[QE-users] Questions related to vibrational analysis (for both molecule and adsorbate)--update

[Paolo Giannozzi]

On Fri, Mar 13, 2020 at 4:22 AM Shen, Ziheng <zshen83 at gatech.edu> wrote:

1) When doing frequency analysis for molecules, I expected to get zero or
> extremely small value for the first six frequencies (i.e. translational &
> rotational modes). According to suggestions from those previously posted
> problems, I tried to apply more restrict convergence thresholds and ASR. It
> seems that ASR help a lot to reduce the number. But I still got frequencies
> at ~50 level. Is it possible to completely remove those small values? Or
> are those values small enough to be neglected?
>

They are small enough to be neglected. They can be removed by applying the
ASR to the computed dynamical matrix. See the various kinds of ASR in codes
"dynmat" and "matdyn", in particular the "zero-dim" one. Note that  more
sophisticated ASR than "simple" can be surprising slow.

2) My ultimate goal is to perform frequency analysis for adsorbate so that
> I can both determine transition state structures and apply ZPE corrections.
> I tried to use “nat_todo” to fix the surface atoms and only did calculation
> for adsorbate (CH in my case). I got crazy result (~10000 cm-1) when using
> large tr2_ph, and got improved results when I decrease the threshold. But I
> still got fairly large translational & rotational frequencies like below
>

I don't think you will obtain anything sensible by fixing the surface atoms
and making the calculation for the adsorbate atoms  only

Paolo


>
>   freq (    1) =     -25.618746 [THz] =    -854.549399 [cm-1]
>      freq (    2) =      -7.333895 [THz] =    -244.632409 [cm-1]
>      freq (    3) =      -6.696884 [THz] =    -223.383991 [cm-1]
>      freq (    4) =      -6.248674 [THz] =    -208.433322 [cm-1]
>      freq (    5) =      -4.947831 [THz] =    -165.041892 [cm-1]
>      freq (    6) =      -2.014699 [THz] =     -67.203109 [cm-1]
>      freq (   37) =       0.571458 [THz] =      19.061786 [cm-1]
>      freq (   38) =       5.754719 [THz] =     191.956759 [cm-1]
>      freq (   39) =      16.488930 [THz] =     550.011494 [cm-1]
>      freq (   40) =      16.563150 [THz] =     552.487199 [cm-1]
>      freq (   41) =      18.255969 [THz] =     608.953585 [cm-1]
>      freq (   42) =      56.121326 [THz] =    1872.005923 [cm-1]
>
> What does negative translational frequencies indicate, is it possible to
> eliminate these imaginary numbers (like using more restrict threshold)?
> And does my result indicate that my structure is most probably not a
> transition state since all the other frequencies are positive?
>
> I’m attaching the input file of pw.x &ph.x below:
> =========================scf input, structure obtained from
> neb.x========================
> &CONTROL
>   Calculation='scf',
>   restart_mode='from_scratch',
>   prefix         = "Ni_ch_ts"
>   outdir         = "./ts/tmp",
>   pseudo_dir     = "./pseudo",
>   tstress        = .true.
>   verbosity      = 'high'
>   tefield      = .true.
>   dipfield     = .true.
> /
> &SYSTEM
>   ibrav                  = 0,
>   nat                    = 14,
>   ntyp                   = 3,
>   ecutwfc                = 65,
>   ecutrho                = 650,
>   Occupations='smearing',
>   smearing='mp',
>   degauss=0.01,
>   nspin=2,
>   starting_magnetization(1)=0.2,
>   eamp        = 0.0
>   edir        = 3
>   emaxpos     = 0.95
>   eopreg      = 0.05
> /
> &ELECTRONS
>   electron_maxstep=250,
>   conv_thr    = 1.D-10,
>   mixing_beta = 0.1,
> /
>
> ATOMIC_SPECIES
> Ni 58.69 ni_pbe_v1.4.uspp.F.UPF
> C  12    C.pbe-n-kjpaw_psl.1.0.0.UPF
> H  1     H.pbe-kjpaw_psl.1.0.0.UPF
> CELL_PARAMETERS { angstrom }
>
>         4.9667177200         0.0000000000         0.0000000000
>         2.4833588600         4.3013037190         0.0000000000
>         0.0000000000         0.0000000000         20.000000000
>
> ATOMIC_POSITIONS { angstrom }
> Ni    0.0000000000    0.0000000000    7.9723500000
> Ni    1.2416800000    2.1506500000    7.9723500000
> Ni    2.4833600000    0.0000000000    7.9723500000
> Ni    3.7250400000    2.1506500000    7.9723500000
> Ni    2.4833600000    1.4337700000   10.0000000000
> Ni    3.7250400000    3.5844200000   10.0000000000
> Ni    4.9667200000    1.4337700000   10.0000000000
> Ni    6.2084000000    3.5844200000   10.0000000000
> Ni    1.2281125212    0.7413038538   12.1124602290
> Ni    2.4833613443    2.9495126082   12.0722664849
> Ni    3.7386101535    0.7413040204   12.1124604793
> Ni    4.9667205066    2.8946406480   11.9560276983
>  C    2.4833610952    1.4972020489   13.1166864267
>  H    2.4833559794    3.1940064219   13.5465576823
>
> K_POINTS { automatic }
> 6 6 1 0 0 0
>
> =======================================ph.x
> input=======================================
> phonons of CH on metal Ni at Gamma
>  &inputph
>  tr2_ph=1.0d-16,
>  prefix='Ni_ch_ts',
>  epsil=.false.,
>  amass(1)=58.69,
>  amass(2)=12.011,
>  amass(3)=1.0,
>  alpha_mix(1)=0.1,
>  outdir='./tmp/',
>  fildyn='CH.dynG',
>  nat_todo= 2,
>  /
>  0.0 0.0 0.0
>  13 14
>
>
> Thanks in advance for anyone that could give suggestions to me!
>
> Best regards
> Ziheng Shen
> PhD student @ Georgia Institute of Technology
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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