[QE-users] how to select the perturbed atoms in phonon single q calculation ?
Omer Mutasim
omermutasim at ymail.com
Thu Oct 29 22:18:41 CET 2020
i have perturbed the molecule with the 3 surface atoms. Also i tried 9 surface atoms connected to it (currently running), however i got the same negative frequencies. Does the frequencies, shown below, have the same order of perturbed atoms ? i.e. the ( 1 - 1) correspond to the first atom, ( 2 - 2) for the second atom ,.. ?what does " I+R " & " A" means ?could the higher frequencies ( > 600 ), at the end, correspond to the molecule ?
below are the results for molecule + 3 surface atoms:
freq ( 1 - 1) = -2644.2 [cm-1] --> A I+R
freq ( 2 - 2) = -2633.2 [cm-1] --> A I+R
freq ( 3 - 3) = -2304.5 [cm-1] --> A I+R
freq ( 4 - 4) = -2238.8 [cm-1] --> A I+R
freq ( 5 - 5) = -2164.5 [cm-1] --> A I+R
freq ( 6 - 6) = -2121.2 [cm-1] --> A I+R
freq ( 7 - 7) = -2104.9 [cm-1] --> A I+R
freq ( 8 - 8) = -2080.8 [cm-1] --> A I+R
freq ( 9 - 9) = -2061.5 [cm-1] --> A I+R
freq ( 10 - 10) = -1925.4 [cm-1] --> A I+R
freq ( 11 - 11) = -1897.1 [cm-1] --> A I+R
freq ( 12 - 12) = -1397.0 [cm-1] --> A I+R
freq ( 13 - 13) = -1234.0 [cm-1] --> A I+R
freq ( 14 - 14) = -1161.7 [cm-1] --> A I+R
freq ( 15 - 15) = -1015.3 [cm-1] --> A I+R
freq (316 -316) = 138.5 [cm-1] --> A I+R
freq (317 -317) = 145.4 [cm-1] --> A I+R
freq (318 -318) = 206.2 [cm-1] --> A I+R
freq (319 -319) = 216.9 [cm-1] --> A I+R
freq (320 -320) = 263.8 [cm-1] --> A I+R
freq (321 -321) = 291.9 [cm-1] --> A I+R
freq (322 -322) = 295.8 [cm-1] --> A I+R
freq (323 -323) = 384.0 [cm-1] --> A I+R
freq (324 -324) = 459.1 [cm-1] --> A I+R
freq (325 -325) = 529.7 [cm-1] --> A I+R
freq (326 -326) = 621.1 [cm-1] --> A I+R
freq (327 -327) = 640.1 [cm-1] --> A I+R
freq (328 -328) = 1190.8 [cm-1] --> A I+R
freq (329 -329) = 1568.2 [cm-1] --> A I+R
freq (330 -330) = 1851.0 [cm-1] --> A I+R
On Thursday, October 29, 2020, 3:52:29 PM GMT+4, Tamas Karpati <tkarpati at gmail.com> wrote:
Dear Omer,
Very well, your simulation completes successfully.
Negative (ie. imaginary) eigenvalues indicate for all-atom
perturbations that your system is not in a local minimum conformation.
In such an overlimited situation, however, these numbers are probably
meaningless. To see what is behind, try to add more and more
atoms to the perturbation pool. The followings might show you
how much of the reactant environment is necessary to account for:
- first add the metal atoms that connect to S or O
- then add metal atoms directly connected to the above metals
- extend further (2 then more metal bond environments).
In principle the all-atom phonon sim. would give you 6 pcs.
of near zero "frequencies" if your structure is a real local minimum.
If not, the no. of imaginary freqs. (also called nimag) informs you
about the dimensions of the E-hypersurface that you need to climb more.
Note: R and P need zero, TS needs exactly one for nimag.
One more point: your molecule was SO2 which decomposed so that
you left out the other O from your simulation (for just 2). It would
be more correct
to do the above steps including all S + 2 O and their direct/indirect
chemical environments... I'm curious what others would say to this.
Good luck,
t
On Thu, Oct 29, 2020 at 11:55 AM Omer Mutasim <omermutasim at ymail.com> wrote:
>
> Dear Dr. Tamas
> i 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 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}
> 11.765383541833 0.0000000000 0.0000000000
> -5.88269177091652 10.1891210324947 0.0000000000
> 0.0000000000 0.0000000000 30.9938690567585
> 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
>
>
>
> On Thursday, October 29, 2020, 02:20:23 PM GMT+4, Tamas Karpati <tkarpati at gmail.com> 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 <omermutasim at ymail.com> 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 <tkarpati at gmail.com> 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 <omermutasim at ymail.com> 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)
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