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<p class="MsoNormal">Hi All,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m trying to compute the vibrational frequencies of adsorbates on a catalyst material. However, when I used ‘nat_todo’ in ph.x input and specified only adsorbate atoms, I’m getting many more non zero frequencies than the expected ‘3N’
values. Also, these are negative. For example, when I consider H atom adsorbed on Mo2N MXene, I get the following output by setting nat_todo = 1 (corresponding to the adsorbed H atom alone):<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">freq ( 1) = -3.783307 [THz] = -126.197541 [cm-1]
<o:p></o:p></p>
<p class="MsoNormal">freq ( 2) = -3.783307 [THz] = -126.197534 [cm-1]
<o:p></o:p></p>
<p class="MsoNormal">freq ( 3) = -2.586423 [THz] = -86.273795 [cm-1]
<o:p></o:p></p>
<p class="MsoNormal">freq ( 4) = -0.000000 [THz] = -0.000013 [cm-1]
<o:p></o:p></p>
<p class="MsoNormal">freq ( 5) = -0.000000 [THz] = -0.000011 [cm-1] <o:p></o:p></p>
<p class="MsoNormal">freq ( 6) = -0.000000 [THz] = -0.000010 [cm-1]<o:p></o:p></p>
<p class="MsoNormal">..<o:p></o:p></p>
<p class="MsoNormal">..<o:p></o:p></p>
<p class="MsoNormal">..<o:p></o:p></p>
<p class="MsoNormal">freq ( 81) = 0.000000 [THz] = 0.000014 [cm-1] <o:p></o:p></p>
<p class="MsoNormal">freq ( 82) = 27.703969 [THz] = 924.104922 [cm-1]
<o:p></o:p></p>
<p class="MsoNormal">freq ( 83) = 27.703973 [THz] = 924.105062 [cm-1]
<o:p></o:p></p>
<p class="MsoNormal">freq ( 84) = 35.034523 [THz] = 1168.625905 [cm-1]
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If I include all atoms in the surface layer together with the H adsorbate in nat_todo (i.e., nat_todo=10), I still get a similar ‘unphysical’ result:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"># mode [cm-1] [THz] IR
<o:p></o:p></p>
<p class="MsoNormal">1 -235.75 -7.0675 0.0000
<o:p></o:p></p>
<p class="MsoNormal">2 -235.75 -7.0675 0.0000 <o:p></o:p></p>
<p class="MsoNormal">3 -232.81 -6.9793 0.0000
<o:p></o:p></p>
<p class="MsoNormal">4 -229.08 -6.8675 0.0000 <o:p></o:p></p>
<p class="MsoNormal">5 -229.08 -6.8675 0.0000 <o:p></o:p></p>
<p class="MsoNormal">6 -224.95 -6.7437 0.0000 <o:p></o:p></p>
<p class="MsoNormal">..<o:p></o:p></p>
<p class="MsoNormal">..<o:p></o:p></p>
<p class="MsoNormal">..<o:p></o:p></p>
<p class="MsoNormal">79 314.67 9.4336 0.0000 <o:p></o:p></p>
<p class="MsoNormal">80 314.67 9.4336 0.0000 <o:p></o:p></p>
<p class="MsoNormal">81 336.83 10.0978 0.0000
<o:p></o:p></p>
<p class="MsoNormal">82 916.50 27.4759 0.0000 <o:p></o:p></p>
<p class="MsoNormal">83 916.50 27.4759 0.0000 <o:p></o:p></p>
<p class="MsoNormal">84 1158.35 34.7263 0.0000 <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The moment I remove nat_todo and compute all the frequencies, I’m getting a meaningful result:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"># mode [cm-1] [THz] IR <o:p></o:p></p>
<p class="MsoNormal">1 -0.00 -0.0000 0.0000 <o:p></o:p></p>
<p class="MsoNormal">2 0.00 0.0000 0.0000
<o:p></o:p></p>
<p class="MsoNormal">3 0.00 0.0000 0.0000 <o:p></o:p></p>
<p class="MsoNormal">4 22.82 0.6841 0.0000 <o:p></o:p></p>
<p class="MsoNormal">5 22.82 0.6841 0.0000
<o:p></o:p></p>
<p class="MsoNormal">6 80.49 2.4131 0.0000 <o:p></o:p></p>
<p class="MsoNormal">7 80.49 2.4131 0.0000 <o:p></o:p></p>
<p class="MsoNormal">..<o:p></o:p></p>
<p class="MsoNormal">..<o:p></o:p></p>
<p class="MsoNormal">..<o:p></o:p></p>
<p class="MsoNormal">79 541.10 16.2217 0.0000
<o:p></o:p></p>
<p class="MsoNormal">80 553.66 16.5984 0.0000 <o:p></o:p></p>
<p class="MsoNormal">81 588.60 17.6459 0.0000
<o:p></o:p></p>
<p class="MsoNormal">82 924.78 27.7243 0.0000
<o:p></o:p></p>
<p class="MsoNormal">83 924.78 27.7243 0.0000 <o:p></o:p></p>
<p class="MsoNormal">84 1170.94 35.1039 0.0000
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">All calculations are geometry optimized to etot_conv_thr = 1.0D-6 and forc_conv_thr = 1.0D-4 followed by an scf with conv_thr = 1.D-12. Following was my ph.in file:<o:p></o:p></p>
<p class="MsoNormal">vibra <o:p></o:p></p>
<p class="MsoNormal">&inputph <o:p></o:p></p>
<p class="MsoNormal">tr2_ph = 1.0d-14
<o:p></o:p></p>
<p class="MsoNormal">prefix='Ti3C2' <o:p></o:p></p>
<p class="MsoNormal">outdir = './' <o:p></o:p></p>
<p class="MsoNormal">search_sym = .false.
<o:p></o:p></p>
<p class="MsoNormal">asr = .true. <o:p></o:p></p>
<p class="MsoNormal">alpha_mix(1) = 0.3 <o:p></o:p></p>
<p class="MsoNormal"># nat_todo = 10<o:p></o:p></p>
<p class="MsoNormal">/ <o:p></o:p></p>
<p class="MsoNormal">0 0 0 <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Is there something that I’m missing out while doing calculations for a subset of atoms? I’d greatly appreciate the help of the community.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you very much!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best Regards,<o:p></o:p></p>
<p class="MsoNormal">Sriram <o:p></o:p></p>
</div>
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