<div dir="ltr"><div>Thank you for taking the time.</div><div><br></div><div>with best regards,</div><div><br></div><div>Mohammad<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Sep 16, 2020 at 11:11 AM <<a href="mailto:pdelugas@sissa.it">pdelugas@sissa.it</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto">Good that at least one of the options worked :-)<div dir="auto"><br></div><div dir="auto">Greetings and best regards</div><div dir="auto">Pietro</div></div><div class="gmail_extra"><br><div class="gmail_quote">Il 16 set 2020 8:19 AM, Mohammad Moaddeli <<a href="mailto:mohammad.moaddeli@gmail.com" target="_blank">mohammad.moaddeli@gmail.com</a>> ha scritto:<br type="attribution"><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Dear Pietro,</div><div><br></div><div>Yes, I had changed both of them. I also tried by changing the second one. but it caused the following error :</div><div><br></div><div>================================================</div><div>.</div><div>.</div><div>.<br></div><div>.<br></div><div> Parallelization info<br> --------------------<br> sticks: dense smooth PW G-vecs: dense smooth PW<br> Min 214 114 32 9544 3716 568<br> Max 215 115 33 9546 3719 571<br> Sum 3433 1829 517 152719 59479 9111<br><br>*** Error in `*** Error in `projwfc.x': *** Error in `projwfc.x': *** Error in `projwfc.x': malloc(): memory corruption: 0x00000000042f2480 ***<br>*** Error in `projwfc.x': malloc(): memory corruption: 0x0000000003466830 ***<br>*** Error in `projwfc.x*** Error in `*** Error in `projwfc.x*** Error in `projwfc.x': malloc(): memory corruption: 0x000000000538c590 ***<br>======= Backtrace: =========<br>/lib64/libc.so.6(+0x82e86)[0x7f966777fe86]<br><br> Gaussian broadening (read from input): ngauss,degauss= 1 0.020000<br><br><br> Calling projwave ....<br>projwfc.x[0xa41cff]<br>projwfc.x[0x44739b]<br>projwfc.x[0x406a9e]<br>/lib64/libc.so.6======= Memory map: ========<br>/lib64/libc.so.6(+0x82e86)[0x7f1ae5cd5e86]<br>/lib64/libc.so.6(__libc_malloc+0x4c)[0x7f1ae5cd8adc]<br>projwfc.x[0xbb24ee]<br>projwfc.x[0xb7d601]<br>projwfc.x[0xbb7173]<br>projwfc.x[0xa41cff]<br>projwfc.x[0x44739b]<br>projwfc.x[0x40b3f7]<br>projwfc.x[0x407143]<br>projwfc.x[0x406a9e]<br>/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f1ae5c75505]<br>projwfc.x[0x4069a9]<br>======= Memory map: ========<br>00400000-00e30000 r-xp 00000000 fd:00 15202532 /codes/qe_6.6/qe-6.6/PP/src/projwfc.x<br>0102f000-01032000 r--p 00a2f000 fd:00 15202532 /codes/qe_6.6/qe-6.6/PP/src/projwfc.x<br>01032000-01152000 rw-p 00a32000 fd:00 15202532 /codes/qe_6.6/qe-6.6/PP/src/projwfc.x<br>01152000-0259f000 rw-p 00000000 00:00 0<br>03e3d000-059b5000 rw-p 00000000 00:00 0 [heap]<br>7f1ad0000000-7f1ad0021000 rw-p 00000000 00:00 0<br>7f1ad0021000-7f1ad4000000 ---p 00000000 00:00 0<br>7f1ad7fd9000-7f1adb77d000 r-xp 00000000 fd:00 3512522 /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_avx2.so<br>7f1adb77d000-7f1adb97c000 ---p 037a4000 fd:00 3512522 /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_avx2.so<br>7f1adb97c000-7f1adb983000 r--p 037a3000 fd:00 3512522 /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_avx2.so<br>7f1adb983000-7f1adb990000 rw-p 037aa000 fd:00 3512522 /opt/intel/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_avx2.so</div><div>.</div><div>.</div><div>.</div><div>
================================================ <br></div><div><br></div><div>I tried to copy the non-zero
<span style="font-size:12pt">PP_PSWFC</span> from the original file before running SCF and finally got the job done. <br></div><div><br></div><div>Best,</div><div><br></div><div>Mohammad</div><div><br></div><div>ShirazU<br></div></div><br><div><div dir="ltr">On Tue, Sep 15, 2020 at 10:00 AM <<a href="mailto:pdelugas@sissa.it" target="_blank">pdelugas@sissa.it</a>> wrote:<br></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto">Hi<div dir="auto">Before or after does not make difference that info is used only for doing the projections. </div><div dir="auto">The pseudo names are written in two places. The one read by the program is the second. Have you changed that one?</div><div dir="auto">Regards </div><div dir="auto">Pietro</div></div><div><br><div>Il 14 set 2020 10:24 PM, Mohammad Moaddeli <<a href="mailto:mohammad.moaddeli@gmail.com" target="_blank">mohammad.moaddeli@gmail.com</a>> ha scritto:<br type="attribution"><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Dear
Pietro,</div><div><br></div><div>Thank you for technical advice.<br></div><div>Should I copy the non-zero
<span style="font-size:12pt">PP_PSWFC</span> from the original file before running SCF?</div><div><br></div><div>Replacing the pseudo file name in
data-file-schema.xml before running projwfc.x results in:</div><div><br></div><div>%%%%%<br></div><div>Error in routine projwave (1):<br> Cannot project on zero atomic wavefunctions!</div><div>%%%%%</div><div><br></div><div>Best,</div><div><br></div><div>Mohammad<br></div></div><br><div><div dir="ltr">On Sun, Sep 13, 2020 at 7:23 PM Pietro Delugas <<a href="mailto:pdelugas@sissa.it" target="_blank">pdelugas@sissa.it</a>> wrote:<br></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><p><span style="font-size:12pt"><u></u> <u></u></span></p><p><span style="font-size:12pt">Hello <u></u><u></u></span></p><p><span style="font-size:12pt"><u></u> <u></u></span></p><p><span style="font-size:12pt">Try to copy the PP_PSWFC from the original file </span>'Si.pbe-nl-rrkjus_psl.1.0.0.UPF' replacing the all 0s one contained in Si.PBE.0.25.UPF. </p><p><u></u> <u></u></p><p>Other thing you can do is to replace the pseudo file name in data-file-schema.xml before running projwfc.x. </p><p><u></u> <u></u></p><p>Hope it helps</p><p>Greetings – Pietro <span style="font-size:12pt"><u></u><u></u></span></p><p><span style="font-size:12pt"><u></u> <u></u></span></p><p>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10</p><p><span style="font-size:12pt"><u></u> <u></u></span></p><div style="border-color:rgb(225,225,225);border-style:solid none none;border-width:1pt medium medium;padding:3pt 0in 0in"><p style="border:medium none;padding:0in"><b>From: </b><a href="mailto:mohammad.moaddeli@gmail.com" target="_blank">Mohammad Moaddeli</a><br><b>Sent: </b>Sunday, September 13, 2020 2:25 PM<br><b>To: </b><a href="mailto:users@lists.quantum-espresso.org" target="_blank">Quantum ESPRESSO users Forum</a><br><b>Subject: </b>Re: [QE-users] DFT-1/2 method</p></div><p><span style="font-size:12pt"><u></u> <u></u></span></p><div><div><p>Dear Giuseppe,</p></div><div><p><u></u> <u></u></p></div><div><p>A pseudopotential from PSlibrary is applied:</p></div><div><p><u></u> <u></u></p></div><div><p>=============================</p></div><div><p>&input<br> title='Si',<br> zed=14.0,<br> config='[Ne] 3s2 3p2 3d-1',<br> iswitch=4<br> dft='PBE'<br> rel = 1,<br>/<br>&test<br> file_pseudo='Si.pbe-nl-rrkjus_psl.1.0.0.UPF',<br> file_pseudopw='Si.PBE.0.25.UPF',<br> configts(1)='3s2 3p2 3d-1',<br> configts(2)='3s2 3p1.75 3d-1',<br> rcutv=1.0<br>/</p></div><div><p>============================= </p></div><div><p>SCF input:</p></div><div><p><u></u> <u></u></p></div><div><p>============================= </p></div><div><p> &control<br> calculation = 'scf'<br> restart_mode='from_scratch',<br> prefix='silicon',<br> tstress = .true.<br> tprnfor = .true.<br> pseudo_dir = './',<br> outdir='tmp'<br>! disk_io = 'none'<br> /<br> &system<br> ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1,<br> ecutwfc =50.0,<br> /<br> &electrons<br> diagonalization='david'<br> mixing_mode = 'plain'<br> mixing_beta = 0.7<br> conv_thr = 1.0d-8<br> /<br>ATOMIC_SPECIES<br> Si 28.086 Si.PBE.0.25.UPF<br>ATOMIC_POSITIONS alat<br> Si 0.00 0.00 0.00<br> Si 0.25 0.25 0.25<br>K_POINTS<br> 10<br> 0.1250000 0.1250000 0.1250000 1.00<br> 0.1250000 0.1250000 0.3750000 3.00<br> 0.1250000 0.1250000 0.6250000 3.00<br> 0.1250000 0.1250000 0.8750000 3.00<br> 0.1250000 0.3750000 0.3750000 3.00<br> 0.1250000 0.3750000 0.6250000 6.00<br> 0.1250000 0.3750000 0.8750000 6.00<br> 0.1250000 0.6250000 0.6250000 3.00<br> 0.3750000 0.3750000 0.3750000 1.00<br> 0.3750000 0.3750000 0.6250000 3.00 </p></div><div><p>============================= </p></div><div><p>To the best of my knowledge ONCVPS could not be run using ld1.x, because of its format.</p></div><div><p><u></u> <u></u></p></div><div><p><u></u> <u></u></p></div><div><p>With best regards,</p></div><div><p><u></u> <u></u></p></div><div><p>Mohammad</p></div><div><p><u></u> <u></u></p></div><div><p>ShirazU</p></div></div><p><u></u> <u></u></p><div><div><p>On Sun, Sep 13, 2020 at 2:59 PM Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>> wrote:</p></div></div><p style="margin-left:4.8pt"><br>Dear Mohammad<br>You are likely using a pseudopotential which does not include atomic <br>pseudo-wavefunctions in the UPF file; maybe, as often reported, one of <br>the ONCVPS contained in the sg15 database. Thus projwfc.x cannot find <br>atomic wavefunctions suitable for performing projections of Kohn-Sham <br>orbitals onto.<br><br>You should look for PSP files containing the pseudowavefunctions, and <br>if you are actually looking for ONCVPS files containing them, you <br>should find what you need here:<br><br><a href="https://github.com/pipidog/ONCVPSP/tree/master/sg15" target="_blank">https://github.com/pipidog/ONCVPSP/tree/master/sg15</a><br><br>HTH<br>Giuseppe<br><br>Quoting Mohammad Moaddeli <<a href="mailto:mohammad.moaddeli@gmail.com" target="_blank">mohammad.moaddeli@gmail.com</a>>:<br><br>> Dear all,<br>><br>> I am trying to run pdos for Si based on the dft-1/2 method implemented by<br>> Leonardo Matheus Marion Jorge. However, the following warning in the scf<br>> run is appeared:<br>><br>> ==================================<br>> Program PWSCF v.6.6 starts on 13Sep2020 at 11:33:39<br>><br>> This program is part of the open-source Quantum ESPRESSO suite<br>> for quantum simulation of materials; please cite<br>> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);<br>> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);<br>> URL <a href="http://www.quantum-espresso.org" target="_blank">http://www.quantum-espresso.org</a>",<br>> in publications or presentations arising from this work. More details<br>> at<br>> <a href="http://www.quantum-espresso.org/quote" target="_blank">http://www.quantum-espresso.org/quote</a><br>><br>> Parallel version (MPI), running on 1 processors<br>><br>> MPI processes distributed on 1 nodes<br>> Fft bands division: nmany = 1<br>> Reading input from <a href="http://scf_si.in" target="_blank">scf_si.in</a><br>><br>> Current dimensions of program PWSCF are:<br>> Max number of different atomic species (ntypx) = 10<br>> Max number of k-points (npk) = 40000<br>> Max angular momentum in pseudopotentials (lmaxx) = 3<br>> WARNING: atomic wfc # 1 for atom typeSi has zero norm<br>> WARNING: atomic wfc # 2 for atom typeSi has zero norm<br>> WARNING: atomic wfc # 3 for atom typeSi has zero norm<br>><br>> Subspace diagonalization in iterative solution of the eigenvalue<br>> problem:<br>> a serial algorithm will be used<br>> .<br>> .<br>> .<br>> ==================================<br>><br>><br>><br>><br>> Therefore pdos could not be computed:<br>><br>><br>><br>><br>> ==================================<br>> Program PROJWFC v.6.6 starts on 13Sep2020 at 11:33:50<br>><br>> This program is part of the open-source Quantum ESPRESSO suite<br>> for quantum simulation of materials; please cite<br>> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);<br>> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);<br>> URL <a href="http://www.quantum-espresso.org" target="_blank">http://www.quantum-espresso.org</a>",<br>> in publications or presentations arising from this work. More details<br>> at<br>> <a href="http://www.quantum-espresso.org/quote" target="_blank">http://www.quantum-espresso.org/quote</a><br>><br>> Parallel version (MPI), running on 1 processors<br>><br>> MPI processes distributed on 1 nodes<br>> Fft bands division: nmany = 1<br>><br>> Reading xml data from directory:<br>><br>> tmp/silicon.save/<br>> WARNING: atomic wfc # 1 for atom typeSi has zero norm<br>> WARNING: atomic wfc # 2 for atom typeSi has zero norm<br>> WARNING: atomic wfc # 3 for atom typeSi has zero norm<br>><br>> IMPORTANT: XC functional enforced from input :<br>> Exchange-correlation= PBE<br>> ( 1 4 3 4 0 0 0)<br>> Any further DFT definition will be discarded<br>> Please, verify this is what you really want<br>><br>><br>> G-vector sticks info<br>> --------------------<br>> sticks: dense smooth PW G-vecs: dense smooth PW<br>> Sum 721 721 211 12627 12627 1989<br>><br>><br>> Gaussian broadening (read from input): ngauss,degauss= 1 0.010000<br>><br>><br>> <br>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>> Error in routine projwave (1):<br>> Cannot project on zero atomic wavefunctions!<br>> <br>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>><br>> stopping ...<br>> ==================================<br>><br>> Is it a limitation in the DFT-1/2 method?<br>><br>> Best regards,<br>><br>> Mohammad<br>><br>> Department of Materials Science and Engineering, School of Engineering,<br>> Shiraz University<br><br><br><br>GIUSEPPE MATTIOLI<br>CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>Via Salaria Km 29,300 - C.P. 10<br>I-00015 - Monterotondo Scalo (RM)<br>Mob (*preferred*) +39 373 7305625<br>Tel + 39 06 90672342 - Fax +39 06 90672316<br>E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br><br>_______________________________________________<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>users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></p><p><span style="font-size:12pt"><u></u> <u></u></span></p></div></div>_______________________________________________<br>
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