Dear Omer, Yes, i meant SO2 gas phase sim. This is an alternative to using the physisorbed slab+SO2 complex as "reactant", R. Question of methodology and the nature of materials. I cannot recall whether S+2O were together (as SO2) or decomposed in your starting structure but in the second case you may use this approach. Also, kinetic parameters are probably easier to derive for the gas phase reactant (?) If your SO2 is in a single piece on the slab in R, then you can drop this idea.
With XCrySDen, to visualize vibrations, you need to use dynmat.x and specify filxsf, then open *.xsf with XCrySDen. Select to visualize forces and use the animation controls to choose which normal mode is to be shown. Expect arrows, not animated vibrations. Such arrows indicate the atomic replacements to do in order to get 1 negative freq. better: move them where the arrows point to, or the exact opposite direction. One by one you can find a real minimum str. Note that unless you do an all-atom phonon, you can never trust those arrows (neither direction nor frequency, even sign). As for H+O (if distant enough, yet in the same simbox), you formally expect the same as for the HO radical -a single bond with a single freq but since this is not a real bond (strength is negligible), freq will be very small (and yes, S=0). t On Thu, Nov 5, 2020 at 5:15 AM Omer Mutasim <omermuta...@ymail.com> wrote: > > Dear Dr. Tamas > > Sorry , what do you mean by “ you most probably need an SO2 simulation > (optimization+phonons) > 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 ? > > I do agree with you , 3-atoms phonon is non-physical, i will include the top > layer also. > > Regarding Xcrysden , I don’t find any axsf file in my output files , how do > you visualise it ? > Another question: > 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. > > By the way , i tried ASE for rate constants, as you recommended, it is really > helpful. > > Thanks a lot for you unwavering help. > > Sent from Yahoo Mail for iPhone > > On Wednesday, November 4, 2020, 10:46 PM, Tamas Karpati <tkarp...@gmail.com> > wrote: > > In addition to my earlier comments, i'd like to mention that for kinetics > you most probably need an SO2 simulation (optimization+phonons) > rather than the same for a surface attached SO2 or SO+O. Big difference! > > Back to the earliers, 3-atoms phonon is so unphysical that it is > recommended to do an all-atom one, or add at least the directly > bonded surface atoms (and extend towards all-atoms if you can). > > In addition, only all-atom phonon will show you whether your big negative > freqs. indicate a non-minimum structure (ie. "freqs" ~ 2nd derivatives > of the PEHS). > With somewhat less atoms you can be lucky, and by visualizing normal > modes (phonons) by eg. XCrysDen will show you where to move atoms > to get into the local minimum. Kinetics theory builds on minima (and TS-es). > Anyways, 3 atoms are too few (also see first section above). > > On Mon, Nov 2, 2020 at 11:29 AM Tamas Karpati <tkarp...@gmail.com> wrote: > > > > Dear Omer, > > > > I guess that your input is fine, your structure is not. > > (By the way, tr2_ph could be lower.) > > > > You woud expect 6 near zero and 3N-6 positive freqs. for a completely > > relaxed minimum structure (and 5 + 3N-5 for a TS). > > This is ruined if you run PH.x on a different potential energy > > hypersurface, PEHS. > > > > It is really very easy to spoil: use a different no. of k point or > > functional > > for PW/vc-relax and PH and you're there. Another temptation is to > > use experimental crystal structure and fix some/most atoms as such. > > These all mean different PEHS'. > > In addition, unconverged relaxation (or too loose convergence), > > while moves on the same PEHS, provides you with inappropriate > > freqs, as it does not bring your structure close enough to the local > > minimum. > > > > I would recommend to reconsider the "life" of your structure > > (origin, optimization method, other parameters) and adjust if necessary. > > t > > > > On Mon, Nov 2, 2020 at 7:43 AM Omer Mutasim <omermuta...@ymail.com> wrote: > > > > > > Dear all > > > > > > 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. > > > > > > Can you please help me to know what is wrong with my input files ? > > > > > > Below are the output & input files: > > > > > > > > > > > > Mode symmetry, C_1 (1) point group: > > > > > > freq ( 1 - 1) = -2762.6 [cm-1] --> A I+R > > > freq ( 2 - 2) = -2570.3 [cm-1] --> A I+R > > > freq ( 3 - 3) = -2460.4 [cm-1] --> A I+R > > > freq ( 4 - 4) = -2423.6 [cm-1] --> A I+R > > > freq ( 5 - 5) = -2356.3 [cm-1] --> A I+R > > > freq ( 6 - 6) = -2158.0 [cm-1] --> A I+R > > > freq ( 7 - 7) = -2151.1 [cm-1] --> A I+R > > > freq ( 8 - 8) = -2067.5 [cm-1] --> A I+R > > > freq ( 9 - 9) = -2034.8 [cm-1] --> A I+R > > > freq ( 10 - 10) = -2025.2 [cm-1] --> A I+R > > > freq ( 11 - 11) = -1864.3 [cm-1] --> A I+R > > > freq ( 12 - 12) = -1804.5 [cm-1] --> A I+R > > > freq ( 13 - 13) = -1099.4 [cm-1] --> A I+R > > > freq ( 14 - 14) = -947.6 [cm-1] --> A I+R > > > freq ( 15 - 15) = -912.5 [cm-1] --> A I+R > > > freq (316 -316) = 179.3 [cm-1] --> A I+R > > > freq (317 -317) = 193.0 [cm-1] --> A I+R > > > freq (318 -318) = 215.8 [cm-1] --> A I+R > > > freq (319 -319) = 240.2 [cm-1] --> A I+R > > > freq (320 -320) = 270.4 [cm-1] --> A I+R > > > freq (321 -321) = 317.0 [cm-1] --> A I+R > > > freq (322 -322) = 370.8 [cm-1] --> A I+R > > > freq (323 -323) = 377.3 [cm-1] --> A I+R > > > freq (324 -324) = 398.3 [cm-1] --> A I+R > > > freq (325 -325) = 417.8 [cm-1] --> A I+R > > > freq (326 -326) = 468.2 [cm-1] --> A I+R > > > freq (327 -327) = 659.0 [cm-1] --> A I+R > > > freq (328 -328) = 1096.6 [cm-1] --> A I+R > > > freq (329 -329) = 1795.5 [cm-1] --> A I+R > > > freq (330 -330) = 2199.3 [cm-1] --> A I+R > > > > > > > > > ph.x input file: > > > > > > phonon calculation at Gamma point. > > > &inputph > > > outdir = './outdir' > > > prefix = 'HS' > > > tr2_ph = 1.0d-09 > > > epsil = .false. > > > amass(1) = 58.69340 > > > amass(2) = 30.97376 > > > amass(3) = 1.00784 > > > amass(4) = 32.065 > > > fildyn = 'HS.dyn' > > > > > > alpha_mix(1)=0.1 > > > > > > recover=.true > > > nogg = .true > > > nat_todo = 5 > > > > > > / > > > 0.0 0.0 0.0 > > > > > > 1 2 37 46 54 > > > > > > > > > > > > scf input file: > > > > > > &CONTROL > > > calculation = "scf" > > > prefix = 'HS' > > > outdir = './outdir' > > > pseudo_dir = '/home/' > > > restart_mode = 'from_scratch' > > > forc_conv_thr = 1.0e-03 > > > etot_conv_thr = 1e-04 > > > nstep = 999 > > > / > > > &SYSTEM > > > ibrav = 0 > > > ecutrho = 200 > > > ecutwfc = 25 > > > nat = 110 > > > ntyp = 4 > > > occupations='smearing',smearing='gaussian',degauss=0.005 > > > vdw_corr = 'DFT-D2' > > > nspin = 2 > > > starting_magnetization(1)= 0.01 > > > / > > > &ELECTRONS > > > conv_thr = 1e-8 > > > electron_maxstep = 200 > > > mixing_mode ='local-TF' > > > mixing_beta = 0.3 > > > / > > > &IONS > > > / > > > K_POINTS {automatic} > > > 3 3 1 0 0 0 > > > 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 > > > H 1.00784 H.pbe-rrkjus_psl.0.1.UPF > > > S 32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF > > > CELL_PARAMETERS {angstrom} > > > 11.76538354 0.0000000000 0.0000000000 > > > -5.8826917709 10.189121032 0.0000000000 > > > 0.0000000000 0.0000000000 30.993869056 > > > ATOMIC_POSITIONS (angstrom) > > > H 0.879694621 3.392266427 10.708999692 > > > S 2.266698845 3.396363162 10.560733430 > > > Ni -2.744571590 4.755054131 0.244939179 > > > Ni 3.134031329 1.363792691 0.248008546 > > > . > > > . > > > . > > > P -1.060403962 1.841094610 1.604930623 > > > P -3.921453199 6.792156181 0.000000000 0 0 0 > > > P 1.960697149 3.396027080 0.000000000 0 0 0 > > > P 7.842906399 0.000000000 0.000000000 0 0 0 > > > > > > > > > regards > > > > > > > > > _______________________________________________ > > > Quantum ESPRESSO is supported by MaX (www.max-centre.eu) > > > users mailing list users@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@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@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users