[QE-users] NEB : path length is increasing
Antoine Jay
ajay at laas.fr
Mon Oct 26 08:25:01 CET 2020
Dear Omer,
I think your initial and final minima have not been well relaxed.
When you fix the initial and final structures in a neb you must have relaxed them before, otherwise, you will have negative energy barriers.
Moreover, you may have rotation of molecules that return local minima if your simulation box is too small.
Regards,
Antoine Jay
LAAS-CNRS
Toulouse, France
Le Lundi, Octobre 26, 2020 06:39 CET, Omer Mutasim <omermutasim at ymail.com> a écrit:
Thanks a lot Dr. Tamas & Dr. Jay. , it is very efficient procedure, it worked for me now for all reaction steps. cheers However for one elementary step , particularly SO2 dissociation ( SO2 = SO+O ) i got the following activation barrier, (it hasn't finished yet, but expected to remain around these values since it doesn't change much): ------------------------------ iteration 297 ------------------------------ activation energy (->) = 0.000000 eV activation energy (<-) = 0.308512 eV image energy (eV) error (eV/A) frozen 1 -92402.4972907 0.036606 T 2 -92402.8008646 0.020347 F 3 -92402.6789202 0.048720 F 4 -92403.2726990 0.102631 F 5 -92403.0642888 0.050277 F 6 -92403.2377599 0.067121 F 7 -92402.8058032 0.029355 T activation energy (->) = 0.000000 eV activation energy (<-) = 0.308512 eV Attached is the MEP curve. As you see in MEP graph , there is oscillation in energies.is it normal to get this oscillated MEP curve for such barrier-less reaction step ? if not, how to get rid of this oscillations ?does using "CI" can increase this barrier a bit ? Thanks in advance RegardsOn Wednesday, October 21, 2020, 11:04:14 PM GMT+4, Omer Mutasim <omermutasim at ymail.com> wrote: Very helpful ideas.But after pre-converging with inexpensive parameters, i will get first & last image that are different than my actual images with higher parameters ( k-pointss, cutoff,..)So then how i can use this pre-converged path for my actual settings?
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On Wednesday, October 21, 2020, 3:06 PM, Tamas Karpati <tkarpati at gmail.com> wrote:Dear Omar, Hope it helps, just some ideas:- I could tell more if you would attach the whole input file (ie. thestructures).- Without knowing the structures only I can give some hints: -- Try using smaller PW basis and lower ecutwfc, ecutrho to speed upyour simulation. -- When you obtain something more reliable result, you can changeback to the higher basis. -- Try leaving opt_scheme at its default value. -- For such a reaction (dissociation of such a polarized molecule) you should expect a barrier, therefore CI_scheme should be anything except for no-CI. -- The best is if you can specify the CI manually in theCLIMBING_IMAGES section (choose the CI_scheme accordingly).Bests, t On Tue, Oct 20, 2020 at 6:53 PM Omer Mutasim <omermutasim at ymail.com> wrote:>> Dear All> I'm doning NEB for dissociation reaction of SO2 to SO +O. But it is not converging for more than a week, and the path length is increasing.> Please tell me what is wrong in my input file:>> below is the input & output files:>> Input file:>> BEGIN> BEGIN_PATH_INPUT> &PATH> restart_mode = 'restart'> string_method = 'neb',> nstep_path = 800,> ds = 1.D0,> opt_scheme = "broyden",> num_of_images = 7,> CI_scheme = 'no-CI',> path_thr = 0.05D0,>> /> END_PATH_INPUT> BEGIN_ENGINE_INPUT> &CONTROL> calculation = "relax"> prefix = 'SO2_neb'> outdir = './outdir'> pseudo_dir = '/home/yQE-test/pseudo/'> restart_mode = 'from_scratch'> forc_conv_thr = 1.0e-03> etot_conv_thr = 1e-04> nstep = 200> !tefield = .TRUE> !dipfield = .TRUE> />> &SYSTEM> ibrav = 0> ecutrho = 270> ecutwfc = 45> nat = 111> ntyp = 4> occupations='smearing',smearing='gaussian',degauss=0.005> vdw_corr = 'DFT-D2'> !edir = 3 , emaxpos = 0.6808, eopreg = 0.08 , eamp = 0.001,> nspin = 2> starting_magnetization(1)= 0.01>> /> &ELECTRONS> conv_thr = 1e-06> electron_maxstep = 200> mixing_mode ='local-TF'> mixing_beta = 0.3>> />> &IONS> />> K_POINTS {automatic}> 3 3 1 0 0 1>> ATOMIC_SPECIES> Ni 58.69340 Ni.pbe-n-rrkjus_psl.0.1.UPF> P 30.97376 P.pbe-n-rrkjus_psl.1.0.0.UPF> S 32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF> O 15.9999 O.pbe-n-rrkjus_psl.1.0.0.UPF> CELL_PARAMETERS {angstrom}> 11.765383541833 0.0000000000 0.0000000000> -5.88269177091652 10.1891210324947 0.0000000000> 0.0000000000 0.0000000000 30.9938690567585> BEGIN_POSITIONS> FIRST_IMAGE> ATOMIC_POSITIONS (angstrom)> S -1.181561037 6.155418563 12.124345096> O -1.100425541 4.672437254 11.356300976> O 0.190308001 6.839217965 11.448732238> Ni -2.738525121 4.763450297 0.239145520> Ni 3.139579474 1.358483744 0.232252034> Ni 3.135766403 8.150575392 0.235327906> Ni -4.673593720 8.104467836 1.780118367> .> .> .> .>> output file:>> Program NEB v.6.4.1 starts on 16Oct2020 at 11:35:32>> This program is part of the open-source Quantum ESPRESSO suite> for quantum simulation of materials; please cite> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);> URL http://www.quantum-espresso.org",> in publications or presentations arising from this work. More details at> http://www.quantum-espresso.org/quote>> Parallel version (MPI), running on 80 processors>> MPI processes distributed on 5 nodes> R & G space division: proc/nbgrp/npool/nimage = 80>> parsing_file_name: input.in> Reading input from pw_1.in> Message from routine read_upf::>>> initial path length = 11.3145 bohr> initial inter-image distance = 1.8857 bohr>> string_method = neb> restart_mode = from_scratch> opt_scheme = broyden> num_of_images = 7> nstep_path = 800> CI_scheme = no-CI> first_last_opt = F> use_freezing = F> ds = 1.0000 a.u.> k_max = 0.1000 a.u.> k_min = 0.1000 a.u.> suggested k_max = 0.6169 a.u.> suggested k_min = 0.6169 a.u.> path_thr = 0.0500 eV / A>> ------------------------------ iteration 1 ------------------------------>> tcpu = 6.2 self-consistency for image 1> tcpu = 3675.5 self-consistency for image 2> tcpu = 7662.5 self-consistency for image 3> tcpu = 11422.7 self-consistency for image 4> tcpu = 15346.3 self-consistency for image 5> tcpu = 19108.7 self-consistency for image 6> tcpu = 22571.1 self-consistency for image 7>> activation energy (->) = 70.216194 eV> activation energy (<-) = 71.022062 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92468.8536637 23.505267 F> 3 -92442.9691259 150.213122 F> 4 -92406.7311409 330.353055 F> 5 -92431.0052901 207.333777 F> 6 -92469.0661237 51.663167 F> 7 -92477.7532028 0.024858 T>> path length = 11.314 bohr> inter-image distance = 1.886 bohr>> ------------------------------ iteration 2 ------------------------------>> tcpu = 26119.7 self-consistency for image 2> tcpu = 28731.5 self-consistency for image 3> tcpu = 31027.4 self-consistency for image 4> tcpu = 34094.2 self-consistency for image 5> tcpu = 36988.0 self-consistency for image 6>> activation energy (->) = 22.531451 eV> activation energy (<-) = 23.337319 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92469.5101428 22.300995 F> 3 -92454.4158842 70.627594 F> 4 -92461.1206812 34.307062 F> 5 -92464.4669859 46.783708 F> 6 -92471.4896125 37.765708 F> 7 -92477.7532028 0.024858 T>> path length = 11.384 bohr> inter-image distance = 1.897 bohr>> ------------------------------ iteration 3 ------------------------------>> tcpu = 39172.0 self-consistency for image 2> tcpu = 41888.0 self-consistency for image 3> tcpu = 44777.8 self-consistency for image 4> tcpu = 47642.0 self-consistency for image 5> tcpu = 50615.2 self-consistency for image 6>> activation energy (->) = 13.435341 eV> activation energy (<-) = 14.241209 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92471.6434742 16.119604 F> 3 -92463.5119937 28.367753 F> 4 -92468.1466546 16.740841 F> 5 -92472.7705146 11.019872 F> 6 -92475.3040517 10.662908 F> 7 -92477.7532028 0.024858 T>> path length = 11.502 bohr> inter-image distance = 1.917 bohr>> ------------------------------ iteration 4 ------------------------------>> tcpu = 53323.8 self-consistency for image 2> tcpu = 56077.9 self-consistency for image 3> tcpu = 59014.9 self-consistency for image 4> tcpu = 61990.6 self-consistency for image 5> tcpu = 64608.8 self-consistency for image 6>> activation energy (->) = 6.530687 eV> activation energy (<-) = 7.336554 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92474.0378392 7.910468 F> 3 -92470.4166483 13.061889 F> 4 -92471.2528453 9.923078 F> 5 -92474.2165523 4.209611 F> 6 -92476.2787664 3.450159 F> 7 -92477.7532028 0.024858 T>> path length = 11.724 bohr> inter-image distance = 1.954 bohr>> ------------------------------ iteration 5 ------------------------------>> tcpu = 67273.9 self-consistency for image 2> tcpu = 70152.2 self-consistency for image 3> tcpu = 73153.1 self-consistency for image 4> tcpu = 76203.5 self-consistency for image 5> tcpu = 78824.8 self-consistency for image 6>> activation energy (->) = 3.710859 eV> activation energy (<-) = 4.516727 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92475.5387437 3.615458 F> 3 -92473.5622985 4.695416 F> 4 -92473.2364760 5.734324 F> 5 -92474.4833513 2.877608 F> 6 -92476.4425910 2.876700 F> 7 -92477.7532028 0.024858 T>> path length = 12.038 bohr> inter-image distance = 2.006 bohr>> ------------------------------ iteration 6 ------------------------------>> tcpu = 81355.0 self-consistency for image 2> tcpu = 84402.5 self-consistency for image 3> tcpu = 87564.5 self-consistency for image 4> tcpu = 90568.2 self-consistency for image 5> tcpu = 93110.5 self-consistency for image 6>> activation energy (->) = 2.560838 eV> activation energy (<-) = 3.366706 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92476.0900010 1.040106 F> 3 -92474.7832671 2.988289 F> 4 -92474.3864972 2.085630 F> 5 -92474.8266397 1.998808 F> 6 -92476.6377600 0.667994 F> 7 -92477.7532028 0.024858 T>> path length = 12.364 bohr> inter-image distance = 2.061 bohr>> ------------------------------ iteration 7 ------------------------------>> tcpu = 95248.7 self-consistency for image 2> tcpu = 98189.3 self-consistency for image 3> tcpu = 101337.9 self-consistency for image 4> tcpu = 104423.7 self-consistency for image 5> tcpu = 107076.7 self-consistency for image 6>> activation energy (->) = 2.125802 eV> activation energy (<-) = 2.931670 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92476.0736630 1.319140 F> 3 -92475.4151167 1.955048 F> 4 -92474.8215329 1.921925 F> 5 -92475.0627346 2.135695 F> 6 -92476.7117640 0.696381 F> 7 -92477.7532028 0.024858 T>> path length = 12.868 bohr> inter-image distance = 2.145 bohr>> ------------------------------ iteration 8 ------------------------------>> tcpu = 108885.3 self-consistency for image 2> tcpu = 111194.4 self-consistency for image 3> tcpu = 113961.2 self-consistency for image 4> tcpu = 116506.3 self-consistency for image 5> tcpu = 118361.2 self-consistency for image 6>> activation energy (->) = 2.073805 eV> activation energy (<-) = 2.879673 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92476.1622863 0.861666 F> 3 -92475.4162307 2.192183 F> 4 -92474.8735300 1.631538 F> 5 -92475.0684015 1.824977 F> 6 -92476.7113576 0.606060 F> 7 -92477.7532028 0.024858 T>> path length = 12.633 bohr> inter-image distance = 2.105 bohr>>> .> .> .> .> .> .> reading file 'SO2_neb.path'>>> string_method = neb> restart_mode = restart> opt_scheme = broyden> num_of_images = 7> nstep_path = 800> CI_scheme = no-CI> first_last_opt = F> use_freezing = F> ds = 1.0000 a.u.> k_max = 0.1000 a.u.> k_min = 0.1000 a.u.> suggested k_max = 0.6169 a.u.> suggested k_min = 0.6169 a.u.> path_thr = 0.0500 eV / A>> ------------------------------ iteration 26 ------------------------------>> tcpu = 6.2 self-consistency for image 2> tcpu = 3713.3 self-consistency for image 3> tcpu = 7137.5 self-consistency for image 4> tcpu = 10796.2 self-consistency for image 5> tcpu = 14447.3 self-consistency for image 6>> activation energy (->) = 0.640765 eV> activation energy (<-) = 1.446632 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92476.3065704 0.250516 F> 3 -92477.0673165 0.278078 F> 4 -92476.7787332 0.431860 F> 5 -92476.4800774 0.453182 F> 6 -92476.5576488 0.296200 F> 7 -92477.7532028 0.024858 T>> path length = 17.545 bohr> inter-image distance = 2.924 bohr>> ------------------------------ iteration 27 ------------------------------>> tcpu = 18237.5 self-consistency for image 2> tcpu = 20736.0 self-consistency for image 3> tcpu = 23008.1 self-consistency for image 4> tcpu = 25721.8 self-consistency for image 5> tcpu = 28310.3 self-consistency for image 6>> activation energy (->) = 0.643277 eV> activation energy (<-) = 1.449145 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92476.3040583 0.235899 F> 3 -92477.0080434 0.474599 F> 4 -92476.8143156 0.678632 F> 5 -92476.4592005 0.597470 F> 6 -92476.4827638 0.224064 F> 7 -92477.7532028 0.024858 T>> path length = 18.367 bohr> inter-image distance = 3.061 bohr>> ------------------------------ iteration 28 ------------------------------>> tcpu = 30382.0 self-consistency for image 2> tcpu = 32498.8 self-consistency for image 3> tcpu = 34597.5 self-consistency for image 4> tcpu = 37250.7 self-consistency for image 5> tcpu = 39649.7 self-consistency for image 6>> activation energy (->) = 0.651733 eV> activation energy (<-) = 1.457601 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92476.2956021 0.236096 F> 3 -92476.9388664 0.680956 F> 4 -92476.8025379 0.874373 F> 5 -92476.3933083 0.734403 F> 6 -92476.4272820 0.239132 F> 7 -92477.7532028 0.024858 T>> path length = 19.115 bohr> inter-image distance = 3.186 bohr>> ------------------------------ iteration 29 ------------------------------>> tcpu = 41622.7 self-consistency for image 2> tcpu = 43787.2 self-consistency for image 3> tcpu = 45892.1 self-consistency for image 4> tcpu = 48482.6 self-consistency for image 5> tcpu = 50617.1 self-consistency for image 6>> activation energy (->) = 0.661553 eV> activation energy (<-) = 1.467420 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92476.2857825 0.249692 F> 3 -92476.8823826 0.778237 F> 4 -92476.7843580 1.002202 F> 5 -92476.3323697 0.748960 F> 6 -92476.3885082 0.238984 F> 7 -92477.7532028 0.024858 T>> path length = 19.742 bohr> inter-image distance = 3.290 bohr>> ------------------------------ iteration 30 ------------------------------>> tcpu = 52474.3 self-consistency for image 2> tcpu = 54679.9 self-consistency for image 3> tcpu = 57012.5 self-consistency for image 4> tcpu = 59877.3 self-consistency for image 5> tcpu = 62490.2 self-consistency for image 6>> activation energy (->) = 0.704760 eV> activation energy (<-) = 1.510628 eV>> image energy (eV) error (eV/A) frozen>> 1 -92476.9473351 0.023792 T> 2 -92476.2668397 0.342411 F> 3 -92476.7810889 0.907920 F> 4 -92476.7414553 1.153276 F> 5 -92476.2425749 0.898295 F> 6 -92476.3370447 0.341313 F> 7 -92477.7532028 0.024858 T>> path length = 20.745 bohr> inter-image distance = 3.457 bohr>> ------------------------------ iteration 31 ------------------------------>> tcpu = 64431.3 self-consistency for image 2> tcpu = 66430.0 self-consistency for image 3> tcpu = 68491.4 self-consistency for image 4> tcpu = 70987.8 self-consistency for image 5>>>>> _______________________________________________> 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_______________________________________________Quantum ESPRESSO is supported by MaX (www.max-centre.eu)users mailing list users at lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
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