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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Dear QE users,</div>
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">Greetings! I’m a beginner of this program and I expected to use QE to find kinetic information of reactions in adsorption processes. Specifically, I’m trying to reproduce the PES
of a published case</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="">CH* + * -> C* + H*</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">where * refers to active site on the Ni(111) surface</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="">So far, I’m able to find the initial state and final state structures. I also got one transition state structure by neb.x. Now I wanted to perform vibrational analysis to confirm
the T.S. strucuture (expecting to see one negative frequency). However, when I did tests on ph.x, I met some troubles. These problems has been asked before in the forum, but I still cannot figure them out by following those given solutions. I appreciate quite
a lot if anyone could provide some hints or advice for my specific case.</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="">First, I did a simple test of ph.x by calculating the frequencies of a single methane molecule. From my previous experience with ORCA, the first 6 frequencies (which represent translational
and rotational modes) should be zero for a molecule. However, the program always returned non-zero values. I followed some previously posted solutions and tried approaches including:</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">1) try more tight forc_thr in geometry relaxation => I decreased forc_thr from default to 1D-5</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">2) try more tight conv_thr in scf calculation => I decreased conv_thr from 1D-8 to 1D-12</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">3) try bigger ecutwfc/ecutrho in scf calculation => I increased ecutwfc from 65Ry to 85Ry</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">4) try to increase the size of unit cell => I increased the length of cubic cell from 20A to 30A</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">5) try more tight tr2_ph and smaller alpha_mix in ph.x => I decreased tr2_ph from default to 1D-16</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">However, none of them worked.
<span style="text-decoration: underline" class="">The input files with highest thresholds for pw.x & ph.x are copied here.</span></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="">=======================================scf input=======================================</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 = "ch4_cell2"</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=""> etot_conv_thr = 1.0D-5</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> forc_conv_thr = 1.0D-5</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 = 5,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> ntyp = 2,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> ecutwfc = 85,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> ecutrho = 850,</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=""> conv_thr = 1.D-12,</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=""> electron_maxstep=250,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">/</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">&IONS</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> ion_dynamics='bfgs'</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">/</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="">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;" class=""> 30 0.0000000000 0.0000000000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> 0.0 30 0.0000000000</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> 0.0000000000 0.0000000000 30</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="">C<span class="Apple-tab-span" style="white-space:pre">
</span>12.998505897 12.669983024 10.000014581</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">H<span class="Apple-tab-span" style="white-space:pre">
</span>14.094202415 12.669376542 10.000895687</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">H<span class="Apple-tab-span" style="white-space:pre">
</span>12.632663345 13.058381752 10.957013019</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">H<span class="Apple-tab-span" style="white-space:pre">
</span>12.632991209 11.646964614 9.857276033</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">H<span class="Apple-tab-span" style="white-space:pre">
</span>12.634287134 13.305064066 9.184810679</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="">1 1 1 0 0 0</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="">=======================================phonon input=======================================</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">phonons of CH4</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='ch4_cell2',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> amass(1)=12.011,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> amass(2)=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='./ts/tmp/',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> fildyn='CH4_cell2.dynG'</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; min-height: 14px;" class="">
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</div>
<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; line-height: normal;" class=""> freq ( 1) = 1.772990 [THz] = 59.140581 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 2) = 4.134960 [THz] = 137.927411 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 3) = 4.480988 [THz] = 149.469657 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 4) = 10.709853 [THz] = 357.242257 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 5) = 11.230300 [THz] = 374.602485 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 6) = 12.538150 [THz] = 418.227663 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 7) = 38.905159 [THz] = 1297.736407 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 8) = 39.196874 [THz] = 1307.466991 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 9) = 39.785039 [THz] = 1327.086048 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 10) = 46.262462 [THz] = 1543.149645 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 11) = 46.466078 [THz] = 1549.941531 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 12) = 89.472569 [THz] = 2984.483660 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 13) = 92.974263 [THz] = 3101.287588 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 14) = 93.136064 [THz] = 3106.684690 [cm-1]</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 15) = 93.343894 [THz] = 3113.617156 [cm-1]</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="">Following the advice from FAQ (“<span style="font-stretch: normal; font-size: 14px; line-height: normal; font-family: Arial; -webkit-font-kerning: none; color: rgb(77, 77, 77); background-color: rgb(255, 255, 255);" class="">if
the nonzero frequencies are small, you can impose the ASR to the dynamical matrix, usually with excellent results”)</span> in QE official website, I also tried to apply asr=true but the calculation didn’t converge. I also saw some users claiming that if the
translational and rotational frequencies are small, it could be due to numerical error and thus they can be negligible. However, I don’t think a frequency that’s around 300 cm-1 can be considered “small”. Could someone please take a look at my input files
and point out some possible errors for me? And in which cases can we say that the frequency is “small”?</div>
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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="">Second, my ultimate goal is to perform frequency analysis for adsorbate so that I can both determine transition state structures and apply ZPE corrections. In the maillist archive,
some users suggested set “nat_todo” to only calculate adsorbates. However, I also got some crazy results by doing so.</div>
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<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="">
<br class="">
</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-12,</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='./ts/tmp/',</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> fildyn='CH_2.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;" class="">==================================phonon output=======================================</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 1 - 1) = -1514178.1 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 2 - 2) = -204586.6 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 3 - 3) = -8039.2 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 4 - 4) = -3220.6 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 5 - 5) = -2283.0 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 6 - 6) = -205.2 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 7 - 7) = -0.0 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 37 - 37) = 1712.6 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 38 - 38) = 2144.7 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 39 - 39) = 3316.3 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 40 - 40) = 7979.5 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 41 - 41) = 186893.8 [cm-1] --> A I+R</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""> freq ( 42 - 42) = 1489603.3 [cm-1] --> A I+R</div>
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<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">I know that tr2_ph here might not be strict enough. However, it still doesn’t make sense to me that the first 6 frequencies have such large values and are negative. Does that imply
this structure is most likely not a transition state? In the manual it says “<span style="font-stretch: normal; font-size: 14px; line-height: normal; font-family: Courier; -webkit-font-kerning: none; background-color: rgb(255, 255, 255); -webkit-text-stroke-color: rgb(0, 0, 0);" class="">this
is an approximation and may not work”</span><span style="-webkit-font-kerning: none; background-color: rgb(255, 255, 255); -webkit-text-stroke-color: rgb(0, 0, 0);" class="">, and I also saw some experienced users in the forum claimed that using “nat_todo”
might have some risk. So is it possible that this function just doesn’t work for my system? How reliable is this function?</span></div>
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Thank you for reading this long question! Thanks in advance for anyone that could give suggestions to me!</div>
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Best regards</div>
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Ziheng Shen</div>
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PhD student @ Georgia Institute of Technology</div>
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