[QE-users] Questions related to vibrational analysis (for both molecule and adsorbate)--update
Paolo Giannozzi
p.giannozzi at gmail.com
Tue Mar 17 15:46:22 CET 2020
On Mon, Mar 16, 2020 at 1:53 AM Shen, Ziheng <zshen83 at gatech.edu> wrote:
>
> 1) May I ask is there any literature that can prove it’s feasible to
> neglect the small frequencies?
>
no idea, but you can easily verify whether the neglect of almost-zero
frequencies has any effect: if you impose the ASR on dynamical matrices,
only frequencies of translational modes (and of rotational ones for a
molecule) should change, while all other frequencies should stay almost the
same.
2) I saw you also replied to others that “nat_todo” does not make any
> sense, but there were still people claimed that they got some useful
> results. I read from some books (like the one written by D.Sholl) saying
> that it’s possible to calculate only frequencies of adsorbates which could
> save computational resources. Some other ab initial calculation software
> (like VASP) also have similar functions to calculate adsorbates only. Why
> is “nat_todo” not working here?
>
Presumably it doesn't work because it is not sufficient to just ignore all
surface atoms and compute the dynamical matrix restricted to adsorbate
atoms only. I guess there are tricks to approximated phonons for an
adsorbate on a surface by computing a "reduced" dynamical matrix for the
adsorbate only, in which the information on the adsorbate-surface
interactions is "refolded", but I don't know any. This same question has
been asked over and over again in the list and nobody (that I remember)
ever gave an answer.
Paolo
Best regards
Ziheng Shen
PhD student @ Georgia Institute of Technology
On Mar 15, 2020, at 7:00 AM, users-request at lists.quantum-espresso.org wrote:
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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