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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Dear QE users,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Greetings! Last week I posted a problem related to vibration analysis (<a href="https://www.mail-archive.com/users@lists.quantum-espresso.org/msg37294.html" class="">https://www.mail-archive.com/users@lists.quantum-espresso.org/msg37294.html</a>),
unfortunately I didn’t get responses. In the past week I did several trials and got some new results. But I still cannot completely figure out my confusions. I would really appreciate it if some one could give me some advice and instructions.</div>
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Basically my question is:</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: "PingFang SC";" class="">
<span style="font-stretch: normal; line-height: normal; font-family: Helvetica;" class="">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>
<div style="margin: 0px; font-stretch: normal; line-height: normal; font-family: "PingFang SC";" class="">
Following are the I/O file of ph.x:</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">=======================================phonon input=======================================</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">phonons of CH4</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> &inputph</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> tr2_ph=1.0d-16,</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> prefix='ch4_cell2',</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> amass(1)=12.011,</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> amass(2)=1.0,</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> alpha_mix(1)=0.1,</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> asr=.true.</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> outdir='./ts/tmp/',</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> fildyn='CH4_cell3.dynG'</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> /</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures; background-color: #ffffff" class=""> 0.0 0.0 0.0</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="text-decoration: underline" class="">The calculated frequencies are:</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">=======================================phonon output=======================================</div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 1) =<span class="Apple-tab-span" style="white-space:pre">
</span>-0.507756 [THz] = -16.936932 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 2) =<span class="Apple-tab-span" style="white-space:pre">
</span>-0.459728 [THz] = -15.334860 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 3) =<span class="Apple-tab-span" style="white-space:pre">
</span>-0.271000 [THz] =<span class="Apple-tab-span" style="white-space:pre"> </span>
-9.039597 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 4) =<span class="Apple-tab-span" style="white-space:pre">
</span> 1.535467 [THz] =<span class="Apple-tab-span" style="white-space:pre"> </span>
51.217660 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 5) =<span class="Apple-tab-span" style="white-space:pre">
</span> 1.705940 [THz] =<span class="Apple-tab-span" style="white-space:pre"> </span>
56.904033 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 6) =<span class="Apple-tab-span" style="white-space:pre">
</span> 1.741249 [THz] =<span class="Apple-tab-span" style="white-space:pre"> </span>
58.081818 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 7) =<span class="Apple-tab-span" style="white-space:pre">
</span>38.593830 [THz] = 1287.351595 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 8) =<span class="Apple-tab-span" style="white-space:pre">
</span>38.610060 [THz] = 1287.892987 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 9) =<span class="Apple-tab-span" style="white-space:pre">
</span>38.618418 [THz] = 1288.171751 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 10) =<span class="Apple-tab-span" style="white-space:pre">
</span>45.381162 [THz] = 1513.752629 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 11) =<span class="Apple-tab-span" style="white-space:pre">
</span>45.388200 [THz] = 1513.987398 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 12) =<span class="Apple-tab-span" style="white-space:pre">
</span>89.406470 [THz] = 2982.278836 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 13) =<span class="Apple-tab-span" style="white-space:pre">
</span>92.546906 [THz] = 3087.032485 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(255, 255, 255);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> freq ( 14) =<span class="Apple-tab-span" style="white-space:pre">
</span>92.772395 [THz] = 3094.554013 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures; background-color: #ffffff" class=""> freq ( 15) =<span class="Apple-tab-span" style="white-space:pre">
</span>92.773975 [THz] = 3094.606712 [cm-1]</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
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<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">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>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
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</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 1) = -25.618746 [THz] = -854.549399 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 2) = -7.333895 [THz] = -244.632409 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 3) = -6.696884 [THz] = -223.383991 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 4) = -6.248674 [THz] = -208.433322 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 5) = -4.947831 [THz] = -165.041892 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 6) = -2.014699 [THz] = -67.203109 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 37) = 0.571458 [THz] = 19.061786 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 38) = 5.754719 [THz] = 191.956759 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 39) = 16.488930 [THz] = 550.011494 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 40) = 16.563150 [THz] = 552.487199 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 41) = 18.255969 [THz] = 608.953585 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 42) = 56.121326 [THz] = 1872.005923 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">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;" class="">And does my result indicate that my structure is most probably not a transition state since all the other frequencies are positive?</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">I’m attaching the input file of pw.x &ph.x below:</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">=========================scf input, structure obtained from neb.x========================</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">&CONTROL</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> Calculation='scf',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> restart_mode='from_scratch',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> prefix = "Ni_ch_ts"</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> outdir = "./ts/tmp",</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> pseudo_dir = "./pseudo",</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> tstress = .true.</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> verbosity = 'high'</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> tefield = .true.</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> dipfield = .true.</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">/</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">&SYSTEM</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> ibrav = 0,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> nat = 14,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> ntyp = 3,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> ecutwfc = 65,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> ecutrho = 650,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> Occupations='smearing',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> smearing='mp',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> degauss=0.01,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> nspin=2,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> starting_magnetization(1)=0.2,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> eamp = 0.0</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> edir = 3</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> emaxpos = 0.95</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> eopreg = 0.05</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">/</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">&ELECTRONS</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> electron_maxstep=250,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> conv_thr = 1.D-10,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> mixing_beta = 0.1,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">/</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
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</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">ATOMIC_SPECIES</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 58.69 ni_pbe_v1.4.uspp.F.UPF</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">C 12 C.pbe-n-kjpaw_psl.1.0.0.UPF</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">H 1 H.pbe-kjpaw_psl.1.0.0.UPF</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">CELL_PARAMETERS { angstrom }</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> 4.9667177200 0.0000000000 0.0000000000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> 2.4833588600 4.3013037190 0.0000000000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> 0.0000000000 0.0000000000 20.000000000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">ATOMIC_POSITIONS { angstrom }</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 0.0000000000 0.0000000000 7.9723500000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 1.2416800000 2.1506500000 7.9723500000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 2.4833600000 0.0000000000 7.9723500000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 3.7250400000 2.1506500000 7.9723500000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 2.4833600000 1.4337700000 10.0000000000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 3.7250400000 3.5844200000 10.0000000000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 4.9667200000 1.4337700000 10.0000000000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 6.2084000000 3.5844200000 10.0000000000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 1.2281125212 0.7413038538 12.1124602290</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 2.4833613443 2.9495126082 12.0722664849</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 3.7386101535 0.7413040204 12.1124604793</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ni 4.9667205066 2.8946406480 11.9560276983</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> C 2.4833610952 1.4972020489 13.1166864267</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> H 2.4833559794 3.1940064219 13.5465576823</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">K_POINTS { automatic }</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">6 6 1 0 0 0</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">=======================================ph.x input=======================================</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">phonons of CH on metal Ni at Gamma</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> &inputph</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> tr2_ph=1.0d-16,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> prefix='Ni_ch_ts',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> epsil=.false.,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> amass(1)=58.69,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> amass(2)=12.011,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> amass(3)=1.0,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> alpha_mix(1)=0.1,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> outdir='./tmp/',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> fildyn='CH.dynG',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> nat_todo= 2,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> /</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> 0.0 0.0 0.0</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> 13 14 </div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
<br class="">
</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 14px;" class="">
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Thanks in advance for anyone that could give suggestions to me! </div>
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Best regards</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Ziheng Shen</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">PhD student @ Georgia Institute of Technology</div>
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