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<p>Dear Shenli and Paolo,</p>
<p><br>
</p>
<p><font color="black"><font size="3"><span style="font-size:12pt;">> I used Iurii’s input, it works well using QE 6.4.1, but would crash using QE 6.4 (not sure if this is because a compilation issue as I just used the module on the cluster)</span></font></font></p>
<p><font color="black"><font size="3"><span style="font-size:12pt;"><br>
</span></font></font></p>
<p><font color="black"><font size="3"><span style="font-size:12pt;">Ok. Your system has 6 fractional translations. In QE 6.4 there is a bug in the HP code to compute U using DFPT when there are fractional translations - there is no this bug in QE 6.4.1. I am
wondering if this is also a bug for DFPT+U phonon code in QE 6.4. In any case, the version QE 6.4.1 is working fine, so I think there is no point in trying to figure out what is wrong with QE 6.4 (if there is indeed an issue, as you say that you are not sure
about the compilation). <br>
</span></font></font></p>
<p><font color="black"><font size="3"><span style="font-size:12pt;"><br>
</span></font></font></p>
<p><font color="black"><font size="3"><span style="font-size:12pt;"></span></font></font><font color="black"><font size="3"><span style="font-size:12pt;">> I verified each different parameters using QE 6.4.1 (add/remove nbnd, change ecutwfc/ecutrho ratio, conv_thr
and add ‘’ for outdir), and found ecutwfc/ecutrho is the reason for my previous crash.</span></font></font></p>
<p><font color="black"><font size="3"><span style="font-size:12pt;"><br>
</span></font></font></p>
<p><font color="black"><font size="3"><span style="font-size:12pt;">Ok, thanks for sharing this information!<br>
</span></font></font></p>
<p><font color="black"><font size="3"><span style="font-size:12pt;"><br>
</span></font></font></p>
<p><font color="black"><font size="3"><span style="font-size:12pt;"><span lang="en-US"><font color="black"><font size="3"><span style="font-size:12pt;">> I set the occupations to be “fixed” because I want to calculate dielectric constant, it seems the ph.x
program will complain if I use “smearing”, even if it converges to an insulating state</span></font></font></span><br>
</span></font></font></p>
<div><br>
</div>
<div>Ok. Yes, epsil=.true. with smearing will not work.<br>
</div>
<div><br>
</div>
<div>Greetings,</div>
<div>Iurii<br>
</div>
<div><br>
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<font size="3" face="'Times New Roman', Times, serif" color="808080">--<br>
Dr. Iurii Timrov<br>
Postdoctoral Researcher<br>
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<font size="3" face="'Times New Roman', Times, serif" color="808080"><font size="3" face="'Times New Roman', Times, serif" color="808080">Swiss Federal Institute of Technology Lausanne (EPFL<font color="808080"><font face="'Times New Roman', Times, serif">)</font></font></font><br>
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<font size="3" face="'Times New Roman', Times, serif" color="808080">CH-1015 Lausanne, Switzerland<br>
+41 21 69 34 881</font></div>
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<a href="http://people.epfl.ch/265334" tabindex="0" id="LPNoLP">http://people.epfl.ch/265334</a><br>
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<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of Shenli Zhang <shlzhang@uchicago.edu><br>
<b>Sent:</b> Wednesday, November 13, 2019 5:46:27 PM<br>
<b>To:</b> Quantum ESPRESSO users Forum<br>
<b>Subject:</b> Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)</font>
<div> </div>
</div>
<div>
<div class="WordSection1">
<p>Dear <span style="font-size:12.0pt;color:black">Iurii and Paolo,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Thank you so much for all the advice! It works for me now. And I’ve tested a bit to see which factor matters:<o:p></o:p></span></p>
<ol style="margin-top:0in" start="1" type="1">
<li style="color:black;mso-list:l0 level1 lfo1"><span style="font-size:12.0pt">I used Iurii’s input, it works well using QE 6.4.1, but would crash using QE 6.4 (not sure if this is because a compilation issue as I just used the module on the cluster)<o:p></o:p></span></li><li style="color:black;mso-list:l0 level1 lfo1"><span style="font-size:12.0pt">I verified each different parameters using QE 6.4.1 (add/remove nbnd, change ecutwfc/ecutrho ratio, conv_thr and add ‘’ for outdir), and found ecutwfc/ecutrho is the reason for my
previous crash.<o:p></o:p></span></li><li style="color:black;mso-list:l0 level1 lfo1"><span style="font-size:12.0pt">I set the occupations to be “fixed” because I want to calculate dielectric constant, it seems the ph.x program will complain if I use “smearing”, even if it converges to an insulating
state.<o:p></o:p></span></li></ol>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Thank you!<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Shenli<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">-- <o:p></o:p></p>
<div>
<p class="MsoNormal"><span style="color:black">Shenli Zhang</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Postdoc <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Pritzker School of Molecular Engineering</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">The University of Chicago</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><span style="color:black">5640 South Ellis Avenue, Chicago, IL 60637</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">users <users-bounces@lists.quantum-espresso.org> on behalf of Timrov Iurii <iurii.timrov@epfl.ch><br>
<b>Reply-To: </b>Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br>
<b>Date: </b>Wednesday, November 13, 2019 at 4:54 AM<br>
<b>To: </b>Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br>
<b>Subject: </b>Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div id="divtagdefaultwrapper">
<p><span style="font-size:12.0pt;color:black">Dear Shenli and Paolo,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">I changed a bit the input for PW and PH and it did not crash for me (only at the very end, for some reason). I used QE 6.4.1, 8 cores, ifort 15.0.2 20150121.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">The input and output files are here (available temporary):<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><a href="https://drive.google.com/open?id=1Z4fSndJZPcK_A5PVa3hMsft8IGqXWHZB">https://drive.google.com/open?id=1Z4fSndJZPcK_A5PVa3hMsft8IGqXWHZB</a><o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">For reference, I show here only the input files:<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">&control<br>
calculation='scf',<br>
restart_mode='from_scratch',<br>
prefix='LCO'<br>
pseudo_dir = '/scratch/timrov/q-e-qe-6.4.1/pseudo/',<br>
outdir='/scratch/timrov/q-e-qe-6.4.1/tempdir/'<br>
/<br>
&system<br>
ibrav = -5,<br>
celldm(1) = 10.1352,<br>
celldm(4) = 0.47876847,<br>
nat = 10,<br>
ntyp = 3,<br>
ecutwfc = 40.0<br>
ecutrho = 320.0<br>
occupations='fixed'<br>
lda_plus_u = .true.,<br>
lda_plus_u_kind = 0,<br>
U_projection_type = 'atomic',<br>
Hubbard_U(2) = 3.0<br>
/<br>
&electrons<br>
conv_thr = 1.d-14<br>
mixing_beta = 0.7<br>
/<br>
ATOMIC_SPECIES<br>
La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF<br>
Co 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF<br>
O 16 O.pbe-n-kjpaw_psl.1.0.0.UPF<br>
ATOMIC_POSITIONS {crystal}<br>
O 0.312627155 0.750000000 0.187372845<br>
O 0.750000000 0.187372845 0.312627155<br>
O 0.187372845 0.312627155 0.750000000<br>
O 0.687372845 0.250000000 0.812627155<br>
O 0.812627155 0.687372845 0.250000000<br>
O 0.250000000 0.812627155 0.687372845<br>
Co 0.000000000 0.000000000 0.000000000<br>
Co 0.500000000 0.500000000 0.500000000<br>
La 0.250000000 0.250000000 0.250000000<br>
La 0.750000000 0.750000000 0.750000000<br>
K_POINTS {automatic}<br>
4 4 4 0 0 0<o:p></o:p></span></p>
</div>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">phonons of LCO at Gamma<br>
&inputph<br>
prefix = 'LCO',<br>
outdir='/scratch/timrov/q-e-qe-6.4.1/tempdir/',<br>
tr2_ph = 1.0d-14,<br>
epsil = .true.<br>
fildyn='LCO.dynG',<br>
/<br>
0.000000000000000 0.000000000000000 0.000000000000000<o:p></o:p></span></p>
</div>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Shenli: Could you try please to use exactly the same inputs as me with QE 6.4.1 and see what happens?<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Paolo: I do not know what to say why you obtain NaN's... Do you use exactly the same input as Shenli?<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Greetings,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Iurii<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:Times;color:gray">--<br>
Dr. Iurii Timrov<br>
Postdoctoral Researcher</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:Times;color:gray">STI - IMX - THEOS and NCCR - MARVEL</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:Times;color:gray">Swiss Federal Institute of Technology Lausanne (EPFL)</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:Times;color:gray">CH-1015 Lausanne, Switzerland<br>
+41 21 69 34 881</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><a href="http://people.epfl.ch/265334">http://people.epfl.ch/265334</a><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> users <users-bounces@lists.quantum-espresso.org> on behalf of Paolo Giannozzi <p.giannozzi@gmail.com><br>
<b>Sent:</b> Wednesday, November 13, 2019 11:13:09 AM<br>
<b>To:</b> Quantum ESPRESSO users Forum<br>
<b>Subject:</b> Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)</span><span style="font-size:12.0pt;color:black">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">It doesn't segfaults for me but it produces NaN's. Note that:<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">- SCF convergence with fixed occupancies is very bad. I started from the charge density and wavefunctions obtained with smearing.<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:12.0pt;color:black">- outdir='rhomb_U3', between ' '<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Paolo<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">On Tue, Nov 12, 2019 at 10:52 PM Shenli Zhang <<a href="mailto:shlzhang@uchicago.edu">shlzhang@uchicago.edu</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Dear Iurii,</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Thank you so much for your reply. The output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred” is not in the output file of ph.x, but
is in the output file generated by the slurm system, which is a job scheduler for the cluster I use. In the ph.x output, there is no error message, but the program just stopped in the line “Calculating the dnsorth_cart matrix…” </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">I double checked the memory setting, it doesn’t seem to be the problem here. As I’ve increased the number of CPUs used to the point where I could actually
run DFPT+U on an orthorhombic supercell of the same system. </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">And thanks for the advice on the parameter settings. I reduced the ecutrho/ecutwfc here in order to do a quick test. I tried the ultrasoft pseudopotentials,
and the error still persists. And yes my system is a nonmagnetic insulator and the scf calculation converged successfully. </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">The reason I think this error is probably due to the unit cell shape is because I also created an orthorhombic supercell of the same system with the same
parameter settings, and I could run the DFPT+U without any problem.</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Regards,</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Shenli</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">-- </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Shenli Zhang</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Postdoc</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Pritzker School of Molecular Engineering</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">The University of Chicago</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">5640 South Ellis Avenue, Chicago, IL 60637</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<div style="border:none;border-top:solid windowtext 1.0pt;padding:3.0pt 0in 0in 0in;border-color:currentcolor currentcolor">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>> on behalf of Timrov Iurii <<a href="mailto:iurii.timrov@epfl.ch" target="_blank">iurii.timrov@epfl.ch</a>><br>
<b>Reply-To: </b>Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
<b>Date: </b>Tuesday, November 12, 2019 at 11:31 AM<br>
<b>To: </b>"<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>" <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
<b>Subject: </b>Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p><span style="font-size:12.0pt;color:black">Dear Shenli Zhang,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">> with an output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred”<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Was is printed in the output file of the PHonon calculation after the crash?
<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Check if you have enough RAM to run DFPT+U, because it is heavy.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Your input for a PW SCF calculation has some problem:<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">- ecutrho/ecutwfc = 4 - this is true for norm-conserving pseudopotentials. But you are using PAW, for which the ratio should be 8 or more. Try to use DFPT+U with ultrasoft pseudopotentials (the ratio should be also
8 or more).<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">- nbnd=50 - this is not needed: just remove it from the input file<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">- occupations='fixed' : is your system a nonmagnetic insulator? Did your PW SCF calculation converged successfully?<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">- conv_thr=1.0d-12 : I suggest to try conv_thr=1.0d-14 if you plan to compute phonons afterwards.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">HTH<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Regards,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Iurii<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:Times;color:gray">--<br>
Dr. Iurii Timrov<br>
Postdoctoral Researcher</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:Times;color:gray">STI - IMX - THEOS and NCCR - MARVEL</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:Times;color:gray">Swiss Federal Institute of Technology Lausanne (EPFL)</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;font-family:Times;color:gray">CH-1015 Lausanne, Switzerland<br>
+41 21 69 34 881</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:12.0pt;color:black"><a href="http://people.epfl.ch/265334" target="_blank">http://people.epfl.ch/265334</a><o:p></o:p></span></p>
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<div id="gmail-m_-2060381739345997068divRplyFwdMsg">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="color:black">From:</span></b><span style="color:black"> users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>>
on behalf of Shenli Zhang <<a href="mailto:shlzhang@uchicago.edu" target="_blank">shlzhang@uchicago.edu</a>><br>
<b>Sent:</b> Tuesday, November 12, 2019 5:57:47 PM<br>
<b>To:</b> <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
<b>Subject:</b> [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1) </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Dear all,</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">I’m testing phonon calculations using ph.x with DFPT+U in QE 6.4 and QE 6.4.1, however the calculation always stops at the line “Calculating the dnsorth_cart
matrix…” with an output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred”</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">I ran my system without U successfully. And I also ran the LiCoO2 +U example successfully. The only difference I can think of between my input file and
the example file is the unit cell shape, where my LaCoO3 system has a rhombohedral unit cell and the example LiCoO2 has an orthorhombic one. Could this be a problem or did I make some mistakes?</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Attached are the input files for my system LCO. Thank you!</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">SCF calculation input:</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">&control</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> calculation='scf'</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> prefix='LaCoO3p_relax'</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> outdir=rhomb_U3</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> pseudo_dir = '/home/shlzhang/QE_simulation/LaCoO3/pseudo',</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">/</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">&system</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> nbnd=50</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> ibrav=-5, celldm(1)=10.1352, celldm(4) =0.47876847, nat=10, ntyp= 3,</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> ecutwfc =90, ecutrho =360, !for PAW ecutrho=4*ecutwfc, but need test</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> occupations='fixed' !energy units in Ry</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> lda_plus_u=.true. Hubbard_U(2)=3</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">/</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">&electrons</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">conv_thr=1.0d-12</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">/</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">&ions</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">/</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">&cell</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">!cell_dofree='shape'</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">/</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">ATOMIC_SPECIES</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Co 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">O 16 O.pbe-n-kjpaw_psl.1.0.0.UPF</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">ATOMIC_POSITIONS (crystal)</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">O 0.312627155 0.750000000 0.187372845</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">O 0.750000000 0.187372845 0.312627155</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">O 0.187372845 0.312627155 0.750000000</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">O 0.687372845 0.250000000 0.812627155</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">O 0.812627155 0.687372845 0.250000000</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">O 0.250000000 0.812627155 0.687372845</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Co -0.000000000 0.000000000 -0.000000000</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Co 0.500000000 0.500000000 0.500000000</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">La 0.250000000 0.250000000 0.250000000</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">La 0.750000000 0.750000000 0.750000000</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">K_POINTS automatic</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> 4 4 4 0 0 0</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Phonon calculation input:</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">phonons of bulk LaCoO3 at Gamma</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">&inputph</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> prefix='LaCoO3p_relax'</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> outdir=rhomb_U3</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> fildyn='LaCoO3.dyn'</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> max_seconds=82800</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> tr2_ph=1.0d-14</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> verbosity='debug'</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> amass(1)=138.9055</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> amass(2)=58.9332</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> amass(3)=16</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> epsil=.true.</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> trans=.true.</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">/</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">0.00000000000 0.000000000000 0.000000000000000 </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black"> </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">-- </span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Shenli Zhang</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Postdoc</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">Pritzker School of Molecular Engineering</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">The University of Chicago</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:black">5640 South Ellis Avenue, Chicago, IL 60637</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
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-- <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:12.0pt;color:black">Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<o:p></o:p></span></p>
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