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<p>The k-points were chosen by observing the total energy and how it converges. At around 42 to 51 k-points, the total energy of the system converged. I have tried using a lower degauss (0.001) with the same mesh and the results at the gamma k and m points
were not agreeable with literature. In fact at the K point there was a negative phonon! </p>
<p>I should also mention that I have tried very similar calculations with other pseudopotentials (Ultrasoft GGA C.pbe-rrkjus.upf, Ultrasoft LDA C.pz-rrkjus, Norm Conserving Blyp C.blyp-mt.upf) the results were the same. The kpoints and ecutwfc were chosen by
observing how the total energy converges with respect to changes in these parameters. Similarly the results were not reasonable, with negative values in some areas and even maximas and minimas at non-high symmetry points. </p>
<p><br>
</p>
<p>Regards,</p>
<p>Faris</p>
<br>
<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> pw_forum-bounces@pwscf.org <pw_forum-bounces@pwscf.org> on behalf of stefano de gironcoli <degironc@sissa.it><br>
<b>Sent:</b> 21 April 2016 19:51<br>
<b>To:</b> PWSCF Forum<br>
<b>Subject:</b> Re: [Pw_forum] Graphene Phonons Not Working</font>
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<div class="moz-cite-prefix">Dear Abualnaja ,<br>
<br>
how did you chose the smearing and k-point combination ?<br>
your degauss (0.1 Ry =1.36 eV) looks huge to me, while your k-point grid looks very dense.<br>
mp smearing is a good choice for *real* metals (with a significant dos(e_F)) even if someone would favor mv smearing. I think that in the case of graphene with vanishing dos(e_F) the simpler gaussian broadening should be fine and possibly preferable.<br>
<br>
stefano<br>
<br>
<br>
On 21/04/2016 20:32, Abualnaja, Faris wrote:<br>
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<p>Apologies all in the q2r and matdyn files zasr and asr should both be 'simple' and NOT 'crystal'</p>
<br>
<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a>
<a class="moz-txt-link-rfc2396E" href="mailto:pw_forum-bounces@pwscf.org"><pw_forum-bounces@pwscf.org></a> on behalf of Abualnaja, Faris
<a class="moz-txt-link-rfc2396E" href="mailto:f.abualnaja15@imperial.ac.uk"><f.abualnaja15@imperial.ac.uk></a><br>
<b>Sent:</b> 21 April 2016 16:42<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
<b>Subject:</b> [Pw_forum] Graphene Phonons Not Working</font>
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<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">To whom it may concern,</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><br>
</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">I've been having trouble lately trying to produce graphene phonon dispersion plots. I am currently using quantum-espresso/5.0.2. I ran an scf calculation using an LDA norm conserving
pseudo potential (C.pz-vbc.UPF). I found an optimised lattice parameter of 4.698 (Bohr) using a vc-relax calculation. I then ran an scf with the optimised lattice parameter and ecutwfc. I then proceeded onto producing a band structure with the following k-points
in units of 2pi/a (Gamma (0,0,0) - K (0.33333, 0.57735027, 0) - M (0.5, 0.28867513, 0)). The band structure agrees with literature, where the dirac points meet at the K point. I then moved on to calculating the phonon at each k (or q) point. I ran the scf
calculation once again in a new directory, I ran the phonon at gamma, K, and M. the results seemed to agree with literature. However, when I ran the phonon dispersion calculation, the results go all over the place. The gamma k and m points are the same but
the curve is not expected. Obviously, after running the ph.x I ran a q2r.x calculation, followed by a matdyn.x calculation. To be clear I checked my k-points, I checked the k-path, the mp grid I used was 12x12x1 when calculating the phonon dispersion and 48x48x1
when running an scf calculation. Also, to clarify I did the tutorial for Al and Si and produced correct plots. Below are my input files:</p>
<p style="">------------------------------------------------------------------------------------------------------------------------------------</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">-------- SCF ---------------------------------------------------------------------------------------------------------------------</p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">&CONTROL</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> prefix = 'graphene'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> pseudo_dir = '/home/fa2215/bin/upf_files'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> calculation = 'scf'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> restart_mode = 'from_scratch'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> verbosity = 'high'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> tprnfor = .TRUE.</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> tstress = .TRUE.</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> etot_conv_thr = 1.0D-4</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> forc_conv_thr = 1.0D-3</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> nstep = 50000</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> wf_collect = .TRUE.</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">/</span></p>
<p class="x_p2" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"></span><br>
</p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">&SYSTEM</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> ibrav = 4</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> celldm(1) = 4.698</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> celldm(3) = 18.616</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> nat = 2</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> ntyp = 1</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> nbnd = 10</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> ecutwfc = 110</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> ecutrho = 440</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> occupations = 'smearing'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> smearing = 'mp'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> degauss = 0.1</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">/</span></p>
<p class="x_p2" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"></span><br>
</p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">&ELECTRONS</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> diagonalization = 'david'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> electron_maxstep = 1000</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> conv_thr = 1.0e-8</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> mixing_beta = 0.3</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">/</span></p>
<p class="x_p2" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"></span><br>
</p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">ATOMIC_SPECIES</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> C 12.01 C.pz-vbc.UPF</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">ATOMIC_POSITIONS crystal</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> C 0.6666666666 0.3333333333 0.0000000000</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> C 0.3333333333 0.6666666666 0.0000000000</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">K_POINTS (automatic)</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">48 48 1 0 0 0</span></p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">------------------------------------------------------------------------------------------------------------------------------------</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style=""></span></p>
<p style="">------------------------------------------------------------------------------------------------------------------------------------<br>
</p>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<p style="">------------------------------------------------------------------------------------------------------------------------------------</p>
</div>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style="">------ PHONON ---------------------------------------------------------------------------------------------------------------------</span><br>
</p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">Phonon Dispersion of graphene</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> &inputph</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> tr2_ph=1.0d-12</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> ldisp=.true.</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> nq1=12 nq2=12 nq3=1</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> prefix='graphene'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> amass(1)=12.01</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> outdir='/work/fa2215/Computational_Data/Graphene/Flat_Graphene/NM_PZ_LDA/Phonon_Calc/Disp/Disp2'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> fildyn='graphene.dyn'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> /</span></p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style="">------------------------------------------------------------------------------------------------------------------------------------</span><br>
</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style=""></span></p>
<p style="">------------------------------------------------------------------------------------------------------------------------------------<br>
</p>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<p style="">------------------------------------------------------------------------------------------------------------------------------------</p>
</div>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style="">----------- Q2R --------------------------------------------------------------------------------------------------------------------<br>
</span></p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style=""></span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">&input</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> fildyn='graphene.dyn', zasr='crystal', flfrc='graphene.fc'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">/</span></p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style="">-</span>-----------------------------------------------------------------------------------------------------------------------------------</p>
<p style="">------------------------------------------------------------------------------------------------------------------------------------</p>
<p style="">------------------------------------------------------------------------------------------------------------------------------------</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style="">-------- MATDYN -------------------------------------------------------------------------------------------------------------------<br>
</span></p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style=""></span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">&input</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> asr='crystal' </span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> amass(1)=12.01</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> flfrc='graphene.fc'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> flfrq='graphene.freq'</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1">/</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> 219</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> 0.000000 0.000000 0.000000 1.0</span></p>
<p class="x_p1" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
<span class="x_s1"> : : : :</span></p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><span style="">------------------------------------------------------------------------------------------------------------------------------------</span><br>
</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><br>
</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">So to recap my procedure was as follows:</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><br>
</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">scf</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">phonon disp</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">q2r</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">matdyn</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><br>
</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">Let me know if anything is unclear and thank you for your help!</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><br>
</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">Best,</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><br>
</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">Faris</p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><br>
</p>
<br>
</div>
</div>
</div>
</div>
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