<div dir="ltr"><div><div><div><div><div><div><div><div><div><div><div><div>Dear Dr. Seitsonen,<br><br></div>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:<br><br>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. <br><br>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.<br><br></div>3) I've added the 'ecutrho' parameter and picked a value of ecutrho=12*ecutwfc. This hasn't changed my answers either.<br><br></div>For relaxing, I've made the following changes to my original script:<br><br></div>&control<br></div> calculation='relax'<br><br></div>&ions<br></div> ion_dynamics='bfgs'<br><br></div>&cell<br></div> cell_dynamics='bfgs'<br></div> press_conv_thr=0.4,<br></div> cell_factor=3.0<br><br></div>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?<br><br>Thanks,<br>Prabhakar Marepalli<br><div><div><div><div><div><div><div><div><div><div><br><br></div></div></div></div></div></div></div></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 2, 2015 at 1:16 PM, Ari P Seitsonen <span dir="ltr"><<a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Dear Prabhakar,<br>
<br>
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.<br>
<br>
Good Luck, :)<br>
<br>
apsi<br>
<br>
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=<u></u>*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=<u></u>-=*=-=*=-=*=-=*=-<br>
Ari Paavo Seitsonen / <a href="mailto:Ari.P.Seitsonen@iki.fi" target="_blank">Ari.P.Seitsonen@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" target="_blank">http://www.iki.fi/~apsi/</a><br>
Ecole Normale Supérieure (ENS), Département de Chimie, Paris<br>
Mobile (F) : <a href="tel:%2B33%20789%2037%2024%2025" value="+33789372425" target="_blank">+33 789 37 24 25</a> (CH) : <a href="tel:%2B41%2079%2071%2090%20935" value="+41797190935" target="_blank">+41 79 71 90 935</a><div class="HOEnZb"><div class="h5"><br>
<br>
<br>
On Fri, 2 Jan 2015, Prabhakar Marepalli wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello everyone,<br>
<br>
I'm trying to compute phonon dispersion properties of graphene nanoribbon<br>
using Quantum Espresso. My unit cell is a simple armchair structure with 4<br>
atoms per unit cell. It looks like below:<br>
<br>
0----0<br>
/ \<br>
0 0<br>
<br>
The above structure is replicated in the y-direction (the periodic<br>
direction) while the x-direction is confined. Using the above structure,<br>
here is the outline of the problems I'm running into:<br>
<br>
1) Negative phonon frequencies (not only at gamma point, but at all other<br>
k-points)<br>
<br>
2) I tried using 'asr' but that doesn't seem to fix the problem.<br>
<br>
3) I understand that the problem might be due to instability of the<br>
structure (I did notice that the forces on atoms in scf calculation is<br>
non-zero , forces of the magnitude 0.2 to 0.4).<br>
<br>
4) When I try to relax the structure using 'ion_dynamics', the forces did go<br>
down but the structure is relaxed so much that it is no longer graphene<br>
nanoribbon.<br>
<br>
Can you please give me some pointers on how to approach this problem, i.e.<br>
how do I get rid of negative frequencies while relaxing the structure that<br>
constrains it to look like a nanoribbon ?<br>
<br>
Thanks for your time!<br>
<br>
Here are my input files:<br>
<br>
pw.x (this doesn't include the ion_dynamics relaxation).<br>
<br>
&control<br>
calculation='scf'<br>
restart_mode='from_scratch',<br>
tstress = .true.<br>
tprnfor = .true.<br>
prefix='gnr_arm',<br>
pseudo_dir = '/work/02420/pm24229/QE/QE/<u></u>pseudo/',<br>
outdir = '/home1/02420/pm24229/tmp/',<br>
/<br>
&system<br>
ibrav= 0, nat= 4, ntyp= 1, nbnd= 20,<br>
ecutwfc =25.0, occupations='smearing', smearing='marzari-vanderbilt',<br>
degauss=0.02<br>
/<br>
&electrons<br>
diagonalization='cg'<br>
conv_thr = 1.0d-12<br>
mixing_beta = 0.7<br>
/<br>
ATOMIC_SPECIES<br>
C 12.0107 C.pbe-rrkjus.UPF<br>
<br>
CELL_PARAMETERS {angstrom}<br>
2.5546 0.00000000 0.00000000<br>
0.00000000 10.0 0.00000000<br>
0.00000000 0.00000000 2.00000000<br>
<br>
ATOMIC_POSITIONS {angstrom}<br>
C 0.0 0.0 0.0<br>
C 1.2773 0.7375 0.000<br>
C 1.2773 2.2125 0.00<br>
C 0.0 2.95 0.0<br>
<br>
K_POINTS automatic<br>
20 1 1 1 1 1<br>
<br>
ph.x<br>
<br>
phonons on kspace<br>
&inputph<br>
tr2_ph=1.0d-14,<br>
prefix='gnr_arm',<br>
ldisp=.true.,<br>
nq1=20, nq2=1, nq3=1<br>
amass(1)=12.0107,<br>
outdir='/home1/02420/pm24229/<u></u>tmp/',<br>
fildyn='gnr_dyn',<br>
/<br>
<br>
Thanks,<br>
Prabhakar Marepalli<br>
<br>
<br>
<br>
</blockquote>
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