[QE-users] how to select the perturbed atoms in phonon single q calculation ?

[Omer Mutasim]

 Dear Dr. TamasI have just checked it, it is what i'm looking to exactly.what is the syntax for nat_todo ? it is not clear from ph.x documentation Can you please clarify it ?

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Syntax:

atom(1) atom(2) ... atom(nat_todo) 

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ph.x: input description


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    On Wednesday, October 28, 2020, 05:45:15 PM GMT+4, Tamas Karpati <tkarpati at gmail.com> wrote:  
 
 Dear Omer,

Did you try to use the nat_todo option in your PH.x input file?
(Do not forget to list the perturbed atom indices on the last line.)

ASE can use QE as "calculator" and I think it can do what you want.
If not, use Phonopy.

HTH,
  t

On Wed, Oct 28, 2020 at 1:28 PM Omer Mutasim <omermutasim at ymail.com> wrote:
>
>
> Dear all
>
>  I need to calculate the the virbrational frequencies of adsorbate molecule on surface using phonon single q calculation  , in order to estimate the partition function (for entropy ,reaction rate constants). so my questions go like:
>
>  I have a large supercell (110 atoms) which means a high degrees of freedom (330 DOF) ,  so i want to decrease this DOF , by perturbing only adsorbate molecule and the the two uppermost layers
>
> how to select the perturbed atoms in quantum espresso ?
> I have heard that it can be done by finite difference method, which wasn't employed in QE.
> However, i have seen a post where Dr. Paolo Giannozzi said: " it can be performed by two finite-difference calculations with opposite displacements "
> So , can you please tell me, what are the steps involved in doing this finite-difference method mentioned by Dr. Paolo ? or any other procedure that can be do the same ?
>
>
>  Thanks in advance
>
>
>
>
> Omer Elmutasim
> Research Assistant
> Chemical Engineering Department
> Khalifa university- UAE
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