[QE-users] Questions related to vibrational analysis (for both molecule and adsorbate)--update
Shen, Ziheng
zshen83 at gatech.edu
Mon Mar 16 01:53:22 CET 2020
Thank you so much Paolo!
I also have some follow up questions, I would appreciate it if you could help me with them!
1) May I ask is there any literature that can prove it’s feasible to neglect the small frequencies? And is this also a same criteria for a slab system (if I calculate frequencies for all modes)?
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?
Thanks again for your help!
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<mailto:users-request at lists.quantum-espresso.org> wrote:
On Fri, Mar 13, 2020 at 4:22 AM Shen, Ziheng <zshen83 at gatech.edu<mailto: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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