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Thank you so much Paolo!
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<div class="">I also have some follow up questions, I would appreciate it if you could help me with them!<br class="">
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</div>
<div class="">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)?</div>
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<div class="">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 class="">Thanks again for your help!</div>
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<div class="" style="margin: 0px; font-stretch: normal; line-height: normal;">Best regards</div>
<div class="" style="margin: 0px; font-stretch: normal; line-height: normal;">Ziheng Shen</div>
<div class="" style="margin: 0px; font-stretch: normal; line-height: normal;">PhD student @ Georgia Institute of Technology</div>
<div class="" style="margin: 0px; font-stretch: normal; line-height: normal;"><br class="">
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<blockquote type="cite" class="">
<div class="">On Mar 15, 2020, at 7:00 AM, <a href="mailto:users-request@lists.quantum-espresso.org" class="">
users-request@lists.quantum-espresso.org</a> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">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; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">zshen83@gatech.edu</a><span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">>
wrote:</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">1)
When doing frequency analysis for molecules, I expected to get zero or</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
extremely small value for the first six frequencies (i.e. translational &<br class="">
rotational modes). According to suggestions from those previously posted<br class="">
problems, I tried to apply more restrict convergence thresholds and ASR. It<br class="">
seems that ASR help a lot to reduce the number. But I still got frequencies<br class="">
at ~50 level. Is it possible to completely remove those small values? Or<br class="">
are those values small enough to be neglected?<br class="">
<br class="">
</blockquote>
<br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">They
are small enough to be neglected. They can be removed by applying the</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">ASR
to the computed dynamical matrix. See the various kinds of ASR in codes</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">"dynmat"
and "matdyn", in particular the "zero-dim" one. Note that more</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">sophisticated
ASR than "simple" can be surprising slow.</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">2)
My ultimate goal is to perform frequency analysis for adsorbate so that</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
I can both determine transition state structures and apply ZPE corrections.<br class="">
I tried to use ?nat_todo? to fix the surface atoms and only did calculation<br class="">
for adsorbate (CH in my case). I got crazy result (~10000 cm-1) when using<br class="">
large tr2_ph, and got improved results when I decrease the threshold. But I<br class="">
still got fairly large translational & rotational frequencies like below<br class="">
<br class="">
</blockquote>
<br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">I
don't think you will obtain anything sensible by fixing the surface atoms</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">and
making the calculation for the adsorbate atoms only</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Paolo</span><br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); 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; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br class="">
freq ( 1) = -25.618746 [THz] = -854.549399 [cm-1]<br class="">
freq ( 2) = -7.333895 [THz] = -244.632409 [cm-1]<br class="">
freq ( 3) = -6.696884 [THz] = -223.383991 [cm-1]<br class="">
freq ( 4) = -6.248674 [THz] = -208.433322 [cm-1]<br class="">
freq ( 5) = -4.947831 [THz] = -165.041892 [cm-1]<br class="">
freq ( 6) = -2.014699 [THz] = -67.203109 [cm-1]<br class="">
freq ( 37) = 0.571458 [THz] = 19.061786 [cm-1]<br class="">
freq ( 38) = 5.754719 [THz] = 191.956759 [cm-1]<br class="">
freq ( 39) = 16.488930 [THz] = 550.011494 [cm-1]<br class="">
freq ( 40) = 16.563150 [THz] = 552.487199 [cm-1]<br class="">
freq ( 41) = 18.255969 [THz] = 608.953585 [cm-1]<br class="">
freq ( 42) = 56.121326 [THz] = 1872.005923 [cm-1]<br class="">
<br class="">
What does negative translational frequencies indicate, is it possible to<br class="">
eliminate these imaginary numbers (like using more restrict threshold)?<br class="">
And does my result indicate that my structure is most probably not a<br class="">
transition state since all the other frequencies are positive?<br class="">
<br class="">
I?m attaching the input file of pw.x &ph.x below:<br class="">
=========================scf input, structure obtained from<br class="">
neb.x========================<br class="">
&CONTROL<br class="">
Calculation='scf',<br class="">
restart_mode='from_scratch',<br class="">
prefix = "Ni_ch_ts"<br class="">
outdir = "./ts/tmp",<br class="">
pseudo_dir = "./pseudo",<br class="">
tstress = .true.<br class="">
verbosity = 'high'<br class="">
tefield = .true.<br class="">
dipfield = .true.<br class="">
/<br class="">
&SYSTEM<br class="">
ibrav = 0,<br class="">
nat = 14,<br class="">
ntyp = 3,<br class="">
ecutwfc = 65,<br class="">
ecutrho = 650,<br class="">
Occupations='smearing',<br class="">
smearing='mp',<br class="">
degauss=0.01,<br class="">
nspin=2,<br class="">
starting_magnetization(1)=0.2,<br class="">
eamp = 0.0<br class="">
edir = 3<br class="">
emaxpos = 0.95<br class="">
eopreg = 0.05<br class="">
/<br class="">
&ELECTRONS<br class="">
electron_maxstep=250,<br class="">
conv_thr = 1.D-10,<br class="">
mixing_beta = 0.1,<br class="">
/<br class="">
<br class="">
ATOMIC_SPECIES<br class="">
Ni 58.69 ni_pbe_v1.4.uspp.F.UPF<br class="">
C 12 C.pbe-n-kjpaw_psl.1.0.0.UPF<br class="">
H 1 H.pbe-kjpaw_psl.1.0.0.UPF<br class="">
CELL_PARAMETERS { angstrom }<br class="">
<br class="">
4.9667177200 0.0000000000 0.0000000000<br class="">
2.4833588600 4.3013037190 0.0000000000<br class="">
0.0000000000 0.0000000000 20.000000000<br class="">
<br class="">
ATOMIC_POSITIONS { angstrom }<br class="">
Ni 0.0000000000 0.0000000000 7.9723500000<br class="">
Ni 1.2416800000 2.1506500000 7.9723500000<br class="">
Ni 2.4833600000 0.0000000000 7.9723500000<br class="">
Ni 3.7250400000 2.1506500000 7.9723500000<br class="">
Ni 2.4833600000 1.4337700000 10.0000000000<br class="">
Ni 3.7250400000 3.5844200000 10.0000000000<br class="">
Ni 4.9667200000 1.4337700000 10.0000000000<br class="">
Ni 6.2084000000 3.5844200000 10.0000000000<br class="">
Ni 1.2281125212 0.7413038538 12.1124602290<br class="">
Ni 2.4833613443 2.9495126082 12.0722664849<br class="">
Ni 3.7386101535 0.7413040204 12.1124604793<br class="">
Ni 4.9667205066 2.8946406480 11.9560276983<br class="">
C 2.4833610952 1.4972020489 13.1166864267<br class="">
H 2.4833559794 3.1940064219 13.5465576823<br class="">
<br class="">
K_POINTS { automatic }<br class="">
6 6 1 0 0 0<br class="">
<br class="">
=======================================ph.x<br class="">
input=======================================<br class="">
phonons of CH on metal Ni at Gamma<br class="">
&inputph<br class="">
tr2_ph=1.0d-16,<br class="">
prefix='Ni_ch_ts',<br class="">
epsil=.false.,<br class="">
amass(1)=58.69,<br class="">
amass(2)=12.011,<br class="">
amass(3)=1.0,<br class="">
alpha_mix(1)=0.1,<br class="">
outdir='./tmp/',<br class="">
fildyn='CH.dynG',<br class="">
nat_todo= 2,<br class="">
/<br class="">
0.0 0.0 0.0<br class="">
13 14<br class="">
<br class="">
<br class="">
Thanks in advance for anyone that could give suggestions to me!<br class="">
<br class="">
Best regards<br class="">
Ziheng Shen<br class="">
PhD student @ Georgia Institute of Technology</blockquote>
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