[QE-users] users Digest, Vol 157, Issue 26
Anibal Thiago Bezerra
anibal.bezerra at unifal-mg.edu.br
Tue Sep 15 02:03:59 CEST 2020
Dear Quantum Espresso Users and Developers,
I'm using simple.x to get the dielectric function for a gold-Aluminium
alloy. With pure systems (Au and Al), I had no problems at all. For the
alloy, the supercell has 12 atoms and the calculation ran with the
parameters similar to the ones in the example. However, I got an
anisotropic response. I already evaluate such a structure using epsilon,
and it returned isotropic dielectric function as expected for a cubic
lattice (I had to use as many k-point as I could do the calculation - for a
coarse grid, epsilon.x returned anisotropic response too).
Therefore, I increased the k-point (from 20 20 20 to 30 30 30, and to 40 40
40) in the simple.x and simple_ip.x calculations, and I failed. Simple.x
finished the calculations with no errors (at least no error messages). The
simple_IP, however, was abruptly finished by the MPI manager with the
following message:
k-point block: 1093
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 13719 RUNNING AT quantum01= EXIT CODE: 9
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
Intel(R) MPI Library troubleshooting guide:
https://software.intel.com/node/561764
===================================================================================
After a kick search, I've found that such kind of error occurs when some
exception like division by zero happens. I've tried to tweak the
parameters, the number of bands (I increased the number of bands, I used
the same number of bands as the KS-states, I tried to use the non-local
commutator, I increased the parameter s, and also decreased it). Hence, I
had no success.
Do you have any hint? Any workaround?
Thanks a lot for your help!!
Best!
Anibal Bezerra
The Federal University of Alfenas
Alfenas
Brazil
Em sáb., 29 de ago. de 2020 às 07:01, <
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> Today's Topics:
>
> 1. Re: Wrong electron number in superposition of atomic charge
> densities (Colonna Nicola (PSI))
> 2. ?magnetization ? for slab surface (Omer Mutasim)
> 3. Regarding input file for hp.x (Mohad Abbasnejad)
> 4. Pseudo potential (tanmay chaki)
> 5. Re: Pseudo potential (Yuvam Bhateja)
> 6. Re: Pseudo potential (tanmay chaki)
> 7. Projection of e_g and t_2g in PDOS (Mohad Abbasnejad)
> 8. [SUSPECT ATTACHMENT REMOVED] Error in routine davcio (10)?
> (Vasilios Passias)
> 9. Re: [SUSPECT ATTACHMENT REMOVED] Error in routine davcio
> (10)? (Paolo Giannozzi)
> 10. Re: Error in routine davcio (10)? (Vasilios Passias)
> 11. Re: Problems running make pw (Aaron Celestian)
> 12. Re: Problems running make pw (Paolo Giannozzi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 28 Aug 2020 10:37:03 +0000
> From: "Colonna Nicola (PSI)" <nicola.colonna at psi.ch>
> To: "users at lists.quantum-espresso.org"
> <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Wrong electron number in superposition of
> atomic charge densities
> Message-ID: <87a9eb14f89648398ca62f35b78d2d99 at psi.ch>
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Paolo, dear Pietro,
>
>
> thank you for the quick answer and for the advise!
>
> I'm currently trying to re-generate the pseudo with the Vanderbilt code,
> but facing extra complications.
>
> I let you know if the fix works as soon as I'll be able to get the new
> atomic rho.
>
>
> Thanks again,
>
>
> Nicola
>
>
>
>
>
>
> -----------------------------------------------------
> PAUL SCHERRER INSTITUT
> Nicola S. Colonna
> WHGA/150
> CH-5232 Villigen-PSI
> ________________________________
> Da: users <users-bounces at lists.quantum-espresso.org> per conto di Pietro
> Davide Delugas <pdelugas at sissa.it>
> Inviato: venerd? 28 agosto 2020 09:22:18
> A: users at lists.quantum-espresso.org
> Oggetto: Re: [QE-users] Wrong electron number in superposition of atomic
> charge densities
>
> Ciao Nicola
>
> Quick and I don't know how dirty: generate a pseudo with 12 electrons
> copy the rhoatom section from there and copy it in place of the 11
> electrons rhoat in the pseudo you've been using.
> greetings - Pietro
>
>
> On 8/27/20 5:28 PM, Colonna Nicola (PSI) wrote:
>
> Dear QE experts,
>
>
> I recently perfomed a scf PBEsol calculation for Tb2Ti2O7 (attached the
> input file).
>
> I would like to plot the difference between the scf charge density and
> the superposition
>
> of atomic charge. For this purpose I used the PostProcessing tool
> (plut_num = 9).
>
>
> I expected the integral of this difference to be ~0 , but I found it to
> be 4. After a quick check
>
> I realized that the Ti pseudopotetial (GBRV-1.4,
> ti_pbesol_v1.4.uspp.F.UPF) was generated
>
> in an ionized configuration with just 1 electron (instead of 2 ) in the
> 3d orbital. Since there
>
> are 4 Ti in the primitive cell, I think this is the reason for the odd
> result described above.
>
>
> Indeed during the initialization of a scf calculation for an isolated Ti
> atom I got:
>
>
>
> Initial potential from superposition of free atoms
> Check: negative starting charge= -0.001319
> starting charge 10.99996, renormalised to 12.00000
>
>
> However this renormalization is not done in the PP, and in any case I do
> not think it would make sense there.
>
>
> That said, my feeling is that I cannot completely trust the charge
> density difference.
>
> Do you have any advise on how to solve this problem (beside changing
> pseudo)?
>
>
> Thank you in advance and best regards,
>
>
> Nicola Colonna
>
>
>
> -----------------------------------------------------
> PAUL SCHERRER INSTITUT
> Nicola S. Colonna
> WHGA/150
> CH-5232 Villigen-PSI
>
>
>
> _______________________________________________
> 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
>
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> ------------------------------
>
> Message: 2
> Date: Fri, 28 Aug 2020 12:01:06 +0000 (UTC)
> From: Omer Mutasim <omermutasim at ymail.com>
> To: Quantum ESPRESSO Users Forum <users at lists.quantum-espresso.org>
> Subject: [QE-users] ?magnetization ? for slab surface
> Message-ID: <719721452.308382.1598616066269 at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear allI?m doing slab calculations for NiP2 using QE.I have checked the
> magnetism for bulk, and the total magnetization converged to zero , so
> should i set ? total-magnetization =0? for further calculation of slab &
> complex system( molecule + slab ? ) or i should set ?nspin=1? ? Or i have
> to set ?starting_magnetization? for both Ni & P ? What are the suitable
> values ??
> I?m really confused about magnetism , ?why should i set ?starting-mag? for
> P atoms while it?s not magnetic ??I will be grateful if you resolve my
> confusion andtelling me the criteria for setting magnetism for such NiP2
> systems.
>
> Omer Elmutasim?Research Assistant?Center for Catalysis &
> separation?Khalifa University?
>
> Sent from Yahoo Mail for iPhone
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> ------------------------------
>
> Message: 3
> Date: Fri, 28 Aug 2020 20:02:46 +0430
> From: Mohad Abbasnejad <mohaddeseh.abbasnejad at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: [QE-users] Regarding input file for hp.x
> Message-ID:
> <CAApze+QnS2VZ7LCaS2hOAjbDN9QPv41xgqwO6Gx_i-cboUW=
> BQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello QE users
> There are two basic questions for preparing input files for hp.x
> 1. In the NiO examples in the HP folder, there are two Ni atoms, namely NI1
> and Ni2. Fortunately, hubbard parameters are obtained the same for both.
> But for my structure Ti1 and Ti2 and Ti3 have different u values. in all of
> the literature just one U is reported for the metallic element. Is it OK to
> report 3 different U values by linear response method or not?
>
> 2. Is it necessary to relax the structure before starting the calculation
> of U parameters by linear response? In fact, the obtained U values from
> relax calculation and without relaxation are totally different with each
> other.
>
> Any help would be appreciated.
>
> Regards,
> Mohaddeseh
> --
> ---------------------------------------------------------
> Mohaddeseh Abbasnejad,
> Assistant Professor of Physics,
> Faculty of Physics,
> Shahid Bahonar University of Kerman,
> Kerman, Iran
> P.O. Box 76169-133
> Tel: +98 34 31322199
> Fax: +98 34 33257434
> Cellphone: +98 917 731 7514
> E-Mail: mohaddeseh.abbasnejad at gmail.com
> Website: academicstaff.uk.ac.ir/moabbasnejad
> ---------------------------------------------------------
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> Message: 4
> Date: Fri, 28 Aug 2020 22:37:37 +0530
> From: tanmay chaki <tanmaychaki at gmail.com>
> To: users at lists.quantum-espresso.org
> Subject: [QE-users] Pseudo potential
> Message-ID:
> <
> CABF7XsegDx+fSvXUrsOV2-VmenMPkgGtZ9QU5ka7D8x7wE2tBw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello QE users,
> Is there any specific Pseudo potential for spin polarized calculation?
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> ------------------------------
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> Message: 5
> Date: Fri, 28 Aug 2020 22:43:21 +0530
> From: Yuvam Bhateja <yuvamb16 at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Pseudo potential
> Message-ID:
> <
> CADw1Vdz+zP0XbZUA7yMEQsG6htERmUmp+2-FafKzT16MTGVHxA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hey,
>
> As per my knowledge, there's no specific pseudopotential for spin
> calculation.
>
> You need to use commands like nspin and starting_magnetization in order to
> start your spin calculation.
>
> Your choice of XC Functional can affect the results in your spin
> calculation.
>
> Let me know if it helps.
>
> Regards
> Yuvam Bhateja
>
> On Fri, 28 Aug 2020, 10:38 pm tanmay chaki, <tanmaychaki at gmail.com> wrote:
>
> > Hello QE users,
> > Is there any specific Pseudo potential for spin polarized calculation?
> > _______________________________________________
> > 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: Fri, 28 Aug 2020 23:16:33 +0530
> From: tanmay chaki <tanmaychaki at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Pseudo potential
> Message-ID:
> <CABF7XscJLgevg6i8=uNqura=
> qZ7ETFkOSsC7vnJs2o5AwVTpnw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Thanks for your suggestions
>
> On Fri, 28 Aug, 2020, 10:43 pm Yuvam Bhateja, <yuvamb16 at gmail.com> wrote:
>
> > Hey,
> >
> > As per my knowledge, there's no specific pseudopotential for spin
> > calculation.
> >
> > You need to use commands like nspin and starting_magnetization in order
> to
> > start your spin calculation.
> >
> > Your choice of XC Functional can affect the results in your spin
> > calculation.
> >
> > Let me know if it helps.
> >
> > Regards
> > Yuvam Bhateja
> >
> > On Fri, 28 Aug 2020, 10:38 pm tanmay chaki, <tanmaychaki at gmail.com>
> wrote:
> >
> >> Hello QE users,
> >> Is there any specific Pseudo potential for spin polarized calculation?
> >> _______________________________________________
> >> 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: 7
> Date: Fri, 28 Aug 2020 23:11:05 +0430
> From: Mohad Abbasnejad <mohaddeseh.abbasnejad at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: [QE-users] Projection of e_g and t_2g in PDOS
> Message-ID:
> <
> CAApze+RrdPAOsE0bad60GmFuKtS4LJMcyNWHez4VDTiQf+uEJA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello QE users
> I want to plot e_g and t_2g sub-bands of d orbitals in PDOS.
> Can someone help me with this?
> any help would be appreciated.
>
> Thanks
> Mohaddeseh
> --
> ---------------------------------------------------------
> Mohaddeseh Abbasnejad,
> Assistant Professor of Physics,
> Faculty of Physics,
> Shahid Bahonar University of Kerman,
> Kerman, Iran
> P.O. Box 76169-133
> Tel: +98 34 31322199
> Fax: +98 34 33257434
> Cellphone: +98 917 731 7514
> E-Mail: mohaddeseh.abbasnejad at gmail.com
> Website: academicstaff.uk.ac.ir/moabbasnejad
> ---------------------------------------------------------
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> ------------------------------
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> Message: 8
> Date: Fri, 28 Aug 2020 14:40:04 -0500
> From: Vasilios Passias <billy.passias at gmail.com>
> To: users at lists.quantum-espresso.org
> Subject: [QE-users] [SUSPECT ATTACHMENT REMOVED] Error in routine
> davcio (10)?
> Message-ID:
> <CA+BV=ckm6LSD=
> q-g5uVFgyyLXUARvp0oFQxDTAPWdKqBpDKH9A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello fellow quantum espresso users.
>
> Recently, I tried running a relaxation calculation. The convergence
> thresholds on the total energy and total force are such that I need to run
> this relaxation calculation multiple times. The first relaxation run, with
> restart_mode = 'from_scratch' , ran fine for the max_time I had set.
>
> Then I set restart_mode = 'restart' and I ran this relaxation calculation
> again, expecting it to continue where it left off.
>
> Instead I got the following error: error in routine davcio (10): error
> while reading from file.
>
> All of the files associated with this error are in the same folder as my
> input and output files. Why is this happening? Should I just re-run this
> calculation?
>
> I have my input, output, job submission, and crash files attached in this
> email.
>
>
> Thank you for your time and input.
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> ------------------------------
>
> Message: 9
> Date: Fri, 28 Aug 2020 23:10:52 +0200
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] [SUSPECT ATTACHMENT REMOVED] Error in routine
> davcio (10)?
> Message-ID:
> <
> CAPMgbCumkS729QRZuh1dJeZMnd3d-JNMQ_rYf3DBi1wPz+zLWA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Fri, Aug 28, 2020 at 9:40 PM Vasilios Passias <billy.passias at gmail.com>
> wrote:
>
> I have my input, output, job submission, and crash files attached in this
> > email.
> >
>
> you have, but the software of the mailing list didn't like them
>
> Paolo
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
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> ------------------------------
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> Message: 10
> Date: Fri, 28 Aug 2020 16:21:54 -0500
> From: Vasilios Passias <billy.passias at gmail.com>
> To: users at lists.quantum-espresso.org
> Subject: Re: [QE-users] Error in routine davcio (10)?
> Message-ID:
> <CA+BV=
> cnmJ02S+VNHg-ShXeC4sju15EzyJ7UqQyGPevxyMx59ig at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> There was a problem with the files I attached in my previous email, so I
> will input them in here:
>
> My input file:
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> *&CONTROL calculation = 'relax', restart_mode = 'restart', pseudo_dir =
> '/home/passias2/qe-6.3/pseudo/' etot_conv_thr = 1.0d-4, forc_conv_thr =
> 1.0d-3, max_seconds = 2.196d+5/&SYSTEM ibrav = 0, nat = 56, ntyp =
> 2, occupations = 'smearing', smearing = 'marzari-vanderbilt', degauss =
> 1.0d-3, ecutwfc = 25.0, ecutrho = 100.0, noncolin = .true. lspinorb =
> .true./&ELECTRONS conv_thr = 1.0d-8, mixing_beta = 0.1/&IONSion_dynamics =
> 'bfgs'/ATOMIC_SPECIES Bi 208.980 Bi.rel-pbe-dn-kjpaw_psl.1.0.0.UPF Na
> 22.989 Na.rel-pbe-spn-kjpaw_psl.0.2.UPFK_POINTS automatic8 8 1 0 0
> 0CELL_PARAMETERS angstrom5.44800000000000 0.00000000000000
> 0.000000000000000.00000000000000 9.65500000000000
> 0.000000000000000.00000000000000 0.00000000000000
> 51.45404266545082ATOMIC_POSITIONS angstromNa 0.0000000000 2.4137500000
> 10.0000000000 Na 0.0000000000 7.2412500000 10.0000000000 Na 2.7240000000
> 5.6288650000 11.5727021333 Na 0.0000000000 0.8013650000 13.1454042665 Na
> 0.0000000000 4.0261350000 13.1454042665 Na 2.7240000000 8.8536350000
> 11.5727021333 Bi 2.7240000000 2.4137500000 11.5727021333 Bi 0.0000000000
> 7.2412500000 13.1454042665 Na 2.7240000000 2.4137500000 14.7181063998 Na
> 2.7240000000 7.2412500000 14.7181063998 Na 0.0000000000 5.6288650000
> 16.2908085331 Na 2.7240000000 0.8013650000 17.8635106664 Na 2.7240000000
> 4.0261350000 17.8635106664 Na 0.0000000000 8.8536350000 16.2908085331 Bi
> 0.0000000000 2.4137500000 16.2908085331 Bi 2.7240000000 7.2412500000
> 17.8635106664 Na 0.0000000000 2.4137500000 19.4362127996 Na 0.0000000000
> 7.2412500000 19.4362127996 Na 2.7240000000 5.6288650000 21.0089149329 Na
> 0.0000000000 0.8013650000 22.5816170662 Na 0.0000000000 4.0261350000
> 22.5816170662 Na 2.7240000000 8.8536350000 21.0089149329 Bi 2.7240000000
> 2.4137500000 21.0089149329 Bi 0.0000000000 7.2412500000 22.5816170662 Na
> 2.7240000000 2.4137500000 24.1543191995 Na 2.7240000000 7.2412500000
> 24.1543191995 Na 0.0000000000 5.6288650000 25.7270213327 Na 2.7240000000
> 0.8013650000 27.2997234660 Na 2.7240000000 4.0261350000 27.2997234660 Na
> 0.0000000000 8.8536350000 25.7270213327 Bi 0.0000000000 2.4137500000
> 25.7270213327 Bi 2.7240000000 7.2412500000 27.2997234660 Na 0.0000000000
> 2.4137500000 28.8724255993 Na 0.0000000000 7.2412500000 28.8724255993 Na
> 2.7240000000 5.6288650000 30.4451277325 Na 0.0000000000 0.8013650000
> 32.0178298658 Na 0.0000000000 4.0261350000 32.0178298658 Na 2.7240000000
> 8.8536350000 30.4451277325 Bi 2.7240000000 2.4137500000 30.4451277325 Bi
> 0.0000000000 7.2412500000 32.0178298658 Na 2.7240000000 2.4137500000
> 33.5905319991 Na 2.7240000000 7.2412500000 33.5905319991 Na 0.0000000000
> 5.6288650000 35.1632341324 Na 2.7240000000 0.8013650000 36.7359362656 Na
> 2.7240000000 4.0261350000 36.7359362656 Na 0.0000000000 8.8536350000
> 35.1632341324 Bi 0.0000000000 2.4137500000 35.1632341324 Bi 2.7240000000
> 7.2412500000 36.7359362656 Na 2.7240000000 2.4137500000 5.2818936002 Na
> 2.7240000000 7.2412500000 5.2818936001Na 0.0000000000 5.6288650000
> 6.8545957335 Na 2.7240000000 0.8013650000 8.4272978666 Na 2.7240000000
> 4.0261350000 8.4272978666Na 0.0000000000 8.8536350000 6.8545957335 Bi
> 0.0000000000 2.4137500000 6.8545957335 Bi 2.7240000000 7.2412500000
> 8.4272978667 *
>
>
> My output file:
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> * The initial density is read from file :
> ./pwscf.save/charge-density negative rho (up, down): 3.771E-01
> 0.000E+00 Starting wfcs from file Checking if some PAW data can be
> deallocated... total cpu time spent up to now is 15.7 secs
> Self-consistent Calculation iteration # 1 ecut= 25.00 Ry
> beta= 0.10 Calculation restarted from kpoint # 20 Davidson
> diagonalization with
> overlap
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc11"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping
> ...
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc3"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping
> ...
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc13"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping
> ...
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc14"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping
> ...
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc10"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping
> ...
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc5"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping
> ...
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc2"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping
> ...
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc17"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping
> ...
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc16"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping
> ...
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine davcio (10): error while reading from file
>
> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc20"
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> stopping ...*
>
>
> Other relevant information:
>
>
>
>
>
>
>
>
>
>
>
> *Warning: Process to core binding is enabled and OMP_NUM_THREADS is set to
> non-zero (1) valueIf your program has OpenMP sections, this can cause
> over-subscription of cores and consequently poor performanceTo avoid this,
> please re-run your application after setting MV2_ENABLE_AFFINITY=0Use
> MV2_USE_THREAD_WARNING=0 to suppress this message[cli_12]: aborting
> job:application called MPI_Abort(MPI_COMM_WORLD, 1) - process
> 12[mpiexec at golub220] HYDT_bscd_pbs_wait_for_completion
> (tools/bootstrap/external/pbs_wait.c:67): tm_poll(obit_event) failed with
> TM error 17002[mpiexec at golub220] HYDT_bsci_wait_for_completion
> (tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for
> completion[proxy:0:0 at golub220] HYD_pmcd_pmip_control_cmd_cb
> (pm/pmiserv/pmip_cb.c:911): assert (!closed) failed[proxy:0:0 at golub220]
> HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback
> returned error status[proxy:0:0 at golub220] main (pm/pmiserv/pmip.c:202):
> demux engine error waiting for event*
>
>
>
> On Fri, Aug 28, 2020 at 2:40 PM Vasilios Passias <billy.passias at gmail.com>
> wrote:
>
> > Hello fellow quantum espresso users.
> >
> > Recently, I tried running a relaxation calculation. The convergence
> > thresholds on the total energy and total force are such that I need to
> run
> > this relaxation calculation multiple times. The first relaxation run,
> with
> > restart_mode = 'from_scratch' , ran fine for the max_time I had set.
> >
> > Then I set restart_mode = 'restart' and I ran this relaxation calculation
> > again, expecting it to continue where it left off.
> >
> > Instead I got the following error: error in routine davcio (10):
> error
> > while reading from file.
> >
> > All of the files associated with this error are in the same folder as my
> > input and output files. Why is this happening? Should I just re-run
> this
> > calculation?
> >
> > I have my input, output, job submission, and crash files attached in this
> > email.
> >
> >
> > Thank you for your time and input.
> >
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 11
> Date: Fri, 28 Aug 2020 15:37:29 -0700
> From: Aaron Celestian <acelestian at nhm.org>
> To: users at lists.quantum-espresso.org
> Subject: Re: [QE-users] Problems running make pw
> Message-ID: <DE536194-7BC9-411D-944E-DDBD55CABC04 at nhm.org>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Paolo and Kelsey,
>
> I?m brand new to this list and QE, and I?m having the same problem as
> Kelsey. The '-fallow-argument-mismatch' warning is present for me. I?ve
> read through most of the archives looking for clues for solving this, but I
> wasn?t able to find a solution to what I?m doing wrong. The ?./configure?
> worked without errors/warnings. I do see that the FFLAGS set in the
> configure output:
> setting FFLAGS... -O3 -g -fallow-argument-mismatch
>
>
> This is one line of many from the ?make pw? screen output:
> f951: Warning: Nonexistent include directory
> '/Users/acelesti/QE//FoX/finclude' [-Wmissing-include-dirs]
> mpif90 -O3 -g -fallow-argument-mismatch -cpp -D__FFTW -D__MPI
> -Duse_beef - I/Users/acelesti/QE//include
> -I/Users/acelesti/QE//FoX/finclude
> -I/Users/acelesti/QE//S3DE/iotk/include/ -c iotk_write.f90
>
> tried a 'make clean' and redo 'make all', and the problem persists.
>
> I checked my fortran version and I get:
>
> $ gfortran --version
> GNU Fortran (Homebrew GCC 10.2.0) 10.2.0
> mpirun (Open MPI) 4.0.5
>
>
> But checking gcc version and I get:
> $ gcc --version
> Configured with:
> --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
> Apple clang version 11.0.3 (clang-1103.0.32.62)
> Target: x86_64-apple-darwin19.6.0
> Thread model: posix
>
>
> Any suggestions would be greatly appreciated!
>
> Aaron
> Running MacOS 10.5.6
> Trying QE version 6.6
>
>
>
>
> Aaron J. Celestian, Ph.D.
> Associate Curator, Mineral Sciences
> Natural History Museum of Los Angeles County
> Adj. Associate Professor, USC Earth Sciences
> Affiliate Research Scientist, NASA Jet Propulsion Laboratory
> Research <https://sites.google.com/nhm.org/aaron-celestian/home> | Blog
> <https://medium.com/@aaron.celestian> | Website <
> https://sites.google.com/nhm.org/aaron-celestian/home>
>
>
>
> gcc 10? check for the presence of "-fallow-argument-mismatch" in
> compilation flags. "configure" should automatically add it, though.
>
> Paolo
>
> On Fri, Aug 14, 2020 at 12:33 AM Kelsey Levine <
> krl52 at cornell.edu
> > wrote:
>
> >
> Dear QE Users,
>
> >
> >
> I am trying to set up Quantum Espresso 6.5 and have run into a problem
>
> >
> after running make pw. ./configure runs successfully, but make pw returns
>
> >
> the following:
>
> >
> *mp.f90:173:24:*
>
> >
> >
> 173 | CALL MPI_GATHER(mydata, 1, MPI_INTEGER, alldata, 1,
>
> >
> MPI_INTEGER, root, group, IERR)
>
> >
> | *1*
>
> >
> ......
>
> >
> 197 | CALL MPI_GATHER(mydata, msglen, MPI_INTEGER, alldata,
>
> >
> msglen, MPI_INTEGER, root, group, IERR)
>
> >
> | 2
>
> >
> *Error:* Rank mismatch between actual argument at *(1)* and actual
>
> >
> argument at (2) (rank-1 and scalar)
>
> >
> make[1]: *** [mp.o] Error 1
>
> >
> make: *** [libutil] Error 1
>
> >
> >
> The rank mismatch / type mismatch error displays numerous times before
>
> >
> the compilation actually stops, so I?m not sure if that is actually
> causing
>
> >
> the error 1 or if it is just a warning. It seems like it might be an issue
>
> >
> with the complier so I tried upgrading gcc to 11.0.3 but to no avail. I am
>
> >
> at a loss for how to solve this issue so any suggestions are appreciated.
>
> >
> >
> Thank You
>
> >
> Kelsey
>
> >
> Cornell University
>
> >
> _______________________________________________
>
> >
> 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
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 12
> Date: Sat, 29 Aug 2020 08:38:48 +0200
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Problems running make pw
> Message-ID:
> <CAPMgbCsq=O=d_uWowxS=G7=LpNLKB=vO4Ui9tOYZTXrCx7U=
> Tw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Sat, Aug 29, 2020 at 12:37 AM Aaron Celestian <acelestian at nhm.org>
> wrote:
>
> >
> > * f951:* *Warning:* Nonexistent include directory '
> > */Users/acelesti/QE//FoX/finclude*' [*-Wmissing-include-dirs*]
> > mpif90 -O3 -g -fallow-argument-mismatch -cpp -D__FFTW -D__MPI -Duse_beef
> > - I/Users/acelesti/QE//include -I/Users/acelesti/QE//FoX/finclude
> > -I/Users/acelesti/QE//S3DE/iotk/include/ -c iotk_write.f90
> >
>
> this is a warning, not an error. Where is the error?
>
> Paolo
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
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>
> ------------------------------
>
> Subject: Digest Footer
>
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