[QE-users] how to select the perturbed atoms in phonon single q calculation ?
Omer Mutasim
omermutasim at ymail.com
Fri Oct 30 12:54:49 CET 2020
Dear Dr. Tamas,Thanks for the clarification.I think the problem might be the K ponits ( 1 1 1 ) i am using in my scf input file , i will increase it to ( 3 3 1 ) , then i will let you know the results.I’m really learning a lot form you, Thanks a lot
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On Friday, October 30, 2020, 1:17 PM, Tamas Karpati <tkarpati at gmail.com> wrote:
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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