On Mon, Sep 23, 2019 at 12:24 PM Mayuri Bora <mayu...@tezu.ernet.in> wrote:
Can we do PBE+GGA with SOC and VdW correction in NM/FM in QE? > Because i have tried for the same but segmentation fault is observed as > mentioned below > the code stops with an error message if you try to run noncolinear or spinorbit calculations with a vdW-DF functional (e.g. input_dft='vdW-DF') or with XDM (not currently impemented). DFT-D2 and DFT-D3 are completely independent from the electronic structure. I don't know about Tkatchenko-Scheffler but it shouldn't crash because it uses just the charge density. Please explain under which exact circumstances the code crashes. Paolo cp: missing destination file operand after > ‘/global/home/sushantk/mayuri/SOC/soc_vdwcorr/’ > Try 'cp --help' for more information. > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > libintlc.so.5 00007F49A83B4C05 Unknown Unknown Unknown > libintlc.so.5 00007F49A83B2827 Unknown Unknown Unknown > libifcoremt.so.5 00007F49AA141962 Unknown Unknown Unknown > libifcoremt.so.5 00007F49AA1417B6 Unknown Unknown Unknown > libifcoremt.so.5 00007F49AA096CAD Unknown Unknown Unknown > libifcoremt.so.5 00007F49AA0A8FAD Unknown Unknown Unknown > libpthread.so.0 00007F49AA62B100 Unknown Unknown Unknown > pw.x 000000000053E3E3 Unknown Unknown Unknown > pw.x 00000000005354DD Unknown Unknown Unknown > pw.x 0000000000529284 Unknown Unknown Unknown > pw.x 0000000000524E11 Unknown Unknown Unknown > pw.x 000000000057C092 Unknown Unknown Unknown > pw.x 00000000004DB3B9 Unknown Unknown Unknown > pw.x 0000000000406670 Unknown Unknown Unknown > pw.x 0000000000406523 Unknown Unknown Unknown > pw.x 000000000040648E Unknown Unknown Unknown > libc.so.6 00007F49A7FFBB15 Unknown Unknown Unknown > pw.x 0000000000406399 Unknown Unknown Unknown > > real 0m27.796s > user 0m49.701s > sys 0m2.100s > > Send users mailing list submissions to > > users@lists.quantum-espresso.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.quantum-espresso.org/mailman/listinfo/users > > or, via email, send a message with subject or body 'help' to > > users-requ...@lists.quantum-espresso.org > > > > You can reach the person managing the list at > > users-ow...@lists.quantum-espresso.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of users digest..." > > > > > > Today's Topics: > > > > 1. Fw: Can we do LDA+U with SOC for FM/AFM systems in QE > > (David Kostov) > > 2. Re: Error during compilation in the step of make all command > > (Will DeBenedetti) > > 3. Re: Fw: Can we do LDA+U with SOC for FM/AFM systems in QE > > (Lorenzo Paulatto) > > 4. QE+Wannier90 (=?gbk?B?emh5?=) > > 5. Re: QE+Wannier90 (TERSOO ATSUE) > > 6. Re: QE+Wannier90 (=?gbk?B?emh5?=) > > 7. Re: Convergence of calculating Hubbard parameters from DFPT > > (Christoph Wolf) > > 8. Re: Error during compilation in the step of make all command (???) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sun, 22 Sep 2019 11:57:22 +0000 (UTC) > > From: David Kostov <d...@yahoo.com> > > To: Quantum ESPRESSO Users Forum <users@lists.quantum-espresso.org> > > Subject: [QE-users] Fw: Can we do LDA+U with SOC for FM/AFM systems in > > QE > > Message-ID: <1117481007.4909079.1569153442...@mail.yahoo.com> > > Content-Type: text/plain; charset="utf-8" > > > > Hello again, > > I am still waiting for a support for my issue. > > Thank youD > > > > ----- Forwarded Message ----- From: David Kostov <d...@yahoo.com>To: > > Quantum ESPRESSO Users Forum <users@lists.quantum-espresso.org>Sent: > > Friday, September 20, 2019, 5:24:39 p.m. CSTSubject: Can we do LDA+U > > with SOC for FM/AFM systems in QE > > Dear QE community > > > > I wanted to structure optimization for my system considering both Hub-U > > and SOC. But I am getting the following error with vc-relax. > > > > Error in routine force_hub (1): > > ????? forces in full LDA+U scheme are not yet implemented > > > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > ???? stopping ... > > > > > > > > This is a ferromagnetic system. In the scf.in I have defined : > > ??? starting_magnetization(1)=0.5, > > ??? starting_magnetization(2)=0.0, > > ??? lda_plus_u = .true., > > ??? lda_plus_u_kind = 1, > > ??? Hubbard_U(1) = 4.00, > > ??? noncolin= .true. > > ??? lspinorb= .true. > > I have not defined nspin there. Can someone please let me know what is > > wrong with my input? > > > > > > > > I tried removing? "lda_plus_u = .true.," and "lda_plus_u_kind = 1" , Then > > it works, but I noticed vc-relax calculation has finished in a one cycle > > (it has directly given the final structure) and it is the experimental > > structure which is in the scf.in. I am doubtful about that results too. > > > > I appreciate your support to this problem. If I brief my system again, it > > is FM and I need to include both Hub-U and SOC. > > Thank youD. > > > > > > > > > > > > > > > > > > > > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190922/3d77e816/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 2 > > Date: Sun, 22 Sep 2019 08:11:38 -0400 > > From: Will DeBenedetti <wj...@cornell.edu> > > To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> > > Subject: Re: [QE-users] Error during compilation in the step of make > > all command > > Message-ID: > > < > cang7sujcjfvnb0hksbmroz3zxihrj-ztucyqgju3zjg4+j+...@mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Sheng-Chinh, > > > > I also recall having this error at some point. Usually 99.99% of these > > errors have to do with PATH variables being incorrectly set. For a number > > of reasons, I do not use the Python that ships with Macs, I instead use > > virtual environments using Anaconda (not an endorsement, just a much > > painless way of using software that Apple will soon deprecate). I was > able > > to get the test suite running by creating a virtual environment using > > Python 2.7.something and activating this environment using condo > activate > > name_of_environment > > > > As per the documentation you will to run make run-tests-foo, then the > > tests will run serially or in parallel. Keep in mind only PW, CP, PH, and > > EPW binaries are supported. Make sure you have statically lined these > four > > binaries as per my previous message and verify using otool -L otherwise > > the > > tests will crash. I have a 4-core processor and the tests took quite some > > time running in parallel on the Intel compiler suite. Running on gFortran > > will be slower. > > > > Will DeBenedetti > > > > > > > > On Sun, Sep 22, 2019 at 2:03 AM ??? <r03223...@ntu.edu.tw> wrote: > > > >> Hi Will, > >> > >> Thanks so much for the info. I?ve checked libraries of pw.x and it seems > >> good for them with static addresses. So, I carried out calculations, > >> such > >> as scf and vc_relax, and they worked smoothly. Thus, I think the absence > >> of > >> messages I mentioned in previous e-mail was caused by some of the bins > >> having dynamic addresses. And it could be fixed by replacing their > >> addresses. > >> > >> Besides, when I ran test files (make run-tests-pw-serial) in the > >> file--test-suite, the system showed the message below. > >> > >> env: python2: No such file or directory > >> make: *** [run-tests-pw-serial] Error 127 > >> > >> I?ve tried several ways to address it. I checked the installation of > >> python2 and its version was 2.7.16. Besides, I also made a symbolic link > >> to > >> direct the system to the location of python 2.7 using the command as > >> follows, but still no joy. Have you ever experienced the situation? > >> > >> ln -s /opt/local/bin/python2.7 > >> > /Users/hayashikiyoshisatoshi/Desktop/q-e-qe-6.4.1/q-e-qe-6.4.1/test-suite/python2 > >> > >> > >> Thank you for considering my request. > >> Sheng-Chih Lin > >> r03223...@ntu.edu.tw > >> > >> > >> > >> > >> Will DeBenedetti <wj...@cornell.edu> ? 2019?9?22? ??9:52 ??? > >> > >> Hi Sheng-Chinh, > >> > >> Have you looked to see if you have made QE binaries? These will be in > >> the > >> /qe/bin On my machine these are located here: /Users/wjid/qe/bin > >> > >> Using ls shows the following after running `make all`: > >> > >> wjid$ ls > >> alpha2f.x neb.x > >> average.x open_grid.x > >> band.eps path_interpolation.x > >> bands.x ph.x > >> bse_main.x phcg.x > >> cell2ibrav.x plan_avg.x > >> cp.x plotband.x > >> dist.x plotproj.x > >> dos.x plotrho.x > >> dynmat.x pmw.x > >> epa.x pp.x > >> epsilon.x ppacf.x > >> ev.x projwfc.x > >> fd.x pw.x > >> fd_ef.x pw2bgw.x > >> fd_ifc.x pw2critic.x > >> fermi_proj.x pw2gw.x > >> fermi_velocity.x pw2wannier90.x > >> fqha.x pw4gww.x > >> fs.x pwcond.x > >> generate_rVV10_kernel_table.x pwi2xsf.x > >> generate_vdW_kernel_table.x q2qstar.x > >> gww.x q2r.x > >> gww_fit.x q2trans.x > >> head.x q2trans_fd.x > >> hp.x simple.x > >> ibrav2cell.x simple_bse.x > >> initial_state.x simple_ip.x > >> iotk spectra_correction.x > >> iotk.x sumpdos.x > >> iotk_print_kinds.x turbo_davidson.x > >> kpoints.x turbo_eels.x > >> lambda.x turbo_lanczos.x > >> ld1.x turbo_spectrum.x > >> manycp.x wannier_ham.x > >> manypw.x wannier_plot.x > >> matdyn.x wfck2r.x > >> molecularnexafs.x wfdd.x > >> molecularpdos.x xspectra.x > >> > >> Then you should verify that your binaries are linked properly by using > >> otool, which is the linux equivalent of ldd. > >> > >> The command to show which shared libraries are linked with this binary > >> use > >> otool -L (in terminal) > >> > >> wjid$ otool -L pw.x > >> pw.x: > >> > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_scalapack_lp64.dylib > >> (compatibility version 0.0.0, current version 0.0.0) > >> > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_intel_lp64.dylib > >> (compatibility version 0.0.0, current version 0.0.0) > >> > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_intel_thread.dylib > >> (compatibility version 0.0.0, current version 0.0.0) > >> > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_core.dylib > >> (compatibility version 0.0.0, current version 0.0.0) > >> > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_blacs_mpich_lp64.dylib > >> (compatibility version 0.0.0, current version 0.0.0) > >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version > >> 1252.50.4) > >> /usr/local/bin/mpich-install/lib/libmpifort.12.dylib (compatibility > >> version 14.0.0, current version 14.7.0) > >> /usr/local/bin/mpich-install/lib/libmpi.12.dylib (compatibility version > >> 14.0.0, current version 14.7.0) > >> /usr/local/bin/mpich-install/lib/libpmpi.12.dylib (compatibility version > >> 14.0.0, current version 14.7.0) > >> > >> The output shows which MKL and mpich libraries are linked to the pw.x > >> binary. > >> > >> Like I said in my previous email, if you have system integrity > >> protection > >> enabled (it is by default) linking to dynamic libraries is disabled by > >> default. These binaries will look like plotrho.x as below: > >> > >> wjid$ otool -L plotrho.x > >> plotrho.x: > >> @rpath/libmkl_scalapack_ilp64.dylib (compatibility version 0.0.0, > >> current > >> version 0.0.0) > >> @rpath/libmkl_intel_ilp64.dylib (compatibility version 0.0.0, current > >> version 0.0.0) > >> @rpath/libmkl_intel_thread.dylib (compatibility version 0.0.0, current > >> version 0.0.0) > >> @rpath/libmkl_core.dylib (compatibility version 0.0.0, current version > >> 0.0.0) > >> @rpath/libmkl_blacs_mpich_ilp64.dylib (compatibility version 0.0.0, > >> current version 0.0.0) > >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version > >> 1252.50.4) > >> /usr/local/bin/mpich-install/lib/libmpifort.12.dylib (compatibility > >> version 14.0.0, current version 14.7.0) > >> /usr/local/bin/mpich-install/lib/libmpi.12.dylib (compatibility version > >> 14.0.0, current version 14.7.0) > >> /usr/local/bin/mpich-install/lib/libpmpi.12.dylib (compatibility version > >> 14.0.0, current version 14.7.0) > >> > >> To get around this, you can replace the dynamic link with a static > >> address > >> using install_name_tool command as below. For my setup this looks like > >> the > >> following: > >> > >> install_name_tool -change "@rpath@rpath/libmkl_scalapack_ilp64.dylib" > " > >> /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/ > >> lib/libmkl_scalapack_lp64.dylib" </Path/To/Binary> > >> > >> Note that the above command is a one-liner. Repeat this until all of > >> the @rpath/..../ are gone. > >> > >> Will DeBenedetti > >> Cornell University > >> > >> > >> > >> On Sat, Sep 21, 2019 at 9:14 PM ??? <r03223...@ntu.edu.tw> wrote: > >> > >>> Hi Will, > >>> > >>> Thanks for reaching out to me. But, I am really new to QE and do not > >>> understand what files I need to identify. Can you give me more details? > >>> > >>> Also, I leave the message, as follows, I got in the end of the ?'make > >>> all'' command. Hope this can help identify the problem. > >>> > >>> ld: warning: text-based stub file > >>> > /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory.tbd > >>> and library file > >>> > /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory > >>> are out of sync. Falling back to library file for linking. > >>> ld: warning: text-based stub file > >>> /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS.tbd > >>> and > >>> library file > >>> /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS are > >>> out of > >>> sync. Falling back to library file for linking. > >>> ( cd ../../bin ; ln -fs ../GWW/bse/bse_main.x . ) > >>> > >>> Thank you for considering my request. > >>> Sheng-Chih Lin > >>> r03223...@ntu.edu.tw > >>> > >>> > >>> > >>> > >>> Will DeBenedetti <wj...@cornell.edu> ? 2019?9?21? ??10:28 ??? > >>> > >>> Path/To/QE/Binaries > >>> > >>> > >>> _______________________________________________ > >>> Quantum ESPRESSO is supported by MaX > >>> (www.max-centre.eu/quantum-espresso) > >>> users mailing list users@lists.quantum-espresso.org > >>> https://lists.quantum-espresso.org/mailman/listinfo/users > >> > >> _______________________________________________ > >> Quantum ESPRESSO is supported by MaX > >> (www.max-centre.eu/quantum-espresso) > >> users mailing list users@lists.quantum-espresso.org > >> https://lists.quantum-espresso.org/mailman/listinfo/users > >> > >> > >> _______________________________________________ > >> Quantum ESPRESSO is supported by MaX > >> (www.max-centre.eu/quantum-espresso) > >> users mailing list users@lists.quantum-espresso.org > >> https://lists.quantum-espresso.org/mailman/listinfo/users > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190922/893a30ed/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 3 > > Date: Sun, 22 Sep 2019 16:59:04 +0200 > > From: Lorenzo Paulatto <paul...@gmail.com> > > To: users@lists.quantum-espresso.org > > Subject: Re: [QE-users] Fw: Can we do LDA+U with SOC for FM/AFM > > systems in QE > > Message-ID: <5b9787f6-49e2-56f6-de2a-85080cc5f...@gmail.com> > > Content-Type: text/plain; charset=utf-8; format=flowed > > > >> > >> I wanted to structure optimization for my system considering both Hub-U > >> and SOC. But I am getting the following error with vc-relax. > >> > >> Error in routine force_hub (1): > >> ????? forces in full LDA+U scheme are not yet implemented > > > > Dear David, > > if it is not implemented, you have to implement it, or pay someone to do > > it. > > > > Regarding the relax converging in one step, you provide no proof that > > you are not starting from the optimum structure already, and you're not > > providing the example to test it. If the problem is that you are > > doubtful, try to run with a different geometry, and see if it moves from > > there. > > > > kind regards > > > > > > -- > > Lorenzo Paulatto - Paris > > > > > > ------------------------------ > > > > Message: 4 > > Date: Sun, 22 Sep 2019 23:14:27 +0800(CST) > > From: "zhy" <zh...@mails.jlu.edu.cn> > > To: "qe-users" <users@lists.quantum-espresso.org> > > Subject: [QE-users] QE+Wannier90 > > Message-ID: <46brb81vgdzl...@mails.jlu.edu.cn> > > Content-Type: text/plain; charset="us-ascii" > > > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190922/2961c4a1/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 5 > > Date: Sun, 22 Sep 2019 16:41:31 +0100 > > From: TERSOO ATSUE <tatsue1...@stu.ui.edu.ng> > > To: zhy <zh...@mails.jlu.edu.cn>, Quantum ESPRESSO users Forum > > <users@lists.quantum-espresso.org> > > Subject: Re: [QE-users] QE+Wannier90 > > Message-ID: > > < > ca+mgmuf1raw5btc6rmab6nn0r4ku14wmlgheekwewrykhr-...@mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Your pw2wan.in file should have the same outdir as that of scf and nscf > > calculations. i.e. './' instead of './scf/' > > > > Atsue Tersoo > > PhD student, Department of Physics, University of Ibadan, Nigeria. > > > > On Sun, Sep 22, 2019, 4:12 PM zhy <zh...@mails.jlu.edu.cn> wrote: > > > >> Dear all, > >> I'm trying to calculate the on-site energy and hopping integral with > >> QE+wannier90 codes. I follow the example in PP/WAN90 folder. I can > >> successfully obtain the results of scf/nscf. But When I ran pw2wannier.x > >> , > >> I have the following error message: > >> > >> Error in routine pw_readfile (1): > >> error opening xml data file > >> > >> I don't know how to deal with this problem ,here are my input files: > >> SCF > >> &control > >> calculation = 'scf', > >> prefix='FonC' > >> restart_mode = 'from_scratch' > >> pseudo_dir = './', > >> outdir = './', > >> / > >> &system > >> ibrav=0, > >> nat = 32, > >> ntyp = 3, > >> ecutwfc = 60 > >> / > >> &electrons > >> diagonalization = 'david' > >> mixing_mode = 'plain' > >> mixing_beta = 0.7 > >> conv_thr = 1.0d-14 > >> / > >> ATOMIC_SPECIES > >> C 12.001 C.pbe-n-kjpaw_psl.1.0.0.UPF > >> H 1.008 H.pbe-kjpaw_psl.1.0.0.UPF > >> F 18.998 F.pbe-n-kjpaw_psl.1.0.0.UPF > >> CELL_PARAMETERS (angstrom) > >> 48.000000000 0.000000000 0.000000000 > >> 0.000000000 20.000000000 0.000000000 > >> 0.000000000 0.000000000 4.293155000 > >> ATOMIC_POSITIONS (angstrom) > >> C 16.632525610 9.569503948 2.927891272 > >> C 16.545259875 9.629176757 1.470576513 > >> C 17.850691078 9.585423811 0.754490962 > >> C 17.827635231 9.570337507 3.615716314 > >> C 19.080218182 9.576439365 2.891004118 > >> C 19.062192466 9.584694603 1.456081864 > >> C 20.305559560 9.582090847 0.735285100 > >> C 20.298541126 9.582092110 3.593817815 > >> C 21.539490394 9.583742823 2.873080392 > >> C 21.532237250 9.581402390 1.442075124 > >> C 22.769711337 9.581834464 0.721157484 > >> C 22.765824718 9.583198123 3.582568309 > >> C 24.002537847 9.582700549 2.862585777 > >> C 23.997462153 9.582700549 1.430569373 > >> C 25.234175282 9.583198123 0.710586841 > >> C 25.230288663 9.581834464 3.571997666 > >> C 26.467762750 9.581402390 2.851080026 > >> C 26.460509606 9.583742823 1.420074758 > >> C 27.701458874 9.582092110 0.699337335 > >> C 27.694440440 9.582090847 3.557870050 > >> C 28.937807534 9.584694603 2.837073286 > >> C 28.919781818 9.576439365 1.402151032 > >> C 30.172364768 9.570337507 0.677438836 > >> C 30.149308922 9.585423811 3.538664188 > >> C 31.454740125 9.629176757 2.822578637 > >> C 31.367474391 9.569503948 1.365263878 > >> H 15.683581257 9.629398010 3.455819108 > >> H 15.845674242 8.871191822 1.073707384 > >> H 32.154325758 8.871191822 3.219447766 > >> H 32.316418743 9.629398010 0.837336042 > >> F 32.129822432 10.893202999 3.147752934 > >> F 15.870177298 10.893202999 1.145402526 > >> K_POINTS AUTOMATIC > >> 1 1 11 0 0 0 > >> > >> NSCF > >> &CONTROL > >> prefix = 'FonC' > >> calculation = 'nscf' > >> pseudo_dir = './' > >> outdir = './' > >> / > >> &SYSTEM > >> ibrav = 0 > >> ntyp = 3 > >> nat = 32 > >> ecutwfc = 80 > >> / > >> &ELECTRONS > >> conv_thr = 1.0d-10 > >> / > >> ATOMIC_SPECIES > >> C 12.001 C.pbe-n-kjpaw_psl.1.0.0.UPF > >> H 1.008 H.pbe-kjpaw_psl.1.0.0.UPF > >> F 18.998 F.pbe-n-kjpaw_psl.1.0.0.UPF > >> CELL_PARAMETERS (angstrom) > >> 48.000000000 0.000000000 0.000000000 > >> 0.000000000 20.000000000 0.000000000 > >> 0.000000000 0.000000000 4.293155000 > >> ATOMIC_POSITIONS (angstrom) > >> C 16.632525610 9.569503948 2.927891272 > >> C 16.545259875 9.629176757 1.470576513 > >> C 17.850691078 9.585423811 0.754490962 > >> C 17.827635231 9.570337507 3.615716314 > >> C 19.080218182 9.576439365 2.891004118 > >> C 19.062192466 9.584694603 1.456081864 > >> C 20.305559560 9.582090847 0.735285100 > >> C 20.298541126 9.582092110 3.593817815 > >> C 21.539490394 9.583742823 2.873080392 > >> C 21.532237250 9.581402390 1.442075124 > >> C 22.769711337 9.581834464 0.721157484 > >> C 22.765824718 9.583198123 3.582568309 > >> C 24.002537847 9.582700549 2.862585777 > >> C 23.997462153 9.582700549 1.430569373 > >> C 25.234175282 9.583198123 0.710586841 > >> C 25.230288663 9.581834464 3.571997666 > >> C 26.467762750 9.581402390 2.851080026 > >> C 26.460509606 9.583742823 1.420074758 > >> C 27.701458874 9.582092110 0.699337335 > >> C 27.694440440 9.582090847 3.557870050 > >> C 28.937807534 9.584694603 2.837073286 > >> C 28.919781818 9.576439365 1.402151032 > >> C 30.172364768 9.570337507 0.677438836 > >> C 30.149308922 9.585423811 3.538664188 > >> C 31.454740125 9.629176757 2.822578637 > >> C 31.367474391 9.569503948 1.365263878 > >> H 15.683581257 9.629398010 3.455819108 > >> H 15.845674242 8.871191822 1.073707384 > >> H 32.154325758 8.871191822 3.219447766 > >> H 32.316418743 9.629398010 0.837336042 > >> F 32.129822432 10.893202999 3.147752934 > >> F 15.870177298 10.893202999 1.145402526 > >> K_POINTS {crystal_b} > >> 50 > >> 0.0000 0.0000 0.0000 0.0200 > >> 0.0000 0.0000 0.0200 0.0200 > >> 0.0000 0.0000 0.0400 0.0200 > >> 0.0000 0.0000 0.0600 0.0200 > >> 0.0000 0.0000 0.0800 0.0200 > >> 0.0000 0.0000 0.1000 0.0200 > >> 0.0000 0.0000 0.1200 0.0200 > >> 0.0000 0.0000 0.1400 0.0200 > >> 0.0000 0.0000 0.1600 0.0200 > >> 0.0000 0.0000 0.1800 0.0200 > >> 0.0000 0.0000 0.2000 0.0200 > >> 0.0000 0.0000 0.2200 0.0200 > >> 0.0000 0.0000 0.2400 0.0200 > >> 0.0000 0.0000 0.2600 0.0200 > >> 0.0000 0.0000 0.2800 0.0200 > >> 0.0000 0.0000 0.3000 0.0200 > >> 0.0000 0.0000 0.3200 0.0200 > >> 0.0000 0.0000 0.3400 0.0200 > >> 0.0000 0.0000 0.3600 0.0200 > >> 0.0000 0.0000 0.3800 0.0200 > >> 0.0000 0.0000 0.4000 0.0200 > >> 0.0000 0.0000 0.4200 0.0200 > >> 0.0000 0.0000 0.4400 0.0200 > >> 0.0000 0.0000 0.4600 0.0200 > >> 0.0000 0.0000 0.4800 0.0200 > >> 0.0000 0.0000 0.5000 0.0200 > >> 0.0000 0.0000 0.5200 0.0200 > >> 0.0000 0.0000 0.5400 0.0200 > >> 0.0000 0.0000 0.5600 0.0200 > >> 0.0000 0.0000 0.5800 0.0200 > >> 0.0000 0.0000 0.6000 0.0200 > >> 0.0000 0.0000 0.6200 0.0200 > >> 0.0000 0.0000 0.6400 0.0200 > >> 0.0000 0.0000 0.6600 0.0200 > >> 0.0000 0.0000 0.6800 0.0200 > >> 0.0000 0.0000 0.7000 0.0200 > >> 0.0000 0.0000 0.7200 0.0200 > >> 0.0000 0.0000 0.7400 0.0200 > >> 0.0000 0.0000 0.7600 0.0200 > >> 0.0000 0.0000 0.7800 0.0200 > >> 0.0000 0.0000 0.8000 0.0200 > >> 0.0000 0.0000 0.8200 0.0200 > >> 0.0000 0.0000 0.8400 0.0200 > >> 0.0000 0.0000 0.8600 0.0200 > >> 0.0000 0.0000 0.8800 0.0200 > >> 0.0000 0.0000 0.9000 0.0200 > >> 0.0000 0.0000 0.9200 0.0200 > >> 0.0000 0.0000 0.9400 0.0200 > >> 0.0000 0.0000 0.9600 0.0200 > >> 0.0000 0.0000 0.9800 0.0200 > >> > >> PW2WAN.in > >> &inputpp > >> outdir = './scf/' > >> prefix = 'FonC' > >> seedname = 'FonC.sa' > >> spin_component = 'none' > >> write_mmn = .true. > >> write_amn = .true. > >> write_unk = .false. > >> wan_mode = 'standalone' > >> / > >> > >> > >> _______________________________________________ > >> Quantum ESPRESSO is supported by MaX > >> (www.max-centre.eu/quantum-espresso) > >> users mailing list users@lists.quantum-espresso.org > >> https://lists.quantum-espresso.org/mailman/listinfo/users > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190922/251969f7/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 6 > > Date: Mon, 23 Sep 2019 09:34:58 +0800(CST) > > From: "zhy" <zh...@mails.jlu.edu.cn> > > To: "TERSOO ATSUE " > > <tatsue1...@stu.ui.edu.ng>,"Quantum ESPRESSO > users > > Forum" <users@lists.quantum-espresso.org> > > Subject: Re: [QE-users] QE+Wannier90 > > Message-ID: <46c6m62zlszl...@mails.jlu.edu.cn> > > Content-Type: text/plain; charset="us-ascii" > > > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190923/e27d0189/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 7 > > Date: Mon, 23 Sep 2019 10:34:17 +0900 > > From: Christoph Wolf <wolf.christoph@qns.science> > > To: Quantum Espresso users Forum <users@lists.quantum-espresso.org> > > Subject: Re: [QE-users] Convergence of calculating Hubbard parameters > > from DFPT > > Message-ID: > > < > camc_g_76sxzgy7fjnywa_vr1z6ojxpumzc2nlo4jvd+zxfz...@mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear Gaoxue, > > > > I cannot see the attached output but I was wondering what range of alpha > > you were using? In my experience small alpha ranges give very reliable > > linear responses and they do not change the resulting U by more than the > > uncertainty from inversion. > > > > HTH! > > Chris > > > > -- > > Postdoctoral Researcher > > Center for Quantum Nanoscience, Institute for Basic Science > > Ewha Womans University, Seoul, South Korea > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190923/2e8e181d/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 8 > > Date: Mon, 23 Sep 2019 10:14:12 +0800 > > From: ??? <r03223...@ntu.edu.tw> > > To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org> > > Subject: Re: [QE-users] Error during compilation in the step of make > > all command > > Message-ID: <93e029c2-7122-4e94-9bed-74653e176...@ntu.edu.tw> > > Content-Type: text/plain; charset="utf-8" > > > > Dear Will, > > > > Thanks so much for your help. Using the virtual environment by anaconda, > > now I can run the overall test system smoothly, despite some failed > tests. > > > > Thank you for considering my request. > > Sheng-Chih Lin > > r03223...@ntu.edu.tw > > > > > > > > > >> Will DeBenedetti <wj...@cornell.edu> ? 2019?9?22? ??8:11 ??? > >> > >> Hi Sheng-Chinh, > >> > >> I also recall having this error at some point. Usually 99.99% of these > >> errors have to do with PATH variables being incorrectly set. For a > >> number of reasons, I do not use the Python that ships with Macs, I > >> instead use virtual environments using Anaconda (not an endorsement, > >> just a much painless way of using software that Apple will soon > >> deprecate). I was able to get the test suite running by creating a > >> virtual environment using Python 2.7.something and activating this > >> environment using condo activate name_of_environment > >> > >> As per the documentation you will to run make run-tests-foo, then the > >> tests will run serially or in parallel. Keep in mind only PW, CP, PH, > >> and EPW binaries are supported. Make sure you have statically lined > >> these four binaries as per my previous message and verify using otool -L > >> otherwise the tests will crash. I have a 4-core processor and the tests > >> took quite some time running in parallel on the Intel compiler suite. > >> Running on gFortran will be slower. > >> > >> Will DeBenedetti > >> > >> > >> > >> On Sun, Sep 22, 2019 at 2:03 AM ??? <r03223...@ntu.edu.tw > >> <mailto:r03223...@ntu.edu.tw>> wrote: > >> Hi Will, > >> > >> Thanks so much for the info. I?ve checked libraries of pw.x and it seems > >> good for them with static addresses. So, I carried out calculations, > >> such as scf and vc_relax, and they worked smoothly. Thus, I think the > >> absence of messages I mentioned in previous e-mail was caused by some of > >> the bins having dynamic addresses. And it could be fixed by replacing > >> their addresses. > >> > >> Besides, when I ran test files (make run-tests-pw-serial) in the > >> file--test-suite, the system showed the message below. > >> > >> env: python2: No such file or directory > >> make: *** [run-tests-pw-serial] Error 127 > >> > >> I?ve tried several ways to address it. I checked the installation of > >> python2 and its version was 2.7.16. Besides, I also made a symbolic link > >> to direct the system to the location of python 2.7 using the command as > >> follows, but still no joy. Have you ever experienced the situation? > >> > >> ln -s /opt/local/bin/python2.7 > >> > /Users/hayashikiyoshisatoshi/Desktop/q-e-qe-6.4.1/q-e-qe-6.4.1/test-suite/python2 > >> > >> > >> Thank you for considering my request. > >> Sheng-Chih Lin > >> r03223...@ntu.edu.tw <mailto:r03223...@ntu.edu.tw> > >> > >> > >> > >> > >>> Will DeBenedetti <wj...@cornell.edu <mailto:wj...@cornell.edu>> ? > >>> 2019?9?22? ??9:52 ??? > >>> > >>> Hi Sheng-Chinh, > >>> > >>> Have you looked to see if you have made QE binaries? These will be in > >>> the /qe/bin On my machine these are located here: /Users/wjid/qe/bin > >>> > >>> Using ls shows the following after running `make all`: > >>> > >>> wjid$ ls > >>> alpha2f.x neb.x > >>> average.x open_grid.x > >>> band.eps path_interpolation.x > >>> bands.x ph.x > >>> bse_main.x phcg.x > >>> cell2ibrav.x plan_avg.x > >>> cp.x plotband.x > >>> dist.x plotproj.x > >>> dos.x plotrho.x > >>> dynmat.x pmw.x > >>> epa.x pp.x > >>> epsilon.x ppacf.x > >>> ev.x projwfc.x > >>> fd.x pw.x > >>> fd_ef.x pw2bgw.x > >>> fd_ifc.x pw2critic.x > >>> fermi_proj.x pw2gw.x > >>> fermi_velocity.x pw2wannier90.x > >>> fqha.x pw4gww.x > >>> fs.x pwcond.x > >>> generate_rVV10_kernel_table.x pwi2xsf.x > >>> generate_vdW_kernel_table.x q2qstar.x > >>> gww.x q2r.x > >>> gww_fit.x q2trans.x > >>> head.x q2trans_fd.x > >>> hp.x simple.x > >>> ibrav2cell.x simple_bse.x > >>> initial_state.x simple_ip.x > >>> iotk spectra_correction.x > >>> iotk.x sumpdos.x > >>> iotk_print_kinds.x turbo_davidson.x > >>> kpoints.x turbo_eels.x > >>> lambda.x turbo_lanczos.x > >>> ld1.x turbo_spectrum.x > >>> manycp.x wannier_ham.x > >>> manypw.x wannier_plot.x > >>> matdyn.x wfck2r.x > >>> molecularnexafs.x wfdd.x > >>> molecularpdos.x xspectra.x > >>> > >>> Then you should verify that your binaries are linked properly by using > >>> otool, which is the linux equivalent of ldd. > >>> > >>> The command to show which shared libraries are linked with this binary > >>> use otool -L (in terminal) > >>> > >>> wjid$ otool -L pw.x > >>> pw.x: > >>> > > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_scalapack_lp64.dylib > >>> (compatibility version 0.0.0, current version 0.0.0) > >>> > > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_intel_lp64.dylib > >>> (compatibility version 0.0.0, current version 0.0.0) > >>> > > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_intel_thread.dylib > >>> (compatibility version 0.0.0, current version 0.0.0) > >>> > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_core.dylib > >>> (compatibility version 0.0.0, current version 0.0.0) > >>> > > /opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_blacs_mpich_lp64.dylib > >>> (compatibility version 0.0.0, current version 0.0.0) > >>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > >>> version 1252.50.4) > >>> /usr/local/bin/mpich-install/lib/libmpifort.12.dylib (compatibility > >>> version 14.0.0, current version 14.7.0) > >>> /usr/local/bin/mpich-install/lib/libmpi.12.dylib (compatibility > >>> version 14.0.0, current version 14.7.0) > >>> /usr/local/bin/mpich-install/lib/libpmpi.12.dylib (compatibility > >>> version 14.0.0, current version 14.7.0) > >>> > >>> The output shows which MKL and mpich libraries are linked to the pw.x > >>> binary. > >>> > >>> Like I said in my previous email, if you have system integrity > >>> protection enabled (it is by default) linking to dynamic libraries is > >>> disabled by default. These binaries will look like plotrho.x as below: > >>> > >>> wjid$ otool -L plotrho.x > >>> plotrho.x: > >>> @rpath/libmkl_scalapack_ilp64.dylib (compatibility version 0.0.0, > >>> current version 0.0.0) > >>> @rpath/libmkl_intel_ilp64.dylib (compatibility version 0.0.0, > current > >>> version 0.0.0) > >>> @rpath/libmkl_intel_thread.dylib (compatibility version 0.0.0, > current > >>> version 0.0.0) > >>> @rpath/libmkl_core.dylib (compatibility version 0.0.0, current > version > >>> 0.0.0) > >>> @rpath/libmkl_blacs_mpich_ilp64.dylib (compatibility version 0.0.0, > >>> current version 0.0.0) > >>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > >>> version 1252.50.4) > >>> /usr/local/bin/mpich-install/lib/libmpifort.12.dylib (compatibility > >>> version 14.0.0, current version 14.7.0) > >>> /usr/local/bin/mpich-install/lib/libmpi.12.dylib (compatibility > >>> version 14.0.0, current version 14.7.0) > >>> /usr/local/bin/mpich-install/lib/libpmpi.12.dylib (compatibility > >>> version 14.0.0, current version 14.7.0) > >>> > >>> To get around this, you can replace the dynamic link with a static > >>> address using install_name_tool command as below. For my setup this > >>> looks like the following: > >>> > >>> install_name_tool -change "@rpath@rpath/libmkl_scalapack_ilp64.dylib" > >>> > "/opt/intel/compilers_and_libraries_2019.4.233/mac/mkl/lib/libmkl_scalapack_lp64.dylib" > >>> </Path/To/Binary> > >>> > >>> Note that the above command is a one-liner. Repeat this until all of > >>> the @rpath/..../ are gone. > >>> > >>> Will DeBenedetti > >>> Cornell University > >>> > >>> > >>> > >>> On Sat, Sep 21, 2019 at 9:14 PM ??? <r03223...@ntu.edu.tw > >>> <mailto:r03223...@ntu.edu.tw>> wrote: > >>> Hi Will, > >>> > >>> Thanks for reaching out to me. But, I am really new to QE and do not > >>> understand what files I need to identify. Can you give me more details? > >>> > >>> Also, I leave the message, as follows, I got in the end of the ?'make > >>> all'' command. Hope this can help identify the problem. > >>> > >>> ld: warning: text-based stub file > >>> > /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory.tbd > >>> and library file > >>> > /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory > >>> are out of sync. Falling back to library file for linking. > >>> ld: warning: text-based stub file > >>> /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS.tbd > >>> and library file > >>> /System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS are > >>> out of sync. Falling back to library file for linking. > >>> ( cd ../../bin ; ln -fs ../GWW/bse/bse_main.x . ) > >>> > >>> Thank you for considering my request. > >>> Sheng-Chih Lin > >>> r03223...@ntu.edu.tw <mailto:r03223...@ntu.edu.tw> > >>> > >>> > >>> > >>> > >>>> Will DeBenedetti <wj...@cornell.edu <mailto:wj...@cornell.edu>> ? > >>>> 2019?9?21? ??10:28 ??? > >>>> > >>>> Path/To/QE/Binaries > >>> > >>> _______________________________________________ > >>> Quantum ESPRESSO is supported by MaX > >>> (www.max-centre.eu/quantum-espresso > >>> <http://www.max-centre.eu/quantum-espresso>) > >>> users mailing list users@lists.quantum-espresso.org > >>> <mailto:users@lists.quantum-espresso.org> > >>> https://lists.quantum-espresso.org/mailman/listinfo/users > >>> <https://lists.quantum-espresso.org/mailman/listinfo/users > >_______________________________________________ > >>> Quantum ESPRESSO is supported by MaX > >>> (www.max-centre.eu/quantum-espresso > >>> <http://www.max-centre.eu/quantum-espresso>) > >>> users mailing list users@lists.quantum-espresso.org > >>> <mailto:users@lists.quantum-espresso.org> > >>> https://lists.quantum-espresso.org/mailman/listinfo/users > >>> <https://lists.quantum-espresso.org/mailman/listinfo/users> > >> _______________________________________________ > >> Quantum ESPRESSO is supported by MaX ( > www.max-centre.eu/quantum-espresso > >> <http://www.max-centre.eu/quantum-espresso>) > >> users mailing list users@lists.quantum-espresso.org > >> <mailto:users@lists.quantum-espresso.org> > >> https://lists.quantum-espresso.org/mailman/listinfo/users > >> <https://lists.quantum-espresso.org/mailman/listinfo/users > >_______________________________________________ > >> Quantum ESPRESSO is supported by MaX > >> (www.max-centre.eu/quantum-espresso) > >> users mailing list users@lists.quantum-espresso.org > >> https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190923/1a5a4cd4/attachment-0001.html > > > > > > ------------------------------ > > > > Subject: Digest Footer > > > > _______________________________________________ > > users mailing list > > users@lists.quantum-espresso.org > > https://lists.quantum-espresso.org/mailman/listinfo/users > > > > ------------------------------ > > > > End of users Digest, Vol 146, Issue 15 > > ************************************** > > > > > Mayuri Bora > Researh Scholar > Advanced Functional Material Laboratory > Tezpur University > Napaam > http://www.tezu.ernet.in/afml/ > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for > the individual named. 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_______________________________________________ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users