[QE-users] users Digest, Vol 146, Issue 15
Mayuri Bora
mayu219 at tezu.ernet.in
Mon Sep 23 12:24:12 CEST 2019
Hi all,
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-
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 at 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-request at lists.quantum-espresso.org
>
> You can reach the person managing the list at
> users-owner at 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 <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...
> 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 <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
> -------------- 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 <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...
> 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 <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
> -------------- 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" <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>
> 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 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
> -------------- 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: ??? <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
>
> -------------- 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 at 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. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message.
More information about the users
mailing list