[gpaw-users] Phonon calculation for 12C/13C graphene?

[Toma Susi]

Hi Chris,

Ah, now I realized what went wrong: although I had changed the masses for the phonon calculation (which doesn’t actually affect the forces), my plotting script was reading the original POSCAR structure, and that of course defaulted all the C masses into the normal isotope when calculating the bands.

Sorry for the confusion, and many thanks for helping me sort this out!

Cheers,
Toma


> On 05 Jan 2016, at 19:27, Christopher Patrick <chripa at fysik.dtu.dk> wrote:
> 
> Hi Toma,
> 
> This is very strange.  I took your script and structure and did my own calculation.  To save time, I reduced the supercell sampling to 3x3x1 and kpoints to myk=3.  As a result, the bandstructure looks very bad.  However, I do see that if I change the masses (simply by atoms[i].mass = something) I do change the phonon frequencies (see attached). 
> 
> Just to be clear, you should only have to do the force calculations once; once all the pickle files are in the directory, your script should run on a single cpu in a few seconds.
> 
> There must be something else going on that we are missing.  What happens if you add
> 
> import pylab as plt
> plt.figure(1, (8, 6))
> plt.axes([.1, .07, .67, .85])
> for n in range(len(omega_kn[0])):
>    omega_n = omega_kn[:, n]
>    plt.plot(q, omega_n, 'k-', lw=2)
> 
> plt.xticks(Q, point_names, fontsize=18)
> plt.yticks(fontsize=18)
> plt.xlim(q[0], q[-1])
> plt.ylabel("Frequency ($\mathrm{meV}$)", fontsize=22)
> plt.grid('on')
> plt.show()
> 
> to the bottom of your script (so that it plots the bandstructure straightaway).
> 
> Chris
> ________________________________________
> From: Toma Susi [toma.susi at univie.ac.at]
> Sent: 05 January 2016 16:41
> To: Christopher Patrick
> Cc: gpaw-users
> Subject: Re: [gpaw-users] Phonon calculation for 12C/13C graphene?
> 
> Hi,
> 
> I tested with a crazy mass value for one atom, and double-checked that this was correctly input by inserting a “print(atoms.get_masses())” into the script.
> 
> Again, no difference whatsoever in the band structure.
> 
> -Toma
> 
> 
>> On 05 Jan 2016, at 11:21, Toma Susi <toma.susi at univie.ac.at> wrote:
>> 
>> Hi Chris,
>> 
>> Thanks for your reply! You can find the structure attached.
>> 
>> I did not check with an absurd mass, but that’s a great idea, will do so now.
>> 
>> -Toma
>> 
>> 
>> <POSCARgra11_k42_crlx>
>> 
>> 
>>> On 05 Jan 2016, at 11:16, Christopher Patrick <chripa at fysik.dtu.dk> wrote:
>>> 
>>> Hi Toma,
>>> 
>>> Sorry for the delay in replying.  Just to help me reproduce your calculation, could you possibly send the structure that your script is reading in?
>>> 
>>> You say that the phonon bands are absolutely unchanged from a "normal" calculation... does that mean if you choose a crazy value (e.g. 100000.) for atoms[1].mass,
>>> nothing happens either?
>>> 
>>> Best wishes,
>>> 
>>> Chris
>>> ________________________________________
>>> From: gpaw-users-bounces at listserv.fysik.dtu.dk [gpaw-users-bounces at listserv.fysik.dtu.dk] on behalf of Toma Susi [toma.susi at univie.ac.at]
>>> Sent: 29 December 2015 11:21
>>> To: gpaw-users
>>> Subject: [gpaw-users] Phonon calculation for 12C/13C graphene?
>>> 
>>> Dear GPAW users,
>>> 
>>> I have been running calculations with the primitive two-atom graphene unit cell, expanded into a supercell for a phonon band structure calculation, and after some help from the list a while back, these are now quite successful.
>>> 
>>> However, I would like to run a calculation for mixed graphene, ie. graphene with one atom of 12C and another of 13C to see how this affects the phonon bands. In ASE, it seems to be possible to specify the atom isotope by changing the “mass” attribute.
>>> 
>>> Thus, in my script, after reading in the structure, I have specified:
>>> 
>>> atoms[0].mass = 12.0
>>> atoms[1].mass = 13.003355
>>> 
>>> And this does seem to change the masses as desired, at least in an interactive run. The rest of the calculation runs as normal, but in the end, the phonon bands are absolutely unchanged from a “normal” calculation. I’ve attached the script.
>>> 
>>> Is there another way to do this, or is this not possible at all for some reason?
>>> 
>>> Thank you!
>>> 
>>> 
>>> ________________________________
>>> Dr. Toma Susi
>>> Principal investigator
>>> FWF Project HeQuCoG
>>> University of Vienna, Austria
>>> 
>>> http://mostlyphysics.net
>>> 
>>> "Love is the only emotion that enhances our intelligence."
>>> -Humberto Maturana
>>> 
>> 
> 
> <crazy_mass1.png><crazy_mass2.png><usual_mass.png>