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<p class="MsoNormal"><span style="font-size:11.0pt">Dear Iurii,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">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
</span><span style="font-size:11.0pt;color:black">“Calculating the dnsorth_cart matrix…” </span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">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. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">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. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Shenli<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-- <o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Shenli Zhang</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Postdoc</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Pritzker School of Molecular Engineering</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">The University of Chicago</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:black">5640 South Ellis Avenue, Chicago, IL 60637</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><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 Timrov Iurii <iurii.timrov@epfl.ch><br>
<b>Reply-To: </b>Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org><br>
<b>Date: </b>Tuesday, November 12, 2019 at 11:31 AM<br>
<b>To: </b>"users@lists.quantum-espresso.org" <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>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p><span style="font-size:12.0pt;color:black">Dear </span><span style="color:black">Shenli Zhang</span><span style="font-size:12.0pt;color:black">,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="color:black">> 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><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="color:black">Was is printed in the output file of the PHonon calculation after the crash?
</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="color:black">Check if you have enough RAM to run DFPT+U, because it is heavy.</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="color:black">Your input for a PW SCF calculation has some problem:</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p><span style="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).</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p><span style="color:black">- nbnd=50 - this is not needed: just remove it from the input file</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p><span style="color:black">- occupations='fixed' : is your system a nonmagnetic insulator? Did your PW SCF calculation converged successfully?</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
<p><span style="color:black">- conv_thr=1.0d-12 : I suggest to try conv_thr=1.0d-14 if you plan to compute phonons afterwards.</span><span style="font-size:12.0pt;color:black"><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"><span style="font-family:Times;color:gray">--<br>
Dr. Iurii Timrov<br>
Postdoctoral Researcher</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Times;color:gray">STI - IMX - THEOS and NCCR - MARVEL</span><span style="color:black"><o:p></o:p></span></p>
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<div name="divtagdefaultwrapper">
<p class="MsoNormal"><span style="font-family:Times;color:gray">Swiss Federal Institute of Technology Lausanne (EPFL)</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:Times;color:gray">CH-1015 Lausanne, Switzerland<br>
+41 21 69 34 881</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="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="font-size:11.0pt;color:black">From:</span></b><span style="font-size:11.0pt;color:black"> users <users-bounces@lists.quantum-espresso.org> on behalf of Shenli Zhang <shlzhang@uchicago.edu><br>
<b>Sent:</b> Tuesday, November 12, 2019 5:57:47 PM<br>
<b>To:</b> users@lists.quantum-espresso.org<br>
<b>Subject:</b> [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)</span><span style="font-size:11.0pt">
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Dear all,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;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><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;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><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Attached are the input files for my system LCO. Thank you!</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">SCF calculation input:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">&control</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> calculation='scf'</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> prefix='LaCoO3p_relax'</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> outdir=rhomb_U3</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> pseudo_dir = '/home/shlzhang/QE_simulation/LaCoO3/pseudo',</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">/</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">&system</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> nbnd=50</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> ibrav=-5, celldm(1)=10.1352, celldm(4) =0.47876847, nat=10, ntyp= 3,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> ecutwfc =90, ecutrho =360, !for PAW ecutrho=4*ecutwfc, but need test</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> occupations='fixed' !energy units in Ry</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> lda_plus_u=.true. Hubbard_U(2)=3</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">/</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">&electrons</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">conv_thr=1.0d-12</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">/</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">&ions</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">/</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">&cell</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">!cell_dofree='shape'</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">/</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">ATOMIC_SPECIES</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Co 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">O 16 O.pbe-n-kjpaw_psl.1.0.0.UPF</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">ATOMIC_POSITIONS (crystal)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">O 0.312627155 0.750000000 0.187372845</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">O 0.750000000 0.187372845 0.312627155</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">O 0.187372845 0.312627155 0.750000000</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">O 0.687372845 0.250000000 0.812627155</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">O 0.812627155 0.687372845 0.250000000</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">O 0.250000000 0.812627155 0.687372845</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Co -0.000000000 0.000000000 -0.000000000</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Co 0.500000000 0.500000000 0.500000000</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">La 0.250000000 0.250000000 0.250000000</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">La 0.750000000 0.750000000 0.750000000</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">K_POINTS automatic</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> 4 4 4 0 0 0</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Phonon calculation input:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">phonons of bulk LaCoO3 at Gamma</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">&inputph</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> prefix='LaCoO3p_relax'</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> outdir=rhomb_U3</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> fildyn='LaCoO3.dyn'</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> max_seconds=82800</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> tr2_ph=1.0d-14</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> verbosity='debug'</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> amass(1)=138.9055</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> amass(2)=58.9332</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> amass(3)=16</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> epsil=.true.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black"> trans=.true.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">/</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">0.00000000000 0.000000000000 0.000000000000000 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-- </span><o:p></o:p></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Shenli Zhang</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Postdoc</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Pritzker School of Molecular Engineering</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">The University of Chicago</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:black">5640 South Ellis Avenue, Chicago, IL 60637</span><o:p></o:p></p>
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