<div dir="ltr"><div dir="ltr">On Fri, Mar 13, 2020 at 4:22 AM Shen, Ziheng <<a href="mailto:zshen83@gatech.edu">zshen83@gatech.edu</a>> wrote:</div><div dir="ltr"><br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;"><span style="font-stretch:normal;line-height:normal;font-family:Helvetica">1)
</span>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?
</div></blockquote><div><br></div><div>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.<br></div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">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</div></blockquote><div><br></div><div>I don't think you will obtain anything sensible by fixing the surface atoms and making the calculation for the adsorbate atoms only</div><div><br></div><div>Paolo<br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">
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<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 1) = -25.618746 [THz] = -854.549399 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 2) = -7.333895 [THz] = -244.632409 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 3) = -6.696884 [THz] = -223.383991 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 4) = -6.248674 [THz] = -208.433322 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 5) = -4.947831 [THz] = -165.041892 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 6) = -2.014699 [THz] = -67.203109 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 37) = 0.571458 [THz] = 19.061786 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 38) = 5.754719 [THz] = 191.956759 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 39) = 16.488930 [THz] = 550.011494 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 40) = 16.563150 [THz] = 552.487199 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 41) = 18.255969 [THz] = 608.953585 [cm-1]</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> freq ( 42) = 56.121326 [THz] = 1872.005923 [cm-1]</div>
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<div style="margin:0px;font-stretch:normal;line-height:normal">What does negative translational frequencies indicate, is it possible to eliminate these imaginary numbers (like using more restrict threshold)?</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">And does my result indicate that my structure is most probably not a transition state since all the other frequencies are positive?</div>
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<div style="margin:0px;font-stretch:normal;line-height:normal">I’m attaching the input file of pw.x &ph.x below:</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">=========================scf input, structure obtained from neb.x========================</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">&CONTROL</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> Calculation='scf',</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> restart_mode='from_scratch',</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> prefix = "Ni_ch_ts"</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> outdir = "./ts/tmp",</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> pseudo_dir = "./pseudo",</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> tstress = .true.</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> verbosity = 'high'</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> tefield = .true.</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> dipfield = .true.</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">/</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">&SYSTEM</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> ibrav = 0,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> nat = 14,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> ntyp = 3,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> ecutwfc = 65,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> ecutrho = 650,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> Occupations='smearing',</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> smearing='mp',</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> degauss=0.01,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> nspin=2,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> starting_magnetization(1)=0.2,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> eamp = 0.0</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> edir = 3</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> emaxpos = 0.95</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> eopreg = 0.05</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">/</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">&ELECTRONS</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> electron_maxstep=250,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> conv_thr = 1.D-10,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> mixing_beta = 0.1,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">/</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:14px">
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<div style="margin:0px;font-stretch:normal;line-height:normal">ATOMIC_SPECIES</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 58.69 ni_pbe_v1.4.uspp.F.UPF</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">C 12 C.pbe-n-kjpaw_psl.1.0.0.UPF</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">H 1 H.pbe-kjpaw_psl.1.0.0.UPF</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">CELL_PARAMETERS { angstrom }</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> 4.9667177200 0.0000000000 0.0000000000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> 2.4833588600 4.3013037190 0.0000000000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> 0.0000000000 0.0000000000 20.000000000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">ATOMIC_POSITIONS { angstrom }</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 0.0000000000 0.0000000000 7.9723500000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 1.2416800000 2.1506500000 7.9723500000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 2.4833600000 0.0000000000 7.9723500000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 3.7250400000 2.1506500000 7.9723500000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 2.4833600000 1.4337700000 10.0000000000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 3.7250400000 3.5844200000 10.0000000000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 4.9667200000 1.4337700000 10.0000000000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 6.2084000000 3.5844200000 10.0000000000</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 1.2281125212 0.7413038538 12.1124602290</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 2.4833613443 2.9495126082 12.0722664849</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 3.7386101535 0.7413040204 12.1124604793</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">Ni 4.9667205066 2.8946406480 11.9560276983</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> C 2.4833610952 1.4972020489 13.1166864267</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> H 2.4833559794 3.1940064219 13.5465576823</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">K_POINTS { automatic }</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">6 6 1 0 0 0</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:14px">
<br>
</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">=======================================ph.x input=======================================</div>
<div style="margin:0px;font-stretch:normal;line-height:normal">phonons of CH on metal Ni at Gamma</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> &inputph</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> tr2_ph=1.0d-16,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> prefix='Ni_ch_ts',</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> epsil=.false.,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> amass(1)=58.69,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> amass(2)=12.011,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> amass(3)=1.0,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> alpha_mix(1)=0.1,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> outdir='./tmp/',</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> fildyn='CH.dynG',</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> nat_todo= 2,</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> /</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> 0.0 0.0 0.0</div>
<div style="margin:0px;font-stretch:normal;line-height:normal"> 13 14 </div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:14px">
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</div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:14px">
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<div style="margin:0px;font-stretch:normal;line-height:normal">Thanks in advance for anyone that could give suggestions to me! </div>
<div style="margin:0px;font-stretch:normal;line-height:normal;min-height:14px">
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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>
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