<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
        {font-family:"Cambria Math";
        panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
        {font-family:Calibri;
        panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
        {margin:0in;
        font-size:11.0pt;
        font-family:"Calibri",sans-serif;}
span.EmailStyle17
        {mso-style-type:personal-compose;
        font-family:"Calibri",sans-serif;
        color:windowtext;}
.MsoChpDefault
        {mso-style-type:export-only;
        font-family:"Calibri",sans-serif;}
@page WordSection1
        {size:8.5in 11.0in;
        margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
        {page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72" style="word-wrap:break-word">
<div class="WordSection1">
<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>
<p>=====-----=====-----=====<br>
Notice: The information contained in this e-mail<br>
message and/or attachments to it may contain <br>
confidential or privileged information. If you are <br>
not the intended recipient, any dissemination, use, <br>
review, distribution, printing or copying of the <br>
information contained in this e-mail message <br>
and/or attachments to it are strictly prohibited. If <br>
you have received this communication in error, <br>
please notify us by reply e-mail or telephone and <br>
immediately and permanently delete the message <br>
and any attachments. Thank you</p>

<p></p></body>
</html>