Thanks a lot for the help to both prof. Matteo Cococcioni and prof. Giuseppe Mattioli. Best Regards, Tommaso. Il giorno 29/mag/2014, alle ore 12:00, pw_forum-request at pwscf.org ha scritto:
> 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: Fermi energy (Giuseppe Mattioli) > 2. Re: multiples site Hubbard U (Matteo Cococcioni) > 3. Re: pw2wannier.x error (Giovanni Pizzi) > 4. Problem Regarding neb calculation (RAMESWAR BHATTACHARJEE) > 5. R: Fermi energy (DELLACA' Valentina (CRF)) > 6. Re: ibrav7 doesn't show the structure of BaNi2As2 correctly > (David Foster) > 7. Re: ibrav7 doesn't show the structure of BaNi2As2 correctly > (David Foster) > 8. Re: ibrav7 doesn't show the structure of BaNi2As2 correctly > (Tone Kokalj) > 9. Re: ibrav7 doesn't show the structure of BaNi2As2 correctly > (David Foster) > 10. Re: ibrav7 doesn't show the structure of BaNi2As2 correctly > (David Foster) > 11. Re: ibrav7 doesn't show the structure of BaNi2As2 correctly > (Tone Kokalj) > 12. Hubbard U (Tommy) > 13. Re: Graphene_fixed calculation (Higuchi Toshiharu) > 14. How to add supercell to QE i/p file (siddheshwar chopra) > 15. Re: ibrav7 doesn't show the structure of BaNi2As2 correctly > (David Foster) > 16. Re: How to add supercell to QE i/p file (Sridhar Sadasivam) > 17. Re: How to add supercell to QE i/p file (siddheshwar chopra) > 18. Reg: To calculate EOS using Quantum espresso. > (Peram sreenivasa reddy) > 19. Conductivity measurements using QE... (siddheshwar chopra) > 20. Counterpoise correction (Francis Jing) > 21. resp_mat.f90 (Tommaso Francese) > 22. Re: Hubbard U (Giuseppe Mattioli) > 23. Re: Counterpoise correction (Ari P Seitsonen) > 24. Re: Counterpoise correction (Tone Kokalj) > 25. Re: Counterpoise correction (Giovanni Cantele) > 26. Re: resp_mat.f90 (Matteo Cococcioni) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 May 2014 12:07:03 +0200 > From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it> > Subject: Re: [Pw_forum] Fermi energy > To: pw_forum at pwscf.org > Message-ID: > <20140528120703.Horde.7xfbZeBgnhETLYmgtlb9ng2 at webmail.sic.rm.cnr.it> > Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes > > > Dear Valentina > >> Is it already the Fermi Energy defined in the article by Zunger? > > Definitely not! You should individuate the valence band maximum and > use the corresponding eigenvalue in the formula as a constant. The > Fermi level is the variable (you calculate the formation energy at a > given Fermi level, and, possibly, the transition level between two > different charge states of the same defect). The rationale is that the > position of transition levels should be independent on the Fermi > level. I may suggest (but do not tell prof. Zunger, please...) that > Van de Walle's paper is somewhat clearer: > > Van de Walle, C. G.; Neugebauer, J.; J. Appl. Phys. 2004, 95, 3851. > > A very recent review by Pacchioni and Di Valentin, which improves in > some details the calculation of transition levels, can be found here: > > http://pubs.acs.org/doi/pdf/10.1021/ar4002944 > > There is also another detail, often hidden into the papers. When you > perform the calculations in a plane-wave/pseudopotential PBC > framework, if you change the total charge, you also insert a > background charge that shift the potential (defined up to a constant > value) and, in turn, the eigenvalues. You should insert some DeltaV > value in the formation energy formula to recover the shift. If the > supercell is large, and the dielectric constant of the host matrix is > high (let us say a >100-atom cell of TiO2, for instance), then DeltaV > is negligibly small. Otherwise you can find something around some > tenths of eV. However, Pacchioni and Di Valentin have tested a > workaround for the estimate of DeltaV (see the review). > >> occupations='smearing' with degauss =1d-20 > > I hope that it is degauss =1d-2 > > HTH > > Giuseppe > > Giuseppe Mattioli > ISM-CNR > Italy > > Quoting "DELLACA' Valentina (CRF)" <valentina.dellaca at crf.it>: > >> Hi, >> We are computing the formation energies of charged defects in >> supercells. We are referring to Lany and Zunger, Phys. Rev. B 78, >> 235104 (2008) Eq. (1). >> The Fermi energy used here is defined as Ev (valence band maximun) >> + delta E Fermi ; i.e. is defined with respect the valence band >> maximum. >> The system we are working with is an insulator, and we are using >> occupations='smearing' with degauss =1d-20 in order to have the >> Fermi Energy written in the log file.( Please, tell me if we are >> doing something wrong here!) >> The question is: the Fermi Energy that I read in the log file, is >> defined respect to what? Is it already the Fermi Energy defined in >> the article by Zunger? >> Thanks, >> Regards >> Valentina >> >> >> Valentina Dellac? >> Group Materials Labs >> PA&CT - Materials CAE Development & Virtual Analysis >> >> >> Centro Ricerche Fiat S.C.p.A. >> Sede legale e amministrativa: Strada Torino, 50 >> 10043 Orbassano (TO), Italia >> Tel +39 011 9083138 >> Fax +39 011 9083666 >> >> www.crf.it<http://www.crf.it> > > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: <giuseppe.mattioli at ism.cnr.it> > > > > ------------------------------ > > Message: 2 > Date: Wed, 28 May 2014 12:18:43 +0200 > From: Matteo Cococcioni <matteo at umn.edu> > Subject: Re: [Pw_forum] multiples site Hubbard U > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <CAMZASgFkre8Bo2cVnPD2k2kWZueKoP0cS+hi7OYEgS0oCMvWCA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Tommaso, > > the same supercell is good for both. You can calculate the U for both > atomic species at the same time simply including both responses in the same > response matrices. > > hope this helps. > > Matteo > > > On Wed, May 28, 2014 at 11:47 AM, Tommaso Francese < > neutrinofrancese at gmail.com> wrote: > >> Dear all, >> i?m working on a Yttria doped Zirconia, YSZ. I have understood how to >> calculate the U values for a single site, but how can i calculate the U >> values for both the transition metal inside the same structure, e.g. Zr and >> Y in YSZ structure? Do i have to build a supercell even in this case? >> Thanks in advance, >> Tommaso Francese. >> Universit? C? Foscari of Venice. >> _______________________________________________ >> 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/20140528/918d1aa2/attachment-0001.html > > > ------------------------------ > > Message: 3 > Date: Wed, 28 May 2014 14:06:31 +0200 > From: Giovanni Pizzi <giovanni.pizzi at epfl.ch> > Subject: Re: [Pw_forum] pw2wannier.x error > To: pw_forum at pwscf.org > Message-ID: <5385D147.9030208 at epfl.ch> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Rajdeep, > at a quick glance everything seems ok, if you want a quantitative > comparison you can also check the sample output files that we > distributed with the paper: http://dx.doi.org/10.1016/j.cpc.2014.05.004 > (follow 'program summary URL', then 'download'). > > If you have further questions specific on Wannier90, I suggest you to > write on the Wannier mailing list rather than here (see instructions > here: http://www.wannier.org/forum.html ) > > Best, > > Giovanni > > > On 05/27/2014 12:06 PM, Rajdeep Banerjee wrote: >> Dear Giovanni Pizzi, >> Thank you very much for your generous >> help. I think wannier90-2.0.0 is compatible with espresso-5.0.3. Can >> you please check the attached input and output files >> (Si_boltzmann.tar.gz ) to see if there's any discrepancy (as I'm just >> a beginner in wannier )Here's a step by step list of the things I did: >> 1. downloaded "espresso+PHonon-5.0.3.tar.gz" >> 2. unpacked: tar -zxvf espresso+PHonon-5.0.3.tar.gz >> 3. cd espresso-5.0.3 >> 4. ./configure --enable-parallel >> 5. make pw >> 6. make pp >> >> I downloaded wannier90-2.0.0: >> 1. cp ./config/make.sys.gfort ./make.sys >> 2. make >> >> Then I ran the files in ./examples/example16/ >> >>>> path/espresso-5.0.3/bin/pw.x < Si.scf > Si.scf.out >>>> path/espresso-5.0.3/bin/pw.x < Si.nscf > Si.nscf.out >>>> pathforwannier2.0.0/wannier90.x -pp Si >>>> path/espresso-5.0.3/bin/pw2wannier90.x < Si.pw2wan > Si.pw2wan.out >>>> pathforwannier2.0.0/wannier90.x Si >>>> pathforwannier2.0.0/postw90.x Si >> >> All these were run in serial and parallel (except of course >> wannier90.x) without error. >> >> Thanks a lot. >> >> Rajdeep Banerjee >> JNCASR >> Bangalore, India >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > -- > Giovanni Pizzi > Post-doctoral Research Scientist > EPFL STI IMX THEOS > MXC 340 (B?timent MXC) > Station 12 > CH-1015 Lausanne (Switzerland) > Phone: +41 21 69 31124 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140528/133729e3/attachment-0001.html > > > ------------------------------ > > Message: 4 > Date: Wed, 28 May 2014 19:11:18 +0530 > From: RAMESWAR BHATTACHARJEE <bitub22 at gmail.com> > Subject: [Pw_forum] Problem Regarding neb calculation > To: pw_forum at pwscf.org > Message-ID: > <CAHPw7QHmEPaForNh0e=776_rM1SbJDt1iJAF-VeQ+ba_M-mkZw at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > I am performing a neb calculation for 1,5 -hydrogen shift.I gave no of > image 10.But those image i am getting very terrible ,they are very high > energetic.I tried many times but I am getting the same.My input is given > below > --------------------------------------------------------------------------------------------------------------------------------- > BEGIN > BEGIN_PATH_INPUT > &PATH > restart_mode = 'from_scratch' > string_method = 'neb', > nstep_path = 250, > ds = 2.D0, > opt_scheme = "broyden", > num_of_images = 10, > k_max = 0.3D0, > k_min = 0.2D0, > path_thr = 0.1D0, > CI_scheme = "auto", > / > END_PATH_INPUT > BEGIN_ENGINE_INPUT > &CONTROL > outdir = > '/work/spad/rameswar/NEB_acoh/neb_pentadiene/' , > pseudo_dir = '/work/spad/espresso-5.0/pseudo/' , > prefix = 'pentadiene' , > > / > &SYSTEM > ibrav = 0, > celldm(1) = 1.8903 > nat = 13, > ntyp = 2, > ecutwfc = 30 , > ecutrho = 300 , > occupations = 'smearing' , > smearing = 'gaussian' > degauss = 0.01 > tot_charge=0, > nosym = .true. > / > &ELECTRONS > electron_maxstep = 1000 , > conv_thr = 1.0d-6 > mixing_beta = 0.3 , > diagonalization='david' > diago_david_ndim = 4 > / > &IONS > upscale = 100 , > > / > &CELL > cell_dynamics='bfgs', > press = 0.0 > / > ATOMIC_SPECIES > H 1.008 H.pbe-van_ak.UPF > C 12.0107 C.pbe-van_ak.UPF > > BEGIN_POSITIONS > FIRST_IMAGE > ATOMIC_POSITIONS angstrom > C 1.31953600 0.39251400 -0.19343100 > H 2.06529200 0.99605700 -0.71272700 > C 0.05078000 1.08150100 0.07624800 > H 0.14286600 2.15744500 0.22388600 > C -1.19511100 0.56812000 0.11418900 > H -2.00384900 1.26564900 0.33037400 > C 1.66688000 -0.85585100 0.16169100 > H 1.00988300 -1.50109900 0.73605200 > H 2.64463400 -1.25497800 -0.09145400 > C -1.61619400 -0.85095500 -0.13977400 > H -0.86303200 -1.40706100 -0.70511400 > H -1.79063100 -1.39166100 0.80077400 > H -2.56051200 -0.87631800 -0.69533200 > LAST_IMAGE > ATOMIC_POSITIONS angstrom > C -1.19534800 0.56802500 -0.11421000 > H -2.00438700 1.26537500 -0.32984500 > C 0.05037100 1.08169200 -0.07634100 > H 0.14251100 2.15766000 -0.22366400 > C 1.31930100 0.39264000 0.19337400 > H 2.06491000 0.99644800 0.71260700 > C -1.61573100 -0.85129100 0.13977700 > H -1.78972900 -1.39225000 -0.80073900 > H -2.56016400 -0.87714600 0.69510400 > C 1.66702300 -0.85563500 -0.16164600 > H -0.86209300 -1.40685600 0.70503200 > H 1.01027200 -1.50148700 -0.73565400 > H 2.64498300 -1.25433600 0.09143800 > > END_POSITIONS > > K_POINTS gamma > > CELL_PARAMETERS > 20.00 0.000 0.000 > 0.000 20.000 0.000 > 0.000 0.000 20.0000 > END_ENGINE_INPUT > END > > ------------------------------------------------------------------------------------------------------------------------------- > > > and the coordinate of the images are > ----------------------------------------------------------------------------------------------------------------------------------- > first_image > C 1.3195360000 0.3925140000 -0.1934310000 > H 2.0652920000 0.9960570000 -0.7127270000 > C 0.0507800000 1.0815010000 0.0762480000 > H 0.1428660000 2.1574450000 0.2238860000 > C -1.1951110000 0.5681200000 0.1141890000 > H -2.0038490000 1.2656490000 0.3303740000 > C 1.6668800000 -0.8558510000 0.1616910000 > H 1.0098830000 -1.5010990000 0.7360520000 > H 2.6446340000 -1.2549780000 -0.0914540000 > C -1.6161940000 -0.8509550000 -0.1397740000 > H -0.8630320000 -1.4070610000 -0.7051140000 > H -1.7906310000 -1.3916610000 0.8007740000 > H -2.5605120000 -0.8763180000 -0.6953320000 > intermediate_image 1 > C 1.0416235670 0.4096826261 -0.1847281913 > H 1.6124607436 1.0267761067 -0.6708528399 > C 0.0537058850 1.0860702728 0.0596630422 > H 0.1428460638 2.1576140221 0.1739526568 > C -0.9199608069 0.5450727328 0.1232272746 > H -1.5512985038 1.2363516284 0.3734291705 > C 1.2981007866 -0.8528495649 0.1593086615 > H 0.6962406140 -1.4898303363 0.5653138105 > H 2.0674711412 -1.2145164128 -0.0045940149 > C -1.2504287178 -0.8463507998 -0.1379062740 > H -0.8587514466 -1.4116254973 -0.5513732775 > H -1.4782928984 -1.4045884656 0.6307027960 > H -1.9830206898 -0.9185018154 -0.6095645184 > intermediate_image 2 > C 0.7697708965 0.4198288397 -0.1781298039 > H 1.1576798732 1.0584049209 -0.6299548953 > C 0.0600373019 1.1062813519 0.0442962608 > H 0.1428386007 2.1578869519 0.1237678121 > C -0.6539753372 0.5118928036 0.1335399475 > H -1.0971330198 1.2078106990 0.4173145558 > C 0.9212569220 -0.8438869413 0.1580428030 > H 0.3810863513 -1.4792141963 0.3937583913 > H 1.4957342148 -1.1792660778 0.0820502918 > C -0.8723392467 -0.8299444788 -0.1292797358 > H -0.8589855856 -1.4266486470 -0.3986380386 > H -1.1648720529 -1.4181501883 0.4604625178 > H -1.4102486256 -0.9617493545 -0.5293429090 > intermediate_image 3 > C 0.5152709718 0.4164260568 -0.1815486968 > H 0.6986982750 1.0908440287 -0.5905036296 > C 0.0627472742 1.1566352211 0.0253546832 > H 0.1427755023 2.1583161254 0.0731925773 > C -0.4014949867 0.4650729032 0.1571386960 > H -0.6390783549 1.1795902675 0.4645508606 > C 0.5324329659 -0.8140711069 0.1540264641 > H 0.0657799714 -1.4716702851 0.2203884887 > H 0.9349463549 -1.1638419454 0.1759490522 > C -0.4781050609 -0.8230493527 -0.1175326270 > H -0.8714517559 -1.4255596409 -0.2343839151 > H -0.8508633194 -1.4331811207 0.2942385733 > H -0.8406517784 -1.0123247430 -0.4715073100 > intermediate_image 4 > C 0.2787694936 0.4133995319 -0.2941708064 > H 0.2088503172 1.1275631771 -0.5637816490 > C 0.0568888419 1.1950962371 0.0007780485 > H 0.1429175143 2.1583892534 0.0190973599 > C -0.1552204492 0.4306419342 0.2908511281 > H -0.1530540411 1.1512497159 0.5343678558 > C 0.2537009233 -0.7461400629 0.2226441223 > H -0.2467315902 -1.4712624484 0.0300927454 > H 0.3135381160 -1.1855709022 0.3223140066 > C -0.2037123083 -0.7564542621 -0.1926243029 > H -0.8859977082 -1.4104737852 -0.0664084280 > H -0.5323440561 -1.4522500049 0.1159392834 > H -0.2064322945 -1.1310654114 -0.4267527875 > intermediate_image 5 > C -0.1115876668 0.4269928554 -0.3008617870 > H -0.0930377972 1.1470010345 -0.5409666281 > C 0.0562258918 1.1965905485 0.0009822449 > H 0.1429224793 2.1584063967 -0.0123636558 > C 0.2356282630 0.4153249469 0.3020697380 > H 0.1487946133 1.1318737416 0.5598152551 > C -0.1611903412 -0.7542762665 0.2105957709 > H -0.4990534627 -1.4540644055 -0.0949995760 > H -0.1257034359 -1.1406838592 0.4153835240 > C 0.2115378755 -0.7429183752 -0.2366369732 > H -0.8859304121 -1.4104266076 0.0446838834 > H -0.2812713037 -1.4700597929 -0.0039106157 > H 0.2339335275 -1.1806735747 -0.3382816195 > intermediate_image 6 > C -0.4014272064 0.4649683123 -0.1571127693 > H -0.6391673180 1.1792736818 -0.4642506604 > C 0.0626008101 1.1566646778 -0.0254538503 > H 0.1426587089 2.1583862967 -0.0729547358 > C 0.5150783912 0.4165784260 0.1814594883 > H 0.6984705317 1.0911965754 0.5905762897 > C -0.4777203227 -0.8233191632 0.1176047364 > H -0.8502910428 -1.4334542304 -0.2940406376 > H -0.8403177395 -1.0130648561 0.4712712403 > C 0.5321642170 -0.8138536755 -0.1539666924 > H -0.8711631070 -1.4255566070 0.2342325112 > H 0.0656390413 -1.4717233751 -0.2200530275 > H 0.9349299266 -1.1630804517 -0.1760670382 > intermediate_image 7 > C -0.6540926426 0.5117847521 -0.1335649407 > H -1.0974670860 1.2075139819 -0.4169306314 > C 0.0598067280 1.1063825854 -0.0443914639 > H 0.1426416757 2.1580055595 -0.1235459667 > C 0.7696384692 0.4199588647 0.1780830306 > H 1.1574983643 1.0587665913 0.6299769792 > C -0.8720278169 -0.8301974232 0.1292812646 > H -1.1642569308 -1.4185234487 -0.4603486709 > H -1.4100522160 -0.9625446967 0.5291524682 > C 0.9212481920 -0.8436552585 -0.1580088351 > H -0.8584542009 -1.4265788672 0.3985788894 > H 0.3811905012 -1.4793813800 -0.3934381793 > H 1.4959376694 -1.1785749433 -0.0821162445 > intermediate_image 8 > C -0.9201430644 0.5449713763 -0.1232516573 > H -1.5517343360 1.2360652468 -0.3729725461 > C 0.0533905907 1.0862173983 -0.0597553868 > H 0.1425698921 2.1577810033 -0.1737307337 > C 1.0414389172 0.4098096406 0.1846752988 > H 1.6121794999 1.0271532518 0.6708041505 > C -1.2500420892 -0.8466659630 0.1379098688 > H -1.4775338524 -1.4050691232 -0.6306277600 > H -1.9827488578 -0.9193111730 0.6093589204 > C 1.2981731324 -0.8526231990 -0.1592693760 > H -0.8580137776 -1.4114702974 0.5512968311 > H 0.6964863918 -1.4901087050 -0.5649549149 > H 2.0677428150 -1.2138519535 0.0045539681 > last_image > C -1.1953480000 0.5680250000 -0.1142100000 > H -2.0043870000 1.2653750000 -0.3298450000 > C 0.0503710000 1.0816920000 -0.0763410000 > H 0.1425110000 2.1576600000 -0.2236640000 > C 1.3193010000 0.3926400000 0.1933740000 > H 2.0649100000 0.9964480000 0.7126070000 > C -1.6157310000 -0.8512910000 0.1397770000 > H -1.7897290000 -1.3922500000 -0.8007390000 > H -2.5601640000 -0.8771460000 0.6951040000 > C 1.6670230000 -0.8556350000 -0.1616460000 > H -0.8620930000 -1.4068560000 0.7050320000 > H 1.0102720000 -1.5014870000 -0.7356540000 > H 2.6449830000 -1.2543360000 0.0914380000 > > ------------------------------------------------------------------------------------------------------------------------- > > So can anybody help me to sort out the problem.I am also getting the same > result for acetic acid dimer proton transfer also.All suggestion will be > highly appreciated.Thank you. > > Best regards > Rameswar Bhattacharjee > Dept.of Spectroscopy > IACS Kolkata, > India. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140528/62e282cd/attachment-0001.html > > > ------------------------------ > > Message: 5 > Date: Wed, 28 May 2014 16:18:54 +0200 > From: "DELLACA' Valentina (CRF)" <valentina.dellaca at crf.it> > Subject: [Pw_forum] R: Fermi energy > To: PWSCF Forum <pw_forum at pwscf.org>, Giuseppe Mattioli > <giuseppe.mattioli at ism.cnr.it> > Cc: "SGROI Mauro Francesco \(CRF\)" <mauro.sgroi at crf.it> > Message-ID: > <006F1CBCC91B524BB5A44CB8147B0060E30FD9974A at MXCL12.fgremc.it> > Content-Type: text/plain; charset="utf-8" > > Dear Giuseppe, > Thanks a lot. Indeed it was a 1d-2. > I am going to read the articles you suggested. > Best regards, > Valentina > > Valentina Dellac? > Group Materials Labs > PA&CT ? Materials CAE Development & Virtual Analysis > > ? > Centro Ricerche Fiat S.C.p.A. > Sede legale e amministrativa: Strada Torino, 50 > 10043 Orbassano (TO), Italia > Tel? +39 011 9083138 > Fax +39 011 9083666 > > www.crf.it > > > -----Messaggio originale----- > Da: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] Per > conto di Giuseppe Mattioli > Inviato: mercoled? 28 maggio 2014 12:07 > A: pw_forum at pwscf.org > Oggetto: Re: [Pw_forum] Fermi energy > > > Dear Valentina > >> Is it already the Fermi Energy defined in the article by Zunger? > > Definitely not! You should individuate the valence band maximum and use the > corresponding eigenvalue in the formula as a constant. The Fermi level is the > variable (you calculate the formation energy at a given Fermi level, and, > possibly, the transition level between two different charge states of the > same defect). The rationale is that the position of transition levels should > be independent on the Fermi level. I may suggest (but do not tell prof. > Zunger, please...) that Van de Walle's paper is somewhat clearer: > > Van de Walle, C. G.; Neugebauer, J.; J. Appl. Phys. 2004, 95, 3851. > > A very recent review by Pacchioni and Di Valentin, which improves in some > details the calculation of transition levels, can be found here: > > http://pubs.acs.org/doi/pdf/10.1021/ar4002944 > > There is also another detail, often hidden into the papers. When you perform > the calculations in a plane-wave/pseudopotential PBC framework, if you change > the total charge, you also insert a background charge that shift the > potential (defined up to a constant > value) and, in turn, the eigenvalues. You should insert some DeltaV value in > the formation energy formula to recover the shift. If the supercell is large, > and the dielectric constant of the host matrix is high (let us say a > >100-atom cell of TiO2, for instance), then DeltaV is negligibly small. > Otherwise you can find something around some tenths of eV. However, Pacchioni > and Di Valentin have tested a workaround for the estimate of DeltaV (see the > review). > >> occupations='smearing' with degauss =1d-20 > > I hope that it is degauss =1d-2 > > HTH > > Giuseppe > > Giuseppe Mattioli > ISM-CNR > Italy > > Quoting "DELLACA' Valentina (CRF)" <valentina.dellaca at crf.it>: > >> Hi, >> We are computing the formation energies of charged defects in >> supercells. We are referring to Lany and Zunger, Phys. Rev. B 78, >> 235104 (2008) Eq. (1). >> The Fermi energy used here is defined as Ev (valence band maximun) >> + delta E Fermi ; i.e. is defined with respect the valence band >> maximum. >> The system we are working with is an insulator, and we are using >> occupations='smearing' with degauss =1d-20 in order to have the Fermi >> Energy written in the log file.( Please, tell me if we are doing >> something wrong here!) The question is: the Fermi Energy that I read >> in the log file, is defined respect to what? Is it already the Fermi >> Energy defined in the article by Zunger? >> Thanks, >> Regards >> Valentina >> >> >> Valentina Dellac? >> Group Materials Labs >> PA&CT - Materials CAE Development & Virtual Analysis >> >> >> Centro Ricerche Fiat S.C.p.A. >> Sede legale e amministrativa: Strada Torino, 50 >> 10043 Orbassano (TO), Italia >> Tel +39 011 9083138 >> Fax +39 011 9083666 >> >> www.crf.it<http://www.crf.it> > > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent libres et ?gaux en > droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? > commune > - Article 2 - Le but de toute association politique est la conservation des > droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - 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 > > > > ------------------------------ > > Message: 6 > Date: Wed, 28 May 2014 08:51:58 -0700 (PDT) > From: David Foster <davidfoster751 at yahoo.com> > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org, tone.kokalj at ijs.si > Message-ID: > <1401292318.90978.YahooMailBasic at web125404.mail.ne1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Prof. Kokalj > Thank you very much for your kindness. I checked the positions that I > gathered from MS Visualizer to prepare ibrav=7 input. I have attached two cif > files, one belonging to primitive_p1, and the other belonging to > conventional_p1 (here p1 means no symmetry or all atoms). Both files I > generated from MS. You can see that the lattice parameters that have been > used for crystal positions of atoms (from primitive_p1.cif) all belong to the > primitive. Please check the files. > If the files areopened with other programs such as Vesta, you can see the > positions of file primitive_p1.cif are relative to primitive translational > vectors. > It will be appreciated if you help. > PS: I generated nanotube (ibrav=12) by this method and everything is OK. If > it is necessary, I can send it too. > Thanks again, and sorry for delay. > > Regards > > David Foster > > Ph.D. Student of Chemistry > > -------------------------------------------- > On Tue, 5/27/14, Tone Kokalj <tone.kokalj at ijs.si> wrote: > > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org > Date: Tuesday, May 27, 2014, 11:56 PM > > On Tue, 2014-05-27 at 10:50 -0700, > David Foster wrote: >> Dear Prof. Kokalj >> Thank you again for your guide. I usually use it, but > introducing 0<ibrav<14 in cases which there are > symmetry, increases speed of calculations. > > In this case, one way to convert is this: first convert > from > "crystal-conventional" coordinates to Cartesian and then > from Cartesian > to "crystal-primitive". This involves a bit of matrix > algebra and > "octave" program comes very handy in this respect. > > Regards. > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint > attachments. > See:? http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: conventional_p1.cif > Type: x-unknown/x-cif > Size: 2148 bytes > Desc: not available > Url : > http://pwscf.org/pipermail/pw_forum/attachments/20140528/c023eedd/attachment-0002.bin > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: primitive_p1.cif > Type: x-unknown/x-cif > Size: 1600 bytes > Desc: not available > Url : > http://pwscf.org/pipermail/pw_forum/attachments/20140528/c023eedd/attachment-0003.bin > > > ------------------------------ > > Message: 7 > Date: Wed, 28 May 2014 08:59:35 -0700 (PDT) > From: David Foster <davidfoster751 at yahoo.com> > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org, tone.kokalj at ijs.si > Message-ID: > <1401292775.76552.YahooMailBasic at web125402.mail.ne1.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Prof. Kokalj > Please change .bin extensions to .cif to see the files. > Regards > > David Foster > > Ph.D. Student of Chemistry > > -------------------------------------------- > On Tue, 5/27/14, Tone Kokalj <tone.kokalj at ijs.si> wrote: > > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org > Date: Tuesday, May 27, 2014, 11:56 PM > > On Tue, 2014-05-27 at 10:50 -0700, > David Foster wrote: >> Dear Prof. Kokalj >> Thank you again for your guide. I usually use it, but > introducing 0<ibrav<14 in cases which there are > symmetry, increases speed of calculations. > > In this case, one way to convert is this: first convert > from > "crystal-conventional" coordinates to Cartesian and then > from Cartesian > to "crystal-primitive". This involves a bit of matrix > algebra and > "octave" program comes very handy in this respect. > > Regards. > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint > attachments. > See:? http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > > ------------------------------ > > Message: 8 > Date: Wed, 28 May 2014 18:25:20 +0200 > From: Tone Kokalj <tone.kokalj at ijs.si> > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org > Message-ID: <1401294320.27691.90.camel at catalyst.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Wed, 2014-05-28 at 08:51 -0700, David Foster wrote: >> Dear Prof. Kokalj >> Thank you very much for your kindness. I checked the positions that I >> gathered from MS Visualizer to prepare ibrav=7 input. > > Don't know what is MS Visualizer. Anyway I took a closer look and > realized that the problem is the lattice definition, which is different > in the two cases (MS Visualizer vs QE). All you need to do is to swap > the columns, i.e., this will work for ibrav=7: > > ATOMIC_POSITIONS crystal > Ba 0.00000 0.00000 0.00000 > As 0.00000 0.34710 0.34710 > As 0.00000 0.65290 0.65290 > Ni 0.50000 0.75000 0.25000 > Ni 0.50000 0.25000 0.75000 > > > Regards, Tone > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > ------------------------------ > > Message: 9 > Date: Wed, 28 May 2014 09:37:16 -0700 (PDT) > From: David Foster <davidfoster751 at yahoo.com> > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org, tone.kokalj at ijs.si > Message-ID: > <1401295036.32140.YahooMailBasic at web125401.mail.ne1.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Prof. Kokalj > > Thank you for your help. The problem is solved with your help. > > Thanks again. > > Regards > > David Foster > > Ph.D. Student of Chemistry > > -------------------------------------------- > On Wed, 5/28/14, Tone Kokalj <tone.kokalj at ijs.si> wrote: > > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org > Date: Wednesday, May 28, 2014, 9:25 AM > > On Wed, 2014-05-28 at 08:51 -0700, > David Foster wrote: >> Dear Prof. Kokalj >> Thank you very much for your kindness. I checked the > positions that I gathered from MS Visualizer to prepare > ibrav=7 input. > > Don't know what is MS Visualizer. Anyway I took a closer > look and > realized that the problem is the lattice definition, which > is different > in the two cases (MS Visualizer vs QE). All you need to do > is to swap > the columns, i.e., this will work for ibrav=7: > > ATOMIC_POSITIONS crystal > ? Ba? ? 0.00000? ? > 0.00000???0.00000 > ? As? ? 0.00000? ? > 0.34710???0.34710 > ? As? ? 0.00000? ? > 0.65290???0.65290 > ? Ni? ? 0.50000? ? > 0.75000???0.25000 > ? Ni? ? 0.50000? ? > 0.25000???0.75000 > > > Regards, Tone > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint > attachments. > See:? http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > > ------------------------------ > > Message: 10 > Date: Wed, 28 May 2014 10:43:08 -0700 (PDT) > From: David Foster <davidfoster751 at yahoo.com> > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org, tone.kokalj at ijs.si > Message-ID: > <1401298988.32807.YahooMailBasic at web125404.mail.ne1.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Prof. Kokalj > > Maybe this question bored you, but it is important for me. Sorry for any > inconvenience. > > Would you please give me more information that how to recognize the > difference in the lattice definition. If I am right in both softwares (QE and > MS) A=B<C. > > So, how did you recognize the difference? > > Regards > > David Foster > > Ph.D. Student of Chemistry > > -------------------------------------------- > On Wed, 5/28/14, Tone Kokalj <tone.kokalj at ijs.si> wrote: > > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org > Date: Wednesday, May 28, 2014, 9:25 AM > > On Wed, 2014-05-28 at 08:51 -0700, > David Foster wrote: >> Dear Prof. Kokalj >> Thank you very much for your kindness. I checked the > positions that I gathered from MS Visualizer to prepare > ibrav=7 input. > > Don't know what is MS Visualizer. Anyway I took a closer > look and > realized that the problem is the lattice definition, which > is different > in the two cases (MS Visualizer vs QE). All you need to do > is to swap > the columns, i.e., this will work for ibrav=7: > > ATOMIC_POSITIONS crystal > ? Ba? ? 0.00000? ? > 0.00000???0.00000 > ? As? ? 0.00000? ? > 0.34710???0.34710 > ? As? ? 0.00000? ? > 0.65290???0.65290 > ? Ni? ? 0.50000? ? > 0.75000???0.25000 > ? Ni? ? 0.50000? ? > 0.25000???0.75000 > > > Regards, Tone > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint > attachments. > See:? http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > > ------------------------------ > > Message: 11 > Date: Wed, 28 May 2014 22:25:31 +0200 > From: Tone Kokalj <tone.kokalj at ijs.si> > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org > Message-ID: <1401308731.27236.31.camel at catalyst.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Wed, 2014-05-28 at 10:43 -0700, David Foster wrote: >> Dear Prof. Kokalj >> >> Maybe this question bored you, but it is important for me. Sorry for any >> inconvenience. >> >> Would you please give me more information that how to recognize the >> difference in the lattice definition. >> If I am right in both softwares (QE and MS) A=B<C. >> >> So, how did you recognize the difference? > > Actually I didn't (at least initially). But from experience I know that > such kinds of problems are typically due to mismatches in lattice > definitions. Your reference to A=B<C pertains to conventional > tetragonal-body-centered cell. This typically implies that conventional > lattice vectors are > > V1=(a,0,0) > V2=(0,b,0) > V3=(0,0,c) > > But then there are multiple choices how to choose primitive vectors. The > QE definition is (see INPUT_PW.txt): > > v1=(a/2)(1,-1,c/a) > v2=(a/2)(1,1,c/a) > v3=(a/2)(-1,-1,c/a) > > but it can equally well be this (1st and 3rd vectors swapped): > > v1=(a/2)(-1,-1,c/a) > v2=(a/2)(1,1,c/a) > v3=(a/2)(1,-1,c/a) > > or any other possibility. To see what effect this have when the > coordinates are specified in fractions of lattice vectors (i.e. crystal > coordinates), consider these two possibilities (patch appropriately your > input file): > > > &system > ibrav=0, celldm(1)=7.83745, > ... > > CELL_PARAMETERS > 0.5 -0.5 1.400757 > 0.5 0.5 1.400757 > -0.5 -0.5 1.400757 > > ATOMIC_POSITIONS crystal > Ba 0.00000 0.00000 0.00000 > As 0.34710 0.34710 0.00000 > As 0.65290 0.65290 0.00000 > Ni 0.75000 0.25000 0.50000 > Ni 0.25000 0.75000 0.50000 > > > versus: > > > &system > ibrav=0, celldm(1)=7.83745, > ... > CELL_PARAMETERS > -0.5 -0.5 1.400757 > 0.5 0.5 1.400757 > 0.5 -0.5 1.400757 > > ATOMIC_POSITIONS crystal > Ba 0.00000 0.00000 0.00000 > As 0.34710 0.34710 0.00000 > As 0.65290 0.65290 0.00000 > Ni 0.75000 0.25000 0.50000 > Ni 0.25000 0.75000 0.50000 > > > The second version gives correct structure, but the first version not. > > > Regards, Tone > > > PS: David, please just call me "Tone" w/o any "prof." prefix, which I am not. > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > ------------------------------ > > Message: 12 > Date: Wed, 28 May 2014 23:10:46 +0200 > From: Tommy <neutrinofrancese at gmail.com> > Subject: [Pw_forum] Hubbard U > To: "Pw_forum at pwscf.org" <Pw_forum at pwscf.org> > Message-ID: <53865107.220dc30a.7520.044f at mx.google.com> > Content-Type: text/plain; charset="windows-1252" > > Dear all, > i'm working on a Yttria doped Zirconia, YSZ. I have understood how to > calculate the U values for a single site, but how can i calculate the U > values for both the transition metal inside the same structure, e.g. Zr and Y > in YSZ structure? Do i have to build a supercell even in this case? Do you > think that i need to calculate also the oxygen U contribute? > Sorry for the trivial question, but I'm deeply interested in the method and > understand every feature. > Thanks in advance, > Tommaso Francese. > Universit? C? Foscari of Venice. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140528/2219ca4f/attachment-0001.html > > > ------------------------------ > > Message: 13 > Date: Thu, 29 May 2014 07:49:10 +0900 > From: "Higuchi Toshiharu" <toshihigu at r7.dion.ne.jp> > Subject: Re: [Pw_forum] Graphene_fixed calculation > To: "'Ari Paavo Seitsonen'" <Ari.P.Seitsonen at iki.fi>, "'PWSCF Forum'" > <pw_forum at pwscf.org> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="UTF-8" > > Dear Dr. Seitsonen, > > Thank you very much for your kindness reply. > I changed the k points, however the band gap was not 0 eV. > If you have any comment, please teach me. > > k-point(automatic) HOMO LUMO band gap > 40 40 1 1 1 1 -0.8642 eV -0.6635 eV 0.2007 eV > 40 40 1 0 0 0 -0.9682 eV -0.5618 eV 0.4064 eV > 40 40 1 0 0 1 -0.9686 eV -0.5622 eV 0.4064 eV > > (band gap = LUMO - HOMO) > *********************************************** > Dr. Toshiharu Higuchi > University of Tsukuba/ Japan > E-Mail: toshihigu at r7.dion.ne.jp > *********************************************** > > > -----Original Message----- > From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On > Behalf Of Ari P Seitsonen > Sent: Tuesday, May 27, 2014 7:08 PM > To: PWSCF Forum > Subject: Re: [Pw_forum] Graphene_fixed calculation > > > Dear Toshiharu Higuchi, > > How did you determine the band gap? Do you have a k point exactly at the > point K of the Brillouin zone? I would guess no, and like I mentioned > recently, I do not think that shifting the Monkhorst-Pack k point grid away > from the Gamma (or Gamma-bar in two dimensions) point is a good idea. > > Greetings, > > apsi > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > Institut f?r Chemie der Universit?t Z?rich, CH-8057 Z?rich > Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 > > > On Tue, 27 May 2014, Higuchi Toshiharu wrote: > >> >> Dear Quantum-ESRESSO users, >> >> I would like to calculate the local density of state of graphene and >> graphene >> >> related materials. >> >> Using the following pw.in file, I calculated the scf under ?occupation >> = fixed?, >> >> and get the HOMO = -0.8642 eV, and LUMO = -0.6635 eV. This results >> indicate >> >> that this graphene is an insulator having a band gap of 0.2007 eV. >> >> However, this model is half-metal having a band gap of 0.0 eV, if I >> calculated by >> >> this process: (1)SCF (smearing) -> nscf (tetrahedra) -> ProjWFC. >> >> Why will it become the error when I set ?occupation = fixed?? >> >> I would really appreciate if you teach me. >> >> ****************************************************************** >> >> &CONTROL >> >> title = 'Graphene_1A2' , >> >> calculation = 'scf' , >> >> restart_mode = 'from_scratch' , >> >> outdir = '/home/user/tmp/' , >> >> pseudo_dir = >> '/home/user/espresso-5.0.1/espresso-5.0.1/pseudo/' , >> >> prefix = 'Graphene_1A2' , >> >> verbosity = 'high' , >> >> / >> >> &SYSTEM >> >> ibrav = 4, >> >> celldm(1) = 4.6595, >> >> celldm(3) = 4.0571, >> >> nat = 2, >> >> ntyp = 1, >> >> ecutwfc = 40 , >> >> ecutrho = 200 , >> >> nbnd = 150, >> >> occupations = 'fixed' , >> >> degauss = 0.02 , >> >> smearing = 'gaussian' , >> >> exxdiv_treatment = 'gygi-baldereschi' , >> >> / >> >> &ELECTRONS >> >> electron_maxstep = 100, >> >> conv_thr = 1.D-8 , >> >> / >> >> ATOMIC_SPECIES >> >> C 12.01100 C.pz-rrkjus.UPF >> >> ATOMIC_POSITIONS angstrom >> >> C 0.000000000 0.000000000 0.000000000 >> >> C 1.232850116 0.706423116 0.000000000 >> >> K_POINTS automatic >> >> 40 40 1 1 1 1 >> >> >> >> ********************************************************************** >> **************** >> >> Toshiharu Higuchi >> >> University of Tsukuba/ Japan >> >> E-Mail: toshihigu at r7.dion.ne.jp >> >> ********************************************************************** >> **************** >> >> >> >> >> > > > > > ------------------------------ > > Message: 14 > Date: Thu, 29 May 2014 05:01:21 +0530 > From: siddheshwar chopra <sidhusai at gmail.com> > Subject: [Pw_forum] How to add supercell to QE i/p file > To: pw_forum at pwscf.org > Message-ID: > <CAMWZ2mfhpXCAQ0LG0rvLyVe4H67SMPaV7S7NxmPk11gsKEXRiw at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear users, > Somebody please help me in making my first i/p file in QE for graphene. I > want to find band gap of a 4x4x1 supercell of graphene.. > Also how do we find k point path? Please help... > > Regards, > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140529/479feb0d/attachment-0001.html > > > ------------------------------ > > Message: 15 > Date: Wed, 28 May 2014 18:14:50 -0700 (PDT) > From: David Foster <davidfoster751 at yahoo.com> > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org, tone.kokalj at ijs.si > Message-ID: > <1401326090.91340.YahooMailBasic at web125404.mail.ne1.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Tone > Thank you. It was very helpful. > Regards > > David Foster > > Ph.D. Student of Chemistry > > -------------------------------------------- > On Wed, 5/28/14, Tone Kokalj <tone.kokalj at ijs.si> wrote: > > Subject: Re: [Pw_forum] ibrav7 doesn't show the structure of BaNi2As2 > correctly > To: pw_forum at pwscf.org > Date: Wednesday, May 28, 2014, 1:25 PM > > On Wed, 2014-05-28 at 10:43 -0700, > David Foster wrote: >> ? Dear Prof. Kokalj >> >> Maybe this question bored you, but it is important for > me. Sorry for any inconvenience. >> >> Would you please give me more information that how to > recognize the difference in the lattice definition. >> If I am right in both softwares (QE and MS) A=B<C. >> >> So, how did you recognize the difference? > > Actually I didn't (at least initially). But from experience > I know that > such kinds of problems are typically due to mismatches in > lattice > definitions. Your reference to A=B<C pertains to > conventional > tetragonal-body-centered cell. This typically implies that > conventional > lattice vectors are > > V1=(a,0,0) > V2=(0,b,0) > V3=(0,0,c) > > But then there are multiple choices how to choose primitive > vectors. The > QE definition is (see INPUT_PW.txt): > > v1=(a/2)(1,-1,c/a)? > v2=(a/2)(1,1,c/a) > v3=(a/2)(-1,-1,c/a) > > but it can equally well be this (1st and 3rd vectors > swapped): > > v1=(a/2)(-1,-1,c/a) > v2=(a/2)(1,1,c/a) > v3=(a/2)(1,-1,c/a) > > or any other possibility.? To see what effect this have > when the > coordinates are specified in fractions of lattice vectors > (i.e. crystal > coordinates), consider these two possibilities (patch > appropriately your > input file): > > > &system > ? ???ibrav=0,? celldm(1)=7.83745, > ... > > CELL_PARAMETERS > ? 0.5 -0.5 1.400757 > ? 0.5? 0.5 1.400757 > -0.5 -0.5 1.400757 > > ATOMIC_POSITIONS crystal > ? Ba? ? > ???0.00000???0.00000???0.00000? > > ? As? ? > ???0.34710???0.34710???0.00000? > > ? As? ? > ???0.65290???0.65290???0.00000? > > ? Ni? ? > ???0.75000???0.25000???0.50000? > > ? Ni? ? > ???0.25000???0.75000???0.50000? > > > > versus: > > > &system > ? ???ibrav=0,? celldm(1)=7.83745, > ... > CELL_PARAMETERS > -0.5 -0.5 1.400757 > ? 0.5? 0.5 1.400757 > ? 0.5 -0.5 1.400757 > > ATOMIC_POSITIONS crystal > ? Ba? ? > ???0.00000???0.00000???0.00000? > > ? As? ? > ???0.34710???0.34710???0.00000? > > ? As? ? > ???0.65290???0.65290???0.00000? > > ? Ni? ? > ???0.75000???0.25000???0.50000? > > ? Ni? ? > ???0.25000???0.75000???0.50000? > > > > The second version gives correct structure, but the first > version not. > > > Regards, Tone > > > PS: David, please just call me "Tone" w/o any "prof." > prefix, which I am not. > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint > attachments. > See:? http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > > ------------------------------ > > Message: 16 > Date: Thu, 29 May 2014 09:57:52 +0530 > From: Sridhar Sadasivam <sridhu88 at gmail.com> > Subject: Re: [Pw_forum] How to add supercell to QE i/p file > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <CANTo9TuSaAgsvJHDNPu3vf1iGR4=S78TrcA+JeYxhMgW264_+A at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > I usually just write a small code to generate supercells. Knowing the > primitive lattice vectors and basis atoms (2 for graphene), it is very easy > to write a small code that can be used to generate a NxN supercell. You can > then also visualize in XCrysden to make sure that you have generated the > structure correctly. > > You can use XCrysden to get the k-point path as well. Just remember that > the k-point path obtained from XCrysden is in crystal units. > Sridhar > > > On Thu, May 29, 2014 at 5:01 AM, siddheshwar chopra <sidhusai at > gmail.com>wrote: > >> Dear users, >> Somebody please help me in making my first i/p file in QE for graphene. I >> want to find band gap of a 4x4x1 supercell of graphene.. >> Also how do we find k point path? Please help... >> >> Regards, >> >> _______________________________________________ >> 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/20140529/2a9ab218/attachment-0001.html > > > ------------------------------ > > Message: 17 > Date: Thu, 29 May 2014 10:38:55 +0530 > From: siddheshwar chopra <sidhusai at gmail.com> > Subject: Re: [Pw_forum] How to add supercell to QE i/p file > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <CAMWZ2mcx71YVZ8cJXESG4GyJ9vBY=ari+1g=mGdhesF1gUKr2Q at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Sridhar, > Could you share that code with us? > Also I know how to make a supercell using Avogadro.. > I need to know HOW should I add that supercell in the QE i/p file? I would > be glad if you could provide me on such i/p file which contains say 4x4x1 > supercell of graphene. > > Regards, > > > On Thu, May 29, 2014 at 9:57 AM, Sridhar Sadasivam <sridhu88 at > gmail.com>wrote: > >> I usually just write a small code to generate supercells. Knowing the >> primitive lattice vectors and basis atoms (2 for graphene), it is very easy >> to write a small code that can be used to generate a NxN supercell. You can >> then also visualize in XCrysden to make sure that you have generated the >> structure correctly. >> >> You can use XCrysden to get the k-point path as well. Just remember that >> the k-point path obtained from XCrysden is in crystal units. >> Sridhar >> >> >> On Thu, May 29, 2014 at 5:01 AM, siddheshwar chopra <sidhusai at >> gmail.com>wrote: >> >>> Dear users, >>> Somebody please help me in making my first i/p file in QE for graphene. I >>> want to find band gap of a 4x4x1 supercell of graphene.. >>> Also how do we find k point path? Please help... >>> >>> Regards, >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > *Dr. Siddheshwar chopra,* > > > *M.Sc., Ph.D (Physics)Assistant Professor (Physics),* > *Amity University, Noida, India.* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140529/a413cacc/attachment-0001.html > > > ------------------------------ > > Message: 18 > Date: Thu, 29 May 2014 12:41:43 +0530 > From: Peram sreenivasa reddy <peramsreenivas at gmail.com> > Subject: [Pw_forum] Reg: To calculate EOS using Quantum espresso. > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <CAC0U+wVY9PN7e0u6=Eb8OrVT5dNgKruHd05yP9O3Dx-+=orzbg at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear PWSCF Forum, > > I want to calculate the equation of state by using Quamtum Espresso. > > I have the Volume and total energy values for different lattice parameter > values of the same compound. > > Now i want to to calculate the equation of state by using Quantum Espresso. > > Please help me. > > Thank you very much in advance. > > Thanking you. > > -- > *P.V.SREENIVASA REDDY* > > *Research ScholarDepartment of Physics * > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140529/a3b596a9/attachment-0001.html > > > ------------------------------ > > Message: 19 > Date: Thu, 29 May 2014 12:50:15 +0530 > From: siddheshwar chopra <sidhusai at gmail.com> > Subject: [Pw_forum] Conductivity measurements using QE... > To: PWSCF-QE Forum <Pw_forum at pwscf.org> > Message-ID: > <CAMWZ2mexun7ozJ8Ww5gmtwpW1cZpcOtBU4=_KRSaOY3OxzhNyQ at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Users, > I am new to QE and wish to know if we can measure the electronic > conductivity of a thin films by varying electrodes (Au,Ag etc)? If yes how > can we go about it? > > Regards, > > -- > *Dr. Siddheshwar chopra,* > > > *M.Sc., Ph.D (Physics)Assistant Professor (Physics),* > *Amity University, Noida, India.* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140529/a2e871e5/attachment-0001.html > > > ------------------------------ > > Message: 20 > Date: Thu, 29 May 2014 16:50:26 +0800 > From: Francis Jing <francijing at gmail.com> > Subject: [Pw_forum] Counterpoise correction > To: pw_forum at pwscf.org > Message-ID: > <CACg4Yc2Acjjh0xLczkKHMwjLqFiKhzt18u+TPANnCA6ArUDeZQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I want to study weak interactions using vdw-DF, and have two questions: > > 1. How to do counterpoise correction? > I have searched the manual and the web, but cannot find a detailed > instruction. > In the Gaussian program, it is done by setting atoms as ghost. So how can I > use ghost atoms in PWscf? > > 2. The vdw-DF already has a good description of weak interactions, so is > there any need to do counterpoise correction? > > Thanks, > Francis > > -- > Zhifeng (Francis) Jing > Graduate Student in Physical Chemistry > School of Chemistry and Chemical Engineering > Shanghai Jiao Tong University > http://sun.sjtu.edu.cn > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140529/2dc6943b/attachment-0001.html > > > ------------------------------ > > Message: 21 > Date: Thu, 29 May 2014 10:58:47 +0200 > From: Tommaso Francese <neutrinofrancese at gmail.com> > Subject: [Pw_forum] resp_mat.f90 > To: pw_forum at pwscf.org > Message-ID: <461816BF-94A4-4A81-ADA1-5836588431A9 at gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all QE users, > shall i ask you where i can find the reps_mat.f90 script exactly and all the > script used in > http://media.quantum-espresso.org/santa_barbara_2009_07/slides-exercices/Handson_ldau.pdf > ? > Thanks in advance, > Tommaso > Universit? C? Foscari of Venice > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140529/5a13f1bf/attachment-0001.html > > > ------------------------------ > > Message: 22 > Date: Thu, 29 May 2014 11:02:21 +0200 > From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it> > Subject: Re: [Pw_forum] Hubbard U > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <201405291102.21842.giuseppe.mattioli at ism.cnr.it> > Content-Type: Text/Plain; charset="iso-8859-1" > > > Dear Tommaso > Regarding the metal ions, Matteo Cococcioni already answered your question: > you can use the same supercell to calculate both the linear response > values. Regarding the O, it is often useful/mandatory to use an on-site > correction in transition metal oxides, because if you correct only the metal > you may completely miss the p-d coupling. But a reasonable estimate of the U > value for O is not very easy. You may be interested in this paper, which > investigates the double U(Ti,O) correction in intrinsic and defective TiO2: > > Mattioli, et al.; J. Phys. Chem. C 2010, 114, 21694. > > J. J. Gong pointed out some days ago an alternative method to estimate the ab > initio U value in fully occupied (or almost fully occupied) bands, which > is often the case of O 2p bands in oxides. It could be interesting to know > the opinion of the QE "U-developers" on the possibility to implement the > related Hartree-Fock calculation. Anyway the method is discussed here: > > Mosey, et al.; J. Chem Phys. 2008, 129, 014103 > > Finally, the implementation of the U+V correction (see Leiria Campo and > Cococcioni; J. Phys.: Condens. Matter 2010, 22, 055602), which would be very > useful in covalent compounds, should be added to the next QE release. For a > comprehensive review, you may also be interested in: > > Himmetoglu, et al.; Int. J. Quantum Chem. 2014, 114, 14. > > HTH > > Giuseppe > > On Wednesday 28 May 2014 23:10:46 Tommy wrote: >> Dear all, >> i'm working on a Yttria doped Zirconia, YSZ. I have understood how to >> calculate the U values for a single site, but how can i calculate the U >> values for both the transition metal inside the same structure, e.g. Zr >> and Y in YSZ structure? Do i have to build a supercell even in this case? >> Do you think that i need to calculate also the oxygen U contribute? Sorry >> for the trivial question, but I'm deeply interested in the method and >> understand every feature. Thanks in advance, >> Tommaso Francese. >> Universit? C? Foscari of Venice. > > > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: <giuseppe.mattioli at ism.cnr.it> > http://www.ism.cnr.it/english/staff/mattiolig > ResearcherID: F-6308-2012 > > > > ------------------------------ > > Message: 23 > Date: Thu, 29 May 2014 11:05:47 +0200 (CEST) > From: Ari P Seitsonen <Ari.P.Seitsonen at iki.fi> > Subject: Re: [Pw_forum] Counterpoise correction > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <alpine.LSU.2.00.1405291103290.229963 at pcihserv.uzh.ch> > Content-Type: text/plain; charset="utf-8" > > > Dear Francis, > > When using plane waves there is no need for the counterpoise correction > as there is no basis set superposition error (in a given cell the basis > set does not depend on how many or which kind of atoms are in the cell). > Please check the literature on plane wave basis sets for further > explanation. > > Greetings from Zurich, > > apsi > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ > Institut f?r Chemie der Universit?t Z?rich, CH-8057 Z?rich > Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 > > > On Thu, 29 May 2014, Francis Jing wrote: > >> Dear all, >> >> I want to study weak interactions using vdw-DF, and have two questions: >> >> 1. How to do counterpoise correction? >> I have searched the manual and the web, but cannot find a detailed >> instruction. >> In the Gaussian program, it is done by setting atoms as ghost. So how can I >> use ghost atoms in PWscf? >> >> 2. The vdw-DF already has a good description of weak interactions, so is >> there any need to do counterpoise correction? >> >> Thanks, >> Francis >> >> -- >> Zhifeng (Francis) JingGraduate Student in Physical Chemistry >> School of Chemistry and Chemical Engineering >> Shanghai Jiao Tong University >> http://sun.sjtu.edu.cn >> > > ------------------------------ > > Message: 24 > Date: Thu, 29 May 2014 11:06:49 +0200 > From: Tone Kokalj <tone.kokalj at ijs.si> > Subject: Re: [Pw_forum] Counterpoise correction > To: pw_forum at pwscf.org > Message-ID: <1401354409.27236.36.camel at catalyst.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Thu, 2014-05-29 at 16:50 +0800, Francis Jing wrote: >> Dear all, >> >> >> I want to study weak interactions using vdw-DF, and have two >> questions: >> >> >> 1. How to do counterpoise correction? >> I have searched the manual and the web, but cannot find a detailed >> instruction. > > You have not find any instruction, because there is no basis-set > superposition error with plane-wave basis set, hence the counterpoise > correction = 0. > > Regards, > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > ------------------------------ > > Message: 25 > Date: Thu, 29 May 2014 11:26:13 +0200 > From: Giovanni Cantele <giovanni.cantele at spin.cnr.it> > Subject: Re: [Pw_forum] Counterpoise correction > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4B2D8046-3E42-4538-8EB1-32D8BA63B91E at spin.cnr.it> > Content-Type: text/plain; charset="us-ascii" > > > On 29 May 2014, at 10:50, Francis Jing <francijing at gmail.com> wrote: > >> Dear all, >> >> I want to study weak interactions using vdw-DF, and have two questions: >> >> 1. How to do counterpoise correction? >> I have searched the manual and the web, but cannot find a detailed >> instruction. >> In the Gaussian program, it is done by setting atoms as ghost. So how can I >> use ghost atoms in PWscf? >> >> 2. The vdw-DF already has a good description of weak interactions, so is >> there any need to do counterpoise correction? >> >> Thanks, >> Francis >> >> -- >> Zhifeng (Francis) Jing >> Graduate Student in Physical Chemistry >> School of Chemistry and Chemical Engineering >> Shanghai Jiao Tong University >> http://sun.sjtu.edu.cn >> _______________________________________________ >> > > > Dear Francis, > > PWscf uses plane waves which is not a localised basis set. The counterpoise > method allows to correct the basis set superposition error, > arising when using finite, localised basis sets. > > > Giovanni > > -- > > Giovanni Cantele, PhD > CNR-SPIN > c/o Dipartimento di Fisica > Universita' di Napoli "Federico II" > Complesso Universitario M. S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > e-mail: giovanni.cantele at spin.cnr.it > Phone: +39 081 676910 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.na.infn.it/~cantele > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140529/bb4e2428/attachment-0001.html > > > ------------------------------ > > Message: 26 > Date: Thu, 29 May 2014 11:47:05 +0200 > From: Matteo Cococcioni <matteo at umn.edu> > Subject: Re: [Pw_forum] resp_mat.f90 > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <CAMZASgFzc6XbQZVk2Zf=Y0qoA8kuJdaMiC0h7R1nm=qKMAHbuA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Tommaso, > > it should be in the tar file you can download that contains the examples to > run. > > best, > > Matteo > > > On Thu, May 29, 2014 at 10:58 AM, Tommaso Francese < > neutrinofrancese at gmail.com> wrote: > >> Dear all QE users, >> shall i ask you where i can find the reps_mat.f90 script exactly and all >> the script used in >> http://media.quantum-espresso.org/santa_barbara_2009_07/slides-exercices/Handson_ldau.pdf >> ? >> Thanks in advance, >> Tommaso >> Universit? C? Foscari of Venice >> >> _______________________________________________ >> 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/20140529/489e2b1d/attachment-0001.html > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > End of Pw_forum Digest, Vol 82, Issue 30 > ****************************************
