[QE-users] Phonon: negative frequencies for adsorbate molecule using "nat-todo" option
Tamas Karpati
tkarpati at gmail.com
Mon Nov 2 11:29:36 CET 2020
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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