Dear Dr. Tamasi tried "nogg", and it does work. However, the frequencies are
negative for the perturbed molecule atoms (HS) . I only perturbed the
molecule.Given that the molecule is stable, i.e. not a transition state.Below
are the output & input files:
output:
Mode symmetry, C_1 (1) point group:
freq ( 1 - 1) = -3417.3 [cm-1] --> A I+R freq
( 2 - 2) = -2660.2 [cm-1] --> A I+R freq ( 3 - 3)
= -2139.6 [cm-1] --> A I+R freq ( 4 - 4) =
-1453.3 [cm-1] --> A I+R freq ( 5 - 5) = -1358.9
[cm-1] --> A I+R freq ( 6 - 6) = -1036.4 [cm-1]
--> A I+R freq (325 -325) = 1030.9 [cm-1] --> A
I+R freq (326 -326) = 1151.4 [cm-1] --> A
I+R freq (327 -327) = 1295.7 [cm-1] --> A I+R
freq (328 -328) = 1579.7 [cm-1] --> A I+R freq (329
-329) = 2857.6 [cm-1] --> A I+R freq (330 -330) =
3310.5 [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)=0.3 nogg
= .true nat_todo = 2
/0.0 0.0 0.0
1 2
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}1 1 1 0 0 0ATOMIC_SPECIESNi 58.69340
Ni.pbe-n-rrkjus_psl.0.1.UPFP 30.97376 P.pbe-n-rrkjus_psl.1.0.0.UPFH 1.00784
H.pbe-rrkjus_psl.0.1.UPFS 32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF
CELL_PARAMETERS {angstrom} 11.765383541833 0.0000000000
0.0000000000 -5.88269177091652 10.1891210324947 0.0000000000
0.0000000000 0.0000000000 30.9938690567585ATOMIC_POSITIONS
(angstrom)H 0.879694621 3.392266427 10.708999692S 2.266698845
3.396363162 10.560733430Ni -2.744571590 4.755054131 0.244939179Ni
3.134031329 1.363792691 0.248008546...P -1.060403962 1.841094610
1.604930623P -3.921453199 6.792156181 0.000000000 0 0 0P
1.960697149 3.396027080 0.000000000 0 0 0P 7.842906399
0.000000000 0.000000000 0 0 0
On Thursday, October 29, 2020, 02:20:23 PM GMT+4, Tamas Karpati
<[email protected]> wrote:
did you try nogg=.true. ?
if not, i suggest you to apply the minimum necessary amount of
parameters in your input file.
On Wed, Oct 28, 2020 at 3:14 PM Omer Mutasim <[email protected]> wrote:
>
> I just tried but i got the following error message:
>
> "
> Error in routine phq_readin (1):
> gamma_gamma tricks with nat_todo not available. Use nogg=.true.
>
> "
> i'm doing single q phonon calculation
> any help ?
> On Wednesday, October 28, 2020, 05:45:15 PM GMT+4, Tamas Karpati
> <[email protected]> wrote:
>
>
> Dear Omer,
>
> Did you try to use the nat_todo option in your PH.x input file?
> (Do not forget to list the perturbed atom indices on the last line.)
>
> ASE can use QE as "calculator" and I think it can do what you want.
> If not, use Phonopy.
>
> HTH,
> t
>
> On Wed, Oct 28, 2020 at 1:28 PM Omer Mutasim <[email protected]> wrote:
> >
> >
> > Dear all
> >
> > I need to calculate the the virbrational frequencies of adsorbate molecule
> >on surface using phonon single q calculation , in order to estimate the
> >partition function (for entropy ,reaction rate constants). so my questions
> >go like:
> >
> > I have a large supercell (110 atoms) which means a high degrees of freedom
> >(330 DOF) , so i want to decrease this DOF , by perturbing only adsorbate
> >molecule and the the two uppermost layers
> >
> > how to select the perturbed atoms in quantum espresso ?
> > I have heard that it can be done by finite difference method, which wasn't
> > employed in QE.
> > However, i have seen a post where Dr. Paolo Giannozzi said: " it can be
> > performed by two finite-difference calculations with opposite displacements
> > "
> > So , can you please tell me, what are the steps involved in doing this
> > finite-difference method mentioned by Dr. Paolo ? or any other procedure
> > that can be do the same ?
> >
> >
> > Thanks in advance
> >
> >
> >
> >
> > Omer Elmutasim
> > Research Assistant
> > Chemical Engineering Department
> > Khalifa university- UAE
>
> > _______________________________________________
> > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> > users mailing list [email protected]
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> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
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>
> _______________________________________________
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_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list [email protected]
https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list [email protected]
https://lists.quantum-espresso.org/mailman/listinfo/users
