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Dear Dr. Tamas <div><br></div><div>Sorry , what do you mean by “ <span style="-webkit-text-size-adjust: auto;">you most probably need an SO2 simulation (optimization+phonons)</span></div>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 ? <div><br><div>I do agree with you , 3-atoms phonon is non-physical, i will include the top layer also. </div><div><br></div><div>Regarding Xcrysden , I don’t find any axsf file in my output files , how do you visualise it ? </div><div>Another question: </div><div>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.</div><div><br></div><div>By the way , i tried ASE for rate constants, as you recommended, it is really helpful. </div><div><br><div><div>Thanks a lot for you unwavering help. </div><div><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 Wednesday, November 4, 2020, 10:46 PM, Tamas Karpati <tkarpati@gmail.com> wrote:</p><blockquote class="iosymail"><div dir="ltr">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"><div class="yqt1265326108" id="yqtfd74199"><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 mailing list <a shape="rect" ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br clear="none">> > <a shape="rect" href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br clear="none">_______________________________________________<br clear="none">Quantum ESPRESSO is supported by MaX (www.max-centre.eu)<br clear="none">users mailing list <a shape="rect" ymailto="mailto:users@lists.quantum-espresso.org" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br clear="none"><a shape="rect" href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br clear="none"></div></div><blockquote></blockquote></blockquote></div></div></div></div>
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