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<div dir="auto">Dear Iurii,</div>
<div dir="auto"><br>
</div>
<div dir="auto">Thanks very much for your kind reply.</div>
<div dir="auto">And I am sorry for my mistake.</div>
<div dir="auto"><br>
</div>
<div id="composer_signature" dir="auto">Best regards,
<div>LIANG Xiongyi</div>
<div>Department of Materials Science and Engineering</div>
<div>City University of Hongkong </div>
</div>
<div dir="auto"><br>
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</div>
<div>-------- Original message --------</div>
<div>From: Timrov Iurii <iurii.timrov@epfl.ch> </div>
<div>Date: 23/10/2020 21:42 (GMT+08:00) </div>
<div>To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> </div>
<div>Subject: Re: [QE-users] ph.x calculation with DPT+U </div>
<div><br>
</div>
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<p>Dear <span lang="zh-CN"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US">LIANG Xiongyi</span></span></font></span>,</p>
<p><br>
</p>
<p><span lang="zh-CN"></p>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US">> Have you run DFPT+U by ph.x?</span></span></font></div>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US"><br>
</span></span></font></div>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US">Yes, of course. I am one of the coauthors of this paper:</span></span></font></div>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US"><a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.101.064305" class="OWAAutoLink" id="LPlnk991366">https://journals.aps.org/prb/abstract/10.1103/PhysRevB.101.064305</a><br>
</span></span></font></div>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US"><br>
</span></span></font></div>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US">> How many day it will take? One week? One month?</span></span></font></div>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US"><br>
</span></span></font></div>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US">It depends on many factors (size of your system, k-mesh, q-mesh, cutoff, number of cores that you use,...)<br>
</span></span></font></div>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US"><br>
</span></span></font></div>
<div style="margin:0"><font size="2" face="DengXian" style="font-family:DengXian,serif,"EmojiFont""><span style="font-size:11pt"><span lang="en-US">> It there any strategy to accelerate it? Using NCPP? Or USPP? </span></span></font></div>
</span>
<p></p>
<p><br>
</p>
<p>In order to speed up the DFPT+U calculation you should use more core and parallelize efficiently your calculation (over plane waves, k points, q points, ...)</p>
<p><br>
</p>
<p>Greetings,</p>
<p>Iurii</p>
<p><br>
</p>
<p>P.S.: My first name is Iurii, not Lurii. Just copy-paste it in order to avoid making mistakes.<br>
</p>
<p><br>
</p>
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<font size="3" face="'Times New Roman', Times, serif" color="808080">--<br>
Dr. Iurii TIMROV<br>
Postdoctoral Researcher<br>
<font color="808080"><font face="'Times New Roman', Times, serif"></font></font></font></div>
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<font size="3" face="'Times New Roman', Times, serif" color="808080">STI - IMX <font color="808080">
<font face="'Times New Roman', Times, serif">- THEOS</font></font></font><font size="3" face="'Times New Roman', Times, serif" color="808080"> and NCCR - MARVEL<br>
</font></div>
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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>
</font></div>
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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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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> users <users-bounces@lists.quantum-espresso.org> on behalf of LEUNG Clarence <liangxy123@hotmail.com><br>
<b>Sent:</b> Friday, October 23, 2020 3:33:02 PM<br>
<b>To:</b> Quantum Espresso users Forum<br>
<b>Subject:</b> Re: [QE-users] ph.x calculation with DPT+U</font>
<div> </div>
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<p class="MsoNormal"><span lang="EN-US">Dear Lurii,</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Have you run DFPT+U by ph.x?</span></p>
<p class="MsoNormal"><span lang="EN-US">How many day it will take? One week? One month?</span></p>
<p class="MsoNormal"><span lang="EN-US">It there any strategy to accelerate it? Using NCPP? Or USPP?
</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks!</span></p>
<p class="MsoNormal"><span lang="EN-US">Best regards,</span></p>
<p class="MsoNormal"><span lang="EN-US">LIANG Xiongyi</span></p>
<p class="MsoNormal"><span lang="EN-US">Postdoctoral Fellow</span></p>
<p class="MsoNormal"><span lang="EN-US">City University of Hong Kong</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="border:none; padding:0cm"><b><span lang="EN-US">From:
</span></b><span lang="EN-US"><a href="mailto:iurii.timrov@epfl.ch">Timrov Iurii</a><br>
<b>Sent: </b>2020</span>年<span lang="EN-US">10</span>月<span lang="EN-US">19</span>日<span lang="EN-US"> 5:33<br>
<b>To: </b><a href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br>
<b>Subject: </b>Re: [QE-users] ph.x calculation with DPT+U</span></p>
</div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt; font-family:SimSun"> </span></p>
<div id="divtagdefaultwrapper">
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">Dear Liang,</span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">> It is very slow, it is normal?</span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">Yes</span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">> My system consists of 80 atoms...</span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">For such a large system DFPT+U is expected to be very slow, in particular because the calculation of d2ns_bare matrix (second "bare" derivative of the occupation matrix ns) is computationally
very expensive. I suggest to use the frozen-phonon approach (Phonopy).</span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">Greetings,</span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">Iurii</span></p>
<p><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman",serif; color:gray">--<br>
Dr. Iurii TIMROV<br>
Postdoctoral Researcher</span><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"></span></p>
</div>
<div name="divtagdefaultwrapper">
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman",serif; color:gray">STI - IMX - THEOS and NCCR - MARVEL</span><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"></span></p>
</div>
<div name="divtagdefaultwrapper">
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman",serif; color:gray">Swiss Federal Institute of Technology Lausanne (EPFL)</span><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"></span></p>
</div>
<div name="divtagdefaultwrapper">
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Times New Roman",serif; color:gray">CH-1015 Lausanne, Switzerland<br>
+41 21 69 34 881</span><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"></span></p>
</div>
<div name="divtagdefaultwrapper">
<p class="MsoNormal"><span lang="EN-US"><a href="http://people.epfl.ch/265334"><span style="font-family:"Calibri",sans-serif">http://people.epfl.ch/265334</span></a></span><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"></span></p>
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<p class="MsoNormal"><span lang="EN-US"><img border="0" width="460" height="2" id="Horizontal_x0020_Line_x0020_1" src="cid:image002.png@01D6A97E.4CE3A890" style="width:4.7899in; height:.0252in"></span><span lang="EN-US" style="font-family:SimSun"></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">From:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> users <users-bounces@lists.quantum-espresso.org> on behalf of LEUNG Clarence
<liangxy123@hotmail.com><br>
<b>Sent:</b> Saturday, October 17, 2020 8:53:18 AM<br>
<b>To:</b> users@lists.quantum-espresso.org<br>
<b>Subject:</b> [QE-users] ph.x calculation with DPT+U</span><span lang="EN-US"> </span>
</p>
<div>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">Dear QEusers,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">Recently, I do ph.x calculation with DPT+U in QE6.6. However, it is very very slow. The output file running for four days as follows:</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> Atomic wfc used for the projector on the Hubbard manifold are NOT orthogonalized
</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> Calculating the dnsbare matrix...</span></p>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
</div>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> Calculating the dnsorth_cart matrix...</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> Alpha used in Ewald sum = 2.8000</span></p>
</div>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
</div>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> Calculating the d2ns_bare matrix. It might take a while!</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> k point # 1 out of 2</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"><br>
The specification of my server is two nodes with 64 cores (Xeon e5) and 512G RAMs. My system consists of 80 atoms, and the input files of ph.x si as follows:</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">&INPUTPH
</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> outdir='',</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> prefix='',</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> tr2_ph = 1d-12,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> ldisp = .true. ,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> fildyn ='' ,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> epsil=.false.,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> trans=.true.,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> nq1 = 1 ,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> nq2 = 1 ,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> nq3 = 1 ,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> nat_todo = 1,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> alpha_mix(1) = 0.07,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">/</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">79</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">It is very slow, it is normal? It is very appreciated that give me some advices.</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">Best regards,</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">LIANG</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">Postdoc</span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif; color:black">City University of Hong Kong</span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt; font-family:SimSun"> </span></p>
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