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, <[email protected]> wrote: > Send Pw_forum mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > 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 <[email protected]> > Subject: Re: [Pw_forum] Hybrid Calculation > To: pw_forum <[email protected]> > Message-ID: > <CA+g44DuQbRWw8TxJxVTyUzMf_-y8hM8Q=K+zzn3zyH6Uui9yXQ@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" <[email protected]> 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 > [email protected] > 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 <[email protected]> > Subject: [Pw_forum] Problem in post-processing and work function > calculation > To: PWSCF Forum <[email protected]> > Message-ID: > <[email protected]. > 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 <[email protected]> > Subject: Re: [Pw_forum] Hybrid Calculation > To: PWSCF Forum <[email protected]> > Message-ID: > <CAPMgbCu4q760X-6obnoiFRvyD2EBr7LzDxaqXaN51- > [email protected]> > 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 <[email protected]> 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 > > [email protected] > > 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 <[email protected]> > Subject: Re: [Pw_forum] Hybrid Calculation > To: [email protected] > 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 <[email protected]>: > > > 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" <[email protected]> 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 > > [email protected] > > 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: <[email protected]> > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > End of Pw_forum Digest, Vol 125, Issue 24 > ***************************************** >
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