From guntram.schmidt at chemie.uni-halle.de Mon Aug 1 12:08:42 2011 From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt) Date: Mon, 01 Aug 2011 12:08:42 +0200 Subject: [Pw_forum] How to convince QE from local lapack/blas? In-Reply-To: <61A00C8B-E1AF-4FAF-B140-238805CEF4F0@democritos.it> References: <4E28041D.6050101@chemie.uni-halle.de> <299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg> <4E2F1616.8080905@chemie.uni-halle.de> <0FA242DB-AA44-4B5C-BA79-992927CEBB5A@ihpc.a-star.edu.sg> <61A00C8B-E1AF-4FAF-B140-238805CEF4F0@democritos.it> Message-ID: <4E367B2A.8010007@chemie.uni-halle.de> Dear Paolo! Thanks a lot for this clearification! It finally got me to be able to use essl, though. I had to use -D__ESSL instead of D_LINUX_ESSL (suggested by ./configure)! Finally a last question: Is is meaningfull to have the internal lapack loaded after the external one? I mean: LAPACK_LIBS = -lessl -L/gpfs/usrurz/lib64 -llapack /gpfs/home/aasfu/espresso-4.3.2/lapack-3.2/lapack.a vs. LAPACK_LIBS = -lessl -L/gpfs/usrurz/lib64 -llapack /gpfs/usrurz/lib64/liblapack.a beeing our local compiled version. Thank you, Guntram Am 27.07.2011 22:31, schrieb Paolo Giannozzi: > > On Jul 27, 2011, at 5:40 , Michael Sullivan wrote: > >> If I'm not wrong, that just means that you're not using ESSL. > > it is true that by linking lapack before essl, the lapack version > of lapack routines is linked, not the essl version. However > the fft and blas from essl are linked (unless there is a > copy of blas into lapack, which shouldn't be the case). > The resulting loss of performances should be minor. > If fft and blas from essl are not linked, the loss of > performances is much larger. > > Final clarification: > > -D__ESSL means that the fft routines of essl are used, and > that the calls of some lapack routines follow the essl syntax, > not the lapack syntax; > > -D__LINUX_ESSL means that the fft routines of essl are used, > and that the calls of lapack routines follow the lapack syntax. > > In all cases, it is convenient to link essl before lapack (essl does > not contain all lapack routines, just a subset, so not linking lapack > may result in missing symbols). If the lapack replacements in essl > do not follow the lapack syntax (IBM SP machines, typically), > -D__ESSL should be used. If they follow the lapack syntax, or if > they do not contain lapack replacements (IBM BlueGene and other > strange IBM machines), -D__LINUX_ESSL should be used. > > Complicated? blame the geniuses who wrote lapack replacements > with the same names but called in a different way > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From wonvein at gmail.com Mon Aug 1 12:47:37 2011 From: wonvein at gmail.com (WANG Wei) Date: Mon, 1 Aug 2011 19:47:37 +0900 Subject: [Pw_forum] Problem with modifying the QE code for the spin-polarized vdW-DF calculation Message-ID: Dear QE developers, As well known, the non-local vdW correlation is not defined for spin-polarised systems. However, I noted that some codes (such as vasp, Junolo) can evaluate the non-local vdW correlation energy on the sum of the spin-up and spin-down densities. Is it a good approximation? Because my systems consist of charged defects, I have to modify the QE code to support the spin-polarized vdW-DF calculation. (1) Firstly, I modified the /PW/stres_nonloc_dft.f90 file. I defined the rho_valence(:, :) and replaced the "rho" in the " CALL stress_vdW_DF(rho, rho_core, sigma_nonloc_dft)" with "rho_valence", namely ################################# real(DP), intent(in) :: rho (dfftp%nnr, nspin), rho_core (dfftp%nnr) real(DP), intent(inout) :: sigma_nonloc_dft (3, 3) integer ::nspin, inlc real(DP), allocatable :: rho_valence(:, :) integer :: l, m, i allocate(rho_valence(dfftp%nnr, 1)) sigma_nonloc_dft(:,:) = 0.d0 inlc = get_inlc() if (inlc==1 .or. inlc==2) then if (nspin>4) call errore('stres_vdW_DF', & 'vdW+DF non implemented in non-collinear magnetic calculations',1) ! get the valence charge density do i=1, nspin rho_valence(:,1)=rho_valence(:,1)+rho(:,i) end do CALL stress_vdW_DF(rho_valence, rho_core, sigma_nonloc_dft) end if return deallocate(rho_valence) end subroutine stres_nonloc_dft ################################# (2) Secondly, I commented out all the "call errore('xc_vdW_DF','vdW functional not implemented for spin polarized runs', size(rho_valence,2)-1)". Moreover, I also modified the subroutine dv_drho_vdw. ################################# !! Delta rho in real space do i=1,nspin CALL invfft ('Dense', drho(:,i), dfftp) drho_real(:) = drho_real(:)+REAL( drho(:,i) ) end do ################################# My question is: Are there other parts need to modify? Best Regards, WANG -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110801/1fdb77ac/attachment.htm From giannozz at democritos.it Mon Aug 1 13:02:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 1 Aug 2011 13:02:46 +0200 Subject: [Pw_forum] How to convince QE from local lapack/blas? In-Reply-To: <4E367B2A.8010007@chemie.uni-halle.de> References: <4E28041D.6050101@chemie.uni-halle.de> <299E6A96-12FD-4C30-8756-7DC6987C805B@ihpc.a-star.edu.sg> <4E2F1616.8080905@chemie.uni-halle.de> <0FA242DB-AA44-4B5C-BA79-992927CEBB5A@ihpc.a-star.edu.sg> <61A00C8B-E1AF-4FAF-B140-238805CEF4F0@democritos.it> <4E367B2A.8010007@chemie.uni-halle.de> Message-ID: <1B51D277-C607-4A5D-84EC-BBCFE7E60769@democritos.it> On Aug 1, 2011, at 12:08 , Guntram Schmidt wrote: > Is it meaningful to have the internal lapack loaded after > the external one? I mean: > > LAPACK_LIBS = -lessl -L/gpfs/usrurz/lib64 -llapack > /gpfs/home/aasfu/espresso-4.3.2/lapack-3.2/lapack.a > > vs. > > LAPACK_LIBS = -lessl -L/gpfs/usrurz/lib64 -llapack it shouldn't make any difference: lapack routines should be linked from essl if present there, from /gpfs/usrurz/lib64 if not. Nothing should be linked from the internal library. The best way to be sure is "experimental computer science", i.e., to try and see what happens. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From thomas.gruber at physik.tu-freiberg.de Mon Aug 1 13:32:37 2011 From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber) Date: Mon, 01 Aug 2011 13:32:37 +0200 Subject: [Pw_forum] repeated band structure calculation in splittet phonon calculation Message-ID: <4E368ED5.2020703@physik.tu-freiberg.de> Dear All, In a phonon calculation with a different k-point grid than in a scf calculation a band structure calculation is needed for every q-point, but not for every irreducible representations. Now I want to split this phonon calculation in every q-point and every irreducible representations. But when I do that, there will be a band structure calculation in every job, but only one per q-point is necessary. How can I save the band structure calculation to be read for every job? Every job will be run on one core, because I got problems with the final run. The program was looking for a *.wfc file and I used wf_collect = .true. in the scf run. Everything worked fine with Version 4.3.1 when I didn't used wf_collect and did all jobs on one core. Or did I something wrong and it should work? Regards, Thomas From Heiles at cluster.pc.chemie.tu-darmstadt.de Mon Aug 1 14:08:55 2011 From: Heiles at cluster.pc.chemie.tu-darmstadt.de (Sven Heiles) Date: Mon, 01 Aug 2011 14:08:55 +0200 Subject: [Pw_forum] Increasing FFT grid for charge density analyses Message-ID: <4E369757.2060604@cluster.pc.chemie.tu-darmstadt.de> Dear all! I have performed calculations for small molecules in QuantumEspresso v4.2.1. For post-processing I intend to analyse the charge transfer via Bader analyses. http://theory.cm.utexas.edu/vtsttools/bader/ For this purpose I have generated a cube file with pp.x and nx,y,z=120. Unfortunately I am not able to increase the FFT grid for the output file by increasing nx,y,z and therefore I am not able to test the convergence of the Bader analyses. Is it because I am using the gamma-point specific algortihm or is there another way to improfe the grid? Best wishes Sven -- Dipl. Ing. Sven Heiles Technische Universit?t Darmstadt AK Sch?fer Eduard-Zintl-Institut Petersenstra?e 20 D-64287 Darmstadt ? Germany Phone: ++49-(0)6151-164397 Fax: ++49-(0)6151-166024 Web: http://www.tu-darmstadt.de/fb/ch/cluster/schaefer.tud From m.abbasnejad at gmail.com Mon Aug 1 15:01:05 2011 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Mon, 1 Aug 2011 17:31:05 +0430 Subject: [Pw_forum] About the Frozen Phonon Method Message-ID: Dear users, I have plotted the harmonic frequency (obtained within the frozen phonon approach) of Diamond as a function of atomic displacements (small displacements in the [1 1 1] direction, u(1)=?(u,u,u) and u(2)=?(-u,-u,-u) are the displacements of two atoms in the basis). I expect to see a range of displacements that tend to the similar frequency, but there is no convergence in the plot. Also, the displacements with the same amplitude but different in sign, do not tend to the same frequency, which is not what I expect, too. The plot is attached. I was wondering if anyone could help me to find the source of error. I should expect the mentioned symmetry, right? Why there is no convergence? Thanks in advance. Yours, Mohaddeseh --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110801/4036e4b0/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: fig..pdf Type: application/pdf Size: 38632 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110801/4036e4b0/attachment-0001.pdf From baroni at sissa.it Mon Aug 1 16:03:59 2011 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 1 Aug 2011 16:03:59 +0200 Subject: [Pw_forum] About the Frozen Phonon Method In-Reply-To: References: Message-ID: <4EE86CC9-72B4-4565-9D10-FB055D8DC851@sissa.it> Hi Mohaddesh. I do not understand why you say that the calculated frequency (which, I assume you define as 2 * Delta E / u^2 ???) does not converge as u->0. According to your plot, it does, and to a reasonable value. The finite slope of your plot around u=0 seems to me nothing but a manifestation of cubic anharmonicity ... What's wrong in this? SB On Aug 1, 2011, at 3:01 PM, mohaddeseh abbasnejad wrote: > > Dear users, > > I have plotted the harmonic frequency (obtained within the frozen phonon approach) of Diamond as a function of atomic displacements (small displacements in the [1 1 1] direction, u(1)=?(u,u,u) and u(2)=?(-u,-u,-u) are the displacements of two atoms in the basis). I expect to see a range of displacements that tend to the similar frequency, but there is no convergence in the plot. Also, the displacements with the same amplitude but different in sign, do not tend to the same frequency, which is not what I expect, too. The plot is attached. > I was wondering if anyone could help me to find the source of error. I should expect the mentioned symmetry, right? Why there is no convergence? > > Thanks in advance. > > Yours, > Mohaddeseh > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110801/ab3afc9c/attachment.htm From m.abbasnejad at gmail.com Mon Aug 1 16:56:13 2011 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Mon, 1 Aug 2011 19:26:13 +0430 Subject: [Pw_forum] About the Frozen Phonon Method In-Reply-To: <4EE86CC9-72B4-4565-9D10-FB055D8DC851@sissa.it> References: <4EE86CC9-72B4-4565-9D10-FB055D8DC851@sissa.it> Message-ID: Dear Prof. Baroni Thanks for your reply. I wonder shouldn't the plot show the same frequency for a range of displacements? And the same freq. for the range to be the harmonic frequency? or the zero displacement limit, is the harmonic frequency? And when I test the displacements with the same amplitude, but different in sign (regarding the inward and outward atomic movements in the basis) I do not get the same results. Shouldn't the plot have symmetry vs. the vertical axis? Thank You again Mohaddeseh On Mon, Aug 1, 2011 at 6:33 PM, Stefano Baroni wrote: > Hi Mohaddesh. I do not understand why you say that the calculated frequency > (which, I assume you define as 2 * Delta E / u^2 ???) does not converge as > u->0. According to your plot, it does, and to a reasonable value. The finite > slope of your plot around u=0 seems to me nothing but a manifestation of > cubic anharmonicity ... What's wrong in this? SB > > On Aug 1, 2011, at 3:01 PM, mohaddeseh abbasnejad wrote: > > > Dear users, > > I have plotted the harmonic frequency (obtained within the frozen phonon > approach) of Diamond as a function of atomic displacements (small > displacements in the [1 1 1] direction, u(1)=?(u,u,u) and > u(2)=?(-u,-u,-u) are the displacements of two atoms in the basis). I expect > to see a range of displacements that tend to the similar frequency, but > there is no convergence in the plot. Also, the displacements with the same > amplitude but different in sign, do not tend to the same frequency, which is > not what I expect, too. The plot is attached. > I was wondering if anyone could help me to find the source of error. I > should expect the mentioned symmetry, right? Why there is no convergence? > > Thanks in advance. > > Yours, > Mohaddeseh > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110801/d123df66/attachment.htm From fratesi at mater.unimib.it Mon Aug 1 18:01:06 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Mon, 1 Aug 2011 18:01:06 +0200 (CEST) Subject: [Pw_forum] question about LDOS calculation within boxes using pp.x In-Reply-To: References: Message-ID: Dear Habibi, > I have been trying to use pp.x on a Cr(001) slab, and I would like to calculate PDOS in a box above de surface. I guess you are referring to projwfc.x rather than pp.x > As a matter of fact, I would like to see the decrease of the > wavefunctions in the vacuum, by analysing the PDOS in boxes at different > heights. Maybe you could be more interested in using indeed pp.x to extract the DOS as a function of position. To make the distinction clear (?): 1) the local DOS is a function of position and energy, say D(r,E); 2) projwfc.x allows to compute and plot *as a function of E*, the integral of D in a specified volume (box) 3) pp.x allows to compute and plot *as a function of r*, the integral of D in a specified energy window (see plot_num=10) It seems to me that this last point is what you are interested in. You have to choose your energy window. Alternatively, pick up just one wavefunction (plot_num=7). > After a calculation on small boxes, I would like to have, now, an > average type box, on the whole surface, so let's say a pavement-like > box. > > After a pp.x regular PDOS calculation, I have noticed that the > segmentation along x and y direction is 30, I thought that regarding > this information, I could take a box with a width of 30 on x and y > direction for another pp.x calculation with the boxes to get the big box > I need. If your FFT grid contains 30 points, you can select the full cell (in that direction) by putting irmin=1 and irmax=30. See example16. (irmin=0, from your input, is equivalent to 30; the first and last points you specify are INCLUDED). > Hence, pp.x generates a .xsf file for visualizing the boxes. When I > would calculate it with a small box (width=2 on x and y directions, ie > irmin(1)=1, irmax(1)=3 in the pp.x input file), I could see the box with > xcrysden. However, using the big values (30) for my boxes boundaries, I > cannot visualize them. But I still get a result about ldos in the boxes. The box is visualized as xsf files with 3D datagrids, valued 1.0 inside the box volume and 0 outside (visualize them as isosurfaces with isovalue 0.5). If the box is as large as the unit cell, all values are =1.0 and no isosurface=0.5 can be shown. There's no box boundary, in a periodic world. > My questions are the following : how can I be sure that the ldos > calculation are actually done within my big boxes boundaries? Is it > correct to use that big segmentation in the first place? Try a few tests to practice: compute the LDOS in the full cell; compute it in two halves; ... Notice that augmentation charge contribution is not included, so you should use norm-conserving pseudopotentials if you want to compare this to the full DOS. Hope this helps, Guido Fratesi -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca From baroni at sissa.it Mon Aug 1 20:03:53 2011 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 1 Aug 2011 20:03:53 +0200 Subject: [Pw_forum] About the Frozen Phonon Method In-Reply-To: References: <4EE86CC9-72B4-4565-9D10-FB055D8DC851@sissa.it> Message-ID: On Aug 1, 2011, at 4:56 PM, mohaddeseh abbasnejad wrote: > Dear Prof. Baroni > > Thanks for your reply. > I wonder shouldn't the plot show the same frequency for a range of displacements? what range? why should it? > And the same freq. for the range to be the harmonic frequency? or the zero displacement limit, is the harmonic frequency? yes, by definition > And when I test the displacements with the same amplitude, but different in sign (regarding the inward and outward atomic movements in the basis) I do not get the same results. why should you? > Shouldn't the plot have symmetry vs. the vertical axis? why? please, try you best to answer my questions, and I will make my best to let you understand SB > > Thank You again > Mohaddeseh > > > On Mon, Aug 1, 2011 at 6:33 PM, Stefano Baroni wrote: > Hi Mohaddesh. I do not understand why you say that the calculated frequency (which, I assume you define as 2 * Delta E / u^2 ???) does not converge as u->0. According to your plot, it does, and to a reasonable value. The finite slope of your plot around u=0 seems to me nothing but a manifestation of cubic anharmonicity ... What's wrong in this? SB > > On Aug 1, 2011, at 3:01 PM, mohaddeseh abbasnejad wrote: > >> >> Dear users, >> >> I have plotted the harmonic frequency (obtained within the frozen phonon approach) of Diamond as a function of atomic displacements (small displacements in the [1 1 1] direction, u(1)=?(u,u,u) and u(2)=?(-u,-u,-u) are the displacements of two atoms in the basis). I expect to see a range of displacements that tend to the similar frequency, but there is no convergence in the plot. Also, the displacements with the same amplitude but different in sign, do not tend to the same frequency, which is not what I expect, too. The plot is attached. >> I was wondering if anyone could help me to find the source of error. I should expect the mentioned symmetry, right? Why there is no convergence? >> >> Thanks in advance. >> >> Yours, >> Mohaddeseh >> --------------------------------------------------------- >> >> Mohaddeseh Abbasnejad, >> Room No. 323, Department of Physics, >> University of Tehran, North Karegar Ave., >> Tehran, P.O. Box: 14395-547- IRAN >> E-Mail: m.abbasnejad at gmail.com >> Website: http://physics.ut.ac.ir >> >> --------------------------------------------------------- >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +98 917 731 7514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110801/63e69320/attachment-0001.htm From chenhanghuipwscf at gmail.com Tue Aug 2 03:49:34 2011 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Mon, 1 Aug 2011 21:49:34 -0400 Subject: [Pw_forum] Hubbard U on Eu 4f orbitals Message-ID: To whom it may concern, I have a naive question. I would like to run a LSDA+U calculation on EuO. I checked the subroutine tabd.f90 and found that the default number of localized electrons for Eu 4f is 6. However, since Eu has 4f^7 5d^0 6s^2 atomic configuration, why is the number NOT 7? Thank you very much. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110801/69ec84f4/attachment.htm From jiachen at princeton.edu Tue Aug 2 05:05:16 2011 From: jiachen at princeton.edu (jia chen) Date: Mon, 1 Aug 2011 23:05:16 -0400 Subject: [Pw_forum] Hubbard U on Eu 4f orbitals In-Reply-To: References: Message-ID: I guess this number doesn't really matter, hope some one can confirm or correct me, thanks you very much. On Mon, Aug 1, 2011 at 9:49 PM, hanghui chen wrote: > To whom it may concern, > ???? I have a naive question. I would like to run a LSDA+U calculation on > EuO. I checked the subroutine tabd.f90 and found that the default number of > localized electrons for Eu 4f is 6. However, since Eu has 4f^7 5d^0 6s^2 > atomic configuration, why is the number NOT 7? > ???? Thank you very much. > > Hanghui Chen > Department of Physics > Yale University > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Jia Chen From m.abbasnejad at gmail.com Tue Aug 2 08:18:41 2011 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Tue, 2 Aug 2011 10:48:41 +0430 Subject: [Pw_forum] About the Frozen Phonon Method In-Reply-To: References: <4EE86CC9-72B4-4565-9D10-FB055D8DC851@sissa.it> Message-ID: Dear Prof. Baroni Thanks again > Dear Prof. Baroni > > Thanks for your reply. > I wonder shouldn't the plot show the same frequency for a range of > displacements? > > > what range? why should it? > > -- Because if we are in the neighberhood of a minimum "where a quadratic could be fitted", any displacement in that range should result the same frequency. By displacement, I mean the same pattern but different in amplitude. > And the same freq. for the range to be the harmonic frequency? or the zero > displacement limit, is the harmonic frequency? > > > yes, by definition > > And when I test the displacements with the same amplitude, but different > in sign (regarding the inward and outward atomic movements in the basis) I > do not get the same results. > > > why should you? > > Shouldn't the plot have symmetry vs. the vertical axis? > > > why? > -- Consider for example a linear chain of atoms, with 2 atoms per basis. The optical mode is the result of the outward movement of the atoms (The one in +a/2 moves towards +x and the one in -a/2 moves towards -x). I expect that if I displace the atoms in an inward movement with the same amplitude as the outward, I should see the same frequency (The one in +a/2 moves towards -x and the one in -a/2 moves towards +x) because the 2 patterns present the same mode, right? That is what I've done in the case of Diamond. Is my expectation wrong? > > please, try you best to answer my questions, and I will make my best to let > you understand > > SB > > Mohaddeseh > Thank You again > Mohaddeseh > > > On Mon, Aug 1, 2011 at 6:33 PM, Stefano Baroni wrote: > >> Hi Mohaddesh. I do not understand why you say that the calculated >> frequency (which, I assume you define as 2 * Delta E / u^2 ???) does not >> converge as u->0. According to your plot, it does, and to a reasonable >> value. The finite slope of your plot around u=0 seems to me nothing but a >> manifestation of cubic anharmonicity ... What's wrong in this? SB >> >> On Aug 1, 2011, at 3:01 PM, mohaddeseh abbasnejad wrote: >> >> >> Dear users, >> >> I have plotted the harmonic frequency (obtained within the frozen phonon >> approach) of Diamond as a function of atomic displacements (small >> displacements in the [1 1 1] direction, u(1)=?(u,u,u) and >> u(2)=?(-u,-u,-u) are the displacements of two atoms in the basis). I expect >> to see a range of displacements that tend to the similar frequency, but >> there is no convergence in the plot. Also, the displacements with the same >> amplitude but different in sign, do not tend to the same frequency, which is >> not what I expect, too. The plot is attached. >> I was wondering if anyone could help me to find the source of error. I >> should expect the mentioned symmetry, right? Why there is no convergence? >> >> Thanks in advance. >> >> Yours, >> Mohaddeseh >> --------------------------------------------------------- >> >> Mohaddeseh Abbasnejad, >> Room No. 323, Department of Physics, >> University of Tehran, North Karegar Ave., >> Tehran, P.O. Box: 14395-547- IRAN >> E-Mail: m.abbasnejad at gmail.com >> Website: http://physics.ut.ac.ir >> >> --------------------------------------------------------- >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> --- >> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - >> Trieste >> http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / >> stefanobaroni (skype) >> >> La morale est une logique de l'action comme la logique est une morale de >> la pens?e - Jean Piaget >> >> Please, if possible, don't send me MS Word or PowerPoint attachments >> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > --------------------------------------------------------- > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +98 917 731 7514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > --------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/6b6385e0/attachment.htm From giannozz at democritos.it Tue Aug 2 09:12:57 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 2 Aug 2011 09:12:57 +0200 Subject: [Pw_forum] Hubbard U on Eu 4f orbitals In-Reply-To: References: Message-ID: <8B4B4265-1255-4E1E-93EC-51BC8112AB6B@democritos.it> On Aug 2, 2011, at 3:49 , hanghui chen wrote: > I checked the subroutine tabd.f90 and found that the default > number of localized electrons for Eu 4f is 6. However, since Eu > has 4f^7 5d^0 6s^2 atomic configuration, why is the number NOT 7? because whoever filled that table assumed trivalent Eu? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Aug 2 09:14:36 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 2 Aug 2011 09:14:36 +0200 Subject: [Pw_forum] Increasing FFT grid for charge density analyses In-Reply-To: <4E369757.2060604@cluster.pc.chemie.tu-darmstadt.de> References: <4E369757.2060604@cluster.pc.chemie.tu-darmstadt.de> Message-ID: <9663B556-1CD1-4DDB-8C36-85213502D607@democritos.it> On Aug 1, 2011, at 14:08 , Sven Heiles wrote: > For this purpose I have generated a cube file with pp.x and > nx,y,z=120. > Unfortunately I am not able to increase the FFT grid for the output > file what aren't you able? what happens? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From gabriele.sclauzero at epfl.ch Tue Aug 2 10:27:21 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 2 Aug 2011 10:27:21 +0200 Subject: [Pw_forum] Segmentation fault on relaxed structure in vc-relax on QE4.3.1 In-Reply-To: <1FA8802D-1DFE-48E5-8DA6-678001203DE5@dipteris.unige.it> References: <5DCDB2A2-4C90-4B12-BF41-66420303C182@democritos.it> <1FA8802D-1DFE-48E5-8DA6-678001203DE5@dipteris.unige.it> Message-ID: <7B36BC3C-3B8A-4F8C-B091-00B0542A038B@epfl.ch> I think you should file a bug report here http://qe-forge.org/tracker/?func=add&group_id=10&atid=133 HTH GS Il giorno 29/lug/2011, alle ore 12.51, Marino Vetuschi Zuccolini ha scritto: > Paolo, > the problem is still there. How can I report the bug on qe-forge. I've already an account. > > Thank you > > m. > > On 28 Jul 2011, at 18:14, Marino Vetuschi Zuccolini wrote: > >> I've compiled the 4.3.2 version of QE and the bug it is not present apparently on some tests I did. >> I will follow your suggestion if it will still present. >> >> Thank you very much. >> >> m. >> On 28 Jul 2011, at 17:38, Paolo Giannozzi wrote: >> >>> >>> On Jul 26, 2011, at 13:50 , Marino Vetuschi Zuccolini wrote: >>> >>>> during the computation of the last SCF cycle *on relaxed structure* >>>> this segmentation fault error (repeated for each process) happens >>> >>> a problem in the last step of a variable-cell optimization was fixed >>> in v.4.3.2. Please file a bug report on qe-forge if still present. >>> >>> P. >>> --- >>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >>> Phone +39-0432-558216, fax +39-0432-558222 >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> ******************************************************* >> Marino Vetuschi Zuccolini >> zucco at dipteris.unige.it >> Researcher / Geochemist >> Laboratory of Geochemistry >> >> DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova >> Tel. ++39 010 3538136 Fax. ++39 010 352169 >> Corso Europa 26, 16132 - Genova - Italy >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > ******************************************************* > Marino Vetuschi Zuccolini > zucco at dipteris.unige.it > Researcher / Geochemist > Laboratory of Geochemistry > > DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova > Tel. ++39 010 3538136 Fax. ++39 010 352169 > Corso Europa 26, 16132 - Genova - Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/ab0a4af4/attachment.htm From Heiles at cluster.pc.chemie.tu-darmstadt.de Tue Aug 2 10:38:49 2011 From: Heiles at cluster.pc.chemie.tu-darmstadt.de (Sven Heiles) Date: Tue, 02 Aug 2011 10:38:49 +0200 Subject: [Pw_forum] Increasing FFT grid for charge density analyses In-Reply-To: <9663B556-1CD1-4DDB-8C36-85213502D607@democritos.it> References: <4E369757.2060604@cluster.pc.chemie.tu-darmstadt.de> <9663B556-1CD1-4DDB-8C36-85213502D607@democritos.it> Message-ID: <4E37B799.4050608@cluster.pc.chemie.tu-darmstadt.de> In order to check for the convergence of the Bader charge I have to change the grid which is plotted to the cube file. As far as I understand the input I do that by changing nx,ny,nz. If I do so no matter if I use 40,40,40; 60,60,60 or 120,120,120 the cube file always consists of a 240x240x240 grid. So is it possible to change the FFT grid which is used when the cube file is plotted? Sven Am 02.08.2011 09:14, schrieb Paolo Giannozzi: > On Aug 1, 2011, at 14:08 , Sven Heiles wrote: > >> For this purpose I have generated a cube file with pp.x and >> nx,y,z=120. >> Unfortunately I am not able to increase the FFT grid for the output >> file > what aren't you able? what happens? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dipl. Ing. Sven Heiles Technische Universit?t Darmstadt AK Sch?fer Eduard-Zintl-Institut Petersenstra?e 20 D-64287 Darmstadt ? Germany Phone: ++49-(0)6151-164397 Fax: ++49-(0)6151-166024 Web: http://www.tu-darmstadt.de/fb/ch/cluster/schaefer.tud From tone.kokalj at ijs.si Tue Aug 2 10:42:50 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 02 Aug 2011 10:42:50 +0200 Subject: [Pw_forum] Increasing FFT grid for charge density analyses In-Reply-To: <4E37B799.4050608@cluster.pc.chemie.tu-darmstadt.de> References: <4E369757.2060604@cluster.pc.chemie.tu-darmstadt.de> <9663B556-1CD1-4DDB-8C36-85213502D607@democritos.it> <4E37B799.4050608@cluster.pc.chemie.tu-darmstadt.de> Message-ID: <1312274570.4116.2.camel@catalyst.ijs.si> On Tue, 2011-08-02 at 10:38 +0200, Sven Heiles wrote: > In order to check for the convergence of the Bader charge I have to > change the grid which is > plotted to the cube file. > > As far as I understand the input I do that by changing nx,ny,nz. If I do > so no matter if I use 40,40,40; 60,60,60 or 120,120,120 the cube file always > consists of a 240x240x240 grid. > > So is it possible to change the FFT grid which is used when > the cube file is plotted? Increase the ecutrho in the pw.x input file (you may go over 1000 ry as to get a very dense mesh), do a new pw.x calculation, and the rest will follow. 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 From giannozz at democritos.it Tue Aug 2 10:54:11 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 02 Aug 2011 10:54:11 +0200 Subject: [Pw_forum] Increasing FFT grid for charge density analyses In-Reply-To: <4E37B799.4050608@cluster.pc.chemie.tu-darmstadt.de> References: <4E369757.2060604@cluster.pc.chemie.tu-darmstadt.de> <9663B556-1CD1-4DDB-8C36-85213502D607@democritos.it> <4E37B799.4050608@cluster.pc.chemie.tu-darmstadt.de> Message-ID: <1312275251.6899.8.camel@fe12lx.fisica.uniud.it> On Tue, 2011-08-02 at 10:38 +0200, Sven Heiles wrote: > As far as I understand the input I do that by changing nx,ny,nz. If I do > so no matter if I use 40,40,40; 60,60,60 or 120,120,120 the cube file always > consists of a 240x240x240 grid. there are only a few (documented) cases in which you can use your own grid instead of the FFT grid. These cases are implemented using a "Slow" FT. If you try this on a 120x120x120 grid, it will take more time that the rest of the calculation. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From gabriele.sclauzero at epfl.ch Tue Aug 2 11:35:50 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 2 Aug 2011 11:35:50 +0200 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: References: Message-ID: <127AA0F8-4184-4DE6-82B1-09F96377C076@epfl.ch> Hello, Il giorno 28/lug/2011, alle ore 23.03, chengyu yang ha scritto: > Dear All, > I am trying to calculate the complex bands and the transmission of a (5,5) defectless carbon nanotube using PWCOND.x, however, the calculation process is very slow and I can see it kind of stopped at the point: ngper, shell number = 2809 299. Your value of ngper is quite large for this kind of calculations, you can't afford it without using a lot of processors in a parallel calculation. Moreover, as far as I know the calculation of the complex bands is not completely parallelized at the moment, hence if your leads have a very large cross section and contain really a lot of atoms, I'm afraid that the calculation is hardly feasible with the current implementation. In your case, the calculation should be feasible with 8-16 processors in parallel (if nodes have enough memory), but only if you use USPP, so that you will be able to reduce the ecutwfc down to 30-35 Ry. In the PWcond input file I would reduce epsproj to 10^-5 or 10^-6, depending on the level of accuracy required (but you should do a small test on this). HTH GS > My input files are like this: > > ################################################################################## > scf input file: > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > prefix = '55' , > / > &SYSTEM > ibrav = 6, > celldm(1) = 21.764541128,celldm(3)=0.213765379 > nat = 20, > ntyp = 1, > ecutwfc = 75 , > / > &ELECTRONS > conv_thr = 1.0d-8 , > mixing_beta = 0.7 , > / > ATOMIC_SPECIES > C 12.01100 C.pz-vbc.UPF > > ATOMIC_POSITIONS angstrom > > C 3.409595 0.000000 -1.231179 > C 3.113484 1.389805 -1.231179 > C 2.758420 2.004110 -0.000000 > C 1.701954 2.954436 -0.000000 > C 1.053623 3.242718 -1.231179 > C -0.359664 3.390572 -1.231179 > C -1.053623 3.242718 -0.000000 > C -2.283903 2.531625 -0.000000 > C -2.758420 2.004110 -1.231179 > C -3.335768 0.705684 -1.231179 > C -3.409595 0.000000 -0.000000 > C -3.113484 -1.389805 -0.000000 > C -2.758420 -2.004110 -1.231179 > C -1.701954 -2.954436 -1.231179 > C -1.053623 -3.242718 0.000000 > C 0.359664 -3.390572 0.000000 > C 1.053623 -3.242718 -1.231179 > C 2.283903 -2.531625 -1.231179 > C 2.758420 -2.004110 0.000000 > C 3.335768 -0.705684 0.000000 > > > > > K_POINTS automatic > 1 1 5 0 0 0 > > > ############################################################################### > > pwcond.in file: > > > &inputcond > prefixl='55' > band_file ='bands.cnt55' > ikind=0 > energy0=4.d0 > denergy=-0.1d0 > ewind=3.d0 > epsproj=1.d-4 > delgep = 1.d-9 > cutplot = 3.d0 > / > 1 > 0.0 0.0 1.0 > 5 > > ########################################################### > and the output file: > > GEOMETRY: > > lattice parameter (a_0) = 21.7645 a.u. > the volume = 2203.8697 (a.u.)^3 > the cross section = 473.6953 (a.u.)^2 > l of the unit cell = 0.2138 (a_0) > number of atoms/cell = 20 > number of atomic types = 1 > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 1.0000 0.0000 0.0000 ) > a(2) = ( 0.0000 1.0000 0.0000 ) > a(3) = ( 0.0000 0.0000 0.2138 ) > > > Cartesian axes > > site n. atom positions (a_0 units) > 1 C tau( 1)=( 0.2960 0.0000 0.1069 ) > 2 C tau( 2)=( 0.2703 0.1207 0.1069 ) > 3 C tau( 3)=( 0.2395 0.1740 0.2138 ) > 4 C tau( 4)=( 0.1478 0.2565 0.2138 ) > 5 C tau( 5)=( 0.0915 0.2816 0.1069 ) > 6 C tau( 6)=( -0.0312 0.2944 0.1069 ) > 7 C tau( 7)=( -0.0915 0.2816 0.2138 ) > 8 C tau( 8)=( -0.1983 0.2198 0.2138 ) > 9 C tau( 9)=( -0.2395 0.1740 0.1069 ) > 10 C tau( 10)=( -0.2896 0.0613 0.1069 ) > 11 C tau( 11)=( -0.2960 0.0000 0.2138 ) > 12 C tau( 12)=( -0.2703 -0.1207 0.2138 ) > 13 C tau( 13)=( -0.2395 -0.1740 0.1069 ) > 14 C tau( 14)=( -0.1478 -0.2565 0.1069 ) > 15 C tau( 15)=( -0.0915 -0.2816 0.2138 ) > 16 C tau( 16)=( 0.0312 -0.2944 0.2138 ) > 17 C tau( 17)=( 0.0915 -0.2816 0.1069 ) > 18 C tau( 18)=( 0.1983 -0.2198 0.1069 ) > 19 C tau( 19)=( 0.2395 -0.1740 0.2138 ) > 20 C tau( 20)=( 0.2896 -0.0613 0.2138 ) > > nr1s = 120 > nr2s = 120 > nr3s = 27 > nrx1s = 120 > nrx2s = 120 > nrx3s = 27 > nr1 = 120 > nr2 = 120 > nr3 = 27 > nrx1 = 120 > nrx2 = 120 > nrx3 = 27 > > _______________________________ > Radii of nonlocal spheres: > > type ibeta ang. mom. radius (a_0 units) > C 1 0 0.0593 > ----- General information ----- > > ----- Complex band structure calculation ----- > > nrx = 120 > nry = 120 > nz1 = 11 > > > energy0 = 4.0E+00 > denergy = -1.0E-01 > nenergy = 5 > ecut2d = 7.5E+01 > ewind = 3.0E+00 > epsproj = 1.0E-04 > > > number of k_|| points= 1 > cryst. coord. > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > ----- Information about left lead ----- > > nocros = 10 > noins = 10 > norb = 30 > norbf = 30 > nrz = 27 > > iorb type ibeta ang. mom. m position (a_0) > 1 1 1 0 1 taunew( 1)=( 0.2395 0.1740 0.0000) > 2 1 1 0 1 taunew( 2)=( 0.1478 0.2565 0.0000) > 3 1 1 0 1 taunew( 3)=( -0.0915 0.2816 0.0000) > 4 1 1 0 1 taunew( 4)=( -0.1983 0.2198 0.0000) > 5 1 1 0 1 taunew( 5)=( -0.2960 0.0000 0.0000) > 6 1 1 0 1 taunew( 6)=( -0.2703 -0.1207 0.0000) > 7 1 1 0 1 taunew( 7)=( -0.0915 -0.2816 0.0000) > 8 1 1 0 1 taunew( 8)=( 0.0312 -0.2944 0.0000) > 9 1 1 0 1 taunew( 9)=( 0.2395 -0.1740 0.0000) > 10 1 1 0 1 taunew( 10)=( 0.2896 -0.0613 0.0000) > 11 1 1 0 1 taunew( 11)=( 0.2960 0.0000 0.1069) > 12 1 1 0 1 taunew( 12)=( 0.2703 0.1207 0.1069) > 13 1 1 0 1 taunew( 13)=( 0.0915 0.2816 0.1069) > 14 1 1 0 1 taunew( 14)=( -0.0312 0.2944 0.1069) > 15 1 1 0 1 taunew( 15)=( -0.2395 0.1740 0.1069) > 16 1 1 0 1 taunew( 16)=( -0.2896 0.0613 0.1069) > 17 1 1 0 1 taunew( 17)=( -0.2395 -0.1740 0.1069) > 18 1 1 0 1 taunew( 18)=( -0.1478 -0.2565 0.1069) > 19 1 1 0 1 taunew( 19)=( 0.0915 -0.2816 0.1069) > 20 1 1 0 1 taunew( 20)=( 0.1983 -0.2198 0.1069) > 21 1 1 0 1 taunew( 21)=( 0.2395 0.1740 0.2138) > 22 1 1 0 1 taunew( 22)=( 0.1478 0.2565 0.2138) > 23 1 1 0 1 taunew( 23)=( -0.0915 0.2816 0.2138) > 24 1 1 0 1 taunew( 24)=( -0.1983 0.2198 0.2138) > 25 1 1 0 1 taunew( 25)=( -0.2960 0.0000 0.2138) > 26 1 1 0 1 taunew( 26)=( -0.2703 -0.1207 0.2138) > 27 1 1 0 1 taunew( 27)=( -0.0915 -0.2816 0.2138) > 28 1 1 0 1 taunew( 28)=( 0.0312 -0.2944 0.2138) > 29 1 1 0 1 taunew( 29)=( 0.2395 -0.1740 0.2138) > 30 1 1 0 1 taunew( 30)=( 0.2896 -0.0613 0.2138) > k slab z(k) z(k+1) crossing(iorb=1,norb) > 1 0.0000 0.0079 0.0079 111111111100000000000000000000 > 2 0.0079 0.0158 0.0079 111111111100000000000000000000 > 3 0.0158 0.0238 0.0079 111111111100000000000000000000 > 4 0.0238 0.0317 0.0079 111111111100000000000000000000 > 5 0.0317 0.0396 0.0079 111111111100000000000000000000 > 6 0.0396 0.0475 0.0079 111111111100000000000000000000 > 7 0.0475 0.0554 0.0079 111111111111111111110000000000 > 8 0.0554 0.0633 0.0079 111111111111111111110000000000 > 9 0.0633 0.0713 0.0079 000000000011111111110000000000 > 10 0.0713 0.0792 0.0079 000000000011111111110000000000 > 11 0.0792 0.0871 0.0079 000000000011111111110000000000 > 12 0.0871 0.0950 0.0079 000000000011111111110000000000 > 13 0.0950 0.1029 0.0079 000000000011111111110000000000 > 14 0.1029 0.1108 0.0079 000000000011111111110000000000 > 15 0.1108 0.1188 0.0079 000000000011111111110000000000 > 16 0.1188 0.1267 0.0079 000000000011111111110000000000 > 17 0.1267 0.1346 0.0079 000000000011111111110000000000 > 18 0.1346 0.1425 0.0079 000000000011111111110000000000 > 19 0.1425 0.1504 0.0079 000000000011111111110000000000 > 20 0.1504 0.1583 0.0079 000000000011111111111111111111 > 21 0.1583 0.1663 0.0079 000000000011111111111111111111 > 22 0.1663 0.1742 0.0079 000000000000000000001111111111 > 23 0.1742 0.1821 0.0079 000000000000000000001111111111 > 24 0.1821 0.1900 0.0079 000000000000000000001111111111 > 25 0.1900 0.1979 0.0079 000000000000000000001111111111 > 26 0.1979 0.2058 0.0079 000000000000000000001111111111 > 27 0.2058 0.2138 0.0079 000000000000000000001111111111 > > k( 1) = ( 0.0000000 0.0000000), wk = 1.0000000 > > ngper, shell number = 2809 299 > #################################################################################### > the output file stopped there, and I couldn't see the process. Maybe it takes long time cause I found it took 1 hour to calculate a transmission. > I don't quite understand the parameters setting, I have adjusted the ewind, epsproj, nzl, according to the postings on this forum. However, > the result seemed not change. > > I appreciate everyone who could give me some advice. > Thank you! > > Regards. > > Chengyu Yang > Material Science and Engineering, > University of Central Florida, USA > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/08ce46bf/attachment-0001.htm From Heiles at cluster.pc.chemie.tu-darmstadt.de Tue Aug 2 11:40:56 2011 From: Heiles at cluster.pc.chemie.tu-darmstadt.de (Sven Heiles) Date: Tue, 02 Aug 2011 11:40:56 +0200 Subject: [Pw_forum] Increasing FFT grid for charge density analyses In-Reply-To: <1312274570.4116.2.camel@catalyst.ijs.si> References: <4E369757.2060604@cluster.pc.chemie.tu-darmstadt.de> <9663B556-1CD1-4DDB-8C36-85213502D607@democritos.it> <4E37B799.4050608@cluster.pc.chemie.tu-darmstadt.de> <1312274570.4116.2.camel@catalyst.ijs.si> Message-ID: <4E37C628.6000509@cluster.pc.chemie.tu-darmstadt.de> Thanks for the help! I'll give it a try. Regards Sven Am 02.08.2011 10:42, schrieb Tone Kokalj: > On Tue, 2011-08-02 at 10:38 +0200, Sven Heiles wrote: >> In order to check for the convergence of the Bader charge I have to >> change the grid which is >> plotted to the cube file. >> >> As far as I understand the input I do that by changing nx,ny,nz. If I do >> so no matter if I use 40,40,40; 60,60,60 or 120,120,120 the cube file always >> consists of a 240x240x240 grid. >> >> So is it possible to change the FFT grid which is used when >> the cube file is plotted? > Increase the ecutrho in the pw.x input file (you may go over 1000 ry as > to get a very dense mesh), do a new pw.x calculation, and the rest will > follow. > > Regards, Tone -- Dipl. Ing. Sven Heiles Technische Universit?t Darmstadt AK Sch?fer Eduard-Zintl-Institut Petersenstra?e 20 D-64287 Darmstadt ? Germany Phone: ++49-(0)6151-164397 Fax: ++49-(0)6151-166024 Web: http://www.tu-darmstadt.de/fb/ch/cluster/schaefer.tud From guntram.schmidt at chemie.uni-halle.de Tue Aug 2 11:46:51 2011 From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt) Date: Tue, 02 Aug 2011 11:46:51 +0200 Subject: [Pw_forum] Interpretation of vc-relax / pi-pi-stack Message-ID: <4E37C78B.9020309@chemie.uni-halle.de> Dear solid-state-theorists ;-), I'm wondering what the vc-relax-result of an optimizing of a measured crystal structure can tell me. I have a sodium salt of a benzene-sulfonic acid (Na+ -O3S-Ph type) and the optimization at vdW-rpb-rrkjus-level grows the unit cell significantly along the pi-pi-stacking! The measured crystal structure has an approx. intercentroid distance of 3.5 A which grows to app. 5 A after "optimization". This happens with two different salts of this type. I thought, vdW was capable of treating such interactions - isn't it? Or do I have to modify my input-parameters (attached)? Thanks, Guntram ---------------------------------------- &control calculation = 'vc-relax' restart_mode='from_scratch', prefix='zacdatenzschmidti2t0537i2t0537', tstress = .true. tprnfor = .true. pseudo_dir = '/gpfs/home/aasfu/espresso-4.3.1/pseudo/', outdir='/gpfs/home/aasfu/tmp/' verbosity = 'high' / &system ibrav = 14, A = 6.6986, B = 22.181, C = 6.1146, cosAB = 0, cosAC = -.1452369383, cosBC = 0, nat = 88, ntyp = 5, ecutwfc = 70, ecutrho = 700, input_dft = 'vdW-DF', occupations = 'smearing' , degauss = 0.05D0 , smearing = 'gaussian', / &electrons conv_thr = 1.0d-5 electron_maxstep= 1000 / &ions / &CELL press = 0.0, / ATOMIC_SPECIES S 32.066 S.rpb-rrkjus.UPF Na 22.98977 Na.rpb-rrkjus.UPF C 12.011 C.rpb-rrkjus.UPF H 1.00794 H.rpb-rrkjus.UPF O 15.9994 O.rpb-rrkjus.UPF ATOMIC_POSITIONS angstrom O 5.189644 1.223060 1.773489 ... K_POINTS automatic 1 1 1 0 0 0 ------------------------------------------ From gabriele.sclauzero at epfl.ch Tue Aug 2 11:47:24 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 2 Aug 2011 11:47:24 +0200 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: References: <4E327A29.2010400@materials.ox.ac.uk> Message-ID: <42D46A19-38FE-4A4D-B84F-3E64201E1F3F@epfl.ch> Il giorno 29/lug/2011, alle ore 17.42, chengyu yang ha scritto: > Dear Dr. Marzari and all, > Thanks very much. I will try wannier . Here are some other questions, > 1.If I want to do research on the properties of carbon nanotube/metal system, I saw them using NEGF , but I didn't see NEGF package in Quantum Espresso, does this mean I should try other codes like SIESTA? As you already know (from your previous email), ballistic transport calculations can be performed with the PWcond code in the QE package. PWcond does not use NEGF technique, if you want to use that you will need to move to another code (for instance, the Want code should be directly interfaced with PWscf). > 2.If I want to research the conductivity properties of carbon nanotube/metal system under magnetic field, which code should I use?Can Quantum Espresso handle this? I don't believe this has been considered/implemented so far. > I learned a little about the quantum transport, but I still didn't find the right code to deal with such a complicated proplem. > Sorry I am a newie in this field, and I don't have quite a strong physics background. Before dealing with a complicated physics problem it sounds reasonable to first acquire a solid background and start with simpler problems, don't you think so? HTH GS > Thank you again. > > Chengyu Yang > Materials Science and Engineering,University of Central Florida > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/b7731676/attachment.htm From gabriele.sclauzero at epfl.ch Tue Aug 2 11:56:22 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 2 Aug 2011 11:56:22 +0200 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: References: <4E327A29.2010400@materials.ox.ac.uk> Message-ID: <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> Il giorno 29/lug/2011, alle ore 21.16, chengyu yang ha scritto: > Dear All, > After two hours , my transmission calculation comes out a result. And you couldn't wait for a couple of hours before writing to the forum saying that you were in trouble?... Assuming that your PWscf calculation has been converged, the important thing here is to look at the basis set reduction performed by PWcond: ngper, shell number = 2809 299 ngper, n2d = 2809 472 It looks to me that the n2d could be too small compared to the original size of the basis set (ngper). As I wrote in my previous email, you should try to decrease epsproj and check that the results (i.e. the complex bands) do not change appreciably. The eigenvalues at real k from PWcond need to be on the top of the band structure computed with PWscf. Also compare with previous theoretical results, I guess that there should be several works about the conductance of CNTs. cuplot is needed only to plot the scattering states. I guess that you do not need them at this stage. HTH GS > But I thought it may be not converged and didn't get the final result. > May anybody have a look at my output file? I attached in this email. > My input file is like this: > &inputcond > prefixl='55' > tran_file='trans.cnt55', > ikind=0 > energy0=4.d0 > denergy=-0.1d0 > ewind=3.d0 > epsproj=1.d-4 > delgep = 1.d-9 > cutplot = 3.d0 > / > 1 > 0.0 0.0 1.0 > 5 > > > Is there somebody that can give me an advice? > I really appreciate it. > > Chengyu Yang > Materials Science and Engineering, > University of Central Florida, USA > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/01ac829c/attachment.htm From halin at ifm.liu.se Tue Aug 2 12:04:41 2011 From: halin at ifm.liu.se (Hans Lind) Date: Tue, 2 Aug 2011 12:04:41 +0200 Subject: [Pw_forum] Ways to reduce disk i/o when doing phonon calculations with ph.x Message-ID: When doing large phonon calculations (dozens of atoms, distributed over 1000s of nodes) ph.x ends up doing a very large amount of disk i/o. This wouldn't be so much of a problem on systems with distributed disks, each node having access to its own hard drive. But on systems with a central disk the i/o causes system wide slowdowns as the disk can't keep up. Is there some way to reduce the disk i/o to manageable levels, I have tried setting "reduce_io='low'" but it is just not enough. Or do I have to resort to using distributed disk systems?. Are the developers working on some way to reduce the disk i/o in future versions? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/1aab2614/attachment-0001.htm From padmaja_patnaik at yahoo.co.uk Tue Aug 2 14:31:16 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Tue, 2 Aug 2011 13:31:16 +0100 (BST) Subject: [Pw_forum] Error in calculations Message-ID: <1312288276.13703.YahooMailClassic@web28514.mail.ukl.yahoo.com> Hi All After generating fully relativistic ultra-soft pseudopotential when i do the scf calculations it stops giving the following massage. running the scf calculation for Cr..../testrun: line 77: 16136 Segmentation fault????? $PW_COMMAND < cr.scf.in > cr.scf.out Error condition encountered during test: exit status = 139 Aborting Can anybody please advise on this. Thanks in advance, regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/8e58f569/attachment.htm From kolbba5 at wfu.edu Tue Aug 2 15:21:35 2011 From: kolbba5 at wfu.edu (Kolb, Brian) Date: Tue, 2 Aug 2011 09:21:35 -0400 Subject: [Pw_forum] Interpretation of vc-relax / pi-pi-stack In-Reply-To: <4E37C78B.9020309@chemie.uni-halle.de> References: <4E37C78B.9020309@chemie.uni-halle.de> Message-ID: Hi Guntram, In general, the results of an optimization will differ from experiment. This is especially true with vdW-DF, which has been shown to give binding distances that are too large in general. That being said, I agree that the difference between your computed result and experiment seems excessive. Assuming all your atomic coordinates and cell parameters are correct, one potential trouble I see in your input file is the "conv_thr" parameter. 1e-5 is quite a poor convergence criterion, especially for a variable-cell relaxation run. Forces and stresses tend to be harder to converge than energies so you often need very low energy convergence thresholds for relaxation runs. I generally don't run any relaxation calculation without a cutoff of 1e-8 or better. Without seeing your output I can't know if this will help but it's good practice in any case. If these are ionic systems you're doing, as it seems they are, you might need to do spin-polarization calculations. Unfortunately, there is no rigorous way to do spin polarization at present using vdW-DF. Just as a check you could try a spin polarized run with the Grimme corrections (london=.true. in the &system section). If you could attach an output file, I might be able to tell you a bit more. Hope this helps, Brian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/8aa983f1/attachment.htm From guntram.schmidt at chemie.uni-halle.de Tue Aug 2 16:43:04 2011 From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt) Date: Tue, 02 Aug 2011 16:43:04 +0200 Subject: [Pw_forum] 0: in pw-output In-Reply-To: References: <4E37C78B.9020309@chemie.uni-halle.de> Message-ID: <4E380CF8.5090503@chemie.uni-halle.de> Dear All, I'm running QE on a cluster, driven by IBM loadleveler and I always get a 0: in the beginning of each line of the output-file. This seems to be related to the threads calculating, as there is sometimes other numbers in the range of processors I'm using before the :. Does anybody know this artifact and where it comes from? How can I prevent it? Thanks a lot, Guntram From giannozz at democritos.it Tue Aug 2 17:03:54 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 2 Aug 2011 17:03:54 +0200 Subject: [Pw_forum] Error in calculations In-Reply-To: <1312288276.13703.YahooMailClassic@web28514.mail.ukl.yahoo.com> References: <1312288276.13703.YahooMailClassic@web28514.mail.ukl.yahoo.com> Message-ID: On Aug 2, 2011, at 14:31 , Padmaja Patnaik wrote: > running the scf calculation for Cr..../testrun: line 77: 16136 > Segmentation fault > [...] Can anybody please advise on this. nobody can, as explained many times. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Aug 2 18:03:44 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 2 Aug 2011 18:03:44 +0200 Subject: [Pw_forum] Ways to reduce disk i/o when doing phonon calculations with ph.x In-Reply-To: References: Message-ID: On Aug 2, 2011, at 12:04 , Hans Lind wrote: > When doing large phonon calculations (dozens of atoms, distributed > over 1000s of nodes) > ph.x ends up doing a very large amount of disk i/o [...]. I have > tried setting "reduce_io='low'" it works only for pw.x > Or do I have to resort to using distributed disk systems? It depends. If you have calculations involving "dozens" of atoms, you can perform a single irrep/wave-vector calculation on each node, working on local disks. Then, you have just to perform a final run that "collects" all the pieces. The latter involves only partial dynamical matrices, i.e. a small amount of data. The infrastructure to do this is in place in all recent versions, since it has been use for grid computing. > Are the developers working on some way to reduce the disk i/o in > future versions? there are projects of extending linear-response routines towards large systems. Interested in joining the effort? Note that there are only two ways to reduce I/O: - store things into memory - recalculate things instead of storing them In the first case, you need more RAM; in the second, more CPU. No way out. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Aug 2 18:33:38 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 2 Aug 2011 18:33:38 +0200 Subject: [Pw_forum] 0: in pw-output In-Reply-To: <4E380CF8.5090503@chemie.uni-halle.de> References: <4E37C78B.9020309@chemie.uni-halle.de> <4E380CF8.5090503@chemie.uni-halle.de> Message-ID: <36905FE3-BCCF-456D-82C8-9B9A57CDD6F9@democritos.it> On Aug 2, 2011, at 16:43 , Guntram Schmidt wrote: > I'm running QE on a cluster, driven by IBM loadleveler and I always > get a 0: in the beginning of each line of the output-file. once upon a time, when dinosaurs were roaming the world and outputs were printed to typewriters, a "0" in the first character meant "double spacing", while a "1" meant "next page". Maybe you have set a loadleveler option that produces double-spaced output :-) ? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Aug 2 18:54:26 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 2 Aug 2011 18:54:26 +0200 Subject: [Pw_forum] repeated band structure calculation in splittet phonon calculation In-Reply-To: <4E368ED5.2020703@physik.tu-freiberg.de> References: <4E368ED5.2020703@physik.tu-freiberg.de> Message-ID: <6902C646-F611-40DD-80E3-03041B0F389C@democritos.it> On Aug 1, 2011, at 13:32 , Thomas Gruber wrote: > In a phonon calculation with a different k-point grid than in a scf > calculation a band structure calculation is needed for every q-point, > but not for every irreducible representations. Now I want to split > this > phonon calculation in every q-point and every irreducible > representations. But when I do that, there will be a band structure > calculation in every job, but only one per q-point is necessary. > How can I save the band structure calculation to be read for every > job? In principle you could just copy the results for the needed band structure, but I am not sure the code will recognize that the data is there. You may need to modify the code. Keeping track of all possible cases is not easy. Typically the calculation of bands is a small part wrt a phonon calculation. The ultimate solution is to speed up the calculation of bands, but this would require some ideas and some serious work > Or did I something wrong and it should work? what should work in which case and with which version of the code exactly? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From padmaja_patnaik at yahoo.co.uk Tue Aug 2 19:47:33 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Tue, 2 Aug 2011 18:47:33 +0100 (BST) Subject: [Pw_forum] Doubt in input file Message-ID: <1312307253.87015.YahooMailClassic@web28508.mail.ukl.yahoo.com> Hi All While doing fully relativistic calculations one has to? mention "noncolin= .TRUE., lspinorb= .TRUE.," in the scf input. If then I proceed to do nscf? calculations for DOS then should I mention these to variables again in the input? Please suggest. With thanks and regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/9e9764de/attachment.htm From baroni at sissa.it Tue Aug 2 19:50:47 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 2 Aug 2011 19:50:47 +0200 Subject: [Pw_forum] About the Frozen Phonon Method In-Reply-To: References: <4EE86CC9-72B4-4565-9D10-FB055D8DC851@sissa.it> Message-ID: <808F3EE8-A00B-4594-921D-68F21E091A88@sissa.it> On Aug 2, 2011, at 8:18 AM, mohaddeseh abbasnejad wrote: > Dear Prof. Baroni > > Thanks again >> Dear Prof. Baroni >> >> Thanks for your reply. >> I wonder shouldn't the plot show the same frequency for a range of displacements? > > what range? why should it? > > > -- Because if we are in the neighberhood of a minimum "where a quadratic could be fitted", any displacement in that range should result the same frequency. By displacement, I mean the same pattern but different in amplitude. who said this? around a minimum, the only thing you can say is that the Taylor expansion of the energy in powers of the atomic displacements lacks any linear terms. In general, it has both quadratic terms (which are the one you are interested in), as well as higher order terms ... No reason why the Taylor expansion should be *exactly* quadratic (which is what would give rise to a "same frequency"). Note however, that it is your definition of frequency that is probably flawed. I suspect that you define the frequency as the ratio between the energy variation and the square of the displacement, which obviously depends on the magnitude of the displacement, if the energy variation is not exactly quadratic. The correct definition, instead, is the *limit* of that ration when the displacement goes to zero. That limit is obviously well defined, independently of the magnitude of any particular distortion that you may consider. > >> And the same freq. for the range to be the harmonic frequency? or the zero displacement limit, is the harmonic frequency? > > yes, by definition See the above discussion > >> And when I test the displacements with the same amplitude, but different in sign (regarding the inward and outward atomic movements in the basis) I do not get the same results. > > why should you? > >> Shouldn't the plot have symmetry vs. the vertical axis? > > why? > > -- Consider for example a linear chain of atoms, with 2 atoms per basis. The optical mode is the result of the outward movement of the atoms (The one in +a/2 moves towards +x and the one in -a/2 moves towards -x). I expect that if I displace the atoms in an inward movement with the same amplitude as the outward, I should see the same frequency (The one in +a/2 moves towards -x and the one in -a/2 moves towards +x) because the 2 patterns present the same mode, right? That is what I've done in the case of Diamond. Is my expectation wrong? Yes. If the Taylor expansion of the energy difference vs displacement has cubic terms (as it usually has, but in very special cases dictated by symmetry), there is no reason why the energy difference should be even with respect to energy displacement. Actually, it usually isn't ... Hope this clarifies a bit the situation ... Take care SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/0838a7ae/attachment-0001.htm From halin at ifm.liu.se Tue Aug 2 20:21:45 2011 From: halin at ifm.liu.se (Hans Lind) Date: Tue, 2 Aug 2011 20:21:45 +0200 Subject: [Pw_forum] Ways to reduce disk i/o when doing phonon calculations with ph.x In-Reply-To: References: Message-ID: Ok, thanks for the answer. > It depends. If you have calculations involving "dozens" of atoms, you > can perform a > single irrep/wave-vector calculation on each node, working on local > disks. Then, you > have just to perform a final run that "collects" all the pieces. The > latter involves only > partial dynamical matrices, i.e. a small amount of data. The > infrastructure to do this > is in place in all recent versions, since it has been use for grid > computing. If you mean what is described in the "GRID" examples, then I am already doing it that way. The calculations would take far too long otherwise and exceed the wall-time. But it doesn't help with only a single central disk system. Also, when doing such separation of irrep it repeats the initial wavefunction calculation (I think that is what it does at first) for each irrep calculation or group of irrep, which in the case of large systems becomes very time consuming and I've noticed can take longer than to calculate a single irrep afterwards Of course, I can always run on another system with distributed disks I just have less resources there and these phonon calculation take a lot of time to run. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/e4f071ef/attachment.htm From halin at ifm.liu.se Tue Aug 2 20:27:27 2011 From: halin at ifm.liu.se (Hans Lind) Date: Tue, 2 Aug 2011 20:27:27 +0200 Subject: [Pw_forum] Ways to reduce disk i/o when doing phonon calculations with ph.x In-Reply-To: References: Message-ID: Just saw the comment to Thomas Gruber about recalculations or band structures in separated irrep, no need to comment on my questions on it. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/5106ec4e/attachment.htm From jen7182 at hotmail.com Tue Aug 2 21:25:09 2011 From: jen7182 at hotmail.com (Jennifer Wohlwend) Date: Tue, 2 Aug 2011 15:25:09 -0400 Subject: [Pw_forum] q vectors Message-ID: I'm trying to perform electron-phonon coupling calcualtions and I was wondering how do you get the q vectors? Thank you!! J.W. Universal Technology Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/021f2cda/attachment.htm From elie.moujaes at hotmail.co.uk Tue Aug 2 22:20:40 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 2 Aug 2011 21:20:40 +0100 Subject: [Pw_forum] electronic DOS for a GB system of 60 atoms Message-ID: Dear all,I am trying to reproduce calculations done on the electronic DOS of a 60 carbon system. I have got that the DOS is around 0.2 at the Fermi level whereas the calculations done previously got that it is exactly zero. In addition their curve seems sharper than mine. I used degauss=0.01 in nscf and scf calculations. the grid for scf was 4 4 1 whilst it was 9 9 1 for nscf. You will find attached the ps file of the DOS. Can anyone advise me on that?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/74686d85/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: GBm.dos.ps Type: application/postscript Size: 42117 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110802/74686d85/attachment-0001.ps From jenaparadies at googlemail.com Tue Aug 2 22:35:16 2011 From: jenaparadies at googlemail.com (Lars Matthes) Date: Tue, 2 Aug 2011 22:35:16 +0200 Subject: [Pw_forum] electronic DOS for a GB system of 60 atoms In-Reply-To: References: Message-ID: Dear Elie, it looks like you have way too few k-points for your nscf calculation. For a well converged DOS it isnecessary to have sufficient dense k-grid. By increasing the number of k-points you'll see, that the DOS will be much smoother, because up to know the 'waves' in your DOS doesn't seem to be physical, I think they are artificial and a result of a low k-sampling. If the grid is dense enough and your DOS doesn't change anymore you can also decrease the smearing and improve the behaviour of your spectra close to the gap. Hope that helps Lars 2011/8/2 Elie Moujaes > Dear all, > > I am trying to reproduce calculations done on the electronic DOS of a 60 > carbon system. I have got that the DOS is around 0.2 at the Fermi level > whereas the calculations done previously got that it is exactly zero. In > addition their curve seems sharper than mine. I used degauss=0.01 in nscf > and scf calculations. the grid for scf was 4 4 1 whilst it was 9 9 1 for > nscf. You will find attached the ps file of the DOS. Can anyone advise me on > that? > > Thanks > > Elie Moujaes > > University of Nottingham > NG7 2RD > UK > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Lars Matthes Institut f?r Festk?rpertheorie und -optik Friedrich-Schiller-Universit?t Jena Max-Wien-Platz 1 07743 Jena Germany Phone: +49.3641.947163 Mail: Lars.Matthes at uni-jena.de -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/5a40bb60/attachment.htm From elie.moujaes at hotmail.co.uk Tue Aug 2 22:36:42 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Tue, 2 Aug 2011 21:36:42 +0100 Subject: [Pw_forum] electronic DOS for a GB system of 60 atoms In-Reply-To: References: , Message-ID: Dear Lars, Thanks very much for your help. Elie Date: Tue, 2 Aug 2011 22:35:16 +0200 From: jenaparadies at googlemail.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] electronic DOS for a GB system of 60 atoms Dear Elie, it looks like you have way too few k-points for your nscf calculation. For a well converged DOS it isnecessary to have sufficient dense k-grid. By increasing the number of k-points you'll see, that the DOS will be much smoother, because up to know the 'waves' in your DOS doesn't seem to be physical, I think they are artificial and a result of a low k-sampling. If the grid is dense enough and your DOS doesn't change anymore you can also decrease the smearing and improve the behaviour of your spectra close to the gap. Hope that helps Lars 2011/8/2 Elie Moujaes Dear all, I am trying to reproduce calculations done on the electronic DOS of a 60 carbon system. I have got that the DOS is around 0.2 at the Fermi level whereas the calculations done previously got that it is exactly zero. In addition their curve seems sharper than mine. I used degauss=0.01 in nscf and scf calculations. the grid for scf was 4 4 1 whilst it was 9 9 1 for nscf. You will find attached the ps file of the DOS. Can anyone advise me on that? ThanksElie Moujaes University of NottinghamNG7 2RDUK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Lars Matthes Institut f?r Festk?rpertheorie und -optik Friedrich-Schiller-Universit?t Jena Max-Wien-Platz 1 07743 Jena Germany Phone: +49.3641.947163 Mail: Lars.Matthes at uni-jena.de _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/c32d7703/attachment.htm From bamideleibrahim at yahoo.com Wed Aug 3 05:07:49 2011 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Tue, 2 Aug 2011 20:07:49 -0700 (PDT) Subject: [Pw_forum] how to plot infrared and raman spectra Message-ID: <1312340869.55387.YahooMailNeo@web39420.mail.mud.yahoo.com> ?Dear all, ?? I perform infrared and raman cross-section calculation but don't know how to process the out data to get a graphical result. ?? I will be delighted to if anybody can help me on how to do this. Thanks ? Adetunji Bamidele Ibrahim Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/b7bdb798/attachment.htm From bamideleibrahim at yahoo.com Wed Aug 3 06:29:44 2011 From: bamideleibrahim at yahoo.com (bamidele ibrahim) Date: Tue, 2 Aug 2011 21:29:44 -0700 (PDT) Subject: [Pw_forum] QHA compilation error Message-ID: <1312345784.48007.YahooMailNeo@web39401.mail.mud.yahoo.com> Dear all, ? I am trying to compile QHA with QE 4.3 version. After run ./Compile, it's gives this error; ifort -O3? -c? tetra.f make: ifort: Command not found make: *** [tetra.o] Error 127 ifort -O3?? -c? Debye.f90 make: ifort: Command not found make: *** [Debye.o] Error 127 ifort -FR -c? Mean_square_displacement.f90 make: ifort: Command not found make: *** [Mean_square_displacement.o] Error 127 ln: creating symbolic link `tetra.x': File exists ln: creating symbolic link `phonon_dos.x': File exists ln: creating symbolic link `Debye.x': File exists ln: creating symbolic link `Atom_projected_properties.x': File exists ln: creating symbolic link `F_QHA.x': File exists ln: creating symbolic link `Ghost_DOS.x': File exists ln: creating symbolic link `Partial_phonon_DOS.x': File exists ln: creating symbolic link `Mean_square_displacement.x': File exists ln: creating symbolic link `atom_info.x': File exists Please, kindly help me out on this. ? Adetunji Bamidele Ibrahim Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110802/0d8809ab/attachment.htm From m.abbasnejad at gmail.com Wed Aug 3 07:03:05 2011 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Wed, 3 Aug 2011 09:33:05 +0430 Subject: [Pw_forum] About the Frozen Phonon Method In-Reply-To: <808F3EE8-A00B-4594-921D-68F21E091A88@sissa.it> References: <4EE86CC9-72B4-4565-9D10-FB055D8DC851@sissa.it> <808F3EE8-A00B-4594-921D-68F21E091A88@sissa.it> Message-ID: Dear Prof. Baroni, Thank you so much. It clarified a lot. Yours, Mohaddeseh On Tue, Aug 2, 2011 at 10:20 PM, Stefano Baroni wrote: > > On Aug 2, 2011, at 8:18 AM, mohaddeseh abbasnejad wrote: > > Dear Prof. Baroni > > Thanks again > >> Dear Prof. Baroni >> >> Thanks for your reply. >> I wonder shouldn't the plot show the same frequency for a range of >> displacements? >> >> >> what range? why should it? >> >> > -- Because if we are in the neighberhood of a minimum "where a quadratic > could be fitted", any displacement in that range should result the same > frequency. By displacement, I mean the same pattern but different in > amplitude. > > > who said this? around a minimum, the only thing you can say is that the > Taylor expansion of the energy in powers of the atomic displacements lacks > any linear terms. In general, it has both quadratic terms (which are the one > you are interested in), as well as higher order terms ... No reason why the > Taylor expansion should be *exactly* quadratic (which is what would give > rise to a "same frequency"). Note however, that it is your definition of > frequency that is probably flawed. I suspect that you define the frequency > as the ratio between the energy variation and the square of the > displacement, which obviously depends on the magnitude of the displacement, > if the energy variation is not exactly quadratic. The correct definition, > instead, is the *limit* of that ration when the displacement goes to zero. > That limit is obviously well defined, independently of the magnitude of any > particular distortion that you may consider. > > > >> And the same freq. for the range to be the harmonic frequency? or the >> zero displacement limit, is the harmonic frequency? >> >> >> yes, by definition >> > > See the above discussion > > >> And when I test the displacements with the same amplitude, but different >> in sign (regarding the inward and outward atomic movements in the basis) I >> do not get the same results. >> >> >> why should you? >> >> Shouldn't the plot have symmetry vs. the vertical axis? >> >> >> why? >> > > -- Consider for example a linear chain of atoms, with 2 atoms per basis. > The optical mode is the result of the outward movement of the atoms (The one > in +a/2 moves towards +x and the one in -a/2 moves towards -x). I expect > that if I displace the atoms in an inward movement with the same amplitude > as the outward, I should see the same frequency (The one in +a/2 moves > towards -x and the one in -a/2 moves towards +x) because the 2 patterns > present the same mode, right? That is what I've done in the case of Diamond. > Is my expectation wrong? > > > Yes. If the Taylor expansion of the energy difference vs displacement has > cubic terms (as it usually has, but in very special cases dictated by > symmetry), there is no reason why the energy difference should be even with > respect to energy displacement. Actually, it usually isn't ... > > Hope this clarifies a bit the situation ... > > Take care > SB > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- --------------------------------------------------------- Mohaddeseh Abbasnejad, Room No. 323, Department of Physics, University of Tehran, North Karegar Ave., Tehran, P.O. Box: 14395-547- IRAN Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 Cellphone: +98 917 731 7514 E-Mail: m.abbasnejad at gmail.com Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/9523c4fc/attachment-0001.htm From prasenjit.jnc at gmail.com Wed Aug 3 08:00:01 2011 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Wed, 3 Aug 2011 11:30:01 +0530 Subject: [Pw_forum] IOTK error while restarting using QE4.3.1 Message-ID: Dear all, I am using Quantum espresso 4.3.1. It has been compiled with gfortran 4.1.2 and openmpi-1.5. The code has been compiled on a desktop having Intel(R) Core(TM)2 Quad CPU Q9650. When I am trying to restart the scf calculation it is giving me the following IOTK error: # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_end (iotk_scan.spp:233) # CVS Revision: 1.23 # foundl # ERROR IN: iotk_close_read (iotk_files.spp:645) # CVS Revision: 1.20 However, the same input file restarts perfectly fine for QE-4.2.1 compiled in the same machine using the same versions of gfortran and mpi. The input file for bulk PbS is given below: &CONTROL calculation = 'scf', prefix='Pb-S', restart_mode = 'restart', tstress = .TRUE., tprnfor=.true. pseudo_dir ='.', outdir='.' wf_collect=.true. / &SYSTEM ibrav= 2, celldm(1) = 11.37, nat= 2, ntyp= 2, nspin = 1, ecutwfc = 40., ecutrho=400 / &ELECTRONS conv_thr=1.0d-8, mixing_mode = 'plain' mixing_beta = 0.3, / ATOMIC_SPECIES Pb 196.966569 Pb.pbe-d-van.UPF S 32.0 S.pbe-van_bm.UPF ATOMIC_POSITIONS (crystal) Pb 0.00000 0.00000 0.00000 S 0.50000 0.50000 0.50000 K_POINTS {automatic} 8 8 8 0 0 0 Does anyone have similar experience with version 4.3.1 and gfortran compilers? Is it some problem with the compiler or there is some bug in QE4.3.1? With regards, Prasenjit -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From gabriele.sclauzero at epfl.ch Wed Aug 3 10:26:52 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 3 Aug 2011 10:26:52 +0200 Subject: [Pw_forum] Doubt in input file In-Reply-To: <1312307253.87015.YahooMailClassic@web28508.mail.ukl.yahoo.com> References: <1312307253.87015.YahooMailClassic@web28508.mail.ukl.yahoo.com> Message-ID: <8C47158A-82F0-49B2-BFD4-E67535854104@epfl.ch> Il giorno 02/ago/2011, alle ore 19.47, Padmaja Patnaik ha scritto: > Hi All > While doing fully relativistic calculations one has to mention "noncolin= .TRUE., lspinorb= .TRUE.," in the scf input. > Yes > If then I proceed to do nscf calculations for DOS then should I mention these to variables again in the input? > Yes > Please suggest. > I did > > With thanks and regards > You're welcome Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/c52f5a94/attachment.htm From fabrizio.gala at uniroma1.it Wed Aug 3 14:33:27 2011 From: fabrizio.gala at uniroma1.it (fabrizio gala) Date: Wed, 03 Aug 2011 14:33:27 +0200 Subject: [Pw_forum] compiling error during the installation of the GPU release of Quantum ESpresso Message-ID: <4E394017.5080802@uniroma1.it> Dear all, during the installation of the GPU-enabled release of QE on a 64-bit Linux Pc with (gfortran+gcc+openmpi), the following error occurs: make[1]: Entering directory `/home/fabri/espresso-PRACE/PW' [....] mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__CUDA -D__CUDA_MEM_PINNED -D__GPU_NVIDIA_20 -D__CUDA_QE_TIMING -D__MPI -D__PARA -I../include -I/usr/local/cuda//include -I../iotk/src -I../Modules -I. -c addusdens.f90 addusdens.f90:121.12: IF (err) THEN 1 Error: IF clause at (1) requires a scalar LOGICAL expression make[1]: *** [addusdens.o] Error 1 make[1]: Leaving directory `/home/fabri/espresso-PRACE/PW' make: *** [pw] Error 2 Could anybody give me some hints? thank you in advance -- Dr. Fabrizio Gala Dipartimento di Scienze di Base e Applicate per l'Ingegneria, Sezione di Fisica. La Sapienza,University of Rome and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM) via A. Scarpa 14-16 00161 Rome - ITALY phone: +390649766545 fax: +390644240183 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/d61ddf57/attachment.htm From robinshy at gmail.com Wed Aug 3 15:29:55 2011 From: robinshy at gmail.com (Robin H) Date: Wed, 3 Aug 2011 21:29:55 +0800 Subject: [Pw_forum] problem with creating the pseudopotential of Zn In-Reply-To: <36f98ebe.3d22.131579d6572.Coremail.flux_ray12@163.com> References: <36f98ebe.3d22.131579d6572.Coremail.flux_ray12@163.com> Message-ID: thanks for your valuable advice,my problem was resolved at once.You are so kind to give me the help! And I'm so sorry to reply the letter late because of a vacation. ? 2011?7?23? ??11:29?GAO Zhe ??? > when lloc=2, d orbital should be the last one~ > I am not good at PP generation and theory, but your problem can be fixed > with such modifications ( I am not sure whether LD1 code supports > Revised-PBE, and I met a negative rho problem if I used RRKJ method ): > *&input > zed = 30. > rel = 1, > config = '[Ar] 3d10 4s1 4p1' , > iswitch = 3, > dft = 'PBE' > / > &inputp > lloc = 1 , > pseudotype = 3 , > file_pseudopw = 'Zn.PBE.UPF' , > nlcc = .true. , > tm = .true. , > > / > 5 > 3D 3 2 10.00 0.00 1.80 2.00 > 3D 3 2 0.00 0.05 1.80 2.00 > 4S 1 0 1.00 0.00 1.80 2.00 > 4S 1 0 0.00 0.05 1.80 2.00 > 4P 2 1 1.00 0.00 1.80 2.10 > * > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-07-23 16:45:13,"Robin H" wrote: > > Hi,everyone.I have tried many times to creat the PP of Zn,but the problems > come out everytime.Even if I correct the one,then there will be anthoer.Zn > is one of the transition iron atom,and I'm not sure my input items are all > proper for it.This is my input file for ld1.x .And the next is the wrong > information.I need some help. > *input :* > &input > title='Zn' > zed=30. > rel=1, > config='[Ar] 3d10.00 4s1.00 4p1.00', > iswitch=3, > dft='revPBE' > / > &inputp > lloc=2, > pseudotype=3, > file_pseudopw='Zn.revPBE.UPF', > author='ADC', > / > 6 > 3D 3 2 10.00 0.00 1.80 2.00 > 3D 3 2 0.00 0.05 1.80 2.00 > 4S 1 0 1.00 0.00 1.80 2.00 > 4S 1 0 0.00 0.05 1.80 2.00 > 4P 2 1 1.00 0.00 1.80 2.10 > 4P 2 1 0.00 0.05 1.80 2.10 > > > > *wrong information :* > * *Program LD1 v.4.3.1 starts on 23Jul2011 at 16:29: 5 > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > URL http://www.quantum-espresso.org", > in publications or presentations arising from this work. More details > at > > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > Parallel version (MPI), running on 1 processors > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from ld1_readin : error # 1 > only one local channel > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/b06b30cf/attachment.htm From eariel99 at gmail.com Wed Aug 3 17:24:11 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Wed, 3 Aug 2011 11:24:11 -0400 Subject: [Pw_forum] Raman on DFT-false-metals Message-ID: Hi, I would like to calculate a Raman spectrum with PHONON for an insulator that is metallic in LDA and GGA. Is it possible to introduce easily a scissors shift to open the gap and allow the Raman calculation? -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). Translate from spanish here http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/dc935be2/attachment-0001.htm From yshzhang88 at yahoo.com Wed Aug 3 18:50:48 2011 From: yshzhang88 at yahoo.com (Yongsheng Zhang) Date: Wed, 3 Aug 2011 09:50:48 -0700 (PDT) Subject: [Pw_forum] ld1.x generate Sb PP Message-ID: <1312390248.10088.YahooMailNeo@web31801.mail.mud.yahoo.com> Dear PP experts, I spend long long time to generate the Sb PBE pseudopotential. The "best" one I get is still not very successful to get the good experimental or VASP-PAW lattice constants. exp??? :??????????? 4.308420000000000???????? 4.308419999850220???????? 11.27460000000000 PAW-PBE:???? 4.387963702059904???????? 4.387963701901805???????? 11.42545713239960 PP-PBE:??????? 4.44711025 ? ? ? ? ? ? ? ? ? ?? 4.44858214 ? ? ? ? ? ? ? ? ? ? 11.81877927 The c-direction is significantly different to the experimental data and PAW results. And I notice in the PP database, there has a PW91 Sb PP. Using the PW91 PP, the theoretical lattice constants are quite good. (4.35479533, 4.35557221,? 11.32102582). The my Sb PP input file is: &input ??? title='Sb' ??? zed=51. ??? rel=1, ??? rlderiv=2.2, ??? eminld=-2.0, ??? emaxld=2.0, ??? deld=0.01, ??? nld=3, ??? config='[Kr] 4d10.0 5s2.0 5p3.0' ??? iswitch=3, ??? dft='PBE' ?/ ?&inputp ?? pseudotype=3, ?? lloc=1, ?? rho0=0.001, ?? file_pseudopw='Sb.pbe.UPF', ?? nlcc = .true., ?? author='YS-Zhang', ?/ 4 4D? 3? 2 10.00? 0.00? 1.60? 2.00? 1 4D? 3? 2? 0.00 -1.70? 1.60? 2.00? 1 5S? 1? 0? 2.00? 0.00? 2.10? 2.10? 1 5P? 2? 1? 3.00? 0.00? 2.30? 2.30? 1 During the tests, I didn't find any ghost state and the largest difference between PP and AE is ???? 3 2???? 4D?? 1(10.00)?????? -6.59082?????? -6.55589?????? -0.03493 ???? 1 0???? 5S?? 1( 0.00)?????? -4.49315?????? -4.49962??????? 0.00647 ???? 2 1???? 5P?? 1( 0.00)?????? -3.63377?????? -3.64128??????? 0.00751 ???? dEtot_ae =????? 10.908350 Ry ???? dEtot_ps =????? 10.913263 Ry,?? Delta E=????? -0.004913 Ry Please help me improve the Sb PP input file. Thank you very much. Yongsheng Zhang Northwestern University Dept. of Materials Science and Eng. 2220 Campus Dr. Evanston, IL 60208 From deepak.p.thakur at gmail.com Wed Aug 3 19:49:38 2011 From: deepak.p.thakur at gmail.com (dipak thakur) Date: Wed, 3 Aug 2011 23:19:38 +0530 Subject: [Pw_forum] Regarding supercell dimensions Message-ID: I am nobe to quantum espresso and using supercell for first time. Can any one help me in understanding few things regarding the supecell determination? The following is a typical input file I am using (copied from one of the earlier post). CONTROL title = 'Graphene mono layer' calculation = "relax" , restart_mode = 'from_scratch' , outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , etot_conv_thr = 1.0E-4 , forc_conv_thr = 1.0D-3 , nstep=50, dt=40, prefix='1MLG_Ti_H2', / &SYSTEM ibrav = 0., ntyp = 2 , nat = 33 , ecutwfc = 50.0 , ecutrho = 400.0, / &ELECTRONS electron_maxstep = 300., conv_thr = 1.0d-8 , mixing_mode = 'plain', mixing_beta = 0.5, diagonalization = 'cg' , diago_cg_maxiter = 50, / &IONS / CELL_PARAMETERS 16.12131954 9.383047808 0.0000000 0.00000000 18.658162370 0.0000000 0.0000000 0.0000000 56.6893424 ATOMIC_SPECIES C 12.0107 C.pbe-van_ak.UPF Ti 47.8670 Ti.pbe-sp-van_ak.UPF ATOMIC_POSITIONS angstrom C 2.89163 7.40219 1.8862 C 3.59292 8.63832 1.8826 C 3.60349 6.16702 1.8884 C 5.0186 8.64501 1.8612 C 5.0215 6.16598 1.8904 C 5.73302 7.40522 1.8718 C 1.47184 7.39616 1.891 C 2.89112 9.87066 1.886 C 2.89471 4.93264 1.8916 C 5.73319 9.8885 1.8612 C 5.73643 4.9413 1.8924 C 7.16348 7.41203 1.882 C 1.47474 4.9269 1.8924 C 0.762281 8.62783 1.8946 C 0.763134 6.16172 1.8914 C 1.4715 9.86335 1.8934 C 3.60341 11.1095 1.8868 C 5.02124 11.1239 1.882 C 3.60512 3.70156 1.8932 C 5.02645 3.70789 1.891 C 7.87807 8.65532 1.8816 C 7.16373 9.89497 1.872 C 7.16203 4.94814 1.8954 C 7.87619 6.17677 1.8996 C 5.73634 12.3522 1.8872 C 0.772689 3.69102 1.898 C 0.762793 1.22003 1.8968 C 7.87645 11.1337 1.8894 C 7.16203 12.3587 1.889 C 7.87201 13.5922 1.8942 C 2.89479 2.46619 1.8922 C 1.47482 2.45878 1.8952 Ti 6.41604 8.65974 3.74 K_POINTS {automatic} 6.0 6.0 1.0 1.0 1.0 1.0 Can anyone help me understanding how are these Cell parameters calculated? Also in some cases celld(m) are used. Can anyone comment on these also? How are the cell parameters and lattice constant or atomic spacing related? Any clue would be of great help. Thanks in advance. Rgds Deepak -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/6951fbc5/attachment.htm From hmortizmn1 at gmail.com Thu Aug 4 00:07:58 2011 From: hmortizmn1 at gmail.com (Henry Ortiz) Date: Wed, 3 Aug 2011 17:07:58 -0500 Subject: [Pw_forum] problem with Sc-pseudo Message-ID: Dear all ... I have been working with the pseudo Sc.pbe-nsp-van.UPF obtained from the database at the quantum-espresso web page. In order to test it I set up a calculation for ScN, with Rs and Zb structure but I got really bad frequencies. After some check, it seems to me that the problem relies on the Sc pseudo. Does anybody have experience with this pseudos or if you happen to have a good Sc soft pseudo it will greatly appreciate it? or if no, can somebody help me or giving me some hints on how to create a good soft pseudo? Thanks in advance -- Henry Ortiz CINVESTAV-Quer?taro Mexico -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110803/f4fd420b/attachment.htm From renpj at dicp.ac.cn Thu Aug 4 04:05:58 2011 From: renpj at dicp.ac.cn (Ren PJ) Date: Thu, 4 Aug 2011 10:05:58 +0800 Subject: [Pw_forum] Run example error in qe-gipaw Message-ID: <20110804100558.78c7b535@ren-desktop> Dear all, I have installed qe-gipaw, but when I try to run the tests in the example/ directory I always get the error info like: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from seqopn : error # 98 error opening quartz.gipaw_recover %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Before run gipaw.x, I have run pw.x calculation with no error. Does anyone meet the same problem? Thank you all Pengju Ren Dalian Institute of Chemical Physics From mohnish.iitk at gmail.com Thu Aug 4 05:54:54 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 4 Aug 2011 09:24:54 +0530 Subject: [Pw_forum] Regarding supercell dimensions In-Reply-To: References: Message-ID: Dear Deepak! There no cell parameter in your input. You have to take the experimental value of the lattice constant available or dig out some paper in which the relevant calculations are done. See the INPUT_PW.txt in DOC folder of espresso distribution. The meaning of parameters are very clearly mentioned there. And next time please mention your affiliation so that we should know whom we are interacting with. On Wed, Aug 3, 2011 at 11:19 PM, dipak thakur wrote: > I am nobe to quantum espresso and using supercell for first time. > Can any one help me in understanding few things regarding the supecell > determination? > > The following is a typical input file I am using (copied from one of the > earlier post). > > CONTROL > title = 'Graphene mono layer' > calculation = "relax" , > restart_mode = 'from_scratch' , > outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' , > pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' , > > etot_conv_thr = 1.0E-4 , > forc_conv_thr = 1.0D-3 , > nstep=50, > dt=40, > prefix='1MLG_Ti_H2', > / > &SYSTEM > ibrav = 0., > > ntyp = 2 , > nat = 33 , > ecutwfc = 50.0 , > ecutrho = 400.0, > / > &ELECTRONS > electron_maxstep = 300., > conv_thr = 1.0d-8 , > > mixing_mode = 'plain', > mixing_beta = 0.5, > diagonalization = 'cg' , > diago_cg_maxiter = 50, > / > &IONS > / > CELL_PARAMETERS > 16.12131954 9.383047808 0.0000000 > > 0.00000000 18.658162370 0.0000000 > 0.0000000 0.0000000 56.6893424 > ATOMIC_SPECIES > C 12.0107 C.pbe-van_ak.UPF > Ti 47.8670 Ti.pbe-sp-van_ak.UPF > ATOMIC_POSITIONS angstrom > C 2.89163 7.40219 1.8862 > > C 3.59292 8.63832 1.8826 > C 3.60349 6.16702 1.8884 > C 5.0186 8.64501 1.8612 > C 5.0215 6.16598 1.8904 > C 5.73302 7.40522 1.8718 > > C 1.47184 7.39616 1.891 > C 2.89112 9.87066 1.886 > C 2.89471 4.93264 1.8916 > C 5.73319 9.8885 1.8612 > C 5.73643 4.9413 1.8924 > > C 7.16348 7.41203 1.882 > C 1.47474 4.9269 1.8924 > C 0.762281 8.62783 1.8946 > C 0.763134 6.16172 1.8914 > C 1.4715 9.86335 1.8934 > > C 3.60341 11.1095 1.8868 > C 5.02124 11.1239 1.882 > C 3.60512 3.70156 1.8932 > C 5.02645 3.70789 1.891 > C 7.87807 8.65532 1.8816 > > C 7.16373 9.89497 1.872 > C 7.16203 4.94814 1.8954 > C 7.87619 6.17677 1.8996 > C 5.73634 12.3522 1.8872 > C 0.772689 3.69102 1.898 > > C 0.762793 1.22003 1.8968 > C 7.87645 11.1337 1.8894 > C 7.16203 12.3587 1.889 > C 7.87201 13.5922 1.8942 > C 2.89479 2.46619 1.8922 > > C 1.47482 2.45878 1.8952 > Ti 6.41604 8.65974 3.74 > K_POINTS {automatic} > 6.0 6.0 1.0 1.0 1.0 1.0 > > Can anyone help me understanding how are these Cell parameters calculated? > > Also in some cases celld(m) are used. Can anyone comment on these also? > How are the cell parameters and lattice constant or atomic spacing related? > > Any clue would be of great help. > > Thanks in advance. > > > Rgds > Deepak > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/0b9e6c5b/attachment.htm From mohnish.iitk at gmail.com Thu Aug 4 06:36:57 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 4 Aug 2011 10:06:57 +0530 Subject: [Pw_forum] large error in RuO2 lattice parameter Message-ID: Dear QE users, 2.7438 I want to study RuO2 surfaces. I did calculation of ruthenium metal and found the lattice constant right(experimental = 2.70 and 1.584, I got 2.7438 and 1.582) But after doing calculation of bulk ruthenium oxide I am getting very different lattice parameter as compared to the experimental value. Experimental value is 4.494 and 3.107 and I am getting the value of 4.6421 and 3.1888. Can anybody please tell from where the discrepancy is coming? Thanks a lot in advance *input file* &control calculation = 'vc-relax', restart_mode='restart', nstep=100 outdir='/home/mohnish/Desktop/Ruo2-bulk', pseudo_dir='/home/mohnish/Desktop/Ruo2-bulk', prefix='Ruo2', tstress = .true., tprnfor = .true., / &system ibrav= 6, a = 4.6379, c = 3.1844,nat= 6, ntyp= 2, ecutwfc = 40,ecutrho=400,occupations='smearing',degauss=0.01,smearing='gaussian' / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 startingpot = 'file' startingwfc = 'file' / &IONS ion_dynamics='bfgs' / &CELL cell_dynamics = 'bfgs' / ATOMIC_SPECIES Ru 101.07 Ru.pbe-n-van.UPF O 15.099 O.pbe-rrkjus.UPF ATOMIC_POSITIONS (crystal) Ru 0.00000000 0.00000000 0.00000000 Ru 0.50000000 0.50000000 0.50000000 O 0.30600000 0.30600000 0.00000000 O 0.69400000 0.69400000 0.00000000 O 0.19400000 0.80600000 0.50000000 O 0.80600000 0.19400000 0.50000000 K_POINTS (automatic) 10 10 12 0 0 0 *Section of output file,* bfgs converged in 8 scf cycles and 4 bfgs steps (criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00) End of BFGS Geometry Optimization Final enthalpy = -227.8256404205 Ry Begin final coordinates new unit-cell volume = 463.72196 a.u.^3 ( 68.71650 Ang^3 ) CELL_PARAMETERS (alat= 8.76436083) 1.000910330 0.000000000 0.000000000 0.000000000 1.000910330 0.000000000 0.000000000 0.000000000 0.687553615 ATOMIC_POSITIONS (crystal) Ru 0.000000000 0.000000000 0.000000000 Ru 0.500000000 0.500000000 0.500000000 O 0.306258404 0.306258404 0.000000000 O 0.693741596 0.693741596 0.000000000 O 0.193741596 0.806258404 0.500000000 O 0.806258404 0.193741596 0.500000000 End final coordinates -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/ada00234/attachment-0001.htm From gulzarahmed61 at gmail.com Thu Aug 4 09:32:47 2011 From: gulzarahmed61 at gmail.com (gulzar ahmed) Date: Thu, 4 Aug 2011 13:02:47 +0530 Subject: [Pw_forum] Error Message-ID: I am getting error in Error: Function 'waveunit' at (1) has no IMPLICIT type -- GUL AHMED (M) 99820-94533 Save trees. Print Only When Necessary -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/ff558092/attachment.htm From mahdi_fn109 at yahoo.com Thu Aug 4 10:18:24 2011 From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri) Date: Thu, 4 Aug 2011 01:18:24 -0700 (PDT) Subject: [Pw_forum] problem in K_point selection. Message-ID: <1312445904.30602.YahooMailNeo@web43145.mail.sp1.yahoo.com> Dear all, I have an error in output file for scf calculation,? ? ? ? ? k( ? 24) = ( ?-0.4285714 ? 0.4123930 ? 0.0000000), wk = ? 0.0816327 ? ? ? ? k( ? 25) = ( ?-0.4285714 ?-0.0824786 ? 0.0000000), wk = ? 0.0816327 ? ? ?G cutoff = ? 83.6540 ?( ?23611 G-vectors) ? ? FFT grid: ( 20, 20,160) ? ? ?G cutoff = ? 57.9143 ?( ?13733 G-vectors) ?smooth grid: ( 15, 15,135) rank 3 in job 24 ?mzmr-desktop_51851 ? caused collective abort of all ranks ? exit status of rank 3: killed by signal 11? how can i fix this error? I think it appear from wrong ?k_point? and ?ecutwfc?. The following is a k_point and ecutwfc: ecutwfc =50 , ecutrho = 300 , K_POINTS {automatic} 7 ?6 ?1 ? ? 0 ?0 ?0 Can anyone help me? Thanks in advance. ? Mahdi Faghih nasiri MSC, Guilan University, Rasht, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/d71283de/attachment.htm From mahdi_fn109 at yahoo.com Thu Aug 4 10:18:23 2011 From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri) Date: Thu, 4 Aug 2011 01:18:23 -0700 (PDT) Subject: [Pw_forum] problem in K_Point selection. Message-ID: <1312445903.55358.YahooMailNeo@web43131.mail.sp1.yahoo.com> I have an error in output file for scf calculation,? ? ? ? ? ?k( ? 24) = ( ?-0.4285714 ? 0.4123930 ? 0.0000000), wk = ? 0.0816327 ? ? ? ? ?k( ? 25) = ( ?-0.4285714 ?-0.0824786 ? 0.0000000), wk = ? 0.0816327 ? ? ? ? ?G cutoff = ? 83.6540 ?( ?23611 G-vectors) ? ? FFT grid: ( 20, 20,160) ? ? ? ? ?G cutoff = ? 57.9143 ?( ?13733 G-vectors) ?smooth grid: ( 15, 15,135) ? ? ? ? ?rank 3 in job 24 ?mzmr-desktop_51851 ? caused collective abort of all ranks ? ? ? ? ?exit status of rank 3: killed by signal 11? how can i fix this error? I think it appear from wrong ?k_point? and ?ecutwfc?. The following is a k_point and ecutwfc: ? ? ? ? ? ecutwfc =50 , ? ? ? ? ? ecutrho = 300 , ? ? ? ? ? K_POINTS {automatic} ? ? ? ? ? 7 ?6 ?1 ? ? 0 ?0 ?0 Can anyone help me? Thanks in advance. ? Mahdi Faghih nasiri MSC, Guilan University, Rasht, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/fee82dec/attachment.htm From robinshy at gmail.com Thu Aug 4 11:30:12 2011 From: robinshy at gmail.com (Robin H) Date: Thu, 4 Aug 2011 17:30:12 +0800 Subject: [Pw_forum] anyone meets the problem like this? Message-ID: Dear all,anyone who used revPBE to creat PP has meet the warning like this : !!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!! Message from routine ld1_readin: US requires at least two energies per channel 4P !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! I am anxious to know how to resolve it. Welcome any suggestion. my input is : &input title='Zn' zed=30. rel=1, config='[Ar] 3d10.00 4s1.00 4p1.00', iswitch=3, dft='revPBE' / &inputp lloc=1, pseudotype=3, tm=.true., file_pseudopw='Zn.revPBE.UPF', / 5 3D 3 2 10.00 0.00 1.80 2.00 3D 3 2 0.00 0.05 1.80 2.00 4S 1 0 1.00 0.00 1.80 2.00 4S 1 0 0.00 0.05 1.80 2.00 4P 2 1 1.00 0.00 1.80 2.10 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/c87c88bd/attachment.htm From zafartariq2003 at yahoo.com Thu Aug 4 11:39:03 2011 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Thu, 4 Aug 2011 02:39:03 -0700 (PDT) Subject: [Pw_forum] About abbrevations of thermo.f Message-ID: <1312450743.95871.YahooMailNeo@web65416.mail.ac4.yahoo.com> I am calculating thermal properties using example "example_EOS" (thermo program). I get out put but I can not understand the abbrevation "bs.d". Whereas some abbrevations (according to me) **vol.d ==> P vs. V at various temperatures **alpha.d ==> Thermal Exancivity Vs T **bt.d ==> Bulk modulus vs T at various pressures ** Cp.d ==> Cp vs T at various Pressures ** Cv.d ==> Cv vs T at various pressures ** ga.d ==> Thermal gruension Parameter ** stp.d ==> Entrop vs T at various pressures **AM I RIGHT ** Also tell me what is 4th term in weight (input and input_QHA present in QHA directry of thermo program) ****input******* #v,#q,#freq,#unit 10,72,6,1 P= -4.2000 V= 128.0000 E= -34.511049940 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 389.703600000 389.703600000 689.271300000 -0.083333000 0.083333000 -0.083333000 65.161900000 65.161900000 111.638700000 388.319400000 388.319400000 685.533400000 -0.166667000 0.166667000 -0.166667000 125.786900000 125.786900000 218.804400000 384.646500000 384.646500000 674.502500000 . . . . . weight 0.0000000 0.0000000 0.0000000 0.0011574 <=== how we can calculate it? -0.0833333 0.0833333 -0.0833333 0.0092593 -0.1666667 0.1666667 -0.1666667 0.0092593 -0.2500000 0.2500000 -0.2500000 0.0092593 -0.3333333 0.3333333 -0.3333333 0.0092593 -0.4166667 0.4166667 -0.4166667 0.0092593 ....... ...... ..... ? Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,PakistanBest Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/979b330a/attachment.htm From prayerz.omo at gmail.com Thu Aug 4 11:50:52 2011 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Thu, 4 Aug 2011 05:50:52 -0400 Subject: [Pw_forum] pw.x seg. faults with EXX Message-ID: Ciao Tutti, I am trying to do a calculation with the PBE0 functional. I compiled pw.x using -DEXX. However, I got the following message when I tried to run. (If I replace input_dft='pbe0' with input_dft='pbe', I don't have this error but this is obviously not what I want. Thanks in advance for any help. XC functional enforced from input : Exchange-correlation = PBE0 (6484) EXX-fraction = 0.25 !!! Any further DFT definition will be discarded !!! Please, verify this is what you really want ! file O.pbe-mt.UPF: wavefunction(s) 0S 0P 0D renormalized Subspace diagonalization in iterative solution of the eigenvalue problem: a serial algorithm will be used [compute-1-7:09041] *** Process received signal *** [compute-1-7:09041] Signal: Segmentation fault (11) [compute-1-7:09041] Signal code: Address not mapped (1) [compute-1-7:09041] Failing at address: 0x5 o. Postdoctoral Fellow, ICTP, Trieste, ITALY -- ***************** Seek GOD! ************* From prayerz.omo at gmail.com Thu Aug 4 13:04:15 2011 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Thu, 4 Aug 2011 07:04:15 -0400 Subject: [Pw_forum] pw.x seg. faults with EXX In-Reply-To: References: Message-ID: Ciao ancora Tutti, It seems I diagnosed the problem: with the pbe0 hybrid, it seems you cannot set ecutrho to more than 4 times ecutwfc. I don't know why. The default seems to be ecutrho = 4 X ecutwfc so I just removed my specification for ecutrho and it runs without segfault. So far it is still running. Grazie. o. On Thu, Aug 4, 2011 at 5:50 AM, Omololu Akin-Ojo wrote: > Ciao Tutti, > > I am trying to do a calculation with the PBE0 functional. I compiled > pw.x using -DEXX. However, I got the following message when I tried to > run. (If I replace input_dft='pbe0' with input_dft='pbe', I don't have > this error but this is obviously not what I want. > Thanks in advance for any help. > > ? ? XC functional enforced from input : > ? ? Exchange-correlation ? ? ?= PBE0 (6484) > ? ? EXX-fraction ? ? ? ? ? ? ?= ? ? ? ?0.25 > ? ? !!! Any further DFT definition will be discarded > ? ? !!! Please, verify this is what you really want ! > > ? ? file O.pbe-mt.UPF: wavefunction(s) ?0S 0P 0D renormalized > > ? ? Subspace diagonalization in iterative solution of the eigenvalue problem: > ? ? a serial algorithm will be used > > [compute-1-7:09041] *** Process received signal *** > [compute-1-7:09041] Signal: Segmentation fault (11) > [compute-1-7:09041] Signal code: Address not mapped (1) > [compute-1-7:09041] Failing at address: 0x5 > > > o. > > Postdoctoral Fellow, > ICTP, Trieste, ITALY > > -- > ***************** Seek GOD! ************* > -- ***************** Seek GOD! ************* From padmaja_patnaik at yahoo.co.uk Thu Aug 4 13:24:29 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Thu, 4 Aug 2011 12:24:29 +0100 (BST) Subject: [Pw_forum] Error in example22 Message-ID: <1312457069.2563.YahooMailClassic@web28505.mail.ukl.yahoo.com> Hi All Example22 deals with fully relativistic pseudopotential. When I ran the example its running without error. But then I tried to calculate the density of states for Pt with fully relativistic pseudopotential and its giving the following error. running DOS calculation for Pt...Aborted Error condition encountered during test: exit status = 134 Aborting I tried to generate full relativistic pseudopotential for Si, C and Cr and for all the cases the scf calculations are running but it gives the same (above) error in DOS calculation (which I communicated in the my last mail to this forum). But thinking that I might have done something wrong I tried with the given relativistic pseudopotential case for Pt in the code. But that also gives the same error. Can anybody please help me finding out my probable mistake? Thanking in advance, regards Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/3ef82f2a/attachment.htm From moronaphtaly84 at gmail.com Thu Aug 4 15:07:50 2011 From: moronaphtaly84 at gmail.com (naphtaly moro) Date: Thu, 4 Aug 2011 15:07:50 +0200 Subject: [Pw_forum] pw.x seg. faults with EXX Message-ID: Dear Omolou It is because one sets the ecutrho to greater than for for ultrasoft PP, but since EXX as implemented in QE uses normconserving pp it is not hence necessary to increase the ecutrho to more than 4 Kind Regards ============================================== OUMA, Cecil Naphtaly Moro PhD. Student Physics Department, University of Pretoria, South Africa Office 5-61, NW-1 Building Cell: +27 721385182 ============================================== "Clouds are not spheres, mountains are not cones, coastlines are not circles, and bark is not smooth, nor does lightning travel in a straight line." - Benoit Mandelbrot On Thu, Aug 4, 2011 at 1:04 PM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/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. Error (gulzar ahmed) > 2. problem in K_point selection. (Mahdi Faqieh nasiri) > 3. problem in K_Point selection. (Mahdi Faqieh nasiri) > 4. anyone meets the problem like this? (Robin H) > 5. About abbrevations of thermo.f (zafar rasheed) > 6. pw.x seg. faults with EXX (Omololu Akin-Ojo) > 7. Re: pw.x seg. faults with EXX (Omololu Akin-Ojo) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 4 Aug 2011 13:02:47 +0530 > From: gulzar ahmed > Subject: [Pw_forum] Error > To: Pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > I am getting error in Error: Function 'waveunit' at (1) has no IMPLICIT > type > > -- > GUL AHMED > (M) 99820-94533 > Save trees. Print Only When Necessary > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110804/ff558092/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Thu, 4 Aug 2011 01:18:24 -0700 (PDT) > From: Mahdi Faqieh nasiri > Subject: [Pw_forum] problem in K_point selection. > To: "pw_forum at pwscf.org" > Message-ID: > <1312445904.30602.YahooMailNeo at web43145.mail.sp1.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I have an error in output file for scf calculation,? > > > ? ? ? ? k( ? 24) = ( ?-0.4285714 ? 0.4123930 ? 0.0000000), wk = ? 0.0816327 > ? ? ? ? k( ? 25) = ( ?-0.4285714 ?-0.0824786 ? 0.0000000), wk = ? 0.0816327 > > ? ? ?G cutoff = ? 83.6540 ?( ?23611 G-vectors) ? ? FFT grid: ( 20, 20,160) > ? ? ?G cutoff = ? 57.9143 ?( ?13733 G-vectors) ?smooth grid: ( 15, 15,135) > rank 3 in job 24 ?mzmr-desktop_51851 ? caused collective abort of all ranks > ? exit status of rank 3: killed by signal 11? > > > how can i fix this error? > I think it appear from wrong ?k_point? and ?ecutwfc?. > The following is a k_point and ecutwfc: > > ecutwfc =50 , > ecutrho = 300 , > > K_POINTS {automatic} > 7 ?6 ?1 ? ? 0 ?0 ?0 > > Can anyone help me? > > Thanks in advance. > ? > Mahdi Faghih nasiri > MSC, > Guilan University, > Rasht, Iran. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110804/d71283de/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Thu, 4 Aug 2011 01:18:23 -0700 (PDT) > From: Mahdi Faqieh nasiri > Subject: [Pw_forum] problem in K_Point selection. > To: "pw_forum at pwscf.org" > Message-ID: > <1312445903.55358.YahooMailNeo at web43131.mail.sp1.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > I have an error in output file for scf calculation,? > > > ? ? ? ? ?k( ? 24) = ( ?-0.4285714 ? 0.4123930 ? 0.0000000), wk = ? > 0.0816327 > ? ? ? ? ?k( ? 25) = ( ?-0.4285714 ?-0.0824786 ? 0.0000000), wk = ? > 0.0816327 > > ? ? ? ? ?G cutoff = ? 83.6540 ?( ?23611 G-vectors) ? ? FFT grid: ( 20, > 20,160) > ? ? ? ? ?G cutoff = ? 57.9143 ?( ?13733 G-vectors) ?smooth grid: ( 15, > 15,135) > ? ? ? ? ?rank 3 in job 24 ?mzmr-desktop_51851 ? caused collective abort of > all ranks > ? ? ? ? ?exit status of rank 3: killed by signal 11? > > > how can i fix this error? > I think it appear from wrong ?k_point? and ?ecutwfc?. > The following is a k_point and ecutwfc: > > ? ? ? ? ? ecutwfc =50 , > ? ? ? ? ? ecutrho = 300 , > > ? ? ? ? ? K_POINTS {automatic} > ? ? ? ? ? 7 ?6 ?1 ? ? 0 ?0 ?0 > > Can anyone help me? > > Thanks in advance. > ? > Mahdi Faghih nasiri > MSC, > Guilan University, > Rasht, Iran. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110804/fee82dec/attachment-0001.htm > > ------------------------------ > > Message: 4 > Date: Thu, 4 Aug 2011 17:30:12 +0800 > From: Robin H > Subject: [Pw_forum] anyone meets the problem like this? > To: Pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all,anyone who used revPBE to creat PP has meet the warning like this > : > !!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!! > Message from routine ld1_readin: > US requires at least two energies per channel 4P > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > I am anxious to know how to resolve it. Welcome any suggestion. > my input is : > &input > title='Zn' > zed=30. > rel=1, > config='[Ar] 3d10.00 4s1.00 4p1.00', > iswitch=3, > dft='revPBE' > / > &inputp > lloc=1, > pseudotype=3, > tm=.true., > file_pseudopw='Zn.revPBE.UPF', > / > 5 > 3D 3 2 10.00 0.00 1.80 2.00 > 3D 3 2 0.00 0.05 1.80 2.00 > 4S 1 0 1.00 0.00 1.80 2.00 > 4S 1 0 0.00 0.05 1.80 2.00 > 4P 2 1 1.00 0.00 1.80 2.10 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110804/c87c88bd/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Thu, 4 Aug 2011 02:39:03 -0700 (PDT) > From: zafar rasheed > Subject: [Pw_forum] About abbrevations of thermo.f > To: forum forum > Message-ID: > <1312450743.95871.YahooMailNeo at web65416.mail.ac4.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > I am calculating thermal properties using example "example_EOS" (thermo > program). I get out put but I can not understand the abbrevation "bs.d". > Whereas some abbrevations (according to me) > **vol.d ==> P vs. V at various temperatures > **alpha.d ==> Thermal Exancivity Vs T > **bt.d ==> Bulk modulus vs T at various pressures > ** Cp.d ==> Cp vs T at various Pressures > ** Cv.d ==> Cv vs T at various pressures > ** ga.d ==> Thermal gruension Parameter > ** stp.d ==> Entrop vs T at various pressures > **AM I RIGHT ** > Also tell me what is 4th term in weight (input and input_QHA present in QHA > directry of thermo program) > ****input******* > #v,#q,#freq,#unit > 10,72,6,1 > P= -4.2000 V= 128.0000 E= -34.511049940 > 0.000000000 0.000000000 0.000000000 > 0.000000000 > 0.000000000 > 0.000000000 > 389.703600000 > 389.703600000 > 689.271300000 > -0.083333000 0.083333000 -0.083333000 > 65.161900000 > 65.161900000 > 111.638700000 > 388.319400000 > 388.319400000 > 685.533400000 > -0.166667000 0.166667000 -0.166667000 > 125.786900000 > 125.786900000 > 218.804400000 > 384.646500000 > 384.646500000 > 674.502500000 > . > . > . > . > . > weight > 0.0000000 0.0000000 0.0000000 0.0011574 <=== how we can calculate it? > -0.0833333 0.0833333 -0.0833333 0.0092593 > -0.1666667 0.1666667 -0.1666667 0.0092593 > -0.2500000 0.2500000 -0.2500000 0.0092593 > -0.3333333 0.3333333 -0.3333333 0.0092593 > -0.4166667 0.4166667 -0.4166667 0.0092593 > ....... > ...... > ..... > ? > > Muhammad Zafar > PhD Scholar > Department of Physics > The Islamia University of Bahawalpur,PakistanBest Regards > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110804/979b330a/attachment-0001.htm > > ------------------------------ > > Message: 6 > Date: Thu, 4 Aug 2011 05:50:52 -0400 > From: Omololu Akin-Ojo > Subject: [Pw_forum] pw.x seg. faults with EXX > To: PWSCF Forum > Message-ID: > > > Content-Type: text/plain; charset=ISO-8859-1 > > Ciao Tutti, > > I am trying to do a calculation with the PBE0 functional. I compiled > pw.x using -DEXX. However, I got the following message when I tried to > run. (If I replace input_dft='pbe0' with input_dft='pbe', I don't have > this error but this is obviously not what I want. > Thanks in advance for any help. > > XC functional enforced from input : > Exchange-correlation = PBE0 (6484) > EXX-fraction = 0.25 > !!! Any further DFT definition will be discarded > !!! Please, verify this is what you really want ! > > file O.pbe-mt.UPF: wavefunction(s) 0S 0P 0D renormalized > > Subspace diagonalization in iterative solution of the eigenvalue > problem: > a serial algorithm will be used > > [compute-1-7:09041] *** Process received signal *** > [compute-1-7:09041] Signal: Segmentation fault (11) > [compute-1-7:09041] Signal code: Address not mapped (1) > [compute-1-7:09041] Failing at address: 0x5 > > > o. > > Postdoctoral Fellow, > ICTP, Trieste, ITALY > > -- > ***************** Seek GOD! ************* > > > ------------------------------ > > Message: 7 > Date: Thu, 4 Aug 2011 07:04:15 -0400 > From: Omololu Akin-Ojo > Subject: Re: [Pw_forum] pw.x seg. faults with EXX > To: PWSCF Forum > Message-ID: > > > Content-Type: text/plain; charset=ISO-8859-1 > > Ciao ancora Tutti, > > It seems I diagnosed the problem: with the pbe0 hybrid, it seems you > cannot set ecutrho to more than 4 times ecutwfc. I don't know why. The > default seems to be ecutrho = 4 X ecutwfc so I just removed my > specification for ecutrho and it runs without segfault. So far it is > still running. > > Grazie. > > o. > > On Thu, Aug 4, 2011 at 5:50 AM, Omololu Akin-Ojo > wrote: > > Ciao Tutti, > > > > I am trying to do a calculation with the PBE0 functional. I compiled > > pw.x using -DEXX. However, I got the following message when I tried to > > run. (If I replace input_dft='pbe0' with input_dft='pbe', I don't have > > this error but this is obviously not what I want. > > Thanks in advance for any help. > > > > ? ? XC functional enforced from input : > > ? ? Exchange-correlation ? ? ?= PBE0 (6484) > > ? ? EXX-fraction ? ? ? ? ? ? ?= ? ? ? ?0.25 > > ? ? !!! Any further DFT definition will be discarded > > ? ? !!! Please, verify this is what you really want ! > > > > ? ? file O.pbe-mt.UPF: wavefunction(s) ?0S 0P 0D renormalized > > > > ? ? Subspace diagonalization in iterative solution of the eigenvalue > problem: > > ? ? a serial algorithm will be used > > > > [compute-1-7:09041] *** Process received signal *** > > [compute-1-7:09041] Signal: Segmentation fault (11) > > [compute-1-7:09041] Signal code: Address not mapped (1) > > [compute-1-7:09041] Failing at address: 0x5 > > > > > > o. > > > > Postdoctoral Fellow, > > ICTP, Trieste, ITALY > > > > -- > > ***************** Seek GOD! ************* > > > > > > -- > ***************** Seek GOD! ************* > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 50, Issue 13 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/345aefbd/attachment-0001.htm From gabriele.sclauzero at epfl.ch Thu Aug 4 15:39:27 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Thu, 4 Aug 2011 15:39:27 +0200 Subject: [Pw_forum] anyone meets the problem like this? In-Reply-To: References: Message-ID: <986BFB4A-A184-4C68-96D7-512E617DFC75@epfl.ch> Dear Robin, the message looks quite self-explanatory to me. If it does not mean anything to you, then you need to go through the theory of Ultrasoft (US) pseudopotentials and have a look at the documentation of the ld1 code. If you want to pseudize a channel in the norm-conserving recipe, while keeping the others in the US style, then you have to specify the rcutus equal to rcut for that channel, for instance: 4P 2 1 1.00 0.00 1.80 1.80 works with no warnings. Moreover, also your input produces the same US PP even if you get that warning, because the code tries to understand what you really wanted, and it does correctly. HTH GS Il giorno 04/ago/2011, alle ore 11.30, Robin H ha scritto: > Dear all,anyone who used revPBE to creat PP has meet the warning like this : > !!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!! > Message from routine ld1_readin: > US requires at least two energies per channel 4P > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > I am anxious to know how to resolve it. Welcome any suggestion. > my input is : > &input > title='Zn' > zed=30. > rel=1, > config='[Ar] 3d10.00 4s1.00 4p1.00', > iswitch=3, > dft='revPBE' > / > &inputp > lloc=1, > pseudotype=3, > tm=.true., > file_pseudopw='Zn.revPBE.UPF', > / > 5 > 3D 3 2 10.00 0.00 1.80 2.00 > 3D 3 2 0.00 0.05 1.80 2.00 > 4S 1 0 1.00 0.00 1.80 2.00 > 4S 1 0 0.00 0.05 1.80 2.00 > 4P 2 1 1.00 0.00 1.80 2.10 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/f950e122/attachment.htm From gabriele.sclauzero at epfl.ch Thu Aug 4 15:42:52 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Thu, 4 Aug 2011 15:42:52 +0200 Subject: [Pw_forum] anyone meets the problem like this? In-Reply-To: References: Message-ID: <3429723D-77FF-40F3-9223-16A24A4C43E5@epfl.ch> Sorry, I forgot to say two things: 1. please specify a more meaningful subject in your next posts on the forum 2. please sign your emails with your name and affiliation as also written here http://www.quantum-espresso.org/wiki/index.php/Pw_users Thanks GS > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/6f6b45c4/attachment.htm From giannozz at democritos.it Thu Aug 4 17:45:50 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 4 Aug 2011 17:45:50 +0200 Subject: [Pw_forum] problem in K_Point selection. In-Reply-To: <1312445903.55358.YahooMailNeo@web43131.mail.sp1.yahoo.com> References: <1312445903.55358.YahooMailNeo@web43131.mail.sp1.yahoo.com> Message-ID: <3D8CA7C1-706B-4648-A2E6-E8A9A9530227@democritos.it> On Aug 4, 2011, at 10:18 , Mahdi Faqieh nasiri wrote: > rank 3 in job 24 mzmr-desktop_51851 caused collective > abort of all ranks > exit status of rank 3: killed by signal 11 > > how can i fix this error? see the FAQ and the user guide P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Thu Aug 4 17:48:10 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 4 Aug 2011 17:48:10 +0200 Subject: [Pw_forum] Error In-Reply-To: References: Message-ID: <14BA6811-95AE-4D04-BC07-62B3A9A22648@democritos.it> On Aug 4, 2011, at 9:32 , gulzar ahmed wrote: > I am getting error in Error: Function 'waveunit' at (1) has no > IMPLICIT type if are you applying for the contest on "most obscure message ever", this is not the correct place. You are getting error WHEN DOING WHAT??? --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ttduyle at gmail.com Thu Aug 4 18:16:10 2011 From: ttduyle at gmail.com (Duy Le) Date: Thu, 4 Aug 2011 12:16:10 -0400 Subject: [Pw_forum] problem in K_point selection. In-Reply-To: <1312445904.30602.YahooMailNeo@web43145.mail.sp1.yahoo.com> References: <1312445904.30602.YahooMailNeo@web43145.mail.sp1.yahoo.com> Message-ID: On Thu, Aug 4, 2011 at 4:18 AM, Mahdi Faqieh nasiri wrote: > Dear all, > I have an error in output file for scf calculation, > > ? ? ? ? k( ? 24) = ( ?-0.4285714 ? 0.4123930 ? 0.0000000), wk = ? 0.0816327 > ? ? ? ? k( ? 25) = ( ?-0.4285714 ?-0.0824786 ? 0.0000000), wk = ? 0.0816327 > ? ? ?G cutoff = ? 83.6540 ?( ?23611 G-vectors) ? ? FFT grid: ( 20, 20,160) > ? ? ?G cutoff = ? 57.9143 ?( ?13733 G-vectors) ?smooth grid: ( 15, 15,135) > rank 3 in job 24 ?mzmr-desktop_51851 ? caused collective abort of all ranks > ? exit status of rank 3: killed by signal 11 > > how can i fix this error? > I think it appear from wrong ?k_point? and ?ecutwfc?. > The following is a k_point and ecutwfc: > ecutwfc =50 , > ecutrho = 300 , > K_POINTS {automatic} > 7 ?6 ?1 ? ? 0 ?0 ?0 This should not relate to QE (QE error usually comes with a CRASH information) You should check your compilation, network connection, MPI, hardware,... Also, you should try to run with less number of cores if possible. -------------------------------------------------- Duy Le PhD Candidate Department of Physics University of Central Florida. "Men don't need hand to do things" > Mahdi Faghih nasiri > MSC, > Guilan University, > Rasht, Iran. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From ttduyle at gmail.com Thu Aug 4 18:35:27 2011 From: ttduyle at gmail.com (Duy Le) Date: Thu, 4 Aug 2011 12:35:27 -0400 Subject: [Pw_forum] large error in RuO2 lattice parameter In-Reply-To: References: Message-ID: On Thu, Aug 4, 2011 at 12:36 AM, mohnish pandey wrote: > Dear QE users, > 2.7438 > I want to study RuO2 surfaces. I did calculation of ruthenium metal and > found the lattice constant right(experimental = 2.70 and 1.584, I got 2.7438 > and 1.582) But after doing calculation of bulk ruthenium oxide I am getting > very different lattice parameter as compared to the experimental value. > Experimental value is 4.494 and 3.107 and I am getting the value of 4.6421 > and 3.1888. > Can anybody please tell from where the discrepancy is coming? It comes from the difference between theory and experiment. If you check literature of similar calculation (S. Hong et al, surf. sci. 2010), you will see that your numbers are really good. -------------------------------------------------- Duy Le PhD Candidate Department of Physics University of Central Florida. "Men don't need hand to do things" > Thanks a lot in advance > > input file > > &control > ??? calculation = 'vc-relax', > ??? restart_mode='restart', > ??? nstep=100 > ??? outdir='/home/mohnish/Desktop/Ruo2-bulk', > ??? pseudo_dir='/home/mohnish/Desktop/Ruo2-bulk', > ??? prefix='Ruo2', > ??? tstress = .true., > ??? tprnfor = .true., > ? / > ? &system > ??? ibrav=? 6, a = 4.6379, c = 3.1844,nat=? 6, ntyp= 2, > ??? ecutwfc = > 40,ecutrho=400,occupations='smearing',degauss=0.01,smearing='gaussian' > ? / > ? &electrons > ?? diagonalization='david' > ?? mixing_mode = 'plain' > ?? mixing_beta = 0.7 > ?? conv_thr = 1.0d-8 > ?? startingpot = 'file' > ?? startingwfc = 'file' > ?/ > &IONS > ?ion_dynamics='bfgs' > / > &CELL > ?cell_dynamics = 'bfgs' > / > ATOMIC_SPECIES > ? Ru 101.07 Ru.pbe-n-van.UPF > ? O? 15.099 O.pbe-rrkjus.UPF > ?ATOMIC_POSITIONS (crystal) > Ru? 0.00000000? 0.00000000? 0.00000000 > Ru? 0.50000000? 0.50000000? 0.50000000 > O?? 0.30600000? 0.30600000? 0.00000000 > O?? 0.69400000? 0.69400000? 0.00000000 > O?? 0.19400000? 0.80600000? 0.50000000 > O?? 0.80600000? 0.19400000? 0.50000000 > ?K_POINTS (automatic) > ?10 10 12 0 0 0 > > > Section of output file, > > bfgs converged in?? 8 scf cycles and?? 4 bfgs steps > ???? (criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00) > > ???? End of BFGS Geometry Optimization > > ???? Final enthalpy =??? -227.8256404205 Ry > Begin final coordinates > ???? new unit-cell volume =??? 463.72196 a.u.^3 (??? 68.71650 Ang^3 ) > > CELL_PARAMETERS (alat=? 8.76436083) > ?? 1.000910330?? 0.000000000?? 0.000000000 > ?? 0.000000000?? 1.000910330?? 0.000000000 > ?? 0.000000000?? 0.000000000?? 0.687553615 > > ATOMIC_POSITIONS (crystal) > Ru?????? 0.000000000?? 0.000000000?? 0.000000000 > Ru?????? 0.500000000?? 0.500000000?? 0.500000000 > O??????? 0.306258404?? 0.306258404?? 0.000000000 > O??????? 0.693741596?? 0.693741596?? 0.000000000 > O??????? 0.193741596?? 0.806258404?? 0.500000000 > O??????? 0.806258404?? 0.193741596?? 0.500000000 > End final coordinates > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Senior Project Associate, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From deepak.p.thakur at gmail.com Thu Aug 4 19:06:50 2011 From: deepak.p.thakur at gmail.com (dipak thakur) Date: Thu, 4 Aug 2011 22:36:50 +0530 Subject: [Pw_forum] Help regarding supercell Message-ID: Sir, Good evening. I think I was unable to convey my message correctly. Kindly go through the input file below. --------------------------------------------------------------------------------------------------------- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ &CONTROL title = Graphene mono layer , calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/root/tmp/' , pseudo_dir = '/root/Desktop/QUANTUM_ESPRESSO/pseudo/' , prefix = graphene , disk_io = 'default' , verbosity = 'default' , etot_conv_thr = 1.D-4 , forc_conv_thr = 1.D-3 , nstep = 50 , dt = 40 , / &SYSTEM ibrav = 0, celldm(1) = 1.0000000, celldm(2) = 1.0000000, celldm(3) = 0.5000000, nat = 32, ntyp = 1, ecutwfc = 50 , ecutrho = 400 , occupations = 'smearing' , smearing = 'methfessel-paxton' , nspin = 1 , lda_plus_u = .false. , / &ELECTRONS electron_maxstep = 300, conv_thr = 1.0d-8 , mixing_mode = 'plain' , mixing_beta = 0.5 , diagonalization = 'cg' , diago_cg_maxiter = 50, / &IONS / CELL_PARAMETERS 16.121319540 9.383047808 0.000000000 0.000000000 18.658162370 0.000000000 0.000000000 0.000000000 56.689342400 ATOMIC_SPECIES C 12.01070 C.pbe-van_bm.UPF ATOMIC_POSITIONS angstrom C 2.891630000 7.402190000 2.000000000 C 3.592920000 8.638320000 2.000000000 C 3.603490000 6.167020000 2.000000000 C 5.018600000 8.645010000 2.000000000 C 5.021500000 6.165980000 2.000000000 C 5.733020000 7.405220000 2.000000000 C 1.471840000 7.396160000 2.000000000 C 2.891120000 9.870660000 2.000000000 C 2.894710000 4.932640000 2.000000000 C 5.733190000 9.888500000 2.000000000 C 5.736430000 4.941300000 2.000000000 C 7.163480000 7.412030000 2.000000000 C 1.474740000 4.926900000 2.000000000 C 0.762281000 8.627830000 2.000000000 C 0.763134000 6.161720000 2.000000000 C 1.471500000 9.863350000 2.000000000 C 3.603410000 11.109500000 2.000000000 C 5.021240000 11.123900000 2.000000000 C 3.605120000 3.701560000 2.000000000 C 5.026450000 3.707890000 2.000000000 C 7.878070000 8.655320000 2.000000000 C 7.163730000 9.894970000 2.000000000 C 7.162030000 4.948140000 2.000000000 C 7.876190000 6.176770000 2.000000000 C 5.736340000 12.352200000 2.000000000 C 0.772689000 3.691020000 2.000000000 C 0.762793000 1.220030000 2.000000000 C 7.876450000 11.133700000 2.000000000 C 7.162030000 12.358700000 2.000000000 C 7.872010000 13.592200000 2.000000000 C 2.894790000 2.466190000 2.000000000 C 1.474820000 2.458780000 2.000000000 K_POINTS automatic 6 6 1 1 1 1 --------------------------------------------------------------------------------------------------------- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I am desparately trying to understand how to determine: 1. The CELL_PARAMETERS 16.121319540 9.383047808 0.000000000 0.000000000 18.658162370 0.000000000 0.000000000 0.000000000 56.689342400 (or how are they determined in this case) - This is again a copy of earlier post. 2. The celldm(1) = 1.0000000, celldm(2) = 1.0000000, celldm(3) = 0.5000000, How do I fix them. Is there any software and/or technique to do this? or Is there any mathematical relation that would be able to provide me these values. The cell parameters are given to a precision upto 9th decimal place. Secondly, the celldm(3) =0.5, does it mean that it would divide the value 56.689342400 by 2 and can similar logic be applied to celldm(1) and celldm(2)? Thirdly, if I view the geometry in XcrySDen, it show vacuum layers in Z direction, but no gap/vacuum in x and y direction? I have seen this in many papers published till date and is trying to understand these things. Doesn't the adjacent supercell (in x and y direction) interact with the supercell under consideration? Also is there relation between the co-ordinates of the atom, the CELL PARAMETERS and celldm()? I hereby request you to kindly help me in this regard. Deepak Thakur Research Student Swami Ramanand Teerth Marathwada University, Vishnupuri, Nanded, Maharashtra, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/e5f1f2c1/attachment.htm From ttduyle at gmail.com Thu Aug 4 19:13:23 2011 From: ttduyle at gmail.com (Duy Le) Date: Thu, 4 Aug 2011 13:13:23 -0400 Subject: [Pw_forum] Help regarding supercell In-Reply-To: References: Message-ID: If ibrav=0, you must NOT specify celldm(2-6), according to the manual. http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id3775702 More info can be found there in regarding celldm, ibrav, CELL_PARAMETTERS PS: you should not change subject of your email. This would help to keep your email in the same thread, and help others to understand well your situation. -------------------------------------------------- Duy Le PhD Candidate Department of Physics University of Central Florida. "Men don't need hand to do things" On Thu, Aug 4, 2011 at 1:06 PM, dipak thakur wrote: > Sir, > > Good evening. > > I think I was unable to convey my message correctly. > > Kindly go through the input file below. > --------------------------------------------------------------------------------------------------------- > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > ?&CONTROL > ?????????????????????? title = Graphene mono layer , > ???????????????? calculation = 'relax' , > ??????????????? restart_mode = 'from_scratch' , > ????????????????????? outdir = '/root/tmp/' , > ????????????????? pseudo_dir = '/root/Desktop/QUANTUM_ESPRESSO/pseudo/' , > ????????????????????? prefix = graphene , > ???????????????????? disk_io = 'default' , > ?????????????????? verbosity = 'default' , > ?????????????? etot_conv_thr = 1.D-4 , > ?????????????? forc_conv_thr = 1.D-3 , > ?????????????????????? nstep = 50 , > ????????????????????????? dt = 40 , > ?/ > ?&SYSTEM > ?????????????????????? ibrav = 0, > ?????????????????? celldm(1) = 1.0000000, > ??? ??? ? ? ? ? ?? celldm(2) = 1.0000000, > ??? ??? ? ? ? ? ?? celldm(3) = 0.5000000, > ???????????????????????? nat = 32, > ??????????????????????? ntyp = 1, > ???????????????????? ecutwfc = 50 , > ???????????????????? ecutrho = 400 , > ???????????????? occupations = 'smearing' , > ??????????????????? smearing = 'methfessel-paxton' , > ?????????????????????? nspin = 1 , > ????????????????? lda_plus_u = .false. , > ?/ > ?&ELECTRONS > ??????????? electron_maxstep = 300, > ??????????????????? conv_thr = 1.0d-8 , > ???????????????? mixing_mode = 'plain' , > ???????????????? mixing_beta = 0.5 , > ???????????? diagonalization = 'cg' , > ??????????? diago_cg_maxiter = 50, > ?/ > ?&IONS > ?/ > CELL_PARAMETERS > ??? 16.121319540??? 9.383047808??? 0.000000000 > ???? 0.000000000?? 18.658162370??? 0.000000000 > ???? 0.000000000??? 0.000000000?? 56.689342400 > ATOMIC_SPECIES > ??? C?? 12.01070? C.pbe-van_bm.UPF > ATOMIC_POSITIONS angstrom > ??? C????? 2.891630000??? 7.402190000??? 2.000000000 > ??? C????? 3.592920000??? 8.638320000??? 2.000000000 > ??? C????? 3.603490000??? 6.167020000??? 2.000000000 > ??? C????? 5.018600000??? 8.645010000??? 2.000000000 > ??? C????? 5.021500000??? 6.165980000??? 2.000000000 > ??? C????? 5.733020000??? 7.405220000??? 2.000000000 > ??? C????? 1.471840000??? 7.396160000??? 2.000000000 > ??? C????? 2.891120000??? 9.870660000??? 2.000000000 > ??? C????? 2.894710000??? 4.932640000??? 2.000000000 > ??? C????? 5.733190000??? 9.888500000??? 2.000000000 > ??? C????? 5.736430000??? 4.941300000??? 2.000000000 > ??? C????? 7.163480000??? 7.412030000??? 2.000000000 > ??? C????? 1.474740000??? 4.926900000??? 2.000000000 > ??? C????? 0.762281000??? 8.627830000??? 2.000000000 > ??? C????? 0.763134000??? 6.161720000??? 2.000000000 > ??? C????? 1.471500000??? 9.863350000??? 2.000000000 > ??? C????? 3.603410000?? 11.109500000??? 2.000000000 > ??? C????? 5.021240000?? 11.123900000??? 2.000000000 > ??? C????? 3.605120000??? 3.701560000??? 2.000000000 > ??? C????? 5.026450000??? 3.707890000??? 2.000000000 > ??? C????? 7.878070000??? 8.655320000??? 2.000000000 > ??? C????? 7.163730000??? 9.894970000??? 2.000000000 > ??? C????? 7.162030000??? 4.948140000??? 2.000000000 > ??? C????? 7.876190000??? 6.176770000??? 2.000000000 > ??? C????? 5.736340000?? 12.352200000??? 2.000000000 > ??? C????? 0.772689000??? 3.691020000??? 2.000000000 > ??? C????? 0.762793000??? 1.220030000??? 2.000000000 > ??? C????? 7.876450000?? 11.133700000??? 2.000000000 > ??? C????? 7.162030000?? 12.358700000??? 2.000000000 > ??? C????? 7.872010000?? 13.592200000??? 2.000000000 > ??? C????? 2.894790000??? 2.466190000??? 2.000000000 > ??? C????? 1.474820000??? 2.458780000??? 2.000000000 > K_POINTS automatic > ? 6 6 1?? 1 1 1 > > --------------------------------------------------------------------------------------------------------- > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > I am desparately trying to understand how to determine: > 1. The > CELL_PARAMETERS > ??? 16.121319540??? 9.383047808??? 0.000000000 > ???? 0.000000000?? 18.658162370??? 0.000000000 > ???? 0.000000000??? 0.000000000?? 56.689342400 > (or how are they determined in this case) - This is again a copy of earlier > post. > 2. The????????? celldm(1) = 1.0000000, > ??? ??? ? ? ? ? ?? celldm(2) = 1.0000000, > ??? ??? ? ? ? ? ?? celldm(3) = 0.5000000, > ?????????????????? How do I fix them. > Is there any software and/or technique to do this? or Is there any > mathematical relation that would be able to provide me these values. > The cell parameters are given to a precision upto 9th decimal place. > > Secondly, the celldm(3) =0.5, does it mean that it would divide the value > 56.689342400 by 2 and can similar logic be applied to celldm(1) and > celldm(2)? > Thirdly, if I view the geometry in XcrySDen, it show vacuum layers in Z > direction, but no gap/vacuum in x and y direction? I have seen this in many > papers published till date and is trying to understand these things. > Doesn't the adjacent supercell (in x and y direction) interact with the > supercell under consideration? > Also is there relation between the co-ordinates of the atom, the CELL > PARAMETERS and celldm()? > > I hereby request you to kindly help me in this regard. > > Deepak Thakur > Research Student > Swami Ramanand Teerth Marathwada University, > Vishnupuri, Nanded, > Maharashtra, > India. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From gabriele.sclauzero at epfl.ch Thu Aug 4 17:52:46 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Thu, 4 Aug 2011 17:52:46 +0200 Subject: [Pw_forum] Error in example22 In-Reply-To: <1312457069.2563.YahooMailClassic@web28505.mail.ukl.yahoo.com> References: <1312457069.2563.YahooMailClassic@web28505.mail.ukl.yahoo.com> Message-ID: <298F3227-2006-4918-8750-E549B133CFDD@epfl.ch> The error code issued by the shell script alone is not useful. Please provide more information (at least the output of the DOS calculations). With so little information no one will be able to help you... GS Il giorno 04/ago/2011, alle ore 13.24, Padmaja Patnaik ha scritto: > Hi All > > Example22 deals with fully relativistic pseudopotential. When I ran the example its running without error. But then I tried to calculate the density of states for Pt with fully relativistic pseudopotential and its giving the following error. > > running DOS calculation for Pt...Aborted > Error condition encountered during test: exit status = 134 > Aborting > > I tried to generate full relativistic pseudopotential for Si, C and Cr and for all the cases the scf calculations are running but it gives the same (above) error in DOS calculation (which I communicated in the my last mail to this forum). But thinking that I might have done something wrong I tried with the given relativistic pseudopotential case for Pt in the code. But that also gives the same error. Can anybody please help me finding out my probable mistake? Thanking in advance, > regards > > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/cd95ba9f/attachment-0001.htm From giannozz at democritos.it Thu Aug 4 22:35:25 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 4 Aug 2011 22:35:25 +0200 Subject: [Pw_forum] IOTK error while restarting using QE4.3.1 In-Reply-To: References: Message-ID: On Aug 3, 2011, at 8:00 , Prasenjit Ghosh wrote: > When I am trying to restart the scf calculation it is giving me the > following IOTK error it is very likely a compiler problem > However, the same input file restarts perfectly fine for QE-4.2.1 > compiled > in the same machine using the same versions of gfortran and mpi doesn't mean much, unfortunately P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From padmaja_patnaik at yahoo.co.uk Fri Aug 5 06:15:50 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Fri, 5 Aug 2011 05:15:50 +0100 (BST) Subject: [Pw_forum] Error in example22 In-Reply-To: Message-ID: <1312517750.93208.YahooMailClassic@web28505.mail.ukl.yahoo.com> DOS output file has 474 lines. So quite a big one to add here. Adding the last few lines. It stops suddenly during the calculations without any error message in the dos.out file. Last lines of dos.out file are: k =-0.3333-1.0000 0.0000???? band energies (ev): ??? 11.4826? 11.4826? 11.9471? 11.9471? 14.5757? 14.5757? 16.4971? 16.4971 ????????? k =-0.5000-1.0000 0.0000???? band energies (ev): ??? 11.9360? 11.9360? 12.9428? 12.9428? 13.1796? 13.1796? 15.8993? 15.8993 ???? the Fermi energy is??? 12.6210 ev Also attaching the input file for scf and dos calcualtions below. scf input file: --------------------- ?&system ??? ibrav=? 2, celldm(1) =7.42, nat=? 1, ntyp= 1, ??? lspinorb=.true., ??? noncolin=.true., ??? starting_magnetization=0.0, ??? occupations='smearing', ??? degauss=0.02, ??? smearing='mp', ??? ecutwfc =30.0, ??? ecutrho =250.0, ?/ ?&electrons ??? mixing_beta = 0.7, ??? conv_thr =? 1.0d-8 ?/ ATOMIC_SPECIES Pt? 0.0?? Ptrel.RRKJ3.UPF ATOMIC_POSITIONS Pt? 0.0000000?? 0.00000000?? 0.0 K_POINTS AUTOMATIC 4 4 4 1 1 1 EOF DOS input file: --------------------- cat > pt.dos.in << EOF ?&control ??? calculation='nscf' ??? prefix='pt', ??? pseudo_dir = '$PSEUDO_DIR/', ??? outdir='$TMP_DIR/' ?/ ?&system ?? ibrav=? 2, celldm(1) =7.42, nat=? 1, ntyp= 1, ??? lspinorb=.true., ??? noncolin=.true., ??? starting_magnetization=0.0, ??? ecutwfc =30.0, ??? ecutrho =250.0, nbnd=8, ??? occupations='tetrahedra' ?/ ?&electrons ??? conv_thr = 1.0e-10 ??? mixing_beta = 0.7 ?/ ATOMIC_SPECIES Pt? 0.0?? Ptrel.RRKJ3.UPF ATOMIC_POSITIONS Pt? 0.0000000?? 0.00000000?? 0.0 K_POINTS {automatic} ?12 12 12 0 0 0 EOF Thanks and regards, Padmaja Patnaik Research Scholar Dept of Physics IIT Bombay Mumbai, India - Message: 3 Date: Thu, 4 Aug 2011 17:52:46 +0200 From: Gabriele Sclauzero Subject: Re: [Pw_forum] Error in example22 To: PWSCF Forum Message-ID: <298F3227-2006-4918-8750-E549B133CFDD at epfl.ch> Content-Type: text/plain; charset="iso-8859-1" The error code issued by the shell script alone is not useful. Please provide more information (at least the output of the DOS calculations). With so little information no one will be able to help you... GS Il giorno 04/ago/2011, alle ore 13.24, Padmaja Patnaik ha scritto: > Hi All > > Example22 deals with fully relativistic pseudopotential. When I ran the example its running without error. But then I tried to calculate the density of states for Pt with fully relativistic pseudopotential and its giving the following error. > > running DOS calculation for Pt...Aborted > Error condition encountered during test: exit status = 134 > Aborting > > I tried to generate full relativistic pseudopotential for Si, C and Cr and for all the cases the scf calculations are running but it gives the same (above) error in DOS calculation (which I communicated in the my last mail to this forum). But thinking that I might have done something wrong I tried with the given relativistic pseudopotential case for Pt in the code. But that also gives the same error. Can anybody please help me finding out my probable mistake? Thanking in advance, > regards > > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA ???PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/2ebd827e/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Fri Aug 5 08:09:52 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 05 Aug 2011 08:09:52 +0200 Subject: [Pw_forum] IOTK error while restarting using QE4.3.1 In-Reply-To: References: Message-ID: In data 04 agosto 2011 alle ore 22:35:25, Paolo Giannozzi ha scritto: > it is very likely a compiler problem I've had several reports of lkpoints_dir=.false. with only one kpoint causes every sort of errors, luckily I have no time to investigate the matter properly due to holiday... just check that it is not your case. regards -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From prayerz.omo at gmail.com Fri Aug 5 08:24:05 2011 From: prayerz.omo at gmail.com (Omololu Akin-Ojo) Date: Fri, 5 Aug 2011 08:24:05 +0200 Subject: [Pw_forum] pw.x seg. faults with EXX In-Reply-To: References: Message-ID: Thank you, Naphtaly, I think I understand your explanation. It will be nice if the program prints out an appropriate error message instead of seg-faulting -- this way, others users do not waste their time trying to fix the problem like I did. Thanks again. o. On Thu, Aug 4, 2011 at 3:07 PM, naphtaly moro wrote: > Dear Omolou > It is because one sets the ecutrho to greater than for for ultrasoft PP, but > since EXX as implemented in QE uses normconserving pp it is not hence > necessary to increase the ecutrho to more than 4 > Kind Regards > ============================================== > OUMA, Cecil Naphtaly Moro > PhD. Student > Physics Department, University of Pretoria, South Africa > Office 5-61, NW-1 Building > Cell: +27 721385182 > ============================================== > > "Clouds are not spheres, mountains are not cones, coastlines are not > circles, > and bark is not smooth, nor does lightning travel in a straight line." - > Benoit Mandelbrot > > > > On Thu, Aug 4, 2011 at 1:04 PM, wrote: >> >> Send Pw_forum mailing list submissions to >> ? ? ? ?pw_forum at pwscf.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> ? ? ? ?http://www.democritos.it/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. Error (gulzar ahmed) >> ? 2. problem in K_point selection. (Mahdi Faqieh nasiri) >> ? 3. problem in K_Point selection. (Mahdi Faqieh nasiri) >> ? 4. anyone meets the problem like this? (Robin H) >> ? 5. About abbrevations of thermo.f (zafar rasheed) >> ? 6. pw.x seg. faults with EXX (Omololu Akin-Ojo) >> ? 7. Re: pw.x seg. faults with EXX (Omololu Akin-Ojo) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 4 Aug 2011 13:02:47 +0530 >> From: gulzar ahmed >> Subject: [Pw_forum] Error >> To: Pw_forum at pwscf.org >> Message-ID: >> >> ? >> Content-Type: text/plain; charset="iso-8859-1" >> >> I am getting error in Error: Function 'waveunit' at (1) has no IMPLICIT >> type >> >> -- >> GUL AHMED >> (M) 99820-94533 >> Save trees. Print Only When Necessary >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20110804/ff558092/attachment-0001.htm >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 4 Aug 2011 01:18:24 -0700 (PDT) >> From: Mahdi Faqieh nasiri >> Subject: [Pw_forum] problem in K_point selection. >> To: "pw_forum at pwscf.org" >> Message-ID: >> ? ? ? ?<1312445904.30602.YahooMailNeo at web43145.mail.sp1.yahoo.com> >> Content-Type: text/plain; charset="utf-8" >> >> Dear all, >> >> I have an error in output file for scf calculation,? >> >> >> ? ? ? ? k( ? 24) = ( ?-0.4285714 ? 0.4123930 ? 0.0000000), wk = ? >> 0.0816327 >> ? ? ? ? k( ? 25) = ( ?-0.4285714 ?-0.0824786 ? 0.0000000), wk = ? >> 0.0816327 >> >> ? ? ?G cutoff = ? 83.6540 ?( ?23611 G-vectors) ? ? FFT grid: ( 20, 20,160) >> ? ? ?G cutoff = ? 57.9143 ?( ?13733 G-vectors) ?smooth grid: ( 15, 15,135) >> rank 3 in job 24 ?mzmr-desktop_51851 ? caused collective abort of all >> ranks >> ? exit status of rank 3: killed by signal 11? >> >> >> how can i fix this error? >> I think it appear from wrong ?k_point? and ?ecutwfc?. >> The following is a k_point and ecutwfc: >> >> ecutwfc =50 , >> ecutrho = 300 , >> >> K_POINTS {automatic} >> 7 ?6 ?1 ? ? 0 ?0 ?0 >> >> Can anyone help me? >> >> Thanks in advance. >> ? >> Mahdi Faghih nasiri >> MSC, >> Guilan University, >> Rasht, Iran. >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20110804/d71283de/attachment-0001.htm >> >> ------------------------------ >> >> Message: 3 >> Date: Thu, 4 Aug 2011 01:18:23 -0700 (PDT) >> From: Mahdi Faqieh nasiri >> Subject: [Pw_forum] problem in K_Point selection. >> To: "pw_forum at pwscf.org" >> Message-ID: >> ? ? ? ?<1312445903.55358.YahooMailNeo at web43131.mail.sp1.yahoo.com> >> Content-Type: text/plain; charset="utf-8" >> >> I have an error in output file for scf calculation,? >> >> >> ? ? ? ? ?k( ? 24) = ( ?-0.4285714 ? 0.4123930 ? 0.0000000), wk = ? >> 0.0816327 >> ? ? ? ? ?k( ? 25) = ( ?-0.4285714 ?-0.0824786 ? 0.0000000), wk = ? >> 0.0816327 >> >> ? ? ? ? ?G cutoff = ? 83.6540 ?( ?23611 G-vectors) ? ? FFT grid: ( 20, >> 20,160) >> ? ? ? ? ?G cutoff = ? 57.9143 ?( ?13733 G-vectors) ?smooth grid: ( 15, >> 15,135) >> ? ? ? ? ?rank 3 in job 24 ?mzmr-desktop_51851 ? caused collective abort of >> all ranks >> ? ? ? ? ?exit status of rank 3: killed by signal 11? >> >> >> how can i fix this error? >> I think it appear from wrong ?k_point? and ?ecutwfc?. >> The following is a k_point and ecutwfc: >> >> ? ? ? ? ? ecutwfc =50 , >> ? ? ? ? ? ecutrho = 300 , >> >> ? ? ? ? ? K_POINTS {automatic} >> ? ? ? ? ? 7 ?6 ?1 ? ? 0 ?0 ?0 >> >> Can anyone help me? >> >> Thanks in advance. >> ? >> Mahdi Faghih nasiri >> MSC, >> Guilan University, >> Rasht, Iran. >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20110804/fee82dec/attachment-0001.htm >> >> ------------------------------ >> >> Message: 4 >> Date: Thu, 4 Aug 2011 17:30:12 +0800 >> From: Robin H >> Subject: [Pw_forum] anyone meets the problem like this? >> To: Pw_forum at pwscf.org >> Message-ID: >> >> ? >> Content-Type: text/plain; charset="iso-8859-1" >> >> Dear all,anyone who used revPBE to creat PP has meet the warning like this >> : >> ? ? !!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!! >> ? ? Message from routine ld1_readin: >> ? ? US requires at least two energies per channel 4P >> ? ? !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> >> I am anxious to know how to resolve it. Welcome any suggestion. >> my input is : >> ?&input >> ? ?title='Zn' >> ? ?zed=30. >> ? ?rel=1, >> ? ?config='[Ar] 3d10.00 4s1.00 4p1.00', >> ? ?iswitch=3, >> ? ?dft='revPBE' >> ?/ >> ?&inputp >> ? lloc=1, >> ? pseudotype=3, >> ? tm=.true., >> ? file_pseudopw='Zn.revPBE.UPF', >> ?/ >> 5 >> 3D ?3 ?2 ?10.00 ?0.00 ?1.80 ?2.00 >> 3D ?3 ?2 ? 0.00 ?0.05 ?1.80 ?2.00 >> 4S ?1 ?0 ?1.00 ? 0.00 ?1.80 ?2.00 >> 4S ?1 ?0 ?0.00 ? 0.05 ?1.80 ?2.00 >> 4P ?2 ?1 ?1.00 ? 0.00 ?1.80 ?2.10 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20110804/c87c88bd/attachment-0001.htm >> >> ------------------------------ >> >> Message: 5 >> Date: Thu, 4 Aug 2011 02:39:03 -0700 (PDT) >> From: zafar rasheed >> Subject: [Pw_forum] About abbrevations of thermo.f >> To: forum forum >> Message-ID: >> ? ? ? ?<1312450743.95871.YahooMailNeo at web65416.mail.ac4.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> I am calculating thermal properties using example "example_EOS" (thermo >> program). I get out put but I can not understand the abbrevation "bs.d". >> Whereas some abbrevations (according to me) >> **vol.d ==> P vs. V at various temperatures >> **alpha.d ==> Thermal Exancivity Vs T >> **bt.d ==> Bulk modulus vs T at various pressures >> ** Cp.d ==> Cp vs T at various Pressures >> ** Cv.d ==> Cv vs T at various pressures >> ** ga.d ==> Thermal gruension Parameter >> ** stp.d ==> Entrop vs T at various pressures >> **AM I RIGHT ** >> Also tell me what is 4th term in weight (input and input_QHA present in >> QHA directry of thermo program) >> ****input******* >> #v,#q,#freq,#unit >> 10,72,6,1 >> P= -4.2000 V= 128.0000 E= -34.511049940 >> 0.000000000 0.000000000 0.000000000 >> 0.000000000 >> 0.000000000 >> 0.000000000 >> 389.703600000 >> 389.703600000 >> 689.271300000 >> -0.083333000 0.083333000 -0.083333000 >> 65.161900000 >> 65.161900000 >> 111.638700000 >> 388.319400000 >> 388.319400000 >> 685.533400000 >> -0.166667000 0.166667000 -0.166667000 >> 125.786900000 >> 125.786900000 >> 218.804400000 >> 384.646500000 >> 384.646500000 >> 674.502500000 >> . >> . >> . >> . >> . >> weight >> 0.0000000 0.0000000 0.0000000 0.0011574 <=== how we can calculate it? >> -0.0833333 0.0833333 -0.0833333 0.0092593 >> -0.1666667 0.1666667 -0.1666667 0.0092593 >> -0.2500000 0.2500000 -0.2500000 0.0092593 >> -0.3333333 0.3333333 -0.3333333 0.0092593 >> -0.4166667 0.4166667 -0.4166667 0.0092593 >> ....... >> ...... >> ..... >> ? >> >> Muhammad Zafar >> PhD Scholar >> Department of Physics >> The Islamia University of Bahawalpur,PakistanBest Regards >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://www.democritos.it/pipermail/pw_forum/attachments/20110804/979b330a/attachment-0001.htm >> >> ------------------------------ >> >> Message: 6 >> Date: Thu, 4 Aug 2011 05:50:52 -0400 >> From: Omololu Akin-Ojo >> Subject: [Pw_forum] pw.x seg. faults with EXX >> To: PWSCF Forum >> Message-ID: >> >> ? >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Ciao Tutti, >> >> I am trying to do a calculation with the PBE0 functional. I compiled >> pw.x using -DEXX. However, I got the following message when I tried to >> run. (If I replace input_dft='pbe0' with input_dft='pbe', I don't have >> this error but this is obviously not what I want. >> Thanks in advance for any help. >> >> ? ? XC functional enforced from input : >> ? ? Exchange-correlation ? ? ?= PBE0 (6484) >> ? ? EXX-fraction ? ? ? ? ? ? ?= ? ? ? ?0.25 >> ? ? !!! Any further DFT definition will be discarded >> ? ? !!! Please, verify this is what you really want ! >> >> ? ? file O.pbe-mt.UPF: wavefunction(s) ?0S 0P 0D renormalized >> >> ? ? Subspace diagonalization in iterative solution of the eigenvalue >> problem: >> ? ? a serial algorithm will be used >> >> [compute-1-7:09041] *** Process received signal *** >> [compute-1-7:09041] Signal: Segmentation fault (11) >> [compute-1-7:09041] Signal code: Address not mapped (1) >> [compute-1-7:09041] Failing at address: 0x5 >> >> >> o. >> >> Postdoctoral Fellow, >> ICTP, Trieste, ITALY >> >> -- >> ***************** Seek GOD! ************* >> >> >> ------------------------------ >> >> Message: 7 >> Date: Thu, 4 Aug 2011 07:04:15 -0400 >> From: Omololu Akin-Ojo >> Subject: Re: [Pw_forum] pw.x seg. faults with EXX >> To: PWSCF Forum >> Message-ID: >> >> ? >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Ciao ancora Tutti, >> >> It seems I diagnosed the problem: with the pbe0 hybrid, it seems you >> cannot set ecutrho to more than 4 times ecutwfc. I don't know why. The >> default seems to be ecutrho = 4 X ecutwfc so I just removed my >> specification for ecutrho and it runs without segfault. So far it is >> still running. >> >> Grazie. >> >> o. >> >> On Thu, Aug 4, 2011 at 5:50 AM, Omololu Akin-Ojo >> wrote: >> > Ciao Tutti, >> > >> > I am trying to do a calculation with the PBE0 functional. I compiled >> > pw.x using -DEXX. However, I got the following message when I tried to >> > run. (If I replace input_dft='pbe0' with input_dft='pbe', I don't have >> > this error but this is obviously not what I want. >> > Thanks in advance for any help. >> > >> > ? ? XC functional enforced from input : >> > ? ? Exchange-correlation ? ? ?= PBE0 (6484) >> > ? ? EXX-fraction ? ? ? ? ? ? ?= ? ? ? ?0.25 >> > ? ? !!! Any further DFT definition will be discarded >> > ? ? !!! Please, verify this is what you really want ! >> > >> > ? ? file O.pbe-mt.UPF: wavefunction(s) ?0S 0P 0D renormalized >> > >> > ? ? Subspace diagonalization in iterative solution of the eigenvalue >> > problem: >> > ? ? a serial algorithm will be used >> > >> > [compute-1-7:09041] *** Process received signal *** >> > [compute-1-7:09041] Signal: Segmentation fault (11) >> > [compute-1-7:09041] Signal code: Address not mapped (1) >> > [compute-1-7:09041] Failing at address: 0x5 >> > >> > >> > o. >> > >> > Postdoctoral Fellow, >> > ICTP, Trieste, ITALY >> > >> > -- >> > ***************** Seek GOD! ************* >> > >> >> >> >> -- >> ***************** Seek GOD! ************* >> >> >> ------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> End of Pw_forum Digest, Vol 50, Issue 13 >> **************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ***************** Seek GOD! ************* From prasenjit.jnc at gmail.com Fri Aug 5 08:54:39 2011 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Fri, 5 Aug 2011 12:24:39 +0530 Subject: [Pw_forum] IOTK error while restarting using QE4.3.1 In-Reply-To: References: Message-ID: Thanks Paolo and Lorenzo. > I've had several reports of lkpoints_dir=.false. with only one kpoint > causes every sort of errors, luckily I have no time to investigate the > matter properly due to holiday... just check that it is not your case. > > regards > Lorenzo, I am not setting this flag in the input file.....I am using the default value which is .true. Also in the *.save directories, I have all the k-points directories.....So I think it is not the case. Regards, Prasenjit -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From gabriele.sclauzero at epfl.ch Fri Aug 5 12:11:45 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Fri, 5 Aug 2011 12:11:45 +0200 Subject: [Pw_forum] Error in example22 In-Reply-To: <1312517750.93208.YahooMailClassic@web28505.mail.ukl.yahoo.com> References: <1312517750.93208.YahooMailClassic@web28505.mail.ukl.yahoo.com> Message-ID: What you show is the output of a non-self consistent field (NSCF) calculation. I think that when you speak of DOS calculation most of the people here understand a dos.x run (or at least I did...) I've tried your input files and they work fine for me! Your nscf run stops almost at the end, just before (or while) writing the data to disk. Are you sure that you specified prefix and outdir correctly? (be careful that an empty value of $TMP_DIR would cause problems, obviously...) HTH GS Il giorno 05/ago/2011, alle ore 06.15, Padmaja Patnaik ha scritto: > DOS output file has 474 lines. So quite a big one to add here. Adding the last few lines. It stops suddenly during the calculations without any error message in the dos.out file. Last lines of dos.out file are: > k =-0.3333-1.0000 0.0000 band energies (ev): > > 11.4826 11.4826 11.9471 11.9471 14.5757 14.5757 16.4971 16.4971 > > k =-0.5000-1.0000 0.0000 band energies (ev): > > 11.9360 11.9360 12.9428 12.9428 13.1796 13.1796 15.8993 15.8993 > > the Fermi energy is 12.6210 ev > > Also attaching the input file for scf and dos calcualtions below. > scf input file: > --------------------- > &system > ibrav= 2, celldm(1) =7.42, nat= 1, ntyp= 1, > lspinorb=.true., > noncolin=.true., > starting_magnetization=0.0, > occupations='smearing', > degauss=0.02, > smearing='mp', > ecutwfc =30.0, > ecutrho =250.0, > / > &electrons > mixing_beta = 0.7, > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > Pt 0.0 Ptrel.RRKJ3.UPF > ATOMIC_POSITIONS > Pt 0.0000000 0.00000000 0.0 > K_POINTS AUTOMATIC > 4 4 4 1 1 1 > EOF > > DOS input file: > --------------------- > > cat > pt.dos.in << EOF > &control > calculation='nscf' > prefix='pt', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav= 2, celldm(1) =7.42, nat= 1, ntyp= 1, > lspinorb=.true., > noncolin=.true., > starting_magnetization=0.0, > ecutwfc =30.0, > ecutrho =250.0, nbnd=8, > occupations='tetrahedra' > / > &electrons > conv_thr = 1.0e-10 > mixing_beta = 0.7 > / > > ATOMIC_SPECIES > Pt 0.0 Ptrel.RRKJ3.UPF > ATOMIC_POSITIONS > Pt 0.0000000 0.00000000 0.0 > K_POINTS {automatic} > 12 12 12 0 0 0 > EOF > > Thanks and regards, > > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > > - > Message: 3 > Date: Thu, 4 Aug 2011 17:52:46 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] Error in example22 > To: PWSCF Forum > Message-ID: <298F3227-2006-4918-8750-E549B133CFDD at epfl.ch> > Content-Type: text/plain; charset="iso-8859-1" > > The error code issued by the shell script alone is not useful. Please provide more information (at least the output of the DOS calculations). With so little information no one will be able to help you... > > GS > > Il giorno 04/ago/2011, alle ore 13.24, Padmaja Patnaik ha scritto: > > > Hi All > > > > Example22 deals with fully relativistic pseudopotential. When I ran the example its running without error. But then I tried to calculate the density of states for Pt with fully relativistic pseudopotential and its giving the following error. > > > > running DOS calculation for Pt...Aborted > > Error condition encountered during test: exit status = 134 > > Aborting > > > > I tried to generate full relativistic pseudopotential for Si, C and Cr and for all the cases the scf calculations are running but it gives the same (above) error in DOS calculation (which I communicated in the my last mail to this forum). But thinking that I might have done something wrong I tried with the given relativistic pseudopotential case for Pt in the code. But that also gives the same error. Can anybody please help me finding out my probable mistake? Thanking in advance, > > regards > > > > Padmaja Patnaik > > Research Scholar > > Dept of Physics > > IIT Bombay > > Mumbai, India > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/4c36ad29/attachment.htm From thomas.gruber at physik.tu-freiberg.de Fri Aug 5 14:02:47 2011 From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber) Date: Fri, 05 Aug 2011 14:02:47 +0200 Subject: [Pw_forum] repeated band structure calculation in, splittet phonon calculation In-Reply-To: References: Message-ID: <4E3BDBE7.2090505@physik.tu-freiberg.de> >> Or did I something wrong and it should work? >> > what should work in which case and with which version of the code > exactly? > > I wanted to know, if I can use "wf_collect = .true." in an scf run, which is used for input of an splittet phonon calculation with QE 4.3.1. Part of the &inputph for ph.x would look like this. to create the pattern: nq1=3,nq2=2,nq3=3, start_irr=0, last_irr=0, run mode 11 on q-point 8: nq1=3,nq2=2,nq3=3, start_q=8, last_q=8, start_irr=11, last_irr=11, and the final run with all the *.xml file: nq1=3,nq2=2,nq3=3, When I calculate everything on one core, it works. But when I run the scf on multiple cores and use "wf_collect = .true." then the following error occurs, when I run the splittet jobs on multiple core (but not on one core) or at the final run (even with one core): from openfilq : error # 1 file $prefix.wfc not found Thanks already for your help. Thomas From giannozz at democritos.it Fri Aug 5 14:44:44 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 5 Aug 2011 14:44:44 +0200 Subject: [Pw_forum] q vectors In-Reply-To: References: Message-ID: <08B78182-1C69-43B3-B5E8-8B111847E3E4@democritos.it> On Aug 2, 2011, at 21:25 , Jennifer Wohlwend wrote: > > I'm trying to perform electron-phonon coupling calcualtions and > I was wondering how do you get the q vectors? as a uniform grid, by specifying the number of points along each vector generating the reciprocal lattice. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 5 14:46:12 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 5 Aug 2011 14:46:12 +0200 Subject: [Pw_forum] Raman on DFT-false-metals In-Reply-To: References: Message-ID: <0780405C-0BD4-4085-897A-DDE708D7A063@democritos.it> On Aug 3, 2011, at 17:24 , Eduardo Ariel Menendez Proupin wrote: > I would like to calculate a Raman spectrum with PHONON for an > insulator > that is metallic in LDA and GGA. Is it possible to introduce easily > a scissors > shift to open the gap and allow the Raman calculation? it is possible, but it is not implemented right now P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 5 14:50:08 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 5 Aug 2011 14:50:08 +0200 Subject: [Pw_forum] pw.x seg. faults with EXX In-Reply-To: References: Message-ID: On Aug 5, 2011, at 8:24 , Omololu Akin-Ojo wrote: > It will be nice if the program prints out an appropriate error message > instead of seg-faulting -- this way, others users do not waste their > time trying to fix the problem like I did. Do you realize how stupid is what you have written? --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Fri Aug 5 14:53:09 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 5 Aug 2011 14:53:09 +0200 Subject: [Pw_forum] compiling error during the installation of the GPU release of Quantum ESpresso In-Reply-To: <4E394017.5080802@uniroma1.it> References: <4E394017.5080802@uniroma1.it> Message-ID: <7EC195D8-6B4A-436D-91BC-00F053FBC128@democritos.it> On Aug 3, 2011, at 14:33 , fabrizio gala wrote: > IF (err) THEN > 1 > Error: IF clause at (1) requires a scalar LOGICAL expression assuming that err is an integer variable, the correct syntax is "IF ( err > 0 ) THEN" Some compilers accept integers in logical expressions (0=.false., 1=.true.) but this is nonstandard P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From raamesh123 at rediffmail.com Fri Aug 5 14:49:05 2011 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 5 Aug 2011 12:49:05 -0000 Subject: [Pw_forum] =?utf-8?q?Help_regarding_supercell_=28Deepak_Tahkur=29?= In-Reply-To: Message-ID: <1312480763.S.38106.25097.F.H.TnB3X2ZvcnVtLXJlcXVlc3RAcHdzY2Yub3JnAFB3X2ZvcnVtIERpZ2VzdCwgVm9sIDUwLCBJc3N1ZSAxNg__.f6-145-74.old.1312548545.14461@webmail.rediffmail.com> Dear Deepak "Thirdly, if I view the geometry in XcrySDen, it show vacuum layers in Z direction, but no gap/vacuum in x and y direction? I have seen this in many papers published till date and is trying to understand these things. Doesn't the adjacent supercell (in x and y direction) interact with the supercell under consideration?" The question is not complete Deepak. In case of thin film or surface studies people will a vacuum layers only in the Z direction. But if you want to isolate group of atoms or molecules you need to have vacuum layer in all three crystallographic direction. you can refer to this paper http://rmp.aps.org/abstract/RMP/v64/i4/p1045_1 With regards K. Ramesh Kumar Research Scholar Department of Physics IIT-Madras Chennai-600 036 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/37bf9dd9/attachment-0001.htm From member at linkedin.com Fri Aug 5 15:51:13 2011 From: member at linkedin.com (Alex An via LinkedIn) Date: Fri, 5 Aug 2011 13:51:13 +0000 (UTC) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <463199627.1941280.1312552273812.JavaMail.app@ela4-bed80.prod> LinkedIn ------------ Alex An requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Alex Accept invitation from Alex An http://www.linkedin.com/e/-iqpnjm-gqz7qg7k-31/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I85780408_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pve30Qc3wTdjx9bTl4ljsQlQR9bPcNdz8NejwSdPcLrCBxbOYWrSlI/EML_comm_afe/ View invitation from Alex An http://www.linkedin.com/e/-iqpnjm-gqz7qg7k-31/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I85780408_60/0MdBYUc3gMe3sRe4ALqnpPbOYWrSlI/svi/ ------------------------------------------ DID YOU KNOW that LinkedIn can find the answers to your most difficult questions? 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URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/aa231cfe/attachment.htm From member at linkedin.com Fri Aug 5 15:52:49 2011 From: member at linkedin.com (Alex An via LinkedIn) Date: Fri, 5 Aug 2011 13:52:49 +0000 (UTC) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <427608120.1944704.1312552369167.JavaMail.app@ela4-bed80.prod> LinkedIn ------------ Alex An requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Alex Accept invitation from Alex An http://www.linkedin.com/e/-iqpnjm-gqz7shq6-44/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I85781014_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pvd34McjwTdjx9bTl4ljsQlQR9bPcNdz8NejwSdPcLrCBxbOYWrSlI/EML_comm_afe/ View invitation from Alex An http://www.linkedin.com/e/-iqpnjm-gqz7shq6-44/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I85781014_60/0MdBYQcj0Ne3sRe4ALqnpPbOYWrSlI/svi/ ------------------------------------------ DID YOU KNOW that LinkedIn can find the answers to your most difficult questions? Post those vexing questions on LinkedIn Answers to tap into the knowledge of the world's foremost business experts: http://www.linkedin.com/e/-iqpnjm-gqz7shq6-44/ask/inv-23/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/b5b4ca7f/attachment.htm From bdslipun at gmail.com Fri Aug 5 16:10:37 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Fri, 5 Aug 2011 19:40:37 +0530 Subject: [Pw_forum] elastic constants Message-ID: how can elastic constants determined in espresso code for a cubic system -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/60171add/attachment.htm From fabrizio.gala at uniroma1.it Fri Aug 5 16:18:28 2011 From: fabrizio.gala at uniroma1.it (fabrizio gala) Date: Fri, 05 Aug 2011 16:18:28 +0200 Subject: [Pw_forum] compiling error during the installation of the GPU release of Quantum ESpresso In-Reply-To: <7EC195D8-6B4A-436D-91BC-00F053FBC128@democritos.it> References: <4E394017.5080802@uniroma1.it> <7EC195D8-6B4A-436D-91BC-00F053FBC128@democritos.it> Message-ID: <4E3BFBB4.3070204@uniroma1.it> thanks for your fast reply, unfortunately, after having corrected the syntax as you told me, the following compiling error occurs: make[2]: Entering directory `/home/fabri/espresso-PRACE/PW/cuda' /usr/local/cuda/bin/nvcc -O3 --ptxas-options=-v -arch sm_20 -gencode arch=compute_20,code=compute_20 -I../../include -I../include -I/usr/local/cuda//include -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__CUDA -D__CUDA_MEM_PINNED -D__GPU_NVIDIA_20 -D__CUDA_QE_TIMING -D__MPI -D__PARA -c vloc_psi.cu -o vloc_psi_cuda.o In file included from /usr/local/cuda//include/cuda_runtime.h:59:0, from :0: /usr/local/cuda//include/host_config.h:82:2: error: #error -- unsupported GNU version! gcc 4.5 and up are not supported! In file included from vloc_psi.cu:16:0: ../../include/cuda_env.h:26:17: fatal error: mpi.h: No such file or directory compilation terminated. make[2]: *** [libpwcuda.a] Error 1 make[2]: Leaving directory `/home/fabri/espresso-PRACE/PW/cuda' mpif90 -g -o pw.x \ pwscf.o libpw.a libpwcuda.a ../Modules/libqemod.a ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -llapack -lblas -lfftw3 -lblas -L/usr/local/cuda//lib64 -lcudart -lcublas -lcufft -lcublas -lcuda gfortran: error: libpwcuda.a: No such file or directory make[1]: *** [pw.x] Error 1 make[1]: Leaving directory `/home/fabri/espresso-PRACE/PW' make: *** [pw] Error 2 which seems to me more tricky.. any suggestion? Il 05/08/11 14:53, Paolo Giannozzi ha scritto: > On Aug 3, 2011, at 14:33 , fabrizio gala wrote: > >> IF (err) THEN >> 1 >> Error: IF clause at (1) requires a scalar LOGICAL expression > assuming that err is an integer variable, the correct syntax is "IF > ( err> 0 ) THEN" > Some compilers accept integers in logical expressions (0=.false., > 1=.true.) but > this is nonstandard > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Fabrizio Gala Dipartimento di Scienze di Base e Applicate per l'Ingegneria, Sezione di Fisica. La Sapienza,University of Rome and Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM) via A. Scarpa 14-16 00161 Rome - ITALY phone: +390649766545 fax: +390644240183 From lmartinsamos at gmail.com Fri Aug 5 17:00:14 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Fri, 5 Aug 2011 17:00:14 +0200 Subject: [Pw_forum] compiling error during the installation of the GPU release of Quantum ESpresso In-Reply-To: <4E3BFBB4.3070204@uniroma1.it> References: <4E394017.5080802@uniroma1.it> <7EC195D8-6B4A-436D-91BC-00F053FBC128@democritos.it> <4E3BFBB4.3070204@uniroma1.it> Message-ID: Dear Fabrizio there is a specific mailing list for questions/problems with the GPU implementation ( q-e-gpgpu at qeforge.qe-forge.org). You can subscribe at http://qe-forge.org/mailman/listinfo/q-e-gpgpu . best regards Layla 2011/8/5 fabrizio gala > thanks for your fast reply, > unfortunately, after having corrected the syntax as you told me, the > following compiling error occurs: > > make[2]: Entering directory `/home/fabri/espresso-PRACE/PW/cuda' > /usr/local/cuda/bin/nvcc -O3 --ptxas-options=-v -arch sm_20 -gencode > arch=compute_20,code=compute_20 -I../../include -I../include > -I/usr/local/cuda//include -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__CUDA > -D__CUDA_MEM_PINNED -D__GPU_NVIDIA_20 -D__CUDA_QE_TIMING -D__MPI > -D__PARA -c vloc_psi.cu -o vloc_psi_cuda.o > In file included from /usr/local/cuda//include/cuda_runtime.h:59:0, > from :0: > /usr/local/cuda//include/host_config.h:82:2: error: #error -- > unsupported GNU version! gcc 4.5 and up are not supported! > In file included from vloc_psi.cu:16:0: > ../../include/cuda_env.h:26:17: fatal error: mpi.h: No such file or > directory > compilation terminated. > make[2]: *** [libpwcuda.a] Error 1 > make[2]: Leaving directory `/home/fabri/espresso-PRACE/PW/cuda' > mpif90 -g -o pw.x \ > pwscf.o libpw.a libpwcuda.a ../Modules/libqemod.a ../flib/ptools.a > ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -llapack -lblas > -lfftw3 -lblas -L/usr/local/cuda//lib64 -lcudart -lcublas -lcufft > -lcublas -lcuda > gfortran: error: libpwcuda.a: No such file or directory > make[1]: *** [pw.x] Error 1 > make[1]: Leaving directory `/home/fabri/espresso-PRACE/PW' > make: *** [pw] Error 2 > > which seems to me more tricky.. > any suggestion? > > > Il 05/08/11 14:53, Paolo Giannozzi ha scritto: > > On Aug 3, 2011, at 14:33 , fabrizio gala wrote: > > > >> IF (err) THEN > >> 1 > >> Error: IF clause at (1) requires a scalar LOGICAL expression > > assuming that err is an integer variable, the correct syntax is "IF > > ( err> 0 ) THEN" > > Some compilers accept integers in logical expressions (0=.false., > > 1=.true.) but > > this is nonstandard > > > > P. > > --- > > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > Dr. Fabrizio Gala > Dipartimento di Scienze di Base e Applicate per l'Ingegneria, > Sezione di Fisica. > La Sapienza,University of Rome > and > Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia > (CNISM) > > via A. Scarpa 14-16 > 00161 Rome - ITALY > phone: +390649766545 > fax: +390644240183 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/f40a4733/attachment.htm From mikeat4999 at gmail.com Fri Aug 5 17:06:22 2011 From: mikeat4999 at gmail.com (mike at.) Date: Fri, 5 Aug 2011 18:06:22 +0300 Subject: [Pw_forum] pw.x seg. faults with EXX In-Reply-To: References: Message-ID: Omolulu On Fri, Aug 5, 2011 at 9:24 AM, Omololu Akin-Ojo wrote: > Thank you, Naphtaly, I think I understand your explanation. > > It will be nice if the program prints out an appropriate error message > instead of seg-faulting -- this way, others users do not waste their > The "seg-fault" IS an "approppriate" error message imho. http://en.wikipedia.org/wiki/Segmentation_fault > time trying to fix the problem like I did. > > Thanks again. > > o. > > On Thu, Aug 4, 2011 at 3:07 PM, naphtaly moro > wrote: > > Dear Omolou > > It is because one sets the ecutrho to greater than for for ultrasoft PP, > but > > since EXX as implemented in QE uses normconserving pp it is not hence > > necessary to increase the ecutrho to more than 4 > > Kind Regards > > ============================================== > > OUMA, Cecil Naphtaly Moro > > PhD. Student > > Physics Department, University of Pretoria, South Africa > > Office 5-61, NW-1 Building > > Cell: +27 721385182 > > ============================================== > > > > "Clouds are not spheres, mountains are not cones, coastlines are not > > circles, > > and bark is not smooth, nor does lightning travel in a straight line." - > > Benoit Mandelbrot > > > > > > > > On Thu, Aug 4, 2011 at 1:04 PM, wrote: > >> > >> Send Pw_forum mailing list submissions to > >> pw_forum at pwscf.org > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> http://www.democritos.it/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..." > -- M. O. ATAMBO mikeat4999 at gmail.com student, computational material science group Chepkoilel university college. Department of Physics -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/b7166c65/attachment-0001.htm From baroni at sissa.it Fri Aug 5 17:41:40 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 5 Aug 2011 17:41:40 +0200 Subject: [Pw_forum] elastic constants In-Reply-To: References: Message-ID: As with any other periodic code, I guess: by calculating the stress response to a given strain. If you go through the QE users' manual, I am pretty sure you will find how to instruct QE to calculate the stress tensor (look how to set the variable "tstress"). A HTH By the way: would you be so kind as to sign future posts to this forum, including your academic affiliation? Thanks - SB On Aug 5, 2011, at 4:10 PM, bhabya sahoo wrote: > how can elastic constants determined in espresso code for a cubic system > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/921bbf6c/attachment.htm From member at linkedin.com Fri Aug 5 20:31:22 2011 From: member at linkedin.com (Thaneshwor Kaloni via LinkedIn) Date: Fri, 5 Aug 2011 18:31:22 +0000 (UTC) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <2014678760.2761116.1312569082920.JavaMail.app@ela4-bed82.prod> LinkedIn ------------ Thaneshwor Kaloni requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Thaneshwor Accept invitation from Thaneshwor Kaloni http://www.linkedin.com/e/-iqpnjm-gqzhqq79-5i/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I85901619_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pvej4Scj0Vdjx9bSxckj4Ps6V7bPsPcjwNdz4TdPcLrCBxbOYWrSlI/EML_comm_afe/ View invitation from Thaneshwor Kaloni http://www.linkedin.com/e/-iqpnjm-gqzhqq79-5i/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I85901619_60/0MdBYVcjoNc3ARe4ALqnpPbOYWrSlI/svi/ ------------------------------------------ Why might connecting with Thaneshwor Kaloni be a good idea? Have a question? Thaneshwor Kaloni's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Thaneshwor Kaloni and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/-iqpnjm-gqzhqq79-5i/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/e7b8a0c8/attachment.htm From baroni at sissa.it Fri Aug 5 21:15:28 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 5 Aug 2011 21:15:28 +0200 Subject: [Pw_forum] Invitation to connect on LinkedIn In-Reply-To: <2014678760.2761116.1312569082920.JavaMail.app@ela4-bed82.prod> References: <2014678760.2761116.1312569082920.JavaMail.app@ela4-bed82.prod> Message-ID: Please, everybody: stop sending linkdln invitations (as well as any other social network activities) to this forum. Thanks - SB On Aug 5, 2011, at 8:31 PM, Thaneshwor Kaloni via LinkedIn wrote: > LinkedIn > Thaneshwor Kaloni requested to add you as a connection on LinkedIn: > veronica, > > I'd like to add you to my professional network on LinkedIn. > > - Thaneshwor > > > Accept > View invitation from Thaneshwor Kaloni > > > > WHY MIGHT CONNECTING WITH THANESHWOR KALONI BE A GOOD IDEA? > > Have a question? Thaneshwor Kaloni's network will probably have an answer > You can use LinkedIn Answers to distribute your professional questions to Thaneshwor Kaloni and your extended network. You can get high-quality answers from experienced professionals. > > > ? 2011, LinkedIn Corporation > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110805/4164fd6f/attachment.htm From ivan.girotto at ichec.ie Fri Aug 5 21:38:32 2011 From: ivan.girotto at ichec.ie (Ivan Girotto) Date: Fri, 05 Aug 2011 20:38:32 +0100 Subject: [Pw_forum] compiling error during the installation of the GPU release of Quantum ESpresso In-Reply-To: <4E3BFBB4.3070204@uniroma1.it> References: <4E394017.5080802@uniroma1.it> <7EC195D8-6B4A-436D-91BC-00F053FBC128@democritos.it> <4E3BFBB4.3070204@uniroma1.it> Message-ID: <4E3C46B8.7070501@ichec.ie> Hi Fabrizio, we never met this problem. I would ask you to try with a gcc compiler version < 4.5, or with Intel compiler if you have one available. Please let me know if a different compiler can fix your problem. Otherwise we'll further investigate. Regards, Ivan -- Girotto Ivan - ivan.girotto at ichec.ie ICHEC - Computational Group - http://www.ichec.ie The Tower - 7th floor Trinity Technology& Enterprise Campus Grand Canal Quay - Dublin 2 - Ireland +353-1-5241608 ex. 32 (ph) / +353-1-7645845 (fax) On 05/08/2011 15:18, fabrizio gala wrote: > thanks for your fast reply, > unfortunately, after having corrected the syntax as you told me, the > following compiling error occurs: > > make[2]: Entering directory `/home/fabri/espresso-PRACE/PW/cuda' > /usr/local/cuda/bin/nvcc -O3 --ptxas-options=-v -arch sm_20 -gencode > arch=compute_20,code=compute_20 -I../../include -I../include > -I/usr/local/cuda//include -D__GFORTRAN -D__STD_F95 -D__FFTW3 -D__CUDA > -D__CUDA_MEM_PINNED -D__GPU_NVIDIA_20 -D__CUDA_QE_TIMING -D__MPI > -D__PARA -c vloc_psi.cu -o vloc_psi_cuda.o > In file included from /usr/local/cuda//include/cuda_runtime.h:59:0, > from:0: > /usr/local/cuda//include/host_config.h:82:2: error: #error -- > unsupported GNU version! gcc 4.5 and up are not supported! > In file included from vloc_psi.cu:16:0: > ../../include/cuda_env.h:26:17: fatal error: mpi.h: No such file or > directory > compilation terminated. > make[2]: *** [libpwcuda.a] Error 1 > make[2]: Leaving directory `/home/fabri/espresso-PRACE/PW/cuda' > mpif90 -g -o pw.x \ > pwscf.o libpw.a libpwcuda.a ../Modules/libqemod.a ../flib/ptools.a > ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a -llapack -lblas > -lfftw3 -lblas -L/usr/local/cuda//lib64 -lcudart -lcublas -lcufft > -lcublas -lcuda > gfortran: error: libpwcuda.a: No such file or directory > make[1]: *** [pw.x] Error 1 > make[1]: Leaving directory `/home/fabri/espresso-PRACE/PW' > make: *** [pw] Error 2 > > which seems to me more tricky.. > any suggestion? > > > Il 05/08/11 14:53, Paolo Giannozzi ha scritto: >> On Aug 3, 2011, at 14:33 , fabrizio gala wrote: >> >>> IF (err) THEN >>> 1 >>> Error: IF clause at (1) requires a scalar LOGICAL expression >> assuming that err is an integer variable, the correct syntax is "IF >> ( err> 0 ) THEN" >> Some compilers accept integers in logical expressions (0=.false., >> 1=.true.) but >> this is nonstandard >> >> P. >> --- >> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > From robinshy at gmail.com Sat Aug 6 05:29:44 2011 From: robinshy at gmail.com (Robin H) Date: Sat, 6 Aug 2011 11:29:44 +0800 Subject: [Pw_forum] anyone meets the problem like this? In-Reply-To: <986BFB4A-A184-4C68-96D7-512E617DFC75@epfl.ch> References: <986BFB4A-A184-4C68-96D7-512E617DFC75@epfl.ch> Message-ID: Dear Gabriele? thanks for your sincerely suggestions. It's a good lesson for me. Robin H Department of physics, Tongji University NO.1239, Siping raod,Shanghai,China 2011/8/4 Gabriele Sclauzero > Dear Robin, > > the message looks quite self-explanatory to me. If it does not mean > anything to you, then you need to go through the theory of Ultrasoft (US) > pseudopotentials and have a look at the documentation of the ld1 code. > If you want to pseudize a channel in the norm-conserving recipe, while > keeping the others in the US style, then you have to specify the rcutus > equal to rcut for that channel, > for instance: > > 4P 2 1 1.00 0.00 1.80 1.80 > > works with no warnings. > Moreover, also your input produces the same US PP even if you get that > warning, because the code tries to understand what you really wanted, and it > does correctly. > > HTH > > GS > > Il giorno 04/ago/2011, alle ore 11.30, Robin H ha scritto: > > Dear all,anyone who used revPBE to creat PP has meet the warning like > this : > !!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!! > Message from routine ld1_readin: > US requires at least two energies per channel 4P > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > I am anxious to know how to resolve it. Welcome any suggestion. > my input is : > &input > title='Zn' > zed=30. > rel=1, > config='[Ar] 3d10.00 4s1.00 4p1.00', > iswitch=3, > dft='revPBE' > / > &inputp > lloc=1, > pseudotype=3, > tm=.true., > file_pseudopw='Zn.revPBE.UPF', > / > 5 > 3D 3 2 10.00 0.00 1.80 2.00 > 3D 3 2 0.00 0.05 1.80 2.00 > 4S 1 0 1.00 0.00 1.80 2.00 > 4S 1 0 0.00 0.05 1.80 2.00 > 4P 2 1 1.00 0.00 1.80 2.10 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110806/6d77fa25/attachment.htm From foursea at 163.com Sat Aug 6 08:18:14 2011 From: foursea at 163.com (lilonghua) Date: Sat, 6 Aug 2011 14:18:14 +0800 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 References: <201108061136234844372@163.com> Message-ID: <201108061418142181751@163.com> I think the problem is caused by the character length. when the input character len<=79, everything is all right! 2011-08-06 lilonghua ???? lilonghua ????? 2011-08-06 11:36:23 ???? pw_forum ??? ??? QE v4.3.2 failed to read the input file of v4.3 Dear all, I have compiled the lastest version of QE. However, pw.x v4.3.2 failed to read the input file of v4.3, even the EXX_example in v4.3.2. the Error message is: " from read_namelists : error # 17 reading namelist system" I don't find significant changes of variables in document of pwscf v4.3.2. And pwscf v4.3 is ok to perform the EXX_example of v4.3.2 (actually, those examples are same to that of v4.3). So, what's happen to the io of v4.3.2? and how to solve it? Best regards, Longhua Li 2011-08-06 ---------------------------------------- lilonghua -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110806/b1225821/attachment.htm From foursea at 163.com Sat Aug 6 05:36:24 2011 From: foursea at 163.com (lilonghua) Date: Sat, 6 Aug 2011 11:36:24 +0800 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 Message-ID: <201108061136234844372@163.com> Dear all, I have compiled the lastest version of QE. However, pw.x v4.3.2 failed to read the input file of v4.3, even the EXX_example in v4.3.2. the Error message is: " from read_namelists : error # 17 reading namelist system" I don't find significant changes of variables in document of pwscf v4.3.2. And pwscf v4.3 is ok to perform the EXX_example of v4.3.2 (actually, those examples are same to that of v4.3). So, what's happen to the io of v4.3.2? and how to solve it? Best regards, Longhua Li 2011-08-06 ---------------------------------------- lilonghua From flux_ray12 at 163.com Sun Aug 7 16:04:05 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Sun, 7 Aug 2011 22:04:05 +0800 (CST) Subject: [Pw_forum] the meaning of gx, gy and gz in PDOS of phonon from QHA code Message-ID: <435ff3a3.4628.131a48ec687.Coremail.flux_ray12@163.com> Dear PWscf Developer and Users: I am using QHA code to calculate thermodynamic properties for highly-ordered doping cubic system, such like: ibrav = 1 , ATOMIC_POSITION crystal A 0.0 0.0 0.0 B 0.0 0.5 0.5 B 0.5 0.0 0.5 B 0.5 0.5 0.0 C 0.5 0.0 0.0 C 0.0 0.5 0.0 C 0.0 0.0 0.5 C 0.5 0.5 0.5 When I checked the files named projected_DOS.Xi, except the PDOS of Xi atom itself, gx, gy and gz are also listed in the last three columns. At beginning, I thought gx, gy and gz must represent the vibrations on x,y,z directions, respectively. However, I found the values of gx, gy and gz are significantly different with each other, especially for the atom with different kinds elements as nearest neighbor atoms. Since my model is cubic and with high symmetry, the vibration in x,y,z directions should be same. So I think they may not mean the vibrations on x,y,z's direction. Then, would any one like to tell me the meaning of them? I am really puzzled by this data~~~ Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110807/c5dcc6e3/attachment.htm From lmartinsamos at gmail.com Mon Aug 8 11:55:09 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 8 Aug 2011 11:55:09 +0200 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 In-Reply-To: <201108061418142181751@163.com> References: <201108061136234844372@163.com> <201108061418142181751@163.com> Message-ID: Dear lilonghua could you send please the input file that causes the problem you mentioned? thank you very much Layla 2011/8/6 lilonghua > ** > I think the problem is caused by the character length. when the input > character len<=79, everything is all right! > > > 2011-08-06 > ------------------------------ > lilonghua > ------------------------------ > *????* lilonghua > *?????* 2011-08-06 11:36:23 > *????* pw_forum > *???* > *???* QE v4.3.2 failed to read the input file of v4.3 > Dear all, > > I have compiled the lastest version of QE. However, pw.x v4.3.2 failed to read the input file of v4.3, even the EXX_example in v4.3.2. the Error message is: > " from read_namelists : error # 17 > reading namelist system" > > I don't find significant changes of variables in document of pwscf v4.3.2. And pwscf v4.3 is ok to perform the EXX_example of v4.3.2 (actually, those examples are same to that of v4.3). So, what's happen to the io of v4.3.2? and how to solve it? > Best regards, > Longhua Li > 2011-08-06 > ---------------------------------------- > lilonghua > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/06d03a5b/attachment.htm From lmartinsamos at gmail.com Mon Aug 8 12:39:01 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Mon, 8 Aug 2011 12:39:01 +0200 Subject: [Pw_forum] Run example error in qe-gipaw Message-ID: Dear Pengju, I just try qe-gipaw example without finding any problem. One of the thing that could give some difficulties is the fact that the out dir is set to /tmp/ceresoli. Maybe you could try to change outdir to something else. bests regards Layla -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/519a68c1/attachment.htm From robinshy at gmail.com Mon Aug 8 12:45:17 2011 From: robinshy at gmail.com (Robin H) Date: Mon, 8 Aug 2011 18:45:17 +0800 Subject: [Pw_forum] vdw-df2 In-Reply-To: References: Message-ID: I think you can use revPBE to produce the PPs for using,and in your calculation you can set the input_dft='vDW-DF',that's what the example mean.Could you tell me where you find the information of the example? Thanks. Robin H 2011/7/28 DONG Rui > Hi, all > > I have something not clear about the vdw-df implementation. > > It is mentioned in the example that we'd better use revised pbe when using > the vdw-df, but "revPBE" itself is another xc-functional? What do we do now? > > Do we write the input_dft="revPBE+vdW-DF2"? > > or we do "revPBE" first and use the result to restart a "vdW-DF2" > calculation? > > Thank you very much for help! > > -- > Sincerely, > > Rui DONG > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/a0acbb89/attachment.htm From izaakw89 at yahoo.com Mon Aug 8 20:06:33 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Mon, 8 Aug 2011 11:06:33 -0700 (PDT) Subject: [Pw_forum] Co Pseudopotential In-Reply-To: References: Message-ID: <1312826793.38160.YahooMailNeo@web43406.mail.sp1.yahoo.com> Hello everyone, I am trying to calculate the magnetic spin of Co adsorbed onto a surface. The literature that I am comparing my values with says the Co spin?is 3/2 from an all-electron calculation and I am getting S=1. The pseudopotential that I am using for Co is Co.pbe-nd-rrkjus.UPF. Is there something about this pseudopotential that is giving me an incorrect spin? Should I be using a different pseudopotential? Thanks for any help. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/d4c5398b/attachment.htm From heatherjkulik at gmail.com Mon Aug 8 20:23:50 2011 From: heatherjkulik at gmail.com (heather kulik) Date: Mon, 8 Aug 2011 11:23:50 -0700 Subject: [Pw_forum] Co Pseudopotential In-Reply-To: <1312826793.38160.YahooMailNeo@web43406.mail.sp1.yahoo.com> References: <1312826793.38160.YahooMailNeo@web43406.mail.sp1.yahoo.com> Message-ID: <04E4FE8EED214DF9AB4FE2E594D97AAA@gmail.com> Izaak, If you really are getting S=1 for the total spin in your calculation, then you have an even number of electrons in your system. Neutral cobalt has an odd number of valence electrons, 3d74s2, (hence the S=3/2) so this likely means that you have an odd number of electrons in whatever you chose for your surface. That's not to say you couldn't run into other problems. If you mean you see S=1 locally, e.g. from PDOS, you are likely getting charge transfer between the atom and the surface, and you may observe something that looks like S=1 on Co. I would need more information about your "all electron calculation" reference from the literature (i.e. is it Co on the same surface and with the same functional?) in order to suggest anything further. Hope that helps, Heather Kulik Stanford University On Monday, August 8, 2011 at 11:06 AM, Izaak Williamson wrote: > Hello everyone, > > I am trying to calculate the magnetic spin of Co adsorbed onto a surface. The literature that I am comparing my values with says the Co spin is 3/2 from an all-electron calculation and I am getting S=1. The pseudopotential that I am using for Co is Co.pbe-nd-rrkjus.UPF. Is there something about this pseudopotential that is giving me an incorrect spin? Should I be using a different pseudopotential? > > Thanks for any help. > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/2398fe74/attachment.htm From chengyu.young at gmail.com Mon Aug 8 21:14:58 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Mon, 8 Aug 2011 15:14:58 -0400 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> References: <4E327A29.2010400@materials.ox.ac.uk> <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> Message-ID: Thank you Dr.Sclauzero and all, I've changed the pseudo potential to USPP, set the ecutwfc down to 35, and reduce theepsproj=1.d-5, and I ran the whole procedure to calculate the band structure of my (5,5) CNT again. This time the procedure runs well and faster until I got to the bands.x step, I got " negative rho (up, down): 0.502E-03 0.000E+00" at the bands.out, and it stopped there. I couldn't proceed further. My another question is about the K points, I could generate a k point path via Xcrysden, but I couldn't generate the all the k points I need to input manually for the 'nscf' input as in the examples. I defined 50 k points in Xcrysden, however, the final result was only the few high symmetry points I defined. I don't know how to get all the k points the 'nscf' needs? I've tried the kpoints.x, but I don't know how the mesh n1,n2,n3 can be connected to the k point path by Xcrysden, and how I should set up them. Thanks beforehand for anyone who can explain these things to me, I really appreciate it. Best regards. Chengyu Yang Material Science, University of Central Florida USA 2011/8/2 Gabriele Sclauzero > > Il giorno 29/lug/2011, alle ore 21.16, chengyu yang ha scritto: > > Dear All, > After two hours , my transmission calculation comes out a result. > > > And you couldn't wait for a couple of hours before writing to the forum > saying that you were in trouble?... > > Assuming that your PWscf calculation has been converged, the important > thing here is to look at the basis set reduction performed by PWcond: > > ngper, shell number = 2809 299 > ngper, n2d = 2809 472 > > It looks to me that the n2d could be too small compared to the original > size of the basis set (ngper). As I wrote in my previous email, you should > try to decrease epsproj and check that the results (i.e. the complex bands) > do not change appreciably. The eigenvalues at real k from PWcond need to be > on the top of the band structure computed with PWscf. > Also compare with previous theoretical results, I guess that there should > be several works about the conductance of CNTs. > cuplot is needed only to plot the scattering states. I guess that you do > not need them at this stage. > > HTH > > GS > > But I thought it may be not converged and didn't get the final result. > May anybody have a look at my output file? I attached in this email. > My input file is like this: > &inputcond > prefixl='55' > tran_file='trans.cnt55', > ikind=0 > energy0=4.d0 > denergy=-0.1d0 > ewind=3.d0 > epsproj=1.d-4 > delgep = 1.d-9 > cutplot = 3.d0 > / > 1 > 0.0 0.0 1.0 > 5 > > > Is there somebody that can give me an advice? > I really appreciate it. > > Chengyu Yang > Materials Science and Engineering, > University of Central Florida, USA > > _______________________________________________ > > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > * PH H2 462, Station 3, CH-1015 Lausanne* > > > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/2e06099f/attachment-0001.htm From jiachen at princeton.edu Mon Aug 8 22:55:26 2011 From: jiachen at princeton.edu (jia chen) Date: Mon, 8 Aug 2011 16:55:26 -0400 Subject: [Pw_forum] Co Pseudopotential In-Reply-To: <1312826793.38160.YahooMailNeo@web43406.mail.sp1.yahoo.com> References: <1312826793.38160.YahooMailNeo@web43406.mail.sp1.yahoo.com> Message-ID: Hi, I did lots of calculations by this one, works decently and I did atomic calculation, total magnetization is 3.0. On Mon, Aug 8, 2011 at 2:06 PM, Izaak Williamson wrote: > Hello everyone, > > I am trying to calculate the magnetic spin of Co adsorbed onto a surface. > The literature that I am comparing my values with says the Co spin is 3/2 > from an all-electron calculation and I am getting S=1. The pseudopotential > that I am using for Co is Co.pbe-nd-rrkjus.UPF. Is there something about > this pseudopotential that is giving me an incorrect spin? Should I be using > a different pseudopotential? > > Thanks for any help. > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Jia Chen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/76e3c5ca/attachment.htm From CJH085 at bham.ac.uk Mon Aug 8 23:15:43 2011 From: CJH085 at bham.ac.uk (Christopher Heard) Date: Mon, 8 Aug 2011 22:15:43 +0100 Subject: [Pw_forum] Pd pseudopotential Message-ID: <4406F1904F879A4D9FE86E310EA663410213768B1892@mbx5.adf.bham.ac.uk> Hello all, I want to do some structure relaxations on Pd particles, and I noticed all the available pseudopotentials have electronic configuration d9s1. I would have thought d10 is more likely, and am worried as to whether I will therefore have to treat all calculations as openshell, with either a fixed tot_magnetization, or worse, with full magnetic convergence with a guess at starting_magnetization. Both will slow me down a lot, and I'd rather not have to. Does anyone know, firstly if indeed I will have to do these magnetic calculations, and secondly, why d9s1 should be more stable than closed shell? Thanks, Chris ----------------------------------- PhD student, University of Birmingham, UK ----------------------------------- From izaakw89 at yahoo.com Tue Aug 9 01:16:50 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Mon, 8 Aug 2011 16:16:50 -0700 (PDT) Subject: [Pw_forum] Co Pseudopotential In-Reply-To: <04E4FE8EED214DF9AB4FE2E594D97AAA@gmail.com> References: <1312826793.38160.YahooMailNeo@web43406.mail.sp1.yahoo.com> <04E4FE8EED214DF9AB4FE2E594D97AAA@gmail.com> Message-ID: <1312845410.41661.YahooMailNeo@web43412.mail.sp1.yahoo.com> Thank you Heather and Jia for your replies. For a single Co atom, I do get the total magnetization of 3 but when Co is on a surface, its spin polarization comes out to be 2, which is S=1. The all-electron calculations were also done using pbe functional and on the same surface and with the same coverage of Co. Heather, what do you mean by locally? I do calculate the spin polarization from pdos. The whole system does have an even number of electrons but why does it result in S=1? Any explanation would be appreciated. -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/8eb63a4e/attachment.htm From heatherjkulik at gmail.com Tue Aug 9 02:02:51 2011 From: heatherjkulik at gmail.com (heather kulik) Date: Mon, 8 Aug 2011 17:02:51 -0700 Subject: [Pw_forum] Co Pseudopotential In-Reply-To: <1312845410.41661.YahooMailNeo@web43412.mail.sp1.yahoo.com> References: <1312826793.38160.YahooMailNeo@web43406.mail.sp1.yahoo.com> <04E4FE8EED214DF9AB4FE2E594D97AAA@gmail.com> <1312845410.41661.YahooMailNeo@web43412.mail.sp1.yahoo.com> Message-ID: Total magnetization as printed in the code is equivalent to nelup-neldw. You cannot get an odd total magnetization if you have an even number of electrons. The total magnetization is only the same as the magnetization on cobalt if cobalt is the only atom in your simulation cell with a magnetic moment. If, as you have indicated, you have created a surface with an odd number of electrons, it must also have a net spin or, alternatively, charge transfer may occur between Co and the surface so that the surface has no net spin. Either way, mulliken population analysis, projections onto a localized basis, or some alternative approach is required to approximately identify the magnetic moment on each atom. If you provide the reference you're comparing to, it might be clearer what you are trying to compare against. Hope that helps, Heather Kulik Stanford University On Monday, August 8, 2011 at 4:16 PM, Izaak Williamson wrote: > Thank you Heather and Jia for your replies. For a single Co atom, I do get the total magnetization of 3 but when Co is on a surface, its spin polarization comes out to be 2, which is S=1. The all-electron calculations were also done using pbe functional and on the same surface and with the same coverage of Co. > > Heather, what do you mean by locally? I do calculate the spin polarization from pdos. The whole system does have an even number of electrons but why does it result in S=1? Any explanation would be appreciated. > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/a3ebde1e/attachment.htm From jiachen at princeton.edu Tue Aug 9 02:25:56 2011 From: jiachen at princeton.edu (jia chen) Date: Mon, 8 Aug 2011 20:25:56 -0400 Subject: [Pw_forum] Co Pseudopotential In-Reply-To: <1312845410.41661.YahooMailNeo@web43412.mail.sp1.yahoo.com> References: <1312826793.38160.YahooMailNeo@web43406.mail.sp1.yahoo.com> <04E4FE8EED214DF9AB4FE2E594D97AAA@gmail.com> <1312845410.41661.YahooMailNeo@web43412.mail.sp1.yahoo.com> Message-ID: Hi, If I understand you correctly, there is electron transfer between the surface and the Co atom which makes the spin polarization of Co atom to be 1. Not very surprising to me. On Mon, Aug 8, 2011 at 7:16 PM, Izaak Williamson wrote: > Thank you Heather and Jia for your replies. For a single Co atom, I do get > the total magnetization of 3 but when Co is on a surface, its spin > polarization comes out to be 2, which is S=1. The all-electron calculations > were also done using pbe functional and on the same surface and with the > same coverage of Co. > > Heather, what do you mean by locally? I do calculate the spin polarization > from pdos. The whole system does have an even number of electrons but why > does it result in S=1? Any explanation would be appreciated. > > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Jia Chen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/b2c4bb69/attachment.htm From chengyu.young at gmail.com Tue Aug 9 03:53:09 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Mon, 8 Aug 2011 21:53:09 -0400 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: References: <4E327A29.2010400@materials.ox.ac.uk> <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> Message-ID: Hi all. As an update I calculated the bandstructure assuming that the negative rho has little effect on the final result, and then I got a bandstructure with a certain lines in it. I am hoping if anyone can tell me how to get all the k point for the nscf input, so I can get a more smooth bandstructure finally. Thank you. Best regards. Chengyu Yang MMAE, University of Central Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110808/12326d11/attachment.htm From mayankaditya at gmail.com Tue Aug 9 09:24:17 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Tue, 9 Aug 2011 12:54:17 +0530 Subject: [Pw_forum] convergence of Phonon Message-ID: Dear all I am doing phonon calculation of a magnetic system, have not included any magnetic interaction on it. I am calculating phonon at 2x2x2 mesh (6 q points). I got the phonon frequency +ve at 5 q point while at one q point it is negative. I have check this with 24 x24x24 k point and with very high ecut and observed this particular phonon mode doesn't converge with k point while rest is converged. is it because of not taking in to account the magnetic part or something else. -- Mayank BHABHA ATOMIC RESEARCH CENTER MUMBAI, INDIA Office: ?022-25595606 Home: 9920397437 / 9869834437 From lorenzo.paulatto at impmc.upmc.fr Tue Aug 9 09:43:40 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 09 Aug 2011 09:43:40 +0200 Subject: [Pw_forum] Pd pseudopotential In-Reply-To: <4406F1904F879A4D9FE86E310EA663410213768B1892@mbx5.adf.bham.ac.uk> References: <4406F1904F879A4D9FE86E310EA663410213768B1892@mbx5.adf.bham.ac.uk> Message-ID: In data 08 agosto 2011 alle ore 23:15:43, Christopher Heard ha scritto: > Both will slow me down a lot, and I'd rather not have to. > Does anyone know, firstly if indeed I will have to do these magnetic > calculations, and secondly, why d9s1 should be more stable than closed > shell? Dear Chriss, the reference configuration used to generate a good-quality pseudopotential have no influence on its behaviour when used in a bulk system. On the other hand, if the pseudo is low quality it should not be used at all. best regards -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From flux_ray12 at 163.com Tue Aug 9 10:26:16 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 9 Aug 2011 16:26:16 +0800 (CST) Subject: [Pw_forum] convergence of Phonon In-Reply-To: References: Message-ID: <1ea4af7.5b2d.131ada6379f.Coremail.flux_ray12@163.com> I think you can try to reduce the alpha_mix(1), 0.7 by default, for a better convergency~ P.S.: This suggestion was original from by Prof. Isaev, and it works well in a lot of cases. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-09 15:24:17,"mayank gupta" wrote: >Dear all > > >I am doing phonon calculation of a magnetic system, have not included >any magnetic interaction on it. I am calculating phonon at 2x2x2 mesh >(6 q points). I got the phonon frequency +ve at 5 q point while at >one q point it is negative. I have check this with 24 x24x24 k point >and with very high ecut and observed this particular phonon mode >doesn't converge with k point while rest is converged. is it because >of not taking in to account the magnetic part or something else. > > > >-- >Mayank > >BHABHA ATOMIC RESEARCH CENTER >MUMBAI, INDIA >Office: 022-25595606 >Home: 9920397437 / 9869834437 >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110809/f25e0307/attachment.htm From renpj at dicp.ac.cn Tue Aug 9 11:02:55 2011 From: renpj at dicp.ac.cn (Ren PJ) Date: Tue, 9 Aug 2011 17:02:55 +0800 Subject: [Pw_forum] Run example error in qe-gipaw In-Reply-To: References: Message-ID: <20110809170255.567f6c7b@ren-desktop> On Mon, 8 Aug 2011 12:39:01 +0200 Layla Martin-Samos wrote: > Dear Pengju, I just try qe-gipaw example without finding any problem. > One of the thing that could give some difficulties is the fact that > the out dir is set to /tmp/ceresoli. Maybe you could try to change > outdir to something else. > > bests regards > > Layla Thanks for your reply. I have contact to Mr. Ceresoli, and now I know the reason is I use gfortran compiler. I Change gfortran to ifort, there is no error. Mr. Ceresoli say it is a bug of gfortran. Pengju From baroni at sissa.it Tue Aug 9 11:12:33 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 9 Aug 2011 11:12:33 +0200 Subject: [Pw_forum] convergence of Phonon In-Reply-To: References: Message-ID: it may depend on a Kohn anomaly (which are particularly sensitive to k-point sampling) SB On Aug 9, 2011, at 9:24 AM, mayank gupta wrote: > Dear all > > > I am doing phonon calculation of a magnetic system, have not included > any magnetic interaction on it. I am calculating phonon at 2x2x2 mesh > (6 q points). I got the phonon frequency +ve at 5 q point while at > one q point it is negative. I have check this with 24 x24x24 k point > and with very high ecut and observed this particular phonon mode > doesn't converge with k point while rest is converged. is it because > of not taking in to account the magnetic part or something else. > > > > -- > Mayank > > BHABHA ATOMIC RESEARCH CENTER > MUMBAI, INDIA > Office: 022-25595606 > Home: 9920397437 / 9869834437 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110809/0112875e/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Tue Aug 9 11:57:41 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it) Date: Tue, 9 Aug 2011 11:57:41 +0200 Subject: [Pw_forum] Co Pseudopotential In-Reply-To: References: <1312826793.38160.YahooMailNeo@web43406.mail.sp1.yahoo.com> <04E4FE8EED214DF9AB4FE2E594D97AAA@gmail.com> <1312845410.41661.YahooMailNeo@web43412.mail.sp1.yahoo.com> Message-ID: <20110809115741.mhxps97a68wooogg@webmail.sic.rm.cnr.it> Really not surprising... I've performed some calculations on Co-phthalocyanine, that is, a Co(II) ion "dressed" by an organic molecule (odd number of electrons, S=1/2 on cobalt), in contact with a Pb surface (even number of electrons). A charge transfer of one electron from the Co atom to the Pb slab quenches the Co magnetic moment to S=0, as also measured by spin-polarized STM. As Heather and Jia say, it may be very important to know if some charge transfer process between your "undressed" (:-)) Co atom and your (metal?) slab takes place. It should depend on the relative positions of the Co electronic levels with respect to the metal Fermi energy (enough k points...?). You may check this also by using the pp.x code in order to subtract the Co and slab charge density to the total (Co+slab) charge density, thus obtaining an .xsf charge density plot you can look at with xcrysden. Beyond GGA methods (GGA+U on the 3d shell of Co?) may be also useful, if you are able to calculate/estimate a meaningful value for the Hubbard U. HTH. Without looking at your real system it is unlikely we can advice you more than this, I suppose... Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting jia chen : > Hi, > > If I understand you correctly, there is electron transfer between the > surface and the Co atom which makes the spin polarization of Co atom to be > 1. Not very surprising to me. > > On Mon, Aug 8, 2011 at 7:16 PM, Izaak Williamson wrote: > >> Thank you Heather and Jia for your replies. For a single Co atom, I do get >> the total magnetization of 3 but when Co is on a surface, its spin >> polarization comes out to be 2, which is S=1. The all-electron calculations >> were also done using pbe functional and on the same surface and with the >> same coverage of Co. >> >> Heather, what do you mean by locally? I do calculate the spin polarization >> from pdos. The whole system does have an even number of electrons but why >> does it result in S=1? Any explanation would be appreciated. >> >> >> -- >> Izaak Williamson >> Research Assistant >> Physics Department >> Boise State University >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Jia Chen > From beata_bp at gazeta.pl Tue Aug 9 14:09:49 2011 From: beata_bp at gazeta.pl (beata_bp Gazeta.pl) Date: Tue, 9 Aug 2011 14:09:49 +0200 Subject: [Pw_forum] Compilation QE4.3.1 under Cygwin (gcc, g++4.6.1) Message-ID: Hi everyone, I know that in fact it isn't QE , but gfortran compiler problem, but maybe there is a simple solution how to avoid it for the time being. I am trying to compile PW (QE4.3.1) under Cygwin (gcc, g++4.6.1). The config passed succesfully. And make pw gives the following error: Below is also the last line of compilation script: gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3 -I../include -I../iotk/src -I../Modules -I. -c realus.f90 realus.f90: In function 'augmentation_qq': realus.f90:3004:0: error: insn does not satisfy its constraints: (insn 373 372 237 13 (set (reg/v/f:SI 10 st(2) [orig:281 op ] [281]) (mem/c:SI (plus:SI (reg/f:SI 7 sp) (const_int 36 [0x24])) [0 S4 A32])) realus.f90:2939 50 {*movsi_internal} (nil)) realus.f90:3004:0: internal compiler error: in reload_cse_simpl postreload.c:403 Please submit a full bug report, with preprocessed source if appropriate. See for instructions. make[1]: *** [realus.o] Error 1 make[1]: Leaving directory `/cygdrive/c/cygwin/espresso-4.3/PW' make: *** [pw] Error 2 Best Regards and Thanks in advance for any suggestion Beata Paluchowska Institute of Atomic Energy, ?wierk-Otwock Poland. From chengyu.young at gmail.com Tue Aug 9 17:37:16 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Tue, 9 Aug 2011 11:37:16 -0400 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: References: <4E327A29.2010400@materials.ox.ac.uk> <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> Message-ID: Dr. Sclaizero and all, Thanks for your reply. It really gave me a clue.However, about the k points, I still have some problem. (1) I heard that to calculate bandstructure, one need to use more than 20 k points to get a reliable result, that's why I was looking for more k points. I did only use the three high symmetry k points in the nscf calculation, but the final result seems to be too simple to be true. I attached them for you to have a look. (2) In the conductance example for Al, I see they used 50 k points to get a bandstructure, and I was wondering how did they get them? I can only find at most 10 high symmetry points for Al. Do we need the same amount/scale of K point ? If so, how? k points in the al.nscf.in: K_POINTS 50 0.00 0.00 0.00000000 0.00000000 0.00 0.00 0.00721538 0.00721538 0.00 0.00 0.01443075 0.01443075 0.00 0.00 0.02164613 0.02164613 0.00 0.00 0.02886150 0.02886150 0.00 0.00 0.03607688 0.03607688 0.00 0.00 0.04329225 0.04329225 0.00 0.00 0.05050763 0.05050763 0.00 0.00 0.05772300 0.05772300 0.00 0.00 0.06493838 0.06493838 0.00 0.00 0.07215375 0.07215375 0.00 0.00 0.07936913 0.07936913 0.00 0.00 0.08658450 0.08658450 0.00 0.00 0.09379988 0.09379988 0.00 0.00 0.10101525 0.10101525 0.00 0.00 0.10823063 0.10823063 0.00 0.00 0.11544601 0.11544601 0.00 0.00 0.12266138 0.12266138 0.00 0.00 0.12987676 0.12987676 0.00 0.00 0.13709213 0.13709213 0.00 0.00 0.14430751 0.14430751 0.00 0.00 0.15152288 0.15152288 0.00 0.00 0.15873826 0.15873826 0.00 0.00 0.16595363 0.16595363 0.00 0.00 0.17316901 0.17316901 0.00 0.00 0.18038438 0.18038438 0.00 0.00 0.18759976 0.18759976 0.00 0.00 0.19481513 0.19481513 0.00 0.00 0.20203051 0.20203051 0.00 0.00 0.20924588 0.20924588 0.00 0.00 0.21646126 0.21646126 0.00 0.00 0.22367663 0.22367663 0.00 0.00 0.23089201 0.23089201 0.00 0.00 0.23810739 0.23810739 0.00 0.00 0.24532276 0.24532276 0.00 0.00 0.25253814 0.25253814 0.00 0.00 0.25975351 0.25975351 0.00 0.00 0.26696889 0.26696889 0.00 0.00 0.27418426 0.27418426 0.00 0.00 0.28139964 0.28139964 0.00 0.00 0.28861501 0.28861501 0.00 0.00 0.29583039 0.29583039 0.00 0.00 0.30304576 0.30304576 0.00 0.00 0.31026114 0.31026114 0.00 0.00 0.31747651 0.31747651 0.00 0.00 0.32469189 0.32469189 0.00 0.00 0.33190726 0.33190726 0.00 0.00 0.33912264 0.33912264 0.00 0.00 0.34633802 0.34633802 0.00 0.00 0.35355339 0.35355339 Thanks for your patience. Best regards. Chengyu Yang MMAE,University of Central Florida > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110809/5c2e9858/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: 55bands1.ps Type: application/postscript Size: 3107 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110809/5c2e9858/attachment-0002.ps -------------- next part -------------- A non-text attachment was scrubbed... Name: 55bands3.ps Type: application/postscript Size: 3107 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110809/5c2e9858/attachment-0003.ps From mahdi_fn109 at yahoo.com Tue Aug 9 17:49:19 2011 From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri) Date: Tue, 9 Aug 2011 08:49:19 -0700 (PDT) Subject: [Pw_forum] (no subject) Message-ID: <1312904959.70429.YahooMailNeo@web43136.mail.sp1.yahoo.com> Dear all, i'm trying to plot bandstracture. i do 'scf', 'nscf', 'bands' and ./bands.x . now i have 2 diffrent Fermi Energy in 'scf' and 'nscf'. i don't know to use which of them in plotbands calculation now. Fermi Energy in 'scf' out or Fermi Energy in 'nscf' out. ? Mahdi Faghih nasiri MSC, Guilan University, Rasht, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110809/12730658/attachment.htm From gabriele.sclauzero at epfl.ch Tue Aug 9 18:40:28 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 9 Aug 2011 18:40:28 +0200 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: References: <4E327A29.2010400@materials.ox.ac.uk> <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> Message-ID: <34226655-1604-4F5A-95D0-88865428CA42@epfl.ch> Dear Chengyu Yang, (1) the number of k-points you need to use in order to get a nice band structure plot depends obviously on the details of the geometry (in particular, on the size of the BZ, which is related to the size of the unit cell, and on the number and "flatness" of the bands, to resolve correctly the band crossings) and also on the lenght of your path, obviously. Your band structure doesn't tell much to me, since I've never computed CNTs so far, but you could easily check your results with the available literature. (2) Which example are you speaking of? Your questions look obscure to me. Please try to be more clear and explain exactly what you are refering to (bulk Al or Al wire? conductance, complex band structure, or standard electronic structure calculation? Where are those 50 k-points? I can't find them...) HTH Gabriele SclaUzero PS: there is no need to send also a duplicate message to my email address since I'm (obviously) subscribed to this mailing list and I can get your posts through the list Il giorno 09/ago/2011, alle ore 17.37, chengyu yang ha scritto: > Dr. Sclaizero and all, > Thanks for your reply. It really gave me a clue.However, about the k points, I still have some problem. > (1) I heard that to calculate bandstructure, one need to use more than 20 k points to get a reliable result, that's why I was looking for more k points. I did only use the three high symmetry k points in the nscf calculation, but the final result seems to be too simple to be true. I attached them for you to have a look. > (2) In the conductance example for Al, I see they used 50 k points to get a bandstructure, and I was wondering how did they get them? I can only find at most 10 high symmetry points for Al. Do we need the same amount/scale of K point ? If so, how? > > k points in the al.nscf.in: > > K_POINTS > 50 > 0.00 0.00 0.00000000 0.00000000 > 0.00 0.00 0.00721538 0.00721538 > 0.00 0.00 0.01443075 0.01443075 > 0.00 0.00 0.02164613 0.02164613 > 0.00 0.00 0.02886150 0.02886150 > 0.00 0.00 0.03607688 0.03607688 > 0.00 0.00 0.04329225 0.04329225 > 0.00 0.00 0.05050763 0.05050763 > 0.00 0.00 0.05772300 0.05772300 > 0.00 0.00 0.06493838 0.06493838 > 0.00 0.00 0.07215375 0.07215375 > 0.00 0.00 0.07936913 0.07936913 > 0.00 0.00 0.08658450 0.08658450 > 0.00 0.00 0.09379988 0.09379988 > 0.00 0.00 0.10101525 0.10101525 > 0.00 0.00 0.10823063 0.10823063 > 0.00 0.00 0.11544601 0.11544601 > 0.00 0.00 0.12266138 0.12266138 > 0.00 0.00 0.12987676 0.12987676 > 0.00 0.00 0.13709213 0.13709213 > 0.00 0.00 0.14430751 0.14430751 > 0.00 0.00 0.15152288 0.15152288 > 0.00 0.00 0.15873826 0.15873826 > 0.00 0.00 0.16595363 0.16595363 > 0.00 0.00 0.17316901 0.17316901 > 0.00 0.00 0.18038438 0.18038438 > 0.00 0.00 0.18759976 0.18759976 > 0.00 0.00 0.19481513 0.19481513 > 0.00 0.00 0.20203051 0.20203051 > 0.00 0.00 0.20924588 0.20924588 > 0.00 0.00 0.21646126 0.21646126 > 0.00 0.00 0.22367663 0.22367663 > 0.00 0.00 0.23089201 0.23089201 > 0.00 0.00 0.23810739 0.23810739 > 0.00 0.00 0.24532276 0.24532276 > 0.00 0.00 0.25253814 0.25253814 > 0.00 0.00 0.25975351 0.25975351 > 0.00 0.00 0.26696889 0.26696889 > 0.00 0.00 0.27418426 0.27418426 > 0.00 0.00 0.28139964 0.28139964 > 0.00 0.00 0.28861501 0.28861501 > 0.00 0.00 0.29583039 0.29583039 > 0.00 0.00 0.30304576 0.30304576 > 0.00 0.00 0.31026114 0.31026114 > 0.00 0.00 0.31747651 0.31747651 > 0.00 0.00 0.32469189 0.32469189 > 0.00 0.00 0.33190726 0.33190726 > 0.00 0.00 0.33912264 0.33912264 > 0.00 0.00 0.34633802 0.34633802 > 0.00 0.00 0.35355339 0.35355339 > > > Thanks for your patience. > > Best regards. > > Chengyu Yang > MMAE,University of Central Florida > > > > > <55bands1.ps><55bands3.ps>_______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110809/df24bd96/attachment.htm From chengyu.young at gmail.com Tue Aug 9 19:02:30 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Tue, 9 Aug 2011 13:02:30 -0400 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: <34226655-1604-4F5A-95D0-88865428CA42@epfl.ch> References: <4E327A29.2010400@materials.ox.ac.uk> <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> <34226655-1604-4F5A-95D0-88865428CA42@epfl.ch> Message-ID: Dear Dr. Sclaizero and all, The example is from the example 1 ,in the *Complex band structures and ballistic conductance* in the hands-on tutorial of quantum espresso, and it's about the bandstructure of bulk Al along the 001 direction. I am now pasting the input script for the nscf calculation here, at the end you would see the 50 K points: al.nscf.in &control calculation='nscf' restart_mode='from_scratch', pseudo_dir = '$PSEUDO_DIR', outdir='$TMP_DIR' prefix='al' / &system ibrav = 6, celldm(1) =5.3, celldm(3) =1.414, nat= 2, ntyp= 1, ecutwfc = 15.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.01 / &electrons conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Al 26.98 Al.vbc.UPF ATOMIC_POSITIONS Al 0. 0. 0.0 Al 0.5 0.5 0.707 K_POINTS 50 0.00 0.00 0.00000000 0.00000000 0.00 0.00 0.00721538 0.00721538 0.00 0.00 0.01443075 0.01443075 0.00 0.00 0.02164613 0.02164613 0.00 0.00 0.02886150 0.02886150 0.00 0.00 0.03607688 0.03607688 0.00 0.00 0.04329225 0.04329225 0.00 0.00 0.05050763 0.05050763 0.00 0.00 0.05772300 0.05772300 0.00 0.00 0.06493838 0.06493838 0.00 0.00 0.07215375 0.07215375 0.00 0.00 0.07936913 0.07936913 0.00 0.00 0.08658450 0.08658450 0.00 0.00 0.09379988 0.09379988 0.00 0.00 0.10101525 0.10101525 0.00 0.00 0.10823063 0.10823063 0.00 0.00 0.11544601 0.11544601 0.00 0.00 0.12266138 0.12266138 0.00 0.00 0.12987676 0.12987676 0.00 0.00 0.13709213 0.13709213 0.00 0.00 0.14430751 0.14430751 0.00 0.00 0.15152288 0.15152288 0.00 0.00 0.15873826 0.15873826 0.00 0.00 0.16595363 0.16595363 0.00 0.00 0.17316901 0.17316901 0.00 0.00 0.18038438 0.18038438 0.00 0.00 0.18759976 0.18759976 0.00 0.00 0.19481513 0.19481513 0.00 0.00 0.20203051 0.20203051 0.00 0.00 0.20924588 0.20924588 0.00 0.00 0.21646126 0.21646126 0.00 0.00 0.22367663 0.22367663 0.00 0.00 0.23089201 0.23089201 0.00 0.00 0.23810739 0.23810739 0.00 0.00 0.24532276 0.24532276 0.00 0.00 0.25253814 0.25253814 0.00 0.00 0.25975351 0.25975351 0.00 0.00 0.26696889 0.26696889 0.00 0.00 0.27418426 0.27418426 0.00 0.00 0.28139964 0.28139964 0.00 0.00 0.28861501 0.28861501 0.00 0.00 0.29583039 0.29583039 0.00 0.00 0.30304576 0.30304576 0.00 0.00 0.31026114 0.31026114 0.00 0.00 0.31747651 0.31747651 0.00 0.00 0.32469189 0.32469189 0.00 0.00 0.33190726 0.33190726 0.00 0.00 0.33912264 0.33912264 0.00 0.00 0.34633802 0.34633802 0.00 0.00 0.35355339 0.35355339 Thank you! Best regards. Chengyu Yang MMAE, University of Central Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110809/1fc1c1b9/attachment-0001.htm From mahdi_fn109 at yahoo.com Wed Aug 10 02:21:11 2011 From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri) Date: Tue, 9 Aug 2011 17:21:11 -0700 (PDT) Subject: [Pw_forum] Fermi Energy Message-ID: <1312935671.51560.YahooMailNeo@web43135.mail.sp1.yahoo.com> Dear all, i'm trying to plot bandstracture. i do 'scf', 'nscf', 'bands' and ./bands.x . now i have 2 diffrent Fermi Energy in 'scf' and 'nscf'. i don't know to use which of them in plotbands calculation now. Fermi Energy in 'scf' out or Fermi Energy in 'nscf' out. ? Mahdi Faghih nasiri MSC, Guilan University, Rasht, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110809/ca17f2ab/attachment.htm From chengyu.young at gmail.com Wed Aug 10 04:19:58 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Tue, 9 Aug 2011 22:19:58 -0400 Subject: [Pw_forum] Fermi Energy In-Reply-To: <1312935671.51560.YahooMailNeo@web43135.mail.sp1.yahoo.com> References: <1312935671.51560.YahooMailNeo@web43135.mail.sp1.yahoo.com> Message-ID: Use the Fermi energy in scf. Chengyu MMAE,University of Central Florida US -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110809/855b9088/attachment.htm From davgumo at me.com Wed Aug 10 05:35:10 2011 From: davgumo at me.com (davgumo) Date: Wed, 10 Aug 2011 03:35:10 +0000 (GMT) Subject: [Pw_forum] Calculation of log_w Message-ID: <80eef5ac-4051-67d5-d797-92c0767a9c48@me.com> Hello all, In a post dated Jun 25 2010, Professor Isaev said that lambda.x is an?obsolete code now, he claims that the calculation of log_w is now implemented into the matdyn.x code.? My question is how can I use matdyn.x to calculate log_w. My goal is to produce a value for Tc but i've been having trouble getting reproducible numbers with the lambda.x code. I work with Graphite intercalation compounds. Please professor Eyvas Isaev, any help you can provide to me is much appreciated.? David Guzman M Department of Physics & Astronomy California State University-Los Angeles -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/26cce4e9/attachment.htm From mayankaditya at gmail.com Wed Aug 10 09:44:28 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Wed, 10 Aug 2011 13:14:28 +0530 Subject: [Pw_forum] Convergence of Phonon with K points Message-ID: Dear Sir It's magnetic oxide SrFeO2. Kohn anomaloy occurs in metallic system. Should I further increase k points or do something else. Thanks > it may depend on a Kohn anomaly (which are particularly sensitive to k-point sampling) > SB > > On Aug 9, 2011, at 9:24 AM, mayank gupta wrote: > >> Dear all >> >> >> I am doing phonon calculation of a magnetic system, have not included >> any magnetic interaction on it. I am calculating phonon at 2x2x2 mesh >> (6 q points). I got the phonon frequency +ve at 5 q point while at >> one q point it is negative. I have check this with 24 x24x24 k point >> and with very high ecut and observed this particular phonon mode >> doesn't converge with k point while rest is converged. is it because >> of not taking in to account the magnetic part or something else. >> >> >> -- Mayank BHABHA ATOMIC RESEARCH CENTER MUMBAI, INDIA Office: ?022-25595606 Home: 9920397437 / 9869834437 From prasenjit.jnc at gmail.com Wed Aug 10 11:19:57 2011 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Wed, 10 Aug 2011 14:49:57 +0530 Subject: [Pw_forum] Convergence of Phonon with K points In-Reply-To: References: Message-ID: For which phonons are you getting the imaginary frequencies? If it is for the acoustic modes at gamma point, then it tells that your structure is not stable.....however if it is for other k-points, it is an indication that your cell parameters are not well optimized. Prasenjit On 10 August 2011 13:14, mayank gupta wrote: > Dear Sir > > It's magnetic oxide SrFeO2. Kohn anomaloy occurs in metallic system. > Should I further increase k points or do something else. > > Thanks > > >> it may depend on a Kohn anomaly (which are particularly sensitive to k-point sampling) >> SB >> >> On Aug 9, 2011, at 9:24 AM, mayank gupta wrote: >> >>> Dear all >>> >>> >>> I am doing phonon calculation of a magnetic system, ?have not included >>> any magnetic interaction on it. I am calculating phonon at ?2x2x2 mesh >>> (6 q points). I got the phonon frequency +ve at 5 q point ?while at >>> one q point it is negative. I have check this with 24 x24x24 k point >>> and with very high ecut and observed ?this particular phonon mode >>> doesn't converge with k point while rest is converged. is it because >>> of not taking in to account the magnetic part or something else. >>> >>> >>> > > -- > Mayank > > BHABHA ATOMIC RESEARCH CENTER > MUMBAI, INDIA > Office: ?022-25595606 > Home: 9920397437 / 9869834437 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From gabriele.sclauzero at epfl.ch Wed Aug 10 12:09:43 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 10 Aug 2011 12:09:43 +0200 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: References: <4E327A29.2010400@materials.ox.ac.uk> <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> <34226655-1604-4F5A-95D0-88865428CA42@epfl.ch> Message-ID: <3F40C7E2-6250-4C93-889E-D5DE8DD71F56@epfl.ch> Il giorno 09/ago/2011, alle ore 19.02, chengyu yang ha scritto: > Dear Dr. Sclaizero and all, > The example is from the example 1 ,in the Complex band structures and ballistic conductance in the hands-on tutorial of quantum espresso, and it's about the bandstructure of bulk Al along the 001 direction. I am now pasting the input script for the nscf calculation here, at the end you would see the 50 K points: OK, so you're speaking of bulk Al. (from your previous email) > (2) In the conductance example for Al, I see they used 50 k points to get a bandstructure, and I was wondering how did they get them? It should be just a straight k-point path connecting Gamma to X in the BZ of fcc Al. > I can only find at most 10 high symmetry points for Al. In this 50 k-point path there should be just 2 high-symmetry points (Gamma and X), I don't understand why you bother about the other points. > Do we need the same amount/scale of K point ? If so, how? The number of points you want to include along the transport direction to check up to which accuracy the band structure of PWscf is reproduced by PWcond is up to you. I would use, let's say, 20-30 points in the nscf calculation, such that the successive bands.x run can resolve the band-crossings and one can plot a nice band structure with lines. Then you need to perform a PWcond run for a set of scattering energies {e_1, e_2,...} in the intersting range and superimpose the resulting (e_i,k) points (for k real) to the previously obtained band structure. These points should fall on the lines corresponding to the PWscf band structure. HTH Mr. SclaUzero > > al.nscf.in > > > &control > calculation='nscf' > restart_mode='from_scratch', > pseudo_dir = '$PSEUDO_DIR', > outdir='$TMP_DIR' > prefix='al' > / > &system > ibrav = 6, > celldm(1) =5.3, > celldm(3) =1.414, > nat= 2, > ntyp= 1, > ecutwfc = 15.0, > occupations='smearing', > smearing='methfessel-paxton', > degauss=0.01 > / > &electrons > conv_thr = 1.0e-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Al 26.98 Al.vbc.UPF > ATOMIC_POSITIONS > Al 0. 0. 0.0 > Al 0.5 0.5 0.707 > K_POINTS > 50 > 0.00 0.00 0.00000000 0.00000000 > 0.00 0.00 0.00721538 0.00721538 > 0.00 0.00 0.01443075 0.01443075 > 0.00 0.00 0.02164613 0.02164613 > 0.00 0.00 0.02886150 0.02886150 > 0.00 0.00 0.03607688 0.03607688 > 0.00 0.00 0.04329225 0.04329225 > 0.00 0.00 0.05050763 0.05050763 > 0.00 0.00 0.05772300 0.05772300 > 0.00 0.00 0.06493838 0.06493838 > 0.00 0.00 0.07215375 0.07215375 > 0.00 0.00 0.07936913 0.07936913 > 0.00 0.00 0.08658450 0.08658450 > 0.00 0.00 0.09379988 0.09379988 > 0.00 0.00 0.10101525 0.10101525 > 0.00 0.00 0.10823063 0.10823063 > 0.00 0.00 0.11544601 0.11544601 > 0.00 0.00 0.12266138 0.12266138 > 0.00 0.00 0.12987676 0.12987676 > 0.00 0.00 0.13709213 0.13709213 > 0.00 0.00 0.14430751 0.14430751 > 0.00 0.00 0.15152288 0.15152288 > 0.00 0.00 0.15873826 0.15873826 > 0.00 0.00 0.16595363 0.16595363 > 0.00 0.00 0.17316901 0.17316901 > 0.00 0.00 0.18038438 0.18038438 > 0.00 0.00 0.18759976 0.18759976 > 0.00 0.00 0.19481513 0.19481513 > 0.00 0.00 0.20203051 0.20203051 > 0.00 0.00 0.20924588 0.20924588 > 0.00 0.00 0.21646126 0.21646126 > 0.00 0.00 0.22367663 0.22367663 > 0.00 0.00 0.23089201 0.23089201 > 0.00 0.00 0.23810739 0.23810739 > 0.00 0.00 0.24532276 0.24532276 > 0.00 0.00 0.25253814 0.25253814 > 0.00 0.00 0.25975351 0.25975351 > 0.00 0.00 0.26696889 0.26696889 > 0.00 0.00 0.27418426 0.27418426 > 0.00 0.00 0.28139964 0.28139964 > 0.00 0.00 0.28861501 0.28861501 > 0.00 0.00 0.29583039 0.29583039 > 0.00 0.00 0.30304576 0.30304576 > 0.00 0.00 0.31026114 0.31026114 > 0.00 0.00 0.31747651 0.31747651 > 0.00 0.00 0.32469189 0.32469189 > 0.00 0.00 0.33190726 0.33190726 > 0.00 0.00 0.33912264 0.33912264 > 0.00 0.00 0.34633802 0.34633802 > 0.00 0.00 0.35355339 0.35355339 > > Thank you! > Best regards. > > Chengyu Yang > MMAE, University of Central Florida > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/7c4a6f3c/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Wed Aug 10 13:46:32 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 10 Aug 2011 13:46:32 +0200 Subject: [Pw_forum] Compilation QE4.3.1 under Cygwin (gcc, g++4.6.1) In-Reply-To: References: Message-ID: On Tue, 09 Aug 2011 14:09:49 +0200, beata_bp Gazeta.pl wrote: > insn does not satisfy its constraints: as far as i can see, there is not workaround for this bug (); you have to update gcc... -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From baroni at sissa.it Wed Aug 10 14:30:49 2011 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 10 Aug 2011 14:30:49 +0200 Subject: [Pw_forum] Convergence of Phonon with K points In-Reply-To: References: Message-ID: <72E64614-07D9-4EAD-B189-27C9AEAAD74D@sissa.it> Dear Mayank, have you plotted the electronic energy bands? are you sure that the the system is not (semi-) metallic, possibly because of some shortcomings of the XC functional you are using? more generally, imaginary frequencies signal a mechanical instability of your system. if the instability occurs at a finite wave-vector, that means that he system may undergo a transition to a structure whose (larger) unit cell is commensurate with the instability wave-vector. If the instability occurs at q=0, then some distortions of atomic positions may occur, which in turn may determine a distortion of the cell shape. If it is a sound velocity that vanishes, this finally indicates an elastic instability of the shape of the unit cell. in any case, more insight is needed, which in turn would probably require more work from you. remember: no pain, no gain! good luck, SB On Aug 10, 2011, at 9:44 AM, mayank gupta wrote: > Dear Sir > > It's magnetic oxide SrFeO2. Kohn anomaloy occurs in metallic system. > Should I further increase k points or do something else. > > Thanks > > >> it may depend on a Kohn anomaly (which are particularly sensitive to k-point sampling) >> SB >> >> On Aug 9, 2011, at 9:24 AM, mayank gupta wrote: >> >>> Dear all >>> >>> >>> I am doing phonon calculation of a magnetic system, have not included >>> any magnetic interaction on it. I am calculating phonon at 2x2x2 mesh >>> (6 q points). I got the phonon frequency +ve at 5 q point while at >>> one q point it is negative. I have check this with 24 x24x24 k point >>> and with very high ecut and observed this particular phonon mode >>> doesn't converge with k point while rest is converged. is it because >>> of not taking in to account the magnetic part or something else. >>> >>> >>> > > -- > Mayank > > BHABHA ATOMIC RESEARCH CENTER > MUMBAI, INDIA > Office: 022-25595606 > Home: 9920397437 / 9869834437 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/db78e195/attachment.htm From elie.moujaes at hotmail.co.uk Wed Aug 10 15:44:17 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Wed, 10 Aug 2011 14:44:17 +0100 Subject: [Pw_forum] phonon calculations for a system of 60 atoms Message-ID: Hello all, i am doing a phonon calculation for a system of 60 carbon atoms. I have two small questions: (1) what is the safe value that I can set to tr2_ph and get good results? I am doing the calculations for a tr2_ph=1.0D-10 but it is taking a long timee and I have got like 180 modes of irreducible representations. (2) I am doing phonon calculations at special points (Gamma, M, X) separately. Is there a way to collect these to get the phonon band dispersion later? Thanks Elie Mouaesuniversity of NottinghamNottinghamNG7 2RD -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/f7435f5f/attachment.htm From joshiniharika20 at yahoo.in Wed Aug 10 09:53:50 2011 From: joshiniharika20 at yahoo.in (Niharika Joshi) Date: Wed, 10 Aug 2011 13:23:50 +0530 (IST) Subject: [Pw_forum] Problem in Xspectra calculation Message-ID: <1312962830.28050.YahooMailClassic@web95709.mail.in.yahoo.com> Hi, I was trying the tutorial examples for the X-ray absorption spectra calculation for diamond. The examples were downloaded from the following site: http://www.ictp.it/~rgebauer/Matteo_XAS.tar.gz when I execute the Xspectra input file the execution terminates with the error message: wrong fft dimensions. The Quantum esspresso version that i am using is esspresso 4.3 and executing as stated below, /opt/MPI/lam-7.1.4/lam/bin/mpirun -np 12 /home/Desktop/espresso-4.3/bin/xspectra.x < input file >output file & Any idea what could be wrong? -Niharika -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/f6102040/attachment.htm From beata_bp at gazeta.pl Wed Aug 10 17:02:55 2011 From: beata_bp at gazeta.pl (beata_bp Gazeta.pl) Date: Wed, 10 Aug 2011 17:02:55 +0200 Subject: [Pw_forum] Compilation QE4.3.1 under Cygwin (gcc, g++4.6.1) In-Reply-To: References: Message-ID: Thanks for your answer, Lorenzo The problem is that seems to me that I had used the latest version (4.6.1)of gcc - but bug 485729 has been reported to be fixed in 4.4.0... Best regards. Beata. Institute of Atomic Energy, ?wierk-Otwock Poland 2011/8/10 Lorenzo Paulatto : > On Tue, 09 Aug 2011 14:09:49 +0200, beata_bp Gazeta.pl > wrote: > >> insn does not satisfy its constraints: > > > as far as i can see, there is not workaround for this bug you have to update > gcc... > > -- > Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: ? http://www-int.impmc.upmc.fr/~paulatto/ > mail: ?23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From chengyu.young at gmail.com Wed Aug 10 17:34:53 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Wed, 10 Aug 2011 11:34:53 -0400 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: <3F40C7E2-6250-4C93-889E-D5DE8DD71F56@epfl.ch> References: <4E327A29.2010400@materials.ox.ac.uk> <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> <34226655-1604-4F5A-95D0-88865428CA42@epfl.ch> <3F40C7E2-6250-4C93-889E-D5DE8DD71F56@epfl.ch> Message-ID: Dear Mr. Sclauzero and all, It seems nice to me. But in the example 1 ,(in the *Complex band structures and ballistic conductance* in the hands-on tutorial of quantum espresso), the pwcond.x comes first, then they gave the nscf script , and then ran the pw.x and bands.x in following steps. Is that making any difference from what you said? Thanks. Chengyu Yang Materials Science,University of Central Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/c57595bd/attachment.htm From mohnish.iitk at gmail.com Wed Aug 10 18:02:23 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 10 Aug 2011 21:32:23 +0530 Subject: [Pw_forum] Problem in Xspectra calculation In-Reply-To: <1312962830.28050.YahooMailClassic@web95709.mail.in.yahoo.com> References: <1312962830.28050.YahooMailClassic@web95709.mail.in.yahoo.com> Message-ID: Dear Niharika! Its very hard to answer without taking a look a look at your input file. And please mention your affiliation so that we know that whom we are interacting with.. On Wed, Aug 10, 2011 at 1:23 PM, Niharika Joshi wrote: > Hi, > I was trying the tutorial examples for the X-ray absorption spectra > calculation for diamond. > The examples were downloaded from the following site: > http://www.ictp.it/~rgebauer/Matteo_XAS.tar.gz > when I execute the Xspectra input file the execution terminates with the > error message: wrong fft dimensions. > The Quantum esspresso version that i am using is esspresso 4.3 and > executing as stated below, > /opt/MPI/lam-7.1.4/lam/bin/mpirun -np 12 > /home/Desktop/espresso-4.3/bin/xspectra.x < input file >output file & > Any idea what could be wrong? > -Niharika > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/6e1cd469/attachment-0001.htm From gabriele.sclauzero at epfl.ch Wed Aug 10 19:13:41 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 10 Aug 2011 19:13:41 +0200 Subject: [Pw_forum] Slow calculation of (5, 5) CNT transmission and complex bands. In-Reply-To: References: <4E327A29.2010400@materials.ox.ac.uk> <8E6228BD-EA25-49B9-925D-45AA65B7A3FD@epfl.ch> <34226655-1604-4F5A-95D0-88865428CA42@epfl.ch> <3F40C7E2-6250-4C93-889E-D5DE8DD71F56@epfl.ch> Message-ID: Il giorno 10/ago/2011, alle ore 17.34, chengyu yang ha scritto: > > Dear Mr. Sclauzero and all, > It seems nice to me. But in the example 1 ,(in the Complex band structures and ballistic conductance in the hands-on tutorial of quantum espresso), the pwcond.x comes first, then they gave the nscf script , and then ran the pw.x and bands.x in following steps. > Is that making any difference from what you said? The important thing is that the SCF pw.x run comes first, because both the NSCF pw.x run and the pwcond.x run will read the self-consistent potential produced by the SCF run (and stored in outdir/prefix). The nscf run and the pwcond run are in principle independent from each other. HTH GS > Thanks. > > Chengyu Yang > Materials Science,University of Central Florida > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/f5c651cb/attachment.htm From prasenjit.jnc at gmail.com Wed Aug 10 19:41:43 2011 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Wed, 10 Aug 2011 23:11:43 +0530 Subject: [Pw_forum] Convergence of Phonon with K points In-Reply-To: <72E64614-07D9-4EAD-B189-27C9AEAAD74D@sissa.it> References: <72E64614-07D9-4EAD-B189-27C9AEAAD74D@sissa.it> Message-ID: Ciao Stefano, Thanks for a clear explanation. Prasenjit On 10 August 2011 18:00, Stefano Baroni wrote: > Dear Mayank, > have you plotted the electronic energy bands? are you sure that the the > system is not (semi-) metallic, possibly because of some shortcomings of the > XC functional you are using? > more generally, imaginary frequencies signal a mechanical instability of > your system. if the instability occurs at a finite wave-vector, that means > that he system may undergo a transition to a structure whose (larger) unit > cell is commensurate with the instability wave-vector. If the instability > occurs at q=0, then some distortions of atomic positions may occur, which in > turn may determine a distortion of the cell shape. If it is a sound velocity > that vanishes, this finally indicates an elastic instability of the shape of > the unit cell. > in any case, more insight is needed, which in turn would probably require > more work from you. > remember: no pain, no gain! > good luck, > SB > > On Aug 10, 2011, at 9:44 AM, mayank gupta wrote: > > Dear Sir > > It's magnetic oxide SrFeO2. Kohn anomaloy occurs in metallic system. > Should I further increase k points or do something else. > > Thanks > > > it may depend on a Kohn anomaly (which are particularly sensitive to k-point > sampling) > > SB > > On Aug 9, 2011, at 9:24 AM, mayank gupta wrote: > > Dear all > > > I am doing phonon calculation of a magnetic system, ?have not included > > any magnetic interaction on it. I am calculating phonon at ?2x2x2 mesh > > (6 q points). I got the phonon frequency +ve at 5 q point ?while at > > one q point it is negative. I have check this with 24 x24x24 k point > > and with very high ecut and observed ?this particular phonon mode > > doesn't converge with k point while rest is converged. is it because > > of not taking in to account the magnetic part or something else. > > > > > -- > Mayank > > BHABHA ATOMIC RESEARCH CENTER > MUMBAI, INDIA > Office: ?022-25595606 > Home: 9920397437 / 9869834437 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Stefano Baroni - SISSA??&??DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me?[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni > (skype) > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > Please, if possible, don't??send me MS Word or PowerPoint attachments > Why? See:??http://www.gnu.org/philosophy/no-word-attachments.html > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PRASENJIT GHOSH, Assistant Professor, IISER Pune, First floor, Central Tower, Sai Trinity Building Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India Phone: +91 (20) 2590 8203 Fax: +91 (20) 2589 9790 From member at linkedin.com Wed Aug 10 22:56:58 2011 From: member at linkedin.com (Mehrnoosh Hazrati via LinkedIn) Date: Wed, 10 Aug 2011 20:56:58 +0000 (UTC) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <2069396455.38358.1313009818748.JavaMail.app@ela4-bed84.prod> LinkedIn ------------ Mehrnoosh Hazrati requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Mehrnoosh Accept invitation from Mehrnoosh Hazrati http://www.linkedin.com/e/-iqpnjm-gr6s584c-13/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I88295372_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pvczsPdjAOe3x9bSlmoSFVqmETbPAOdPgRej8Oe3cLrCBxbOYWrSlI/EML_comm_afe/ View invitation from Mehrnoosh Hazrati http://www.linkedin.com/e/-iqpnjm-gr6s584c-13/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I88295372_60/0MdBYOdPcRej8Ue4ALqnpPbOYWrSlI/svi/ ------------------------------------------ DID YOU KNOW you can showcase your professional knowledge on LinkedIn to receive job/consulting offers and enhance your professional reputation? Posting replies to questions on LinkedIn Answers puts you in front of the world's professional community. http://www.linkedin.com/e/-iqpnjm-gr6s584c-13/abq/inv-24/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/cdd8e9bd/attachment.htm From wang.riping.81 at gmail.com Thu Aug 11 06:22:44 2011 From: wang.riping.81 at gmail.com (Riping WANG) Date: Thu, 11 Aug 2011 13:22:44 +0900 Subject: [Pw_forum] symmetry not found in pw.x and ph.x Message-ID: Dear pwforum, I am calculating scf for a ibrav=4 structure with espresso-4.3.2. But it can not find the symmetry. In the output file, it report "no symmetry found". I am also calculation with ph.x with the same. the phonon mode is not identified. I confirmed the atomic positions in the input file. It is consistent with 32 point symmetry (space group 154). I tried ibrav=2 and 12, they can find symmetry and phonon modes, even with atomic positions slightly different from point symmety formula.. So I am wondering: what kind of situation, the code can not find symmtery? Is there any suggestion to make it find symmetry? I attached the input file and output file of pw.x followiing. Thanks very much for you attention and helps. Best withes. WANG Riping 2011.8.11 &CONTROL calculation = scf , restart_mode = 'from_scratch' , prefix = alpo4-154.0_0 , pseudo_dir = '~/pseudo', outdir = outdir , nstep = 500 , max_seconds = 360000 , etot_conv_thr = 5.0D-6 , forc_conv_thr = 1.0D10 , tprnfor = .true. / &system ibrav = 4 , celldm(1) = 9.471757419 , celldm(3) = 2.21251394 , nat = 18 , ntyp = 3 , ecutwfc = 50.0 , ecutrho = 400.0 , / &electrons conv_thr = 1.0d-10 , / &ions ion_dynamics = none , / &CELL cell_dynamics = none , press = 0 , press_conv_thr = 0.05D0 , / ATOMIC_SPECIES O 15.9994 O.pbe-van_ak.UPF Al 26.981538 Al.pbe-n-van.UPF P 30.973761 P.pbe-van_ak.UPF ATOMIC_POSITIONS crystal Al 0.4692 0.0000 0.1667 1 0 0 Al 0.0000 0.4692 0.8333 0 1 0 Al 0.5308 0.5308 0.5000 1 1 0 P 0.4694 0.0000 0.6667 1 0 0 P 0.0000 0.4694 0.3333 0 1 0 P 0.5306 0.5306 0.0000 1 1 0 O 0.4160 0.2860 0.1011 O 0.7140 0.1300 0.7678 O 0.8700 0.5840 0.4344 O 0.2860 0.4160 0.8989 O 0.1300 0.7140 0.2322 O 0.5840 0.8700 0.5655 O 0.4150 0.2538 0.6140 O 0.7462 0.1612 0.2807 O 0.8388 0.5850 0.9473 O 0.2538 0.4150 0.3860 O 0.1612 0.7462 0.7193 O 0.5850 0.8388 0.0526 K_POINTS automatic 4 4 3 0 0 0 Program PWSCF v.4.3.2 starts on 11Aug2011 at 11:58: 4 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 3 processors R & G space division: proc/pool = 3 Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... Reading input from stdin Warning: card &IONS ignored Warning: card ION_DYNAMICS = NONE , ignored Warning: card / ignored Warning: card &CELL ignored Warning: card CELL_DYNAMICS = NONE , ignored Warning: card PRESS = 0 , ignored Warning: card PRESS_CONV_THR = 0.05D0 , ignored Warning: card / ignored Subspace diagonalization in iterative solution of the eigenvalue problem: a serial algorithm will be used Parallelization info -------------------- sticks: dense smooth PW G-vecs: dense smooth PW Min 826 412 116 73322 25972 3822 Max 827 413 117 73331 25986 3827 Sum 2479 1237 349 219979 77939 11473 bravais-lattice index = 4 lattice parameter (alat) = 9.4718 a.u. unit-cell volume = 1628.2022 (a.u.)^3 number of atoms/cell = 18 number of atomic types = 3 number of electrons = 96.00 number of Kohn-Sham states= 48 kinetic-energy cutoff = 50.0000 Ry charge density cutoff = 400.0000 Ry convergence threshold = 1.0E-10 mixing beta = 0.7000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE ( 1 4 3 4 0) EXX-fraction = 0.00 celldm(1)= 9.471757 celldm(2)= 0.000000 celldm(3)= 2.212514 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of alat) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( -0.500000 0.866025 0.000000 ) a(3) = ( 0.000000 0.000000 2.212514 ) reciprocal axes: (cart. coord. in units 2 pi/alat) b(1) = ( 1.000000 0.577350 0.000000 ) b(2) = ( 0.000000 1.154701 0.000000 ) b(3) = ( 0.000000 0.000000 0.451975 ) PseudoPot. # 1 for O read from file: ~/pseudo/O.pbe-van_ak.UPF MD5 check sum: Pseudo is Ultrasoft, Zval = 6.0 Generated by new atomic code, or converted to UPF format Using radial grid of 737 points, 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800 PseudoPot. # 2 for Al read from file: ~/pseudo/Al.pbe-n-van.UPF MD5 check sum: Pseudo is Ultrasoft + core correction, Zval = 3.0 Generated by new atomic code, or converted to UPF format Using radial grid of 893 points, 2 beta functions with: l(1) = 0 l(2) = 1 Q(r) pseudized with 8 coefficients, rinner = 0.900 0.900 0.900 PseudoPot. # 3 for P read from file: ~/pseudo/P.pbe-van_ak.UPF MD5 check sum: Pseudo is Ultrasoft, Zval = 5.0 Generated by new atomic code, or converted to UPF format Using radial grid of 807 points, 6 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 l(5) = 2 l(6) = 2 Q(r) pseudized with 8 coefficients, rinner = 1.100 1.100 1.100 1.100 1.100 atomic species valence mass pseudopotential O 6.00 15.99940 O ( 1.00) Al 3.00 26.98154 Al( 1.00) P 5.00 30.97376 P ( 1.00) No symmetry found Cartesian axes site n. atom positions (alat units) 1 Al tau( 1) = ( 0.4692000 0.0000000 0.3688261 ) 2 Al tau( 2) = ( -0.2346000 0.4063391 1.8436879 ) 3 Al tau( 3) = ( 0.2654000 0.4596863 1.1062570 ) 4 P tau( 4) = ( 0.4694000 0.0000000 1.4750830 ) 5 P tau( 5) = ( -0.2347000 0.4065123 0.7374309 ) 6 P tau( 6) = ( 0.2653000 0.4595131 0.0000000 ) 7 O tau( 7) = ( 0.2730000 0.2476833 0.2236852 ) 8 O tau( 8) = ( 0.6490000 0.1125833 1.6987682 ) 9 O tau( 9) = ( 0.5780000 0.5057588 0.9611161 ) 10 O tau( 10) = ( 0.0780000 0.3602666 1.9888288 ) 11 O tau( 11) = ( -0.2270000 0.6183421 0.5137457 ) 12 O tau( 12) = ( 0.1490000 0.7534421 1.2511766 ) 13 O tau( 13) = ( 0.2881000 0.2197972 1.3584836 ) 14 O tau( 14) = ( 0.6656000 0.1396033 0.6210527 ) 15 O tau( 15) = ( 0.5463000 0.5066249 2.0959145 ) 16 O tau( 16) = ( 0.0463000 0.3594005 0.8540304 ) 17 O tau( 17) = ( -0.2119000 0.6462282 1.5914613 ) 18 O tau( 18) = ( 0.1656000 0.7264221 0.1163782 ) number of k points= 26 cart. coord. in units 2pi/alat k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0416667 k( 2) = ( 0.0000000 0.0000000 0.1506582), wk = 0.0833333 k( 3) = ( 0.0000000 0.2886751 0.0000000), wk = 0.0833333 k( 4) = ( 0.0000000 0.2886751 0.1506582), wk = 0.0833333 k( 5) = ( 0.0000000 -0.5773503 0.0000000), wk = 0.0416667 k( 6) = ( 0.0000000 -0.5773503 0.1506582), wk = 0.0833333 k( 7) = ( 0.2500000 0.4330127 0.0000000), wk = 0.0833333 k( 8) = ( 0.2500000 0.4330127 0.1506582), wk = 0.0833333 k( 9) = ( -0.2500000 0.1443376 0.0000000), wk = 0.0833333 k( 10) = ( 0.2500000 0.1443376 0.0000000), wk = 0.0833333 k( 11) = ( 0.0000000 -0.2886751 0.1506582), wk = 0.0833333 k( 12) = ( -0.2500000 0.1443376 0.1506582), wk = 0.0833333 k( 13) = ( 0.2500000 0.1443376 0.1506582), wk = 0.0833333 k( 14) = ( -0.2500000 -0.1443376 0.1506582), wk = 0.0833333 k( 15) = ( 0.2500000 -0.1443376 0.1506582), wk = 0.0833333 k( 16) = ( 0.5000000 -0.2886751 0.0000000), wk = 0.0416667 k( 17) = ( -0.5000000 -0.2886751 0.0000000), wk = 0.0416667 k( 18) = ( 0.5000000 -0.2886751 0.1506582), wk = 0.0833333 k( 19) = ( -0.5000000 -0.2886751 0.1506582), wk = 0.0833333 k( 20) = ( -0.2500000 0.4330127 0.0000000), wk = 0.0833333 k( 21) = ( 0.5000000 0.0000000 0.0000000), wk = 0.0833333 k( 22) = ( -0.2500000 -0.4330127 0.1506582), wk = 0.0833333 k( 23) = ( -0.2500000 0.4330127 -0.1506582), wk = 0.0833333 k( 24) = ( 0.2500000 -0.4330127 -0.1506582), wk = 0.0833333 k( 25) = ( 0.5000000 0.0000000 0.1506582), wk = 0.0833333 k( 26) = ( -0.5000000 0.0000000 0.1506582), wk = 0.0833333 Dense grid: 219979 G-vectors FFT dimensions: ( 64, 64, 135) Smooth grid: 77939 G-vectors FFT dimensions: ( 45, 45, 96) Largest allocated arrays est. size (Mb) dimensions Kohn-Sham Wavefunctions 2.39 Mb ( 3264, 48) NL pseudopotentials 8.07 Mb ( 3264, 162) Each V/rho on FFT grid 2.81 Mb ( 184320) Each G-vector array 0.56 Mb ( 73326) G-vector shells 0.07 Mb ( 8914) Largest temporary arrays est. size (Mb) dimensions Auxiliary wavefunctions 9.56 Mb ( 3264, 192) Each subspace H/S matrix 0.56 Mb ( 192, 192) Each matrix 0.12 Mb ( 162, 48) Arrays for rho mixing 22.50 Mb ( 184320, 8) Initial potential from superposition of free atoms starting charge 95.99220, renormalised to 96.00000 Starting wfc are 72 atomic wfcs total cpu time spent up to now is 30.1 secs per-process dynamical memory: 60.5 Mb Self-consistent Calculation iteration # 1 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 2.0 total cpu time spent up to now is 98.3 secs total energy = -461.81705211 Ry Harris-Foulkes estimate = -465.06353120 Ry estimated scf accuracy < 4.61917014 Ry iteration # 2 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 4.81E-03, avg # of iterations = 3.0 total cpu time spent up to now is 183.2 secs total energy = -463.04537545 Ry Harris-Foulkes estimate = -464.89517769 Ry estimated scf accuracy < 3.74928200 Ry iteration # 3 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.91E-03, avg # of iterations = 2.2 total cpu time spent up to now is 248.6 secs total energy = -463.78132866 Ry Harris-Foulkes estimate = -463.78151842 Ry estimated scf accuracy < 0.01633610 Ry iteration # 4 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.70E-05, avg # of iterations = 3.0 total cpu time spent up to now is 334.9 secs total energy = -463.79565591 Ry Harris-Foulkes estimate = -463.79691483 Ry estimated scf accuracy < 0.00321029 Ry iteration # 5 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 3.34E-06, avg # of iterations = 2.0 total cpu time spent up to now is 396.0 secs total energy = -463.79574724 Ry Harris-Foulkes estimate = -463.79592447 Ry estimated scf accuracy < 0.00052331 Ry iteration # 6 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 5.45E-07, avg # of iterations = 3.0 total cpu time spent up to now is 471.5 secs total energy = -463.79586898 Ry Harris-Foulkes estimate = -463.79591371 Ry estimated scf accuracy < 0.00010453 Ry iteration # 7 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.09E-07, avg # of iterations = 3.0 total cpu time spent up to now is 536.1 secs total energy = -463.79589022 Ry Harris-Foulkes estimate = -463.79589247 Ry estimated scf accuracy < 0.00000826 Ry iteration # 8 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 8.61E-09, avg # of iterations = 2.0 total cpu time spent up to now is 591.2 secs total energy = -463.79589151 Ry Harris-Foulkes estimate = -463.79589156 Ry estimated scf accuracy < 0.00000067 Ry iteration # 9 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 6.95E-10, avg # of iterations = 2.0 total cpu time spent up to now is 655.0 secs total energy = -463.79589164 Ry Harris-Foulkes estimate = -463.79589171 Ry estimated scf accuracy < 0.00000014 Ry iteration # 10 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.44E-10, avg # of iterations = 2.0 total cpu time spent up to now is 712.5 secs total energy = -463.79589166 Ry Harris-Foulkes estimate = -463.79589166 Ry estimated scf accuracy < 4.4E-09 Ry iteration # 11 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 4.56E-12, avg # of iterations = 3.0 total cpu time spent up to now is 791.6 secs total energy = -463.79589166 Ry Harris-Foulkes estimate = -463.79589166 Ry estimated scf accuracy < 1.3E-09 Ry iteration # 12 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 1.33E-12, avg # of iterations = 2.0 total cpu time spent up to now is 850.1 secs total energy = -463.79589166 Ry Harris-Foulkes estimate = -463.79589166 Ry estimated scf accuracy < 2.2E-10 Ry iteration # 13 ecut= 50.00 Ry beta=0.70 Davidson diagonalization with overlap ethr = 2.28E-13, avg # of iterations = 2.8 total cpu time spent up to now is 913.2 secs End of self-consistent calculation k = 0.0000 0.0000 0.0000 ( 9719 PWs) bands (ev): -18.2892 -18.0881 -18.0867 -15.9173 -15.9156 -15.6028 -15.5923 -15.5905 -15.5665 -15.5576 -15.5529 -15.5503 -7.2679 -6.4153 -6.4127 -4.2540 -4.2515 -3.7637 -3.7619 -3.6202 -3.5868 -3.4079 -3.4061 -3.0504 -0.9591 -0.9561 -0.7449 -0.7435 -0.7311 -0.6583 -0.4266 -0.1731 -0.1724 0.0091 0.0100 0.3102 0.3274 0.3422 0.3426 0.9407 1.0990 1.1019 1.3139 1.6728 1.6740 1.7044 1.7065 1.8290 k = 0.0000 0.0000 0.1507 ( 9791 PWs) bands (ev): -18.2606 -18.1839 -18.0176 -16.0194 -15.7681 -15.6458 -15.5963 -15.5839 -15.5741 -15.5569 -15.5532 -15.5501 -7.1578 -6.8497 -6.0144 -4.5881 -3.9280 -3.7872 -3.7167 -3.6867 -3.6010 -3.5203 -3.2467 -3.1067 -1.0906 -0.8931 -0.7996 -0.7174 -0.6652 -0.6287 -0.3709 -0.2407 -0.0692 -0.0402 0.1734 0.1855 0.2979 0.3232 0.3432 0.9522 0.9906 1.1059 1.3723 1.5241 1.6702 1.7786 1.7914 1.8207 k = 0.0000 0.2887 0.0000 ( 9730 PWs) bands (ev): -18.2028 -18.0635 -18.0394 -15.9736 -15.8951 -15.7409 -15.6275 -15.6122 -15.5962 -15.5852 -15.5731 -15.5553 -6.9070 -6.4340 -6.1449 -4.5657 -4.3553 -3.7248 -3.6578 -3.5693 -3.5436 -3.4765 -3.2220 -3.1165 -1.1419 -0.9691 -0.9373 -0.8182 -0.7052 -0.5524 -0.3345 -0.3186 -0.1866 -0.1364 0.1072 0.1527 0.2525 0.3475 0.4208 1.0729 1.1139 1.1541 1.2769 1.5174 1.5556 1.7135 1.7762 1.7995 k = 0.0000 0.2887 0.1507 ( 9717 PWs) bands (ev): -18.1814 -18.1226 -18.0012 -16.0039 -15.8329 -15.7774 -15.6227 -15.6133 -15.5969 -15.5823 -15.5724 -15.5580 -6.8334 -6.6295 -5.9790 -4.7206 -4.1941 -3.8758 -3.6399 -3.5932 -3.4333 -3.4090 -3.2624 -3.1490 -1.1648 -1.0560 -0.8086 -0.7578 -0.6559 -0.6201 -0.4106 -0.3292 -0.1756 -0.1214 0.0719 0.1708 0.2954 0.3514 0.3973 1.0566 1.1598 1.1796 1.2866 1.3636 1.5813 1.6770 1.8160 1.8562 k = 0.0000-0.5774 0.0000 ( 9752 PWs) bands (ev): -18.0901 -18.0392 -18.0053 -16.0145 -15.9451 -15.8680 -15.6520 -15.6364 -15.6106 -15.6021 -15.5819 -15.5705 -6.4558 -6.3777 -5.9407 -4.8536 -4.4030 -3.9749 -3.6302 -3.5706 -3.5100 -3.2781 -3.1998 -3.0009 -1.2918 -1.0762 -1.0683 -0.8035 -0.7343 -0.5019 -0.3689 -0.3009 -0.2164 -0.1559 -0.0653 0.0759 0.2251 0.3694 0.4393 1.1205 1.1660 1.2487 1.3104 1.3631 1.4223 1.6839 1.7546 1.8830 k = 0.0000-0.5774 0.1507 ( 9714 PWs) bands (ev): -18.0893 -18.0400 -18.0054 -16.0159 -15.9320 -15.8819 -15.6455 -15.6368 -15.6205 -15.5973 -15.5805 -15.5707 -6.4371 -6.3980 -5.9395 -4.8554 -4.3601 -4.0707 -3.6306 -3.5432 -3.4594 -3.2811 -3.1677 -3.0497 -1.2868 -1.1071 -1.0153 -0.8777 -0.6611 -0.5268 -0.4198 -0.3497 -0.1828 -0.1036 -0.0209 0.1102 0.1965 0.2851 0.4885 1.0658 1.1184 1.3026 1.3539 1.3990 1.4486 1.6281 1.7850 1.8486 k = 0.2500 0.4330 0.0000 ( 9737 PWs) bands (ev): -18.0894 -18.0357 -18.0102 -16.0145 -15.9215 -15.8859 -15.6482 -15.6262 -15.6169 -15.6034 -15.5916 -15.5730 -6.4747 -6.3693 -5.8972 -4.7356 -4.5108 -4.1846 -3.5807 -3.4958 -3.4199 -3.3437 -3.2277 -2.9957 -1.2180 -1.0435 -0.9521 -0.8658 -0.7706 -0.6387 -0.3718 -0.2706 -0.2577 -0.0745 0.0016 0.0988 0.1388 0.3787 0.4323 1.0934 1.2037 1.2586 1.3412 1.4066 1.4469 1.6178 1.6624 1.8936 k = 0.2500 0.4330 0.1507 ( 9719 PWs) bands (ev): -18.0808 -18.0535 -18.0009 -16.0154 -15.9125 -15.8940 -15.6410 -15.6292 -15.6179 -15.6087 -15.5968 -15.5656 -6.4513 -6.3968 -5.8929 -4.7509 -4.4560 -4.2412 -3.6092 -3.4868 -3.3978 -3.2902 -3.2025 -3.0608 -1.1946 -1.0517 -1.0015 -0.8280 -0.7645 -0.6548 -0.3837 -0.3060 -0.1825 -0.0975 -0.0051 0.0633 0.2266 0.3345 0.4507 1.0731 1.1491 1.2658 1.3164 1.4230 1.5119 1.6146 1.7064 1.8484 k =-0.2500 0.1443 0.0000 ( 9730 PWs) bands (ev): -18.2029 -18.0641 -18.0391 -15.9727 -15.8938 -15.7377 -15.6268 -15.6091 -15.5967 -15.5860 -15.5783 -15.5578 -6.9074 -6.4361 -6.1428 -4.5649 -4.3540 -3.7244 -3.6592 -3.5703 -3.5452 -3.4751 -3.2216 -3.1163 -1.1419 -0.9683 -0.9364 -0.8197 -0.7046 -0.5528 -0.3343 -0.3185 -0.1881 -0.1364 0.1085 0.1517 0.2534 0.3486 0.4212 1.0719 1.1155 1.1533 1.2771 1.5161 1.5568 1.7140 1.7744 1.7983 k = 0.2500 0.1443 0.0000 ( 9730 PWs) bands (ev): -18.2027 -18.0629 -18.0402 -15.9735 -15.8950 -15.7406 -15.6273 -15.6118 -15.5964 -15.5857 -15.5733 -15.5555 -6.9070 -6.4342 -6.1445 -4.5654 -4.3556 -3.7248 -3.6580 -3.5696 -3.5437 -3.4761 -3.2220 -3.1165 -1.1419 -0.9690 -0.9374 -0.8184 -0.7052 -0.5525 -0.3345 -0.3185 -0.1865 -0.1364 0.1075 0.1521 0.2526 0.3478 0.4209 1.0725 1.1145 1.1538 1.2771 1.5167 1.5559 1.7134 1.7759 1.7993 k = 0.0000-0.2887 0.1507 ( 9717 PWs) bands (ev): -18.1813 -18.1228 -18.0011 -16.0018 -15.8464 -15.7627 -15.6256 -15.6094 -15.6046 -15.5813 -15.5681 -15.5599 -6.8328 -6.6303 -5.9784 -4.7241 -4.1774 -3.9030 -3.6458 -3.5767 -3.4484 -3.3871 -3.2483 -3.1661 -1.1648 -1.0323 -0.8494 -0.7277 -0.6909 -0.5991 -0.4087 -0.3360 -0.1734 -0.1418 0.0787 0.1775 0.3029 0.3452 0.4092 1.0430 1.1107 1.2436 1.2826 1.3812 1.5887 1.7005 1.7490 1.8735 k =-0.2500 0.1443 0.1507 ( 9717 PWs) bands (ev): -18.1814 -18.1229 -18.0011 -16.0007 -15.8458 -15.7591 -15.6251 -15.6069 -15.6036 -15.5845 -15.5711 -15.5628 -6.8334 -6.6308 -5.9777 -4.7226 -4.1773 -3.9019 -3.6477 -3.5786 -3.4473 -3.3866 -3.2482 -3.1660 -1.1645 -1.0316 -0.8498 -0.7290 -0.6901 -0.5991 -0.4065 -0.3373 -0.1744 -0.1432 0.0799 0.1781 0.3025 0.3467 0.4097 1.0439 1.1099 1.2427 1.2827 1.3824 1.5886 1.6997 1.7475 1.8731 k = 0.2500 0.1443 0.1507 ( 9717 PWs) bands (ev): -18.1811 -18.1227 -18.0013 -16.0016 -15.8467 -15.7621 -15.6255 -15.6092 -15.6043 -15.5822 -15.5680 -15.5602 -6.8328 -6.6301 -5.9782 -4.7238 -4.1778 -3.9027 -3.6461 -3.5769 -3.4482 -3.3870 -3.2483 -3.1661 -1.1649 -1.0322 -0.8496 -0.7278 -0.6910 -0.5992 -0.4083 -0.3362 -0.1734 -0.1421 0.0790 0.1774 0.3027 0.3455 0.4095 1.0434 1.1103 1.2433 1.2827 1.3815 1.5885 1.7004 1.7486 1.8734 k =-0.2500-0.1443 0.1507 ( 9717 PWs) bands (ev): -18.1812 -18.1226 -18.0014 -16.0040 -15.8323 -15.7774 -15.6227 -15.6132 -15.5965 -15.5826 -15.5731 -15.5580 -6.8332 -6.6297 -5.9785 -4.7206 -4.1940 -3.8761 -3.6398 -3.5936 -3.4333 -3.4088 -3.2624 -3.1489 -1.1649 -1.0559 -0.8088 -0.7579 -0.6559 -0.6200 -0.4103 -0.3295 -0.1755 -0.1216 0.0720 0.1707 0.2955 0.3513 0.3978 1.0567 1.1599 1.1794 1.2862 1.3638 1.5813 1.6768 1.8155 1.8562 k = 0.2500-0.1443 0.1507 ( 9717 PWs) bands (ev): -18.1815 -18.1228 -18.0012 -16.0033 -15.8302 -15.7757 -15.6228 -15.6105 -15.5961 -15.5827 -15.5765 -15.5618 -6.8336 -6.6307 -5.9778 -4.7200 -4.1923 -3.8763 -3.6407 -3.5952 -3.4330 -3.4085 -3.2624 -3.1485 -1.1646 -1.0553 -0.8083 -0.7586 -0.6555 -0.6203 -0.4093 -0.3312 -0.1761 -0.1215 0.0720 0.1714 0.2964 0.3510 0.3986 1.0568 1.1600 1.1792 1.2864 1.3641 1.5814 1.6762 1.8149 1.8554 k = 0.5000-0.2887 0.0000 ( 9752 PWs) bands (ev): -18.0905 -18.0398 -18.0051 -16.0101 -15.9437 -15.8668 -15.6498 -15.6335 -15.6109 -15.6026 -15.5883 -15.5750 -6.4579 -6.3801 -5.9375 -4.8501 -4.4021 -3.9738 -3.6320 -3.5722 -3.5135 -3.2777 -3.1990 -2.9994 -1.2914 -1.0771 -1.0687 -0.8009 -0.7340 -0.5005 -0.3703 -0.3014 -0.2178 -0.1562 -0.0646 0.0745 0.2273 0.3707 0.4398 1.1219 1.1656 1.2463 1.3118 1.3633 1.4226 1.6832 1.7520 1.8818 k =-0.5000-0.2887 0.0000 ( 9752 PWs) bands (ev): -18.0895 -18.0386 -18.0066 -16.0140 -15.9449 -15.8682 -15.6514 -15.6360 -15.6106 -15.6028 -15.5825 -15.5706 -6.4561 -6.3779 -5.9394 -4.8531 -4.4036 -3.9751 -3.6302 -3.5711 -3.5105 -3.2781 -3.1995 -3.0005 -1.2920 -1.0763 -1.0683 -0.8032 -0.7343 -0.5016 -0.3691 -0.3012 -0.2168 -0.1559 -0.0653 0.0758 0.2254 0.3696 0.4394 1.1209 1.1660 1.2477 1.3109 1.3629 1.4222 1.6836 1.7542 1.8827 k = 0.5000-0.2887 0.1507 ( 9714 PWs) bands (ev): -18.0897 -18.0406 -18.0051 -16.0117 -15.9301 -15.8809 -15.6441 -15.6333 -15.6202 -15.5980 -15.5867 -15.5754 -6.4392 -6.4003 -5.9363 -4.8519 -4.3590 -4.0701 -3.6325 -3.5461 -3.4606 -3.2820 -3.1662 -3.0480 -1.2867 -1.1082 -1.0154 -0.8760 -0.6600 -0.5251 -0.4208 -0.3508 -0.1826 -0.1050 -0.0212 0.1104 0.1988 0.2846 0.4900 1.0639 1.1199 1.3032 1.3547 1.3987 1.4480 1.6273 1.7829 1.8470 k =-0.5000-0.2887 0.1507 ( 9714 PWs) bands (ev): -18.0887 -18.0394 -18.0066 -16.0155 -15.9317 -15.8821 -15.6451 -15.6363 -15.6203 -15.5982 -15.5815 -15.5703 -6.4373 -6.3982 -5.9382 -4.8549 -4.3606 -4.0710 -3.6306 -3.5436 -3.4597 -3.2813 -3.1672 -3.0492 -1.2870 -1.1071 -1.0154 -0.8774 -0.6610 -0.5267 -0.4198 -0.3498 -0.1829 -0.1039 -0.0211 0.1103 0.1970 0.2847 0.4890 1.0651 1.1190 1.3027 1.3541 1.3987 1.4482 1.6278 1.7847 1.8482 k =-0.2500 0.4330 0.0000 ( 9737 PWs) bands (ev): -18.0900 -18.0362 -18.0095 -16.0125 -15.9205 -15.8852 -15.6482 -15.6246 -15.6156 -15.6072 -15.5928 -15.5743 -6.4755 -6.3704 -5.8962 -4.7338 -4.5101 -4.1856 -3.5821 -3.4945 -3.4210 -3.3432 -3.2276 -2.9957 -1.2180 -1.0429 -0.9516 -0.8653 -0.7708 -0.6390 -0.3723 -0.2703 -0.2588 -0.0751 0.0008 0.1004 0.1395 0.3792 0.4330 1.0935 1.2036 1.2592 1.3414 1.4061 1.4461 1.6169 1.6626 1.8931 k = 0.5000 0.0000 0.0000 ( 9737 PWs) bands (ev): -18.0896 -18.0360 -18.0101 -16.0124 -15.9201 -15.8853 -15.6482 -15.6241 -15.6154 -15.6076 -15.5933 -15.5743 -6.4755 -6.3706 -5.8957 -4.7338 -4.5102 -4.1857 -3.5824 -3.4942 -3.4213 -3.3429 -3.2276 -2.9957 -1.2180 -1.0430 -0.9517 -0.8653 -0.7708 -0.6391 -0.3726 -0.2699 -0.2590 -0.0748 0.0005 0.1006 0.1393 0.3789 0.4336 1.0933 1.2036 1.2597 1.3412 1.4057 1.4459 1.6168 1.6626 1.8930 k =-0.2500-0.4330 0.1507 ( 9719 PWs) bands (ev): -18.0808 -18.0535 -18.0009 -16.0154 -15.9126 -15.8940 -15.6411 -15.6293 -15.6167 -15.6097 -15.5968 -15.5655 -6.4514 -6.3967 -5.8929 -4.7510 -4.4558 -4.2414 -3.6088 -3.4870 -3.3981 -3.2904 -3.2022 -3.0608 -1.1946 -1.0515 -1.0016 -0.8282 -0.7647 -0.6544 -0.3839 -0.3060 -0.1823 -0.0974 -0.0050 0.0630 0.2262 0.3347 0.4508 1.0734 1.1488 1.2658 1.3165 1.4224 1.5123 1.6147 1.7067 1.8482 k =-0.2500 0.4330-0.1507 ( 9719 PWs) bands (ev): -18.0815 -18.0536 -18.0005 -16.0135 -15.9116 -15.8933 -15.6412 -15.6280 -15.6156 -15.6118 -15.5990 -15.5669 -6.4523 -6.3977 -5.8919 -4.7494 -4.4547 -4.2426 -3.6098 -3.4876 -3.3970 -3.2906 -3.2020 -3.0609 -1.1947 -1.0511 -1.0011 -0.8280 -0.7646 -0.6546 -0.3844 -0.3065 -0.1828 -0.0977 -0.0054 0.0642 0.2274 0.3343 0.4519 1.0738 1.1483 1.2655 1.3166 1.4228 1.5119 1.6147 1.7061 1.8475 k = 0.2500-0.4330-0.1507 ( 9719 PWs) bands (ev): -18.0816 -18.0535 -18.0006 -16.0136 -15.9109 -15.8939 -15.6409 -15.6278 -15.6186 -15.6081 -15.6004 -15.5667 -6.4520 -6.3980 -5.8919 -4.7491 -4.4554 -4.2421 -3.6096 -3.4878 -3.3976 -3.2893 -3.2028 -3.0608 -1.1945 -1.0510 -1.0014 -0.8280 -0.7644 -0.6548 -0.3845 -0.3062 -0.1826 -0.0978 -0.0058 0.0645 0.2268 0.3354 0.4511 1.0722 1.1498 1.2657 1.3170 1.4234 1.5109 1.6144 1.7057 1.8480 k = 0.5000 0.0000 0.1507 ( 9719 PWs) bands (ev): -18.0810 -18.0537 -18.0009 -16.0134 -15.9109 -15.8937 -15.6413 -15.6276 -15.6157 -15.6115 -15.5997 -15.5670 -6.4520 -6.3981 -5.8913 -4.7493 -4.4550 -4.2426 -3.6096 -3.4880 -3.3973 -3.2902 -3.2020 -3.0609 -1.1947 -1.0510 -1.0013 -0.8279 -0.7644 -0.6548 -0.3851 -0.3064 -0.1826 -0.0973 -0.0054 0.0642 0.2271 0.3346 0.4520 1.0732 1.1487 1.2656 1.3168 1.4228 1.5113 1.6145 1.7059 1.8475 k =-0.5000 0.0000 0.1507 ( 9719 PWs) bands (ev): -18.0810 -18.0537 -18.0009 -16.0134 -15.9111 -15.8935 -15.6406 -15.6274 -15.6186 -15.6089 -15.6007 -15.5667 -6.4519 -6.3982 -5.8913 -4.7491 -4.4553 -4.2423 -3.6100 -3.4879 -3.3971 -3.2895 -3.2028 -3.0607 -1.1945 -1.0511 -1.0014 -0.8279 -0.7646 -0.6547 -0.3844 -0.3068 -0.1824 -0.0979 -0.0055 0.0646 0.2269 0.3348 0.4518 1.0724 1.1494 1.2657 1.3169 1.4237 1.5106 1.6143 1.7058 1.8477 ! total energy = -463.79589166 Ry Harris-Foulkes estimate = -463.79589166 Ry estimated scf accuracy < 3.8E-12 Ry The total energy is the sum of the following terms: one-electron contribution = -239.66672104 Ry hartree contribution = 168.32448929 Ry xc contribution = -126.75238928 Ry ewald contribution = -265.70127063 Ry convergence has been achieved in 13 iterations Forces acting on atoms (Ry/au): atom 1 type 2 force = 0.00036827 0.00002292 -0.00059820 atom 2 type 2 force = 0.00013705 0.00020556 0.00038929 atom 3 type 2 force = 0.00009817 -0.00015317 -0.00016344 atom 4 type 3 force = 0.00071556 0.00002817 -0.00137366 atom 5 type 3 force = 0.00022662 0.00033906 0.00068870 atom 6 type 3 force = 0.00019071 -0.00028185 -0.00040866 atom 7 type 1 force = 0.00033604 0.00002755 0.00006190 atom 8 type 1 force = -0.00030375 -0.00013590 -0.00032493 atom 9 type 1 force = -0.00014438 -0.00019788 -0.00001937 atom 10 type 1 force = -0.00019983 0.00016599 -0.00010529 atom 11 type 1 force = 0.00018213 -0.00023653 0.00007906 atom 12 type 1 force = -0.00080929 0.00045370 0.00115239 atom 13 type 1 force = 0.00060665 -0.00040630 0.00039096 atom 14 type 1 force = -0.00011932 0.00013773 -0.00021200 atom 15 type 1 force = -0.00058975 -0.00029335 0.00029344 atom 16 type 1 force = -0.00064759 0.00026839 -0.00041331 atom 17 type 1 force = 0.00030691 0.00002954 0.00004003 atom 18 type 1 force = -0.00035419 0.00002637 0.00052308 Total force = 0.002481 Total SCF correction = 0.000004 Writing output data file alpo4-154.0_0.save init_run : 26.25s CPU 29.95s WALL ( 1 calls) electrons : 703.87s CPU 883.12s WALL ( 1 calls) forces : 11.24s CPU 15.92s WALL ( 1 calls) Called by init_run: wfcinit : 21.86s CPU 24.92s WALL ( 1 calls) potinit : 0.80s CPU 0.86s WALL ( 1 calls) Called by electrons: c_bands : 571.02s CPU 720.39s WALL ( 13 calls) sum_band : 104.28s CPU 127.95s WALL ( 13 calls) v_of_rho : 3.04s CPU 3.64s WALL ( 14 calls) newd : 26.68s CPU 32.12s WALL ( 14 calls) mix_rho : 0.52s CPU 0.63s WALL ( 13 calls) Called by c_bands: init_us_2 : 4.41s CPU 4.67s WALL ( 728 calls) cegterg : 554.44s CPU 701.58s WALL ( 338 calls) Called by *egterg: h_psi : 420.10s CPU 522.77s WALL ( 1196 calls) s_psi : 40.40s CPU 42.33s WALL ( 1196 calls) g_psi : 3.46s CPU 3.58s WALL ( 832 calls) cdiaghg : 12.32s CPU 12.98s WALL ( 1170 calls) Called by h_psi: add_vuspsi : 40.62s CPU 42.71s WALL ( 1196 calls) General routines calbec : 58.93s CPU 75.22s WALL ( 1560 calls) fft : 3.46s CPU 8.48s WALL ( 231 calls) ffts : 0.09s CPU 0.12s WALL ( 27 calls) fftw : 315.38s CPU 414.00s WALL ( 117346 calls) interpolate : 0.45s CPU 0.74s WALL ( 27 calls) davcio : 0.05s CPU 2.03s WALL ( 1066 calls) Parallel routines fft_scatter : 74.75s CPU 165.11s WALL ( 117604 calls) PWSCF : 12m21.62s CPU 15m29.43s WALL This run was terminated on: 12:13:34 11Aug2011 =------------------------------------------------------------------------------= JOB DONE. =------------------------------------------------------------------------------= -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), +81-858-43-1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110811/49dfbfa5/attachment-0001.htm From giannozz at democritos.it Thu Aug 11 09:11:00 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 11 Aug 2011 09:11:00 +0200 Subject: [Pw_forum] Problem in Xspectra calculation In-Reply-To: <1312962830.28050.YahooMailClassic@web95709.mail.in.yahoo.com> References: <1312962830.28050.YahooMailClassic@web95709.mail.in.yahoo.com> Message-ID: <9BFB38FD-7813-45DA-B714-DAE9631220BC@democritos.it> On Aug 10, 2011, at 9:53 , Niharika Joshi wrote: > wrong fft dimensions > The Quantum espresso version that i am using is espresso 4.3 there is a known problem with XSpectra in version 4.3: http://www.democritos.it/pipermail/pw_forum/2011-April/020230.html Update to the current version (4.3.2) P. -- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From ismotochi at gmail.com Thu Aug 11 10:29:53 2011 From: ismotochi at gmail.com (isaac motochi) Date: Thu, 11 Aug 2011 10:29:53 +0200 Subject: [Pw_forum] Problem in Xspectra calculation In-Reply-To: <9BFB38FD-7813-45DA-B714-DAE9631220BC@democritos.it> References: <1312962830.28050.YahooMailClassic@web95709.mail.in.yahoo.com> <9BFB38FD-7813-45DA-B714-DAE9631220BC@democritos.it> Message-ID: Check in your input .scf.in, there is an element there Ch. If it is carbon since it has same mass as C in atomic species then modify your file appropriately. Isaac University of the Witwatersrand From baroni at sissa.it Thu Aug 11 10:54:17 2011 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 11 Aug 2011 10:54:17 +0200 Subject: [Pw_forum] Invitation to connect on LinkedIn In-Reply-To: <2069396455.38358.1313009818748.JavaMail.app@ela4-bed84.prod> References: <2069396455.38358.1313009818748.JavaMail.app@ela4-bed84.prod> Message-ID: <8671FF45-01D3-4709-8630-C332D1D79A09@sissa.it> Please, STOP here. Thanks - SB On Aug 10, 2011, at 10:56 PM, Mehrnoosh Hazrati via LinkedIn wrote: > LinkedIn > Mehrnoosh Hazrati requested to add you as a connection on LinkedIn: > veronica, > > I'd like to add you to my professional network on LinkedIn. > > - Mehrnoosh > > > Accept > View invitation from Mehrnoosh Hazrati > > > > DID YOU KNOW you can showcase your professional knowledge on LinkedIn to receive job/consulting offers and enhance your professional reputation? > Posting replies to questions on LinkedIn Answers puts you in front of the world's professional community. > > > ? 2011, LinkedIn Corporation > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110811/ed5dd653/attachment.htm From giannozz at democritos.it Thu Aug 11 14:00:01 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 11 Aug 2011 14:00:01 +0200 Subject: [Pw_forum] symmetry not found in pw.x and ph.x In-Reply-To: References: Message-ID: <1EFDC79E-3878-481D-8077-524BED12890C@democritos.it> On Aug 11, 2011, at 6:22 , Riping WANG wrote: > I am calculating scf for a ibrav=4 structure with espresso-4.3.2. > But it can not find the symmetry. http://www.quantum-espresso.org/user_guide/ node52.html#SECTION0001210190000000000000 --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From izaakw89 at yahoo.com Fri Aug 12 00:41:36 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Thu, 11 Aug 2011 15:41:36 -0700 (PDT) Subject: [Pw_forum] Co Pseudopotential Message-ID: <1313102496.25595.YahooMailNeo@web43402.mail.sp1.yahoo.com> The paper I am referring to is: C.Y. Lin, B.A. Jones, Phys Rev B 83, 014413 (2011). They perform an all-electron calculation and find that one electron is forfeit to the surface (so Co has a + charge), yet they still find the spin to be 3/2. When I use pseudopotential calculations on the same system, I get a similar charge (forfeiting one electron to the surface) but my spin is 1. How can this be? -- Izaak Williamson Research Assistant Physics Department Boise State University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110811/2ee48730/attachment.htm From foursea at 163.com Fri Aug 12 08:21:25 2011 From: foursea at 163.com (lilonghua) Date: Fri, 12 Aug 2011 14:21:25 +0800 Subject: [Pw_forum] WAN90_example failed in library mode Message-ID: <201108121421247344418@163.com> Dear all, The "WAN90_example" is ok in test "stand-alone" mode, but failed in "library mode". Error message is : " Wannier mode is: library Setting up... MP grid is 4 x 4 x 4 - Number of atoms is ( 2) - Number of wannier functions is ( 0) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from setup_nnkp : error # 1 wrong excluded band index %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from setup_nnkp : error # 1 ..." I am sure I have compiled pw2wannier90.x with -D__WANLIB and libwannier.a. How can I solve this proplem? 2011-08-12 lilonghua -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110812/856e3705/attachment.htm From nicola.marzari at materials.ox.ac.uk Fri Aug 12 11:25:17 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Fri, 12 Aug 2011 10:25:17 +0100 Subject: [Pw_forum] WAN90_example failed in library mode In-Reply-To: <201108121421247344418@163.com> References: <201108121421247344418@163.com> Message-ID: <4E44F17D.9050309@materials.ox.ac.uk> Dear Lionghua, please post this to the wannier mailing list, rather than pwscf. Also, great to have your name and affiliation in the mail. Thanks! nicola On 8/12/11 7:21 AM, lilonghua wrote: > Dear all, > The "WAN90_example" is ok in test "stand-alone" mode, but failed in > "library mode". Error message is : > " > Wannier mode is: library > Setting up... > MP grid is 4 x 4 x 4 > - Number of atoms is ( 2) > - Number of wannier functions is ( 0) > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from setup_nnkp : error # 1 > wrong excluded band index > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from setup_nnkp : error # 1 > ..." > I am sure I have compiled pw2wannier90.x with -D__WANLIB and libwannier.a. > How can I solve this proplem? > 2011-08-12 > ------------------------------------------------------------------------ > lilonghua -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From rdong at ncsu.edu Fri Aug 12 16:12:12 2011 From: rdong at ncsu.edu (DONG Rui) Date: Fri, 12 Aug 2011 10:12:12 -0400 Subject: [Pw_forum] Temperature rescaling in MD calculation Message-ID: Hi, all, I am doing MD calculation in QuantumEspresso, and have a question now... here are some of the input list * &ions ion_temperature = 'reduce-T', tempw=10, delta_t = 1, nraise=10, pot_extrapolation='second-order', wfc_extrapolation='second-order', / * But I found the rescaling works only when delta_t is a negative number, which is different from what the documentation tells me. Anyone has the same problem? And does anyone know how to heat the system up use the method "reduce-T"? Thank you guys! Rui -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110812/c168b9aa/attachment.htm From crma at sissa.it Fri Aug 12 16:45:12 2011 From: crma at sissa.it (Changru Ma) Date: Fri, 12 Aug 2011 16:45:12 +0200 Subject: [Pw_forum] Temperature rescaling in MD calculation In-Reply-To: References: Message-ID: <15E892A6-9BB1-4B7C-9C49-E4E46A251FDA@sissa.it> Dear Rui, On 12 Aug, 2011, at 16:12, DONG Rui wrote: > Hi, all, > > I am doing MD calculation in QuantumEspresso, and have a question now... > > here are some of the input list > &ions > ion_temperature = 'reduce-T', > tempw=10, > delta_t = 1, > nraise=10, > pot_extrapolation='second-order', > wfc_extrapolation='second-order', > / > > But I found the rescaling works only when delta_t is a negative number, which is different from what the documentation tells me. In Doc/INPUT_PW.txt, I find the following lines: Variable: ion_temperature Type: CHARACTER 'reduce-T' reduce ionic temperature every "nraise" steps by the (negative) value "delta_t" and Variable: delta_t Type: REAL if ion_temperature='reduce-T': every 'nraise' steps the instantaneous temperature is reduced by -delta_T (.e. delta_t is added to the temperature) The instantaneous temperature is calculated at the end of every ionic move and BEFORE rescaling. This is the temperature reported in the main output. For delta_t < 0, the actual average rate of heating or cooling should be roughly C*delta_t/(nraise*dt) (C=1 for an ideal gas, C=0.5 for a harmonic solid, theorem of energy equipartition between all quadratic degrees of freedom). Why delta_t is a negative number is different from the document? > > Anyone has the same problem? And does anyone know how to heat the system up use the method "reduce-T"? I think "reduce-T" is used to quench the system, it reduces ionic temperature every "nraise" steps by the (negative) value "delta_t". To heat the system up, I would suggest you to use other thermostats, like "rescaling", "rescale-v", "rescale-T", "berendsen" or "andersen". Best wishes, Changru > > Thank you guys! > > Rui _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110812/197a7de5/attachment.htm From chengyu.young at gmail.com Fri Aug 12 23:36:20 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Fri, 12 Aug 2011 17:36:20 -0400 Subject: [Pw_forum] Strange bandstructure for metallic carbon nanotube In-Reply-To: References: Message-ID: Hi everybody. I tried to plot the bandstructure for carbon nanotube(5,5), however, the result looks strange. I have 20 carbon atoms in a unitcell, and I set the number of bands(nbnd=80 or 48). nbnd=80 is out of the consideration that conduction bands+valence bands. http://imageshack.us/photo/my-images/51/cnt55bands80.jpg/ nbnd=48 is from the 20% more for metal.(here the carbon nanotube is metallic) http://imageshack.us/photo/my-images/202/cnt55bands48.jpg/ The third picture is after I added no_overlap=.true. in the bands.infile for nbnd =48. http://imageshack.us/photo/my-images/808/cnt55bands48nooverlap.jpg/ All the three pictures are far from the band structure in literature, and I don't know if they are wrong. Can somebody give me an advice and I apprieciate it very much. Thank you! Best regards. Chengyu Yang MMAE University of Central Florida, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110812/7b52ce76/attachment.htm From chengyu.young at gmail.com Fri Aug 12 23:43:54 2011 From: chengyu.young at gmail.com (chengyu yang) Date: Fri, 12 Aug 2011 17:43:54 -0400 Subject: [Pw_forum] Strange bandstructure for metallic carbon nanotube In-Reply-To: References: Message-ID: Hi everybody. Sorry to post this email again cause the image in this one is bigger and easy to see. I tried to plot the bandstructure for carbon nanotube(5,5), however, the result looks strange. I have 20 carbon atoms in a unitcell, and I set the number of bands(nbnd=80 or 48). nbnd=80 is out of the consideration that conduction bands+valence bands. http://imageshack.us/photo/my-images/36/cnt55bands80.jpg/ nbnd=48 is from the 20% more for metal.(here the carbon nanotube is metallic) http://imageshack.us/photo/my-images/163/cnt55bands48.jpg/ The third picture is after I added no_overlap=.true. in the bands.infile for nbnd =48. http://imageshack.us/photo/my-images/850/cnt55bands48nooverlap.jpg/ All the three pictures are far from the band structure in literature, and I don't know if they are wrong. Can somebody give me an advice and I apprieciate it very much. Thank you! Best regards. Chengyu Yang MMAE University of Central Florida, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110812/fb79bad9/attachment.htm From nazari at iasbs.ac.ir Sun Aug 14 10:02:05 2011 From: nazari at iasbs.ac.ir (nazari at iasbs.ac.ir) Date: Sun, 14 Aug 2011 12:32:05 +0430 (IRDT) Subject: [Pw_forum] problem with bands.x ver. 4.3.1 In-Reply-To: <201108121421247344418@163.com> References: <201108121421247344418@163.com> Message-ID: <50248.85.185.211.90.1313308925.squirrel@mail.iasbs.ac.ir>
Dear All, Please find in the attachment two band structures for graphene. Two inputs for them are the same. The only difference is ?in the QES version. It seems that bands.x in QSE version 4.3.1 does not work properly. But the plot with version 4.2 is the same as reported plots for graphene in literature. Would you please let we know what is the problem? regards Fariba Nazari IASBS ? ? ? -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110814/ce3d4a9a/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: QES-4.2.pdf Type: application/pdf Size: 12026 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110814/ce3d4a9a/attachment-0002.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: QES-4.3.1.pdf Type: application/pdf Size: 12061 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110814/ce3d4a9a/attachment-0003.pdf From bdslipun at gmail.com Sun Aug 14 10:55:54 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 14 Aug 2011 14:25:54 +0530 Subject: [Pw_forum] band structure Message-ID: i have calculated the band structure for cscl phase but what is the wrong with this how the kpoints are given in the band structure for cscl phase please tell me -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110814/a6cdefea/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: sc zero b2 .ps Type: application/postscript Size: 145022 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110814/a6cdefea/attachment-0001.ps From mansourehp at gmail.com Sun Aug 14 17:16:56 2011 From: mansourehp at gmail.com (Mansoureh Pashangpour) Date: Sun, 14 Aug 2011 19:46:56 +0430 Subject: [Pw_forum] charge density Message-ID: Dear all how can I set e1(i) and e2(i) to find 2 D rho plot for graphene. thanks alot M. Pashangpour Islamic Azad University Tehran, IRAN From mikeat4999 at gmail.com Mon Aug 15 07:31:41 2011 From: mikeat4999 at gmail.com (mike at.) Date: Mon, 15 Aug 2011 08:31:41 +0300 Subject: [Pw_forum] problem with bands.x ver. 4.3.1 In-Reply-To: <50248.85.185.211.90.1313308925.squirrel@mail.iasbs.ac.ir> References: <201108121421247344418@163.com> <50248.85.185.211.90.1313308925.squirrel@mail.iasbs.ac.ir> Message-ID: Have you tried this: in bands.in file. add no_overlap = true, On Sun, Aug 14, 2011 at 11:02 AM, wrote: > Dear All, > Please find in the attachment two band structures for graphene. Two inputs > for them are the same. The only difference is in the QES version. It seems > that bands.x in QSE version 4.3.1 does not work properly. But the plot with > version 4.2 is the same as reported plots for graphene in literature. > Would you please let we know what is the problem? > > regards > Fariba Nazari > IASBS > > > > > > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- M. O. ATAMBO mikeat4999 at gmail.com student, computational material science group Chepkoilel university college. Department of Physics -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110815/caaf2a82/attachment.htm From zafartariq2003 at yahoo.com Mon Aug 15 08:59:06 2011 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Sun, 14 Aug 2011 23:59:06 -0700 (PDT) Subject: [Pw_forum] (no subject) Message-ID: <1313391546.99825.YahooMailClassic@web65408.mail.ac4.yahoo.com> Dear All I plot ZnO electronic structure using this file given below &control Title = 'ZnO , hcp,a=3.2500,c=5.206 ,c/a=1.6103125', calculation ='scf' restart_mode='from_scratch', pseudo_dir = '/root/Pwscf/pseudo/', outdir ='/root/Pwscf/scratch/' prefix ='ZnO' tstress = .false. tprnfor = .false. / &system ibrav= 4, celldm(1) = 6.132075472, celldm(3) = 1.601846154, nat =4, ntyp =2, ecutwfc =25.0, ecutrho =300.0 occupations ='smearing', smearing='methefessel_paxton', degauss = 0.05, / &electrons diagonalization='cg' , conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Zn 65.409 Zn.pz-van_ak.UPF O 15.9994 O.pz-van_ak.UPF ATOMIC_POSITIONS (crystal) Zn 0.333333333 0.666666667 0.0000000 O 0.333333333 0.666666667 0.3817000 Zn 0.666666667 0.333333333 0.5000000 O 0.666666667 0.333333333 0.8817000 K_POINTS (automatic) 4 4 4 0 0 0 This plot (after changing scf to nscf) is same as experimental and theoretical BUT when I make a cell of 8 atoms (1x1x2 supercell) input is as below &control calculation ='scf' restart_mode='from_scratch', pseudo_dir = '/root/Pwscf/pseudo/', outdir ='/root/Pwscf/scratch/' prefix ='ZnO' tstress = .false. tprnfor = .true. / &system ibrav = 4, celldm(1) = 6.132075472, celldm(3) = 3.203692308, (due to increase in size along Z-direction C= 2*c ) nat = 8, ntyp = 2, ecutwfc = 25.0, ecutrho = 300.0 occupations ='smearing', smearing ='methefessel_paxton', degauss =0.02 / &electrons diagonalization='cg' ,mixing_mode='plain', conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Zn 65.38 Zn.pz-van_ak.UPF O 16.00 O.pz-van_ak.UPF ATOMIC_POSITIONS (crystal) Zn 0.333333333 0.666666667 0.000000000 Zn 0.333333333 0.666666667 0.500000000 Zn 0.666666667 0.333333333 0.250000000 Zn 0.666666667 0.333333333 0.750000000 O 0.333333333 0.666666667 0.190850000 O 0.333333333 0.666666667 0.690850000 O 0.666666667 0.333333333 0.440850000 O 0.666666667 0.333333333 0.940850000 K_POINTS (automatic) 4 4 4 0 0 0 After changing scf to bands the electronic structure is metallic (no band gap) and a I get different electronic structure . Now please guide me how I can get true electronic structure. Thanking in Advance Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110814/5146d361/attachment.htm From zafartariq2003 at yahoo.com Mon Aug 15 12:02:36 2011 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Mon, 15 Aug 2011 03:02:36 -0700 (PDT) Subject: [Pw_forum] problem in electronic structure of ZnO Message-ID: <1313402556.98528.YahooMailClassic@web65414.mail.ac4.yahoo.com> Dear All I plot ZnO electronic structure using this file given below &control Title = 'ZnO , hcp,a=3.2500,c=5.206 ,c/a=1.6103125', calculation ='scf' restart_mode='from_scratch', pseudo_dir = '/root/Pwscf/pseudo/', outdir ='/root/Pwscf/scratch/' prefix ='ZnO' tstress = .false. tprnfor = .false. / &system ibrav= 4, celldm(1) = 6.132075472, celldm(3) = 1.601846154, nat =4, ntyp =2, ecutwfc =25.0, ecutrho =300.0 occupations ='smearing', smearing='methefessel_paxton', degauss = 0.05, / &electrons diagonalization='cg' , conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Zn 65.409 Zn.pz-van_ak.UPF O 15.9994 O.pz-van_ak.UPF ATOMIC_POSITIONS (crystal) Zn 0.333333333 0.666666667 0.0000000 O 0.333333333 0.666666667 0.3817000 Zn 0.666666667 0.333333333 0.5000000 O 0.666666667 0.333333333 0.8817000 K_POINTS (automatic) 4 4 4 0 0 0 This plot (after changing scf to nscf) is same as experimental and theoretical BUT when I make a cell of 8 atoms (1x1x2 supercell) input is as below &control calculation ='scf' restart_mode='from_scratch', pseudo_dir = '/root/Pwscf/pseudo/', outdir ='/root/Pwscf/scratch/' prefix ='ZnO' tstress = .false. tprnfor = .true. / &system ibrav = 4, celldm(1) = 6.132075472, celldm(3) = 3.203692308, (due to increase in size along Z-direction C= 2*c ) nat = 8, ntyp = 2, ecutwfc = 25.0, ecutrho = 300.0 occupations ='smearing', smearing ='methefessel_paxton', degauss =0.02 / &electrons diagonalization='cg' ,mixing_mode='plain', conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Zn 65.38 Zn.pz-van_ak.UPF O 16.00 O.pz-van_ak.UPF ATOMIC_POSITIONS (crystal) Zn 0.333333333 0.666666667 0.000000000 Zn 0.333333333 0.666666667 0.500000000 Zn 0.666666667 0.333333333 0.250000000 Zn 0.666666667 0.333333333 0.750000000 O 0.333333333 0.666666667 0.190850000 O 0.333333333 0.666666667 0.690850000 O 0.666666667 0.333333333 0.440850000 O 0.666666667 0.333333333 0.940850000 K_POINTS (automatic) 4 4 4 0 0 0 After changing scf to bands the electronic structure is metallic (no band gap) and a I get different electronic structure . Now please guide me how I can get true electronic structure. Thanking in Advance Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110815/d80a1674/attachment.htm From uccaati at ucl.ac.uk Mon Aug 15 12:13:27 2011 From: uccaati at ucl.ac.uk (Antonio Tilocca) Date: Mon, 15 Aug 2011 11:13:27 +0100 (BST) Subject: [Pw_forum] Temperature rescaling in MD calculation (DONG Rui) In-Reply-To: References: Message-ID: Hi Rui, the standard Berendsen thermostat implemented in PW works perfectly fine to control the temperature in an MD run. Depending on how far your initial temperature is from the target, the plain isokinetic rescaling ('rescaling' keyword) is another option which might work well in your case. Antonio Tilocca University College London Date: Fri, 12 Aug 2011 10:12:12 -0400 From: DONG Rui Subject: [Pw_forum] Temperature rescaling in MD calculation To: pw_forum at pwscf.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, all, I am doing MD calculation in QuantumEspresso, and have a question now... here are some of the input list * &ions ion_temperature = 'reduce-T', tempw=10, delta_t = 1, nraise=10, pot_extrapolation='second-order', wfc_extrapolation='second-order', / * But I found the rescaling works only when delta_t is a negative number, which is different from what the documentation tells me. Anyone has the same problem? And does anyone know how to heat the system up use the method "reduce-T"? Thank you guys! Rui From guntram.schmidt at chemie.uni-halle.de Mon Aug 15 12:21:12 2011 From: guntram.schmidt at chemie.uni-halle.de (Guntram Schmidt) Date: Mon, 15 Aug 2011 12:21:12 +0200 Subject: [Pw_forum] Dehydration reaction with QE In-Reply-To: <1313391546.99825.YahooMailClassic@web65408.mail.ac4.yahoo.com> References: <1313391546.99825.YahooMailClassic@web65408.mail.ac4.yahoo.com> Message-ID: <4E48F318.2070304@chemie.uni-halle.de> Dear All, I'd like to know, wether QE is capable of modelling a dehydration reaction? As far as I've seen, the NEB method is suitable only for solid-state reactions with retention of the stoichiometry... I have a sodium sulfonate, which degrades from a tetrahydrate to a dihydrate in a topotactic way and I'd like to know, which water molecules are the ones that stay in the crystals and which are the ones, that leave... I tried to simply remove the questioned molecules and do a vc-relax - but it didn't "move" very much. Maybe this method is tuneable - using some "extra forces"? Thanks a lot for help, Guntram Guntram Schmidt University of Halle/Saale, Germany From arvifis at gmail.com Mon Aug 15 18:22:27 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 15 Aug 2011 13:22:27 -0300 Subject: [Pw_forum] problem in electronic structure of ZnO In-Reply-To: <1313402556.98528.YahooMailClassic@web65414.mail.ac4.yahoo.com> References: <1313402556.98528.YahooMailClassic@web65414.mail.ac4.yahoo.com> Message-ID: Dear Muhammad Zafar: In your structure, were optimized the lattice parameter and atomic positions..?? ecutwfc = 25.0 was obtained after a convergence..?? and finally, may be you need increase the k-points values (after a convergence). Best PhD stud. Arles V. Gil Rebaza Institute of Physic of La Plata La Plata - Argentine 2011/8/15 zafar rasheed > Dear All > > I plot ZnO electronic structure using this file given below > > > > &control > > Title = 'ZnO , hcp,a=3.2500,c=5.206 ,c/a=1.6103125', > > calculation ='scf' > > restart_mode='from_scratch', > > pseudo_dir = '/root/Pwscf/pseudo/', > > outdir ='/root/Pwscf/scratch/' > > prefix ='ZnO' > > tstress = .false. > > tprnfor = .false. > > / > > &system > > ibrav= 4, > > celldm(1) = 6.132075472, > > celldm(3) = 1.601846154, > > nat =4, > > ntyp =2, > > ecutwfc =25.0, > > ecutrho =300.0 > > occupations ='smearing', > > smearing='methefessel_paxton', > > degauss = 0.05, > > / > > &electrons > > diagonalization='cg' , > > conv_thr = 1.0e-8 > > mixing_beta = 0.7 > > / > > ATOMIC_SPECIES > > Zn 65.409 Zn.pz-van_ak.UPF > > O 15.9994 O.pz-van_ak.UPF > > ATOMIC_POSITIONS (crystal) > > Zn 0.333333333 0.666666667 0.0000000 > > O 0.333333333 0.666666667 0.3817000 > > Zn 0.666666667 0.333333333 0.5000000 > > O 0.666666667 0.333333333 0.8817000 > > K_POINTS (automatic) > > 4 4 4 0 0 0 > > > > This plot (after changing scf to nscf) is same as experimental and > theoretical > > > > BUT > > > when I make a cell of 8 atoms (1x1x2 supercell) > > input is as below > > > > &control > > calculation ='scf' > > restart_mode='from_scratch', > > pseudo_dir = '/root/Pwscf/pseudo/', > > outdir ='/root/Pwscf/scratch/' > > prefix ='ZnO' > > tstress = .false. > > tprnfor = .true. > > / > > &system > > ibrav = 4, > > celldm(1) = 6.132075472, > > celldm(3) = 3.203692308, (due to increase in size along Z-direction C= 2*c > ) > > nat = 8, > > ntyp = 2, > > ecutwfc = 25.0, > > ecutrho = 300.0 > > occupations ='smearing', > > smearing ='methefessel_paxton', > > degauss =0.02 > > / > > &electrons > > diagonalization='cg' ,mixing_mode='plain', > > conv_thr = 1.0e-8 > > mixing_beta = 0.7 > > / > > ATOMIC_SPECIES > > Zn 65.38 Zn.pz-van_ak.UPF > > O 16.00 O.pz-van_ak.UPF > > ATOMIC_POSITIONS (crystal) > > Zn 0.333333333 0.666666667 0.000000000 > > Zn 0.333333333 0.666666667 0.500000000 > > Zn 0.666666667 0.333333333 0.250000000 > > Zn 0.666666667 0.333333333 0.750000000 > > O 0.333333333 0.666666667 0.190850000 > > O 0.333333333 0.666666667 0.690850000 > > O 0.666666667 0.333333333 0.440850000 > > O 0.666666667 0.333333333 0.940850000 > > K_POINTS (automatic) > > 4 4 4 0 0 0 > > > After changing scf to bands the electronic structure is metallic (no band > gap) and a I get different electronic structure . Now please guide me how I > can get true electronic structure. > > > Thanking in Advance > > > Muhammad Zafar > PhD Scholar > Department of Physics > The Islamia University of Bahawalpur,Pakistan > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110815/c24db579/attachment-0001.htm From mashiatalaaii at gmail.com Mon Aug 15 20:02:20 2011 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Mon, 15 Aug 2011 14:02:20 -0400 Subject: [Pw_forum] experimental Dit and theoretical Dit Message-ID: Dear All, I am working on Si/SiO2 system, at the moment. 1. I was wondering whether the sum of all LDOS calculated from projected wavefunction on the Si at the interface can give me the density of interface states. The question is whether the sum of LDOS of projected wavefunction on the inter-facial atoms is equivalent to planar local density of state at the interface. 2. If positive, the sum of LDOS of all projected wavefunction on all atoms at the interface divided by the surface of the interface is by far higher than the Dit reported from experiment. Actually, I am thinking, no matter how big the structure is, the Dit is still very high. I was wondering whether I miss any point to consider for calculation. I really really appreciate your help. Have a great summer. M Alaaii -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110815/9da8bdab/attachment.htm From bdslipun at gmail.com Tue Aug 16 10:08:57 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 16 Aug 2011 13:38:57 +0530 Subject: [Pw_forum] QHA Message-ID: compilation problem in QHA code error looks below in linux -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110816/773bb57d/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Untitled Document 1 Type: application/octet-stream Size: 4293 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110816/773bb57d/attachment.obj From physics.skgupta at gmail.com Tue Aug 16 10:25:11 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Tue, 16 Aug 2011 13:55:11 +0530 Subject: [Pw_forum] QHA In-Reply-To: References: Message-ID: Dear Sahoo Plz visit the forum, recent some posts are useful. http://www.democritos.it/pipermail/pw_forum/2011-July/021372.html many more suggestion from Prof. Eyvaz Isaev. wishes sanjeev On Tue, Aug 16, 2011 at 1:38 PM, bhabya sahoo wrote: > compilation problem in QHA code error looks below > in linux > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- *Dr. Sanjeev Kumar Gupta* *Post Doctoral Fellow, (Ministry of New and Renewable Energy) Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, India* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110816/40045ab5/attachment.htm From koriro1208 at gmail.com Tue Aug 16 10:27:06 2011 From: koriro1208 at gmail.com (KORIR KIPRONOH) Date: Tue, 16 Aug 2011 09:27:06 +0100 Subject: [Pw_forum] Calculation of surface and nanowire elastic constant Message-ID: Dear QE users, Hi everybody. I'm interested in determining the elastic constants for ZnO polar surface and also for the nanowire(001). I cannot find how this is done and your suggestion would be highly appreciated. -- Korir Kiprono PhD student Politecnico Di Torino Italy koriro1208 at gmail.com From joerg.buchwald at iom-leipzig.de Tue Aug 16 15:16:18 2011 From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald) Date: Tue, 16 Aug 2011 15:16:18 +0200 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 In-Reply-To: References: <201108061136234844372@163.com> <201108061418142181751@163.com> Message-ID: <20110816151618.1bf63c64@PC-Mayr-Mitarb6.pc-flexi> Hi, i have the same problem (with the same error message) with v4.3.2, with v4.3.1 it works fine. here my input file: -- &control calculation='vc-relax' prefix='silicon-vanderbilt', pseudo_dir='/home/joerg/espresso-4.3.1/pseudo' outdir = '/home/joerg/scratch', tstress=.true. disk_io='none' / &system ibrav= 8, celldm(1) =10.33425, celldm(2)=1.0, celldm(3)=10.00, nat= 80, ntyp= 1, ecutwfc = 55.0 / &electrons diagonalization='david' mixing_mode='plain' / &ions / &cell / ATOMIC_SPECIES Si 28.086 Si.pbe-n-van.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 Si 0.50 0.50 0.00 Si 0.75 0.75 0.25 Si 0.50 0.00 0.50 Si 0.75 0.25 0.75 Si 0.00 0.50 0.50 Si 0.25 0.75 0.75 Si 0.00 0.00 1.00 Si 0.25 0.25 1.25 Si 0.50 0.50 1.00 Si 0.75 0.75 1.25 Si 0.50 0.00 1.50 Si 0.75 0.25 1.75 Si 0.00 0.50 1.50 Si 0.25 0.75 1.75 Si 0.00 0.00 2.00 Si 0.25 0.25 2.25 Si 0.50 0.50 2.00 Si 0.75 0.75 2.25 Si 0.50 0.00 2.50 Si 0.75 0.25 2.75 Si 0.00 0.50 2.50 Si 0.25 0.75 2.75 Si 0.00 0.00 3.00 Si 0.25 0.25 3.25 Si 0.50 0.50 3.00 Si 0.75 0.75 3.25 Si 0.50 0.00 3.50 Si 0.75 0.25 3.75 Si 0.00 0.50 3.50 Si 0.25 0.75 3.75 Si 0.00 0.00 4.0 Si 0.25 0.25 4.25 Si 0.50 0.50 4.00 Si 0.75 0.75 4.25 Si 0.50 0.00 4.50 Si 0.75 0.25 4.75 Si 0.00 0.50 4.50 Si 0.25 0.75 4.75 Si 0.00 0.00 5.0 Si 0.25 0.25 5.25 Si 0.50 0.50 5.00 Si 0.75 0.75 5.25 Si 0.50 0.00 5.50 Si 0.75 0.25 5.75 Si 0.00 0.50 5.50 Si 0.25 0.75 5.75 Si 0.00 0.00 6.0 Si 0.25 0.25 6.25 Si 0.50 0.50 6.00 Si 0.75 0.75 6.25 Si 0.50 0.00 6.50 Si 0.75 0.25 6.75 Si 0.00 0.50 6.50 Si 0.25 0.75 6.75 Si 0.00 0.00 7.0 Si 0.25 0.25 7.25 Si 0.50 0.50 7.00 Si 0.75 0.75 7.25 Si 0.50 0.00 7.50 Si 0.75 0.25 7.75 Si 0.00 0.50 7.50 Si 0.25 0.75 7.75 Si 0.00 0.00 8.0 Si 0.25 0.25 8.25 Si 0.50 0.50 8.00 Si 0.75 0.75 8.25 Si 0.50 0.00 8.50 Si 0.75 0.25 8.75 Si 0.00 0.50 8.50 Si 0.25 0.75 8.75 Si 0.00 0.00 9.0 Si 0.25 0.25 9.25 Si 0.50 0.50 9.00 Si 0.75 0.75 9.25 Si 0.50 0.00 9.50 Si 0.75 0.25 9.75 Si 0.00 0.50 9.50 Si 0.25 0.75 9.75 K_POINTS automatic 7 7 7 0 0 0 --- Best, J?rg Buchwald -- J?rg Buchwald Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY From lmartinsamos at gmail.com Tue Aug 16 17:06:54 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Tue, 16 Aug 2011 17:06:54 +0200 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 In-Reply-To: <20110816151618.1bf63c64@PC-Mayr-Mitarb6.pc-flexi> References: <201108061136234844372@163.com> <201108061418142181751@163.com> <20110816151618.1bf63c64@PC-Mayr-Mitarb6.pc-flexi> Message-ID: Dear Jorg and Lilonghua I just have tested the example Jorg sent, and I did not find any input error with 4.3.2. Boh! I do not know! Can you send the output with the exact error message? thank you for your collaboration Layla 2011/8/16 J?rg Buchwald > Hi, > i have the same problem (with the same error message) with v4.3.2, with > v4.3.1 it works fine. > > here my input file: > > -- > > &control > calculation='vc-relax' > prefix='silicon-vanderbilt', > pseudo_dir='/home/joerg/espresso-4.3.1/pseudo' > outdir = '/home/joerg/scratch', > tstress=.true. > disk_io='none' > / > &system > ibrav= 8, celldm(1) =10.33425, celldm(2)=1.0, celldm(3)=10.00, > nat= 80, ntyp= 1, ecutwfc = 55.0 > / > &electrons > diagonalization='david' > mixing_mode='plain' > / > &ions > / > &cell > / > ATOMIC_SPECIES > Si 28.086 Si.pbe-n-van.UPF > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.25 0.25 0.25 > Si 0.50 0.50 0.00 > Si 0.75 0.75 0.25 > Si 0.50 0.00 0.50 > Si 0.75 0.25 0.75 > Si 0.00 0.50 0.50 > Si 0.25 0.75 0.75 > Si 0.00 0.00 1.00 > Si 0.25 0.25 1.25 > Si 0.50 0.50 1.00 > Si 0.75 0.75 1.25 > Si 0.50 0.00 1.50 > Si 0.75 0.25 1.75 > Si 0.00 0.50 1.50 > Si 0.25 0.75 1.75 > Si 0.00 0.00 2.00 > Si 0.25 0.25 2.25 > Si 0.50 0.50 2.00 > Si 0.75 0.75 2.25 > Si 0.50 0.00 2.50 > Si 0.75 0.25 2.75 > Si 0.00 0.50 2.50 > Si 0.25 0.75 2.75 > Si 0.00 0.00 3.00 > Si 0.25 0.25 3.25 > Si 0.50 0.50 3.00 > Si 0.75 0.75 3.25 > Si 0.50 0.00 3.50 > Si 0.75 0.25 3.75 > Si 0.00 0.50 3.50 > Si 0.25 0.75 3.75 > Si 0.00 0.00 4.0 > Si 0.25 0.25 4.25 > Si 0.50 0.50 4.00 > Si 0.75 0.75 4.25 > Si 0.50 0.00 4.50 > Si 0.75 0.25 4.75 > Si 0.00 0.50 4.50 > Si 0.25 0.75 4.75 > Si 0.00 0.00 5.0 > Si 0.25 0.25 5.25 > Si 0.50 0.50 5.00 > Si 0.75 0.75 5.25 > Si 0.50 0.00 5.50 > Si 0.75 0.25 5.75 > Si 0.00 0.50 5.50 > Si 0.25 0.75 5.75 > Si 0.00 0.00 6.0 > Si 0.25 0.25 6.25 > Si 0.50 0.50 6.00 > Si 0.75 0.75 6.25 > Si 0.50 0.00 6.50 > Si 0.75 0.25 6.75 > Si 0.00 0.50 6.50 > Si 0.25 0.75 6.75 > Si 0.00 0.00 7.0 > Si 0.25 0.25 7.25 > Si 0.50 0.50 7.00 > Si 0.75 0.75 7.25 > Si 0.50 0.00 7.50 > Si 0.75 0.25 7.75 > Si 0.00 0.50 7.50 > Si 0.25 0.75 7.75 > Si 0.00 0.00 8.0 > Si 0.25 0.25 8.25 > Si 0.50 0.50 8.00 > Si 0.75 0.75 8.25 > Si 0.50 0.00 8.50 > Si 0.75 0.25 8.75 > Si 0.00 0.50 8.50 > Si 0.25 0.75 8.75 > Si 0.00 0.00 9.0 > Si 0.25 0.25 9.25 > Si 0.50 0.50 9.00 > Si 0.75 0.75 9.25 > Si 0.50 0.00 9.50 > Si 0.75 0.25 9.75 > Si 0.00 0.50 9.50 > Si 0.25 0.75 9.75 > K_POINTS automatic > 7 7 7 0 0 0 > --- > Best, > J?rg Buchwald > > > -- > J?rg Buchwald > Leibniz-Institut fuer Oberflaechenmodifizierung e.V. > Permoserstrasse 15 > 04318 Leipzig > GERMANY > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110816/487d51e1/attachment.htm From joerg.buchwald at iom-leipzig.de Tue Aug 16 17:23:22 2011 From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald) Date: Tue, 16 Aug 2011 17:23:22 +0200 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 In-Reply-To: References: <201108061136234844372@163.com> <201108061418142181751@163.com> <20110816151618.1bf63c64@PC-Mayr-Mitarb6.pc-flexi> Message-ID: <20110816172322.5a8d5f24@PC-Mayr-Mitarb6.pc-flexi> thats strange. here is the output file, it is the same error message, as the one of longhua. -- Program PWSCF v.4.3.2 starts on 16Aug2011 at 15:59: 5 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 8 processors R & G space division: proc/pool = 8 Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 40000 Max angular momentum in pseudopotentials (lmaxx) = 3 Waiting for input... Reading input from stdin %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 17 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 17 reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 17 reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 17 reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 17 reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 17 reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 17 reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... stopping ... stopping ... stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 17 reading namelist system %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -- thx, J?rg J?rg Buchwald Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY From lmartinsamos at gmail.com Tue Aug 16 17:47:06 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Tue, 16 Aug 2011 17:47:06 +0200 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 In-Reply-To: <20110816172322.5a8d5f24@PC-Mayr-Mitarb6.pc-flexi> References: <201108061136234844372@163.com> <201108061418142181751@163.com> <20110816151618.1bf63c64@PC-Mayr-Mitarb6.pc-flexi> <20110816172322.5a8d5f24@PC-Mayr-Mitarb6.pc-flexi> Message-ID: Dear Jorg, if you make an "ls" do you see somewhere (in ./ or in out_dir) a file called "input_tmp.in"? cheers Layla 2011/8/16 J?rg Buchwald > thats strange. > here is the output file, it is the same error message, as the one > of longhua. > > -- > Program PWSCF v.4.3.2 starts on 16Aug2011 at 15:59: 5 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 > (2009); URL http://www.quantum-espresso.org", > in publications or presentations arising from this work. More > details at > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > > Parallel version (MPI), running on 8 processors > R & G space division: proc/pool = 8 > > Current dimensions of program PWSCF are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 40000 > Max angular momentum in pseudopotentials (lmaxx) = 3 > Waiting for input... > Reading input from stdin > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 17 > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 17 > reading namelist system > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 17 > reading namelist system > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > reading namelist system > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 17 > reading namelist system > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 17 > reading namelist system > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 17 > reading namelist system > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 17 > reading namelist system > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > stopping ... > > stopping ... > > stopping ... > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_namelists : error # 17 > reading namelist system > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > -- > > thx, > J?rg > > > J?rg Buchwald > Leibniz-Institut fuer Oberflaechenmodifizierung e.V. > Permoserstrasse 15 > 04318 Leipzig > GERMANY > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110816/8f10ffb0/attachment.htm From joerg.buchwald at iom-leipzig.de Tue Aug 16 18:09:52 2011 From: joerg.buchwald at iom-leipzig.de (=?UTF-8?B?SsO2cmc=?= Buchwald) Date: Tue, 16 Aug 2011 18:09:52 +0200 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 In-Reply-To: References: <201108061136234844372@163.com> <201108061418142181751@163.com> <20110816151618.1bf63c64@PC-Mayr-Mitarb6.pc-flexi> <20110816172322.5a8d5f24@PC-Mayr-Mitarb6.pc-flexi> Message-ID: <20110816180952.0d1fdec9@PC-Mayr-Mitarb6.pc-flexi> Thanks, that was it. I found a forbidden linebreak in input_tmp.in So as mentioned before it was a problem caused by the character length... Regards, J?rg Buchwald -- Leibniz-Institut fuer Oberflaechenmodifizierung e.V. Permoserstrasse 15 04318 Leipzig GERMANY From payam.norouzzadeh at gmail.com Tue Aug 16 21:44:52 2011 From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh) Date: Tue, 16 Aug 2011 14:44:52 -0500 Subject: [Pw_forum] Thermal conductivity and Gruneisen parameters Message-ID: Dear QE users I'm wondering if anybody knows how to calculate thermal conductivity and also Gruneisen parameters by QE. I haven't seen any example file or document about above mentioned quantities. Does anybody know a good document about them? Best regards,Payam Norouzzadeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110816/a5bb9b08/attachment.htm From lo_wan_2005 at hotmail.com Wed Aug 17 08:23:24 2011 From: lo_wan_2005 at hotmail.com (Lo_wan_2005XW) Date: Wed, 17 Aug 2011 14:23:24 +0800 Subject: [Pw_forum] warning for 176 P63/m structure Message-ID: Dear all, I am studying a compound with P63/m structure. But the program complain: warning: symmetry operation # 2 not allowed. fractional translation: 0.0000000 0.0000000 0.5000000 in crystal coordinates warning: symmetry operation # 5 not allowed. fractional translation: 0.0000000 0.0000000 0.5000000 in crystal coordinates warning: symmetry operation # 6 not allowed. fractional translation: 0.0000000 0.0000000 0.5000000 in crystal coordinates warning: symmetry operation # 14 not allowed. fractional translation: 0.0000000 0.0000000 0.5000000 in crystal coordinates warning: symmetry operation # 17 not allowed. fractional translation: 0.0000000 0.0000000 0.5000000 in crystal coordinates warning: symmetry operation # 18 not allowed. fractional translation: 0.0000000 0.0000000 0.5000000 in crystal coordinates Our compound has P63/m structure (176 space group). And following is the setup: -------------------------------------------- &system ibrav= 4, celldm(1) =10.726090, celldm(3)=1.25440, nat= 12, ntyp= 2, ecutwfc =35.0,ecutrho=300 occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05 / &electrons diagonalization='david' mixing_beta = 0.7 / ATOMIC_SPECIES La 138.9055 La.pbe-n-bpaw.UPF Si 28.0855 Si.pbe-n-van.UPF ATOMIC_POSITIONS crystal La 0.00000000 0.00000000 0.50000000 La 0.00000000 0.00000000 0.00000000 Si 0.48000000 0.99000000 0.75000000 Si 0.01000000 0.49000000 0.75000000 Si 0.51000000 0.52000000 0.75000000 Si 0.52000000 0.01000000 0.25000000 Si 0.99000000 0.51000000 0.25000000 Si 0.49000000 0.48000000 0.25000000 Si 0.333333333 0.666666666 0.50000000 Si 0.666666666 0.333333333 0.00000000 Si 0.666666666 0.333333333 0.50000000 Si 0.333333333 0.666666666 0.00000000 K_POINTS automatic 6 6 5 0 0 0 -------------------------------------------- Following is "atomic positions are in cartesian coordinates" printed by the program site n. atom positions (alat units) 1 La tau( 1) = ( 0.0000000 0.0000000 0.6272000 ) 2 La tau( 2) = ( 0.0000000 0.0000000 0.0000000 ) 3 Si tau( 3) = ( -0.0150000 0.8573651 0.9408000 ) 4 Si tau( 4) = ( -0.2350000 0.4243524 0.9408000 ) 5 Si tau( 5) = ( 0.2500000 0.4503332 0.9408000 ) 6 Si tau( 6) = ( 0.5150000 0.0086603 0.3136000 ) 7 Si tau( 7) = ( 0.7350000 0.4416730 0.3136000 ) 8 Si tau( 8) = ( 0.2500000 0.4156922 0.3136000 ) 9 Si tau( 9) = ( 0.0000000 0.5773503 0.6272000 ) 10 Si tau( 10) = ( 0.5000000 0.2886751 0.0000000 ) 11 Si tau( 11) = ( 0.5000000 0.2886751 0.6272000 ) 12 Si tau( 12) = ( 0.0000000 0.5773503 0.0000000 ) I cannot find any error in the setup. So why there is a warning about the symmetry operation? Does it serious problem? Thanks Xiangang Wan Department of Physics Nanjing University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110817/c1e53d21/attachment.htm From degironc at sissa.it Wed Aug 17 09:21:21 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 17 Aug 2011 09:21:21 +0200 Subject: [Pw_forum] warning for 176 P63/m structure In-Reply-To: References: Message-ID: <4E4B6BF1.2020400@sissa.it> Dear Xiangang Wan, there is a section in the manual and a few thousand posts in the mailing list archive explaining this issue. best, Stefano de Gironcoli - SISSA and DEMOCRITOS thereOn 08/17/2011 08:23 AM, Lo_wan_2005XW wrote: > Dear all, > > I am studying a compound with P63/m structure. > > But the program complain: > > warning: symmetry operation # 2 not allowed. fractional translation: > 0.0000000 0.0000000 0.5000000 in crystal coordinates > warning: symmetry operation # 5 not allowed. fractional translation: > 0.0000000 0.0000000 0.5000000 in crystal coordinates > warning: symmetry operation # 6 not allowed. fractional translation: > 0.0000000 0.0000000 0.5000000 in crystal coordinates > warning: symmetry operation # 14 not allowed. fractional translation: > 0.0000000 0.0000000 0.5000000 in crystal coordinates > warning: symmetry operation # 17 not allowed. fractional translation: > 0.0000000 0.0000000 0.5000000 in crystal coordinates > warning: symmetry operation # 18 not allowed. fractional translation: > 0.0000000 0.0000000 0.5000000 in crystal coordinates > > > Our compound has P63/m structure (176 space group). And following is the setup: > > -------------------------------------------- > &system > ibrav= 4, celldm(1) =10.726090, > celldm(3)=1.25440, nat= 12, ntyp= 2, ecutwfc =35.0,ecutrho=300 > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05 > / > &electrons > diagonalization='david' > mixing_beta = 0.7 > / > ATOMIC_SPECIES > La 138.9055 La.pbe-n-bpaw.UPF > Si 28.0855 Si.pbe-n-van.UPF > ATOMIC_POSITIONS crystal > La 0.00000000 0.00000000 0.50000000 > La 0.00000000 0.00000000 0.00000000 > Si 0.48000000 0.99000000 0.75000000 > Si 0.01000000 0.49000000 0.75000000 > Si 0.51000000 0.52000000 0.75000000 > Si 0.52000000 0.01000000 0.25000000 > Si 0.99000000 0.51000000 0.25000000 > Si 0.49000000 0.48000000 0.25000000 > Si 0.333333333 0.666666666 0.50000000 > Si 0.666666666 0.333333333 0.00000000 > Si 0.666666666 0.333333333 0.50000000 > Si 0.333333333 0.666666666 0.00000000 > K_POINTS automatic > 6 6 5 0 0 0 > -------------------------------------------- > > Following is "atomic positions are in cartesian coordinates" printed by the program > > site n. atom positions (alat units) > 1 La tau( 1) = ( 0.0000000 0.0000000 0.6272000 ) > 2 La tau( 2) = ( 0.0000000 0.0000000 0.0000000 ) > 3 Si tau( 3) = ( -0.0150000 0.8573651 0.9408000 ) > 4 Si tau( 4) = ( -0.2350000 0.4243524 0.9408000 ) > 5 Si tau( 5) = ( 0.2500000 0.4503332 0.9408000 ) > 6 Si tau( 6) = ( 0.5150000 0.0086603 0.3136000 ) > 7 Si tau( 7) = ( 0.7350000 0.4416730 0.3136000 ) > 8 Si tau( 8) = ( 0.2500000 0.4156922 0.3136000 ) > 9 Si tau( 9) = ( 0.0000000 0.5773503 0.6272000 ) > 10 Si tau( 10) = ( 0.5000000 0.2886751 0.0000000 ) > 11 Si tau( 11) = ( 0.5000000 0.2886751 0.6272000 ) > 12 Si tau( 12) = ( 0.0000000 0.5773503 0.0000000 ) > > > I cannot find any error in the setup. So why there is a warning about the symmetry operation? Does it serious problem? > > Thanks > > Xiangang Wan > Department of Physics > Nanjing University > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110817/21ef02c6/attachment-0001.htm From foursea at 163.com Wed Aug 17 10:29:35 2011 From: foursea at 163.com (lilonghua) Date: Wed, 17 Aug 2011 16:29:35 +0800 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 Message-ID: <201108171629232658520@163.com> Dear Layla, Sorry to reply so late. Although I have solve this problem by decreasing the character length (<79) of each line, I am glad to attach the input that cause the problem, if you are interest to this problem: &control calculation = 'scf' restart_mode='from_scratch', prefix='silicon', pseudo_dir = '$PSEUDO_DIR/', outdir='./tmp' / &system ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, ecutwfc =12.0, nbnd = 8, input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, exxdiv_treatment='g-b' ! gygi-baldereschi, yukawa, erfc_simple, vcut_ws, vcut_spheric, none ecutvcut=0.7 x_gamma_extrapolation = .true. / &electrons mixing_beta = 0.7 / ATOMIC_SPECIES Si 28.086 Si.pz-vbc.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 K_POINTS 10 0.1250000 0.1250000 0.1250000 1.00 0.1250000 0.1250000 0.3750000 3.00 0.1250000 0.1250000 0.6250000 3.00 0.1250000 0.1250000 0.8750000 3.00 0.1250000 0.3750000 0.3750000 3.00 0.1250000 0.3750000 0.6250000 6.00 0.1250000 0.3750000 0.8750000 6.00 0.1250000 0.6250000 0.6250000 3.00 0.3750000 0.3750000 0.3750000 1.00 0.3750000 0.3750000 0.6250000 3.00 Best regards, Longhua Li 2011-08-17 foursea at 163.com ---------------------------------------- From lmartinsamos at gmail.com Wed Aug 17 10:57:13 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Wed, 17 Aug 2011 10:57:13 +0200 Subject: [Pw_forum] QE v4.3.2 failed to read the input file of v4.3 In-Reply-To: <201108171629232658520@163.com> References: <201108171629232658520@163.com> Message-ID: Thank you very much! Lilonghua! I think that the problem is related with the "home-made and too simple" parser that we now use for dumping the input file! I'll work on improving it! thank you very much for reporting bugs! and helping us improving ESPRESSO. Layla 2011/8/17 lilonghua > Dear Layla, > > Sorry to reply so late. Although I have solve this problem by decreasing > the character length (<79) of each line, I am glad to attach the input that > cause the problem, if you are interest to this problem: > > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='silicon', > pseudo_dir = '$PSEUDO_DIR/', > outdir='./tmp' > > / > &system > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, > ecutwfc =12.0, nbnd = 8, > input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, > exxdiv_treatment='g-b' ! gygi-baldereschi, > yukawa, erfc_simple, vcut_ws, vcut_spheric, none > ecutvcut=0.7 > x_gamma_extrapolation = .true. > / > &electrons > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Si 28.086 Si.pz-vbc.UPF > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.25 0.25 0.25 > K_POINTS > 10 > 0.1250000 0.1250000 0.1250000 1.00 > 0.1250000 0.1250000 0.3750000 3.00 > 0.1250000 0.1250000 0.6250000 3.00 > 0.1250000 0.1250000 0.8750000 3.00 > 0.1250000 0.3750000 0.3750000 3.00 > 0.1250000 0.3750000 0.6250000 6.00 > 0.1250000 0.3750000 0.8750000 6.00 > 0.1250000 0.6250000 0.6250000 3.00 > 0.3750000 0.3750000 0.3750000 1.00 > 0.3750000 0.3750000 0.6250000 3.00 > > > > Best regards, > Longhua Li > 2011-08-17 > foursea at 163.com > ---------------------------------------- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110817/7ee83d51/attachment.htm From nicola.marzari at materials.ox.ac.uk Wed Aug 17 12:41:04 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Wed, 17 Aug 2011 11:41:04 +0100 Subject: [Pw_forum] Thermal conductivity and Gruneisen parameters In-Reply-To: References: Message-ID: <4E4B9AC0.7060601@materials.ox.ac.uk> Dear Payam, for Gruneisen parameters see http://www.sissa.it/cm/thesis/1991/pavone.ps.gz and Phys. Rev. B 71, 205214 (2005) for thermal transport you need phonon lifetimes - see http://www.sissa.it/cm/thesis/1995/debernardi.ps.gz and PRL 106, 045901 (2011) nicola On 8/16/11 8:44 PM, Payam Norouzzadeh wrote: > Dear QE users > > I'm wondering if anybody knows how to calculate thermal conductivity and > also Gruneisen parameters by QE. > I haven't seen any example file or document about above mentioned > quantities. > Does anybody know a good document about them? > > Best regards,Payam Norouzzadeh -- ---------------------------------------------------------------------- Prof Nicola Marzari Department of Materials University of Oxford Chair of Materials Modelling Director, Materials Modelling Laboratory nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM From mashiatalaaii at gmail.com Wed Aug 17 15:31:11 2011 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Wed, 17 Aug 2011 09:31:11 -0400 Subject: [Pw_forum] experimental Dit values versus DFT values Message-ID: Dear All, This is my second email and I highly appreciate your help in this regard. I am working on Si/SiO2 system, at the moment. 1. I was wondering whether the sum of all LDOS calculated from projected wavefunction on the Si at the interface can give me the density of interface states. The question is whether the sum of LDOS of projected wavefunction on the inter-facial atoms is equivalent to planar local density of state at the interface. 2. If positive, the sum of LDOS of all projected wavefunction on all atoms at the interface divided by the surface of the interface is by far higher than the Dit reported from experiment. Actually, I am thinking, no matter how big the structure is, the Dit is still very high. I was wondering whether I miss any point to consider for calculation. I really really appreciate your help. Have a great summer. M Alaaii -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110817/97d3c804/attachment.htm From ttduyle at gmail.com Wed Aug 17 16:00:42 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 17 Aug 2011 10:00:42 -0400 Subject: [Pw_forum] experimental Dit values versus DFT values In-Reply-To: References: Message-ID: I wonder 1. how do you define a Dit? 2. how does the definition compare to the LDOS of atoms at the interface? -------------------------------------------------- Duy Le PhD Candidate Department of Physics University of Central Florida. "Men don't need hand to do things" On Wed, Aug 17, 2011 at 9:31 AM, mashiat alaaii wrote: > Dear All, > This is my second email and I highly appreciate your help in this regard. > I am working on Si/SiO2 system, at the moment. > > ? 1. I was wondering whether the sum of all LDOS calculated from projected > ? wavefunction on the Si at the interface can give me the density of > interface > ? states. The question is whether the sum of LDOS of projected wavefunction > on > ? the inter-facial atoms is equivalent to planar local density of state at > the > ? interface. > ? 2. If positive, the sum of LDOS of all projected wavefunction on all > ? atoms at the interface divided by the surface of the interface is by far > ? higher than the Dit reported from experiment. Actually, I am thinking, no > ? matter how big the structure is, the Dit is still very high. I was > wondering > ? whether I miss any point to consider for calculation. > > I really really appreciate your help. > Have a great summer. > M Alaaii > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From gabriele.sclauzero at epfl.ch Wed Aug 17 16:05:47 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Wed, 17 Aug 2011 16:05:47 +0200 Subject: [Pw_forum] experimental Dit values versus DFT values In-Reply-To: References: Message-ID: Dear Mashiat Alaaii, Il giorno 17/ago/2011, alle ore 15.31, mashiat alaaii ha scritto: > Dear All, > This is my second email and I highly appreciate your help in this regard. Before posting again, please take your time to read: http://www.quantum-espresso.org/wiki/index.php/Pw_users especially second and second-last points in the list. > I am working on Si/SiO2 system, at the moment. > > 1. I was wondering whether the sum of all LDOS calculated from projected > wavefunction on the Si at the interface can give me the density of interface > states. Your terminology is not clear to me, or maybe non-standard. Are you speaking about projected-density of states (PDOS) or local density of states (LDOS)? To my knowledge they are different objects: the first can be computed by projwfc.x, the second by pp.x, both codes included in the post-processing utilities of QE. > The question is whether the sum of LDOS of projected wavefunction on > the inter-facial atoms is equivalent to planar local density of state at the > interface. It's not clear to me what you want to compare, but if they are quantities that you can get from the PP codes, why don't you give a try and let us know? I guess you should compare PDOS integrated up to E_F (and summed over interface atoms) with ILDOS (again up to E_F) integrated over the volume an appropriate interface slab. > 2. If positive, the sum of LDOS of all projected wavefunction on all > atoms at the interface divided by the surface of the interface is by far > higher than the Dit reported from experiment. So you did some calculation. Could you please specify what you have computed and how? > Actually, I am thinking, no > matter how big the structure is, the Dit is still very high. This is very obscure to me. You said that you divided by the surface area... Regards, GS > I was wondering > whether I miss any point to consider for calculation. > > I really really appreciate your help. > Have a great summer. > M Alaaii _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110817/37654e41/attachment-0001.htm From mashiatalaaii at gmail.com Wed Aug 17 16:47:43 2011 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Wed, 17 Aug 2011 10:47:43 -0400 Subject: [Pw_forum] Pw_forum Digest, Vol 50, Issue 43 In-Reply-To: References: Message-ID: Dear Gabriel, Thank you very much for your reply. The problem is: calculating interface states with DFT. The structure is: Si/SiO2 with vacuum in z direction. First I found 3-D DOS and then I tried to get those states on planes parallel to interface. My question is: whether The sum of PDOS on the atoms at the interface presents the planar density of state at the interface. If negative, is there any way to calculate DIt? The dimension of "density of interface state (Dit)" is given by states per cm^2 per eV. Therefore, I divided the sum of PDOS of the interface atoms by the surface area of the cell that I made. However, since the surface is small, the results is 2-3 order of magnitude higher than the experimental results. Even for 3D-DOS, the DOS per eV per volume is very high, because no matter how big the structure is (the structure made for DFT), the volume is still very small; dividing to volume (or surface area, in the case of Dit) results in a very high value. I was wondering whether I am making a mistake or I miss a point in calculating DOS per volume per eV (Dit per surface area per eV). I am really thankful of any king of help and suggestion. Yours M Alaaii On Wed, Aug 17, 2011 at 10:05 AM, wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/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: QE v4.3.2 failed to read the input file of v4.3 (lilonghua) > 2. Re: QE v4.3.2 failed to read the input file of v4.3 > (Layla Martin-Samos) > 3. Re: Thermal conductivity and Gruneisen parameters (Nicola Marzari) > 4. experimental Dit values versus DFT values (mashiat alaaii) > 5. Re: experimental Dit values versus DFT values (Duy Le) > 6. Re: experimental Dit values versus DFT values (Gabriele Sclauzero) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 17 Aug 2011 16:29:35 +0800 > From: "lilonghua" > Subject: Re: [Pw_forum] QE v4.3.2 failed to read the input file of > v4.3 > To: "pw_forum" > Message-ID: <201108171629232658520 at 163.com> > Content-Type: text/plain; charset="us-ascii" > > Dear Layla, > > Sorry to reply so late. Although I have solve this problem by decreasing > the character length (<79) of each line, I am glad to attach the input that > cause the problem, if you are interest to this problem: > > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='silicon', > pseudo_dir = '$PSEUDO_DIR/', > outdir='./tmp' > > / > &system > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, > ecutwfc =12.0, nbnd = 8, > input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, > exxdiv_treatment='g-b' ! gygi-baldereschi, > yukawa, erfc_simple, vcut_ws, vcut_spheric, none > ecutvcut=0.7 > x_gamma_extrapolation = .true. > / > &electrons > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Si 28.086 Si.pz-vbc.UPF > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.25 0.25 0.25 > K_POINTS > 10 > 0.1250000 0.1250000 0.1250000 1.00 > 0.1250000 0.1250000 0.3750000 3.00 > 0.1250000 0.1250000 0.6250000 3.00 > 0.1250000 0.1250000 0.8750000 3.00 > 0.1250000 0.3750000 0.3750000 3.00 > 0.1250000 0.3750000 0.6250000 6.00 > 0.1250000 0.3750000 0.8750000 6.00 > 0.1250000 0.6250000 0.6250000 3.00 > 0.3750000 0.3750000 0.3750000 1.00 > 0.3750000 0.3750000 0.6250000 3.00 > > > > Best regards, > Longhua Li > 2011-08-17 > foursea at 163.com > ---------------------------------------- > > > > > ------------------------------ > > Message: 2 > Date: Wed, 17 Aug 2011 10:57:13 +0200 > From: Layla Martin-Samos > Subject: Re: [Pw_forum] QE v4.3.2 failed to read the input file of > v4.3 > To: PWSCF Forum > Message-ID: > > > Content-Type: text/plain; charset="utf-8" > > Thank you very much! Lilonghua! I think that the problem is related with > the > "home-made and too simple" parser that we now use for dumping the input > file! > > I'll work on improving it! > > thank you very much for reporting bugs! and helping us improving ESPRESSO. > > Layla > > 2011/8/17 lilonghua > > > Dear Layla, > > > > Sorry to reply so late. Although I have solve this problem by decreasing > > the character length (<79) of each line, I am glad to attach the input > that > > cause the problem, if you are interest to this problem: > > > > &control > > calculation = 'scf' > > restart_mode='from_scratch', > > prefix='silicon', > > pseudo_dir = '$PSEUDO_DIR/', > > outdir='./tmp' > > > > / > > &system > > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, > > ecutwfc =12.0, nbnd = 8, > > input_dft='pbe0', nqx1 = 1, nqx2 = 1, nqx3 = 1, > > exxdiv_treatment='g-b' ! > gygi-baldereschi, > > yukawa, erfc_simple, vcut_ws, vcut_spheric, none > > ecutvcut=0.7 > > x_gamma_extrapolation = .true. > > / > > &electrons > > mixing_beta = 0.7 > > / > > ATOMIC_SPECIES > > Si 28.086 Si.pz-vbc.UPF > > ATOMIC_POSITIONS > > Si 0.00 0.00 0.00 > > Si 0.25 0.25 0.25 > > K_POINTS > > 10 > > 0.1250000 0.1250000 0.1250000 1.00 > > 0.1250000 0.1250000 0.3750000 3.00 > > 0.1250000 0.1250000 0.6250000 3.00 > > 0.1250000 0.1250000 0.8750000 3.00 > > 0.1250000 0.3750000 0.3750000 3.00 > > 0.1250000 0.3750000 0.6250000 6.00 > > 0.1250000 0.3750000 0.8750000 6.00 > > 0.1250000 0.6250000 0.6250000 3.00 > > 0.3750000 0.3750000 0.3750000 1.00 > > 0.3750000 0.3750000 0.6250000 3.00 > > > > > > > > Best regards, > > Longhua Li > > 2011-08-17 > > foursea at 163.com > > ---------------------------------------- > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110817/7ee83d51/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Wed, 17 Aug 2011 11:41:04 +0100 > From: Nicola Marzari > Subject: Re: [Pw_forum] Thermal conductivity and Gruneisen parameters > To: PWSCF Forum > Cc: Payam Norouzzadeh > Message-ID: <4E4B9AC0.7060601 at materials.ox.ac.uk> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > Dear Payam, > > > for Gruneisen parameters see > http://www.sissa.it/cm/thesis/1991/pavone.ps.gz > and Phys. Rev. B 71, 205214 (2005) > > for thermal transport you need phonon lifetimes - see > http://www.sissa.it/cm/thesis/1995/debernardi.ps.gz > and PRL 106, 045901 (2011) > > > nicola > > > > On 8/16/11 8:44 PM, Payam Norouzzadeh wrote: > > Dear QE users > > > > I'm wondering if anybody knows how to calculate thermal conductivity and > > also Gruneisen parameters by QE. > > I haven't seen any example file or document about above mentioned > > quantities. > > Does anybody know a good document about them? > > > > Best regards,Payam Norouzzadeh > > > -- > ---------------------------------------------------------------------- > Prof Nicola Marzari Department of Materials University of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > > > ------------------------------ > > Message: 4 > Date: Wed, 17 Aug 2011 09:31:11 -0400 > From: mashiat alaaii > Subject: [Pw_forum] experimental Dit values versus DFT values > To: pw_forum at pwscf.org > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > This is my second email and I highly appreciate your help in this regard. > I am working on Si/SiO2 system, at the moment. > > 1. I was wondering whether the sum of all LDOS calculated from projected > wavefunction on the Si at the interface can give me the density of > interface > states. The question is whether the sum of LDOS of projected wavefunction > on > the inter-facial atoms is equivalent to planar local density of state at > the > interface. > 2. If positive, the sum of LDOS of all projected wavefunction on all > atoms at the interface divided by the surface of the interface is by far > higher than the Dit reported from experiment. Actually, I am thinking, no > matter how big the structure is, the Dit is still very high. I was > wondering > whether I miss any point to consider for calculation. > > I really really appreciate your help. > Have a great summer. > M Alaaii > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110817/97d3c804/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Wed, 17 Aug 2011 10:00:42 -0400 > From: Duy Le > Subject: Re: [Pw_forum] experimental Dit values versus DFT values > To: PWSCF Forum > Message-ID: > > > Content-Type: text/plain; charset=ISO-8859-1 > > I wonder > 1. how do you define a Dit? > 2. how does the definition compare to the LDOS of atoms at the interface? > -------------------------------------------------- > Duy Le > PhD Candidate > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > > On Wed, Aug 17, 2011 at 9:31 AM, mashiat alaaii > wrote: > > Dear All, > > This is my second email and I highly appreciate your help in this regard. > > I am working on Si/SiO2 system, at the moment. > > > > ? 1. I was wondering whether the sum of all LDOS calculated from > projected > > ? wavefunction on the Si at the interface can give me the density of > > interface > > ? states. The question is whether the sum of LDOS of projected > wavefunction > > on > > ? the inter-facial atoms is equivalent to planar local density of state > at > > the > > ? interface. > > ? 2. If positive, the sum of LDOS of all projected wavefunction on all > > ? atoms at the interface divided by the surface of the interface is by > far > > ? higher than the Dit reported from experiment. Actually, I am thinking, > no > > ? matter how big the structure is, the Dit is still very high. I was > > wondering > > ? whether I miss any point to consider for calculation. > > > > I really really appreciate your help. > > Have a great summer. > > M Alaaii > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > ------------------------------ > > Message: 6 > Date: Wed, 17 Aug 2011 16:05:47 +0200 > From: Gabriele Sclauzero > Subject: Re: [Pw_forum] experimental Dit values versus DFT values > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > Dear Mashiat Alaaii, > > Il giorno 17/ago/2011, alle ore 15.31, mashiat alaaii ha scritto: > > > Dear All, > > This is my second email and I highly appreciate your help in this regard. > > Before posting again, please take your time to read: > > http://www.quantum-espresso.org/wiki/index.php/Pw_users > > especially second and second-last points in the list. > > > I am working on Si/SiO2 system, at the moment. > > > > 1. I was wondering whether the sum of all LDOS calculated from > projected > > wavefunction on the Si at the interface can give me the density of > interface > > states. > > Your terminology is not clear to me, or maybe non-standard. > Are you speaking about projected-density of states (PDOS) or local density > of states (LDOS)? > To my knowledge they are different objects: the first can be computed by > projwfc.x, the second by pp.x, both codes included in the post-processing > utilities of QE. > > > The question is whether the sum of LDOS of projected wavefunction on > > the inter-facial atoms is equivalent to planar local density of state > at the > > interface. > > It's not clear to me what you want to compare, but if they are quantities > that you can get from the PP codes, why don't you give a try and let us > know? > I guess you should compare PDOS integrated up to E_F (and summed over > interface atoms) with ILDOS (again up to E_F) integrated over the volume an > appropriate interface slab. > > > 2. If positive, the sum of LDOS of all projected wavefunction on all > > atoms at the interface divided by the surface of the interface is by > far > > higher than the Dit reported from experiment. > > So you did some calculation. Could you please specify what you have > computed and how? > > > Actually, I am thinking, no > > matter how big the structure is, the Dit is still very high. > > This is very obscure to me. You said that you divided by the surface > area... > > > Regards, > > GS > > > I was wondering > > whether I miss any point to consider for calculation. > > > > I really really appreciate your help. > > Have a great summer. > > M Alaaii _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110817/37654e41/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 50, Issue 43 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110817/56a82d62/attachment-0001.htm From hannu.komsa at epfl.ch Wed Aug 17 17:29:22 2011 From: hannu.komsa at epfl.ch (hannu.komsa at epfl.ch) Date: Wed, 17 Aug 2011 17:29:22 +0200 Subject: [Pw_forum] experimental Dit values versus DFT values In-Reply-To: References: Message-ID: <20110817172922.10655bj8jjfca7v6@webmail.epfl.ch> Hello Dit is the number of trapped charges at the interface divided by energy. See for example: http://dx.doi.org/10.1016/S0038-1101(00)00119-2 You need to have electron/hole traps at the interface in order to have non-zero Dit and I guess it only makes sense to look at this within the band gap. It is not the density of interface states per se that originate just from the disruption of the bulk periodicity. The latter can be traps or they can be resonant with the bulk states or whatnot. Anyway, what you should do is to look at the DOS only within the band gap. If you have traps at band gap energies also within the bulk regions, then perhaps local DOS for some region near the interface can be sufficient. If this is indeed what you already did, then perhaps your model needs improvement. It should be possible to construct Si/SiO2 interface model without any trap/gap states, I think. Regards, Hannu-Pekka Komsa EPFL > 1. I was wondering whether the sum of all LDOS calculated from projected > wavefunction on the Si at the interface can give me the density of > interface > states. The question is whether the sum of LDOS of projected wavefunction > on > the inter-facial atoms is equivalent to planar local density of state at > the > interface. > 2. If positive, the sum of LDOS of all projected wavefunction on all > atoms at the interface divided by the surface of the interface is by far > higher than the Dit reported from experiment. Actually, I am thinking, no > matter how big the structure is, the Dit is still very high. I was > wondering > whether I miss any point to consider for calculation. From vovi47 at yahoo.com Wed Aug 17 22:17:32 2011 From: vovi47 at yahoo.com (Vi Vo) Date: Wed, 17 Aug 2011 13:17:32 -0700 (PDT) Subject: [Pw_forum] Ce pseudo potential Message-ID: <1313612252.62872.YahooMailNeo@web114504.mail.gq1.yahoo.com> Dear Stefano, I am sorry to email you on PWSCF forum, since I do not know where to contact you. I found on PWSCF forum the discussioon on Ce PP: http://www.democritos.it/pipermail/pw_forum/2009-March/012235.html Following that discussion, I downloaded the Ce PP and planned to test and use it. I also searched and read 3 papers: PRB 71, 041102(R) (2005) PRB? 72, 237102 (2005) JCP 132, 054110 (2010) which are related to the calculation of Cerium Oxides.? I have a question and appreciate if you could help me to clarify it.? Is the Ce PP on the link (www.democritos.it/~fabris/Ce4_ps_f1d1-pbe-rc1.0.uspp.UPF) the one modified as mentioned in the paper PRB 72, 237102 (2005), or it is the one used in the paper PRB 71, 041102(R) (2005). (I see in the PP the NLCC is .true., but I am not sure). Thank you very much, Vi University of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110817/edcdf852/attachment.htm From abmus007 at gmail.com Thu Aug 18 08:12:22 2011 From: abmus007 at gmail.com (Abolore Musari) Date: Thu, 18 Aug 2011 06:42:22 +0030 Subject: [Pw_forum] Smearing the occupations or not? Message-ID: Dear all, pls just want to calculate the band structure of a compound, but l dont know if its a metal, insulator, semiconductor or semi metal so l want to ask if l can use smearing for occupations in the &system card? in other word l am asking that how do we know when to use smearing for the accupations or tetrahedra or others. thanks for your usual assistance. Musari A.A. UNAAB Nigeria From abmus007 at gmail.com Thu Aug 18 08:18:22 2011 From: abmus007 at gmail.com (Abolore Musari) Date: Thu, 18 Aug 2011 06:48:22 +0030 Subject: [Pw_forum] Smearing the occupations or not? Message-ID: Dear all, pls just want to calculate the band structure of a compound, but l dont know if its a metal, insulator, semiconductor or semi metal so l want to ask if l can use smearing for occupations in the &system card? in other word l am asking that how do we know when to use smearing for the accupations or tetrahedra or others. thanks for your usual assistance. Musari A A. UNAAB Nigeria From zafartariq2003 at yahoo.com Thu Aug 18 08:49:54 2011 From: zafartariq2003 at yahoo.com (zafar rasheed) Date: Wed, 17 Aug 2011 23:49:54 -0700 (PDT) Subject: [Pw_forum] problem in electronic structure of ZnO Message-ID: <1313650194.40352.YahooMailClassic@web65404.mail.ac4.yahoo.com> Dear Eyvaz Isaaev ? ??? I want to calculate electronic band structure of w-ZnO (1x1x2 super cell). But output band strcuture is overlaped. Whereas the band structure of w-ZnO unit cell is same as theoretical and experimental. I make this supercell using PHON code. Due to increase in cell along z-axis? I increase its lattice parameter c 2 times in inputs (celldm=2*c/a). The inputs are attcahed below. &control Title = 'ZnO , hcp,a=3.2500,c=5.206 ,c/a=1.6103125', calculation ='scf' restart_mode='from_scratch', pseudo_dir = '/root/Pwscf/pseudo/', outdir ='/root/Pwscf/scratch/' prefix ='ZnO' tstress = .false. tprnfor = .false. / &system ibrav= 4, celldm(1) = 6.132075472, celldm(3) = 1.601846154, nat =4, ntyp =2, ecutwfc =25.0, ecutrho =300.0 occupations ='smearing', smearing='methefessel_paxton', degauss = 0.02, / &electrons diagonalization='cg' , conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Zn 65.409 Zn.pz-van_ak.UPF O 15.9994 O.pz-van_ak.UPF ATOMIC_POSITIONS (crystal) Zn 0.333333333 0.666666667 0.0000000 O 0.333333333 0.666666667 0.3817000 Zn 0.666666667 0.333333333 0.5000000 O 0.666666667 0.333333333 0.8817000 K_POINTS (automatic) 7 7 7? 0 0 0 This plot (after changing scf to nscf) is same as experimental and theoretical BUT when I make a cell of 8 atoms (1x1x2 supercell) input is as below &control calculation ='nscf' <= or bands restart_mode='from_scratch', pseudo_dir = '/root/Pwscf/pseudo/', outdir ='/root/Pwscf/scratch/' prefix ='ZnO' tstress = .false. tprnfor = .true. / &system ibrav = 4, celldm(1) = 6.132075472, celldm(3) = 3.203692308, (due to increase in size along Z-direction C= 2*c ) nat = 8, ntyp = 2, ecutwfc = 25.0, ecutrho = 300.0 occupations ='smearing', smearing ='methefessel_paxton', degauss =0.02?nbnd=20?nosym=.true. / &electrons diagonalization='cg' ,mixing_mode='plain', conv_thr = 1.0e-8 mixing_beta = 0.7 / ATOMIC_SPECIES Zn 65.38 Zn.pz-van_ak.UPF O 16.00 O.pz-van_ak.UPF ATOMIC_POSITIONS (crystal) Zn 0.333333333 0.666666667 0.000000000 Zn 0.333333333 0.666666667 0.500000000 Zn 0.666666667 0.333333333 0.250000000 Zn 0.666666667 0.333333333 0.750000000 O 0.333333333 0.666666667 0.190850000 O 0.333333333 0.666666667 0.690850000 O 0.666666667 0.333333333 0.440850000 O 0.666666667 0.333333333 0.940850000 K_POINTS 32 ?? 0.0?? 0.0? 0.5? 1 ?? 0.1? -0.1? 0.1? 2 ?? 0.2? -0.2? 0.2? 3 ?? 0.3? -0.3? 0.3? 4 ?? 0.4? -0.4? 0.4? 5 ?? 0.5? -0.5? 0.5? 6 ?? 0.5? -0.5? 0.4? 7 ?? 0.5? -0.5? 0.3? 8 ?? 0.5? -0.5? 0.2? 9 ?? 0.5? -0.5? 0.1? 10 ?? 0.5? -0.5? 0.0? 11 ?? 0.4? -0.4? 0.0? 12 ?? 0.3? -0.3? 0.0? 13 ?? 0.2? -0.2? 0.0? 14 ?? 0.1? -0.1? 0.0? 15 ?? 0.0?? 0.0? 0.0? 16 ?? 0.0?? 0.0? 0.1? 17 ?? 0.0?? 0.0? 0.2? 18 ?? 0.0?? 0.0? 0.3? 19 ?? 0.0?? 0.0? 0.4? 20 ?? 0.0?? 0.0? 0.5? 21 ?? 0.11? 0.11? 0.5 22 ?? 0.22? 0.22? 0.5 23 ?? 0.33? 0.33? 0.5 24 ?? 0.33? 0.33? 0.4 25 ?? 0.33? 0.33? 0.3 26 ?? 0.33? 0.33? 0.2 27 ?? 0.33? 0.33? 0.1 28 ?? 0.33? 0.33? 0.0 29 ?? 0.22? 0.22? 0.0 30 ?? 0.11? 0.11? 0.0 31 ?? 0.00? 0.00? 0.0 32 After changing scf to bands the electronic structure is metallic (no band gap) and a I get different electronic structure . Now please guide me how I can get true electronic structure. Thanking in Advance Muhammad Zafar PhD Scholar Department of Physics The Islamia University of Bahawalpur,Pakistan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110817/850e4c21/attachment-0001.htm From Ari.P.Seitsonen at iki.fi Thu Aug 18 11:40:10 2011 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Thu, 18 Aug 2011 11:40:10 +0200 (CEST) Subject: [Pw_forum] Smearing the occupations or not? In-Reply-To: References: Message-ID: Dear Musari, (or how do you want to be called?) The safest is to start with broadening, calculate the band structure, and reduce the broadening: If the system remains a metal or semi-metal (ie the occupation numbers are not integers), the system is most likely such (at least at the level of DFT or DFT-HF that you have used for the exchange-correlation). Of course there are dangers that your material is strongly-correlated etc (LDA/GGA+U or hybrid functionals might help). In general the GW calculation should be closer to the experiments, if the system decides to be semi-conducting or insulating. Hopefully this helps you a bit. Greetings from Sunny Zurich, apsi -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Physikalisch-Chemisches Institut der Universitaet Zuerich Tel: +41 44 63 54 497 / Mobile: +41 79 71 90 935 On Thu, 18 Aug 2011, Abolore Musari wrote: > Dear all, pls just want to calculate the band structure of a compound, > but l dont know if its a metal, insulator, semiconductor or semi metal > so l want to ask if l can use smearing for occupations in the &system > card? in other word l am asking that how do we know when to use > smearing for the accupations or tetrahedra or others. thanks for your > usual assistance. Musari A A. UNAAB Nigeria > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From vovi47 at yahoo.com Thu Aug 18 17:12:11 2011 From: vovi47 at yahoo.com (Vi Vo) Date: Thu, 18 Aug 2011 08:12:11 -0700 (PDT) Subject: [Pw_forum] How to nscf with LDA+U Message-ID: <1313680331.77508.YahooMailNeo@web114513.mail.gq1.yahoo.com> Dear All, I am doing a test calculation for Ce3Te4, with LDA+U.? I finished the scf run with k-points grid of 9x9x9.? If I would like to run nscf calculation with higher kpt grid, I don't know if there is a special way to do it for LDA+U, or I can just run the nscf as normally done for plain DFT (LDA, PBE,...).? Thank you very much, Vi University of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110818/c2186039/attachment.htm From matteo at umn.edu Thu Aug 18 17:19:27 2011 From: matteo at umn.edu (Matteo Cococcioni) Date: Thu, 18 Aug 2011 10:19:27 -0500 Subject: [Pw_forum] How to nscf with LDA+U In-Reply-To: <1313680331.77508.YahooMailNeo@web114513.mail.gq1.yahoo.com> References: <1313680331.77508.YahooMailNeo@web114513.mail.gq1.yahoo.com> Message-ID: Dear Vi, just try. it should work as for "plain" DFT. Matteo On Thu, Aug 18, 2011 at 10:12 AM, Vi Vo wrote: > Dear All, > > I am doing a test calculation for Ce3Te4, with LDA+U. I finished the scf > run with k-points grid of 9x9x9. If I would like to run nscf calculation > with higher kpt grid, I don't know if there is a special way to do it for > LDA+U, or I can just run the nscf as normally done for plain DFT (LDA, > PBE,...). > > Thank you very much, > > Vi > University of Houston > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110818/4e99d6dd/attachment.htm From CJH085 at bham.ac.uk Thu Aug 18 20:56:47 2011 From: CJH085 at bham.ac.uk (Christopher Heard) Date: Thu, 18 Aug 2011 19:56:47 +0100 Subject: [Pw_forum] Slab relaxation with constrained atoms Message-ID: <4406F1904F879A4D9FE86E310EA66341021378C800A1@mbx5.adf.bham.ac.uk> Dear all, I am trying to perform a slab relaxation calculation, where the geometry of most of the layers is constrained, but the top few are free to rearrange. I intend to then do some work with an adsorbate (also free to relax). Unfortunately, I can't seem to figure out how to constrain the positions of some atoms and not others, in a relaxation calculation. I've trawled the forum and the user guide and the INPUT documentation, so this is my last option. I see one person asked exactly the same question, but there was no reply in the forum archive! I'm sure it's very simple, but thanks to whomever can help, Regards, Chris --------------------------------------------------------------------------- Chris Heard, PhD student, University of Birmingham, UK --------------------------------------------------------------------------- From ismotochi at gmail.com Thu Aug 18 22:40:21 2011 From: ismotochi at gmail.com (isaac motochi) Date: Thu, 18 Aug 2011 23:40:21 +0300 Subject: [Pw_forum] Slab relaxation with constrained atoms In-Reply-To: <4406F1904F879A4D9FE86E310EA66341021378C800A1@mbx5.adf.bham.ac.uk> References: <4406F1904F879A4D9FE86E310EA66341021378C800A1@mbx5.adf.bham.ac.uk> Message-ID: Those that you want constrained, put 0 0 0 after them while those you want to relax, put 1 1 1. Isaac Motochi University of Witwatersrand From CJH085 at bham.ac.uk Thu Aug 18 23:00:12 2011 From: CJH085 at bham.ac.uk (Christopher Heard) Date: Thu, 18 Aug 2011 22:00:12 +0100 Subject: [Pw_forum] Slab relaxation with constrained atoms In-Reply-To: References: <4406F1904F879A4D9FE86E310EA66341021378C800A1@mbx5.adf.bham.ac.uk>, Message-ID: <4406F1904F879A4D9FE86E310EA66341021378C800A2@mbx5.adf.bham.ac.uk> Thank you, just to clarify, do you need to specify any constraint keywords somewhere along with it? Or simply the usual relax input file, just with 1 1 1 or 0 0 0 after the coordinate lines? Thanks again, Chris ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of isaac motochi [ismotochi at gmail.com] Sent: 18 August 2011 15:40 To: PWSCF Forum Subject: Re: [Pw_forum] Slab relaxation with constrained atoms Those that you want constrained, put 0 0 0 after them while those you want to relax, put 1 1 1. Isaac Motochi University of Witwatersrand _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From ismotochi at gmail.com Thu Aug 18 23:33:20 2011 From: ismotochi at gmail.com (isaac motochi) Date: Fri, 19 Aug 2011 00:33:20 +0300 Subject: [Pw_forum] Slab relaxation with constrained atoms In-Reply-To: <4406F1904F879A4D9FE86E310EA66341021378C800A2@mbx5.adf.bham.ac.uk> References: <4406F1904F879A4D9FE86E310EA66341021378C800A1@mbx5.adf.bham.ac.uk> <4406F1904F879A4D9FE86E310EA66341021378C800A2@mbx5.adf.bham.ac.uk> Message-ID: You have calculation='relax' or 'vc-relax' whichever fits your work, check this in the document. then rest is yes to your ques, specify this after coordinate lines From vovi47 at yahoo.com Fri Aug 19 03:25:47 2011 From: vovi47 at yahoo.com (Vi Vo) Date: Thu, 18 Aug 2011 18:25:47 -0700 (PDT) Subject: [Pw_forum] LDA_U, species not in the list Message-ID: <1313717147.16020.YahooMailNeo@web114505.mail.gq1.yahoo.com> Dear All, I am doing LDA+U for a compound (YBCO),? which contains Y, Ba.? These 2 species are not in the list inset_hubbard_I.f90 and tabd.f90.? I added these 2 species in these subroutines.? However, when I run, I got the error: from offset_atom_wfc : error #???????? 2 ???? wrong offset I appreciate if you could let me know if I need to modify something else in other subroutines and what should I change?? Thank you very much, Vi University of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110818/1a671063/attachment.htm From matteo at umn.edu Fri Aug 19 05:09:41 2011 From: matteo at umn.edu (Matteo Cococcioni) Date: Thu, 18 Aug 2011 22:09:41 -0500 Subject: [Pw_forum] LDA_U, species not in the list In-Reply-To: <1313717147.16020.YahooMailNeo@web114505.mail.gq1.yahoo.com> References: <1313717147.16020.YahooMailNeo@web114505.mail.gq1.yahoo.com> Message-ID: Dear Vi, with this little information nobody can help you. please provide the lines you added in the two routines. also provide the name of the pseudopotential you used or specified the electronic configuration they were built on. maybe in set_hubbard_l you specified a value for l that the specific PP does not contain. or something like this. regards, Matteo On Thu, Aug 18, 2011 at 8:25 PM, Vi Vo wrote: > Dear All, > > I am doing LDA+U for a compound (YBCO), which contains Y, Ba. These 2 > species are not in the list in set_hubbard_I.f90 and tabd.f90. I added > these 2 species in these subroutines. However, when I run, I got the error: > from offset_atom_wfc : error # 2 > wrong offset > > I appreciate if you could let me know if I need to modify something else in > other subroutines and what should I change? > > Thank you very much, > > Vi > University of Houston > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110818/ab096305/attachment-0001.htm From elie.moujaes at hotmail.co.uk Fri Aug 19 17:12:52 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 19 Aug 2011 16:12:52 +0100 Subject: [Pw_forum] usage of recover=.true. Message-ID: Dear all, I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? Thanks Elie MoujaesUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110819/4572e0ad/attachment.htm From jlgr at super.unam.mx Sat Aug 20 03:05:52 2011 From: jlgr at super.unam.mx (Jose Luis Gordillo Ruiz) Date: Fri, 19 Aug 2011 20:05:52 -0500 (CDT) Subject: [Pw_forum] discrepancies in tests Message-ID: Hi, I'm installing QE in an opteron 285 computer. I'v tested Intel 11, Intel 12, Pathscale 3.2 and GNU 4.5 compilers, with internal BLAS and LAPACK, and I always got discrepancies in lda+U_force, lda+U_gamma, noncolin-constrain_total and relax2-bfgs_ndim3 and relax2. Additionally, intel and pathscale produce discrepancies in md-pot_extrap2. any suggestions? bests regards, Jose Luis Gordillo Supercomputo - UNAM From rameshchitumalla at gmail.com Sat Aug 20 08:56:32 2011 From: rameshchitumalla at gmail.com (Ramesh Kumar) Date: Sat, 20 Aug 2011 12:26:32 +0530 Subject: [Pw_forum] Serial algorithm Message-ID: Please somebody let me know about "Subspace diagonalization in iterative solution of the eigenvalue problem: a serial algorithm will be used" Thanks in advance -- *With Best Regards: * *CH. Ramesh Kumar, * *Research student, Computational Chemistry Lab, IICT-** ** Hyderabad. * * * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110820/eb0b0268/attachment.htm From siyouber at yahoo.fr Sat Aug 20 11:45:29 2011 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Sat, 20 Aug 2011 10:45:29 +0100 (BST) Subject: [Pw_forum] Re : Thermal conductivity and Gruneisen parameters In-Reply-To: Message-ID: <1313833529.11876.YahooMailClassic@web26507.mail.ukl.yahoo.com> Dear Payam, Thermal conductivity could be obtained through velocity autocorrelation function after running molecular dynamics (CP in QE).( See the book of Frenkel and Smith on page 90). Note that this requires additional postprocessing calculations. As for Gruneisen parameters, one could calculate the specific heat through QHA and the bulk modulus with PW, then use the relationship between them. (See the book of L. Anderson on equations of state, starting from page 6). Hope this helps. ****************************** Bertrand SITAMTZE YOUMBI, Ph D Laboratory of Material Sciences University of Yaound? I-Cameroon --- En date de?: Mar 16.8.11, Payam Norouzzadeh a ?crit?: De: Payam Norouzzadeh Objet: [Pw_forum] Thermal conductivity and Gruneisen parameters ?: pw_forum at pwscf.org Date: Mardi 16 ao?t 2011, 21h44 Dear QE users I'm wondering if anybody knows how to calculate thermal conductivity and also Gruneisen parameters by QE. I haven't seen any example file or document about above mentioned quantities. Does anybody know a good document about them? Best regards,Payam Norouzzadeh -----La pi?ce jointe associ?e suit----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110820/5e761151/attachment.htm From lo_wan_2005 at hotmail.com Sun Aug 21 03:36:33 2011 From: lo_wan_2005 at hotmail.com (Lo_wan_2005XW) Date: Sun, 21 Aug 2011 09:36:33 +0800 Subject: [Pw_forum] K-point in phonon calculation Message-ID: Dear developer and users: Exactly follow the userguide, I am trying to calculate the phonon. Firstly I make a self-consistent calculation with K_POINTS automatic 8 8 8 0 0 0 After the calculation convergent, I start the ph.x calculation. But the calculation is extremely slow, thus I goto the output-file, and find a strange thing. For some q-qoint, I find; number of k points= 1024 Marzari-Vanderbilt smearing, width (Ry)= 0.0500 I understand that phonon may break some symmetry, but how it can go to 1024-k-point when I use 8-8-8 mesh? I already use "start_q=X, last_q=X, recover=.true.," to separate q-point. I also use parallel to speed up the calculation. But it is still extremely slow. My system has only 12 atoms per unit cell, and it seems that some q-point (where it requires 1024 k-points) may need one month! I don't know if there is other method to speed up the calculation? Thanks! Xiangang Wan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110821/60662fe2/attachment.htm From baroni at sissa.it Sun Aug 21 09:23:24 2011 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 21 Aug 2011 09:23:24 +0200 Subject: [Pw_forum] Re : Thermal conductivity and Gruneisen parameters In-Reply-To: <1313833529.11876.YahooMailClassic@web26507.mail.ukl.yahoo.com> References: <1313833529.11876.YahooMailClassic@web26507.mail.ukl.yahoo.com> Message-ID: <3FE00567-F89C-4CFB-825B-0DAC4B718C7F@sissa.it> On Aug 20, 2011, at 11:45 AM, Bertrand SITAMTZE wrote: > Thermal conductivity could be obtained through velocity autocorrelation function > after running molecular dynamics (CP in QE).( See the book of Frenkel and Smith > on page 90). > I do not have Frenkel & Smith's book handy, but I would be surprised if it stated what you say. The calculation of the thermal conductivity through MD requires a proper definition of the energy current which is well known for classical systems (though it involves something more complicated than just velocities), but not yet available, to the best of my knowledge, in DFT. If I am wring, please correct me. > > > As for Gruneisen parameters, one could calculate the specific heat through QHA and the bulk modulus with PW, then use the relationship between them. (See the book of L. Anderson on equations of state, starting from page 6). > Here, I beg to differ as well. First, the calculation of the constant-volume specific heat does not involve any Gruneisen parameters (gamma). The constant-pressure specific heat (Cp) certainly does, but in the sense that you need them in the first place in order to calculate it. Second, It would seem rather innatural to calculate Cp just to estimate some of the parameters used to obtain it! In any case, the expression for Cp in terms of the gammas is an integral from which it would be impossible to obtain back their individual values. > All in all, before asking what QE (or any other code, for that matter) can or cannot do, one should stop for a while and ask oneself what are the most elementary pieces of information needed to compute what we are interested in, and only then ask if any specific code can compute those specific pieces of information. This may take some time, but it is much more instructive than hoping that computer codes can ever be a substitute for our own understanding. In the specific case of the thermal conductivity, one has the choice to follow the quasi-harmonic or the Kubo-Greenwood routes. Nicola Marzari has already given some hints on the former. Dr. Simatze's comments (and my present reply) apply to the latter. As for Gruneisen parameters, you just have just to inspect their definition (gamma = v/omega d (omega) / d (v)), and realize that any code able to compute vibrational frequencies can with little effort calculate them ... QE can calculate phonon frequencies, I will leave the final conclusion to you ... Hope this helps Stefano B --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110821/4462d6b1/attachment.htm From yccheng.nju at gmail.com Sun Aug 21 14:35:36 2011 From: yccheng.nju at gmail.com (=?UTF-8?B?56iL6L+O5pil?=) Date: Sun, 21 Aug 2011 15:35:36 +0300 Subject: [Pw_forum] K-point in phonon calculation In-Reply-To: References: Message-ID: ? 2011?8?21? ??4:36?Lo_wan_2005XW ??? > Dear developer and users: > > Exactly follow the userguide, I am trying to calculate the phonon. > > Firstly I make a self-consistent calculation with > > K_POINTS automatic > 8 8 8 0 0 0 > > After the calculation convergent, I start the ph.x calculation. But the calculation is extremely slow, thus I goto > the output-file, and find a strange thing. > > For some q-qoint, I find; > number of k points= 1024 Marzari-Vanderbilt smearing, width (Ry)= 0.0500 > > 8*8*8=512. If you set the spin polarized scf calculation, I think the number of total k points should multiply 2 again, so there are 1024 kpoints. > > I understand that phonon may break some symmetry, but how it can go to 1024-k-point when I use 8-8-8 mesh? > > I already use "start_q=X, last_q=X, recover=.true.," to separate q-point. I also use parallel to speed up the calculation. > But it is still extremely slow. My system has only 12 atoms per unit cell, and it seems that some q-point > (where it requires 1024 k-points) may need one month! > > I don't know if there is other method to speed up the calculation? > > 1,To make sure pwscf can find all symmetry operation in scf calculation. 2, To reduce the number of k points, ecut energy~ Hope it helps! > > Thanks! > > Xiangang Wan > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Y. C. Cheng Department of Physics Nanjing University Nanjing 210093 P. R. China Tel: 86-25-83592907 Email: yccheng.nju at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110821/37fa470b/attachment.htm From flux_ray12 at 163.com Mon Aug 22 04:36:13 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 22 Aug 2011 10:36:13 +0800 (CST) Subject: [Pw_forum] Can not find minimum free energy by QHA Message-ID: <10da8b04.97f4.131ef5866ac.Coremail.flux_ray12@163.com> Dear QE Developer and Users I am using DFPT+QHA to predict model's properties at high temperature. According to the paper,Ab initio lattice dynamics and phase transformations of ZrO2, Phy Rev B 71, 064301, free energyv.s. volume figure can be plotted at certain temperature for EOS-fitting and so on. Having determined the equlibrium lattice parameter, 8.18 a.u. , of TiC(FCC) by both EOS-fitting and vc-relax, I chose 20 different lattice paramters (7.98~8.38a.u.) and calculated phonon dispersion and thermodynamic properties. However, the free energy kept decreasing as a monotone decreasing function of lattice parameter, even when imaginary frequency began to occur at 8.88a.u.. My DFPT calculation script shows below: cat >TiC_${INT}.scf.in <TiC_${INT}.scf.out cat >TiC_${INT}.ph.in <TiC_${INT}.ph.out QHA is calculated by Prof. Isaev's code which released with QE package. Any suggestion will be welcome. Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/92810b29/attachment.htm From member at linkedin.com Mon Aug 22 05:21:54 2011 From: member at linkedin.com (Thaneshwor Kaloni via LinkedIn) Date: Mon, 22 Aug 2011 03:21:54 +0000 (UTC) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <5300854.6495883.1313983314517.JavaMail.app@ela4-bed84.prod> LinkedIn ------------ Thaneshwor Kaloni requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - Thaneshwor Accept invitation from Thaneshwor Kaloni http://www.linkedin.com/e/-iqpnjm-grmvqmaa-10/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I93340652_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pvczkSc3gPcPB9bSxckj4Ps6V7bPsPcjwNdz4TdPcLrCBxbOYWrSlI/EML_comm_afe/ View invitation from Thaneshwor Kaloni http://www.linkedin.com/e/-iqpnjm-grmvqmaa-10/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I93340652_60/0MdBYOdjoMd3cPekALqnpPbOYWrSlI/svi/ ------------------------------------------ Why might connecting with Thaneshwor Kaloni be a good idea? Have a question? Thaneshwor Kaloni's network will probably have an answer: You can use LinkedIn Answers to distribute your professional questions to Thaneshwor Kaloni and your extended network. You can get high-quality answers from experienced professionals. http://www.linkedin.com/e/-iqpnjm-grmvqmaa-10/ash/inv19_ayn/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/22b2b82b/attachment.htm From physics.skgupta at gmail.com Mon Aug 22 05:48:04 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Mon, 22 Aug 2011 09:18:04 +0530 Subject: [Pw_forum] Invitation to connect on LinkedIn In-Reply-To: <5300854.6495883.1313983314517.JavaMail.app@ela4-bed84.prod> References: <5300854.6495883.1313983314517.JavaMail.app@ela4-bed84.prod> Message-ID: Stop this, Please. SKG On Mon, Aug 22, 2011 at 8:51 AM, Thaneshwor Kaloni via LinkedIn < member at linkedin.com> wrote: > LinkedIn > Thaneshwor Kaloni requested to add you as a connection on LinkedIn: > > veronica, > > I'd like to add you to my professional network on LinkedIn. > > - Thaneshwor > > Accept > View invitation from Thaneshwor Kaloni > > > *WHY MIGHT CONNECTING WITH THANESHWOR KALONI BE A GOOD IDEA?* > > *Have a question? Thaneshwor Kaloni's network will probably have an answer > * > You can use LinkedIn Answersto distribute your professional questions to Thaneshwor Kaloni and your > extended network. You can get high-quality answers from experienced > professionals. > > > ? 2011, LinkedIn Corporation > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- *Dr. Sanjeev Kumar Gupta* *Post Doctoral Fellow, (Ministry of New and Renewable Energy) Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, India* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/a30b0507/attachment.htm From siyouber at yahoo.fr Mon Aug 22 09:13:50 2011 From: siyouber at yahoo.fr (Bertrand SITAMTZE) Date: Mon, 22 Aug 2011 08:13:50 +0100 (BST) Subject: [Pw_forum] Re : Thermal conductivity and Gruneisen parameters In-Reply-To: <3FE00567-F89C-4CFB-825B-0DAC4B718C7F@sissa.it> Message-ID: <1313997230.73245.YahooMailClassic@web26504.mail.ukl.yahoo.com> Dear all, After Prof. Stefano's comments, I will like to indicate that my aim was just to give a contribution, hoping that it will help. If I am wrong in any of my statements, please kindly suggest. Furthermore, everything in my answer has been given with reference and the reader should get acquainted with in order to solve his own problem. Sorry! B. SITAMTZE --- En date de?: Dim 21.8.11, Stefano Baroni a ?crit?: De: Stefano Baroni Objet: Re: [Pw_forum] Re : Thermal conductivity and Gruneisen parameters ?: "PWSCF Forum" Date: Dimanche 21 ao?t 2011, 9h23 On Aug 20, 2011, at 11:45 AM, Bertrand SITAMTZE wrote: Thermal conductivity could be obtained through velocity autocorrelation function? after running molecular dynamics (CP in QE).( See the book of Frenkel and Smith on page 90). I do not have Frenkel & Smith's book handy, but I would be surprised if it stated what you say. The calculation of the thermal conductivity through MD requires a proper definition of the energy current which is well known for classical systems (though it involves something more complicated than just velocities), but not yet available, to the best of my knowledge, in DFT. If I am wring, please correct me. As for Gruneisen parameters, one could calculate the specific heat through QHA and the bulk modulus with PW, then use the relationship between them. (See the book of L. Anderson on equations of state, starting from page 6). Here, I beg to differ as well. First, the calculation of the constant-volume specific heat does not involve any Gruneisen parameters (gamma). The constant-pressure specific heat (Cp) certainly does, but in the sense that you need them in the first place in order to calculate it. Second, It would seem rather innatural to calculate Cp just to estimate some of the parameters used to obtain it! In any case, the expression for Cp in terms of the gammas is an integral from which it would be impossible to obtain back their individual values.? All in all, before asking what QE (or any other code, for that matter) can or cannot do, one should stop for a while and ask oneself what are the most elementary pieces of information needed to compute what we are interested in, and only then ask if any specific code can compute those specific pieces of information. This may take some time, but it is much more instructive than hoping that computer codes can ever be a substitute for our own understanding. In the specific case of the thermal conductivity, one has the choice to follow the quasi-harmonic or the Kubo-Greenwood routes. Nicola Marzari has already given some hints on the former. Dr. Simatze's comments (and my present reply) apply to the latter. As for Gruneisen parameters, you just have just to inspect their definition (gamma = v/omega d (omega) / d (v)), and realize that any code able to compute vibrational frequencies can with little effort calculate them ... QE can calculate phonon frequencies, I will leave the final conclusion to you ... Hope this helpsStefano B ---Stefano Baroni - SISSA??&??DEMOCRITOS National Simulation Center - Triestehttp://stefano.baroni.me?[+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't??send me MS Word or PowerPoint attachmentsWhy? See:??http://www.gnu.org/philosophy/no-word-attachments.html -----La pi?ce jointe associ?e suit----- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/f9d64226/attachment-0001.htm From baroni at sissa.it Mon Aug 22 12:09:37 2011 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 22 Aug 2011 12:09:37 +0200 Subject: [Pw_forum] Re : Thermal conductivity and Gruneisen parameters In-Reply-To: <1313997230.73245.YahooMailClassic@web26504.mail.ukl.yahoo.com> References: <1313997230.73245.YahooMailClassic@web26504.mail.ukl.yahoo.com> Message-ID: Bertrand, All: there is nothing to apologize for, I believe. You started a lively discussion, which a enjoyed participating in. I did not mean to stigmatize anybody or anything, only to give my own contribution to a discussion that is well worth our time. I may have made some wrong or inaccurate statements as well. If anybody thinks that this may be the case, just let us know ... Thank you all for posting in this forum, Best wishes, Stefano B On Aug 22, 2011, at 9:13 AM, Bertrand SITAMTZE wrote: > Dear all, > > After Prof. Stefano's comments, I will like to indicate that my aim > was just to give a contribution, hoping that it will help. > If I am wrong in any of my statements, please kindly suggest. > > Furthermore, everything in my answer has been given with reference > and the reader should get acquainted with in order to solve his own > problem. > > Sorry! > > B. SITAMTZE > > --- En date de : Dim 21.8.11, Stefano Baroni a ?crit : > > De: Stefano Baroni > Objet: Re: [Pw_forum] Re : Thermal conductivity and Gruneisen parameters > ?: "PWSCF Forum" > Date: Dimanche 21 ao?t 2011, 9h23 > > On Aug 20, 2011, at 11:45 AM, Bertrand SITAMTZE wrote: > >> Thermal conductivity could be obtained through velocity autocorrelation function >> after running molecular dynamics (CP in QE).( See the book of Frenkel and Smith >> on page 90). >> > I do not have Frenkel & Smith's book handy, but I would be surprised if it stated what you say. The calculation of the thermal conductivity through MD requires a proper definition of the energy current which is well known for classical systems (though it involves something more complicated than just velocities), but not yet available, to the best of my knowledge, in DFT. If I am wring, please correct me. >> >> >> As for Gruneisen parameters, one could calculate the specific heat through QHA and the bulk modulus with PW, then use the relationship between them. (See the book of L. Anderson on equations of state, starting from page 6). >> > Here, I beg to differ as well. First, the calculation of the constant-volume specific heat does not involve any Gruneisen parameters (gamma). The constant-pressure specific heat (Cp) certainly does, but in the sense that you need them in the first place in order to calculate it. Second, It would seem rather innatural to calculate Cp just to estimate some of the parameters used to obtain it! In any case, the expression for Cp in terms of the gammas is an integral from which it would be impossible to obtain back their individual values. >> > > All in all, before asking what QE (or any other code, for that matter) can or cannot do, one should stop for a while and ask oneself what are the most elementary pieces of information needed to compute what we are interested in, and only then ask if any specific code can compute those specific pieces of information. This may take some time, but it is much more instructive than hoping that computer codes can ever be a substitute for our own understanding. > > In the specific case of the thermal conductivity, one has the choice to follow the quasi-harmonic or the Kubo-Greenwood routes. Nicola Marzari has already given some hints on the former. Dr. Simatze's comments (and my present reply) apply to the latter. As for Gruneisen parameters, you just have just to inspect their definition (gamma = v/omega d (omega) / d (v)), and realize that any code able to compute vibrational frequencies can with little effort calculate them ... QE can calculate phonon frequencies, I will leave the final conclusion to you ... > > Hope this helps > Stefano B > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > > > > -----La pi?ce jointe associ?e suit----- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/14828414/attachment.htm From antonio.msj1 at gmail.com Mon Aug 22 16:03:48 2011 From: antonio.msj1 at gmail.com (Antonio) Date: Mon, 22 Aug 2011 11:03:48 -0300 Subject: [Pw_forum] Phonon Calculations: partial results Message-ID: Dear QE's users. I'm carrying out some phonon calculations using the Espresso4.1. I would like to ask if I can check the partial results, such as the first normal mode calculated. Best regards! -- Doutorando Ant?nio M. Da Silva Jr. NEQC: Nucleo de Estudos em Quimica Computacional Departamento de Quimica - ICE Universidade Federal de Juiz de Fora Campus Universitario S/N 36.036-330 Juiz de Fora - MG - Brasil http://lattes.cnpq.br/0895213089855328 From elie.moujaes at hotmail.co.uk Mon Aug 22 16:06:49 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 22 Aug 2011 15:06:49 +0100 Subject: [Pw_forum] usage of recover=.true. Message-ID: Dear all,I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/72337054/attachment.htm From crma at sissa.it Mon Aug 22 16:17:17 2011 From: crma at sissa.it (Changru Ma) Date: Mon, 22 Aug 2011 16:17:17 +0200 Subject: [Pw_forum] usage of recover=.true. In-Reply-To: References: Message-ID: Dear Elie, In the document Doc/INPUT_PH.txt, variable "recover" is explained clearly: Variable: recover Type: LOGICAL Default: .false. Description: If .true. restart from an interrupted run. So set it to false in your first run and true in the second and the following runs. HTH, Changru On 22 Aug, 2011, at 16:06, Elie Moujaes wrote: > Dear all, > > I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/b461a2f8/attachment-0001.htm From flux_ray12 at 163.com Mon Aug 22 16:21:25 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 22 Aug 2011 22:21:25 +0800 (CST) Subject: [Pw_forum] usage of recover=.true. In-Reply-To: References: Message-ID: <65489225.143b4.131f1de08e5.Coremail.flux_ray12@163.com> If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:06:49,"Elie Moujaes" wrote: Dear all, I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? Thanks Elie Moujaes University of Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/ca0a9564/attachment.htm From elie.moujaes at hotmail.co.uk Mon Aug 22 16:23:16 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 22 Aug 2011 15:23:16 +0100 Subject: [Pw_forum] usage of recover=.true. In-Reply-To: References: , Message-ID: Thanks a lot for the answer. The problem is I started calculating the phonons at the Gamma point. In my system there are 180 modes and something went wrong with the server so it stopped at the 106.I am doing the 180 in one go! Is there a way to save the 106 ones already done! or u suggest that I calculate each one of them in a separate fie and use recover=.true.? ThanksElie From: crma at sissa.it Date: Mon, 22 Aug 2011 16:17:17 +0200 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] usage of recover=.true. Dear Elie, In the document Doc/INPUT_PH.txt, variable "recover" is explained clearly: Variable: recover Type: LOGICAL Default: .false. Description: If .true. restart from an interrupted run. So set it to false in your first run and true in the second and the following runs. HTH,Changru On 22 Aug, 2011, at 16:06, Elie Moujaes wrote:Dear all,I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/d55d7b8b/attachment.htm From elie.moujaes at hotmail.co.uk Mon Aug 22 16:27:33 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 22 Aug 2011 15:27:33 +0100 Subject: [Pw_forum] usage of recover=.true. In-Reply-To: <65489225.143b4.131f1de08e5.Coremail.flux_ray12@163.com> References: , <65489225.143b4.131f1de08e5.Coremail.flux_ray12@163.com> Message-ID: Thank you.I hope it works as I definitely do not want to lose the 105 modes..It took 7 days to do that. But how to re execute the ph.x command..I tried doing the usual:/.../...../ph.x GB60.phG.out but it exited. Is there another way to restart the command? Thanks againElie Date: Mon, 22 Aug 2011 22:21:25 +0800 From: flux_ray12 at 163.com To: pw_forum at pwscf.org Subject: Re: [Pw_forum] usage of recover=.true. If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:06:49,"Elie Moujaes" wrote: Dear all,I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done?ThanksElie MoujaesUniversity of NottinghamNG7 2RDUK _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/a3c78cb1/attachment.htm From gabriele.sclauzero at epfl.ch Mon Aug 22 16:30:56 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 22 Aug 2011 16:30:56 +0200 Subject: [Pw_forum] usage of recover=.true. In-Reply-To: References: , <65489225.143b4.131f1de08e5.Coremail.flux_ray12@163.com> Message-ID: Il giorno 22/ago/2011, alle ore 16.27, Elie Moujaes ha scritto: > Thank you.I hope it works as I definitely do not want to lose the 105 modes..It took 7 days to do that. But how to re execute the ph.x command..I tried doing the usual: > /.../...../ph.x GB60.phG.out but it exited. Could you be more specific? Have you tried to read the output to understand why it did not complete the calculation? HTH GS > Is there another way to restart the command? > > Thanks again > Elie > > Date: Mon, 22 Aug 2011 22:21:25 +0800 > From: flux_ray12 at 163.com > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] usage of recover=.true. > > If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-08-22 22:06:49,"Elie Moujaes" wrote: > Dear all, > > I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > > > > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/5277e6cc/attachment-0001.htm From crma at sissa.it Mon Aug 22 16:34:37 2011 From: crma at sissa.it (Changru Ma) Date: Mon, 22 Aug 2011 16:34:37 +0200 Subject: [Pw_forum] usage of recover=.true. In-Reply-To: References: , Message-ID: <68BE7C68-596E-45FD-AD43-8CA5C5463EC3@sissa.it> No. What I suggested is exactly what you want. In the first calculation, set recover to false, the code will compute the first 105 modes for you. When it is working on the 106th mode, it stops as you said. Then you modify the input file, turn "recover" to true, run the calculation again and the code is able to recover what you have done and start from the 106th mode. I would suggest you to write to another output. In the output, you will see: ? Representation 1 1 modes - Done ? Representation 105 1 modes - Done Representation 106 1 modes - To be done ? HTH Changru On 22 Aug, 2011, at 16:23, Elie Moujaes wrote: > Thanks a lot for the answer. The problem is I started calculating the phonons at the Gamma point. In my system there are 180 modes and something went wrong with the server so it stopped at the 106.I am doing the 180 in one go! Is there a way to save the 106 ones already done! or u suggest that I calculate each one of them in a separate fie and use recover=.true.? > > > Thanks > Elie > > From: crma at sissa.it > Date: Mon, 22 Aug 2011 16:17:17 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] usage of recover=.true. > > Dear Elie, > > In the document Doc/INPUT_PH.txt, variable "recover" is explained clearly: > > Variable: recover > > Type: LOGICAL > Default: .false. > Description: If .true. restart from an interrupted run. > > So set it to false in your first run and true in the second and the following runs. > > HTH, > Changru > > On 22 Aug, 2011, at 16:06, Elie Moujaes wrote: > > Dear all, > > I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Changru Ma > SISSA & Theory at Elettra group > email: crma at sissa.it > tel: +39 040 378 7870 > http://www.sissa.it/~crma > --- > > > _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Changru Ma SISSA & Theory at Elettra group email: crma at sissa.it tel: +39 040 378 7870 http://www.sissa.it/~crma --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/52bdda15/attachment.htm From flux_ray12 at 163.com Mon Aug 22 16:41:13 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Mon, 22 Aug 2011 22:41:13 +0800 (CST) Subject: [Pw_forum] usage of recover=.true. In-Reply-To: References: , <65489225.143b4.131f1de08e5.Coremail.flux_ray12@163.com> Message-ID: <2f1d7848.14616.131f1f027a8.Coremail.flux_ray12@163.com> If you are afraid of losing files, you can copy the corresponding files out as backup before restarting. I just tried restart DFPT once, about 2 months ago. I remember just recover = .t. was needed and everything was fine~ How about the error message in your new output file? -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:27:33,"Elie Moujaes" wrote: Thank you.I hope it works as I definitely do not want to lose the 105 modes..It took 7 days to do that. But how to re execute the ph.x command..I tried doing the usual: /.../...../ph.x GB60.phG.out but it exited. Is there another way to restart the command? Thanks again Elie Date: Mon, 22 Aug 2011 22:21:25 +0800 From:flux_ray12 at 163.com To:pw_forum at pwscf.org Subject: Re: [Pw_forum] usage of recover=.true. If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:06:49,"Elie Moujaes" wrote: Dear all, I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? Thanks Elie Moujaes University of Nottingham NG7 2RD UK _______________________________________________ Pw_forum mailing listPw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/88d00709/attachment.htm From lfhuang at theory.issp.ac.cn Mon Aug 22 16:39:29 2011 From: lfhuang at theory.issp.ac.cn (=?utf-8?B?bGZodWFuZw==?=) Date: Mon, 22 Aug 2011 22:39:29 +0800 Subject: [Pw_forum] =?utf-8?q?Phonon_Calculations=3A_partial_results?= Message-ID: <20110822143929.6402.qmail@ms.hfcas.ac.cn> Dear Antonio: There is a small code that is capable of calculating the partial contribution of each atom in each phonon mode. Link: http://blog.sciencenet.cn/home.php?mod=space&uid=345795&do=blog&quickforward=1&id=422819 Best Wishes! Yours Sincerely L. F. Huang > Date: Mon, 22 Aug 2011 11:03:48 -0300 > From: Antonio > Subject: [Pw_forum] Phonon Calculations: partial results > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Dear QE's users. > > I'm carrying out some phonon calculations using the Espresso4.1. I > would like to ask if I can check the partial results, such as the > first normal mode calculated. > > Best regards! > > -- > Doutorando Ant?nio M. Da Silva Jr. > NEQC: Nucleo de Estudos em Quimica Computacional > Departamento de Quimica - ICE > Universidade Federal de Juiz de Fora > Campus Universitario S/N 36.036-330 > Juiz de Fora - MG - Brasil > http://lattes.cnpq.br/0895213089855328 > ------ ====================================================================== L.F.Huang(???) DFT and phonon physics ====================================================================== Add: Research Laboratory for Computational Materials Sciences, Instutue of Solid State Physics,the Chinese Academy of Sciences, P.O.Box 1129, Hefei 230031, P.R.China Tel: 86-551-5591464-326(office) Fax: 86-551-5591434 ====================================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/36e54423/attachment.htm From elie.moujaes at hotmail.co.uk Mon Aug 22 16:49:25 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Mon, 22 Aug 2011 15:49:25 +0100 Subject: [Pw_forum] usage of recover=.true. (solved) Message-ID: Guys, Thanks a lot for your help. I just checked the output file now and the calculations are running normally. I am at mode 139. Thanks once again for all the suggestions Elie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/8374aa8f/attachment-0001.htm From bdslipun at gmail.com Mon Aug 22 18:21:11 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Mon, 22 Aug 2011 21:51:11 +0530 Subject: [Pw_forum] partial band structure Message-ID: hallo i am doing calculation of band structure in DOS there is no option of getting partial density of states can i calculate that plesase give me suggetions b d sahoo, reserch scolar barc mmbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/a73a6984/attachment.htm From flux_ray12 at 163.com Tue Aug 23 05:15:40 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Tue, 23 Aug 2011 11:15:40 +0800 (CST) Subject: [Pw_forum] partial band structure In-Reply-To: References: Message-ID: <578ce863.5a2a.131f4a2df94.Coremail.flux_ray12@163.com> You can obtain projected DOS by projwfc.x, more detail at the beginning of PP/projwfc.f90 -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-23 00:21:11,"bhabya sahoo" wrote: hallo i am doing calculation of band structure in DOS there is no option of getting partial density of states can i calculate that plesase give me suggetions b d sahoo, reserch scolar barc mmbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/8166fb57/attachment.htm From bdslipun at gmail.com Tue Aug 23 13:46:15 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 23 Aug 2011 17:16:15 +0530 Subject: [Pw_forum] bulk modulus Message-ID: how can one calculate bulk modulus and elastic constants with tempertaure by quantum espresso code b d sahoo reserch scholar barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/0f38bdbc/attachment.htm From aaghafari at yahoo.com Tue Aug 23 14:18:33 2011 From: aaghafari at yahoo.com (ali ghafari) Date: Tue, 23 Aug 2011 05:18:33 -0700 (PDT) Subject: [Pw_forum] B3LYP hybrid density functional Message-ID: <1314101913.44587.YahooMailNeo@web161426.mail.bf1.yahoo.com> Dear All I would like to useB3LYP hybrid density function for correlated system. But I don't know how can I find it for Cu and O. Should I write it by myself? Best Wishes Ghafari -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/462b7bab/attachment.htm From lmartinsamos at gmail.com Tue Aug 23 14:53:55 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Tue, 23 Aug 2011 14:53:55 +0200 Subject: [Pw_forum] B3LYP hybrid density functional In-Reply-To: <1314101913.44587.YahooMailNeo@web161426.mail.bf1.yahoo.com> References: <1314101913.44587.YahooMailNeo@web161426.mail.bf1.yahoo.com> Message-ID: Dear Ali, could you, please, be more explicit in your question? in principle for using B3LYP with pw, you just need to specify in system namelist input_dft="b3lyp", and this is independent of the element. cheers Layla 2011/8/23 ali ghafari > Dear All > > I would like to use B3LYP hybrid density function for correlated system. > But I don't know how can I find it for Cu and O. Should I write it by > myself? > > Best Wishes > Ghafari > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/dcbe7ba3/attachment.htm From bdslipun at gmail.com Tue Aug 23 20:40:29 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 24 Aug 2011 00:10:29 +0530 Subject: [Pw_forum] phonon instability Message-ID: sir i am calculating the phase transition of some carbides the transition from B1 to B2 transition occures at 130 gpa by enthalpy compparison but i am able to find phonon instability at 130 gpa for B1 structure but at the same time i am not able to find the dyanamic stability of B2 phase but it occures high pressure (more than130 gpa ) is there any explanation for this ? is there any relation of thermodyanamical unstability and dyanamical unstability simultaneously? answers are highly appriceted with some reson Bd sahoo reserch scholar barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110824/4b334281/attachment.htm From baroni at sissa.it Tue Aug 23 21:07:33 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 23 Aug 2011 21:07:33 +0200 Subject: [Pw_forum] bulk modulus In-Reply-To: References: Message-ID: using the quasi-harmonic approximation, or constant-pressure ab-initio molecular dynamics (*) - SB (*) if you want a more articulated answer, may I expect a more articulated and well-thought question? On Aug 23, 2011, at 1:46 PM, bhabya sahoo wrote: > how can one calculate bulk modulus and elastic constants with tempertaure > by quantum espresso code > > > > > > > > b d sahoo reserch scholar > > barc mumbai > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/ed106c26/attachment.htm From baroni at sissa.it Tue Aug 23 21:15:30 2011 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 23 Aug 2011 21:15:30 +0200 Subject: [Pw_forum] phonon instability In-Reply-To: References: Message-ID: On Aug 23, 2011, at 8:40 PM, bhabya sahoo wrote: > sir ??? > i am calculating the phase transition of some carbides > the transition from B1 to B2 transition occures at 130 gpa by enthalpy compparison OK > but i am able to find phonon instability at 130 gpa for B1 structure you mean, a phonon (which mode?) goes soft at the same pressure at which the enthalpies of the two phase coincide? > but at the same time i am not able to find the dyanamic stability of B2 phase ??? > but it occures high pressure (more than130 gpa ) ??? > is there any explanation for this ? explanation for WHAT? what are you talking about? may we expect a somewhat more well thought and articulate question? > is there any relation of thermodyanamical unstability > and dyanamical unstability simultaneously? ??? > answers are highly appriceted with some reson well-thought and well documented questions questions would be even more appreciAted for any reAson ... SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/83e276ad/attachment.htm From chenhanghuipwscf at gmail.com Tue Aug 23 22:15:50 2011 From: chenhanghuipwscf at gmail.com (hanghui chen) Date: Tue, 23 Aug 2011 16:15:50 -0400 Subject: [Pw_forum] phonon with LSDA+U Message-ID: To Quantum Espresso community: It seems that in version 4.2 phonon calculations can not be performed with LSDA+U. Is there any fundamental conflict between density functional perturbation theory and LSDA+U? Or is it just that this part is not implemented in PWscf yet? Is there any plan that this part will be implemented in near future? Thank you very much. Hanghui Chen Department of Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/c379da06/attachment-0001.htm From matteo at umn.edu Tue Aug 23 22:25:35 2011 From: matteo at umn.edu (Matteo Cococcioni) Date: Tue, 23 Aug 2011 15:25:35 -0500 Subject: [Pw_forum] phonon with LSDA+U In-Reply-To: References: Message-ID: Dear Hanghui, the lsda+ U has been implemented in the phonon code, but not ported on the current version yet. we need some more time for this. hopefully this will be done soon. regards, Matteo On Tue, Aug 23, 2011 at 3:15 PM, hanghui chen wrote: > To Quantum Espresso community: > It seems that in version 4.2 phonon calculations can not be performed > with LSDA+U. Is there any fundamental conflict between density functional > perturbation theory and LSDA+U? Or is it just that this part is not > implemented in PWscf yet? Is there any plan that this part will be > implemented in near future? > Thank you very much. > > > Hanghui Chen > Department of Physics > Yale University > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Matteo Cococcioni Department of Chemical Engineering and Materials Science, University of Minnesota 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/83ed9047/attachment.htm From foursea at 163.com Wed Aug 24 02:30:05 2011 From: foursea at 163.com (lilonghua) Date: Wed, 24 Aug 2011 08:30:05 +0800 Subject: [Pw_forum] Does SOC conflict with HSE06? Message-ID: <201108231754519374915@163.com> Dear all, Does SOC (spin-orbit coupling) conflict with HSE06 in pwscf? SOC is ok! HSE06 is also OK! But when combining SOC and HSE06, the calculation stop at EXX calculation! This is my input file: &control verbosity='default' ! 'high'|'low'|'minimal' restart_mode='from_scratch' ! 'from_scratch'|'restart' prefix='PbTe' pseudo_dir='./' outdir='./tmp' calculation = 'scf' / &system ibrav=0 nat= 2 ntyp= 2 ecutwfc = 35.0, ecutrho = 140.0 ! ecutrho (4-12*ecutwfc)! occupations='fixed' ! 'tetrahedra'|'smearing'|'fixed'| nbnd= 16 ! number of bands, need special !+++++ DFT Hybride functional +++++ input_dft='hse', nqx1 = 1, nqx2 = 1, nqx3 = 1 exxdiv_treatment='g-b' ! yukawa,erfc_simple,vcut_ws,vcut_spheric,none x_gamma_extrapolation = .true. ! if cut_ws or vcut_spheric, = .false. !exx_fraction =0.25, screening_parameter=0.16 !see Modules/func.f90 lspinorb=.true. noncolin=.true. / &electrons diagonalization='david' ! 'cg'|'-ndiag N' electron_maxstep=300 conv_thr = 1.0e-8 mixing_mode='plain' ! 'TF'|'local-TF' mixing_beta = 0.5 mixing_ndim=8 adaptive_thr=.true. ! use for EXX conv_thr_init=1.d-3 ! use for EXX conv_thr_multi=1.d-1 ! use for EXX / ATOMIC_SPECIES Pb 207.200 Pb.rel-pbe-nc.UPF Te 127.600 Te.rel-pbe-nc.UPF ATOMIC_POSITIONS {crystal} Pb 0.0000000000000 0.0000000000000 0.0000000000000 Te 0.5000000000000 0.5000000000000 0.0000000000000 K_POINTS {automatic} !gamma,crystal_b 4 4 4 0 0 0 CELL_PARAMETERS {cubic} 6.104762563 6.104762563 0.000000000 6.104762563 -6.104762563 0.000000000 6.104762563 0.000000000 6.104762563 Best regards, Longhua Li 2011-08-23 ---------------------------------------- foursea at 163.com From windbellklbh at gmail.com Wed Aug 24 03:09:33 2011 From: windbellklbh at gmail.com (WF) Date: Wed, 24 Aug 2011 09:09:33 +0800 Subject: [Pw_forum] vdW functional in Quantum-Espresso Message-ID: <000701cc61fa$80257b00$80707100$@gmail.com> There are large changes in vdW functional part between version 4.3 and 4.3.1 or later. First, the vdW functional is put in GGA correlation part in funct.f90 in 4.3, but in an independent part (non-local part) in funct.f90 in 4.3.1. Second, the ld1.x refuse to generate pseudo-potential for functional containing vdW part like vdW-DF in 4.3.1 for it is non-local but it is possible to generate something in 4.3. So I have some question about vdW functional. 1. In 4.3, does vdW-DF, or "sla+pw+rpb+vdw" as 1/4/4/9 imply the original GGA correlation in revPBE, "pbc" here, is used? As 4.3.1 allow user to specify GGA correlation and vdW correction simultaneously, and vdW-DF in that version is 1/4/4/0/1, is it reasonable to add GGA correlation in the functional and perform further calculation? I note in literature it is said GGA correlation is small so it is neglected. 2. What is the difference of vdW functional correction in vdW-DF1 and vdW-DF2? 3. If it is impossible to get a pseudo-potential of vdW-DF , what functional in pseudo-potential should I specify to perform calculation later? What is the pp generated by 4.3 actually and can they be used in further calculation? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110824/e6c3ec4b/attachment.htm From bdslipun at gmail.com Wed Aug 24 07:08:27 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 23 Aug 2011 22:08:27 -0700 Subject: [Pw_forum] Fwd: phonon instability In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: Stefano Baroni Date: Tue, Aug 23, 2011 at 12:15 PM Subject: Re: [Pw_forum] phonon instability To: PWSCF Forum On Aug 23, 2011, at 8:40 PM, bhabya sahoo wrote: sir ??? i am calculating the phase transition of some carbides the transition from B1 to B2 transition occures at 130 gpa by enthalpy compparison OK but i am able to find phonon instability at 130 gpa for B1 structure you mean, a phonon (which mode?) goes soft at the same pressure at which the enthalpies of the two phase coincide? TA branch in the gamma -X-R directions for B1 phase - but at the same time i am not able to find the dyanamic stability of B2 phase at 130 gpa ??? but it occures high pressure (more than130 gpa ) ??? is there any explanation for this ? explanation for WHAT? why the phonon instability occures at 130 gpa for B2 strcuture in the gamma -x directions for B2 structure although it is thermodyanamical stable by enthalpy comparison what are you talking about? may we expect a somewhat more well thought and articulate question? is there any relation of thermodyanamical unstability and dyanamical unstability simultaneously? ??? answers are highly appriceted with some reson well-thought and well documented questions questions would be even more appreciAted for any reAson ... SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/010bd5a4/attachment.htm From bdslipun at gmail.com Wed Aug 24 08:39:20 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 23 Aug 2011 23:39:20 -0700 Subject: [Pw_forum] bulk modulus In-Reply-To: References: Message-ID: i want this by quasi harmonic approximation On Tue, Aug 23, 2011 at 12:07 PM, Stefano Baroni wrote: > using the quasi-harmonic approximation, or constant-pressure ab-initio > molecular dynamics (*) - SB > > (*) if you want a more articulated answer, may I expect a more articulated > and well-thought question? > > On Aug 23, 2011, at 1:46 PM, bhabya sahoo wrote: > > > how can one calculate bulk modulus and elastic constants with tempertaure > by quantum espresso code > > > > > > > > b d sahoo reserch scholar > > barc mumbai > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste > http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / > stefanobaroni (skype) > > La morale est une logique de l'action comme la logique est une morale de la > pens?e - Jean Piaget > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/cde59c24/attachment-0001.htm From modaresi.mohsen at gmail.com Wed Aug 24 15:02:36 2011 From: modaresi.mohsen at gmail.com (Mohsen Modaresi) Date: Wed, 24 Aug 2011 06:02:36 -0700 Subject: [Pw_forum] bulk modulus In-Reply-To: References: Message-ID: ?Dear Bhabya Sahoo, we did such a calculations in the case of Garphene and h-Boron-Nitride, but the manuscript does not publish until know. After the publication we are pleased to inform you and send a copy of the manuscript and our input files. On Tue, Aug 23, 2011 at 11:39 PM, bhabya sahoo wrote: > i want this by quasi harmonic approximation > > On Tue, Aug 23, 2011 at 12:07 PM, Stefano Baroni wrote: > >> using the quasi-harmonic approximation, or constant-pressure ab-initio >> molecular dynamics (*) - SB >> >> (*) if you want a more articulated answer, may I expect a more articulated >> and well-thought question? >> >> On Aug 23, 2011, at 1:46 PM, bhabya sahoo wrote: >> >> >> how can one calculate bulk modulus and elastic constants with tempertaure >> by quantum espresso code >> >> >> >> >> >> >> >> b d sahoo reserch scholar >> >> barc mumbai >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> --- >> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - >> Trieste >> http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / >> stefanobaroni (skype) >> >> La morale est une logique de l'action comme la logique est une morale de >> la pens?e - Jean Piaget >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Mohsen Modarresi, PhD student of Solid State Physics, Ferdowsi University of Mashhad, Iran. Phone +98-9133452131 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110824/d34c4e76/attachment.htm From Michael.Mehl at nrl.navy.mil Wed Aug 24 16:08:41 2011 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Wed, 24 Aug 2011 10:08:41 -0400 Subject: [Pw_forum] phonon instability In-Reply-To: References: Message-ID: <4E5505E9.1000601@nrl.navy.mil> If the B1 structure is unstable with respect to the B2 structure above 130 GPa, but the B2 structure is dynamically unstable at and above 130 GPa, there are two possible conclusions: 1) The phonons for the B2 structure were not calculated accurately, or 2) There is a competing structure that is lower in enthalpy than B1 or B2 at 130 GPa Without more information, no one can judge which conclusion is correct, suggest remedies for 1), or possible structure for 2). On 08/23/2011 02:40 PM, bhabya sahoo wrote: > sir > i am calculating the phase transition of some carbides > the transition from B1 to B2 transition occures at 130 gpa by enthalpy > compparison > but i am able to find phonon instability at 130 gpa for B1 structure > but at the same time i am not able to find the dyanamic stability of B2 > phase > but it occures high pressure (more than130 gpa ) > is there any explanation for this ? > > is there any relation of thermodyanamical unstability > and dyanamical unstability simultaneously? > > > answers are highly appriceted with some reson > > > > > > > > > Bd sahoo > reserch scholar > barc mumbai > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From bdslipun at gmail.com Wed Aug 24 16:35:22 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 24 Aug 2011 20:05:22 +0530 Subject: [Pw_forum] phonon instability In-Reply-To: <4E5505E9.1000601@nrl.navy.mil> References: <4E5505E9.1000601@nrl.navy.mil> Message-ID: no i have calculated correctly because the convergence is good with higher k points second is that i have tested zns,wc,NiAs phase none of them have less enthalpy at 130 gpa other thing is that it is stable at above 250 gpa On Wed, Aug 24, 2011 at 7:38 PM, Mike Mehl wrote: > If the B1 structure is unstable with respect to the B2 structure above > 130 GPa, but the B2 structure is dynamically unstable at and above 130 > GPa, there are two possible conclusions: > > 1) The phonons for the B2 structure were not calculated accurately, or > > 2) There is a competing structure that is lower in enthalpy than B1 or > B2 at 130 GPa > > Without more information, no one can judge which conclusion is correct, > suggest remedies for 1), or possible structure for 2). > > > On 08/23/2011 02:40 PM, bhabya sahoo wrote: > > sir > > i am calculating the phase transition of some carbides > > the transition from B1 to B2 transition occures at 130 gpa by enthalpy > > compparison > > but i am able to find phonon instability at 130 gpa for B1 structure > > but at the same time i am not able to find the dyanamic stability of B2 > > phase > > but it occures high pressure (more than130 gpa ) > > is there any explanation for this ? > > > > is there any relation of thermodyanamical unstability > > and dyanamical unstability simultaneously? > > > > > > answers are highly appriceted with some reson > > > > > > > > > > > > > > > > > > Bd sahoo > > reserch scholar > > barc mumbai > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > -- > Michael J. Mehl > Head, Center for Computational Materials Science > Naval Research Laboratory Code 6390 > Washington DC > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110824/9903e9cd/attachment.htm From Michael.Mehl at nrl.navy.mil Wed Aug 24 17:31:02 2011 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Wed, 24 Aug 2011 11:31:02 -0400 Subject: [Pw_forum] phonon instability In-Reply-To: References: <4E5505E9.1000601@nrl.navy.mil> Message-ID: <4E551936.4020709@nrl.navy.mil> ZnS, WC, and NiAs are the likeliest candidates, but not the only ones. The unstable B1 phonons lead to structures which relax to something lower in energy than B1. Since all of your candidate structures have a higher enthalpy than B1 at 130 GPa, it can't be one of those structures. Hence, it's a different structure. It should be frowned upon to hype one's own publications, but if you look at M. J. Mehl, G. L. W. Hart, and S. Curtarolo Journal of Alloys and Compounds, 509, pp. 560-567 (2011) (http://www.sciencedirect.com/science/article/pii/S0925838810021225 or http://arxiv.org/abs/1006.0236) There are examples of how you can find new structures from unstable phonon modes. This case sounds simpler than IrV. It would, of course, help us if we knew which carbides you were working on. On 08/24/2011 10:35 AM, bhabya sahoo wrote: > no i have calculated correctly because the convergence is good with > higher k points > second is that i have tested zns,wc,NiAs phase none of them have less > enthalpy at 130 gpa > other thing is that it is stable at above 250 gpa > > > On Wed, Aug 24, 2011 at 7:38 PM, Mike Mehl > wrote: > > If the B1 structure is unstable with respect to the B2 structure above > 130 GPa, but the B2 structure is dynamically unstable at and above 130 > GPa, there are two possible conclusions: > > 1) The phonons for the B2 structure were not calculated accurately, or > > 2) There is a competing structure that is lower in enthalpy than B1 or > B2 at 130 GPa > > Without more information, no one can judge which conclusion is correct, > suggest remedies for 1), or possible structure for 2). > -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From bdslipun at gmail.com Wed Aug 24 19:07:02 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 24 Aug 2011 22:37:02 +0530 Subject: [Pw_forum] phonon instability In-Reply-To: <4E551936.4020709@nrl.navy.mil> References: <4E5505E9.1000601@nrl.navy.mil> <4E551936.4020709@nrl.navy.mil> Message-ID: ok but i have seen many papers that this B2 unstability due to some anaharmonic contributions or it may be due to band closing phenomenon can u explain this more correctly because i am doing calculation on transition metal carbides On Wed, Aug 24, 2011 at 9:01 PM, Mike Mehl wrote: > ZnS, WC, and NiAs are the likeliest candidates, but not the only ones. > > The unstable B1 phonons lead to structures which relax to something > lower in energy than B1. Since all of your candidate structures have a > higher enthalpy than B1 at 130 GPa, it can't be one of those structures. > Hence, it's a different structure. > > It should be frowned upon to hype one's own publications, but if you look > at > > M. J. Mehl, G. L. W. Hart, and S. Curtarolo > Journal of Alloys and Compounds, 509, pp. 560-567 (2011) > > (http://www.sciencedirect.com/science/article/pii/S0925838810021225 or > http://arxiv.org/abs/1006.0236) > > There are examples of how you can find new structures from unstable > phonon modes. This case sounds simpler than IrV. > > It would, of course, help us if we knew which carbides you were working on. > > On 08/24/2011 10:35 AM, bhabya sahoo wrote: > > no i have calculated correctly because the convergence is good with > > higher k points > > second is that i have tested zns,wc,NiAs phase none of them have less > > enthalpy at 130 gpa > > other thing is that it is stable at above 250 gpa > > > > > > On Wed, Aug 24, 2011 at 7:38 PM, Mike Mehl > > wrote: > > > > If the B1 structure is unstable with respect to the B2 structure > above > > 130 GPa, but the B2 structure is dynamically unstable at and above > 130 > > GPa, there are two possible conclusions: > > > > 1) The phonons for the B2 structure were not calculated accurately, > or > > > > 2) There is a competing structure that is lower in enthalpy than B1 > or > > B2 at 130 GPa > > > > Without more information, no one can judge which conclusion is > correct, > > suggest remedies for 1), or possible structure for 2). > > > > > -- > Michael J. Mehl > Head, Center for Computational Materials Science > Naval Research Laboratory Code 6390 > Washington DC > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110824/fd8e37ab/attachment-0001.htm From Michael.Mehl at nrl.navy.mil Wed Aug 24 19:24:48 2011 From: Michael.Mehl at nrl.navy.mil (Mike Mehl) Date: Wed, 24 Aug 2011 13:24:48 -0400 Subject: [Pw_forum] phonon instability In-Reply-To: References: <4E5505E9.1000601@nrl.navy.mil> <4E551936.4020709@nrl.navy.mil> Message-ID: <4E5533E0.70907@nrl.navy.mil> To keep from boring everyone, I'm taking this off-line. If anyone else wants to participate in the discussion please let me know and I'll add you to the conversation. On 08/24/2011 01:07 PM, bhabya sahoo wrote: > ok but i have seen many papers that this B2 unstability due to some > anaharmonic contributions > or it may be due to band closing phenomenon > can u explain this more correctly because i am doing calculation on > transition metal carbides > On Wed, Aug 24, 2011 at 9:01 PM, Mike Mehl > wrote: > -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC From bdslipun at gmail.com Wed Aug 24 20:06:10 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Wed, 24 Aug 2011 23:36:10 +0530 Subject: [Pw_forum] phonon instability In-Reply-To: <4E5533E0.70907@nrl.navy.mil> References: <4E5505E9.1000601@nrl.navy.mil> <4E551936.4020709@nrl.navy.mil> <4E5533E0.70907@nrl.navy.mil> Message-ID: i am doing the linear response calculation so how can i do frozen phonon calculation On Wed, Aug 24, 2011 at 10:54 PM, Mike Mehl wrote: > To keep from boring everyone, I'm taking this off-line. If anyone else > wants to participate in the discussion please let me know and I'll add > you to the conversation. > > On 08/24/2011 01:07 PM, bhabya sahoo wrote: > > ok but i have seen many papers that this B2 unstability due to some > > anaharmonic contributions > > or it may be due to band closing phenomenon > > can u explain this more correctly because i am doing calculation on > > transition metal carbides > > On Wed, Aug 24, 2011 at 9:01 PM, Mike Mehl > > wrote: > > > > -- > Michael J. Mehl > Head, Center for Computational Materials Science > Naval Research Laboratory Code 6390 > Washington DC > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110824/96af46ed/attachment.htm From flux_ray12 at 163.com Wed Aug 24 20:21:52 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 25 Aug 2011 02:21:52 +0800 (CST) Subject: [Pw_forum] phonon instability In-Reply-To: References: <4E5505E9.1000601@nrl.navy.mil> <4E551936.4020709@nrl.navy.mil> <4E5533E0.70907@nrl.navy.mil> Message-ID: <35d63159.1c0.131fd06e4f2.Coremail.flux_ray12@163.com> As I know, frozen phonon method is not implemented in QE. You can use frozen-ph method either by the free software "phon", http://www.homepages.ucl.ac.uk/~ucfbdxa/, or make it manually like this tutorial: http://www.abinit.org/documentation/helpfiles/for-v6.8/tutorial/lesson_rf1.html, even though it is from Abinit. After all, once we have DFPT, why do you wanna frozen-ph ? -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-25 02:06:10,"bhabya sahoo" wrote: i am doing the linear response calculation so how can i do frozen phonon calculation On Wed, Aug 24, 2011 at 10:54 PM, Mike Mehl wrote: To keep from boring everyone, I'm taking this off-line. If anyone else wants to participate in the discussion please let me know and I'll add you to the conversation. On 08/24/2011 01:07 PM, bhabya sahoo wrote: > ok but i have seen many papers that this B2 unstability due to some > anaharmonic contributions > or it may be due to band closing phenomenon > can u explain this more correctly because i am doing calculation on > transition metal carbides > On Wed, Aug 24, 2011 at 9:01 PM, Mike Mehl > wrote: > -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110825/7832f808/attachment.htm From mtorabi at uwo.ca Wed Aug 24 21:15:09 2011 From: mtorabi at uwo.ca (Amin Torabi) Date: Wed, 24 Aug 2011 15:15:09 -0400 Subject: [Pw_forum] convergence w.r.t ecutwfc Message-ID: Dear experts, Will you please take a look at my input file and convergence table below: I am using PBE USPP for both hydrogen and boron, but calculating energies using PBEsol. (ecutrho is set to 12* ecutwfc.) My question is: 1. Does it look normal? I was expect to seeing 1mRy accuracy at lower ecutwfc values. 2. I didn't use "occupations" or "smearing" and I didn't get any error in output files. Do they affect the convergence? 3. I want to do vc-relax calculation at high pressure. Based on my table, what ecutwfc do you suggest? Thanks in advance. ecutwfc energy 30 -38.28149597 35 -38.28437812 40 -38.28554856 45 -38.28658930 50 -38.28772083 55 -38.28883141 60 -38.28989311 65 -38.29086868 70 -38.29167889 75 -38.29227767 80 -38.29267847 85 -38.29291696 90 -38.29302834 95 -38.29305836 100 -38.29305908 105 -38.29307545 110 -38.29313486 115 -38.29324982 &control pseudo_dir = ** outdir = ** prefix = '$a' tstress = .true tprnfor = .true verbosity = 'low' / &SYSTEM ibrav = 12 celldm(1) = 8.31479435 celldm(2) = 1.3 celldm(3) = 1.4772727273 celldm(4) = -0.260504508642648 nat = 16 ntyp = 2 ecutwfc = $a ecutrho = `expr 12 \* $a` input_dft = 'pbesol' / &ELECTRONS / ATOMIC_SPECIES B 10.811 B.pbe-n-van_ak.UPF H 1.00794 H.pbe-van_ak.UPF ATOMIC_POSITIONS crystal B 0.002 0.146 0.042 H -0.194 0.166 0.140 H 0.196 0.294 -0.005 H 0.104 -0.019 0.112 B -0.002 -0.146 -0.042 H 0.194 -0.166 -0.140 H -0.196 -0.294 0.005 H -0.104 0.019 -0.112 B 0.498 0.354 0.542 H 0.694 0.334 0.640 H 0.304 0.206 0.495 H 0.396 0.519 0.612 B 0.502 0.646 0.458 H 0.306 0.666 0.360 H 0.696 0.794 0.505 H 0.604 0.481 0.388 K_POINTS automatic 8 8 8 0 0 0 -- Amin Torabi Ph.D. Student Chemistry Department The University *of* Western Ontario London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110824/72c76d1c/attachment.htm From baroni at sissa.it Wed Aug 24 21:30:00 2011 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 24 Aug 2011 21:30:00 +0200 Subject: [Pw_forum] phonon instability In-Reply-To: <35d63159.1c0.131fd06e4f2.Coremail.flux_ray12@163.com> References: <4E5505E9.1000601@nrl.navy.mil> <4E551936.4020709@nrl.navy.mil> <4E5533E0.70907@nrl.navy.mil> <35d63159.1c0.131fd06e4f2.Coremail.flux_ray12@163.com> Message-ID: On Aug 24, 2011, at 8:21 PM, GAO Zhe wrote: > As I know, frozen phonon method is not implemented in QE. ??? *ANY* code able to perform total-energy and atomic-force calculations can be used to do frozen phonons ... SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110824/1b5b8398/attachment-0001.htm From flux_ray12 at 163.com Thu Aug 25 05:03:34 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 25 Aug 2011 11:03:34 +0800 (CST) Subject: [Pw_forum] phonon instability In-Reply-To: References: <4E5505E9.1000601@nrl.navy.mil> <4E551936.4020709@nrl.navy.mil> <4E5533E0.70907@nrl.navy.mil> <35d63159.1c0.131fd06e4f2.Coremail.flux_ray12@163.com> Message-ID: <75afc98a.53e7.131fee48498.Coremail.flux_ray12@163.com> Dear Prof. Baroni: Thank you very much for your reply. However, what I wanted to say is, although QE doesn't support frozen-ph as a "function", it can still be calculated through certain steps. Just as elastic constant calculation, we can calculate in any DFT code, but only several code provide it as a "function", such as CASTEP. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-25 03:30:00,"Stefano Baroni" wrote: On Aug 24, 2011, at 8:21 PM, GAO Zhe wrote: As I know, frozen phonon method is not implemented in QE. ??? *ANY* code able to perform total-energy and atomic-force calculations can be used to do frozen phonons ... SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110825/5d4a632d/attachment.htm From colonel.sreekar at gmail.com Thu Aug 25 12:25:30 2011 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Thu, 25 Aug 2011 15:55:30 +0530 Subject: [Pw_forum] constrained magnetization calculation to converge at the ferromagnetic state Message-ID: Respected Sir/Madam, 1. I would like to perform a constrained magnetization calculation for a system, whose unconstrained spin polarized calculation gives an antiferromagnetic state, to converge at the ferromagnetic state. 2. The system is a zigzag graphene nanoribbon(* http://en.wikipedia.org/wiki/Graphene***) and I would like to flip the atomic moment at one of the edge site and constrain both the edge site moments. 3. I calculated the antiferromagnetic edge site moment using PDOS calculation. I used 'lambda' parameter to constrain the moments. 4.Questions: Is 3) the right way to do it? If yes, what should be value of lambda? I used lambda =1 and the scf output (given below) is disturbing... I would like to ask what does "constrained moment : -20.000000" mean and why is the constrain energy so high. If it is not the right way, I would be grateful if you could suggest an alternative. Thanking you, Yours sincerely, Sreekar Guddeti Undergraduate (5th year) Engineering Physics IIT Bombay India PS: The system namelist for scf calculation and the sample output are given below and the complete input file is attached. -------------------------------------- ... ============================================================================== atom number 15 relative position : -3.5000 6.0622 0.0000 charge : 0.983302 magnetization : 0.000256 magnetization/charge: 0.000260 constrained moment : 0.309100 ============================================================================== ============================================================================== atom number 16 relative position : -3.0000 5.7735 0.0000 charge : 1.783674 magnetization : -0.385046 magnetization/charge: -0.215873 constrained moment : -20.000000 ============================================================================== ... ... *constraint energy* (Ryd) = 6095.83663339 --------------------------------- -------------------------------- &SYSTEM ibrav = 12, celldm(1) = 4.608737, celldm(2) = 12.0, celldm(3) = 10.0, celldm(4) = -0.50, nat = 18, ntyp =10, starting_magnetization(2)= 0.3091, starting_magnetization(8)= 0.3091, occupations='smearing', smearing='gauss', degauss=0.01, nspin=2, constrained_magnetization='atomic' lambda = 1 ecutwfc = 50.D0 , report = 2 / -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110825/c5288b4a/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: grapheneznrn10j.scf.in Type: application/octet-stream Size: 2522 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110825/c5288b4a/attachment.obj From arvifis at gmail.com Thu Aug 25 14:08:57 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Thu, 25 Aug 2011 09:08:57 -0300 Subject: [Pw_forum] constrained magnetization calculation to converge at the ferromagnetic state In-Reply-To: References: Message-ID: Dear Sreekar Guddeti, if you want to calculate a constrained magnetization with antiparallel direction between the atom 2 and atom 8, you must to put the "starting_magnetization" tag with opposite value, for example: starting_magnetization(2)= 0.3091, starting_magnetization(8)= -0.3091, best wishes PhD stud. Arles V. Gil Rebaza Instituto de F?sica de La Plata Argentina. 2011/8/25 sreekar guddeti > Respected Sir/Madam, > 1. I would like to perform a constrained magnetization calculation for a > system, whose unconstrained spin polarized calculation gives an > antiferromagnetic state, to converge at the ferromagnetic state. > 2. The system is a zigzag graphene nanoribbon(* > http://en.wikipedia.org/wiki/Graphene***) and I would like to flip the > atomic moment at one of the edge site and constrain both the edge site > moments. > 3. I calculated the antiferromagnetic edge site moment using PDOS > calculation. I used 'lambda' parameter to constrain the moments. > > 4.Questions: Is 3) the right way to do it? If yes, what should be value of > lambda? I used lambda =1 and the scf output (given below) is disturbing... I > would like to ask what does "constrained moment : -20.000000" mean and why > is the constrain energy so high. If it is not the right way, I would be > grateful if you could suggest an alternative. > > Thanking you, > Yours sincerely, > Sreekar Guddeti > Undergraduate (5th year) > Engineering Physics > IIT Bombay > India > > PS: The system namelist for scf calculation and the sample output are given > below and the complete input file is attached. > > > -------------------------------------- > ... > > ============================================================================== > atom number 15 relative position : -3.5000 6.0622 0.0000 > charge : 0.983302 > magnetization : 0.000256 > magnetization/charge: 0.000260 > constrained moment : 0.309100 > > > ============================================================================== > > > ============================================================================== > atom number 16 relative position : -3.0000 5.7735 0.0000 > charge : 1.783674 > magnetization : -0.385046 > magnetization/charge: -0.215873 > constrained moment : -20.000000 > > > ============================================================================== > ... > ... > > *constraint energy* (Ryd) = 6095.83663339 > --------------------------------- > > > > -------------------------------- > &SYSTEM > ibrav = 12, > celldm(1) = 4.608737, > celldm(2) = 12.0, > celldm(3) = 10.0, > celldm(4) = -0.50, > nat = 18, > ntyp =10, > starting_magnetization(2)= 0.3091, > starting_magnetization(8)= 0.3091, > occupations='smearing', > smearing='gauss', > degauss=0.01, > nspin=2, > constrained_magnetization='atomic' > lambda = 1 > ecutwfc = 50.D0 , > report = 2 > > / > > > -- > Sreekar Guddeti > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110825/01a1aa1e/attachment.htm From gabriele.sclauzero at epfl.ch Thu Aug 25 14:15:53 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Thu, 25 Aug 2011 14:15:53 +0200 Subject: [Pw_forum] constrained magnetization calculation to converge at the ferromagnetic state In-Reply-To: References: Message-ID: <3F4BECE9-FBD2-45DF-B00B-FCD4B86CE44E@epfl.ch> Dear Sreekar, I would first try to reduce mixing_beta and also lambda (say, to 0.2 or 0.1). You can then restart the calculation with a larger value of lambda. Don't forget that for USPP you need to specify also ecutrho, and perhaps you don't need such a high ecutwfc. If your USPPs are those on the QE website, I would use ecutwfc=35 and ecutrho=350, for instance. Il giorno 25/ago/2011, alle ore 12.25, sreekar guddeti ha scritto: > Respected Sir/Madam, > 1. I would like to perform a constrained magnetization calculation for a system, whose unconstrained spin polarized calculation gives an antiferromagnetic state, to converge at the ferromagnetic state. > 2. The system is a zigzag graphene nanoribbon(http://en.wikipedia.org/wiki/Graphene) and I would like to flip the atomic moment at one of the edge site and constrain both the edge site moments. > 3. I calculated the antiferromagnetic edge site moment using PDOS calculation. I used 'lambda' parameter to constrain the moments. > > 4.Questions: Is 3) the right way to do it? If yes, what should be value of lambda? I used lambda =1 and the scf output (given below) is disturbing... I would like to ask what does "constrained moment : -20.000000" Indeed this looks suspicious... one should look into the code to understand what's going on. You can have a look into add_bfield.f90, it should not be very difficult to understand how it works. Good luck GS > mean and why is the constrain energy so high. If it is not the right way, I would be grateful if you could suggest an alternative. > > Thanking you, > Yours sincerely, > Sreekar Guddeti > Undergraduate (5th year) > Engineering Physics > IIT Bombay > India > > PS: The system namelist for scf calculation and the sample output are given below and the complete input file is attached. > > > -------------------------------------- > ... > ============================================================================== > atom number 15 relative position : -3.5000 6.0622 0.0000 > charge : 0.983302 > magnetization : 0.000256 > magnetization/charge: 0.000260 > constrained moment : 0.309100 > > ============================================================================== > > ============================================================================== > atom number 16 relative position : -3.0000 5.7735 0.0000 > charge : 1.783674 > magnetization : -0.385046 > magnetization/charge: -0.215873 > constrained moment : -20.000000 > > ============================================================================== > ... > ... > > constraint energy (Ryd) = 6095.83663339 > --------------------------------- > > > > -------------------------------- > &SYSTEM > ibrav = 12, > celldm(1) = 4.608737, > celldm(2) = 12.0, > celldm(3) = 10.0, > celldm(4) = -0.50, > nat = 18, > ntyp =10, > starting_magnetization(2)= 0.3091, > starting_magnetization(8)= 0.3091, > occupations='smearing', > smearing='gauss', > degauss=0.01, > nspin=2, > constrained_magnetization='atomic' > lambda = 1 > ecutwfc = 50.D0 , > report = 2 > > / > > > -- > Sreekar Guddeti > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110825/ba3beab2/attachment-0001.htm From thomas.gruber at physik.tu-freiberg.de Thu Aug 25 16:20:25 2011 From: thomas.gruber at physik.tu-freiberg.de (Thomas Gruber) Date: Thu, 25 Aug 2011 16:20:25 +0200 Subject: [Pw_forum] PAW-pseudo potential in splittet phonon calculation Message-ID: <4E565A29.9060902@physik.tu-freiberg.de> Dear all, I splittet a phonon calculation with start_q, last_q and start_irr & last_irr into each representation. Everything worked perfectly fine with QE 4.3.1 for my system when I use *.pz.vbc-pseudopotential. But I wanted to use PAW-pseudopotentials (which I created with atomPAW) and when I use the same splitting I get differences in the frequencies. I followed the GRID_example for the AlAs system and got the following differences in the frequencies: without splitting: omega( 1-3) = -0.420632 [THz] = -14.030759 [cm-1] omega( 4-6) = 22.373134 [THz] = 746.287424 [cm-1] with splitting: omega( 1-3) = 0.225621 [THz] = 7.525921 [cm-1] omega( 4-6) = 22.384860 [THz] = 746.678569 [cm-1] Did I copied the wrong files for each job or is the a problem with the code when using PAW-pseudopotentials? Regards, Thomas From johanneskreutzer at gmx.at Thu Aug 25 16:44:01 2011 From: johanneskreutzer at gmx.at (Johannes Kreutzer) Date: Thu, 25 Aug 2011 16:44:01 +0200 Subject: [Pw_forum] specifying angles in QE Message-ID: <20110825144401.140620@gmx.net> Dear QE community, have a rather very basic question, but i am absolute beginner in QE Do i have to specify angles in the input (e.g. when specifying the bravais lattice) in grad or rad? i assume its rad, but i want to recheck anyway. Have not found any information in the documentation. thanks in advance johannes -- Johannes Kreutzer Project Assistant IMC TU Wien Getreidemarkt 9 / B0C2 +43 01 58801 165234 NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zur?ck-Garantie! Jetzt informieren: http://www.gmx.net/de/go/freephone From max.n.popov at gmail.com Thu Aug 25 17:40:54 2011 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Thu, 25 Aug 2011 17:40:54 +0200 Subject: [Pw_forum] specifying angles in QE In-Reply-To: <20110825144401.140620@gmx.net> References: <20110825144401.140620@gmx.net> Message-ID: Dear Johannes, one has to specify the cosines of the respective angles. > Do i have to specify angles in the input (e.g. when specifying the bravais > lattice) in grad or rad? > > i assume its rad, but i want to recheck anyway. Have not found any > information in the documentation. > > -- Best regards, Max Popov Ph.D. student Materials center Leoben (MCL), Leoben, Austria. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110825/2a7bf421/attachment.htm From xjin.xmu at gmail.com Fri Aug 26 02:01:47 2011 From: xjin.xmu at gmail.com (jinxi) Date: Fri, 26 Aug 2011 08:01:47 +0800 Subject: [Pw_forum] specifying angles in QE In-Reply-To: <20110825144401.140620@gmx.net> References: <20110825144401.140620@gmx.net> Message-ID: <4E56E26B.6050602@gmail.com> Hi, It is well described in the file /espresso-*.*.*/Doc/INPUT_PW.html(txt), in Namelist &SYSTEM, ibrav, all the input parameters are well explained. On 2011?08?25? 22:44, Johannes Kreutzer wrote: > Dear QE community, > > have a rather very basic question, but i am absolute beginner in QE > > Do i have to specify angles in the input (e.g. when specifying the bravais lattice) in grad or rad? > > i assume its rad, but i want to recheck anyway. Have not found any information in the documentation. > > thanks in advance > > johannes > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110826/fb84d93a/attachment.htm From colonel.sreekar at gmail.com Fri Aug 26 03:04:46 2011 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Fri, 26 Aug 2011 06:34:46 +0530 Subject: [Pw_forum] constrained magnetization calculation to converge at the ferromagnetic state Message-ID: @Arles > Dear Sreekar Guddeti, Respected Mr. Rebaza, Thank you for the reply. if you want to calculate a constrained magnetization > with antiparallel direction between the atom 2 and atom 8, you must to put > the "starting_magnetization" tag with opposite value, for example: > > starting_magnetization(2)= 0.3091, > starting_magnetization(8)= -0.3091, > > I wanted to perform a constrained calculation for the parallel spin configuration. -------------------------------------------------------- @Gabriele > Dear Sreekar, > > Respected Mr. Sclauzero, Thank you for the suggestions and the pointers. I would first try to reduce mixing_beta and also lambda (say, to 0.2 or > 0.1). You can then restart the calculation with a larger value of lambda. > Don't forget that for USPP you need to specify also ecutrho, and perhaps you don't need such a high ecutwfc. > If your USPPs are those on the QE website, I would use ecutwfc=35 and > ecutrho=350, for instance. > > I am using USPPs sourced with the package. It seems like I was using an incorrect algorithm to converge scf calculation. I converged with ecut keeping the default ecutrho at gamma point, then with ecutrho, then with kpoints and finally with smearing width. Questions: 1. Would I be right to assume there is no need to converge the calculation with the mixing_beta? 2. How significant it is to start with different sets of initial_magnetizations for an unconstrained calculation considering its arbitrariness and the increased cost of performing them. Quantitatively, how would one determine the density of the sampling from the possible configurations in the light of the accuracy of the calculation involved. Sincerely, Sreekar Guddeti Undergraduate (5th year) Engineering Physics IIT Bombay India > Respected Sir/Madam, > > 1. I would like to perform a constrained magnetization calculation for a > system, whose unconstrained spin polarized calculation gives an > antiferromagnetic state, to converge at the ferromagnetic state. > > 2. The system is a zigzag graphene nanoribbon( > http://en.wikipedia.org/wiki/Graphene) and I would like to flip the atomic > moment at one of the edge site and constrain both the edge site moments. > > 3. I calculated the antiferromagnetic edge site moment using PDOS > calculation. I used 'lambda' parameter to constrain the moments. > > > > 4.Questions: Is 3) the right way to do it? If yes, what should be value > of lambda? I used lambda =1 and the scf output (given below) is > disturbing... I would like to ask what does "constrained moment : > -20.000000" > > Indeed this looks suspicious... one should look into the code to understand > what's going on. You can have a look into add_bfield.f90, it should not be > very difficult to understand how it works. > > Good luck > > > GS > > > > mean and why is the constrain energy so high. If it is not the right > way, I would be grateful if you could suggest an alternative. > > > > Thanking you, > > Yours sincerely, > > Sreekar Guddeti > > Undergraduate (5th year) > > Engineering Physics > > IIT Bombay > > India > > > > PS: The system namelist for scf calculation and the sample output are > given below and the complete input file is attached. > > > > > > -------------------------------------- > > ... > > > ============================================================================== > > atom number 15 relative position : -3.5000 6.0622 0.0000 > > charge : 0.983302 > > magnetization : 0.000256 > > magnetization/charge: 0.000260 > > constrained moment : 0.309100 > > > > > ============================================================================== > > > > > ============================================================================== > > atom number 16 relative position : -3.0000 5.7735 0.0000 > > charge : 1.783674 > > magnetization : -0.385046 > > magnetization/charge: -0.215873 > > constrained moment : -20.000000 > > > > > ============================================================================== > > ... > > ... > > > > constraint energy (Ryd) = 6095.83663339 > > --------------------------------- > > > > > > > > -------------------------------- > > &SYSTEM > > ibrav = 12, > > celldm(1) = 4.608737, > > celldm(2) = 12.0, > > celldm(3) = 10.0, > > celldm(4) = -0.50, > > nat = 18, > > ntyp =10, > > starting_magnetization(2)= 0.3091, > > starting_magnetization(8)= 0.3091, > > occupations='smearing', > > smearing='gauss', > > degauss=0.01, > > nspin=2, > > constrained_magnetization='atomic' > > lambda = 1 > > ecutwfc = 50.D0 , > > report = 2 > > > > / > > > > > > -- > > Sreekar Guddeti > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110825/ba3beab2/attachment.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 50, Issue 59 > **************************************** > -- Sreekar Guddeti -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110826/adea30f8/attachment.htm From trambui at u.boisestate.edu Fri Aug 26 06:08:39 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Thu, 25 Aug 2011 22:08:39 -0600 Subject: [Pw_forum] Fermi energy in DOS calculation Message-ID: Dear QE users, In DOS calculation, one will obtain a Fermi energy value. And my guess is that it is taken with respect to the bottom of the valence band. Am I correct? I have no experiences in DOS vs. energy whatsoever, and still in the state of figuring things out. I really appreciate any input you have. Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110825/d66759fa/attachment-0001.htm From bdslipun at gmail.com Fri Aug 26 14:29:00 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Fri, 26 Aug 2011 17:59:00 +0530 Subject: [Pw_forum] KPOINTS Message-ID: how can one give the k points in nscf calculation (band structure ) of tetragonal phase (B10) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110826/257a2d66/attachment.htm From bdslipun at gmail.com Fri Aug 26 16:22:33 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Fri, 26 Aug 2011 19:52:33 +0530 Subject: [Pw_forum] Fwd: KPOINTS In-Reply-To: References: Message-ID: ---------- Forwarded message ---------- From: bhabya sahoo Date: Fri, Aug 26, 2011 at 5:59 PM Subject: KPOINTS To: PWSCF Forum how can one give the k points in nscf calculation (band structure ) of tetragonal phase (B10) bd sahoo barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110826/05cc8507/attachment.htm From elie.moujaes at hotmail.co.uk Fri Aug 26 19:31:41 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Fri, 26 Aug 2011 18:31:41 +0100 Subject: [Pw_forum] units of q-vectors when performing the ph.x command Message-ID: dear all, a simple question: what are the units of the q vectors we assign in the ph.in file? is it cartesian or in terms of 2 pi/a? N.B: In my bands file, the points are define in terms of the reciprocal lattice vectors b. Thanks Elie Moujaes University of Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110826/5a4d60b9/attachment.htm From degironc at sissa.it Fri Aug 26 21:55:10 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 26 Aug 2011 21:55:10 +0200 Subject: [Pw_forum] units of q-vectors when performing the ph.x command In-Reply-To: References: Message-ID: <4E57FA1E.5040906@sissa.it> cartesians in units of 2pi/a stefano On 08/26/2011 07:31 PM, Elie Moujaes wrote: > dear all, > > a simple question: what are the units of the q vectors we assign in the ph.in file? is it cartesian or in terms of 2 pi/a? > > N.B: In my bands file, the points are define in terms of the reciprocal lattice vectors b. > > Thanks > > Elie Moujaes > University of Nottingham > NG7 2RD > UK > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110826/a931de78/attachment.htm From mahdi_fn109 at yahoo.com Sat Aug 27 12:32:45 2011 From: mahdi_fn109 at yahoo.com (Mahdi Faqieh nasiri) Date: Sat, 27 Aug 2011 03:32:45 -0700 (PDT) Subject: [Pw_forum] error in epsilon.x calculation Message-ID: <1314441165.78238.YahooMailNeo@web43136.mail.sp1.yahoo.com> Dear all, what means this error in epsilon.x calculation? CRASH ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ? ? ?task # ? ? ? ? 0 ? ? ?from grid_build : error # ? ? ? ? 2 ? ? ?non unifrom kpt grid ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ? Mahdi Faghih nasiri MSC, Guilan University, Rasht, Iran. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110827/75058da1/attachment.htm From modaresi.mohsen at gmail.com Sat Aug 27 12:47:54 2011 From: modaresi.mohsen at gmail.com (Mohsen Modaresi) Date: Sat, 27 Aug 2011 03:47:54 -0700 Subject: [Pw_forum] error in epsilon.x calculation In-Reply-To: <1314441165.78238.YahooMailNeo@web43136.mail.sp1.yahoo.com> References: <1314441165.78238.YahooMailNeo@web43136.mail.sp1.yahoo.com> Message-ID: Dear Mahdi, Before ask a new question check the previous discussion. you should set, nosym = .TRUE. , noinv = .TRUE. , Best Rigards, On Sat, Aug 27, 2011 at 3:32 AM, Mahdi Faqieh nasiri wrote: > Dear all, > what means this error in epsilon.x calculation? > > CRASH > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from grid_build : error # 2 > non unifrom kpt grid > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > Mahdi Faghih nasiri > MSC, > Guilan University, > Rasht, Iran. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Mohsen Modarresi, PhD student of Solid State Physics, Ferdowsi University of Mashhad, Iran. Phone +98-9133452131 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110827/25ceeb4a/attachment.htm From colonel.sreekar at gmail.com Sat Aug 27 13:07:36 2011 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Sat, 27 Aug 2011 16:37:36 +0530 Subject: [Pw_forum] KPOINTS Message-ID: @bhabya Respected Mr. Sahoo, > > how can one give the k points in nscf calculation (band structure ) of > tetragonal phase (B10) > If by this you mean selection of kpoints along a path in the Brillouin zone(generally connecting the symmetry points), I would suggest two options: 1. Use XCrysden (http://www.xcrysden.org/XCrySDen.html) . It has an option for generating kpoints. 2. Write ur own recipe in your favourite language :D ... its fairly simple. Make sure the format is consistent with that used in pwscf. PS: Its a suggestion that you start your mail with a polite address to the community... just a suggestion... chill Sincerely, Sreekar Guddeti Undergraduate (5th year) Engineering Physics IIT Bombay India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110827/2b4f2a90/attachment.htm From kacper.druzbicki at uj.edu.pl Mon Aug 29 00:20:59 2011 From: kacper.druzbicki at uj.edu.pl (=?iso-8859-2?Q?=22Kacper_Dru=BFbicki=22?=) Date: Mon, 29 Aug 2011 00:20:59 +0200 Subject: [Pw_forum] Raman Spectra of Molecular Crystals Message-ID: Dear QE Users, My name is Casper and I am a newbie in Quantum Espresso with some experience in modeling with other periodic codes (mainly CASTEP and DMOL3). Please forgive me bothering you with my question. I don't want to spam QE maillist, but I would like to kindly ask someone for some help in modeling of vibrational spectra of molecular crystals. Could anyone send me any exemplary input which allows to compute IR and Raman spectra of any simple system? I am rather disoriented while reading some manuals etc. and I am not sure how to start. I would really appreciate your help. With best wishes, Casper Kacper Dru?bicki, Faculty of Chemistry, Department of Chemical Physics, Jagiellonian University, Ingardena Street 3, 30-060 Krak?w, Poland phone: +48 12 6632265 From mtorabi at uwo.ca Mon Aug 29 00:34:53 2011 From: mtorabi at uwo.ca (Amin Torabi) Date: Sun, 28 Aug 2011 18:34:53 -0400 Subject: [Pw_forum] convergence w.r.t ecutwfc In-Reply-To: References: Message-ID: Dear QE-users, Will you please take a look at my input file and convergence table below: I am using PBE USPP for both hydrogen and boron, but calculating energies using PBEsol. (ecutrho is set to 12* ecutwfc.) My question is: 1. Does it look normal? I was expecting to see 1mRy accuracy at lower ecutwfc values. 2. I didn't use "occupations" or "smearing" and I didn't get any error in output files. Do they affect the convergence? 3. I want to do vc-relax calculation at high pressure. Based on my table, what ecutwfc do you suggest? Thanks in advance. ecutwfc energy 30 -38.28149597 35 -38.28437812 40 -38.28554856 45 -38.28658930 50 -38.28772083 55 -38.28883141 60 -38.28989311 65 -38.29086868 70 -38.29167889 75 -38.29227767 80 -38.29267847 85 -38.29291696 90 -38.29302834 95 -38.29305836 100 -38.29305908 105 -38.29307545 110 -38.29313486 115 -38.29324982 &control pseudo_dir = ** outdir = ** prefix = '$a' tstress = .true tprnfor = .true verbosity = 'low' / &SYSTEM ibrav = 12 celldm(1) = 8.31479435 celldm(2) = 1.3 celldm(3) = 1.4772727273 celldm(4) = -0.260504508642648 nat = 16 ntyp = 2 ecutwfc = $a ecutrho = `expr 12 \* $a` input_dft = 'pbesol' / &ELECTRONS / ATOMIC_SPECIES B 10.811 B.pbe-n-van_ak.UPF H 1.00794 H.pbe-van_ak.UPF ATOMIC_POSITIONS crystal B 0.002 0.146 0.042 H -0.194 0.166 0.140 H 0.196 0.294 -0.005 H 0.104 -0.019 0.112 B -0.002 -0.146 -0.042 H 0.194 -0.166 -0.140 H -0.196 -0.294 0.005 H -0.104 0.019 -0.112 B 0.498 0.354 0.542 H 0.694 0.334 0.640 H 0.304 0.206 0.495 H 0.396 0.519 0.612 B 0.502 0.646 0.458 H 0.306 0.666 0.360 H 0.696 0.794 0.505 H 0.604 0.481 0.388 K_POINTS automatic 8 8 8 0 0 0 -- Amin Torabi Ph.D. Student Chemistry Department The University *of* Western Ontario London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** -- Amin Torabi Ph.D. Student Chemistry Department The University *of* Western Ontario London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110828/ecda885b/attachment.htm From tfcao at theory.issp.ac.cn Mon Aug 29 05:11:04 2011 From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=) Date: Mon, 29 Aug 2011 11:11:04 +0800 Subject: [Pw_forum] =?utf-8?q?sample=5Fbias_of_STM_simulation?= Message-ID: <20110829031104.8057.qmail@ms.hfcas.ac.cn> Dear QE users I want to get the STM image of hydrogen atoms adsorbed on graphene .So I have to set the parameter "sample_bias" . How can I get it' value. Any suggestions. Thanks in advance. ----?? Sun, 28 Aug 2011 09:22:39 +0200 ??????: ---- > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/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. error in epsilon.x calculation (Mahdi Faqieh nasiri) > 2. Re: error in epsilon.x calculation (Mohsen Modaresi) > 3. Re: KPOINTS (sreekar guddeti) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 27 Aug 2011 03:32:45 -0700 (PDT) > From: Mahdi Faqieh nasiri > Subject: [Pw_forum] error in epsilon.x calculation > To: "pw_forum at pwscf.org" > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > what means this error in epsilon.x calculation? > > CRASH > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > ? ? ?task # ? ? ? ? 0 > ? ? ?from grid_build : error # ? ? ? ? 2 > ? ? ?non unifrom kpt grid > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > ? > Mahdi Faghih nasiri > MSC, > Guilan University, > Rasht, Iran. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110827/75058da1/attachment.html > > ------------------------------ > > Message: 2 > Date: Sat, 27 Aug 2011 03:47:54 -0700 > From: Mohsen Modaresi > Subject: Re: [Pw_forum] error in epsilon.x calculation > To: Mahdi Faqieh nasiri , PWSCF Forum > > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Mahdi, > Before ask a new question check the previous discussion. you should set, > > nosym = .TRUE. , > noinv = .TRUE. , > Best Rigards, > > On Sat, Aug 27, 2011 at 3:32 AM, Mahdi Faqieh nasiri > wrote: > > > Dear all, > > what means this error in epsilon.x calculation? > > > > CRASH > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > task # 0 > > from grid_build : error # 2 > > non unifrom kpt grid > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > Mahdi Faghih nasiri > > MSC, > > Guilan University, > > Rasht, Iran. > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > Mohsen Modarresi, > PhD student of Solid State Physics, Ferdowsi University of Mashhad, Iran. > Phone +98-9133452131 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110827/25ceeb4a/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Sat, 27 Aug 2011 16:37:36 +0530 > From: sreekar guddeti > Subject: Re: [Pw_forum] KPOINTS > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > @bhabya > Respected Mr. Sahoo, > > > > > > how can one give the k points in nscf calculation (band structure ) of > > tetragonal phase (B10) > > > > If by this you mean selection of kpoints along a path in the Brillouin > zone(generally connecting the symmetry points), I would suggest two options: > 1. Use XCrysden (http://www.xcrysden.org/XCrySDen.html) . It has an option > for generating kpoints. > 2. Write ur own recipe in your favourite language :D ... its fairly simple. > Make sure the format is consistent with that used in pwscf. > > PS: Its a suggestion that you start your mail with a polite address to the > community... just a suggestion... chill > > Sincerely, > Sreekar Guddeti > Undergraduate (5th year) > Engineering Physics > IIT Bombay > India > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110827/2b4f2a90/attachment-0001.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 50, Issue 62 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/b1af5de8/attachment-0001.htm From nkxirainbow at gmail.com Mon Aug 29 05:22:00 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 29 Aug 2011 11:22:00 +0800 Subject: [Pw_forum] Raman Spectra of Molecular Crystals In-Reply-To: References: Message-ID: Dear Kacper Dru?bicki: Read the document in your installation directory : /espresso-XXX/examples/README carefully. Then you will find what you need:) 2011/8/29 "Kacper Dru?bicki" > Dear QE Users, > > My name is Casper and I am a newbie in Quantum Espresso with some > experience in modeling with other periodic codes (mainly CASTEP and DMOL3). > Please forgive me bothering you with my question. I don't want to spam QE > maillist, but I would like to kindly ask someone for some help in modeling > of vibrational spectra of molecular crystals. Could anyone send me any > exemplary input which allows to compute IR and Raman spectra of any simple > system? I am rather disoriented while reading some manuals etc. and I am not > sure how to start. I would really appreciate your help. > > With best wishes, > Casper > > Kacper Dru?bicki, > Faculty of Chemistry, > Department of Chemical Physics, > Jagiellonian University, > Ingardena Street 3, 30-060 Krak?w, Poland > phone: +48 12 6632265 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ____________________________________ Hui Wang School of physics, Fudan University, Shanghai, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/846a13a3/attachment.htm From mohnish.iitk at gmail.com Mon Aug 29 09:25:42 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Mon, 29 Aug 2011 12:55:42 +0530 Subject: [Pw_forum] convergence w.r.t ecutwfc In-Reply-To: References: Message-ID: Dear Amin! Are you trying to calculate the energy of BH3 dimer? If it so then the vacuum space you have used is very less, there will be lot of spurious interaction. Increase the vacuum space such that the minimum distance between the images is greater than 15 angstrom. Please try it. On Mon, Aug 29, 2011 at 4:04 AM, Amin Torabi wrote: > Dear QE-users, > > > Will you please take a look at my input file and convergence table below: > > I am using PBE USPP for both hydrogen and boron, but calculating energies > using PBEsol. (ecutrho is set to 12* ecutwfc.) > > My question is: > 1. Does it look normal? I was expecting to see 1mRy accuracy at lower > ecutwfc values. > 2. I didn't use "occupations" or "smearing" and I didn't get any error in > output files. Do they affect the convergence? > 3. I want to do vc-relax calculation at high pressure. Based on my table, > what ecutwfc do you suggest? > > Thanks in advance. > > > > ecutwfc energy > 30 -38.28149597 > 35 -38.28437812 > 40 -38.28554856 > 45 -38.28658930 > 50 -38.28772083 > 55 -38.28883141 > 60 -38.28989311 > 65 -38.29086868 > 70 -38.29167889 > 75 -38.29227767 > 80 -38.29267847 > 85 -38.29291696 > 90 -38.29302834 > 95 -38.29305836 > 100 -38.29305908 > 105 -38.29307545 > 110 -38.29313486 > 115 -38.29324982 > > &control > pseudo_dir = ** > outdir = ** > prefix = '$a' > tstress = .true > tprnfor = .true > verbosity = 'low' > / > &SYSTEM > ibrav = 12 > celldm(1) = 8.31479435 > celldm(2) = 1.3 > celldm(3) = 1.4772727273 > celldm(4) = -0.260504508642648 > nat = 16 > ntyp = 2 > ecutwfc = $a > ecutrho = `expr 12 \* $a` > input_dft = 'pbesol' > / > &ELECTRONS > / > ATOMIC_SPECIES > B 10.811 B.pbe-n-van_ak.UPF > H 1.00794 H.pbe-van_ak.UPF > ATOMIC_POSITIONS crystal > B 0.002 0.146 0.042 > H -0.194 0.166 0.140 > H 0.196 0.294 -0.005 > H 0.104 -0.019 0.112 > B -0.002 -0.146 -0.042 > H 0.194 -0.166 -0.140 > H -0.196 -0.294 0.005 > H -0.104 0.019 -0.112 > B 0.498 0.354 0.542 > H 0.694 0.334 0.640 > H 0.304 0.206 0.495 > H 0.396 0.519 0.612 > B 0.502 0.646 0.458 > H 0.306 0.666 0.360 > H 0.696 0.794 0.505 > H 0.604 0.481 0.388 > K_POINTS automatic > 8 8 8 0 0 0 > > -- > Amin Torabi > Ph.D. Student > Chemistry Department > The University *of* Western Ontario > London, On Canada, N6A 5B7 > Phone: 519-661-2111 Ext: 87871 > **************************************** > > > > -- > Amin Torabi > Ph.D. Student > Chemistry Department > The University *of* Western Ontario > London, On Canada, N6A 5B7 > Phone: 519-661-2111 Ext: 87871 > **************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/5e4ecca6/attachment.htm From jchuang at pub.iams.sinica.edu.tw Mon Aug 29 11:17:52 2011 From: jchuang at pub.iams.sinica.edu.tw (jchuang) Date: Mon, 29 Aug 2011 17:17:52 +0800 Subject: [Pw_forum] The number of bands increases with c-axial Message-ID: <000f01cc662c$8825e200$9871a600$@iams.sinica.edu.tw> Dear all, When I computed the band structure of bi-layer graphene. I found that if I fix the displacement of two layers (3.3A) and other parameters. Change the c-axial (celldm(3)) only. The number of bands will be different. c-axial 17.29 A loss 3 bands 24.62 A equals to the result from VASP (should be the correct one) 29.9 A 2 bands more than 24.62 A 33.2 A 5 bands more than 24.62 A Why 29.9A and 33.2A has more bands compared to 24.62A? For a 2D structure, greater c-axial can generate the correct result. (with the same interlayer displacement) Isn't it right? Best regards, J. C. Huang IAMS, Taiwan ================ following is my input files for 24.62 A ================ Scf.in &control calculation ='scf' restart_mode ='from_scratch' pseudo_dir ='/lustre/lwork/dyyang/bin/espresso-4.0.3/pseudo/' outdir ='./' prefix ='AuC' disk_io='low', wf_collect=.TRUE., / &system ibrav = 0, celldm(1) = 4.65217057370607, nat = 4, ntyp = 1, ecutwfc = 60, ecutrho = 600, occupations = "smearing", smearing = 'mp' degauss = 0.02 / &electrons diagonalization='david' conv_thr = 1.0e-08 mixing_beta = 0.7 / ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF CELL_PARAMETERS (alat) 0.991038192 0.000000000 0.000000000 -0.495519096 0.858264250 0.000000000 0.000000000 0.000000000 10.000581284 ATOMIC_POSITIONS (crystal) C -0.333333333 0.333333333 0.000000000 0 0 0 C 0.333333333 -0.333333333 0.000000000 0 0 0 C -0.333333333 0.333333333 0.132422202 0 0 0 C 0.000000000 0.000000000 0.132422202 0 0 0 K_POINTS (automatic) 16 16 2 0 0 0 Band1.in # self-consistent calculation &control calculation='bands', restart_mode='from_scratch', prefix='AuC', pseudo_dir = '/lustre/lwork/dyyang/bin/espresso-4.0.3/pseudo/', outdir='./' disk_io='low', wf_collect=.TRUE., / &system ibrav=0 celldm(1)=4.65217057370607, nat=4, ntyp=1, nosym=.T., nbnd=50, ecutwfc = 60, ecutrho = 600.0, occupations='smearing', smearing='mp', degauss=0.02 / &electrons diagonalization='david' conv_thr = 1.0e-08 mixing_beta = 0.7 / ATOMIC_SPECIES C 12.0107 C.pz-vbc.UPF CELL_PARAMETERS (alat) 0.991038192 0.000000000 0.000000000 -0.495519096 0.858264250 0.000000000 0.000000000 0.000000000 10.000581284 ATOMIC_POSITIONS (crystal) C -0.333333333 0.333333333 0.000000000 0 0 0 C 0.333333333 -0.333333333 0.000000000 0 0 0 C -0.333333333 0.333333333 0.132422202 0 0 0 C 0.000000000 0.000000000 0.132422202 0 0 0 K_POINTS {crystal} 49 0.50000000 0.00000000 0.00000000 1 0.46875000 0.00000000 0.00000000 2 0.43750000 0.00000000 0.00000000 3 0.40625000 0.00000000 0.00000000 4 0.37500000 0.00000000 0.00000000 5 0.34375000 0.00000000 0.00000000 6 0.31250000 0.00000000 0.00000000 7 0.28125000 0.00000000 0.00000000 8 0.25000000 0.00000000 0.00000000 9 0.21875000 0.00000000 0.00000000 10 0.18750000 0.00000000 0.00000000 11 0.15625000 0.00000000 0.00000000 12 0.12500000 0.00000000 0.00000000 13 0.09375000 0.00000000 0.00000000 14 0.06250000 0.00000000 0.00000000 15 0.03125000 0.00000000 0.00000000 16 0.00000000 0.00000000 0.00000000 17 0.02083333 0.02083333 0.00000000 18 0.04166666 0.04166666 0.00000000 19 0.06249999 0.06249999 0.00000000 20 0.08333332 0.08333332 0.00000000 21 0.10416666 0.10416666 0.00000000 22 0.12499999 0.12499999 0.00000000 23 0.14583332 0.14583332 0.00000000 24 0.16666665 0.16666665 0.00000000 25 0.18749998 0.18749998 0.00000000 26 0.20833331 0.20833331 0.00000000 27 0.22916664 0.22916664 0.00000000 28 0.24999997 0.24999997 0.00000000 29 0.27083331 0.27083331 0.00000000 30 0.29166664 0.29166664 0.00000000 31 0.31249997 0.31249997 0.00000000 32 0.33333330 0.33333330 0.00000000 33 0.34374997 0.31249997 0.00000000 34 0.35416664 0.29166664 0.00000000 35 0.36458331 0.27083331 0.00000000 36 0.37499997 0.24999997 0.00000000 37 0.38541664 0.22916664 0.00000000 38 0.39583331 0.20833331 0.00000000 39 0.40624998 0.18749998 0.00000000 40 0.41666665 0.16666665 0.00000000 41 0.42708332 0.14583332 0.00000000 42 0.43749999 0.12499999 0.00000000 43 0.44791666 0.10416666 0.00000000 44 0.45833333 0.08333333 0.00000000 45 0.46874999 0.06249999 0.00000000 46 0.47916666 0.04166666 0.00000000 47 0.48958333 0.02083333 0.00000000 48 0.50000000 0.00000000 0.00000000 49 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/0712bce3/attachment.htm From modaresi.mohsen at gmail.com Mon Aug 29 12:30:54 2011 From: modaresi.mohsen at gmail.com (Mohsen Modaresi) Date: Mon, 29 Aug 2011 03:30:54 -0700 Subject: [Pw_forum] sample_bias of STM simulation In-Reply-To: <20110829031104.8057.qmail@ms.hfcas.ac.cn> References: <20110829031104.8057.qmail@ms.hfcas.ac.cn> Message-ID: Dear Cao, The WaNT package could simulate coherent transport between two electrodes. In the Landuer-Buttiker formalism by increasing the bias voltage energy window opens and current increases. WaNT cna calculate current in the Landuer-Buttiker approach. On Sun, Aug 28, 2011 at 8:11 PM, Cao TF wrote: > ** > Dear QE users > I want to get the STM image of hydrogen atoms adsorbed on graphene .So I > have to set the parameter "sample_bias" . How can I get it' value. Any > suggestions. Thanks in advance. > > > > ----?? Sun, 28 Aug 2011 09:22:39 +0200 ??????: ---- > > > > Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/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. error in epsilon.x calculation (Mahdi Faqieh nasiri) > > 2. Re: error in epsilon.x calculation (Mohsen Modaresi) > > 3. Re: KPOINTS (sreekar guddeti) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 27 Aug 2011 03:32:45 -0700 (PDT) > > From: Mahdi Faqieh nasiri > > Subject: [Pw_forum] error in epsilon.x calculation > > To: "pw_forum at pwscf.org" > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear all, > > what means this error in epsilon.x calculation? > > > > CRASH > > > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > ? ? ?task # ? ? ? ? 0 > > ? ? ?from grid_build : error # ? ? ? ? 2 > > ? ? ?non unifrom kpt grid > > > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > ? > > Mahdi Faghih nasiri > > MSC, > > Guilan University, > > Rasht, Iran. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110827/75058da1/attachment.html > **> > > > > ------------------------------ > > > > Message: 2 > > Date: Sat, 27 Aug 2011 03:47:54 -0700 > > From: Mohsen Modaresi > > Subject: Re: [Pw_forum] error in epsilon.x calculation > > To: Mahdi Faqieh nasiri , PWSCF Forum > > > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Mahdi, > > Before ask a new question check the previous discussion. you should set, > > > > nosym = .TRUE. , > > noinv = .TRUE. , > > Best Rigards, > > > > On Sat, Aug 27, 2011 at 3:32 AM, Mahdi Faqieh nasiri > > wrote: > > > > > Dear all, > > > what means this error in epsilon.x calculation? > > > > > > CRASH > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > task # 0 > > > from grid_build : error # 2 > > > non unifrom kpt grid > > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > > > > > Mahdi Faghih nasiri > > > MSC, > > > Guilan University, > > > Rasht, Iran. > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > -- > > Mohsen Modarresi, > > PhD student of Solid State Physics, Ferdowsi University of Mashhad, Iran. > > > Phone +98-9133452131 > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110827/25ceeb4a/attachment-0001.htm > **> > > > > ------------------------------ > > > > Message: 3 > > Date: Sat, 27 Aug 2011 16:37:36 +0530 > > From: sreekar guddeti > > Subject: Re: [Pw_forum] KPOINTS > > To: > > pw_forum at pwscf.org > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > @bhabya > > Respected Mr. Sahoo, > > > > > > > > > > how can one give the k points in nscf calculation (band structure ) of > > > > tetragonal phase (B10) > > > > > > > If by this you mean selection of kpoints along a path in the Brillouin > > zone(generally connecting the symmetry points), I would suggest two > options: > > 1. Use XCrysden (http://www.xcrysden.org/XCrySDen.html) . It has an > option > > for generating kpoints. > > 2. Write ur own recipe in your favourite language :D ... its fairly > simple. > > Make sure the format is consistent with that used in pwscf. > > > > PS: Its a suggestion that you start your mail with a polite address to > the > > community... just a suggestion... chill > > > > Sincerely, > > Sreekar Guddeti > > Undergraduate (5th year) > > Engineering Physics > > IIT Bombay > > India > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110827/2b4f2a90/attachment-0001.htm > **> > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 50, Issue 62 > > **************************************** > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Mohsen Modarresi, PhD student of Solid State Physics, Ferdowsi University of Mashhad, Iran. Phone +98-9133452131 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/25f1dcf5/attachment-0001.htm From mtorabi at uwo.ca Mon Aug 29 14:27:06 2011 From: mtorabi at uwo.ca (Amin Torabi) Date: Mon, 29 Aug 2011 08:27:06 -0400 Subject: [Pw_forum] convergence w.r.t ecutwfc In-Reply-To: References: Message-ID: Dear Mohnish, Based on the following experimental papers, diborane has 16 atoms in a monoclinic unit cell (c=4.4A, b=5.72A, a=6.5A and g=105.1deg), and as far as I can understand, this is what XcrysDen is showing Smith, H. W.; Lipscomb, W. N. J. Chem. Phys. 1965, 43, 1060?1064. Jones, D. S.; Lipscomb, W. N. J. Chem. Phys. 1969, 51, 3133?3134 And please notice that the atomic positions are in "crystal". Now, could you please further explain your comment, because I am afraid I didn't get your point. Many thanks Amin On Mon, Aug 29, 2011 at 3:25 AM, mohnish pandey wrote: > Dear Amin! > > Are you trying to calculate the energy of BH3 dimer? If it so then the > vacuum space you have used is very less, there will be lot of spurious > interaction. Increase the vacuum space such that the minimum distance > between the images is greater than 15 angstrom. Please try it. > > On Mon, Aug 29, 2011 at 4:04 AM, Amin Torabi wrote: > >> Dear QE-users, >> >> >> Will you please take a look at my input file and convergence table below: >> >> I am using PBE USPP for both hydrogen and boron, but calculating energies >> using PBEsol. (ecutrho is set to 12* ecutwfc.) >> >> My question is: >> 1. Does it look normal? I was expecting to see 1mRy accuracy at lower >> ecutwfc values. >> 2. I didn't use "occupations" or "smearing" and I didn't get any error in >> output files. Do they affect the convergence? >> 3. I want to do vc-relax calculation at high pressure. Based on my table, >> what ecutwfc do you suggest? >> >> Thanks in advance. >> >> >> >> ecutwfc energy >> 30 -38.28149597 >> 35 -38.28437812 >> 40 -38.28554856 >> 45 -38.28658930 >> 50 -38.28772083 >> 55 -38.28883141 >> 60 -38.28989311 >> 65 -38.29086868 >> 70 -38.29167889 >> 75 -38.29227767 >> 80 -38.29267847 >> 85 -38.29291696 >> 90 -38.29302834 >> 95 -38.29305836 >> 100 -38.29305908 >> 105 -38.29307545 >> 110 -38.29313486 >> 115 -38.29324982 >> >> &control >> pseudo_dir = ** >> outdir = ** >> prefix = '$a' >> tstress = .true >> tprnfor = .true >> verbosity = 'low' >> / >> &SYSTEM >> ibrav = 12 >> celldm(1) = 8.31479435 >> celldm(2) = 1.3 >> celldm(3) = 1.4772727273 >> celldm(4) = -0.260504508642648 >> nat = 16 >> ntyp = 2 >> ecutwfc = $a >> ecutrho = `expr 12 \* $a` >> input_dft = 'pbesol' >> / >> &ELECTRONS >> / >> ATOMIC_SPECIES >> B 10.811 B.pbe-n-van_ak.UPF >> H 1.00794 H.pbe-van_ak.UPF >> ATOMIC_POSITIONS crystal >> B 0.002 0.146 0.042 >> H -0.194 0.166 0.140 >> H 0.196 0.294 -0.005 >> H 0.104 -0.019 0.112 >> B -0.002 -0.146 -0.042 >> H 0.194 -0.166 -0.140 >> H -0.196 -0.294 0.005 >> H -0.104 0.019 -0.112 >> B 0.498 0.354 0.542 >> H 0.694 0.334 0.640 >> H 0.304 0.206 0.495 >> H 0.396 0.519 0.612 >> B 0.502 0.646 0.458 >> H 0.306 0.666 0.360 >> H 0.696 0.794 0.505 >> H 0.604 0.481 0.388 >> K_POINTS automatic >> 8 8 8 0 0 0 >> >> -- >> Amin Torabi >> Ph.D. Student >> Chemistry Department >> The University *of* Western Ontario >> London, On Canada, N6A 5B7 >> Phone: 519-661-2111 Ext: 87871 >> **************************************** >> >> >> >> -- >> Amin Torabi >> Ph.D. Student >> Chemistry Department >> The University *of* Western Ontario >> London, On Canada, N6A 5B7 >> Phone: 519-661-2111 Ext: 87871 >> **************************************** >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > BTech-Mtech, IIT Kanpur > Senior Project Associate, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Amin Torabi Ph.D. Student Chemistry Department The University *of* Western Ontario London, On Canada, N6A 5B7 Phone: 519-661-2111 Ext: 87871 **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/c4d4e12f/attachment.htm From gabriele.sclauzero at epfl.ch Mon Aug 29 14:38:22 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 29 Aug 2011 14:38:22 +0200 Subject: [Pw_forum] sample_bias of STM simulation In-Reply-To: <20110829031104.8057.qmail@ms.hfcas.ac.cn> References: <20110829031104.8057.qmail@ms.hfcas.ac.cn> Message-ID: <8EF86184-E754-44A5-8B3C-56CC5B08DDB6@epfl.ch> Dear Cao, the easiest reply would be: from the experiment (that you want to compare with). HTH GS P.S: A rule of politeness of this forum is to sign posts with your name and affiliation. Another one is not to quote unnecessary text from the forum digest in the new posts. Please take a few seconds to read this before posting again: http://www.quantum-espresso.org/wiki/index.php/Pw_users Il giorno 29/ago/2011, alle ore 05.11, Cao TF ha scritto: > Dear QE users > I want to get the STM image of hydrogen atoms adsorbed on graphene .So I have to set the parameter "sample_bias" . How can I get it' value. Any suggestions. Thanks in advance. > > > > ----?? Sun, 28 Aug 2011 09:22:39 +0200 ??????: ---- > > > > Send Pw_forum mailing list submissions to > > pw_forum at pwscf.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.democritos.it/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. error in epsilon.x calculation (Mahdi Faqieh nasiri) > > 2. Re: error in epsilon.x calculation (Mohsen Modaresi) > > 3. Re: KPOINTS (sreekar guddeti) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Sat, 27 Aug 2011 03:32:45 -0700 (PDT) > > From: Mahdi Faqieh nasiri > > Subject: [Pw_forum] error in epsilon.x calculation > > To: "pw_forum at pwscf.org" > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear all, > > what means this error in epsilon.x calculation? > > > > CRASH > > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > ? ? ?task # ? ? ? ? 0 > > ? ? ?from grid_build : error # ? ? ? ? 2 > > ? ? ?non unifrom kpt grid > > ?%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > ? > > Mahdi Faghih nasiri > > MSC, > > Guilan University, > > Rasht, Iran. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110827/75058da1/attachment.html<>> > > > > ------------------------------ > > > > Message: 2 > > Date: Sat, 27 Aug 2011 03:47:54 -0700 > > From: Mohsen Modaresi > > Subject: Re: [Pw_forum] error in epsilon.x calculation > > To: Mahdi Faqieh nasiri , PWSCF Forum > > > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear Mahdi, > > Before ask a new question check the previous discussion. you should set, > > > > nosym = .TRUE. , > > noinv = .TRUE. , > > Best Rigards, > > > > On Sat, Aug 27, 2011 at 3:32 AM, Mahdi Faqieh nasiri > > wrote: > > > > > Dear all, > > > what means this error in epsilon.x calculation? > > > > > > CRASH > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > task # 0 > > > from grid_build : error # 2 > > > non unifrom kpt grid > > > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > > > > > Mahdi Faghih nasiri > > > MSC, > > > Guilan University, > > > Rasht, Iran. > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > > -- > > Mohsen Modarresi, > > PhD student of Solid State Physics, Ferdowsi University of Mashhad, Iran. > > Phone +98-9133452131 > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110827/25ceeb4a/attachment-0001.htm<>> > > > > ------------------------------ > > > > Message: 3 > > Date: Sat, 27 Aug 2011 16:37:36 +0530 > > From: sreekar guddeti > > Subject: Re: [Pw_forum] KPOINTS > > To: pw_forum at pwscf.org > > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > @bhabya > > Respected Mr. Sahoo, > > > > > > > > > > how can one give the k points in nscf calculation (band structure ) of > > > tetragonal phase (B10) > > > > > > > If by this you mean selection of kpoints along a path in the Brillouin > > zone(generally connecting the symmetry points), I would suggest two options: > > 1. Use XCrysden (http://www.xcrysden.org/XCrySDen.html) . It has an option > > for generating kpoints. > > 2. Write ur own recipe in your favourite language :D ... its fairly simple. > > Make sure the format is consistent with that used in pwscf. > > > > PS: Its a suggestion that you start your mail with a polite address to the > > community... just a suggestion... chill > > > > Sincerely, > > Sreekar Guddeti > > Undergraduate (5th year) > > Engineering Physics > > IIT Bombay > > India > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110827/2b4f2a90/attachment-0001.htm<>> > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 50, Issue 62 > > **************************************** > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/0d8124cf/attachment-0001.htm From antonio.msj1 at gmail.com Mon Aug 29 15:07:21 2011 From: antonio.msj1 at gmail.com (Antonio) Date: Mon, 29 Aug 2011 10:07:21 -0300 Subject: [Pw_forum] Phonon: "data-file.#iq.#irr.xml" files Message-ID: Dear QE' users. In phonon calculations are generated some "data-file.#iq.#irr.xml" files (*.phsave directory). In this files there are two columns. what information are contained there? Best regards. -- Doutorando Ant?nio M. Da Silva Jr. NEQC: Nucleo de Estudos em Quimica Computacional Departamento de Quimica - ICE Universidade Federal de Juiz de Fora Campus Universitario S/N 36.036-330 Juiz de Fora - MG - Brasil http://lattes.cnpq.br/0895213089855328 From Lorenzo.Paulatto at impmc.upmc.fr Mon Aug 29 15:46:35 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 29 Aug 2011 15:46:35 +0200 Subject: [Pw_forum] Phonon: "data-file.#iq.#irr.xml" files In-Reply-To: References: Message-ID: On Mon, 29 Aug 2011 15:07:21 +0200, Antonio wrote: > In phonon calculations are generated some "data-file.#iq.#irr.xml" > files (*.phsave directory). In this files there are two columns. what > information are contained there? Dear Antonio, those are internal files, which are not supposed to be read by the code users... anyway, the columns are the real and imaginary part of the element of line #irr if the dynamical matrix at point #iq best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From antonio.msj1 at gmail.com Mon Aug 29 15:53:31 2011 From: antonio.msj1 at gmail.com (Antonio) Date: Mon, 29 Aug 2011 10:53:31 -0300 Subject: [Pw_forum] Phonon: "data-file.#iq.#irr.xml" files In-Reply-To: References: Message-ID: Dear Lorenzo. Thank you for your contribution. 2011/8/29 Lorenzo Paulatto : > On Mon, 29 Aug 2011 15:07:21 +0200, Antonio wrote: >> In phonon calculations are generated some "data-file.#iq.#irr.xml" >> files (*.phsave directory). In this files there are two columns. what >> information are contained there? > > Dear Antonio, > those are internal files, which are not supposed to be read by the code > users... anyway, the columns are the real and imaginary part of the > element of line #irr if the dynamical matrix at point #iq > > best regards > > -- > Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: ? http://www-int.impmc.upmc.fr/~paulatto/ > mail: ?23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Doutorando Ant?nio M. Da Silva Jr. NEQC: Nucleo de Estudos em Quimica Computacional Departamento de Quimica - ICE Universidade Federal de Juiz de Fora Campus Universitario S/N 36.036-330 Juiz de Fora - MG - Brasil http://lattes.cnpq.br/0895213089855328 From tfcao at theory.issp.ac.cn Mon Aug 29 16:27:26 2011 From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=) Date: Mon, 29 Aug 2011 22:27:26 +0800 Subject: [Pw_forum] (no subject) Message-ID: <20110829142726.15875.qmail@ms.hfcas.ac.cn> Dear Gabriele Sclauzero Thank you very much for the kind reply. I will try to find it from the experiments and try it in my simulations -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/b4f72423/attachment.htm From colonel.sreekar at gmail.com Mon Aug 29 17:11:06 2011 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Mon, 29 Aug 2011 20:41:06 +0530 Subject: [Pw_forum] The number of bands increases with c-axial Message-ID: > > Dear all, > Respected Mr. Huang > When I computed the band structure of bi-layer graphene. > > I found that if I fix the displacement of two layers (3.3A) and other > parameters. Change the c-axial (celldm(3)) only. > > The number of bands will be different. > > > The only possible way I can interpret this (I may be wrong) is the variation in the d-like bands (clutter of bands just above the Fermi level). I did a quick(ecut 30,360 Ry) calculation using your 'c' parameters and I got a similar band structure (I restricted #of bands to 20). I think you may not have scaled the z-coordinates accordingly. To confirm the d-character of the clutter-bands, perform k-resolved DOS calculations... the output is really soothing to the eyes :P. If you intend to perform a precise calculation (of order of 1 meV as your ecut suggests), I may suggest convergence with degauss. Finally, as I too am learning the code, I would like to ask if there is any issue to use other Bravais lattice instead of ibrav=0? 24.62 A equals to the result from VASP (should be the correct one) > why should VASP be 'the correct one'... I wouldnt see it as an authority ;) PS: Let me know if I am wrong. Sincerely, Sreekar Guddeti Undergraduate (5th year) IIT Bombay India -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/b1c2d7e0/attachment.htm From karandeepster at gmail.com Mon Aug 29 17:19:14 2011 From: karandeepster at gmail.com (karan deep) Date: Mon, 29 Aug 2011 20:49:14 +0530 Subject: [Pw_forum] problem in lderiv curves for Sr pseuopotentials Message-ID: i am trying to generate pseudopotentials for LDA in Sr i don't know why logarithmic derivatives are showing extra what u can call them spikes in original wave functions. i am attaching my input as well as ldplot files here thanks for all reply Karandeep Research Scholar Physics Department, IIT, Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/c7f8d0e9/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: sr-ps.in Type: application/octet-stream Size: 946 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110829/c7f8d0e9/attachment-0001.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: gnuplot.ps Type: application/postscript Size: 145147 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110829/c7f8d0e9/attachment-0001.ps From Lorenzo.Paulatto at impmc.upmc.fr Mon Aug 29 17:44:40 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 29 Aug 2011 17:44:40 +0200 Subject: [Pw_forum] problem in lderiv curves for Sr pseuopotentials In-Reply-To: References: Message-ID: On Mon, 29 Aug 2011 17:19:14 +0200, karan deep wrote: > i don't know why logarithmic derivatives are showing extra what u can > call them spikes in original wave functions. i am attaching my input as > well as ldplot files here the original (all-electron) wave functions have nodes, hence the logarithmic derivatives (phi'(r)/phi(r)) have spikes (divergencies) -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From baroni at sissa.it Mon Aug 29 18:20:23 2011 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 29 Aug 2011 18:20:23 +0200 Subject: [Pw_forum] The number of bands increases with c-axial In-Reply-To: References: Message-ID: <0E79CC5D-8867-4680-A580-4FAABDFC8A9A@sissa.it> Dear all: On Aug 29, 2011, at 5:11 PM, sreekar guddeti wrote: > Respected Mr. Huang > > > When I computed the band structure of bi-layer graphene. > > I found that if I fix the displacement of two layers (3.3A) and other > parameters. Change the c-axial (celldm(3)) only. > > The number of bands will be different. ... as it should. It's just a matter of state counting, I believe. Let's consider a simple example, where you compare two structures, one having the c parameter twice as large as the other (say, c and 2c), and let's concentrate on what happens along the z axis. k=0 (kz=0, i should say) of the first structure will correspond to TWO wavevectors (k=0 and k=pi/c) of the second. Hence, when you calculate the band structure of the first, for any value of kz you will obtain twice as many states as in the second (corresponding to kz and kz+pi/c) > The only possible way I can interpret this (I may be wrong) is the variation in the d-like bands (clutter of bands just above the Fermi level). I did a quick(ecut 30,360 Ry) calculation using your 'c' parameters and I got a similar band structure (I restricted #of bands to 20). I think you may not have scaled the z-coordinates accordingly. To confirm the d-character of the clutter-bands, perform k-resolved DOS calculations... the output is really soothing to the eyes :P. If you intend to perform a precise calculation (of order of 1 meV as your ecut suggests), I may suggest convergence with degauss. As said, I think that the explanation is simpler than this, but I may have misunderstood the problem in the first place ... > Finally, as I too am learning the code, I would like to ask if there is any issue to use other Bravais lattice instead of ibrav=0? I do not think so, but ... why not ibrav=0? > 24.62 A equals to the result from VASP (should be the correct one) > why should VASP be 'the correct one'... I wouldnt see it as an authority ;) Here I agree, but I would also argue that the two codes (vasp and pwscf) should result in the same energy bands, when given the same input structure. Is this the case? Hope this helps Stefano B --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/78aa1d81/attachment.htm From mayankaditya at gmail.com Mon Aug 29 19:04:54 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Mon, 29 Aug 2011 22:34:54 +0530 Subject: [Pw_forum] Problem with symmetry in Body center tetragonal structure Message-ID: I am doing phonon calculation for BCT structure with 12 atoms in primitive cell. But in scf calculation the stress tensor is not satisfying the symmetry condition. I mean two diagonal component of stress matrix should be same. And in phonon calculation I got 36 independent branch while according to group theory some of them should be degenerate. Kindly give your comments. Thanks MAYANK BARC MUMBAI, INDIA From gabriele.sclauzero at epfl.ch Mon Aug 29 19:36:12 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Mon, 29 Aug 2011 19:36:12 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <20110829142726.15875.qmail@ms.hfcas.ac.cn> References: <20110829142726.15875.qmail@ms.hfcas.ac.cn> Message-ID: <3E37371B-FFC4-4750-AC03-532BC08B4564@epfl.ch> You're welcome! But you didn't read the posting rules, did you?! Cheers GS Il giorno 29/ago/2011, alle ore 16.27, Cao TF ha scritto: > Dear Gabriele Sclauzero > Thank you very much for the kind reply. I will try to find it from the experiments and try it in my simulations > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/b18e31ff/attachment.htm From bdslipun at gmail.com Mon Aug 29 20:01:04 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Mon, 29 Aug 2011 23:31:04 +0530 Subject: [Pw_forum] input of B10 STRUCTURE Message-ID: WHAT SHOULD BE THE INPUT STRUCTURE OF B10 IN ESPRESSO what should be the value of ibrv either tetragonal primitive or bct and what is the position of atoms in the unit cell(no of atoms) beacause i am not getting the true structure in Crystden view. bd sahoo reserch scholar barc mumbai -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/b513a703/attachment.htm From martins at if.uff.br Mon Aug 29 20:10:59 2011 From: martins at if.uff.br (martins at if.uff.br) Date: Mon, 29 Aug 2011 15:10:59 -0300 Subject: [Pw_forum] Problem with Ni/Ni3Al system Message-ID: <20110829151059.2001434txxckkwmr@webmail.if.uff.br> Dear all, I'm trying to study the Ni/Ni3Al system. For starting, I built a Nx = Ny = Nz = 2 supercell (the Ni and Ni3Al lattice parameters are very close), resulting a 32 atoms system. The input file is: &control calculation = 'vc-relax' restart_mode= 'from_scratch' prefix='NiNi3Al' tstress = .true. tprnfor = .true. pseudo_dir = '/home/martins/programas/espresso-4.2.1/pseudo/', outdir='/home/martins/calculos/QE/NiNi3Al/32at/' / &system ibrav = 1, celldm(1) = 13.45, nat = 32, ntyp = 2, ecutwfc = 50.0, nspin = 2, starting_magnetization(1) = 0.0, starting_magnetization(2) = 0.2, occupations = 'smearing', smearing = 'mv', degauss = 0.02, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-6 / &ions ion_dynamics = 'bfgs' / &cell cell_dynamics = 'bfgs' cell_dofree = 'z' / ATOMIC_SPECIES Al 26.981 Al.pbe-sp-van.UPF Ni 58.693 Ni.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Ni 0.00000 0.00000 0.00000 Ni 0.00000 1.77936 1.77936 Ni 1.77936 1.77936 0.00000 Ni 1.77936 0.00000 1.77936 Ni 3.55872 0.00000 0.00000 Ni 3.55872 1.77936 1.77936 Ni 5.33807 1.77936 0.00000 Ni 5.33807 0.00000 1.77936 Ni 0.00000 3.55872 0.00000 Ni 0.00000 5.33807 1.77936 Ni 1.77936 5.33807 0.00000 Ni 1.77936 3.55872 1.77936 Ni 3.55872 3.55872 0.00000 Ni 3.55872 5.33807 1.77936 Ni 5.33807 5.33807 0.00000 Ni 5.33807 3.55872 1.77936 Al 0.00000 0.00000 3.55872 Ni 0.00000 1.77936 5.33807 Ni 1.77936 1.77936 3.55872 Ni 1.77936 0.00000 5.33807 Al 3.55872 0.00000 3.55872 Ni 3.55872 1.77936 5.33807 Ni 5.33807 1.77936 3.55872 Ni 5.33807 0.00000 5.33807 Al 0.00000 3.55872 3.55872 Ni 0.00000 5.33807 5.33807 Ni 1.77936 5.33807 3.55872 Ni 1.77936 3.55872 5.33807 Al 3.55872 3.55872 3.55872 Ni 3.55872 5.33807 5.33807 Ni 5.33807 5.33807 3.55872 Ni 5.33807 3.55872 5.33807 K_POINTS automatic 2 2 2 0 0 0 However, I've got the following error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from cdiaghg : error # 201 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I did some variations on the input parameters (CG instead of DAVID, DAMP instead of BFGS, ...) and the calculation continue to giving the same error message. Are there some problem with my input file? Any suggestion? I appreciate any help. Best regards, Adriano ------------------------------------ Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense ------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From ivan.girotto at ichec.ie Mon Aug 29 20:52:34 2011 From: ivan.girotto at ichec.ie (Ivan Girotto) Date: Mon, 29 Aug 2011 19:52:34 +0100 Subject: [Pw_forum] Job openings at ICHEC Message-ID: <4E5BDFF2.40805@ichec.ie> Dear all, the Irish Center for High-End Computing (ICHEC ) have recently opened four computational scientist positions . The positions might be of interest to this community as we are seeking to recruit four suitably qualified candidates to deliver the Irish contribution to the Partnership for Advanced Computing in Europe (PRACE). In all the PRACE applications related work packages ICHEC is involved, it has a serious commitment in Material Science area with strong interest to the QE package. I would also like to mention that ICHEC is committed to port the PWscf code on GPU clusters for further PRACE Tier-1 productions. If you are interested in the open positions, you can either directly apply or contact me at my email address (ivan.girotto at ichec.ie). Best regards, Ivan Girotto -- Girotto Ivan -ivan.girotto at ichec.ie ICHEC - Computational Group -http://www.ichec.ie The Tower - 7th floor Trinity Technology& Enterprise Campus Grand Canal Quay - Dublin 2 - Ireland +353-1-5241608 ex. 32 (ph) / +353-1-7645845 (fax) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/5655ca67/attachment.htm From giannozz at democritos.it Mon Aug 29 21:28:53 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 29 Aug 2011 21:28:53 +0200 Subject: [Pw_forum] Problem with symmetry in Body center tetragonal structure In-Reply-To: References: Message-ID: <195E6EE5-FD81-4132-AD62-97B417C1A911@democritos.it> On Aug 29, 2011, at 19:04 , mayank gupta wrote: > I am doing phonon calculation for BCT structure with 12 atoms in > primitive cell. But in scf calculation the stress tensor is not > satisfying the symmetry condition. has your structure the expected symmetry? if so, your stress tensor will also have the expected symmetry. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Aug 29 21:32:15 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 29 Aug 2011 21:32:15 +0200 Subject: [Pw_forum] Fermi energy in DOS calculation In-Reply-To: References: Message-ID: <21440AFC-77D1-4DC5-AAFB-2D2F34C7432F@democritos.it> On Aug 26, 2011, at 6:08 , Tram Bui wrote: > In DOS calculation, one will obtain a Fermi energy value. And my > guess is > that it is taken with respect to the bottom of the valence band. the Fermi energy is taken on the same energy scale as for Kohn-Sham eigenvalues P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Aug 29 21:37:02 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 29 Aug 2011 21:37:02 +0200 Subject: [Pw_forum] Does SOC conflict with HSE06? In-Reply-To: <201108231754519374915@163.com> References: <201108231754519374915@163.com> Message-ID: On Aug 24, 2011, at 2:30 , lilonghua wrote: > SOC is ok! HSE06 is also OK! But when combining SOC and HSE06, > the calculation stop at EXX calculation! how does it stop? with an error message? with a segmentation fault? with no message at all? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Aug 29 21:42:31 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 29 Aug 2011 21:42:31 +0200 Subject: [Pw_forum] Can not find minimum free energy by QHA In-Reply-To: <10da8b04.97f4.131ef5866ac.Coremail.flux_ray12@163.com> References: <10da8b04.97f4.131ef5866ac.Coremail.flux_ray12@163.com> Message-ID: <82A5F624-34FB-43C6-B518-F7E1353EADD5@democritos.it> On Aug 22, 2011, at 4:36 , GAO Zhe wrote: > However, the free energy kept decreasing as a monotone decreasing > function of lattice parameter you mean: the "vibrational free energy" alone, or "the sum of the energy and of the vibrational free energy"? the vibrational free energy should be a small correction to the total energy. P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Mon Aug 29 21:44:57 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 29 Aug 2011 21:44:57 +0200 Subject: [Pw_forum] Serial algorithm In-Reply-To: References: Message-ID: On Aug 20, 2011, at 8:56 , Ramesh Kumar wrote: > Please somebody let me know about > > "Subspace diagonalization in iterative solution of the eigenvalue > problem: > a serial algorithm will be used" do you know how iterative diagonalization (or iterative orthonormalization in Car-Parrinello) works? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From eugeniofs at iq.ufrj.br Mon Aug 29 21:57:02 2011 From: eugeniofs at iq.ufrj.br (Eugenio Furtado) Date: Mon, 29 Aug 2011 16:57:02 -0300 (BRT) Subject: [Pw_forum] Problem with Ni/Ni3Al system In-Reply-To: <322808552.28269.1314647738940.JavaMail.root@mail.iq.ufrj.br> Message-ID: <685820264.28272.1314647822128.JavaMail.root@mail.iq.ufrj.br> Dear brazilian coleague, I didn't find anythig wrong with your input. So, I succeded and it is still running (is now in the first iteration..). Anything wasnt changed... Best regards! Abra?o! Egn ----- Mensagem original ----- De: martins at if.uff.br Para: "pw forum" Enviadas: Segunda-feira, 29 de Agosto de 2011 15:10:59 Assunto: [Pw_forum] Problem with Ni/Ni3Al system Dear all, I'm trying to study the Ni/Ni3Al system. For starting, I built a Nx = Ny = Nz = 2 supercell (the Ni and Ni3Al lattice parameters are very close), resulting a 32 atoms system. The input file is: &control calculation = 'vc-relax' restart_mode= 'from_scratch' prefix='NiNi3Al' tstress = .true. tprnfor = .true. pseudo_dir = '/home/martins/programas/espresso-4.2.1/pseudo/', outdir='/home/martins/calculos/QE/NiNi3Al/32at/' / &system ibrav = 1, celldm(1) = 13.45, nat = 32, ntyp = 2, ecutwfc = 50.0, nspin = 2, starting_magnetization(1) = 0.0, starting_magnetization(2) = 0.2, occupations = 'smearing', smearing = 'mv', degauss = 0.02, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-6 / &ions ion_dynamics = 'bfgs' / &cell cell_dynamics = 'bfgs' cell_dofree = 'z' / ATOMIC_SPECIES Al 26.981 Al.pbe-sp-van.UPF Ni 58.693 Ni.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Ni 0.00000 0.00000 0.00000 Ni 0.00000 1.77936 1.77936 Ni 1.77936 1.77936 0.00000 Ni 1.77936 0.00000 1.77936 Ni 3.55872 0.00000 0.00000 Ni 3.55872 1.77936 1.77936 Ni 5.33807 1.77936 0.00000 Ni 5.33807 0.00000 1.77936 Ni 0.00000 3.55872 0.00000 Ni 0.00000 5.33807 1.77936 Ni 1.77936 5.33807 0.00000 Ni 1.77936 3.55872 1.77936 Ni 3.55872 3.55872 0.00000 Ni 3.55872 5.33807 1.77936 Ni 5.33807 5.33807 0.00000 Ni 5.33807 3.55872 1.77936 Al 0.00000 0.00000 3.55872 Ni 0.00000 1.77936 5.33807 Ni 1.77936 1.77936 3.55872 Ni 1.77936 0.00000 5.33807 Al 3.55872 0.00000 3.55872 Ni 3.55872 1.77936 5.33807 Ni 5.33807 1.77936 3.55872 Ni 5.33807 0.00000 5.33807 Al 0.00000 3.55872 3.55872 Ni 0.00000 5.33807 5.33807 Ni 1.77936 5.33807 3.55872 Ni 1.77936 3.55872 5.33807 Al 3.55872 3.55872 3.55872 Ni 3.55872 5.33807 5.33807 Ni 5.33807 5.33807 3.55872 Ni 5.33807 3.55872 5.33807 K_POINTS automatic 2 2 2 0 0 0 However, I've got the following error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from cdiaghg : error # 201 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I did some variations on the input parameters (CG instead of DAVID, DAMP instead of BFGS, ...) and the calculation continue to giving the same error message. Are there some problem with my input file? Any suggestion? I appreciate any help. Best regards, Adriano ------------------------------------ Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense ------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Eugenio Furtado de Souza Laboratorio de Modelagem Molecular-LABMMOL Universidade Federal do Rio de Janeiro Av. Athos da Silveira Ramos No 149, CT, Bloco A, sala 609 tel: (21) 2562-7132 Cidade Universit?ria, Ilha do Fund?o, Rio de Janeiro-RJ, CEP 21941-90 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/a1241a65/attachment.htm From martins at if.uff.br Mon Aug 29 23:17:34 2011 From: martins at if.uff.br (martins at if.uff.br) Date: Mon, 29 Aug 2011 18:17:34 -0300 Subject: [Pw_forum] Problem with Ni/Ni3Al system Message-ID: <20110829181734.265869369ilotfxq@webmail.if.uff.br> Dear Eugenio, Dear all: > Dear brazilian coleague, I didn't find anythig wrong with your > input. So, I succeded and it is still > running (is now in the > first iteration..). Anything wasnt changed... Best regards! Abra?o! > Egn Motivated by your message, I re-run the calculation, but now using just ONE processor (before, I runned the calculation in four processors, using MPI). Now the program works! Thus, I have two questions: (i) Is it possible to be a version problem? I'm using the 4.3.2 version of the Quantum Espresso. (ii) I can be a compilation problem? In this case I supply other information: I runned other calculations for other supercell dimensions and using MPI (4 processors) and the calculations were fine! Best regards to all, Adriano ------------------------------------ Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense ------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From foursea at 163.com Tue Aug 30 02:51:48 2011 From: foursea at 163.com (lilonghua) Date: Tue, 30 Aug 2011 08:51:48 +0800 Subject: [Pw_forum] Does SOC conflict with HSE06? Message-ID: <201108300851475627351@163.com> Dear Paolo Giannozzi, The error message is about MPI: "Fatal error in PMPI_Barrier: Other MPI error, error stack: PMPI_Barrier(363).................: MPI_Barrier(comm=0x84000005) failed MPIR_Barrier_impl(251)............: MPIR_Bcast_impl(1150).............: ..." some contents of output file are listed as following: "... ... Self-consistent Calculation iteration # 1 ecut= 35.00 Ry beta=0.50 Davidson diagonalization with overlap ethr = 1.00E-02, avg # of iterations = 6.6 ... ... iteration # 3 ecut= 35.00 Ry beta=0.50 Davidson diagonalization with overlap ethr = 7.20E-05, avg # of iterations = 3.3 total cpu time spent up to now is 50.1 secs End of self-consistent calculation k = 0.7071 0.0000 0.0000 ( 1588 PWs) bands (ev): ... ... k = 0.0000 0.0000 0.0000 ( 1639 PWs) bands (ev): -7.0743 -7.0743 -0.6100 -0.6100 2.8041 2.8041 3.9266 3.9266 3.9266 3.9266 7.5157 7.5157 9.6413 9.6413 9.6413 9.6413 10.7299 10.7340 10.8087 10.8418 highest occupied, lowest unoccupied level (ev): 4.8845 4.9068 " ok! ---this is the end of output file. in normal condition, it will print exx information, but in my case (hse+soc), it stops at the end of scf. 2011-08-30 lilonghua foursea at 163.com From didi5158 at gmail.com Tue Aug 30 05:13:57 2011 From: didi5158 at gmail.com (Wang Di) Date: Tue, 30 Aug 2011 11:13:57 +0800 Subject: [Pw_forum] input of B10 STRUCTURE In-Reply-To: References: Message-ID: Dear sahoo: the simplest method is that: no matter the crystal structure are primitive, face, base or body one, simply set the primitive one, then import the position of all atoms in the unit cell. (the position of all atoms can get from the *.cell file using Ms software) wang di 2011/8/30 bhabya sahoo > WHAT SHOULD BE THE INPUT STRUCTURE OF B10 IN ESPRESSO > what should be the value of ibrv either tetragonal primitive or bct and > what is the position of atoms in the unit cell(no of atoms) > beacause i am not getting the true structure in Crystden view. > > > > > > > > > > > > > > > > > bd sahoo > reserch scholar > barc > mumbai > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ----------------------------------------------------------------- *Wang Di** The Crystal Lab,* *AnHui Institute of Optics and Fine Mechanics, *** *Chinese Academy of Sciences,** No350. , Shushanhu Road, Hefei, 230031, China**, E-mail: WangDiean at gmail.com** ,* ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/ad4292be/attachment.htm From bdslipun at gmail.com Tue Aug 30 07:13:35 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 30 Aug 2011 10:43:35 +0530 Subject: [Pw_forum] input of B10 STRUCTURE In-Reply-To: References: Message-ID: where i can find that please clarify me clearly On Tue, Aug 30, 2011 at 8:43 AM, Wang Di wrote: > Dear sahoo: > > the simplest method is that: no matter the crystal structure are primitive, > face, base or body one, simply set the primitive one, then import the > position of all atoms in the unit cell. (the position of all atoms can get > from the *.cell file using Ms software) > > wang di > > 2011/8/30 bhabya sahoo > >> WHAT SHOULD BE THE INPUT STRUCTURE OF B10 IN ESPRESSO >> what should be the value of ibrv either tetragonal primitive or bct and >> what is the position of atoms in the unit cell(no of atoms) >> beacause i am not getting the true structure in Crystden view. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> bd sahoo >> reserch scholar >> barc >> mumbai >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ----------------------------------------------------------------- > *Wang Di** > The Crystal Lab,* > *AnHui Institute of Optics and Fine Mechanics, *** > *Chinese Academy of Sciences,** > No350. , Shushanhu Road, Hefei, 230031, China**, > E-mail: WangDiean at gmail.com** ,* > ----------------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/4d2f9df6/attachment.htm From bdslipun at gmail.com Tue Aug 30 08:12:34 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 30 Aug 2011 11:42:34 +0530 Subject: [Pw_forum] input of B10 STRUCTURE In-Reply-To: References: Message-ID: how can one give the spce group for tetragonal and orthorombhic structures in espresso On Tue, Aug 30, 2011 at 8:43 AM, Wang Di wrote: > Dear sahoo: > > the simplest method is that: no matter the crystal structure are primitive, > face, base or body one, simply set the primitive one, then import the > position of all atoms in the unit cell. (the position of all atoms can get > from the *.cell file using Ms software) > > wang di > > 2011/8/30 bhabya sahoo > >> WHAT SHOULD BE THE INPUT STRUCTURE OF B10 IN ESPRESSO >> what should be the value of ibrv either tetragonal primitive or bct and >> what is the position of atoms in the unit cell(no of atoms) >> beacause i am not getting the true structure in Crystden view. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> bd sahoo >> reserch scholar >> barc >> mumbai >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ----------------------------------------------------------------- > *Wang Di** > The Crystal Lab,* > *AnHui Institute of Optics and Fine Mechanics, *** > *Chinese Academy of Sciences,** > No350. , Shushanhu Road, Hefei, 230031, China**, > E-mail: WangDiean at gmail.com** ,* > ----------------------------------------------------------------- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/0eaaff11/attachment.htm From didi5158 at gmail.com Tue Aug 30 08:31:56 2011 From: didi5158 at gmail.com (Wang Di) Date: Tue, 30 Aug 2011 14:31:56 +0800 Subject: [Pw_forum] input of B10 STRUCTURE In-Reply-To: References: Message-ID: http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id3900444 web of input 2011/8/30 bhabya sahoo > how can one give the spce group for tetragonal and orthorombhic structures > in espresso > > > On Tue, Aug 30, 2011 at 8:43 AM, Wang Di wrote: > >> Dear sahoo: >> >> the simplest method is that: no matter the crystal structure are >> primitive, face, base or body one, simply set the primitive one, then import >> the position of all atoms in the unit cell. (the position of all atoms can >> get from the *.cell file using Ms software) >> >> wang di >> >> 2011/8/30 bhabya sahoo >> >>> WHAT SHOULD BE THE INPUT STRUCTURE OF B10 IN ESPRESSO >>> what should be the value of ibrv either tetragonal primitive or bct and >>> what is the position of atoms in the unit cell(no of atoms) >>> beacause i am not getting the true structure in Crystden view. >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> bd sahoo >>> reserch scholar >>> barc >>> mumbai >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> ----------------------------------------------------------------- >> *Wang Di** >> The Crystal Lab,* >> *AnHui Institute of Optics and Fine Mechanics, *** >> *Chinese Academy of Sciences,** >> No350. , Shushanhu Road, Hefei, 230031, China**, >> E-mail: WangDiean at gmail.com** ,* >> ----------------------------------------------------------------- >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ----------------------------------------------------------------- *Wang Di** The Crystal Lab,* *AnHui Institute of Optics and Fine Mechanics, *** *Chinese Academy of Sciences,** No350. , Shushanhu Road, Hefei, 230031, China**, E-mail: WangDiean at gmail.com** ,* ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/4c72e3c4/attachment-0001.htm From jchuang at pub.iams.sinica.edu.tw Tue Aug 30 08:57:14 2011 From: jchuang at pub.iams.sinica.edu.tw (jchuang) Date: Tue, 30 Aug 2011 14:57:14 +0800 Subject: [Pw_forum] Problem with band structure computation Message-ID: <000001cc66e2$0cae8df0$260ba9d0$@iams.sinica.edu.tw> Dear all, I've got a problem when computing the band structure for mono-layer CaC6. The paper I followed is here (Arxiv preprint arXiv:1105.3736, 2011 - arxiv.org). They got their results from QE, too. The problem is not about QE running process. It's about the result I got from QE simulation. If I set the parameters (atomic positions and celldm) as the same as paper. The band structure I got was different from paper. Some bands are fine, but some are distorted. For example, part of a band with flat shape be tilted. The link for my result is here. (http://imgur.com/fUSna) It looks like something wrong with my atomic structure. But it isn't. I had examined the atomic structure and k-path for many times. To check the validity of atomic positions. I also tried the same structure with VASP. The result from VASP could fit the paper pretty well. To check the validity of input files for QE. (parameters and k-path) I tried to plot the band structure of mono-layer LiC6 with QE. The band structure of LiC6 could fit the paper, too. I had tried to relax the structure or use other pseudo potential files, but still none better. Why I use the correct structure and correct input files, but couldn't get a correct result? Have there been any wrong in my input setting? Could someone please give me any advices or clues? Any suggestions will be greatly appreciated. Best regards, J. C. Huang IAMS, Taiwan ================= the following is my input files ================= Scf.in &control calculation ='scf' restart_mode ='from_scratch' pseudo_dir ='/lustre/lwork/dyyang/bin/espresso-4.0.3/pseudo/' outdir ='./' prefix ='AuC' disk_io='low', wf_collect=.TRUE., / &system ibrav = 4, celldm(1) = 8.050232711, celldm(3) = 4.694835681, nat = 7, ntyp = 2, ecutwfc = 45, ecutrho = 400, occupations = "smearing", smearing = 'gaussian' degauss = 0.002D0 / &electrons diagonalization='david' mixing_mode = 'plain' conv_thr = 1.0e-08 mixing_beta = 0.7 / &ions bfgs_ndim = 3, ATOMIC_SPECIES Ca 40.08 Ca.pz-n-vbc.UPF C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS {crystal} Ca 0.66667 0.33333 0.61200 C 0.33333 0.00000 0.50000 C 0.33333 0.33333 0.50000 C 0.00000 0.33333 0.50000 C 0.00000 0.66667 0.50000 C 0.66667 0.66667 0.50000 C 0.66667 0.00000 0.50000 K_POINTS (automatic) 16 16 1 0 0 0 Band1.in # self-consistent calculation &control calculation='bands', restart_mode='from_scratch', prefix='AuC', pseudo_dir = '/lustre/lwork/dyyang/bin/espresso-4.0.3/pseudo/', outdir='./' tstress = .true. tprnfor = .true. forc_conv_thr = 1.0e-3 / &system ibrav = 4, celldm(1) = 8.050232711, celldm(3) = 4.694835681, nat=7, ntyp=2 ecutwfc =45.0, ecutrho =400, occupations = "smearing", smearing = "gaussian", degauss = 0.002D0, nbnd= 20 / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0e-8 / &ions bfgs_ndim = 3, ATOMIC_SPECIES Ca 40.08 Ca.pz-n-vbc.UPF C 12.0107 C.pz-vbc.UPF ATOMIC_POSITIONS {crystal} Ca 0.66667 0.33333 0.61200 C 0.33333 0.00000 0.50000 C 0.33333 0.33333 0.50000 C 0.00000 0.33333 0.50000 C 0.00000 0.66667 0.50000 C 0.66667 0.66667 0.50000 C 0.66667 0.00000 0.50000 K_POINTS {crystal} 49 0.00000000 0.00000000 0.00000000 1 0.03125000 0.00000000 0.00000000 2 0.06250000 0.00000000 0.00000000 3 0.09375000 0.00000000 0.00000000 4 0.12500000 0.00000000 0.00000000 5 0.15625000 0.00000000 0.00000000 6 0.18750000 0.00000000 0.00000000 7 0.21875000 0.00000000 0.00000000 8 0.25000000 0.00000000 0.00000000 9 0.28125000 0.00000000 0.00000000 10 0.31250000 0.00000000 0.00000000 11 0.34375000 0.00000000 0.00000000 12 0.37500000 0.00000000 0.00000000 13 0.40625000 0.00000000 0.00000000 14 0.43750000 0.00000000 0.00000000 15 0.46875000 0.00000000 0.00000000 16 0.50000000 0.00000000 0.00000000 17 0.48958333 0.02083333 0.00000000 18 0.47916666 0.04166666 0.00000000 19 0.46874999 0.06249999 0.00000000 20 0.45833333 0.08333332 0.00000000 21 0.44791666 0.10416666 0.00000000 22 0.43749999 0.12499999 0.00000000 23 0.42708332 0.14583332 0.00000000 24 0.41666665 0.16666665 0.00000000 25 0.40624998 0.18749998 0.00000000 26 0.39583331 0.20833331 0.00000000 27 0.38541664 0.22916664 0.00000000 28 0.37499997 0.24999997 0.00000000 29 0.36458331 0.27083331 0.00000000 30 0.35416664 0.29166664 0.00000000 31 0.34374997 0.31249997 0.00000000 32 0.33333330 0.33333330 0.00000000 33 0.31249997 0.31249997 0.00000000 34 0.29166664 0.29166664 0.00000000 35 0.27083331 0.27083331 0.00000000 36 0.24999997 0.24999997 0.00000000 37 0.22916664 0.22916664 0.00000000 38 0.20833331 0.20833331 0.00000000 39 0.18749998 0.18749998 0.00000000 40 0.16666665 0.16666665 0.00000000 41 0.14583332 0.14583332 0.00000000 42 0.12499999 0.12499999 0.00000000 43 0.10416666 0.10416666 0.00000000 44 0.08333333 0.08333333 0.00000000 45 0.06249999 0.06249999 0.00000000 46 0.04166666 0.04166666 0.00000000 47 0.02083333 0.02083333 0.00000000 48 0.00000000 0.00000000 0.00000000 49 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/df8cd838/attachment.htm From gabriele.sclauzero at epfl.ch Tue Aug 30 09:33:31 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 30 Aug 2011 09:33:31 +0200 Subject: [Pw_forum] Problem with Ni/Ni3Al system In-Reply-To: <20110829151059.2001434txxckkwmr@webmail.if.uff.br> References: <20110829151059.2001434txxckkwmr@webmail.if.uff.br> Message-ID: <5FFF9B56-B6B0-418C-9E6F-31B04053AD5B@epfl.ch> Dear Adriano, first, why don't you specify ecutrho? Then, which linear algebra libraries are you using (and also which compiler, which OS,...)? GS Il giorno 29/ago/2011, alle ore 20.10, ha scritto: > Dear all, > > I'm trying to study the Ni/Ni3Al system. For starting, I built a Nx = > Ny = Nz = 2 supercell (the Ni and Ni3Al lattice parameters are very > close), resulting a 32 atoms system. The input file is: > > &control > calculation = 'vc-relax' > restart_mode= 'from_scratch' > prefix='NiNi3Al' > tstress = .true. > tprnfor = .true. > pseudo_dir = '/home/martins/programas/espresso-4.2.1/pseudo/', > outdir='/home/martins/calculos/QE/NiNi3Al/32at/' > / > &system > ibrav = 1, > celldm(1) = 13.45, > nat = 32, > ntyp = 2, > ecutwfc = 50.0, > nspin = 2, > starting_magnetization(1) = 0.0, > starting_magnetization(2) = 0.2, > occupations = 'smearing', > smearing = 'mv', > degauss = 0.02, > / > &electrons > diagonalization='david' > mixing_mode = 'plain' > mixing_beta = 0.7 > conv_thr = 1.0d-6 > / > &ions > ion_dynamics = 'bfgs' > / > &cell > cell_dynamics = 'bfgs' > cell_dofree = 'z' > / > ATOMIC_SPECIES > Al 26.981 Al.pbe-sp-van.UPF > Ni 58.693 Ni.pbe-nd-rrkjus.UPF > ATOMIC_POSITIONS angstrom > Ni 0.00000 0.00000 0.00000 > Ni 0.00000 1.77936 1.77936 > Ni 1.77936 1.77936 0.00000 > Ni 1.77936 0.00000 1.77936 > Ni 3.55872 0.00000 0.00000 > Ni 3.55872 1.77936 1.77936 > Ni 5.33807 1.77936 0.00000 > Ni 5.33807 0.00000 1.77936 > Ni 0.00000 3.55872 0.00000 > Ni 0.00000 5.33807 1.77936 > Ni 1.77936 5.33807 0.00000 > Ni 1.77936 3.55872 1.77936 > Ni 3.55872 3.55872 0.00000 > Ni 3.55872 5.33807 1.77936 > Ni 5.33807 5.33807 0.00000 > Ni 5.33807 3.55872 1.77936 > Al 0.00000 0.00000 3.55872 > Ni 0.00000 1.77936 5.33807 > Ni 1.77936 1.77936 3.55872 > Ni 1.77936 0.00000 5.33807 > Al 3.55872 0.00000 3.55872 > Ni 3.55872 1.77936 5.33807 > Ni 5.33807 1.77936 3.55872 > Ni 5.33807 0.00000 5.33807 > Al 0.00000 3.55872 3.55872 > Ni 0.00000 5.33807 5.33807 > Ni 1.77936 5.33807 3.55872 > Ni 1.77936 3.55872 5.33807 > Al 3.55872 3.55872 3.55872 > Ni 3.55872 5.33807 5.33807 > Ni 5.33807 5.33807 3.55872 > Ni 5.33807 3.55872 5.33807 > K_POINTS automatic > 2 2 2 0 0 0 > > However, I've got the following error message: > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > task # 0 > from cdiaghg : error # 201 > diagonalization (ZHEGV*) failed > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > I did some variations on the input parameters (CG instead of DAVID, > DAMP instead of BFGS, ...) and the calculation continue to giving the > same error message. Are there some problem with my input file? Any > suggestion? > > I appreciate any help. Best regards, > > Adriano > > ------------------------------------ > Adriano de Souza Martins > Professor Adjunto III > Departamento de F?sica - ICEx > Polo Universit?rio de Volta Redonda > Universidade Federal Fluminense > ------------------------------------ > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/84ed600d/attachment-0001.htm From elbuesta at icqmail.com Tue Aug 30 11:34:09 2011 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Tue, 30 Aug 2011 05:34:09 -0400 (EDT) Subject: [Pw_forum] Problem with Ni/Ni3Al system In-Reply-To: <5FFF9B56-B6B0-418C-9E6F-31B04053AD5B@epfl.ch> References: <20110829151059.2001434txxckkwmr@webmail.if.uff.br> <5FFF9B56-B6B0-418C-9E6F-31B04053AD5B@epfl.ch> Message-ID: <8CE350F1A2B6140-D50-336@webmail-d063.sysops.aol.com> Dear Adriano, I just tested your input here in our cluster I was not able to reproduce your error. When does it occur, is it in the end of the optimization? Fabio Negreiros Ribeiro CNR - Pisa Il giorno 29/ago/2011, alle ore 20.10, ha scritto: Dear all, I'm trying to study the Ni/Ni3Al system. For starting, I built a Nx = Ny = Nz = 2 supercell (the Ni and Ni3Al lattice parameters are very close), resulting a 32 atoms system. The input file is: &control calculation = 'vc-relax' restart_mode= 'from_scratch' prefix='NiNi3Al' tstress = .true. tprnfor = .true. pseudo_dir = '/home/martins/programas/espresso-4.2.1/pseudo/', outdir='/home/martins/calculos/QE/NiNi3Al/32at/' / &system ibrav = 1, celldm(1) = 13.45, nat = 32, ntyp = 2, ecutwfc = 50.0, nspin = 2, starting_magnetization(1) = 0.0, starting_magnetization(2) = 0.2, occupations = 'smearing', smearing = 'mv', degauss = 0.02, / &electrons diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-6 / &ions ion_dynamics = 'bfgs' / &cell cell_dynamics = 'bfgs' cell_dofree = 'z' / ATOMIC_SPECIES Al 26.981 Al.pbe-sp-van.UPF Ni 58.693 Ni.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Ni 0.00000 0.00000 0.00000 Ni 0.00000 1.77936 1.77936 Ni 1.77936 1.77936 0.00000 Ni 1.77936 0.00000 1.77936 Ni 3.55872 0.00000 0.00000 Ni 3.55872 1.77936 1.77936 Ni 5.33807 1.77936 0.00000 Ni 5.33807 0.00000 1.77936 Ni 0.00000 3.55872 0.00000 Ni 0.00000 5.33807 1.77936 Ni 1.77936 5.33807 0.00000 Ni 1.77936 3.55872 1.77936 Ni 3.55872 3.55872 0.00000 Ni 3.55872 5.33807 1.77936 Ni 5.33807 5.33807 0.00000 Ni 5.33807 3.55872 1.77936 Al 0.00000 0.00000 3.55872 Ni 0.00000 1.77936 5.33807 Ni 1.77936 1.77936 3.55872 Ni 1.77936 0.00000 5.33807 Al 3.55872 0.00000 3.55872 Ni 3.55872 1.77936 5.33807 Ni 5.33807 1.77936 3.55872 Ni 5.33807 0.00000 5.33807 Al 0.00000 3.55872 3.55872 Ni 0.00000 5.33807 5.33807 Ni 1.77936 5.33807 3.55872 Ni 1.77936 3.55872 5.33807 Al 3.55872 3.55872 3.55872 Ni 3.55872 5.33807 5.33807 Ni 5.33807 5.33807 3.55872 Ni 5.33807 3.55872 5.33807 K_POINTS automatic 2 2 2 0 0 0 However, I've got the following error message: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 0 from cdiaghg : error # 201 diagonalization (ZHEGV*) failed %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I did some variations on the input parameters (CG instead of DAVID, DAMP instead of BFGS, ...) and the calculation continue to giving the same error message. Are there some problem with my input file? Any suggestion? I appreciate any help. Best regards, Adriano ------------------------------------ Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense ------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/1bbfaa94/attachment.htm From rameshchitumalla at gmail.com Tue Aug 30 12:29:00 2011 From: rameshchitumalla at gmail.com (Ramesh Kumar) Date: Tue, 30 Aug 2011 15:59:00 +0530 Subject: [Pw_forum] Serial algorithm Message-ID: > > ------------------------------ > On Aug 20, 2011, at 8:56 , Ramesh Kumar wrote: > > > Please somebody let me know about > > > > "Subspace diagonalization in iterative solution of the eigenvalue > > problem: > > a serial algorithm will be used" > > do you know how iterative diagonalization (or iterative > orthonormalization in Car-Parrinello) works? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > Dear Paolo Giannozzi, The iterative diagonalization works both in serial and parallel manner. I am writing my question in detail here. My problem is, when I use the older version of PWScf (v.4.0.1), the output file is writing that the program is using a parallel distributed memory algorithm and when I use the new version (v.4.3.1), a serial algorithm was used. Would you please let me know the possible cause. Thank you. *With Best Regards:* * * *CH. Ramesh Kumar, Research Student, Computational Chemistry Lab, IICT-** Hyderabad. * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/d6e1d7d5/attachment.htm From martins at if.uff.br Tue Aug 30 13:12:42 2011 From: martins at if.uff.br (martins at if.uff.br) Date: Tue, 30 Aug 2011 08:12:42 -0300 Subject: [Pw_forum] Problem with Ni/Ni3Al system Message-ID: <20110830081242.12682n4e2qdjf06i@webmail.if.uff.br> Dear Gabriele and Fabio, thanks for your replies! With relation to the Gabriele's concerns: i) I use gfortran compiler under linux (Debian). The linear algebra packages are the standart for the distribution. I use too the MPICH to run the paralel jobs. ii) With relation to the ecutrho variable, really I did not to improve its value. On the other hand, as Fabio told, the same input file runned in the Fabio's and Eugenio's machines. Moreover, I did some calculations (in paralel) to another supercells and they were fine. Concerning the Fabio's question, the calculation stopped just in the beginning. One more time, thanks! Adriano ------------------------------------ Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense ------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From gabriele.sclauzero at epfl.ch Tue Aug 30 13:46:44 2011 From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero) Date: Tue, 30 Aug 2011 13:46:44 +0200 Subject: [Pw_forum] Problem with Ni/Ni3Al system In-Reply-To: <20110830081242.12682n4e2qdjf06i@webmail.if.uff.br> References: <20110830081242.12682n4e2qdjf06i@webmail.if.uff.br> Message-ID: <9C80DE53-9D97-470C-8024-F8F06FB4EC07@epfl.ch> Il giorno 30/ago/2011, alle ore 13.12, ha scritto: > Dear Gabriele and Fabio, > > thanks for your replies! With relation to the Gabriele's concerns: > > i) I use gfortran compiler under linux (Debian). The linear algebra > packages are the standart for the distribution. Do you mean those included in the QE distribution or those coming with the Debian distribution? I would bet the the first are more reliable. > I use too the MPICH to > run the paralel jobs. > > ii) With relation to the ecutrho variable, really I did not to improve > its value. What do you mean with "improve"? You should check convergence of the calculation also w.r.t. ecutrho when using USPPs. > On the other hand, as Fabio told, the same input file > runned in the Fabio's and Eugenio's machines. Moreover, I did some > calculations (in paralel) to another supercells and they were fine. Did you check your atomic structure carefully (e.g. by using Xcrysden)? > > Concerning the Fabio's question, the calculation stopped just in the > beginning. Then it's likely to be due to either a library problem or a wrong atomic structure (e.g. almost overlapping atoms), in my opinion. HTH GS > > One more time, thanks! > > Adriano > > ------------------------------------ > Adriano de Souza Martins > Professor Adjunto III > Departamento de F?sica - ICEx > Polo Universit?rio de Volta Redonda > Universidade Federal Fluminense > ------------------------------------ > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/aa1ae822/attachment-0001.htm From giannozz at democritos.it Tue Aug 30 14:57:59 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 30 Aug 2011 14:57:59 +0200 Subject: [Pw_forum] Serial algorithm In-Reply-To: References: Message-ID: On Aug 30, 2011, at 12:29 , Ramesh Kumar wrote: > My problem is, when I use the older version of PWScf (v.4.0.1), > the output file is writing that the program is using a parallel > distributed memory algorithm and when I use the new version > (v.4.3.1), a serial algorithm was used. Would you please let > me know the possible cause. different default behavior. The parallel subspace diagonalization is not always convenient wrt the serial one so it is no longer assumed by default. You can explicitly select parallel subspace diagonalization with command-line option "-ndiag N", with N a square integer P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Aug 30 14:59:52 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 30 Aug 2011 14:59:52 +0200 Subject: [Pw_forum] discrepancies in tests In-Reply-To: References: Message-ID: <3EDE91C1-FC71-4202-A756-75A2C440DC41@democritos.it> On Aug 20, 2011, at 3:05 , Jose Luis Gordillo Ruiz wrote: > I always got discrepancies in lda+U_force, lda+U_gamma, > noncolin-constrain_total and relax2-bfgs_ndim3 and relax2. > Additionally, intel and pathscale produce discrepancies in > md-pot_extrap2. > > any suggestions? if they are small, ignore them. The tests you mention yield very easily minor differences between different machines P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From giannozz at democritos.it Tue Aug 30 15:32:23 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 30 Aug 2011 15:32:23 +0200 Subject: [Pw_forum] Problem with band structure computation In-Reply-To: <000001cc66e2$0cae8df0$260ba9d0$@iams.sinica.edu.tw> References: <000001cc66e2$0cae8df0$260ba9d0$@iams.sinica.edu.tw> Message-ID: On Aug 30, 2011, at 8:57 , jchuang wrote: > nbnd= 20 > consider that the highest bands may not be accurately calculated. Try to increase this number P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From elbuesta at icqmail.com Tue Aug 30 16:06:20 2011 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Tue, 30 Aug 2011 10:06:20 -0400 (EDT) Subject: [Pw_forum] Problem with Ni/Ni3Al system In-Reply-To: <20110830081242.12682n4e2qdjf06i@webmail.if.uff.br> References: <20110830081242.12682n4e2qdjf06i@webmail.if.uff.br> Message-ID: <8CE35352095D019-FA0-4902@webmail-d165.sysops.aol.com> "the calculation stopped just in the beginning." Considering that in our machines the job has been running fine for 5 hours, I would guess that the problem is the QE installation, in the libraries more specifically. You could try reinstalling QE using Intel MKL libraries. Fabio -----Original Message----- From: martins To: pw_forum Sent: Tue, Aug 30, 2011 1:12 pm Subject: [Pw_forum] Problem with Ni/Ni3Al system Dear Gabriele and Fabio, thanks for your replies! With relation to the Gabriele's concerns: i) I use gfortran compiler under linux (Debian). The linear algebra packages are the standart for the distribution. I use too the MPICH to run the paralel jobs. ii) With relation to the ecutrho variable, really I did not to improve its value. On the other hand, as Fabio told, the same input file runned in the Fabio's and Eugenio's machines. Moreover, I did some calculations (in paralel) to another supercells and they were fine. Concerning the Fabio's question, Concerning the Fabio's question, the calculation stopped just in the beginning. One more time, thanks! Adriano ------------------------------------ Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense ------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/c61807d2/attachment.htm From rameshchitumalla at gmail.com Tue Aug 30 16:08:10 2011 From: rameshchitumalla at gmail.com (Ramesh Kumar) Date: Tue, 30 Aug 2011 19:38:10 +0530 Subject: [Pw_forum] Serial algorithm In-Reply-To: References: Message-ID: On Aug 30, 2011, at 12:29 , Ramesh Kumar wrote: >* My problem is, when I use the older version of PWScf (v.4.0.1),*>* the output file is writing that the program is using a parallel*>* distributed memory algorithm and when I use the new version*>* (v.4.3.1), a serial algorithm was used. Would you please let*>* me know the possible cause.* different default behavior. The parallel subspace diagonalization is not always convenient wrt the serial one so it is no longer assumed by default. You can explicitly select parallel subspace diagonalization with command-line option "-ndiag N", with N a square integer P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 Dear Paolo Giannozzi, With this command-line option I am able to use the parallel subspace diagonalization. Thank you very much. *With Best Regards:* > * > * > *CH. Ramesh Kumar, > Research Student, > Computational Chemistry Lab, > IICT-** > Hyderabad. > * > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/c2f9eeed/attachment.htm From proffess at yandex.ru Tue Aug 30 16:47:49 2011 From: proffess at yandex.ru (Sergey Lisenkov) Date: Tue, 30 Aug 2011 18:47:49 +0400 Subject: [Pw_forum] Postdoctoral position at the University of South Florida In-Reply-To: References: Message-ID: <492091314715669@web42.yandex.ru> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/6d66296c/attachment.htm From giannozz at democritos.it Tue Aug 30 17:48:10 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 30 Aug 2011 17:48:10 +0200 Subject: [Pw_forum] Does SOC conflict with HSE06? In-Reply-To: <201108231754519374915@163.com> References: <201108231754519374915@163.com> Message-ID: On Aug 24, 2011, at 2:30 , lilonghua wrote: > Does SOC (spin-orbit coupling) conflict with HSE06 in pwscf? with all hybrid functionals, I guess: I do not think spin-orbit calculations are implemented in this case, unfortunately P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From karandeepster at gmail.com Tue Aug 30 17:57:18 2011 From: karandeepster at gmail.com (karan deep) Date: Tue, 30 Aug 2011 21:27:18 +0530 Subject: [Pw_forum] problem in lderiv curves for Sr Message-ID: Thanks for reply sir anther problem is when u keep on decring the value of rlderiv then theses divergences comes in energy range of {0 -2}, and two curves ( all electron ld , pseudo ld ) do not overlap. then is this potential correct. thanks Karandeep Research Scholar Physics Department, IIT, Delhi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110830/88acbdc2/attachment.htm From raghuvir at bcpindia.org Tue Aug 30 20:06:24 2011 From: raghuvir at bcpindia.org (raghuvir at bcpindia.org) Date: Tue, 30 Aug 2011 23:36:24 +0530 Subject: [Pw_forum] Installation ERROR Message-ID: <9472389bc0c6d37de68ec24b8877c328@bcpindia.org> Hi I have recently tried to install quantum espresso onto rocks cluster 5.4.3 (x86_64) using root I tried the installation in /share/apps/espresso-4.5.2 when executed ./configure --prefix=/share/apps/espresso-4.5.2 was successful I found that the configuration searched for some files in /opt/intel/mkl/ (this is not present on the cluster) for the libraries it used default ones provided with QE i succeeded with make all then ls bin/*x listed all the files in the bin directory so i executed: cd tests followed by ./check-pw.x.j (getting executed only by root not by user; IS THIS CORRECT) I am receiving the following error: Checking atom...passed Checking atom-lsda...passed Checking atom-pbe...passed Checking atom-sigmapbe...passed Checking berry...passed Checking berry, step 2 ...######################################################################################################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_end (iotk_scan.f90:241) # CVS Revision: 1.23 # foundl # ERROR IN: iotk_close_read (iotk_files.f90:746) # CVS Revision: 1.20 ######################################################################################################################## -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- FAILED with error condition! Input: berry.in2, Output: berry.out2, Reference: berry.ref2 Aborting Please help me Thanks Raghuvir From giannozz at democritos.it Tue Aug 30 21:21:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 30 Aug 2011 21:21:07 +0200 Subject: [Pw_forum] Installation ERROR In-Reply-To: <9472389bc0c6d37de68ec24b8877c328@bcpindia.org> References: <9472389bc0c6d37de68ec24b8877c328@bcpindia.org> Message-ID: On Aug 30, 2011, at 20:06 , raghuvir at bcpindia.org wrote: > I have recently tried to install quantum espresso [...] > using root looks like a bad idea to me. Just install as a user, copy executables in a public area > # FROM IOTK LIBRARY, VERSION 1.2.0 > # UNRECOVERABLE ERROR (ierr=1) this is a well-known problem with gfortran not compiling iotk properly, apparently. You need to try a different compiler, as explained in the user guide P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 From lorenzo.paulatto at impmc.upmc.fr Tue Aug 30 23:46:12 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 30 Aug 2011 23:46:12 +0200 Subject: [Pw_forum] problem in lderiv curves for Sr In-Reply-To: References: Message-ID: In data 30 agosto 2011 alle ore 17:57:18, karan deep ha scritto: > anther problem is when u keep on decring the value of rlderiv then theses > divergences comes in energy range of {0 -2}, and two curves ( all > electron > ld , pseudo ld ) do not overlap. then is this potential correct. It does not look correct, but I you just did not add enough projectors yet, and the radius of lrderis is too small (it should be slightly larger then every cutoff radius)... -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From windbellklbh at gmail.com Wed Aug 31 04:37:31 2011 From: windbellklbh at gmail.com (WF) Date: Wed, 31 Aug 2011 10:37:31 +0800 Subject: [Pw_forum] Problem with Bi2Se3 SCF converge Message-ID: <000f01cc6786$f1cffc80$d56ff580$@gmail.com> Hello everyone, I am doing calculation of Bi2Se3 with vdW-DF functional, but it really hard to converge. After several iterations it keeps to prompt things like: iteration # 58 ecut= 60.00 Ry beta=0.70 CG style diagonalization c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 2 eigenvalues not converged and will not converge in 1000 iteration. But the calculation of LDA and PBE can converge, however. All pseudo-potential is generated by ld1.x with same parameters except functional. I have tried to change some parameter in SCF but it doesn't seem to be helpful. Is there any suggestion for this problem? Thanks. F,Wu ----------------------------------------------------------- F, Wu College of Chemistry and Molecular Engineering Peking University ---------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110831/72173adc/attachment.htm From tfcao at theory.issp.ac.cn Wed Aug 31 08:27:34 2011 From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=) Date: Wed, 31 Aug 2011 14:27:34 +0800 Subject: [Pw_forum] =?utf-8?q?problems_with_STM_simulation?= Message-ID: <20110831062734.2261.qmail@ms.hfcas.ac.cn> Dear QE users I want to get the STM image of hydrogen chemisorbed on graphene.As it required,I have down the SCF and NSCF calculation. When I try to get the STM image with pp.x, it gives the follow errors. Here I also give my input file,and hope that you can give me some suggestions. &INPUTPP prefix = 'graphene', outdir ='./tmp' , filplot = 'graphene-1.0' , sample_bias = 0.068d0 , plot_num = 5 , / &PLOT nfile = 1, filepp(1) = 'graphene_1.0', weight(1) = 1.0 , iflag = 3, output_format= 5, fileout = 'graphene_1.0.xsf', e1(1)=1,e2(1)=0,e3(1)=0, e1(2)=0,e2(2)=1,e3(2)=0, e1(3)=0,e2(3)=0,e3(3)=1, x0(1)=0,x0(2)=0,x0(3)=0.5, / The output file Program POST-PROC v.4.2.1 starts on 31Aug2011 at 13:51:14 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org", in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO file C.pbe-rrkjus.UPF: wavefunction(s) 2S 2P renormalized file H.pbe-rrkjus.UPF: wavefunction(s) 1S renormalized negative rho (up, down): 0.724E-04 0.103E-03 Calling punch_plot, plot_num = 5 negative rho (up, down): 0.724E-04 0.103E-03 SPIN UP workfunction = -32.0771 +- 18.6272 eV without exchcorr = -16.8136 +- 15.4478 eV SPIN DOWN workfunction = -31.9865 +- 18.6314 eV without exchcorr = -16.8136 +- 15.4478 eV Work function written on file workf Planar mean charge written on file charge Use the true wfcs Sample bias = 0.9252 eV %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ~ ~ ~Research laboratory for Computational Materials Science. Institute of Solid State Physis. CAS -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110831/6bae50f9/attachment.htm From colonel.sreekar at gmail.com Wed Aug 31 09:49:50 2011 From: colonel.sreekar at gmail.com (sreekar guddeti) Date: Wed, 31 Aug 2011 13:19:50 +0530 Subject: [Pw_forum] radius of integration for local charge and magnetization Message-ID: Respected Sir/Madam, First of all I would like to thank all the developers of PWSCF for writing such a beautiful readable code. After following suggestion of Gabriele Sclauzero, I looked at the .f90 files. I don't have experience in FORTRAN, but the explanatory comments are really helpful. I have few questions regarding spin polarized calculations. I would be grateful if you could help me. 1.make_pointlists.f90 determines the radius of integration for local charge and magnetization. In line 110 r_m(nt) = 0.5d0*distmin(nt)/1.2d0 * 0.99d0 integration radius is set to 0.416 of the closest distance from neighbouring atoms. What is the basis for choosing this factor? I got confused when the calculation on graphene ribbon calculation gives low estimate for the local charge. Here C site contains 4 electrons and charge corresponding to 0.416* C-C spacing is ~1.710 e. Does this mean the rest of the charge is diffused in the void? 2. I would like to have the local moments reported after the end of each scf iteration for unconstrained collinear calculation. I set report = 1 , but it works only if i set lambda=0, constrained_magnetization='atomic' forcing it to be a constrained calculation. This workaround doesn't work for tot_magnetization. I think this has got to do with line 491 of electrons.f90. IF ( noncolin .AND. domag .or. i_cons==1) CALL report_mag() How should I modify this line so as to report moments for unconstrained collinear and fixed total_magnetization calculations? 3. The reason I want this is to check the atomic moments and flip one of them to carry out scf calculation of the ferromagnetic state. The PDOS calculation also gives a set of moments. Which set of data should be used for the moments? PS: I have attached relevant input and output below the signature. Sincerely, -- Sreekar Guddeti Undergraduate (5th year) Engineering Physics IIT Bombay India --------------- Input --------------- C-C spacing 2.6616 a.u. --------------- Output lambda=0.0 --------------- Generating pointlists ... new r_m : 0.2382 (alat units) 1.1084 (a.u.) for type 1 new r_m : 0.2382 (alat units) 1.1084 (a.u.) for type 2 new r_m : 0.2382 (alat units) 1.1084 (a.u.) for type 3 new r_m : 0.2382 (alat units) 1.1084 (a.u.) for type 4 ... ... ... ============================================================================== atom number 1 relative position : 0.0000 0.0000 0.0000 charge : 1.698873 magnetization : 0.237509 magnetization/charge: 0.139804 constrained moment : 0.400000 ============================================================================== ============================================================================== atom number 2 relative position : 0.5000 -0.2887 0.0000 charge : 1.585202 magnetization : 0.771066 magnetization/charge: 0.486415 constrained moment : 0.800000 ============================================================================== ============================================================================== atom number 3 relative position : -0.5000 0.8660 0.0000 charge : 1.585089 magnetization : -0.710778 magnetization/charge: -0.448415 constrained moment : -0.700000 ============================================================================== ============================================================================== atom number 4 relative position : 0.0000 0.5774 0.0000 charge : 1.696799 magnetization : -0.180967 magnetization/charge: -0.106652 constrained moment : -0.300000 ============================================================================== -------------------------- PDOS calculation -------------------------- Atom # 1: total charge = 3.9514, s = 0.9101, p = 3.0413, spin up = 1.9279, s = 0.4517, p = 1.4762, spin down = 2.0234, s = 0.4584, p = 1.5651, polarization = -0.0955, s = -0.0066, p = -0.0889, Atom # 2: total charge = 4.1022, s = 0.9810, p = 3.1212, spin up = 2.1723, s = 0.4962, p = 1.6761, spin down = 1.9299, s = 0.4848, p = 1.4451, polarization = 0.2424, s = 0.0114, p = 0.2310, Atom # 3: total charge = 4.1022, s = 0.9811, p = 3.1211, spin up = 1.9299, s = 0.4848, p = 1.4451, spin down = 2.1723, s = 0.4962, p = 1.6761, ------------------------------------------------------------------------------------------ polarization = -0.2424, s = -0.0114, p = -0.2310, (need to flip this moment) ------------------------------------------------------------------------------------------ Atom # 4: total charge = 3.9514, s = 0.9101, p = 3.0412, spin up = 2.0234, s = 0.4584, p = 1.5651, spin down = 1.9279, s = 0.4518, p = 1.4762, polarization = 0.0955, s = 0.0066, p = 0.0889, ------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110831/e58f3fb9/attachment.htm From giannozz at democritos.it Wed Aug 31 12:27:08 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 31 Aug 2011 12:27:08 +0200 Subject: [Pw_forum] problems with STM simulation In-Reply-To: <20110831062734.2261.qmail@ms.hfcas.ac.cn> References: <20110831062734.2261.qmail@ms.hfcas.ac.cn> Message-ID: <1314786428.23049.33.camel@fe12lx.fisica.uniud.it> On Wed, 2011-08-31 at 14:27 +0800, Cao TF wrote: > from davcio : error # 10 > error while reading from file in most cases, this means that the file(s) containing the ewavefunctions are not where they are expected to be P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From flux_ray12 at 163.com Wed Aug 31 13:44:14 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Wed, 31 Aug 2011 19:44:14 +0800 (CST) Subject: [Pw_forum] Can not find minimum free energy by QHA In-Reply-To: <82A5F624-34FB-43C6-B518-F7E1353EADD5@democritos.it> References: <82A5F624-34FB-43C6-B518-F7E1353EADD5@democritos.it> <10da8b04.97f4.131ef5866ac.Coremail.flux_ray12@163.com> Message-ID: Prof. Giannozzi: Thank you very much for your kindly reply. I think this is my problem to understand Fvib. I have also checked Axel van de Walle's Ph.D thesis, and found that free energy should be Fvib+Fconf-TSvib-TSconf. In 0GPa pressure case, Fconf should equal to total energy. Therefore I cannot obtain the right Free Energy vs Volume curve as a result of using Fvib alone. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-30 03:42:31,"Paolo Giannozzi" wrote: > >On Aug 22, 2011, at 4:36 , GAO Zhe wrote: > >> However, the free energy kept decreasing as a monotone decreasing >> function of lattice parameter > >you mean: the "vibrational free energy" alone, or "the sum of the >energy and of the vibrational free energy"? the vibrational free >energy should be a small correction to the total energy. > >P. >--- >Paolo Giannozzi, Dept of Chemistry&Physics&Environment, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110831/0419a2d7/attachment.htm From raghuvir at bcpindia.org Wed Aug 31 15:18:35 2011 From: raghuvir at bcpindia.org (Raghuvir R S Pissurlenkar) Date: Wed, 31 Aug 2011 18:48:35 +0530 Subject: [Pw_forum] Installation ERROR In-Reply-To: References: Message-ID: Thanks Sir I am trying to compile with Intel Compilers (Intel Compose XE 12 the free version) but I recieve an error during configuration, that the configure: WARNING: parallel compiler mpif90 uses gfortran, but serial compiler ifort was detected configure: WARNING: assuming F90=gfortran, discarding ifort I believe this is not good; So I am trying to download Intel Parallel Studio (Is this the one that will help solve the problem for mpi90 issue ??) Also Since I have installed the MKL libraries now the configuration shows The following libraries have been found: BLAS_LIBS= -lmkl_intel_lp64 -lmkl_sequential -lmkl_core LAPACK_LIBS= FFT_LIBS= I mean the libraries that have come with QE are not used. Is that fine or do I specify them too ?? Thanks for your help Regards Raghuvir ----- Original Message ----- From: To: Sent: Wednesday, August 31, 2011 1:07 PM Subject: Pw_forum Digest, Vol 50, Issue 74 > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/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: Installation ERROR (Paolo Giannozzi) > 2. Re: problem in lderiv curves for Sr (Lorenzo Paulatto) > 3. Problem with Bi2Se3 SCF converge (WF) > 4. problems with STM simulation ( Cao TF ) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 30 Aug 2011 21:21:07 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] Installation ERROR > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > On Aug 30, 2011, at 20:06 , raghuvir at bcpindia.org wrote: > >> I have recently tried to install quantum espresso [...] >> using root > > looks like a bad idea to me. Just install as a user, copy executables > in a public area > >> # FROM IOTK LIBRARY, VERSION 1.2.0 >> # UNRECOVERABLE ERROR (ierr=1) > > this is a well-known problem with gfortran not compiling iotk > properly, apparently. You need to try a different compiler, > as explained in the user guide > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > ------------------------------ > > Message: 2 > Date: Tue, 30 Aug 2011 23:46:12 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] problem in lderiv curves for Sr > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 30 agosto 2011 alle ore 17:57:18, karan deep > ha scritto: >> anther problem is when u keep on decring the value of rlderiv then theses >> divergences comes in energy range of {0 -2}, and two curves ( all >> electron >> ld , pseudo ld ) do not overlap. then is this potential correct. > > It does not look correct, but I you just did not add enough projectors > yet, and the radius of lrderis is too small (it should be slightly larger > then every cutoff radius)... > > -- > Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > > ------------------------------ > > Message: 3 > Date: Wed, 31 Aug 2011 10:37:31 +0800 > From: "WF" > Subject: [Pw_forum] Problem with Bi2Se3 SCF converge > To: > Message-ID: <000f01cc6786$f1cffc80$d56ff580$@gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Hello everyone, > > I am doing calculation of Bi2Se3 with vdW-DF functional, but it > really hard to converge. After several iterations it keeps to prompt things > like: > > > > iteration # 58 ecut= 60.00 Ry beta=0.70 > > CG style diagonalization > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > > > and will not converge in 1000 iteration. > > > > But the calculation of LDA and PBE can converge, however. All > pseudo-potential is generated by ld1.x with same parameters except > functional. > > > > I have tried to change some parameter in SCF but it doesn't seem to > be helpful. Is there any suggestion for this problem? > > > > Thanks. > > > > F,Wu > > > > ----------------------------------------------------------- > > F, Wu > > College of Chemistry and Molecular Engineering > > Peking University > > ---------------------------------------------------------- > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110831/72173adc/attachment.html > > ------------------------------ > > Message: 4 > Date: Wed, 31 Aug 2011 14:27:34 +0800 > From: " Cao TF " > Subject: [Pw_forum] problems with STM simulation > To: " pw_forum " > Message-ID: <20110831062734.2261.qmail at ms.hfcas.ac.cn> > Content-Type: text/plain; charset="utf-8" > > Dear QE users > I want to get the STM image of hydrogen chemisorbed on graphene.As it required,I have down the SCF and NSCF calculation. When I try to get the STM image with pp.x, it gives the follow errors. Here I also give my input file,and hope that you can give me some suggestions. > &INPUTPP > prefix = 'graphene', > outdir ='./tmp' , > filplot = 'graphene-1.0' , > sample_bias = 0.068d0 , > plot_num = 5 , > / > &PLOT > nfile = 1, > filepp(1) = 'graphene_1.0', > weight(1) = 1.0 , > iflag = 3, > output_format= 5, > fileout = 'graphene_1.0.xsf', > e1(1)=1,e2(1)=0,e3(1)=0, > e1(2)=0,e2(2)=1,e3(2)=0, > e1(3)=0,e2(3)=0,e3(3)=1, > x0(1)=0,x0(2)=0,x0(3)=0.5, > / > The output file > > Program POST-PROC v.4.2.1 starts on 31Aug2011 at 13:51:14 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please acknowledge > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > URL http://www.quantum-espresso.org", > in publications or presentations arising from this work. More details at > http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO > file C.pbe-rrkjus.UPF: wavefunction(s) 2S 2P renormalized > file H.pbe-rrkjus.UPF: wavefunction(s) 1S renormalized > > negative rho (up, down): 0.724E-04 0.103E-03 > > Calling punch_plot, plot_num = 5 > > negative rho (up, down): 0.724E-04 0.103E-03 > SPIN UP > > workfunction = -32.0771 +- 18.6272 eV > without exchcorr = -16.8136 +- 15.4478 eV > SPIN DOWN > > workfunction = -31.9865 +- 18.6314 eV > without exchcorr = -16.8136 +- 15.4478 eV > > Work function written on file workf > Planar mean charge written on file charge > Use the true wfcs > Sample bias = 0.9252 eV > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from davcio : error # 10 > error while reading from file > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > ~ > ~ > ~Research laboratory for Computational Materials Science. Institute of Solid State Physis. CAS > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110831/6bae50f9/attachment-0001.htm > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 50, Issue 74 > **************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110831/0dfbe07e/attachment-0001.htm From Lorenzo.Paulatto at impmc.upmc.fr Wed Aug 31 15:32:59 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 31 Aug 2011 15:32:59 +0200 Subject: [Pw_forum] Installation ERROR In-Reply-To: References: Message-ID: On Wed, 31 Aug 2011 15:18:35 +0200, Raghuvir R S Pissurlenkar wrote: > I am trying to compile with Intel Compilers (Intel Compose XE 12 the > free version) but I recieve an error during configuration, that the > > configure: WARNING: parallel compiler mpif90 uses gfortran, but serial > compiler ifort was detected > configure: WARNING: assuming F90=gfortran, discarding ifort > > I believe this is not good; So I am trying to download Intel Parallel > Studio (Is this the one that will help solve the problem for mpi90 issue > ??) The message says that the compiler used to compile openmp is gfortran: if you want to compile the parallel versione of QE you must use the same. If you want to compile QE in parallel with ifort you have only one possible solution: recompile openmp with ifort and reinstall it. If I remember correctly, this is done by running the openmp configure like this: ./configure CC=icc CXX=icpc F77=ifort FC=ifort > Also Since I have installed the MKL libraries now the configuration shows > > The following libraries have been found: > BLAS_LIBS= -lmkl_intel_lp64 -lmkl_sequential -lmkl_core > LAPACK_LIBS= > FFT_LIBS= > > I mean the libraries that have come with QE are not used. Is that fine > or do I specify them too ?? This is fine: mkl libraries are normally way faster than the included plain BLAS/LAPACK libraries. If possible, I would suggest you contact directly some experience person at your institution to help you with the compilation. Finally please provide your affiliation (institution/function) when writing this mailing list, it is just to keep track of our user base. best regards -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05