[QE-users] how to select the perturbed atoms in phonon single q calculation ?

Tamas Karpati tkarpati at gmail.com
Fri Oct 30 10:20:19 CET 2020


Dear Omer,

1, Freqs. can be ordered. Atoms can be ordered.
   It is intriguing how you want to compare them.
   But seriously, you have N atoms and 3N normal modes
   or phonons (some are not real modes, though). How
   do you want to order them "the same way"?
2, What is more important, you have a real big no. of
    negative freqs. of high abs. value meaning that your
    structure is away from a stationary point (neighter a local
    minimum nor a TS).
    Your simulations are blindingly fast, thus i suggest to
    perform an all-atom phonon simulation to see if you
    have all positive freqs. after the first 6 (rotation+translation)
    -which six should be small (ideally < 20 /cm but near 100 is OK).

  t

On Fri, Oct 30, 2020 at 4:56 AM Omer Mutasim <omermutasim at ymail.com> wrote:
> 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 Fri, Oct 30, 2020 at 4:56 AM Omer Mutasim <omermutasim at ymail.com> wrote:
>
> below are the results for molecule + 9 surface atoms:
>
>      freq (  1 -  1) =      -2653.0  [cm-1]   --> A               I+R
>      freq (  2 -  2) =      -2647.8  [cm-1]   --> A               I+R
>      freq (  3 -  3) =      -2324.1  [cm-1]   --> A               I+R
>      freq (  4 -  4) =      -2249.4  [cm-1]   --> A               I+R
>      freq (  5 -  5) =      -2179.6  [cm-1]   --> A               I+R
>      freq (  6 -  6) =      -2163.6  [cm-1]   --> A               I+R
>      freq (  7 -  7) =      -2133.7  [cm-1]   --> A               I+R
>      freq (  8 -  8) =      -2118.1  [cm-1]   --> A               I+R
>      freq (  9 -  9) =      -2089.4  [cm-1]   --> A               I+R
>      freq ( 10 - 10) =      -1980.7  [cm-1]   --> A               I+R
>      freq ( 11 - 11) =      -1933.8  [cm-1]   --> A               I+R
>      freq ( 12 - 12) =      -1924.3  [cm-1]   --> A               I+R
>      freq ( 13 - 13) =      -1818.4  [cm-1]   --> A               I+R
>      freq ( 14 - 14) =      -1591.9  [cm-1]   --> A               I+R
>      freq ( 15 - 15) =      -1470.5  [cm-1]   --> A               I+R
>      freq ( 16 - 16) =      -1411.8  [cm-1]   --> A               I+R
>      freq ( 17 - 17) =      -1364.6  [cm-1]   --> A               I+R
>      freq ( 18 - 18) =      -1297.9  [cm-1]   --> A               I+R
>      freq ( 19 - 19) =      -1297.7  [cm-1]   --> A               I+R
>      freq ( 20 - 20) =      -1271.4  [cm-1]   --> A               I+R
>      freq ( 21 - 21) =      -1267.9  [cm-1]   --> A               I+R
>      freq ( 22 - 22) =      -1188.6  [cm-1]   --> A               I+R
>      freq ( 23 - 23) =      -1186.4  [cm-1]   --> A               I+R
>      freq ( 24 - 24) =      -1154.5  [cm-1]   --> A               I+R
>      freq ( 25 - 25) =      -1152.2  [cm-1]   --> A               I+R
>      freq ( 26 - 26) =      -1077.7  [cm-1]   --> A               I+R
>      freq ( 27 - 27) =      -1051.2  [cm-1]   --> A               I+R
>      freq ( 28 - 28) =      -1028.4  [cm-1]   --> A               I+R
>      freq ( 29 - 29) =      -1019.6  [cm-1]   --> A               I+R
>      freq ( 30 - 30) =       -926.6  [cm-1]   --> A               I+R
>      freq ( 31 - 31) =       -914.1  [cm-1]   --> A               I+R
>      freq ( 32 - 32) =       -855.3  [cm-1]   --> A               I+R
>      freq ( 33 - 33) =       -713.5  [cm-1]   --> A               I+R
>      freq (298 -298) =         91.1  [cm-1]   --> A               I+R
>      freq (299 -299) =        102.9  [cm-1]   --> A               I+R
>      freq (300 -300) =        107.6  [cm-1]   --> A               I+R
>      freq (301 -301) =        143.9  [cm-1]   --> A               I+R
>      freq (302 -302) =        175.5  [cm-1]   --> A               I+R
>      freq (303 -303) =        185.7  [cm-1]   --> A               I+R
>      freq (304 -304) =        202.5  [cm-1]   --> A               I+R
>      freq (305 -305) =        266.3  [cm-1]   --> A               I+R
>      freq (306 -306) =        284.1  [cm-1]   --> A               I+R
>      freq (307 -307) =        333.0  [cm-1]   --> A               I+R
>      freq (308 -308) =        349.3  [cm-1]   --> A               I+R
>      freq (309 -309) =        442.5  [cm-1]   --> A               I+R
>      freq (310 -310) =        517.1  [cm-1]   --> A               I+R
>      freq (311 -311) =        571.9  [cm-1]   --> A               I+R
>      freq (312 -312) =        610.2  [cm-1]   --> A               I+R
>      freq (313 -313) =        699.8  [cm-1]   --> A               I+R
>      freq (314 -314) =        755.0  [cm-1]   --> A               I+R
>      freq (315 -315) =        790.9  [cm-1]   --> A               I+R
>      freq (316 -316) =        806.4  [cm-1]   --> A               I+R
>      freq (317 -317) =        847.5  [cm-1]   --> A               I+R
>      freq (318 -318) =        867.3  [cm-1]   --> A               I+R
>      freq (319 -319) =        881.1  [cm-1]   --> A               I+R
>      freq (320 -320) =        903.7  [cm-1]   --> A               I+R
>      freq (321 -321) =        942.0  [cm-1]   --> A               I+R
>      freq (322 -322) =       1029.9  [cm-1]   --> A               I+R
>      freq (323 -323) =       1070.9  [cm-1]   --> A               I+R
>      freq (324 -324) =       1084.6  [cm-1]   --> A               I+R
>      freq (325 -325) =       1214.6  [cm-1]   --> A               I+R
>      freq (326 -326) =       1307.9  [cm-1]   --> A               I+R
>      freq (327 -327) =       1395.9  [cm-1]   --> A               I+R
>      freq (328 -328) =       1450.3  [cm-1]   --> A               I+R
>      freq (329 -329) =       1714.9  [cm-1]   --> A               I+R
>      freq (330 -330) =       1990.8  [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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