>
> N -0.27443 6.95484 6.23894<br>
> H -0.62081 7.52261 5.43481<br>
> H 0.49053 7.51400 6.67228<br>
> H -1.04567 6.85035 6.94166<br>
> C 0.22278 5.63867 5.78043<br>
> H 0.59390 5.07244 6.64552<br>
> H 1.03870 5.79424 5.06035<br>
> H -0.59898 5.09360 5.29641<br>
> Pb 8.86536 2.76857 3.31004<br>
> Br 9.18829 -0.26869 2.99987<br>
> Br 5.92884 2.61224 3.35975<br>
> N 5.60598 0.61332 0.37972<br>
> H 5.25960 1.18110 -0.42441<br>
> H 6.37094 1.17249 0.81306<br>
> H 4.83474 0.50883 1.08244<br>
> C 6.10319 -0.70285 -0.07879<br>
> H 6.47431 -1.26908 0.78630<br>
> H 6.91911 -0.54727 -0.79886<br>
> H 5.28143 -1.24792 -0.56281<br>
> Pb 9.08262 2.95851 9.19659<br>
> Br 8.77027 2.62034 6.23803<br>
> Br 9.40556 -0.07875 8.88642<br>
> Br 6.14611 2.80218 9.24630<br>
> N 5.82325 0.80326 6.26627<br>
> H 5.47687 1.37103 5.46214<br>
> H 6.58821 1.36243 6.69961<br>
> H 5.05201 0.69877 6.96899<br>
> C 6.32046 -0.51291 5.80776<br>
> H 6.69158 -1.07914 6.67285<br>
> H 7.13638 -0.35734 5.08768<br>
> H 5.49870 -1.05798 5.32374<br>
> Pb 8.67410 8.72890 3.49998<br>
> Br 8.36175 8.39073 0.54142<br>
> Br 8.99704 5.69164 3.18981<br>
> Br 5.73759 8.57257 3.54969<br>
> N 5.41472 6.57365 0.56966<br>
> H 5.06835 7.14142 -0.23447<br>
> H 6.17969 7.13281 1.00300<br>
> H 4.64349 6.46916 1.27238<br>
> C 5.91194 5.25747 0.11115<br>
> H 6.28306 4.69125 0.97624<br>
> H 6.72786 5.41305 -0.60893<br>
> H 5.09017 4.71241 -0.37287<br>
> Pb 8.89137 8.91883 9.38653<br>
> Br 8.57901 8.58067 6.42797<br>
> Br 9.21430 5.88157 9.07636<br>
> Br 5.95486 8.76251 9.43623<br>
> N 5.63199 6.76359 6.45621<br>
> H 5.28561 7.33136 5.65208<br>
> H 6.39696 7.32275 6.88955<br>
> H 4.86075 6.65910 7.15893<br>
> C 6.12921 5.44741 5.99770<br>
> H 6.50032 4.88118 6.86279<br>
> H 6.94512 5.60299 5.27762<br>
> H 5.30744 4.90235 5.51367<br>
> END_POSITIONS<br>
> K_POINTS { automatic }<br>
> 2 2 2 0 0 0<br>
> CELL_PARAMETERS (angstrom)<br>
> 11.81285 -0.38251 0.43454<br>
> -0.38251 11.92065 0.37988<br>
> 0.43454 0.37988 11.77310<br>
> END_ENGINE_INPUT<br>
> END<br>
><br>
><br>
><br>
><br>
><br>
> <<a href="https://people.epfl.ch/marko.mladenovic">https://people.epfl.ch/marko.mladenovic</a>><br>
<br>
<br>
<br>
GIUSEPPE MATTIOLI<br>
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
Via Salaria Km 29,300 - C.P. 10<br>
I-00015 - Monterotondo Scalo (RM)<br>
Mob (*preferred*) +39 373 7305625<br>
Tel + 39 06 90672342 - Fax +39 06 90672316<br>
E-mail: <giuseppe.mattioli@ism.cnr.it><br>
<br>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso">www.max-centre.eu/quantum-espresso</a>)<br>
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