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<div class="moz-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<br>
<br>
<br>
On 21/10/2016 17:38, Vikan Manmathan wrote:<br>
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cite="mid:CADCvCZmAJigqb2S66PZKCCJGKRDZKQFjucUp89VVpXg6J6GX=Q@mail.gmail.com"
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<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
class="" style="" id=":1cs.1" tabindex="-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 class="" style="" id=":1cs.2" tabindex="-1">nat</span>_<span
class="" style="" id=":1cs.3" tabindex="-1">todo</span>
option only on metal <span class="" style="" id=":1cs.4"
tabindex="-1">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 class="" style="" id=":1cs.5"
tabindex="-1">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>
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<div><span
style="background-color:rgb(255,255,255)"><b><font
size="2"><span class="" style=""
id=":1cs.7" tabindex="-1">NANDHA</span>
<span class="" style="" id=":1cs.8"
tabindex="-1">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>
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<div>
<div><span style="color:rgb(32,18,77)"><span
class="" style="" id=":1cs.9"
tabindex="-1">IISER</span>, <span
class="" style="" id=":1cs.10"
tabindex="-1">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>
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