<div dir="ltr"><div>Thank you Stefano.<br><br></div>I will try your suggestions.<br></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><span style="background-color:rgb(255,255,255)"><b><font size="2">NANDHA KUMAR V.</font></b></span><br></div><span style="background-color:rgb(238,238,238)"><span></span></span><font color="#0b5394"><font face="tahoma,sans-serif">Research scholar,<br></font></font><div><div><div><div><div><span style="color:rgb(32,18,77)">IISER, PUNE.<span style="background-color:rgb(0,0,0)"><span></span></span><span style="background-color:rgb(243,243,243)"><span></span></span></span><br></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Sat, Oct 22, 2016 at 9:15 AM, stefano de gironcoli <span dir="ltr"><<a href="mailto:degironc@sissa.it" target="_blank">degironc@sissa.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div class="m_6146310233381358802moz-cite-prefix">Dear Vikan,<br>
I dont have direct experience on this problem. here a few things i
would look into:<br>
<br>
from your NEB calculation around the TS you should be able to see
what the unstable mode is expected to look like and how many atoms
are involved.<br>
If you compute interatomic force constants (IFC) only around a
subset of the atoms there is the problem of how you impose the
acoustic sum rule. <br>
One way would be to complete your DynMat using the IFC of the bulk
material (that you could compute separately), and impose ASR on
this model. <br>
To stay on the safe side you could set the mass of the atoms that
you did not compute to a very large number so they do not move. <br>
<br>
stefano<div><div class="h5"><br>
<br>
<br>
On 21/10/2016 17:38, Vikan Manmathan wrote:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<div dir="ltr">
<div>
<div>Dear Developers and Experts,<br>
<br>
</div>
<div>I am interested in studying diffusion of metal clusters
on oxide support. As a first step, I took a simplest case (<span id="m_6146310233381358802:1cs.1">adatom</span>
hopping) and obtained the transition state using CI-NEB
method. I want to find the rate constant for the above, I
need to know the normal mode vibrational frequencies at
initial and transition states. <br>
<br>
</div>
So I calculated the phonon frequencies using frozen atomic
coordinate (<span id="m_6146310233381358802:1cs.2">nat</span>_<span id="m_6146310233381358802:1cs.3">todo</span>
option only on metal <span id="m_6146310233381358802:1cs.4">adatom</span>) since the system size is very
large. I expected the transition state to have one less real
frequencies (3N-1) relative to initial state (3N). However, I
am getting 3N real frequencies for the transition state
(correct me if I am wrong).<br>
<br>
I have also checked it by including more atoms in the linear
response (up to 33 atoms) but still I got 3N real frequencies
for the TS.<br>
<br>
</div>
<div>I have attached the input files and the output file
generated by <span id="m_6146310233381358802:1cs.5">dynmat</span>.x<br>
</div>
<div><br>
</div>
<div>Any suggestion will be highly appreciated.<br>
<br>
</div>
<div>Thanks in advance.<br>
<br>
</div>
<div>regards,<br>
</div>
<div>
<div><br clear="all">
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<div>
<div class="m_6146310233381358802gmail_signature">
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<div><span style="background-color:rgb(255,255,255)"><b><font size="2"><span id="m_6146310233381358802:1cs.7">NANDHA</span>
<span id="m_6146310233381358802:1cs.8">KUMAR</span> V.</font></b></span><br>
</div>
<span style="background-color:rgb(238,238,238)"><span></span></span><font color="#0b5394"><font face="tahoma,sans-serif">Research scholar,<br>
</font></font>
<div>
<div>
<div>
<div>
<div><span style="color:rgb(32,18,77)"><span id="m_6146310233381358802:1cs.9">IISER</span>, <span id="m_6146310233381358802:1cs.10">PUNE</span>.<span style="background-color:rgb(0,0,0)"><span></span></span><span style="background-color:rgb(243,243,243)"><span></span></span></span><br>
</div>
</div>
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<br>
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