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<div class="moz-cite-prefix">On 17/03/20 15:46, Paolo Giannozzi
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAPMgbCva_mOvL_1jWbc9P6gRbVhX_sNDSjCps7t0+2JpbFE4rQ@mail.gmail.com">
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<div dir="ltr">On Mon, Mar 16, 2020 at 1:53 AM Shen, Ziheng <<a
href="mailto:zshen83@gatech.edu" moz-do-not-send="true">zshen83@gatech.edu</a>>
wrote:<br>
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<div>1) May I ask is there any literature that can prove
it’s feasible to neglect the small frequencies? </div>
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<div>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.<br>
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<div>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?
</div>
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<div>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. <br>
</div>
<div><br>
<div>Paolo<br>
</div>
<div><br>
</div>
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<p>I think that if you have light atoms adsorbed on some heavier
material and are looking for the adsorbate related frequencies
then you can diagonalize the reduced matrix and the frequencies
that you obtain should be variational upper bounds to the real
ones....<br>
</p>
<p>just pretend you computed the whole matrix but restrict the
atomic motion to a subset of atoms... so to the extent the modes
are localized on the adsorbate with little involvement of the
substrate you should be ok...</p>
<p>but the low lying frequencies (the ones resonant with the
substrate modes) will be completely wrong. </p>
<p><br>
</p>
<p>one could start with nat_todo equal to just the adsorbate and
then the first shell, then the second one ... and see how things
converge ...</p>
<p>another option (better, but would need some ad hoc coding) would
be to build the dynmat of the nat_todo atoms with interatomic
force constants for the rest of the cell borrowed from some model
(the bulk, or the clean surface) ... and again monitor the
convergence as you include more and more shells of atoms in the
nat_todo.</p>
<p><br>
</p>
<p>stefano<br>
</p>
<p><br>
</p>
<p><br>
</p>
<blockquote type="cite"
cite="mid:CAPMgbCva_mOvL_1jWbc9P6gRbVhX_sNDSjCps7t0+2JpbFE4rQ@mail.gmail.com">
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<div
style="margin:0px;font-stretch:normal;line-height:normal">Best
regards</div>
<div
style="margin:0px;font-stretch:normal;line-height:normal">Ziheng
Shen</div>
<div
style="margin:0px;font-stretch:normal;line-height:normal">PhD
student @ Georgia Institute of Technology</div>
<div
style="margin:0px;font-stretch:normal;line-height:normal"><br>
</div>
<blockquote type="cite">
<div>On Mar 15, 2020, at 7:00 AM, <a
href="mailto:users-request@lists.quantum-espresso.org"
target="_blank" moz-do-not-send="true">
users-request@lists.quantum-espresso.org</a>
wrote:</div>
<br>
<div><span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">On
Fri, Mar 13, 2020 at 4:22 AM Shen, Ziheng <</span><a
href="mailto:zshen83@gatech.edu"
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"
target="_blank" moz-do-not-send="true">zshen83@gatech.edu</a><span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">>
wrote:</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">1)
When doing frequency analysis for molecules, I
expected to get zero or</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<blockquote type="cite"
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">extremely
small value for the first six frequencies (i.e.
translational &<br>
rotational modes). According to suggestions from
those previously posted<br>
problems, I tried to apply more restrict
convergence thresholds and ASR. It<br>
seems that ASR help a lot to reduce the number.
But I still got frequencies<br>
at ~50 level. Is it possible to completely
remove those small values? Or<br>
are those values small enough to be neglected?<br>
<br>
</blockquote>
<br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">They
are small enough to be neglected. They can be
removed by applying the</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">ASR
to the computed dynamical matrix. See the
various kinds of ASR in codes</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">"dynmat"
and "matdyn", in particular the "zero-dim" one.
Note that more</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">sophisticated
ASR than "simple" can be surprising slow.</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">2)
My ultimate goal is to perform frequency
analysis for adsorbate so that</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<blockquote type="cite"
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">I
can both determine transition state structures
and apply ZPE corrections.<br>
I tried to use ?nat_todo? to fix the surface
atoms and only did calculation<br>
for adsorbate (CH in my case). I got crazy
result (~10000 cm-1) when using<br>
large tr2_ph, and got improved results when I
decrease the threshold. But I<br>
still got fairly large translational &
rotational frequencies like below<br>
<br>
</blockquote>
<br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">I
don't think you will obtain anything sensible by
fixing the surface atoms</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">and
making the calculation for the adsorbate atoms
only</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Paolo</span><br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<blockquote type="cite"
style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br>
freq ( 1) = -25.618746 [THz] =
-854.549399 [cm-1]<br>
freq ( 2) = -7.333895 [THz] =
-244.632409 [cm-1]<br>
freq ( 3) = -6.696884 [THz] =
-223.383991 [cm-1]<br>
freq ( 4) = -6.248674 [THz] =
-208.433322 [cm-1]<br>
freq ( 5) = -4.947831 [THz] =
-165.041892 [cm-1]<br>
freq ( 6) = -2.014699 [THz] =
-67.203109 [cm-1]<br>
freq ( 37) = 0.571458 [THz] =
19.061786 [cm-1]<br>
freq ( 38) = 5.754719 [THz] =
191.956759 [cm-1]<br>
freq ( 39) = 16.488930 [THz] =
550.011494 [cm-1]<br>
freq ( 40) = 16.563150 [THz] =
552.487199 [cm-1]<br>
freq ( 41) = 18.255969 [THz] =
608.953585 [cm-1]<br>
freq ( 42) = 56.121326 [THz] =
1872.005923 [cm-1]<br>
<br>
What does negative translational frequencies
indicate, is it possible to<br>
eliminate these imaginary numbers (like using
more restrict threshold)?<br>
And does my result indicate that my structure is
most probably not a<br>
transition state since all the other frequencies
are positive?<br>
<br>
I?m attaching the input file of pw.x &ph.x
below:<br>
=========================scf input, structure
obtained from<br>
neb.x========================<br>
&CONTROL<br>
Calculation='scf',<br>
restart_mode='from_scratch',<br>
prefix = "Ni_ch_ts"<br>
outdir = "./ts/tmp",<br>
pseudo_dir = "./pseudo",<br>
tstress = .true.<br>
verbosity = 'high'<br>
tefield = .true.<br>
dipfield = .true.<br>
/<br>
&SYSTEM<br>
ibrav = 0,<br>
nat = 14,<br>
ntyp = 3,<br>
ecutwfc = 65,<br>
ecutrho = 650,<br>
Occupations='smearing',<br>
smearing='mp',<br>
degauss=0.01,<br>
nspin=2,<br>
starting_magnetization(1)=0.2,<br>
eamp = 0.0<br>
edir = 3<br>
emaxpos = 0.95<br>
eopreg = 0.05<br>
/<br>
&ELECTRONS<br>
electron_maxstep=250,<br>
conv_thr = 1.D-10,<br>
mixing_beta = 0.1,<br>
/<br>
<br>
ATOMIC_SPECIES<br>
Ni 58.69 ni_pbe_v1.4.uspp.F.UPF<br>
C 12 C.pbe-n-kjpaw_psl.1.0.0.UPF<br>
H 1 H.pbe-kjpaw_psl.1.0.0.UPF<br>
CELL_PARAMETERS { angstrom }<br>
<br>
4.9667177200 0.0000000000
0.0000000000<br>
2.4833588600 4.3013037190
0.0000000000<br>
0.0000000000 0.0000000000
20.000000000<br>
<br>
ATOMIC_POSITIONS { angstrom }<br>
Ni 0.0000000000 0.0000000000
7.9723500000<br>
Ni 1.2416800000 2.1506500000
7.9723500000<br>
Ni 2.4833600000 0.0000000000
7.9723500000<br>
Ni 3.7250400000 2.1506500000
7.9723500000<br>
Ni 2.4833600000 1.4337700000
10.0000000000<br>
Ni 3.7250400000 3.5844200000
10.0000000000<br>
Ni 4.9667200000 1.4337700000
10.0000000000<br>
Ni 6.2084000000 3.5844200000
10.0000000000<br>
Ni 1.2281125212 0.7413038538
12.1124602290<br>
Ni 2.4833613443 2.9495126082
12.0722664849<br>
Ni 3.7386101535 0.7413040204
12.1124604793<br>
Ni 4.9667205066 2.8946406480
11.9560276983<br>
C 2.4833610952 1.4972020489
13.1166864267<br>
H 2.4833559794 3.1940064219
13.5465576823<br>
<br>
K_POINTS { automatic }<br>
6 6 1 0 0 0<br>
<br>
=======================================ph.x<br>
input=======================================<br>
phonons of CH on metal Ni at Gamma<br>
&inputph<br>
tr2_ph=1.0d-16,<br>
prefix='Ni_ch_ts',<br>
epsil=.false.,<br>
amass(1)=58.69,<br>
amass(2)=12.011,<br>
amass(3)=1.0,<br>
alpha_mix(1)=0.1,<br>
outdir='./tmp/',<br>
fildyn='CH.dynG',<br>
nat_todo= 2,<br>
/<br>
0.0 0.0 0.0<br>
13 14<br>
<br>
<br>
Thanks in advance for anyone that could give
suggestions to me!<br>
<br>
Best regards<br>
Ziheng Shen<br>
PhD student @ Georgia Institute of Technology</blockquote>
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-- <br>
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<div>Paolo Giannozzi, Dip. Scienze Matematiche
Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
<br>
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