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<div dir="ltr" data-setdir="false"><div><div dir="ltr" data-setdir="false">Great idea. </div><div dir="ltr" data-setdir="false">but how to fix atoms in <span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">lowermost layer(s) in phonon calculation? </span></span></div><div dir="ltr" data-setdir="false"><span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><span><span style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"> my supercell is large (110 atoms ) , i have fixed <span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">lowermost layers</span></span> by setting " 0" ( i.e. 0 0 0) in atomic positions in scf input file ? but it i get the same DOF of 330 , (3*110) ! ,which means ALL atoms were perturbed ! </span></span><br></span></span></div><div dir="ltr" data-setdir="false"><span><span style="color: rgb(0, 0, 0); font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"><span><span style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif;">i guess it i run it this way (DOF = 330) it may take weeks , using 100 cores, to converge.</span></span></span></span></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif;"></div></div><br></div><div><br></div>
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On Tuesday, October 27, 2020, 06:01:35 PM GMT+4, Tamas Karpati <tkarpati@gmail.com> wrote:
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<div><div dir="ltr">Sorry for confusing.<br></div><div dir="ltr"><br></div><div dir="ltr">Single q is OK, k point I don't know but probably also OK<br></div><div dir="ltr">(this one I would check; first use just Gamma here, too).<br></div><div dir="ltr"><br></div><div dir="ltr">With the isolated molecule use the same cell size as with<br></div><div dir="ltr">slab and slab+mol for consistency.<br></div><div dir="ltr"><br></div><div dir="ltr">Atom fixing: fix only the lowermost layer(s) far from reaction center<br></div><div dir="ltr">and keep the contributing atoms (up there) in the phonon simulation.<br></div><div dir="ltr">Do not delete the atoms (that would spoil stoichiometry).<br></div><div dir="ltr">If your slab (and slab+mol) is optimized, this should work (does for me).<br></div><div dir="ltr">Big system offers you quite a DOF. Boo. You'll have some time for a coffee.<br></div><div dir="ltr">Hope it was not a crash (in which case I've no idea).<br></div><div dir="ltr"><br></div><div dir="ltr">On Tue, Oct 27, 2020 at 1:26 PM Omer Mutasim <<a ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br></div><div dir="ltr">><br></div><div dir="ltr">> I mean Single-q phonon calculation (q=0).<br></div><div dir="ltr">> Great, i will use a large unit cell for the isolated molecule.<br></div><div dir="ltr">> Regarding adsorbate molecule : you mentioned : " try to keep uppermost 1~2 atomic layers " , so what should i do for the remaining bottom layers , how prevent the perturbation of these bottom layers ? should i delete them totally or i have to fix them by setting " 0" ( i.e. 0 0 0) in atomic positions ? i tried the latter , but it i get degrees of freedom of 330 ! , which means they were perturbed also !<br></div><div dir="ltr">><br></div><div dir="ltr">> thanks a lot for suggesting these softwares, i will download it.<br></div><div dir="ltr">><br></div><div dir="ltr">> On Tuesday, October 27, 2020, 02:38:16 PM GMT+4, Tamas Karpati <<a ymailto="mailto:tkarpati@gmail.com" href="mailto:tkarpati@gmail.com">tkarpati@gmail.com</a>> wrote:<br></div><div dir="ltr">><br></div><div dir="ltr">><br></div><div dir="ltr">> Omer,<br></div><div dir="ltr">> Congrats!<br></div><div dir="ltr">> What do you mean by Gamma point vibs. (k points or q points)?<br></div><div dir="ltr">> For a single molecule (no slab at all) and large-enough cell i think<br></div><div dir="ltr">> both are OK.<br></div><div dir="ltr">> For rxn-on-slab I would calibrate but guess it's a good approximation.<br></div><div dir="ltr">><br></div><div dir="ltr">> Again, fixing the surf. atoms kills chemistry off... try to keep<br></div><div dir="ltr">> uppermost 1~2 atomic layers in<br></div><div dir="ltr">> (and it's not only precision, it may also affect the qualitative<br></div><div dir="ltr">> description of the process).<br></div><div dir="ltr">><br></div><div dir="ltr">> Did you try to use TAMkin, ASE? I guess you may find them useful to<br></div><div dir="ltr">> derive rate consts.<br></div><div dir="ltr">> (Little Python-ing will be necessary, though.)<br></div><div dir="ltr">> HTH,<br></div><div dir="ltr">> t<br></div><div dir="ltr">><br></div><div dir="ltr">> On Tue, Oct 27, 2020 at 9:13 AM Omer Mutasim <<a ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br></div><div dir="ltr">> ><br></div><div dir="ltr">> > NEB is fine now.<br></div><div dir="ltr">> > I see in your previous message you mentioned phonon calculation to check if the transition state is true (imaginary mode) .<br></div><div dir="ltr">> > I need to calculate the the virbrational frequencies of adsorbate molecule , in order to estimate the partition function (for entropy ,reaction rate constants). so my question goes like:<br></div><div dir="ltr">> > can i use phonon calculation at Gamma point only to get the normal modes of vibrations of molecule ?<br></div><div dir="ltr">> ><br></div><div dir="ltr">> > i have a large supercell (108 atoms) , can i fix the surface atoms to get the vibrations for the molecule only ?<br></div><div dir="ltr">> > does fixing the surface atoms will not affect the precision of molecule's vibrations ?<br></div><div dir="ltr">> ><br></div><div dir="ltr">> > If you i shouldn't fix the surface atoms, How to distinguish between the vibrational frequencies of adsorbate molecule and crystal ?<br></div><div dir="ltr">> > Thanks in advance<br></div><div dir="ltr">> ><br></div><div dir="ltr">> ><br></div><div dir="ltr">> > On Monday, October 26, 2020, 10:09:25 PM GMT+4, Tamas Karpati <<a ymailto="mailto:tkarpati@gmail.com" href="mailto:tkarpati@gmail.com">tkarpati@gmail.com</a>> wrote:<br></div><div dir="ltr">> ><br></div><div dir="ltr">> ><br></div><div dir="ltr">> > Dear Omer,<br></div><div dir="ltr">> ><br></div><div dir="ltr">> > You have shown a figure of a MEP. Most probably image 4 is either R (reactant)<br></div><div dir="ltr">> > or P (product). In one case im2=R, im3=TS, im4=P (and im6 is the diffused P),<br></div><div dir="ltr">> > the other possibility is that im2=diffused R and im4=R then im6=P (im5=TS).<br></div><div dir="ltr">> > Try to judge which is which, then use R and P to start a NEB similarly to<br></div><div dir="ltr">> > your very first input that you have shared (running without a CI).<br></div><div dir="ltr">> ><br></div><div dir="ltr">> > As for your second question, summation of barriers is not very theoretical.<br></div><div dir="ltr">> > The "bottleneck" in a multistep reaction is related the highest barrier.<br></div><div dir="ltr">> > If you are able to derive an Arrhenius-like (or better) rate constant (k)<br></div><div dir="ltr">> > for each step, then -for consecutive reactions- your effective k = k1*k2*...<br></div><div dir="ltr">> > Derive the effective barrier if you like :)<br></div><div dir="ltr">> ><br></div><div dir="ltr">> > HTH,<br></div><div dir="ltr">> > t<br></div><div dir="ltr">> ><br></div><div dir="ltr">> > On Mon, Oct 26, 2020 at 5:28 PM Omer Mutasim <<a ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > you saved my life, thanks a bunch Dr. Tamas<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > I'm only interested in dissociation reaction (SO2 to SO & O) , so i should only consider image 1 & 2 only, based on AXSF file , for running NEB , right ?<br></div><div dir="ltr">> > > what are these two steps you have seen ?<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > i'm doing micro-kinetic modeling for reaction mechanism, so in this case , should i consider the summation of " dissociation barrier " & "diffusion barrier for dissociated SO & O to most stable sites " as the activation barrier for the elementary reaction step SO2 = SO + O ? or i should only consider the dissociation barrier ?<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > Regarding AXSF, it is automatically generated by Quantum Espresso v. 6.4<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > On Monday, October 26, 2020, 07:56:50 PM GMT+4, Tamas Karpati <<a ymailto="mailto:tkarpati@gmail.com" href="mailto:tkarpati@gmail.com">tkarpati@gmail.com</a>> wrote:<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > Dear Omer,<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > 1, SO (being "locally" linear) is not really rotating (just nomenclature)<br></div><div dir="ltr">> > > and such movements are unimportant in this case, I think<br></div><div dir="ltr">> > > 2, as for the NEB: as I said, choose the beginning and end images<br></div><div dir="ltr">> > > of what you consider eg. step 1 and run a NEB like before,<br></div><div dir="ltr">> > > except for replacing your original 2 structures by the new duett.<br></div><div dir="ltr">> > > 2b, do the same for the other elementary step to zoom-in MEP for the<br></div><div dir="ltr">> > > dissociation barrier (I think I saw two steps in your MEP).<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > Attaching the AXSF file was useful, thanks!<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > Please let me ask a stupid question: how do you create such a useful<br></div><div dir="ltr">> > > AXSF file from the NEB job's results? (Sorry for such a trivial one!!)<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > Regards,<br></div><div dir="ltr">> > > t<br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > ><br></div><div dir="ltr">> > > On Mon, Oct 26, 2020 at 4:20 PM Omer Mutasim <<a ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br></div><div dir="ltr">> > > ><br></div><div dir="ltr">> > > ><br></div><div dir="ltr">> > > > Dear Dr. Tamas<br></div><div dir="ltr">> > > > your ideas are very helpful. Your are right.<br></div><div dir="ltr">> > > > i have just noticed that it is a surface reaction + diffusion of dissociated products (SO & O) to most stable sites ( one reaction + 2 diffusion step). Dissociation occurs in image 2 immediately , image 3,4,5 shows diffusion of SO to most stable site (a bit far site , 3 Angstrom), (image 5 is rotation of SO), image 5 shows diffusion of "O" and again rotation of "SO" .<br></div><div dir="ltr">> > > > So how to break down this steps into simpler steps than can be easily handle by NEB ?<br></div><div dir="ltr">> > > > how to deal many rotations of "SO" molecule as it takes most of the images ?<br></div><div dir="ltr">> > > ><br></div><div dir="ltr">> > > > attached is axsf output file for the neb, please view it with xcrysden<br></div><div dir="ltr">> > > > On Monday, October 26, 2020, 06:31:22 PM GMT+4, Tamas Karpati <<a ymailto="mailto:tkarpati@gmail.com" href="mailto:tkarpati@gmail.com">tkarpati@gmail.com</a>> wrote:<br></div><div dir="ltr">> > > ><br></div><div dir="ltr">> > > ><br></div><div dir="ltr">> > > > please note that in case your preoptimized first and/or last structures<br></div><div dir="ltr">> > > > are not the direct reactant and product structures but a R+diffusion<br></div><div dir="ltr">> > > > or P+diffusion step results, your MEP would (and it does) look<br></div><div dir="ltr">> > > > as if you have modelled a two (or even more) steps "reaction" even if<br></div><div dir="ltr">> > > > just one of them is actually "chemistry".<br></div><div dir="ltr">> > > ><br></div><div dir="ltr">> > > > On Mon, Oct 26, 2020 at 3:11 PM Omer Mutasim <<a ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > yes, there is a barrier for the reverse reaction.<br></div><div dir="ltr">> > > > > i have check the initial & final structure again , it was relaxed until force is less than 0.003.<br></div><div dir="ltr">> > > > > I do also agree with you that i should use 1 neb with barrier, and this is what i'm doing exactly.<br></div><div dir="ltr">> > > > > but for this dissociation reaction step (SO2 = SO + O), i think this is the simplest elementary step i can get form SO2 molecule , it can't be broken down into a simpler elementary reaction steps.<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > One this i should mention is that : for the initial structure (SO2*) , I didn't consider the most stable adsorption site for SO2* (E_ads=-0.3 eV), there is neighboring site that is a bit less stable (E_ads = -0.2 eV) which i've used for NEB. I didn't consider the former (most stable site) because the distance between molecule and surface is 3.5 A , , however for the less stable site , the distance is 1.5 A, so i thought it is not proper to consider this physisorbed state in NEB, Please correct me if i'm wrong.<br></div><div dir="ltr">> > > > > thanks a lot for your help.<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > Regards<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > On Monday, October 26, 2020, 05:00:26 PM GMT+4, Tamas Karpati <<a ymailto="mailto:tkarpati@gmail.com" href="mailto:tkarpati@gmail.com">tkarpati@gmail.com</a>> wrote:<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > Dear Omer,<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > I'd like to underline what Antoine has said and suggest that<br></div><div dir="ltr">> > > > > both your first and last structures are saddle points (of order K and L,<br></div><div dir="ltr">> > > > > respectively), rather than minima. Also I agree that your reaction<br></div><div dir="ltr">> > > > > is not barrierless -in accordance with chemical intuition.<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > To make it simple, I recommend<br></div><div dir="ltr">> > > > > - make your 2nd image the first,<br></div><div dir="ltr">> > > > > - make your 6th image the last,<br></div><div dir="ltr">> > > > > - do use more images (even for a single step reaction,<br></div><div dir="ltr">> > > > > but your MEP indicates two TS-es meaning a 2 step reaction<br></div><div dir="ltr">> > > > > which -on more elaboration- may turn out to be an N step one;<br></div><div dir="ltr">> > > > > only you need more points to see its real E-profile).<br></div><div dir="ltr">> > > > > - rerun your NEB job.<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > In fact you should check for imaginary second derivatives by the Phonon code<br></div><div dir="ltr">> > > > > to ensure about each minima/maxima/TS being what they look in such a MEP.<br></div><div dir="ltr">> > > > > Of course, it is painfully slow and many just skip this step.<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > Other ideas:<br></div><div dir="ltr">> > > > > - check the geometry of your 3 local minima and 2 TS-es<br></div><div dir="ltr">> > > > > to see if they correspond to chemically rational structures.<br></div><div dir="ltr">> > > > > - if they look so, decide whether the second minimum is really<br></div><div dir="ltr">> > > > > your product, and if it is so then this should be your last image<br></div><div dir="ltr">> > > > > (and not the 6th as I said above) for rerunning your NEB.<br></div><div dir="ltr">> > > > > - of course, you can model a multistep reaction by a single NEB job,<br></div><div dir="ltr">> > > > > choose the approach that best serves your postprocessing task.<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > Hope this helps,<br></div><div dir="ltr">> > > > > t<br></div><div dir="ltr">> > > > ><br></div><div dir="ltr">> > > > > On Mon, Oct 26, 2020 at 1:40 PM Antoine Jay <<a ymailto="mailto:ajay@laas.fr" href="mailto:ajay@laas.fr">ajay@laas.fr</a>> wrote:<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > There is an energy barrier:<br></div><div dir="ltr">> > > > > > the one between your intermediate minima and your final state.<br></div><div dir="ltr">> > > > > > There is no barrier between initial and intermediate minima.<br></div><div dir="ltr">> > > > > > You should wonder why you have an intermediate minima that is lower in energy (<0.4eV) than the final inserted molecule, this is why I was asking if it was enough relaxed.<br></div><div dir="ltr">> > > > > > Maybe the first exothermic reaction gives enough energy for the second...<br></div><div dir="ltr">> > > > > > But for sure, when you have such a multi-barriers reaction, a 7 images neb is not enough.<br></div><div dir="ltr">> > > > > > If you need accurate results, it is better to have 1 neb per barrier, as you have 1 CI per path.<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Regards,<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Antoine Jay<br></div><div dir="ltr">> > > > > > LAAS-CNRS<br></div><div dir="ltr">> > > > > > Toulouse, France<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Le Lundi, Octobre 26, 2020 09:10 CET, Omer Mutasim <<a ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> a écrit:<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Dear Dr. Jay<br></div><div dir="ltr">> > > > > > I have relaxed the initial and final structures before neb.<br></div><div dir="ltr">> > > > > > Regarding simulation box, i'm using sqrt(3)*sqrt(3) supercell, the other five reaction steps converged well.<br></div><div dir="ltr">> > > > > > However, i have seen in the literature that similar catalyst resulted in such barrier-less dissociation.<br></div><div dir="ltr">> > > > > > So my question goes like : with this oscillated MEP , can i conclude it is barrier-less reaction ? or it is even necessary for barrier-less step to have no oscillation ?<br></div><div dir="ltr">> > > > > > does changing the adsorption site of the reactant (SO2) to less stable site might solve the issue ?<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Regards<br></div><div dir="ltr">> > > > > > On Monday, October 26, 2020, 11:25:36 AM GMT+4, Antoine Jay <<a ymailto="mailto:ajay@laas.fr" href="mailto:ajay@laas.fr">ajay@laas.fr</a>> wrote:<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Dear Omer,<br></div><div dir="ltr">> > > > > > I think your initial and final minima have not been well relaxed.<br></div><div dir="ltr">> > > > > > When you fix the initial and final structures in a neb you must have relaxed them before, otherwise, you will have negative energy barriers.<br></div><div dir="ltr">> > > > > > Moreover, you may have rotation of molecules that return local minima if your simulation box is too small.<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Regards,<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Antoine Jay<br></div><div dir="ltr">> > > > > > LAAS-CNRS<br></div><div dir="ltr">> > > > > > Toulouse, France<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Le Lundi, Octobre 26, 2020 06:39 CET, Omer Mutasim <<a ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> a écrit:<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Thanks a lot Dr. Tamas & Dr. Jay. , it is very efficient procedure, it worked for me now for all reaction steps. cheers<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > 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):<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > ------------------------------ iteration 297 ------------------------------<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > activation energy (->) = 0.000000 eV<br></div><div dir="ltr">> > > > > > activation energy (<-) = 0.308512 eV<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > 1 -92402.4972907 0.036606 T<br></div><div dir="ltr">> > > > > > 2 -92402.8008646 0.020347 F<br></div><div dir="ltr">> > > > > > 3 -92402.6789202 0.048720 F<br></div><div dir="ltr">> > > > > > 4 -92403.2726990 0.102631 F<br></div><div dir="ltr">> > > > > > 5 -92403.0642888 0.050277 F<br></div><div dir="ltr">> > > > > > 6 -92403.2377599 0.067121 F<br></div><div dir="ltr">> > > > > > 7 -92402.8058032 0.029355 T<br></div><div dir="ltr">> > > > > > activation energy (->) = 0.000000 eV<br></div><div dir="ltr">> > > > > > activation energy (<-) = 0.308512 eV<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Attached is the MEP curve. As you see in MEP graph , there is oscillation in energies.<br></div><div dir="ltr">> > > > > > is it normal to get this oscillated MEP curve for such barrier-less reaction step ? if not, how to get rid of this oscillations ?<br></div><div dir="ltr">> > > > > > does using "CI" can increase this barrier a bit ?<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Thanks in advance<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Regards<br></div><div dir="ltr">> > > > > > On Wednesday, October 21, 2020, 11:04:14 PM GMT+4, Omer Mutasim <<a ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Very helpful ideas.<br></div><div dir="ltr">> > > > > > 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,..)<br></div><div dir="ltr">> > > > > > So then how i can use this pre-converged path for my actual settings?<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Sent from Yahoo Mail for iPhone<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > On Wednesday, October 21, 2020, 3:06 PM, Tamas Karpati <<a ymailto="mailto:tkarpati@gmail.com" href="mailto:tkarpati@gmail.com">tkarpati@gmail.com</a>> wrote:<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Dear Omar,<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > Hope it helps, just some ideas:<br></div><div dir="ltr">> > > > > > - I could tell more if you would attach the whole input file (ie. the<br></div><div dir="ltr">> > > > > > structures).<br></div><div dir="ltr">> > > > > > - Without knowing the structures only I can give some hints:<br></div><div dir="ltr">> > > > > > -- Try using smaller PW basis and lower ecutwfc, ecutrho to speed up<br></div><div dir="ltr">> > > > > > your simulation.<br></div><div dir="ltr">> > > > > > -- When you obtain something more reliable result, you can change<br></div><div dir="ltr">> > > > > > back to the higher basis.<br></div><div dir="ltr">> > > > > > -- Try leaving opt_scheme at its default value.<br></div><div dir="ltr">> > > > > > -- For such a reaction (dissociation of such a polarized molecule) you should<br></div><div dir="ltr">> > > > > > expect a barrier, therefore CI_scheme should be anything except for no-CI.<br></div><div dir="ltr">> > > > > > -- The best is if you can specify the CI manually in the<br></div><div dir="ltr">> > > > > > CLIMBING_IMAGES section<br></div><div dir="ltr">> > > > > > (choose the CI_scheme accordingly).<br></div><div dir="ltr">> > > > > > Bests,<br></div><div dir="ltr">> > > > > > t<br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > On Tue, Oct 20, 2020 at 6:53 PM Omer Mutasim <<a ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > Dear All<br></div><div dir="ltr">> > > > > > > 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.<br></div><div dir="ltr">> > > > > > > Please tell me what is wrong in my input file:<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > below is the input & output files:<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > Input file:<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > BEGIN<br></div><div dir="ltr">> > > > > > > BEGIN_PATH_INPUT<br></div><div dir="ltr">> > > > > > > &PATH<br></div><div dir="ltr">> > > > > > > restart_mode = 'restart'<br></div><div dir="ltr">> > > > > > > string_method = 'neb',<br></div><div dir="ltr">> > > > > > > nstep_path = 800,<br></div><div dir="ltr">> > > > > > > ds = 1.D0,<br></div><div dir="ltr">> > > > > > > opt_scheme = "broyden",<br></div><div dir="ltr">> > > > > > > num_of_images = 7,<br></div><div dir="ltr">> > > > > > > CI_scheme = 'no-CI',<br></div><div dir="ltr">> > > > > > > path_thr = 0.05D0,<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > /<br></div><div dir="ltr">> > > > > > > END_PATH_INPUT<br></div><div dir="ltr">> > > > > > > BEGIN_ENGINE_INPUT<br></div><div dir="ltr">> > > > > > > &CONTROL<br></div><div dir="ltr">> > > > > > > calculation = "relax"<br></div><div dir="ltr">> > > > > > > prefix = 'SO2_neb'<br></div><div dir="ltr">> > > > > > > outdir = './outdir'<br></div><div dir="ltr">> > > > > > > pseudo_dir = '/home/yQE-test/pseudo/'<br></div><div dir="ltr">> > > > > > > restart_mode = 'from_scratch'<br></div><div dir="ltr">> > > > > > > forc_conv_thr = 1.0e-03<br></div><div dir="ltr">> > > > > > > etot_conv_thr = 1e-04<br></div><div dir="ltr">> > > > > > > nstep = 200<br></div><div dir="ltr">> > > > > > > !tefield = .TRUE<br></div><div dir="ltr">> > > > > > > !dipfield = .TRUE<br></div><div dir="ltr">> > > > > > > /<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > &SYSTEM<br></div><div dir="ltr">> > > > > > > ibrav = 0<br></div><div dir="ltr">> > > > > > > ecutrho = 270<br></div><div dir="ltr">> > > > > > > ecutwfc = 45<br></div><div dir="ltr">> > > > > > > nat = 111<br></div><div dir="ltr">> > > > > > > ntyp = 4<br></div><div dir="ltr">> > > > > > > occupations='smearing',smearing='gaussian',degauss=0.005<br></div><div dir="ltr">> > > > > > > vdw_corr = 'DFT-D2'<br></div><div dir="ltr">> > > > > > > !edir = 3 , emaxpos = 0.6808, eopreg = 0.08 , eamp = 0.001,<br></div><div dir="ltr">> > > > > > > nspin = 2<br></div><div dir="ltr">> > > > > > > starting_magnetization(1)= 0.01<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > /<br></div><div dir="ltr">> > > > > > > &ELECTRONS<br></div><div dir="ltr">> > > > > > > conv_thr = 1e-06<br></div><div dir="ltr">> > > > > > > electron_maxstep = 200<br></div><div dir="ltr">> > > > > > > mixing_mode ='local-TF'<br></div><div dir="ltr">> > > > > > > mixing_beta = 0.3<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > /<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > &IONS<br></div><div dir="ltr">> > > > > > > /<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > K_POINTS {automatic}<br></div><div dir="ltr">> > > > > > > 3 3 1 0 0 1<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ATOMIC_SPECIES<br></div><div dir="ltr">> > > > > > > Ni 58.69340 Ni.pbe-n-rrkjus_psl.0.1.UPF<br></div><div dir="ltr">> > > > > > > P 30.97376 P.pbe-n-rrkjus_psl.1.0.0.UPF<br></div><div dir="ltr">> > > > > > > S 32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF<br></div><div dir="ltr">> > > > > > > O 15.9999 O.pbe-n-rrkjus_psl.1.0.0.UPF<br></div><div dir="ltr">> > > > > > > CELL_PARAMETERS {angstrom}<br></div><div dir="ltr">> > > > > > > 11.765383541833 0.0000000000 0.0000000000<br></div><div dir="ltr">> > > > > > > -5.88269177091652 10.1891210324947 0.0000000000<br></div><div dir="ltr">> > > > > > > 0.0000000000 0.0000000000 30.9938690567585<br></div><div dir="ltr">> > > > > > > BEGIN_POSITIONS<br></div><div dir="ltr">> > > > > > > FIRST_IMAGE<br></div><div dir="ltr">> > > > > > > ATOMIC_POSITIONS (angstrom)<br></div><div dir="ltr">> > > > > > > S -1.181561037 6.155418563 12.124345096<br></div><div dir="ltr">> > > > > > > O -1.100425541 4.672437254 11.356300976<br></div><div dir="ltr">> > > > > > > O 0.190308001 6.839217965 11.448732238<br></div><div dir="ltr">> > > > > > > Ni -2.738525121 4.763450297 0.239145520<br></div><div dir="ltr">> > > > > > > Ni 3.139579474 1.358483744 0.232252034<br></div><div dir="ltr">> > > > > > > Ni 3.135766403 8.150575392 0.235327906<br></div><div dir="ltr">> > > > > > > Ni -4.673593720 8.104467836 1.780118367<br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > output file:<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > Program NEB v.6.4.1 starts on 16Oct2020 at 11:35:32<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > This program is part of the open-source Quantum ESPRESSO suite<br></div><div dir="ltr">> > > > > > > for quantum simulation of materials; please cite<br></div><div dir="ltr">> > > > > > > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);<br></div><div dir="ltr">> > > > > > > "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);<br></div><div dir="ltr">> > > > > > > URL <a href="http://www.quantum-espresso.org" target="_blank">http://www.quantum-espresso.org</a>",<br></div><div dir="ltr">> > > > > > > in publications or presentations arising from this work. More details at<br></div><div dir="ltr">> > > > > > > <a href="http://www.quantum-espresso.org/quote" target="_blank">http://www.quantum-espresso.org/quote</a><br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > Parallel version (MPI), running on 80 processors<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > MPI processes distributed on 5 nodes<br></div><div dir="ltr">> > > > > > > R & G space division: proc/nbgrp/npool/nimage = 80<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > parsing_file_name: input.in<br></div><div dir="ltr">> > > > > > > Reading input from pw_1.in<br></div><div dir="ltr">> > > > > > > Message from routine read_upf::<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > initial path length = 11.3145 bohr<br></div><div dir="ltr">> > > > > > > initial inter-image distance = 1.8857 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > string_method = neb<br></div><div dir="ltr">> > > > > > > restart_mode = from_scratch<br></div><div dir="ltr">> > > > > > > opt_scheme = broyden<br></div><div dir="ltr">> > > > > > > num_of_images = 7<br></div><div dir="ltr">> > > > > > > nstep_path = 800<br></div><div dir="ltr">> > > > > > > CI_scheme = no-CI<br></div><div dir="ltr">> > > > > > > first_last_opt = F<br></div><div dir="ltr">> > > > > > > use_freezing = F<br></div><div dir="ltr">> > > > > > > ds = 1.0000 a.u.<br></div><div dir="ltr">> > > > > > > k_max = 0.1000 a.u.<br></div><div dir="ltr">> > > > > > > k_min = 0.1000 a.u.<br></div><div dir="ltr">> > > > > > > suggested k_max = 0.6169 a.u.<br></div><div dir="ltr">> > > > > > > suggested k_min = 0.6169 a.u.<br></div><div dir="ltr">> > > > > > > path_thr = 0.0500 eV / A<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 1 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 6.2 self-consistency for image 1<br></div><div dir="ltr">> > > > > > > tcpu = 3675.5 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 7662.5 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 11422.7 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 15346.3 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 19108.7 self-consistency for image 6<br></div><div dir="ltr">> > > > > > > tcpu = 22571.1 self-consistency for image 7<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 70.216194 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 71.022062 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92468.8536637 23.505267 F<br></div><div dir="ltr">> > > > > > > 3 -92442.9691259 150.213122 F<br></div><div dir="ltr">> > > > > > > 4 -92406.7311409 330.353055 F<br></div><div dir="ltr">> > > > > > > 5 -92431.0052901 207.333777 F<br></div><div dir="ltr">> > > > > > > 6 -92469.0661237 51.663167 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 11.314 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 1.886 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 2 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 26119.7 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 28731.5 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 31027.4 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 34094.2 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 36988.0 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 22.531451 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 23.337319 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92469.5101428 22.300995 F<br></div><div dir="ltr">> > > > > > > 3 -92454.4158842 70.627594 F<br></div><div dir="ltr">> > > > > > > 4 -92461.1206812 34.307062 F<br></div><div dir="ltr">> > > > > > > 5 -92464.4669859 46.783708 F<br></div><div dir="ltr">> > > > > > > 6 -92471.4896125 37.765708 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 11.384 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 1.897 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 3 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 39172.0 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 41888.0 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 44777.8 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 47642.0 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 50615.2 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 13.435341 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 14.241209 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92471.6434742 16.119604 F<br></div><div dir="ltr">> > > > > > > 3 -92463.5119937 28.367753 F<br></div><div dir="ltr">> > > > > > > 4 -92468.1466546 16.740841 F<br></div><div dir="ltr">> > > > > > > 5 -92472.7705146 11.019872 F<br></div><div dir="ltr">> > > > > > > 6 -92475.3040517 10.662908 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 11.502 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 1.917 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 4 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 53323.8 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 56077.9 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 59014.9 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 61990.6 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 64608.8 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 6.530687 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 7.336554 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92474.0378392 7.910468 F<br></div><div dir="ltr">> > > > > > > 3 -92470.4166483 13.061889 F<br></div><div dir="ltr">> > > > > > > 4 -92471.2528453 9.923078 F<br></div><div dir="ltr">> > > > > > > 5 -92474.2165523 4.209611 F<br></div><div dir="ltr">> > > > > > > 6 -92476.2787664 3.450159 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 11.724 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 1.954 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 5 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 67273.9 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 70152.2 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 73153.1 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 76203.5 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 78824.8 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 3.710859 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 4.516727 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92475.5387437 3.615458 F<br></div><div dir="ltr">> > > > > > > 3 -92473.5622985 4.695416 F<br></div><div dir="ltr">> > > > > > > 4 -92473.2364760 5.734324 F<br></div><div dir="ltr">> > > > > > > 5 -92474.4833513 2.877608 F<br></div><div dir="ltr">> > > > > > > 6 -92476.4425910 2.876700 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 12.038 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 2.006 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 6 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 81355.0 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 84402.5 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 87564.5 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 90568.2 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 93110.5 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 2.560838 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 3.366706 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92476.0900010 1.040106 F<br></div><div dir="ltr">> > > > > > > 3 -92474.7832671 2.988289 F<br></div><div dir="ltr">> > > > > > > 4 -92474.3864972 2.085630 F<br></div><div dir="ltr">> > > > > > > 5 -92474.8266397 1.998808 F<br></div><div dir="ltr">> > > > > > > 6 -92476.6377600 0.667994 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 12.364 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 2.061 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 7 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 95248.7 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 98189.3 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 101337.9 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 104423.7 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 107076.7 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 2.125802 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 2.931670 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92476.0736630 1.319140 F<br></div><div dir="ltr">> > > > > > > 3 -92475.4151167 1.955048 F<br></div><div dir="ltr">> > > > > > > 4 -92474.8215329 1.921925 F<br></div><div dir="ltr">> > > > > > > 5 -92475.0627346 2.135695 F<br></div><div dir="ltr">> > > > > > > 6 -92476.7117640 0.696381 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 12.868 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 2.145 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 8 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 108885.3 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 111194.4 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 113961.2 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 116506.3 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 118361.2 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 2.073805 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 2.879673 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92476.1622863 0.861666 F<br></div><div dir="ltr">> > > > > > > 3 -92475.4162307 2.192183 F<br></div><div dir="ltr">> > > > > > > 4 -92474.8735300 1.631538 F<br></div><div dir="ltr">> > > > > > > 5 -92475.0684015 1.824977 F<br></div><div dir="ltr">> > > > > > > 6 -92476.7113576 0.606060 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 12.633 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 2.105 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > > .<br></div><div dir="ltr">> > > > > > > reading file 'SO2_neb.path'<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > string_method = neb<br></div><div dir="ltr">> > > > > > > restart_mode = restart<br></div><div dir="ltr">> > > > > > > opt_scheme = broyden<br></div><div dir="ltr">> > > > > > > num_of_images = 7<br></div><div dir="ltr">> > > > > > > nstep_path = 800<br></div><div dir="ltr">> > > > > > > CI_scheme = no-CI<br></div><div dir="ltr">> > > > > > > first_last_opt = F<br></div><div dir="ltr">> > > > > > > use_freezing = F<br></div><div dir="ltr">> > > > > > > ds = 1.0000 a.u.<br></div><div dir="ltr">> > > > > > > k_max = 0.1000 a.u.<br></div><div dir="ltr">> > > > > > > k_min = 0.1000 a.u.<br></div><div dir="ltr">> > > > > > > suggested k_max = 0.6169 a.u.<br></div><div dir="ltr">> > > > > > > suggested k_min = 0.6169 a.u.<br></div><div dir="ltr">> > > > > > > path_thr = 0.0500 eV / A<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 26 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 6.2 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 3713.3 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 7137.5 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 10796.2 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 14447.3 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 0.640765 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 1.446632 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92476.3065704 0.250516 F<br></div><div dir="ltr">> > > > > > > 3 -92477.0673165 0.278078 F<br></div><div dir="ltr">> > > > > > > 4 -92476.7787332 0.431860 F<br></div><div dir="ltr">> > > > > > > 5 -92476.4800774 0.453182 F<br></div><div dir="ltr">> > > > > > > 6 -92476.5576488 0.296200 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 17.545 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 2.924 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 27 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 18237.5 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 20736.0 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 23008.1 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 25721.8 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 28310.3 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 0.643277 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 1.449145 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92476.3040583 0.235899 F<br></div><div dir="ltr">> > > > > > > 3 -92477.0080434 0.474599 F<br></div><div dir="ltr">> > > > > > > 4 -92476.8143156 0.678632 F<br></div><div dir="ltr">> > > > > > > 5 -92476.4592005 0.597470 F<br></div><div dir="ltr">> > > > > > > 6 -92476.4827638 0.224064 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 18.367 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 3.061 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 28 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 30382.0 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 32498.8 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 34597.5 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 37250.7 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 39649.7 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 0.651733 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 1.457601 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92476.2956021 0.236096 F<br></div><div dir="ltr">> > > > > > > 3 -92476.9388664 0.680956 F<br></div><div dir="ltr">> > > > > > > 4 -92476.8025379 0.874373 F<br></div><div dir="ltr">> > > > > > > 5 -92476.3933083 0.734403 F<br></div><div dir="ltr">> > > > > > > 6 -92476.4272820 0.239132 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 19.115 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 3.186 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 29 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 41622.7 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 43787.2 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 45892.1 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 48482.6 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 50617.1 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 0.661553 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 1.467420 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92476.2857825 0.249692 F<br></div><div dir="ltr">> > > > > > > 3 -92476.8823826 0.778237 F<br></div><div dir="ltr">> > > > > > > 4 -92476.7843580 1.002202 F<br></div><div dir="ltr">> > > > > > > 5 -92476.3323697 0.748960 F<br></div><div dir="ltr">> > > > > > > 6 -92476.3885082 0.238984 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 19.742 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 3.290 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 30 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 52474.3 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 54679.9 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 57012.5 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 59877.3 self-consistency for image 5<br></div><div dir="ltr">> > > > > > > tcpu = 62490.2 self-consistency for image 6<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > activation energy (->) = 0.704760 eV<br></div><div dir="ltr">> > > > > > > activation energy (<-) = 1.510628 eV<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > image energy (eV) error (eV/A) frozen<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > 1 -92476.9473351 0.023792 T<br></div><div dir="ltr">> > > > > > > 2 -92476.2668397 0.342411 F<br></div><div dir="ltr">> > > > > > > 3 -92476.7810889 0.907920 F<br></div><div dir="ltr">> > > > > > > 4 -92476.7414553 1.153276 F<br></div><div dir="ltr">> > > > > > > 5 -92476.2425749 0.898295 F<br></div><div dir="ltr">> > > > > > > 6 -92476.3370447 0.341313 F<br></div><div dir="ltr">> > > > > > > 7 -92477.7532028 0.024858 T<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > path length = 20.745 bohr<br></div><div dir="ltr">> > > > > > > inter-image distance = 3.457 bohr<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > ------------------------------ iteration 31 ------------------------------<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > tcpu = 64431.3 self-consistency for image 2<br></div><div dir="ltr">> > > > > > > tcpu = 66430.0 self-consistency for image 3<br></div><div dir="ltr">> > > > > > > tcpu = 68491.4 self-consistency for image 4<br></div><div dir="ltr">> > > > > > > tcpu = 70987.8 self-consistency for image 5<br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > ><br></div><div dir="ltr">> > > > > > > _______________________________________________<br></div><div dir="ltr">> > > > > > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br></div><div dir="ltr">> > > > > > > users mailing list <a ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br></div><div dir="ltr">> > > > > > > <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br></div><div dir="ltr">> > > > > > _______________________________________________<br></div><div dir="ltr">> > > > > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br></div><div dir="ltr">> > > > > > users mailing list <a ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br></div><div dir="ltr">> > > > > > <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > _______________________________________________<br></div><div dir="ltr">> > > > > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br></div><div dir="ltr">> > > > > > users mailing list <a ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br></div><div dir="ltr">> > > > > > <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > ><br></div><div dir="ltr">> > > > > > _______________________________________________<br></div><div dir="ltr">> > > > > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br></div><div dir="ltr">> > > > > > users mailing list <a ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br></div><div dir="ltr">> > > > > > <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br></div><div dir="ltr">> > > > > _______________________________________________<br></div><div dir="ltr">> > > > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br></div><div dir="ltr">> > > > > users mailing list <a ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br></div><div dir="ltr">> > > > > <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br></div><div dir="ltr">> > > > > _______________________________________________<br></div><div dir="ltr">> > > > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br></div><div dir="ltr">> > > > > users mailing list <a ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br></div><div dir="ltr">> > > > > <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br></div><div dir="ltr">> > > > _______________________________________________<br></div><div dir="ltr">> > > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br></div><div dir="ltr">> > > > users mailing list <a ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br></div><div dir="ltr">> > > > <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></div></div>
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