[QE-users] users Digest, Vol 146, Issue 15
Paolo Giannozzi
p.giannozzi at gmail.com
Mon Sep 23 22:05:54 CEST 2019
On Mon, Sep 23, 2019 at 12:24 PM Mayuri Bora <mayu219 at 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
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> >
> > 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 <dkca at yahoo.com>
> > To: Quantum ESPRESSO Users Forum <users at lists.quantum-espresso.org>
> > Subject: [QE-users] Fw: Can we do LDA+U with SOC for FM/AFM systems in
> > QE
> > Message-ID: <1117481007.4909079.1569153442589 at 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 <dkca at yahoo.com>To:
> > Quantum ESPRESSO Users Forum <users at 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...
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> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 22 Sep 2019 08:11:38 -0400
> > From: Will DeBenedetti <wjd74 at cornell.edu>
> > To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> > Subject: Re: [QE-users] Error during compilation in the step of make
> > all command
> > Message-ID:
> > <
> CANG7sujCjFvnb0hksbmRoZ3zXihrJ-ZtUCyQGju3ZJg4+J+D1A at 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 ??? <r03223130 at 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
> >> r03223130 at ntu.edu.tw
> >>
> >>
> >>
> >>
> >> Will DeBenedetti <wjd74 at 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 at 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 ??? <r03223130 at 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
> >>> r03223130 at ntu.edu.tw
> >>>
> >>>
> >>>
> >>>
> >>> Will DeBenedetti <wjd74 at 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 at 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 at 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 at lists.quantum-espresso.org
> >> https://lists.quantum-espresso.org/mailman/listinfo/users
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> >
> > ------------------------------
> >
> > Message: 3
> > Date: Sun, 22 Sep 2019 16:59:04 +0200
> > From: Lorenzo Paulatto <paulatz at gmail.com>
> > To: users at 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-85080cc5f53e at 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" <zhy09 at mails.jlu.edu.cn>
> > To: "qe-users" <users at lists.quantum-espresso.org>
> > Subject: [QE-users] QE+Wannier90
> > Message-ID: <46brb81VgdzLjcG at mails.jlu.edu.cn>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > An HTML attachment was scrubbed...
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> >
> > ------------------------------
> >
> > Message: 5
> > Date: Sun, 22 Sep 2019 16:41:31 +0100
> > From: TERSOO ATSUE <tatsue1203 at stu.ui.edu.ng>
> > To: zhy <zhy09 at mails.jlu.edu.cn>, Quantum ESPRESSO users Forum
> > <users at lists.quantum-espresso.org>
> > Subject: Re: [QE-users] QE+Wannier90
> > Message-ID:
> > <
> CA+mGmUF1Raw5btc6Rmab6nN0R4kU14wmLGHEEKWewRykHr-eYQ at 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 <zhy09 at 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 at lists.quantum-espresso.org
> >> https://lists.quantum-espresso.org/mailman/listinfo/users
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> > ------------------------------
> >
> > Message: 6
> > Date: Mon, 23 Sep 2019 09:34:58 +0800(CST)
> > From: "zhy" <zhy09 at mails.jlu.edu.cn>
> > To: "TERSOO ATSUE "
> > <tatsue1203 at stu.ui.edu.ng>,"Quantum ESPRESSO
> users
> > Forum" <users at lists.quantum-espresso.org>
> > Subject: Re: [QE-users] QE+Wannier90
> > Message-ID: <46c6M62ZLSzLjcN at mails.jlu.edu.cn>
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> >
> > ------------------------------
> >
> > Message: 7
> > Date: Mon, 23 Sep 2019 10:34:17 +0900
> > From: Christoph Wolf <wolf.christoph at qns.science>
> > To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> > Subject: Re: [QE-users] Convergence of calculating Hubbard parameters
> > from DFPT
> > Message-ID:
> > <
> CAMC_G_76sXZgY7FjnywA_vr1Z6OjxPuMZC2nLO4jVd+zXfzubw at 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
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> >
> > ------------------------------
> >
> > Message: 8
> > Date: Mon, 23 Sep 2019 10:14:12 +0800
> > From: ??? <r03223130 at ntu.edu.tw>
> > To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> > Subject: Re: [QE-users] Error during compilation in the step of make
> > all command
> > Message-ID: <93E029C2-7122-4E94-9BED-74653E176655 at 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
> > r03223130 at ntu.edu.tw
> >
> >
> >
> >
> >> Will DeBenedetti <wjd74 at 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 ??? <r03223130 at ntu.edu.tw
> >> <mailto:r03223130 at 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
> >> r03223130 at ntu.edu.tw <mailto:r03223130 at ntu.edu.tw>
> >>
> >>
> >>
> >>
> >>> Will DeBenedetti <wjd74 at cornell.edu <mailto:wjd74 at 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 at 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 ??? <r03223130 at ntu.edu.tw
> >>> <mailto:r03223130 at 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
> >>> r03223130 at ntu.edu.tw <mailto:r03223130 at ntu.edu.tw>
> >>>
> >>>
> >>>
> >>>
> >>>> Will DeBenedetti <wjd74 at cornell.edu <mailto:wjd74 at 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 at lists.quantum-espresso.org
> >>> <mailto:users at 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 at lists.quantum-espresso.org
> >>> <mailto:users at 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 at lists.quantum-espresso.org
> >> <mailto:users at 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 at lists.quantum-espresso.org
> >> https://lists.quantum-espresso.org/mailman/listinfo/users
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> > Subject: Digest Footer
> >
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> >
> > 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/
>
>
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