[Pw_forum] Graphene Nanoribbon (Negative phonon frequencies and structure relaxation)

[Prabhakar Marepalli]

Dear Dr. Seitsonen,

Thanks for checking my script. You are right that the structure I posted
runs in x-direction, but the problems I mentioned are exactly the same for
this script too (I used y-notation as it is easier to draw and explain the
unitcell that way). Also, thanks for pointing about the unitcell plane
distance in z-direction. I've done the following changes:

1) I've increased the lattice constant in z-direction to a very large value
of 10 Angstroms, but it didn't change my answers by a lot.

2) My structure is periodic in all directions, but I've picked the lattice
vectors in y,z directions to be very long that the structure essentially
acts like a 1D.

3) I've added the 'ecutrho' parameter and picked a value of
ecutrho=12*ecutwfc. This hasn't changed my answers either.

For relaxing, I've made the following changes to my original script:

&control
   calculation='relax'

&ions
   ion_dynamics='bfgs'

&cell
   cell_dynamics='bfgs'
   press_conv_thr=0.4,
   cell_factor=3.0

The above relaxation almost changed my nanoribbon lattice to a square
lattice. Can you please suggest if I'm using any of those parameters
incorrectly?

Thanks,
Prabhakar Marepalli



On Fri, Jan 2, 2015 at 1:16 PM, Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>
wrote:

>
> Dear Prabhakar,
>
>   Did you check your structure? To me it looks very weird in 'XCrysDen',
> the planes of the periodic GNR's along z direction only 2 Angstroms apart.
> And yes, you should relax the structure before calculating phonons. And
> your system is periodic in all directions, and the GNR seems to run along
> x, not y like I understood from your description below. Please also read
> the instructions about 'ecutrho' when using ultra-soft pseudo potentials or
> the PAW method.
>
>     Good Luck, :)
>
>        apsi
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=
> -=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>   Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>   Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935
>
>
>
> On Fri, 2 Jan 2015, Prabhakar Marepalli wrote:
>
>  Hello everyone,
>>
>> I'm trying to compute phonon dispersion properties of graphene nanoribbon
>> using Quantum Espresso. My unit cell is a simple armchair structure with 4
>> atoms per unit cell. It looks like below:
>>
>>        0----0
>>       /       \
>>      0        0
>>
>> The above structure is replicated in the y-direction (the periodic
>> direction) while the x-direction is confined. Using the above structure,
>> here is the outline of the problems I'm running into:
>>
>> 1) Negative phonon frequencies (not only at gamma point, but at all other
>> k-points)
>>
>> 2) I tried using 'asr' but that doesn't seem to fix the problem.
>>
>> 3) I understand that the problem might be due to instability of the
>> structure (I did notice that the forces on atoms in scf calculation is
>> non-zero , forces of the magnitude 0.2 to 0.4).
>>
>> 4) When I try to relax the structure using 'ion_dynamics', the forces did
>> go
>> down but the structure is relaxed so much that it is no longer graphene
>> nanoribbon.
>>
>> Can you please give me some pointers on how to approach this problem, i.e.
>> how do I get rid of negative frequencies while relaxing the structure that
>> constrains it to look like a nanoribbon ?
>>
>> Thanks for your time!
>>
>> Here are my input files:
>>
>> pw.x (this doesn't include the ion_dynamics relaxation).
>>
>>  &control
>>     calculation='scf'
>>     restart_mode='from_scratch',
>>     tstress = .true.
>>     tprnfor = .true.
>>     prefix='gnr_arm',
>>     pseudo_dir = '/work/02420/pm24229/QE/QE/pseudo/',
>>     outdir = '/home1/02420/pm24229/tmp/',
>>  /
>>  &system
>>     ibrav=  0, nat=  4, ntyp= 1, nbnd= 20,
>>     ecutwfc =25.0, occupations='smearing', smearing='marzari-vanderbilt',
>>     degauss=0.02
>>  /
>>  &electrons
>>     diagonalization='cg'
>>     conv_thr =  1.0d-12
>>     mixing_beta = 0.7
>>  /
>> ATOMIC_SPECIES
>>  C  12.0107  C.pbe-rrkjus.UPF
>>
>> CELL_PARAMETERS {angstrom}
>>  2.5546 0.00000000 0.00000000
>>  0.00000000 10.0 0.00000000
>>  0.00000000 0.00000000 2.00000000
>>
>> ATOMIC_POSITIONS {angstrom}
>>  C 0.0  0.0  0.0
>>  C 1.2773 0.7375 0.000
>>  C 1.2773 2.2125 0.00
>>  C 0.0  2.95 0.0
>>
>> K_POINTS automatic
>> 20 1 1 1 1 1
>>
>> ph.x
>>
>> phonons on kspace
>>  &inputph
>>   tr2_ph=1.0d-14,
>>   prefix='gnr_arm',
>>   ldisp=.true.,
>>   nq1=20, nq2=1, nq3=1
>>   amass(1)=12.0107,
>>   outdir='/home1/02420/pm24229/tmp/',
>>   fildyn='gnr_dyn',
>>  /
>>
>> Thanks,
>> Prabhakar Marepalli
>>
>>
>>
>>
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