[QE-users] Phonon: negative frequencies for adsorbate molecule using "nat-todo" option
Omer Mutasim
omermutasim at ymail.com
Thu Nov 5 05:15:44 CET 2020
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 <tkarpati at 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 <tkarpati at 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 <omermutasim at 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
> >
> >
> > _______________________________________________
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