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!
Thanks a lot, Marko ________________________________ From: users <[email protected]> on behalf of Giuseppe Mattioli <[email protected]> Sent: Wednesday, November 13, 2019 1:39:34 PM To: Quantum ESPRESSO users Forum Subject: Re: [QE-users] Inconsistency of atomic species in neb.x calculations 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 <[email protected]> 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: <[email protected]> _______________________________________________ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>) users mailing list [email protected] https://lists.quantum-espresso.org/mailman/listinfo/users
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