[Pw_forum] Pw_forum Digest, Vol 125, Issue 24
Chemist
mrbsmith58 at gmail.com
Sat Dec 30 18:51:32 CET 2017
Re: [Pw_forum] Hybrid Calculation
Hello,
Thank you Paolo and Giuseppe for your responses. I will adjust my input
file and make the appropriate changes. I will report later if there are any
additional problems or concerns.
Best,
Brendan
On Sat, Dec 30, 2017 at 6:00 AM, <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to
> pw_forum at pwscf.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://pwscf.org/mailman/listinfo/pw_forum
> or, via email, send a message with subject or body 'help' to
> pw_forum-request at pwscf.org
>
> You can reach the person managing the list at
> pw_forum-owner at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
> 1. Re: Hybrid Calculation (Manu Hegde)
> 2. Problem in post-processing and work function calculation
> (Hooman Yaghoobnejad Asl)
> 3. Re: Hybrid Calculation (Paolo Giannozzi)
> 4. Re: Hybrid Calculation (Giuseppe Mattioli)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 29 Dec 2017 09:44:12 -0500
> From: Manu Hegde <mhegde at uwaterloo.ca>
> Subject: Re: [Pw_forum] Hybrid Calculation
> To: pw_forum <pw_forum at pwscf.org>
> Message-ID:
> <CA+g44DuQbRWw8TxJxVTyUzMf_-y8hM8Q=K+zzn3zyH6Uui9yXQ at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> I am not that expert in hybrid density functional theory. But looking into
> your input seems like you have large cut-off. First start with some simple
> assumptions. Just follow the example in QE libraray. Make sure it works.
> Also you need lot of memory. Hope it helps.
> Manu
> (University of Waterloo)
>
> On Dec 28, 2017 1:39 PM, "Chemist" <mrbsmith58 at gmail.com> wrote:
>
> Hello,
>
> I am attempting to run a hybrid scf calculation on a Pb doped V-oxide
> structure, and I have two questions.
>
> 1) In general, does my input file for such a calculation look correct?
> (input = below)
>
> 2) When running this calculation, I notice that my code crashes with the
> error "dexx is negative!". After doing some searching through the archives,
> The advice suggests to try different exxdiv_treatments - but this gives me
> a host of new problems, such as knowing which ecutvcut to use (and why),
> etc.
>
> I am hoping that someone with expertise can help steer me in the correct
> direction. My input is below. The value for ecut was found by doing a
> convergence study at the gamma point.
>
> Thank you for your time,
> Best,
>
> Brendan Smith
> State University of New York at Buffalo, Ph.D Student, 2nd Year
>
>
> &CONTROL
> calculation = 'scf',
> nstep = 50,
> pseudo_dir = '/projects/academic/alexeyak/brendan/PSEDUO/norm_
> conserving/non_rel/',
> outdir = './',
> prefix = 'x',
> disk_io = 'low',
> /
>
> &SYSTEM
> ibrav = 0,
> nat = 46,
> ntyp = 3,
> nspin = 1,
> nbnd = 235,
> ecutwfc = 90,
> ecutrho = 720,
> occupations = 'smearing',
> smearing = 'gaussian',
> degauss = 0.005,
> nosym = .true.,
> input_dft = 'PBE0'
> /
>
> &ELECTRONS
> electron_maxstep = 300,
> conv_thr = 1.D-7,
> mixing_beta = 0.35,
> /
>
> ATOMIC_SPECIES
> Pb 207.2 Pb.pbe-mt_fhi.UPF
> V 50.9415 V.pbe-mt_fhi.UPF
> O 15.9994 O.pbe-mt_fhi.UPF
>
> K_POINTS automatic
> 1 1 1 0 0 0
>
> CELL_PARAMETERS angstrom
> 15.4779996872 0.0000000000 0.0000000000
> 0.0000000000 3.6440000534 0.0000000000
> -3.3441298425 0.0000000000 9.5546809225
>
> ATOMIC_POSITIONS angstrom
> Pb -1.252373291 0.000000000 3.769703925
> Pb 13.386243452 0.000000000 5.784976998
> Pb 6.486626236 1.822000027 3.769703925
> Pb 5.647243147 1.822000027 5.784976998
> V 4.861534709 0.000000000 0.938269674
> V 7.272335672 0.000000000 8.616411034
> V 12.600534091 1.822000027 0.938269674
> V -0.466664633 1.822000027 8.616411034
> V 1.427260535 0.000000000 1.105476574
> V 10.706608873 0.000000000 8.449204278
> V 9.166260840 1.822000027 1.105476574
> V 2.967609491 1.822000027 8.449204278
> V 3.038442017 0.000000000 3.899265370
> V 9.095428288 0.000000000 5.655415552
> V 10.777441400 1.822000027 3.899265370
> V 1.356427984 1.822000027 5.655415552
> O 0.000000000 0.000000000 0.000000000
> O 7.738999844 1.822000027 0.000000000
> O 12.419713211 0.000000000 0.481555919
> O -0.285843304 0.000000000 9.073124825
> O 4.680713367 1.822000027 0.481555919
> O 7.453156540 1.822000027 9.073124825
> O 9.548904122 0.000000000 0.741443261
> O 2.584965723 0.000000000 8.813237661
> O 1.809904278 1.822000027 0.741443261
> O 10.323965566 1.822000027 8.813237661
> O 6.011811013 0.000000000 2.064766617
> O 6.122059193 0.000000000 7.489914590
> O 13.750810395 1.822000027 2.064766617
> O -1.616941112 1.822000027 7.489914590
> O 3.327103622 0.000000000 2.120183708
> O 8.806766173 0.000000000 7.434497357
> O 11.066103466 1.822000027 2.120183708
> O 1.067766329 1.822000027 7.434497357
> O 0.784110151 0.000000000 2.606516942
> O 11.349759479 0.000000000 6.948164266
> O 8.523110110 1.822000027 2.606516942
> O 3.610759635 1.822000027 6.948164266
> O 10.287975715 0.000000000 4.055961942
> O 1.845894129 0.000000000 5.498718980
> O 2.548975872 1.822000027 4.055961942
> O 9.584893973 1.822000027 5.498718980
> O 4.533116432 0.000000000 4.489744680
> O 7.600753412 0.000000000 5.064936242
> O 12.272116276 1.822000027 4.489744680
> O -0.138246431 1.822000027 5.064936242
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171229/
> 6fff73ab/attachment-0001.html
>
> ------------------------------
>
> Message: 2
> Date: Fri, 29 Dec 2017 11:57:35 -0600
> From: Hooman Yaghoobnejad Asl <hynr8 at mst.edu>
> Subject: [Pw_forum] Problem in post-processing and work function
> calculation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAM_pzMvRiqtJTWQAbyxYZouRHtT3jt9kXVJyHQmvRJmEb0AFFQ at mail.gmail.
> com>
> Content-Type: text/plain; charset="utf-8"
>
> Greetings QE developers and users.
> During the past days I was trying to calculate the work function for a
> LiNiO2(001) slab by following the steps provided in Al(001) PP Examples
> directory. Post-processing Al to get V_bare + V_H potential (plot_num = 11)
> follows as expected, but on getting the macroscopic average using
> average.x, it fails, returning error:
>
>
> *%%%%%%%%%%%%%%%%%%*
> * Error in routine average (1):*
> * nfile is wrong*
> * %%%%%%%%%%%%%%%%%%*
>
> Note that I've just changed the pseudo-potential to PAW and the working
> directory.
> On my own system, doing exactly the same thing wont even pass through the
> post-processing step, returning the following error:
>
> * Calling punch_plot, plot_num = 11*
> * Writing data to file LNO001.pot*
> * Reading data from file LNO001.pot*
>
> * %%%%%%%%%%%%%%%%%%*
> * Error in routine chdens (1):*
> * nx,ny,nz, required*
> * %%%%%%%%%%%%%%%%%%*
>
> I have a few doubts on this:
> 1) Why does it need at all to generate a plotable file (i.e. filepp), even
> though average.x is operating only on the intermediate potential file (i.e.
> filplot); is there any reason for having NAMELIST &PLOT used?
> 2) Any ideas on why I'm getting the nx,ny,nz required on my case, but not
> on Al example?
>
> I tried to supply 20,20,240 as nx,ny,nz, but post processing never ends
> even after 10 hours with 24 processor cores.
> I'm using QE 6.1 on a HPCC, equipped with Xeon E5-2690 v3 compute nodes.
>
> Thanks
> Hooman
> --
>
> *Hooman Yaghoobnejad*
>
> *PhD, Department of Chemistry*
>
> *Missouri University of Science and Technology*
>
> *Rolla, MO 65409*
> *USA*
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171229/
> 8b17b8de/attachment-0001.html
>
> ------------------------------
>
> Message: 3
> Date: Fri, 29 Dec 2017 21:53:35 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: Re: [Pw_forum] Hybrid Calculation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAPMgbCu4q760X-6obnoiFRvyD2EBr7LzDxaqXaN51-
> WXm997ow at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Quick remarks:
> 1. do not set ecutrho > 4*ecutwfc for norm-conserving pseudopotentials
> 2. use "K_POINTS gamma" for k=0: it is faster and takes less memory
> 3. do not specify "nosym" unless you know what it does
>
> Paolo
>
> On Thu, Dec 28, 2017 at 4:31 PM, Chemist <mrbsmith58 at gmail.com> wrote:
>
> > Hello,
> >
> > I am attempting to run a hybrid scf calculation on a Pb doped V-oxide
> > structure, and I have two questions.
> >
> > 1) In general, does my input file for such a calculation look correct?
> > (input = below)
> >
> > 2) When running this calculation, I notice that my code crashes with the
> > error "dexx is negative!". After doing some searching through the
> archives,
> > The advice suggests to try different exxdiv_treatments - but this gives
> me
> > a host of new problems, such as knowing which ecutvcut to use (and why),
> > etc.
> >
> > I am hoping that someone with expertise can help steer me in the correct
> > direction. My input is below. The value for ecut was found by doing a
> > convergence study at the gamma point.
> >
> > Thank you for your time,
> > Best,
> >
> > Brendan Smith
> > State University of New York at Buffalo, Ph.D Student, 2nd Year
> >
> >
> > &CONTROL
> > calculation = 'scf',
> > nstep = 50,
> > pseudo_dir = '/projects/academic/alexeyak/brendan/PSEDUO/norm_
> > conserving/non_rel/',
> > outdir = './',
> > prefix = 'x',
> > disk_io = 'low',
> > /
> >
> > &SYSTEM
> > ibrav = 0,
> > nat = 46,
> > ntyp = 3,
> > nspin = 1,
> > nbnd = 235,
> > ecutwfc = 90,
> > ecutrho = 720,
> > occupations = 'smearing',
> > smearing = 'gaussian',
> > degauss = 0.005,
> > nosym = .true.,
> > input_dft = 'PBE0'
> > /
> >
> > &ELECTRONS
> > electron_maxstep = 300,
> > conv_thr = 1.D-7,
> > mixing_beta = 0.35,
> > /
> >
> > ATOMIC_SPECIES
> > Pb 207.2 Pb.pbe-mt_fhi.UPF
> > V 50.9415 V.pbe-mt_fhi.UPF
> > O 15.9994 O.pbe-mt_fhi.UPF
> >
> > K_POINTS automatic
> > 1 1 1 0 0 0
> >
> > CELL_PARAMETERS angstrom
> > 15.4779996872 0.0000000000 0.0000000000
> > 0.0000000000 3.6440000534 0.0000000000
> > -3.3441298425 0.0000000000 9.5546809225
> >
> > ATOMIC_POSITIONS angstrom
> > Pb -1.252373291 0.000000000 3.769703925
> > Pb 13.386243452 0.000000000 5.784976998
> > Pb 6.486626236 1.822000027 3.769703925
> > Pb 5.647243147 1.822000027 5.784976998
> > V 4.861534709 0.000000000 0.938269674
> > V 7.272335672 0.000000000 8.616411034
> > V 12.600534091 1.822000027 0.938269674
> > V -0.466664633 1.822000027 8.616411034
> > V 1.427260535 0.000000000 1.105476574
> > V 10.706608873 0.000000000 8.449204278
> > V 9.166260840 1.822000027 1.105476574
> > V 2.967609491 1.822000027 8.449204278
> > V 3.038442017 0.000000000 3.899265370
> > V 9.095428288 0.000000000 5.655415552
> > V 10.777441400 1.822000027 3.899265370
> > V 1.356427984 1.822000027 5.655415552
> > O 0.000000000 0.000000000 0.000000000
> > O 7.738999844 1.822000027 0.000000000
> > O 12.419713211 0.000000000 0.481555919
> > O -0.285843304 0.000000000 9.073124825
> > O 4.680713367 1.822000027 0.481555919
> > O 7.453156540 1.822000027 9.073124825
> > O 9.548904122 0.000000000 0.741443261
> > O 2.584965723 0.000000000 8.813237661
> > O 1.809904278 1.822000027 0.741443261
> > O 10.323965566 1.822000027 8.813237661
> > O 6.011811013 0.000000000 2.064766617
> > O 6.122059193 0.000000000 7.489914590
> > O 13.750810395 1.822000027 2.064766617
> > O -1.616941112 1.822000027 7.489914590
> > O 3.327103622 0.000000000 2.120183708
> > O 8.806766173 0.000000000 7.434497357
> > O 11.066103466 1.822000027 2.120183708
> > O 1.067766329 1.822000027 7.434497357
> > O 0.784110151 0.000000000 2.606516942
> > O 11.349759479 0.000000000 6.948164266
> > O 8.523110110 1.822000027 2.606516942
> > O 3.610759635 1.822000027 6.948164266
> > O 10.287975715 0.000000000 4.055961942
> > O 1.845894129 0.000000000 5.498718980
> > O 2.548975872 1.822000027 4.055961942
> > O 9.584893973 1.822000027 5.498718980
> > O 4.533116432 0.000000000 4.489744680
> > O 7.600753412 0.000000000 5.064936242
> > O 12.272116276 1.822000027 4.489744680
> > O -0.138246431 1.822000027 5.064936242
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
>
>
>
> --
> 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 --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20171229/
> 4a545a6b/attachment-0001.html
>
> ------------------------------
>
> Message: 4
> Date: Fri, 29 Dec 2017 23:42:01 +0100
> From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> Subject: Re: [Pw_forum] Hybrid Calculation
> To: pw_forum at pwscf.org
> Message-ID:
> <20171229234201.Horde.LG1qPxlupprEMicj-SamgNC@
> webmail.sic.rm.cnr.it>
> Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes
>
>
> Dear Brendan
> Let me add something more specific:
>
> > 2) When running this calculation, I notice that my code crashes with the
> > error "dexx is negative!". After doing some searching through the
> archives,
> > The advice suggests to try different exxdiv_treatments - but this gives
> me
> > a host of new problems, such as knowing which ecutvcut to use (and why),
> > etc.
>
> Sometimes there is a bit of instability in the algorithm, specially
> when the occupations of KS states oscillate during the scf iterations.
> The strict requirement on dexx has been therefore "softened" in
> version 6.2 (look into electrons.f90) to check the differences. Thus,
> if you are using QE < 6.2 my advice is to update your version. If you
> are already using 6.2 you can try to suppress the call to 'dexx is
> negative' and to see where your calculation is going, but i don't
> recommend it if you don't know what you're doing!
>
> > 1) In general, does my input file for such a calculation look correct?
> > (input = below)
>
> well...
>
> > ecutrho = 720
>
> useless. you are using norm-conserving pseudopotentials. ecutrho
> should be automatically fixed at ecutwfc*4, and you generally don't
> need more than this. Use ecutfock instead, it saves a lot of time. It
> is generally safe to use ecutfock=ecutwfc for geometry optimizations
> and ecutfock=2*ecutwfc for energy/properties calculations.
> adaptive_thr=.true. often provides further speedup.
>
> > nbnd = 235,
> > occupations = 'smearing',
>
> you do not need to specify both. The latter generally provides a
> suitable amount of unoccupied states to work well with noninteger
> occupations, if needed.
>
> > degauss = 0.005,
>
> tight. you should start with a larger value (0.01 Ry = 0.13 eV), which
> generally leads to stable results in the case of
> insulators/semiconductors.
>
> > nosym = .true.,
>
> why?
>
> > K_POINTS automatic
> > 1 1 1 0 0 0
>
> if you want to use gamma then *use* gamma. You save a lot of time
>
> K_POINTS {gamma}
>
> but your structure probably requires a converged (or an *affordably*
> converged...) k-points mesh. In principle you should also check that
> the q-mesh is converged (nqx1=1, nqx2=1, nqx3=1 is the default, but is
> very expensive to use a richer mesh).
>
> HTH
> Giuseppe
>
> Quoting Manu Hegde <mhegde at uwaterloo.ca>:
>
> > I am not that expert in hybrid density functional theory. But looking
> into
> > your input seems like you have large cut-off. First start with some
> simple
> > assumptions. Just follow the example in QE libraray. Make sure it works.
> > Also you need lot of memory. Hope it helps.
> > Manu
> > (University of Waterloo)
> >
> > On Dec 28, 2017 1:39 PM, "Chemist" <mrbsmith58 at gmail.com> wrote:
> >
> > Hello,
> >
> > I am attempting to run a hybrid scf calculation on a Pb doped V-oxide
> > structure, and I have two questions.
> >
> > 1) In general, does my input file for such a calculation look correct?
> > (input = below)
> >
> > 2) When running this calculation, I notice that my code crashes with the
> > error "dexx is negative!". After doing some searching through the
> archives,
> > The advice suggests to try different exxdiv_treatments - but this gives
> me
> > a host of new problems, such as knowing which ecutvcut to use (and why),
> > etc.
> >
> > I am hoping that someone with expertise can help steer me in the correct
> > direction. My input is below. The value for ecut was found by doing a
> > convergence study at the gamma point.
> >
> > Thank you for your time,
> > Best,
> >
> > Brendan Smith
> > State University of New York at Buffalo, Ph.D Student, 2nd Year
> >
> >
> > &CONTROL
> > calculation = 'scf',
> > nstep = 50,
> > pseudo_dir = '/projects/academic/alexeyak/brendan/PSEDUO/norm_
> > conserving/non_rel/',
> > outdir = './',
> > prefix = 'x',
> > disk_io = 'low',
> > /
> >
> > &SYSTEM
> > ibrav = 0,
> > nat = 46,
> > ntyp = 3,
> > nspin = 1,
> > nbnd = 235,
> > ecutwfc = 90,
> > ecutrho = 720,
> > occupations = 'smearing',
> > smearing = 'gaussian',
> > degauss = 0.005,
> > nosym = .true.,
> > input_dft = 'PBE0'
> > /
> >
> > &ELECTRONS
> > electron_maxstep = 300,
> > conv_thr = 1.D-7,
> > mixing_beta = 0.35,
> > /
> >
> > ATOMIC_SPECIES
> > Pb 207.2 Pb.pbe-mt_fhi.UPF
> > V 50.9415 V.pbe-mt_fhi.UPF
> > O 15.9994 O.pbe-mt_fhi.UPF
> >
> > K_POINTS automatic
> > 1 1 1 0 0 0
> >
> > CELL_PARAMETERS angstrom
> > 15.4779996872 0.0000000000 0.0000000000
> > 0.0000000000 3.6440000534 0.0000000000
> > -3.3441298425 0.0000000000 9.5546809225
> >
> > ATOMIC_POSITIONS angstrom
> > Pb -1.252373291 0.000000000 3.769703925
> > Pb 13.386243452 0.000000000 5.784976998
> > Pb 6.486626236 1.822000027 3.769703925
> > Pb 5.647243147 1.822000027 5.784976998
> > V 4.861534709 0.000000000 0.938269674
> > V 7.272335672 0.000000000 8.616411034
> > V 12.600534091 1.822000027 0.938269674
> > V -0.466664633 1.822000027 8.616411034
> > V 1.427260535 0.000000000 1.105476574
> > V 10.706608873 0.000000000 8.449204278
> > V 9.166260840 1.822000027 1.105476574
> > V 2.967609491 1.822000027 8.449204278
> > V 3.038442017 0.000000000 3.899265370
> > V 9.095428288 0.000000000 5.655415552
> > V 10.777441400 1.822000027 3.899265370
> > V 1.356427984 1.822000027 5.655415552
> > O 0.000000000 0.000000000 0.000000000
> > O 7.738999844 1.822000027 0.000000000
> > O 12.419713211 0.000000000 0.481555919
> > O -0.285843304 0.000000000 9.073124825
> > O 4.680713367 1.822000027 0.481555919
> > O 7.453156540 1.822000027 9.073124825
> > O 9.548904122 0.000000000 0.741443261
> > O 2.584965723 0.000000000 8.813237661
> > O 1.809904278 1.822000027 0.741443261
> > O 10.323965566 1.822000027 8.813237661
> > O 6.011811013 0.000000000 2.064766617
> > O 6.122059193 0.000000000 7.489914590
> > O 13.750810395 1.822000027 2.064766617
> > O -1.616941112 1.822000027 7.489914590
> > O 3.327103622 0.000000000 2.120183708
> > O 8.806766173 0.000000000 7.434497357
> > O 11.066103466 1.822000027 2.120183708
> > O 1.067766329 1.822000027 7.434497357
> > O 0.784110151 0.000000000 2.606516942
> > O 11.349759479 0.000000000 6.948164266
> > O 8.523110110 1.822000027 2.606516942
> > O 3.610759635 1.822000027 6.948164266
> > O 10.287975715 0.000000000 4.055961942
> > O 1.845894129 0.000000000 5.498718980
> > O 2.548975872 1.822000027 4.055961942
> > O 9.584893973 1.822000027 5.498718980
> > O 4.533116432 0.000000000 4.489744680
> > O 7.600753412 0.000000000 5.064936242
> > O 12.272116276 1.822000027 4.489744680
> > O -0.138246431 1.822000027 5.064936242
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
> End of Pw_forum Digest, Vol 125, Issue 24
> *****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20171230/9cf9e46f/attachment.html>
More information about the users
mailing list