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I really appreciated your help, thanks a lot Dr. Tamas<br><br><br><a href="https://overview.mail.yahoo.com/?.src=iOS">Sent from Yahoo Mail for iPhone</a><br><br><p class="yahoo-quoted-begin" style="font-size: 15px; color: #715FFA; padding-top: 15px; margin-top: 0">On Thursday, November 5, 2020, 3:57 PM, Tamas Karpati <tkarpati@gmail.com> wrote:</p><blockquote class="iosymail"><div dir="ltr">Dear Omer,<br clear="none"><br clear="none">Yes, i meant SO2 gas phase sim. This is an alternative to using the physisorbed<br clear="none">slab+SO2 complex as "reactant", R. Question of methodology and the nature of<br clear="none">materials. I cannot recall whether S+2O were together (as SO2) or decomposed in<br clear="none">your starting structure but in the second case you may use this approach.<br clear="none">Also, kinetic parameters are probably easier to derive for the gas<br clear="none">phase reactant (?)<br clear="none">If your SO2 is in a single piece on the slab in R, then you can drop this idea.<br clear="none"><br clear="none">With XCrySDen, to visualize vibrations, you need to use dynmat.x and specify<br clear="none">filxsf, then open *.xsf with XCrySDen. Select to visualize forces and use the<br clear="none">animation controls to choose which normal mode is to be shown.<br clear="none">Expect arrows, not animated vibrations. Such arrows indicate the atomic<br clear="none">replacements to do in order to get 1 negative freq. better: move them<br clear="none">where the arrows<br clear="none">point to, or the exact opposite direction. One by one you can find a<br clear="none">real minimum str.<br clear="none">Note that unless you do an all-atom phonon, you can never trust those arrows<br clear="none">(neither direction nor frequency, even sign).<br clear="none"><br clear="none">As for H+O (if distant enough, yet in the same simbox), you formally expect<br clear="none">the same as for the HO radical -a single bond with a single freq but since<br clear="none">this is not a real bond (strength is negligible), freq will be very<br clear="none">small (and yes, S=0).<br clear="none"> t<br clear="none"><div class="yqt0832855780" id="yqtfd11084"><br clear="none">On Thu, Nov 5, 2020 at 5:15 AM Omer Mutasim <<a shape="rect" ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br clear="none">><br clear="none">> Dear Dr. Tamas<br clear="none">><br clear="none">> Sorry , what do you mean by “ you most probably need an SO2 simulation (optimization+phonons)<br clear="none">> rather than the same for a surface attached SO2 or SO+O. Big difference! “ do you mean i should do phonon for SO2 in gas phase ?<br clear="none">><br clear="none">> I do agree with you , 3-atoms phonon is non-physical, i will include the top layer also.<br clear="none">><br clear="none">> Regarding Xcrysden , I don’t find any axsf file in my output files , how do you visualise it ?<br clear="none">> Another question:<br clear="none">> For the reaction : H+O = OH , if i did phonon for the initial state( reactant ) , I should expect to get no vibrational modes at all , right ? I will get only 6 translational modes . So the vibrational entropy will be zero, Please correct me if i am wrong.<br clear="none">><br clear="none">> By the way , i tried ASE for rate constants, as you recommended, it is really helpful.<br clear="none">><br clear="none">> Thanks a lot for you unwavering help.<br clear="none">><br clear="none">> Sent from Yahoo Mail for iPhone<br clear="none">><br clear="none">> On Wednesday, November 4, 2020, 10:46 PM, Tamas Karpati <<a shape="rect" ymailto="mailto:tkarpati@gmail.com" href="mailto:tkarpati@gmail.com">tkarpati@gmail.com</a>> wrote:<br clear="none">><br clear="none">> In addition to my earlier comments, i'd like to mention that for kinetics<br clear="none">> you most probably need an SO2 simulation (optimization+phonons)<br clear="none">> rather than the same for a surface attached SO2 or SO+O. Big difference!<br clear="none">><br clear="none">> Back to the earliers, 3-atoms phonon is so unphysical that it is<br clear="none">> recommended to do an all-atom one, or add at least the directly<br clear="none">> bonded surface atoms (and extend towards all-atoms if you can).<br clear="none">><br clear="none">> In addition, only all-atom phonon will show you whether your big negative<br clear="none">> freqs. indicate a non-minimum structure (ie. "freqs" ~ 2nd derivatives<br clear="none">> of the PEHS).<br clear="none">> With somewhat less atoms you can be lucky, and by visualizing normal<br clear="none">> modes (phonons) by eg. XCrysDen will show you where to move atoms<br clear="none">> to get into the local minimum. Kinetics theory builds on minima (and TS-es).<br clear="none">> Anyways, 3 atoms are too few (also see first section above).<br clear="none">><br clear="none">> On Mon, Nov 2, 2020 at 11:29 AM Tamas Karpati <<a shape="rect" ymailto="mailto:tkarpati@gmail.com" href="mailto:tkarpati@gmail.com">tkarpati@gmail.com</a>> wrote:<br clear="none">> ><br clear="none">> > Dear Omer,<br clear="none">> ><br clear="none">> > I guess that your input is fine, your structure is not.<br clear="none">> > (By the way, tr2_ph could be lower.)<br clear="none">> ><br clear="none">> > You woud expect 6 near zero and 3N-6 positive freqs. for a completely<br clear="none">> > relaxed minimum structure (and 5 + 3N-5 for a TS).<br clear="none">> > This is ruined if you run PH.x on a different potential energy<br clear="none">> > hypersurface, PEHS.<br clear="none">> ><br clear="none">> > It is really very easy to spoil: use a different no. of k point or functional<br clear="none">> > for PW/vc-relax and PH and you're there. Another temptation is to<br clear="none">> > use experimental crystal structure and fix some/most atoms as such.<br clear="none">> > These all mean different PEHS'.<br clear="none">> > In addition, unconverged relaxation (or too loose convergence),<br clear="none">> > while moves on the same PEHS, provides you with inappropriate<br clear="none">> > freqs, as it does not bring your structure close enough to the local minimum.<br clear="none">> ><br clear="none">> > I would recommend to reconsider the "life" of your structure<br clear="none">> > (origin, optimization method, other parameters) and adjust if necessary.<br clear="none">> > t<br clear="none">> ><br clear="none">> > On Mon, Nov 2, 2020 at 7:43 AM Omer Mutasim <<a shape="rect" ymailto="mailto:omermutasim@ymail.com" href="mailto:omermutasim@ymail.com">omermutasim@ymail.com</a>> wrote:<br clear="none">> > ><br clear="none">> > > Dear all<br clear="none">> > ><br clear="none">> > > I'm doing phonon calculation at Gamma point (q) in order to estimate the reaction rate constants for a micro-kinetic model. I have perturbed only the adsorbate molecule with the 3 surface atoms, connected to adsorbate, using "nat-todo" option. However, i got 15 negative frequencies (should be 6 as i know ) ,with high absolute value.<br clear="none">> > ><br clear="none">> > > Can you please help me to know what is wrong with my input files ?<br clear="none">> > ><br clear="none">> > > Below are the output & input files:<br clear="none">> > ><br clear="none">> > ><br clear="none">> > ><br clear="none">> > > Mode symmetry, C_1 (1) point group:<br clear="none">> > ><br clear="none">> > > freq ( 1 - 1) = -2762.6 [cm-1] --> A I+R<br clear="none">> > > freq ( 2 - 2) = -2570.3 [cm-1] --> A I+R<br clear="none">> > > freq ( 3 - 3) = -2460.4 [cm-1] --> A I+R<br clear="none">> > > freq ( 4 - 4) = -2423.6 [cm-1] --> A I+R<br clear="none">> > > freq ( 5 - 5) = -2356.3 [cm-1] --> A I+R<br clear="none">> > > freq ( 6 - 6) = -2158.0 [cm-1] --> A I+R<br clear="none">> > > freq ( 7 - 7) = -2151.1 [cm-1] --> A I+R<br clear="none">> > > freq ( 8 - 8) = -2067.5 [cm-1] --> A I+R<br clear="none">> > > freq ( 9 - 9) = -2034.8 [cm-1] --> A I+R<br clear="none">> > > freq ( 10 - 10) = -2025.2 [cm-1] --> A I+R<br clear="none">> > > freq ( 11 - 11) = -1864.3 [cm-1] --> A I+R<br clear="none">> > > freq ( 12 - 12) = -1804.5 [cm-1] --> A I+R<br clear="none">> > > freq ( 13 - 13) = -1099.4 [cm-1] --> A I+R<br clear="none">> > > freq ( 14 - 14) = -947.6 [cm-1] --> A I+R<br clear="none">> > > freq ( 15 - 15) = -912.5 [cm-1] --> A I+R<br clear="none">> > > freq (316 -316) = 179.3 [cm-1] --> A I+R<br clear="none">> > > freq (317 -317) = 193.0 [cm-1] --> A I+R<br clear="none">> > > freq (318 -318) = 215.8 [cm-1] --> A I+R<br clear="none">> > > freq (319 -319) = 240.2 [cm-1] --> A I+R<br clear="none">> > > freq (320 -320) = 270.4 [cm-1] --> A I+R<br clear="none">> > > freq (321 -321) = 317.0 [cm-1] --> A I+R<br clear="none">> > > freq (322 -322) = 370.8 [cm-1] --> A I+R<br clear="none">> > > freq (323 -323) = 377.3 [cm-1] --> A I+R<br clear="none">> > > freq (324 -324) = 398.3 [cm-1] --> A I+R<br clear="none">> > > freq (325 -325) = 417.8 [cm-1] --> A I+R<br clear="none">> > > freq (326 -326) = 468.2 [cm-1] --> A I+R<br clear="none">> > > freq (327 -327) = 659.0 [cm-1] --> A I+R<br clear="none">> > > freq (328 -328) = 1096.6 [cm-1] --> A I+R<br clear="none">> > > freq (329 -329) = 1795.5 [cm-1] --> A I+R<br clear="none">> > > freq (330 -330) = 2199.3 [cm-1] --> A I+R<br clear="none">> > ><br clear="none">> > ><br clear="none">> > > ph.x input file:<br clear="none">> > ><br clear="none">> > > phonon calculation at Gamma point.<br clear="none">> > > &inputph<br clear="none">> > > outdir = './outdir'<br clear="none">> > > prefix = 'HS'<br clear="none">> > > tr2_ph = 1.0d-09<br clear="none">> > > epsil = .false.<br clear="none">> > > amass(1) = 58.69340<br clear="none">> > > amass(2) = 30.97376<br clear="none">> > > amass(3) = 1.00784<br clear="none">> > > amass(4) = 32.065<br clear="none">> > > fildyn = 'HS.dyn'<br clear="none">> > ><br clear="none">> > > alpha_mix(1)=0.1<br clear="none">> > ><br clear="none">> > > recover=.true<br clear="none">> > > nogg = .true<br clear="none">> > > nat_todo = 5<br clear="none">> > ><br clear="none">> > > /<br clear="none">> > > 0.0 0.0 0.0<br clear="none">> > ><br clear="none">> > > 1 2 37 46 54<br clear="none">> > ><br clear="none">> > ><br clear="none">> > ><br clear="none">> > > scf input file:<br clear="none">> > ><br clear="none">> > > &CONTROL<br clear="none">> > > calculation = "scf"<br clear="none">> > > prefix = 'HS'<br clear="none">> > > outdir = './outdir'<br clear="none">> > > pseudo_dir = '/home/'<br clear="none">> > > restart_mode = 'from_scratch'<br clear="none">> > > forc_conv_thr = 1.0e-03<br clear="none">> > > etot_conv_thr = 1e-04<br clear="none">> > > nstep = 999<br clear="none">> > > /<br clear="none">> > > &SYSTEM<br clear="none">> > > ibrav = 0<br clear="none">> > > ecutrho = 200<br clear="none">> > > ecutwfc = 25<br clear="none">> > > nat = 110<br clear="none">> > > ntyp = 4<br clear="none">> > > occupations='smearing',smearing='gaussian',degauss=0.005<br clear="none">> > > vdw_corr = 'DFT-D2'<br clear="none">> > > nspin = 2<br clear="none">> > > starting_magnetization(1)= 0.01<br clear="none">> > > /<br clear="none">> > > &ELECTRONS<br clear="none">> > > conv_thr = 1e-8<br clear="none">> > > electron_maxstep = 200<br clear="none">> > > mixing_mode ='local-TF'<br clear="none">> > > mixing_beta = 0.3<br clear="none">> > > /<br clear="none">> > > &IONS<br clear="none">> > > /<br clear="none">> > > K_POINTS {automatic}<br clear="none">> > > 3 3 1 0 0 0<br clear="none">> > > ATOMIC_SPECIES<br clear="none">> > > Ni 58.69340 Ni.pbe-n-rrkjus_psl.0.1.UPF<br clear="none">> > > P 30.97376 P.pbe-n-rrkjus_psl.1.0.0.UPF<br clear="none">> > > H 1.00784 H.pbe-rrkjus_psl.0.1.UPF<br clear="none">> > > S 32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF<br clear="none">> > > CELL_PARAMETERS {angstrom}<br clear="none">> > > 11.76538354 0.0000000000 0.0000000000<br clear="none">> > > -5.8826917709 10.189121032 0.0000000000<br clear="none">> > > 0.0000000000 0.0000000000 30.993869056<br clear="none">> > > ATOMIC_POSITIONS (angstrom)<br clear="none">> > > H 0.879694621 3.392266427 10.708999692<br clear="none">> > > S 2.266698845 3.396363162 10.560733430<br clear="none">> > > Ni -2.744571590 4.755054131 0.244939179<br clear="none">> > > Ni 3.134031329 1.363792691 0.248008546<br clear="none">> > > .<br clear="none">> > > .<br clear="none">> > > .<br clear="none">> > > P -1.060403962 1.841094610 1.604930623<br clear="none">> > > P -3.921453199 6.792156181 0.000000000 0 0 0<br clear="none">> > > P 1.960697149 3.396027080 0.000000000 0 0 0<br clear="none">> > > P 7.842906399 0.000000000 0.000000000 0 0 0<br clear="none">> > ><br clear="none">> > ><br clear="none">> > > regards<br clear="none">> > ><br clear="none">> > ><br clear="none">> > > _______________________________________________<br clear="none">> > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br clear="none">> > > users 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