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

Omer Mutasim omermutasim at ymail.com
Thu Oct 29 11:55:15 CET 2020


 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 <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
>
> > _______________________________________________
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