From baroni at sissa.it Sun May 1 12:08:16 2011 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 1 May 2011 12:08:16 +0200 Subject: [Pw_forum] LO-TO splitting in dynmat.x In-Reply-To: <843971.37633.qm@web65712.mail.ac4.yahoo.com> References: <843971.37633.qm@web65712.mail.ac4.yahoo.com> Message-ID: <1D087CEA-E4BC-43AA-9821-B434D8AFCBBE@sissa.it> Eyvaz, All: I beg to differ, here, though it's probably a matter of terminology. On Apr 29, 2011, at 9:41 AM, Eyvaz Isaev wrote: > Dear Wang, > > Let me reiterate: LO-TO splitting takes place ONLY at the Gamma point. I would rather say a LO-TO splitting ALWAYS occur at q/=0 in any crystal, simply because there is no reason why it should not. (if two modes are not related by symmetry, their frequencies usually differ, and LO and TO modes are NOT related by any symmetry operations. Weird things only occur at q=0 in polar materials. See below ... > >For cubic crystals splitting is equal in all directions. > So, for non-cubic LO-TO splitting also occurs and the splitting is different for different directions. That is > why one can see a discontinuity near the Gamma point in phonon dispersion relations. the situation is even a bit more messy (also, see below ...) > >When q is zero, there is no longitude and transverse mode. > Really? How about optical modes? Did you pay attention to "O"? Strictly speaking, I believe Wang is right. At q=0 it makes no sense to speak about longitudinal or transverse modes, simply because it makes no sense to say that the polarization of the mode is parallel (L) or perpendicular (T) to a vector (q) whose norm is 0 (q=0). The problem is, in a polar *and infinite* crystal q=0 modes do not exist (!!!), because the infinite range of the Coulomb interaction makes the dynamical matrix ill-defined at q=0. So, in this case, not only is it impossible to assign a transverse or longitudinal character to a lattice vibration (which would be true for non polar materials as well), but the very concept of lattice vibration breaks down. What one actually calculates when one calculates the LO or TO modes is the q->0 limit of finite-q modes. When the system is non polar, this limit is well defined and independent of the relative orientation of the polarization and wavevector. In polar materials, instead, this limit depends on this relative orientation, hence it is not defined in the q-> limit. So, the L or T character of a lattice vibration is NOT a property of the vibrations at q=0, but only in the q->0 limit. So far, so good, if at small but finite q the polarization of normal modes can be chosen to be parallel or perpendicular to the direction of propagation of the vibration. This is indeed the case for phonons propagating along high-simmetry lines in cubic materials. For low-simmetry lines in cubic materials, or any line in non-cubic materials, this may not even be the case and lattice vibrations in the q->0 limit in general are not longitudinal nor transverse. What continues to be true is that the q->0 limit is that vibrational frequencies will depend on the direction of propagation of the phonon, so that, strictly speaking, lattice-perdiodic vibrations are not well defined ... Hope to have clarified a bit the (admittedly messy) situation ... 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/20110501/f7c5ff99/attachment.htm From baroni at sissa.it Sun May 1 12:17:42 2011 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 1 May 2011 12:17:42 +0200 Subject: [Pw_forum] About time dependent In-Reply-To: References: Message-ID: <3018C0AE-DC4F-44C7-905C-2187C5FB8FE0@sissa.it> Dear Mahdi, not sure I understand what you mean. If you apply an external force to a system of atoms, in the Born-Oppenheimer approximation the atoms will move following a classical trajectory, which can be computed using ab-initio molecular dynamics. QE has several options for doing this. If you want to compute the time-evolution of a system of interacting electrons at clamped nuclei, you can do so using, e.g., time-dependent DFT. I think (but I am not sure and others may confirm or deny ) that the current distribution of QE does contain a code to compute the real-time evolution using TDDFT. I think people from Marzari's group have contributed the code, although I know that other similar codes have been unofficially available for some time now (one was written by Ralph Gebauer). Finally, if you want to treat on a same footing the quantum dynamics of electrons and the classical dynamics of nuclei, then you should venture in a rather unexplored territory, and I am afraid that no tools are currently available within QE. Hoper this helps. Stefano B On Apr 30, 2011, at 10:27 AM, Mahdi Mirnezhad wrote: > Dear users, > Can quantum espresso simulate the time-dependent phenomena? for > example i want to calculate the position of atoms t second after an > external force. It is a non-equilibrium phenomena and the total energy > does not minimum. Is there any way to simulate such phenomena with QE? > I think in principle we could do such a work. If we have the initial > position (wave function) the wave function after t simply could be > written as A0*exp(-ien t), is it correct? > Best Regards > > > Mahdi Mirnezhad > Guilan University, > _______________________________________________ > 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/20110501/b735171d/attachment.htm From funsopaul at yahoo.com Sun May 1 13:24:11 2011 From: funsopaul at yahoo.com (Paul Funso) Date: Sun, 1 May 2011 04:24:11 -0700 (PDT) Subject: [Pw_forum] how to get kopint from xcrysden Message-ID: <259153.23102.qm@web121118.mail.ne1.yahoo.com> Good day all, I am working on orthorhombic system, after doing the graphical selection of k-path from the primitive Brillouin zone, I want to use xcrysden to generate some explicitly generated k-points for this system, which of the points are mine going to put into consideration in order to get the explicit generated k-points that will work for this system. Thank you all for your support. Adebambo Paul Olufunso. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110501/ed64b7d3/attachment-0001.htm From nkxirainbow at gmail.com Sun May 1 13:44:41 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 1 May 2011 19:44:41 +0800 Subject: [Pw_forum] LO-TO splitting in dynmat.x In-Reply-To: <1D087CEA-E4BC-43AA-9821-B434D8AFCBBE@sissa.it> References: <843971.37633.qm@web65712.mail.ac4.yahoo.com> <1D087CEA-E4BC-43AA-9821-B434D8AFCBBE@sissa.it> Message-ID: Dear Professor Stefano Baroni: Thank you for you exhaustive explanation. I am deeply benefited from it. This basic question has been troubling my mind for many years. Thank you very much ?? On Sun, May 1, 2011 at 6:08 PM, Stefano Baroni wrote: > Eyvaz, All: I beg to differ, here, though it's probably a matter of > terminology. > > On Apr 29, 2011, at 9:41 AM, Eyvaz Isaev wrote: > > Dear Wang, > > Let me reiterate: LO-TO splitting takes place ONLY at the Gamma point. > > > I would rather say a LO-TO splitting ALWAYS occur at q/=0 in any crystal, > simply because there is no reason why it should not. (if two modes are not > related by symmetry, their frequencies usually differ, and LO and TO modes > are NOT related by any symmetry operations. Weird things only occur at q=0 > in polar materials. See below ... > > >For cubic crystals splitting is equal in all directions. > So, for non-cubic LO-TO splitting also occurs and the splitting is > different for different directions. That is > why one can see a discontinuity near the Gamma point in phonon dispersion > relations. > > > the situation is even a bit more messy (also, see below ...) > > >When q is zero, there is no longitude and transverse mode. > Really? How about optical modes? Did you pay attention to "O"? > > > Strictly speaking, I believe Wang is right. At q=0 it makes no sense to > speak about longitudinal or transverse modes, simply because it makes no > sense to say that the polarization of the mode is parallel (L) or > perpendicular (T) to a vector (q) whose norm is 0 (q=0). The problem is, in > a polar *and infinite* crystal q=0 modes do not exist (!!!), because the > infinite range of the Coulomb interaction makes the dynamical matrix > ill-defined at q=0. So, in this case, not only is it impossible to assign a > transverse or longitudinal character to a lattice vibration (which would be > true for non polar materials as well), but the very concept of lattice > vibration breaks down. What one actually calculates when one calculates the > LO or TO modes is the q->0 limit of finite-q modes. When the system is non > polar, this limit is well defined and independent of the relative > orientation of the polarization and wavevector. In polar materials, instead, > this limit depends on this relative orientation, hence it is not defined in > the q-> limit. So, the L or T character of a lattice vibration is NOT a > property of the vibrations at q=0, but only in the q->0 limit. > > So far, so good, if at small but finite q the polarization of normal modes > can be chosen to be parallel or perpendicular to the direction of > propagation of the vibration. This is indeed the case for phonons > propagating along high-simmetry lines in cubic materials. For low-simmetry > lines in cubic materials, or any line in non-cubic materials, this may not > even be the case and lattice vibrations in the q->0 limit in general are not > longitudinal nor transverse. What continues to be true is that the q->0 > limit is that vibrational frequencies will depend on the direction of > propagation of the phonon, so that, strictly speaking, lattice-perdiodic > vibrations are not well defined ... > > Hope to have clarified a bit the (admittedly messy) situation ... > > 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 > > > > > _______________________________________________ > 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/20110501/f7cce685/attachment.htm From barfi.koa at gmail.com Mon May 2 08:20:17 2011 From: barfi.koa at gmail.com (B. Koa) Date: Mon, 2 May 2011 10:50:17 +0430 Subject: [Pw_forum] [sum_band.o] Error 1 In-Reply-To: References: Message-ID: Dear Users I have installed gfortran 4.5, MKL 10, and openmpi successfully in the new version of UBUNTU (11.04). Also the configuring step was successful : ./configure MPIF90=mpif90 CC=mpicc F77=gfortran --enable-parallel unfortunately, an error appears when I try to make the binaries of QE4.3 : sum_band.f90:177.28: CALL sym_rho ( nspin_mag, rho%of_g(1,1) ) 1 Error: Element of assumed-shaped or pointer array passed to array dummy argument 'rhog' at (1) sum_band.f90:187.48: IF (.NOT. gamma_only) CALL sym_rho( nspin, rho%kin_g(1,1) ) 1 Error: Element of assumed-shaped or pointer array passed to array dummy argument 'rhog' at (1) make[1]: *** [sum_band.o] Error 1 Formerly, I could make QE4.2 binaries using older compilers in UBUNTU 10.4 but now I can not do it again. I appreciate your suggestions in advance. -- B. Koa National Institutes of Technology (NIT) Patna -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110502/b58c8b9e/attachment.htm From giannozz at democritos.it Mon May 2 08:38:09 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 2 May 2011 08:38:09 +0200 Subject: [Pw_forum] [sum_band.o] Error 1 In-Reply-To: References: Message-ID: <8F5D614D-DCC4-42DF-A904-2CE1775B369C@democritos.it> On May 2, 2011, at 8:20 , B. Koa wrote: > CALL sym_rho ( nspin_mag, rho%of_g(1,1) ) > 1 > Error: Element of assumed-shaped or pointer array passed to array > dummy argument 'rhog' at (1) > sum_band.f90:187.48: > > IF (.NOT. gamma_only) CALL sym_rho( nspin, rho%kin_g(1,1) ) > 1 > Error: Element of assumed-shaped or pointer array passed to array > dummy argument 'rhog' at (1) > make[1]: *** [sum_band.o] Error 1 your version of gfortran doesn't like the above syntax, that seems to me, and to all other compilers, perfectly legitimate. Anyway: just replace rho%of_g(1,1) with rho%of_g and rho%kin_g(1,1) with rho%kin_g. Also see http://qe-forge.org/scm/browser.php?group_id=10, revision 7681 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 Mon May 2 08:38:49 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 02 May 2011 08:38:49 +0200 Subject: [Pw_forum] [sum_band.o] Error 1 In-Reply-To: References: Message-ID: In data 02 maggio 2011 alle ore 08:20:17, B. Koa ha scritto: > CALL sym_rho ( nspin_mag, rho%of_g(1,1) ) > [...] > IF (.NOT. gamma_only) CALL sym_rho( nspin, rho%kin_g(1,1) ) > Formerly, I could make QE4.2 binaries using older compilers in UBUNTU > 10.4 but now I can not do it again. I appreciate your suggestions in > advance. Dear Koa, this is caused by the last version of gfortran non accepting any more a certain syntax. I quote here the solution proposed by Riccardo Di Meo on the developers mailing list: <> So, just change that file accordingly and everything should compile. 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 sclauzer at sissa.it Mon May 2 09:30:09 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 2 May 2011 09:30:09 +0200 Subject: [Pw_forum] Oscillations in macroscopic average of VH+Vbare In-Reply-To: <695642.11777.qm@web43412.mail.sp1.yahoo.com> References: <695642.11777.qm@web43412.mail.sp1.yahoo.com> Message-ID: You need to consider a slab with equally spaced atomic planes (at least in the inner part; you may allow to relax the outern planes, I think) and to choose an appropriate width for the window of the macroscopic average. If you do this correctly, you should not see these oscillations in the slab interior. HTH GS Il giorno 29/apr/2011, alle ore 23.33, Izaak Williamson ha scritto: > Dear all, > > I am trying to calculate the work function for Cu(100) surface with and without bulk reference. The equations used are as follows: > > work function w/o bulkref --> wf1 = Vvac - EF,slab > work function with bulkref --> wf2 = Vvac - Vslab,int + Vbulk,macro - EF,bulk > > The problem is that the macroscopic average of VH+Vbare for the slab is oscillating as a function of z (see 05.png). I do not understand why the macroscopic average is oscillating. We want to see the convergence of the work function with the number of atomic layers in the slab. Due to the oscillation in macroscopic average, the work function dramatically changes when we go from 5 to 6 layers (4.86641 eV to 3.62728 eV, respectively). This makes it hard to see the convergence of wf with number of layers. > > Would it be correct to use the average of the macroscopic average of the peaks and troughs in calculating wf2? Even if we calculate the average of upper oscillations (05.png), I don't know what to do with the trough that comes up just before the vacuum region? > > Thank you for any help. > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University > > <05.png>_______________________________________________ > 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/20110502/155d7579/attachment-0001.htm From sclauzer at sissa.it Mon May 2 10:01:12 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 2 May 2011 10:01:12 +0200 Subject: [Pw_forum] dos vs. pdos.tot In-Reply-To: References: Message-ID: <8E0125FE-C75D-472F-8951-D906C733CE89@sissa.it> Il giorno 27/apr/2011, alle ore 13.20, Masoud Nahali ha scritto: > Dear Mehrnoosh > > I think that atomic states on different atoms are not orthonormal which makes PDOS-tot different from DOS. This statement is not true, please see the header of PP/projwfc.f90: !----------------------------------------------------------------------- PROGRAM projwfc !----------------------------------------------------------------------- ! ! projects wavefunctions onto orthogonalized atomic wavefunctions, ! calculates Lowdin charges, spilling parameter, projected DOS ! or computes the LDOS in a volume given in input as function of energy and moreover it is not the point. The set of atomic states used in projwfc is not complete with respect to the plane wave basis set, i.e. in the general case of a 3D calculation for a solid you cannot make a complete expansion of the KS states using that atomic basis. Please follow similar threads in the forum archives, like this http://www.democritos.it/pipermail/pw_forum/2008-August/009801.html and read Sanchez-Portal et al., Solid State Comm. 95, 685 (1995) HTH GS > I hope it helps. > > > Best Wishes > > Masoud > > -------------- > Masoud Nahali, Ph.D Student at Sharif University of Technology > > > >Mehrnoosh Hazrati Wrote on Wed Apr 27 08:35:51 CEST 2011 > > > >Hi dear QE users, > > >I have a question about DOS diagram : what is the difference between DOS > >gained of the dos.x code and PDOS_tot gained of projwfc.x code output ?! > > >Regards > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110502/fa4ea5f4/attachment.htm From sclauzer at sissa.it Mon May 2 10:07:29 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 2 May 2011 10:07:29 +0200 Subject: [Pw_forum] cesium PP generation regarding semicore state In-Reply-To: References: Message-ID: <2337BF83-4A99-4BB0-AB9B-74B785B1F087@sissa.it> Look at the all-electron wavefunctions and eigenvalues produced by the atomic code. HTH GS Il giorno 28/apr/2011, alle ore 21.01, Tram Bui ha scritto: > Hi Everyone, > The Cs has electron configuartion of [Xe] 6s1. So would you give me some information on how to determine if the semicore state need to be included in the valence? > > Regard, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > _______________________________________________ > 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/20110502/83c86b13/attachment.htm From sclauzer at sissa.it Mon May 2 10:15:52 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 2 May 2011 10:15:52 +0200 Subject: [Pw_forum] how to get kopint from xcrysden In-Reply-To: <259153.23102.qm@web121118.mail.ne1.yahoo.com> References: <259153.23102.qm@web121118.mail.ne1.yahoo.com> Message-ID: Il giorno 01/mag/2011, alle ore 13.24, Paul Funso ha scritto: > Good day all, I am working on orthorhombic system, after doing the graphical selection of k-path from the primitive Brillouin zone, I want to use xcrysden to generate some explicitly generated k-points for this system, which of the points are mine going to put into consideration in order to get the explicit generated k-points that will work for this system. I'm sorry, but I'm having a hard time in trying to understand the above sentence. What do you need exactly? Could you reformulate more clearly, please? Once you have selected the k-point path in the visual tool of xcrysden, you just need to export the points in the .pwscf format and append those lines after the K_POINTS card of pw.x HTH GS P.S.: please supply your affiliation > Thank you all for your support. > > Adebambo Paul Olufunso. > _______________________________________________ > 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/20110502/dbd083df/attachment.htm From mehrnooshhazrati at gmail.com Mon May 2 19:44:33 2011 From: mehrnooshhazrati at gmail.com (Mehrnoosh Hazrati) Date: Mon, 2 May 2011 19:44:33 +0200 Subject: [Pw_forum] dos vs. pdos.tot In-Reply-To: <8E0125FE-C75D-472F-8951-D906C733CE89@sissa.it> References: <8E0125FE-C75D-472F-8951-D906C733CE89@sissa.it> Message-ID: Dear Gabriele, Thank you so much for your reply. On Mon, May 2, 2011 at 10:01 AM, Gabriele Sclauzero wrote: > > Il giorno 27/apr/2011, alle ore 13.20, Masoud Nahali ha scritto: > > *Dear Mehrnoosh > > I think that a**tomic states on different atoms are not orthonormal which makes PDOS-tot different from DOS. * > > This statement is not true, please see the header of PP/projwfc.f90: > > !----------------------------------------------------------------------- > PROGRAM projwfc > !----------------------------------------------------------------------- > ! > ! projects wavefunctions onto orthogonalized atomic wavefunctions, > ! calculates Lowdin charges, spilling parameter, projected DOS > ! or computes the LDOS in a volume given in input as function of energy > > > and moreover it is not the point. > > The set of atomic states used in projwfc is not complete with respect to > the plane wave basis set, i.e. in the general case of a 3D calculation for a > solid you cannot make a complete expansion of the KS states using that > atomic basis. > > Please follow similar threads in the forum archives, like this > http://www.democritos.it/pipermail/pw_forum/2008-August/009801.html > and read > Sanchez-Portal et al., Solid State Comm. 95, 685 (1995) > > > HTH > > GS > > *I hope it helps. > > > * > > Best Wishes > > Masoud > > -------------- > Masoud Nahali, Ph.D Student at Sharif University of Technology > > > *>Mehrnoosh Hazrati* Wrote on W*ed Apr 27 08:35:51 CEST 2011* > > >Hi dear QE users, > > >I have a question about DOS diagram : what is the difference between DOS > >gained of the dos.x code and PDOS_tot gained of projwfc.x code output ?! > > >Regards > > > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > * 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 > > -- * * * """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" * **** Mehrnoosh Kh. Hazrati **** **** Master Student of Computational Physical Chemistry,KNTU,Tehran **** *** Phone : +989123436300 *** *** Mail : mehrnooshhazrati at gmail.com *** * """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110502/4c0e2841/attachment-0001.htm From patricia.a.paredes at gmail.com Mon May 2 21:13:58 2011 From: patricia.a.paredes at gmail.com (Patricia Alejandra Paredes-Olivera) Date: Mon, 2 May 2011 16:13:58 -0300 Subject: [Pw_forum] neb.x with intermediate images Message-ID: When I run neb.x with intermediate images I get a message of error: forrtl: severe (24): end-of-file during read, unit 99, file /home/patricia/neb/prueba.in Image PC Routine Line Source neb.x 000000000097F7DD Unknown Unknown Unknown neb.x 000000000097E2E5 Unknown Unknown Unknown neb.x 0000000000914D29 Unknown Unknown Unknown neb.x 00000000008AA1CA Unknown Unknown Unknown neb.x 00000000008A99C0 Unknown Unknown Unknown neb.x 00000000008D5970 Unknown Unknown Unknown neb.x 0000000000455233 path_gen_inputs_ 164 path_gen_inputs.f90 neb.x 0000000000436DD4 MAIN__ 89 neb.f90 neb.x 0000000000436C22 Unknown Unknown Unknown libc.so.6 0000003F51A1D974 Unknown Unknown Unknown neb.x 0000000000436B49 Unknown Unknown Unknown The input file is the one provided with the example17 with 1 intermediate image: BEGIN BEGIN_PATH_INPUT &PATH restart_mode = 'from_scratch' string_method = 'neb', nstep_path = 20, ds = 2.D0, opt_scheme = "broyden", num_of_images = 3, k_max = 0.3D0, k_min = 0.2D0, CI_scheme = "auto", path_thr = 0.1D0, / END_PATH_INPUT BEGIN_ENGINE_INPUT &CONTROL prefix = "prueba" outdir = "/tmp", pseudo_dir = "/home/patricia/Programas/pwscf/pseudo", / &SYSTEM ibrav = 0, celldm(1) = 1.D0, nat = 3, ntyp = 1, ecutwfc = 20.0D0, ecutrho = 100.0D0, occupations = "smearing", degauss = 0.03D0, / &ELECTRONS conv_thr = 1.D-8, mixing_beta = 0.3D0, / &IONS pot_extrapolation = "second_order", wfc_extrapolation = "second_order", / ATOMIC_SPECIES H 1.00794 C.pbe-rrkjus.UPF BEGIN_POSITIONS FIRST_IMAGE ATOMIC_POSITIONS {bohr} H -2.4165936061 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.8243346657 0.0000000000 0.0000000000 INTERMEDIATE_IMAGE 1 ATOMIC_POSITIONS {bohr} H 0.0000000000 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 LAST_IMAGE ATOMIC_POSITIONS {bohr} H -0.8243346657 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 2.4165936061 0.0000000000 0.0000000000 END_POSITIONS K_POINTS { gamma } CELL_PARAMETERS { cubic } 12.00000 0.00000 0.00000 0.00000 5.00000 0.00000 0.00000 0.00000 5.00000 END_ENGINE_INPUT END Thanks! Patricia Paredes-Olivera INFIQC Universidad Nacional de C?rdoba - Argentina. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110502/5a81410c/attachment.htm From swapnil.chandratre at gmail.com Mon May 2 23:18:53 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 2 May 2011 16:18:53 -0500 Subject: [Pw_forum] Graphene Nanoribbon Message-ID: Hi, I am new to Espresso, I am trying to work with Graphene Nanoribbon(1-d), though I am spending individual time on understanding how to use the software and implement conditions accordingly, can anyone provide a sample input file for a GNR? -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110502/7177c683/attachment.htm From arvifis at gmail.com Tue May 3 00:33:12 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 2 May 2011 19:33:12 -0300 Subject: [Pw_forum] neb.x with intermediate images In-Reply-To: References: Message-ID: If you look in your input file, the intermediate atomic position are wrong. Is impossible put 3 atoms in the same xyz position. INTERMEDIATE_IMAGE 1 ATOMIC_POSITIONS {bohr} H 0.0000000000 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 H 0.0000000000 0.0000000000 0.0000000000 Best. PhD std. Arles V. Gil Rebaza Instituto de F?sica La Plata La Plata - Argentina 2011/5/2 Patricia Alejandra Paredes-Olivera > When I run neb.x with intermediate images I get a message of error: > > forrtl: severe (24): end-of-file during read, unit 99, file > /home/patricia/neb/prueba.in > Image PC Routine Line Source > neb.x 000000000097F7DD Unknown Unknown Unknown > neb.x 000000000097E2E5 Unknown Unknown Unknown > neb.x 0000000000914D29 Unknown Unknown Unknown > neb.x 00000000008AA1CA Unknown Unknown Unknown > neb.x 00000000008A99C0 Unknown Unknown Unknown > neb.x 00000000008D5970 Unknown Unknown Unknown > neb.x 0000000000455233 path_gen_inputs_ 164 > path_gen_inputs.f90 > neb.x 0000000000436DD4 MAIN__ 89 neb.f90 > neb.x 0000000000436C22 Unknown Unknown Unknown > libc.so.6 0000003F51A1D974 Unknown Unknown Unknown > neb.x 0000000000436B49 Unknown Unknown Unknown > > The input file is the one provided with the example17 with 1 intermediate > image: > > BEGIN > BEGIN_PATH_INPUT > &PATH > restart_mode = 'from_scratch' > string_method = 'neb', > nstep_path = 20, > ds = 2.D0, > opt_scheme = "broyden", > num_of_images = 3, > k_max = 0.3D0, > k_min = 0.2D0, > CI_scheme = "auto", > path_thr = 0.1D0, > / > END_PATH_INPUT > BEGIN_ENGINE_INPUT > &CONTROL > prefix = "prueba" > outdir = "/tmp", > pseudo_dir = "/home/patricia/Programas/pwscf/pseudo", > / > &SYSTEM > ibrav = 0, > celldm(1) = 1.D0, > nat = 3, > ntyp = 1, > ecutwfc = 20.0D0, > ecutrho = 100.0D0, > occupations = "smearing", > degauss = 0.03D0, > / > &ELECTRONS > conv_thr = 1.D-8, > mixing_beta = 0.3D0, > / > &IONS > pot_extrapolation = "second_order", > wfc_extrapolation = "second_order", > / > ATOMIC_SPECIES > H 1.00794 C.pbe-rrkjus.UPF > BEGIN_POSITIONS > FIRST_IMAGE > ATOMIC_POSITIONS {bohr} > H -2.4165936061 0.0000000000 0.0000000000 > H 0.0000000000 0.0000000000 0.0000000000 > H 0.8243346657 0.0000000000 0.0000000000 > INTERMEDIATE_IMAGE 1 > ATOMIC_POSITIONS {bohr} > H 0.0000000000 0.0000000000 0.0000000000 > H 0.0000000000 0.0000000000 0.0000000000 > H 0.0000000000 0.0000000000 0.0000000000 > LAST_IMAGE > ATOMIC_POSITIONS {bohr} > H -0.8243346657 0.0000000000 0.0000000000 > H 0.0000000000 0.0000000000 0.0000000000 > H 2.4165936061 0.0000000000 0.0000000000 > END_POSITIONS > K_POINTS { gamma } > CELL_PARAMETERS { cubic } > 12.00000 0.00000 0.00000 > 0.00000 5.00000 0.00000 > 0.00000 0.00000 5.00000 > END_ENGINE_INPUT > END > > Thanks! > > Patricia Paredes-Olivera > INFIQC > Universidad Nacional de C?rdoba - Argentina. > > > > _______________________________________________ > 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/20110502/8945bb93/attachment.htm From patricia.a.paredes at gmail.com Tue May 3 00:51:08 2011 From: patricia.a.paredes at gmail.com (Patricia Alejandra Paredes-Olivera) Date: Mon, 2 May 2011 19:51:08 -0300 Subject: [Pw_forum] neb.x with intermediate images In-Reply-To: References: Message-ID: yes, you are wright, but it is not the wrong positions the reason of the error. I had an error pasting the coordenates in the mail!! Patricia. On Mon, May 2, 2011 at 7:33 PM, Arles V. Gil Rebaza wrote: > If you look in your input file, the intermediate atomic position are wrong. > Is impossible put 3 atoms in the same xyz position. > > INTERMEDIATE_IMAGE 1 > ATOMIC_POSITIONS {bohr} > H 0.0000000000 0.0000000000 0.0000000000 > H 0.0000000000 0.0000000000 0.0000000000 > H 0.0000000000 0.0000000000 0.0000000000 > > Best. > > PhD std. Arles V. Gil Rebaza > Instituto de F?sica La Plata > La Plata - Argentina > > > > 2011/5/2 Patricia Alejandra Paredes-Olivera > >> When I run neb.x with intermediate images I get a message of error: >> >> forrtl: severe (24): end-of-file during read, unit 99, file >> /home/patricia/neb/prueba.in >> Image PC Routine Line >> Source >> neb.x 000000000097F7DD Unknown Unknown >> Unknown >> neb.x 000000000097E2E5 Unknown Unknown >> Unknown >> neb.x 0000000000914D29 Unknown Unknown >> Unknown >> neb.x 00000000008AA1CA Unknown Unknown >> Unknown >> neb.x 00000000008A99C0 Unknown Unknown >> Unknown >> neb.x 00000000008D5970 Unknown Unknown >> Unknown >> neb.x 0000000000455233 path_gen_inputs_ 164 >> path_gen_inputs.f90 >> neb.x 0000000000436DD4 MAIN__ 89 >> neb.f90 >> neb.x 0000000000436C22 Unknown Unknown >> Unknown >> libc.so.6 0000003F51A1D974 Unknown Unknown >> Unknown >> neb.x 0000000000436B49 Unknown Unknown >> Unknown >> >> The input file is the one provided with the example17 with 1 intermediate >> image: >> >> BEGIN >> BEGIN_PATH_INPUT >> &PATH >> restart_mode = 'from_scratch' >> string_method = 'neb', >> nstep_path = 20, >> ds = 2.D0, >> opt_scheme = "broyden", >> num_of_images = 3, >> k_max = 0.3D0, >> k_min = 0.2D0, >> CI_scheme = "auto", >> path_thr = 0.1D0, >> / >> END_PATH_INPUT >> BEGIN_ENGINE_INPUT >> &CONTROL >> prefix = "prueba" >> outdir = "/tmp", >> pseudo_dir = "/home/patricia/Programas/pwscf/pseudo", >> / >> &SYSTEM >> ibrav = 0, >> celldm(1) = 1.D0, >> nat = 3, >> ntyp = 1, >> ecutwfc = 20.0D0, >> ecutrho = 100.0D0, >> occupations = "smearing", >> degauss = 0.03D0, >> / >> &ELECTRONS >> conv_thr = 1.D-8, >> mixing_beta = 0.3D0, >> / >> &IONS >> pot_extrapolation = "second_order", >> wfc_extrapolation = "second_order", >> / >> ATOMIC_SPECIES >> H 1.00794 C.pbe-rrkjus.UPF >> BEGIN_POSITIONS >> FIRST_IMAGE >> ATOMIC_POSITIONS {bohr} >> H -2.4165936061 0.0000000000 0.0000000000 >> H 0.0000000000 0.0000000000 0.0000000000 >> H 0.8243346657 0.0000000000 0.0000000000 >> INTERMEDIATE_IMAGE 1 >> ATOMIC_POSITIONS {bohr} >> H 0.0000000000 0.0000000000 0.0000000000 >> H 0.0000000000 0.0000000000 0.0000000000 >> H 0.0000000000 0.0000000000 0.0000000000 >> LAST_IMAGE >> ATOMIC_POSITIONS {bohr} >> H -0.8243346657 0.0000000000 0.0000000000 >> H 0.0000000000 0.0000000000 0.0000000000 >> H 2.4165936061 0.0000000000 0.0000000000 >> END_POSITIONS >> K_POINTS { gamma } >> CELL_PARAMETERS { cubic } >> 12.00000 0.00000 0.00000 >> 0.00000 5.00000 0.00000 >> 0.00000 0.00000 5.00000 >> END_ENGINE_INPUT >> END >> >> Thanks! >> >> Patricia Paredes-Olivera >> INFIQC >> Universidad Nacional de C?rdoba - Argentina. >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ###---------> Arles V. <---------### > > _______________________________________________ > 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/20110502/49d16f71/attachment-0001.htm From nkxirainbow at gmail.com Tue May 3 04:54:21 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Tue, 3 May 2011 10:54:21 +0800 Subject: [Pw_forum] Graphene Nanoribbon In-Reply-To: References: Message-ID: Dear Swapnil Chandratre: The following is my input file for graphenen ribbon6 for QE4.0. You can find more information at here: http://blog.sina.com.cn/s/blog_5f15ead20100drss.html ############################################################# INPUT FILE OF GRAPHENE RIBBON 6 Input file:graphene.rx.in &CONTROL calculation = 'relax' , restart_mode = ?? outdir = ?? pseudo_dir = ?? etot_conv_thr = 1.0e-4 , forc_conv_thr = 1.0e-3 , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 8, celldm(1) = 4.67689278, celldm(2) = 8.623989813, celldm(3) = 4.048794087, nat = 12, ntyp = 2,// the largest ntype=10 ecutwfc = 60.D0 , ecutrho = 500.D0 , nosym = .false. , nbnd = 36, nelec = 48, occupations = 'smearing' , degauss = 0.02 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = 1.0, starting_magnetization(2) = -0.5, / &ELECTRONS conv_thr = 1.D-6 , mixing_mode = 'plain' , mixing_beta = 0.7D0 , diagonalization = 'david' , diago_david_ndim = 8, / &IONS ion_dynamics = 'damp' , pot_extrapolation = 'second_order' , wfc_extrapolation = 'second_order' , / ATOMIC_SPECIES C1 12.00000 C.pbe-rrkjus.UPF C2 12.00000 C.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal C1 0.000000000 0.236465542 0.000000000 C2 0.500000000 0.265456486 0.000000000 C1 0.500000000 0.334092417 0.000000000 C2 0.000000000 0.366772814 0.000000000 C1 0.000000000 0.433673757 0.000000000 C2 0.500000000 0.466640035 0.000000000 C1 0.500000000 0.533360168 0.000000000 C2 0.000000000 0.566326232 0.000000000 C1 0.000000000 0.633227130 0.000000000 C2 0.500000000 0.665907475 0.000000000 C1 0.500000000 0.734543349 0.000000000 C2 0.000000000 0.763534596 0.000000000 K_POINTS automatic 13 1 1 0 0 0 On Tue, May 3, 2011 at 5:18 AM, swapnil chandratre < swapnil.chandratre at gmail.com> wrote: > Hi, > > I am new to Espresso, I am trying to work with Graphene Nanoribbon(1-d), > though I am spending individual time on understanding how to use the > software and implement conditions accordingly, can anyone provide a sample > input file for a GNR? > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > > _______________________________________________ > 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/20110503/894a6a1a/attachment.htm From swapnil.chandratre at gmail.com Tue May 3 05:09:48 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 2 May 2011 22:09:48 -0500 Subject: [Pw_forum] Graphene Nanoribbon In-Reply-To: References: Message-ID: Hi, Thank you for your quick response, but is it not required to satisfy the dangling bonds with h2 passivation (as I see just the C atoms here). The other query I had is Graphene is Semi Metallic, it can show semi conducting properties if designed in ArmChair configuration with proper geometry, is there any specific thing to keep in mind if I want to explore that aspect. On Mon, May 2, 2011 at 9:54 PM, xirainbow wrote: > Dear Swapnil Chandratre: > The following is my input file for graphenen ribbon6 for QE4.0. > You can find more information at here: > http://blog.sina.com.cn/s/blog_5f15ead20100drss.html > > ############################################################# > INPUT FILE OF GRAPHENE RIBBON 6 > Input file:graphene.rx.in > &CONTROL > calculation = 'relax' , > restart_mode = ?? > outdir = ?? > pseudo_dir = ?? > etot_conv_thr = 1.0e-4 , > forc_conv_thr = 1.0e-3 , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM > ibrav = 8, > celldm(1) = 4.67689278, > celldm(2) = 8.623989813, > celldm(3) = 4.048794087, > nat = 12, > ntyp = 2,// the largest ntype=10 > ecutwfc = 60.D0 , > ecutrho = 500.D0 , > nosym = .false. , > nbnd = 36, > nelec = 48, > occupations = 'smearing' , > degauss = 0.02 , > smearing = 'gaussian' , > nspin = 2 , > starting_magnetization(1) = 1.0, > starting_magnetization(2) = -0.5, > / > &ELECTRONS > conv_thr = 1.D-6 , > mixing_mode = 'plain' , > mixing_beta = 0.7D0 , > diagonalization = 'david' , > diago_david_ndim = 8, > / > &IONS > ion_dynamics = 'damp' , > pot_extrapolation = 'second_order' , > wfc_extrapolation = 'second_order' , > / > ATOMIC_SPECIES > C1 12.00000 C.pbe-rrkjus.UPF > C2 12.00000 C.pbe-rrkjus.UPF > ATOMIC_POSITIONS crystal > C1 0.000000000 0.236465542 0.000000000 > C2 0.500000000 0.265456486 0.000000000 > C1 0.500000000 0.334092417 0.000000000 > C2 0.000000000 0.366772814 0.000000000 > C1 0.000000000 0.433673757 0.000000000 > C2 0.500000000 0.466640035 0.000000000 > C1 0.500000000 0.533360168 0.000000000 > C2 0.000000000 0.566326232 0.000000000 > C1 0.000000000 0.633227130 0.000000000 > C2 0.500000000 0.665907475 0.000000000 > C1 0.500000000 0.734543349 0.000000000 > C2 0.000000000 0.763534596 0.000000000 > K_POINTS automatic > 13 1 1 0 0 0 > > > > > > On Tue, May 3, 2011 at 5:18 AM, swapnil chandratre < > swapnil.chandratre at gmail.com> wrote: > >> Hi, >> >> I am new to Espresso, I am trying to work with Graphene Nanoribbon(1-d), >> though I am spending individual time on understanding how to use the >> software and implement conditions accordingly, can anyone provide a sample >> input file for a GNR? >> >> -- >> Regards, >> Swapnil Chandratre >> Graduate Student >> Dept. of Mechanical Engineering, >> University of Houston, >> Houston, TX >> (M)-713-294-9546 >> >> _______________________________________________ >> 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110502/337d8e8a/attachment.htm From nkxirainbow at gmail.com Tue May 3 05:20:34 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Tue, 3 May 2011 11:20:34 +0800 Subject: [Pw_forum] Graphene Nanoribbon In-Reply-To: References: Message-ID: Dear Swapnil Chandratre: Thank you for your quick response, but is it not required to satisfy the > dangling bonds with h2 passivation (as I see just the C atoms here). > You have to add H by yourself. Do not you know how to add atoms? > The other query I had is Graphene is Semi Metallic, it can show semi > conducting properties if designed in ArmChair configuration with proper > geometry, is there any specific thing to keep in mind if I want to explore > that aspect. > I think you should know how to explore semi metallic property of two dimensional graphene, before dealing with nanoribbon. If you don't know the origin of semi-metallic graphene, you would not know how to explore it in nanoribbon. > > > On Mon, May 2, 2011 at 9:54 PM, xirainbow wrote: > >> Dear Swapnil Chandratre: >> The following is my input file for graphenen ribbon6 for QE4.0. >> You can find more information at here: >> http://blog.sina.com.cn/s/blog_5f15ead20100drss.html >> >> ############################################################# >> INPUT FILE OF GRAPHENE RIBBON 6 >> Input file:graphene.rx.in >> &CONTROL >> calculation = 'relax' , >> restart_mode = ?? >> outdir = ?? >> pseudo_dir = ?? >> etot_conv_thr = 1.0e-4 , >> forc_conv_thr = 1.0e-3 , >> tstress = .true. , >> tprnfor = .true. , >> / >> &SYSTEM >> ibrav = 8, >> celldm(1) = 4.67689278, >> celldm(2) = 8.623989813, >> celldm(3) = 4.048794087, >> nat = 12, >> ntyp = 2,// the largest ntype=10 >> ecutwfc = 60.D0 , >> ecutrho = 500.D0 , >> nosym = .false. , >> nbnd = 36, >> nelec = 48, >> occupations = 'smearing' , >> degauss = 0.02 , >> smearing = 'gaussian' , >> nspin = 2 , >> starting_magnetization(1) = 1.0, >> starting_magnetization(2) = -0.5, >> / >> &ELECTRONS >> conv_thr = 1.D-6 , >> mixing_mode = 'plain' , >> mixing_beta = 0.7D0 , >> diagonalization = 'david' , >> diago_david_ndim = 8, >> / >> &IONS >> ion_dynamics = 'damp' , >> pot_extrapolation = 'second_order' , >> wfc_extrapolation = 'second_order' , >> / >> ATOMIC_SPECIES >> C1 12.00000 C.pbe-rrkjus.UPF >> C2 12.00000 C.pbe-rrkjus.UPF >> ATOMIC_POSITIONS crystal >> C1 0.000000000 0.236465542 0.000000000 >> C2 0.500000000 0.265456486 0.000000000 >> C1 0.500000000 0.334092417 0.000000000 >> C2 0.000000000 0.366772814 0.000000000 >> C1 0.000000000 0.433673757 0.000000000 >> C2 0.500000000 0.466640035 0.000000000 >> C1 0.500000000 0.533360168 0.000000000 >> C2 0.000000000 0.566326232 0.000000000 >> C1 0.000000000 0.633227130 0.000000000 >> C2 0.500000000 0.665907475 0.000000000 >> C1 0.500000000 0.734543349 0.000000000 >> C2 0.000000000 0.763534596 0.000000000 >> K_POINTS automatic >> 13 1 1 0 0 0 >> >> >> >> >> >> On Tue, May 3, 2011 at 5:18 AM, swapnil chandratre < >> swapnil.chandratre at gmail.com> wrote: >> >>> Hi, >>> >>> I am new to Espresso, I am trying to work with Graphene Nanoribbon(1-d), >>> though I am spending individual time on understanding how to use the >>> software and implement conditions accordingly, can anyone provide a sample >>> input file for a GNR? >>> >>> -- >>> Regards, >>> Swapnil Chandratre >>> Graduate Student >>> Dept. of Mechanical Engineering, >>> University of Houston, >>> Houston, TX >>> (M)-713-294-9546 >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > > _______________________________________________ > 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/20110503/0d638464/attachment-0001.htm From swapnil.chandratre at gmail.com Tue May 3 06:10:00 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 2 May 2011 23:10:00 -0500 Subject: [Pw_forum] Graphene Nanoribbon In-Reply-To: References: Message-ID: Hi, I know how to get the H passivated graphene structure, and regarding semi conducting property, can you help getting started by hinting at some literature. On Mon, May 2, 2011 at 10:20 PM, xirainbow wrote: > Dear Swapnil Chandratre: > > Thank you for your quick response, but is it not required to satisfy the >> dangling bonds with h2 passivation (as I see just the C atoms here). >> > You have to add H by yourself. > Do not you know how to add atoms? > > >> The other query I had is Graphene is Semi Metallic, it can show semi >> conducting properties if designed in ArmChair configuration with proper >> geometry, is there any specific thing to keep in mind if I want to explore >> that aspect. >> > I think you should know how to explore semi metallic property of two > dimensional graphene, before dealing with nanoribbon. If you don't know the > origin of semi-metallic graphene, you would not know how to explore it in > nanoribbon. > > >> >> >> On Mon, May 2, 2011 at 9:54 PM, xirainbow wrote: >> >>> Dear Swapnil Chandratre: >>> The following is my input file for graphenen ribbon6 for QE4.0. >>> You can find more information at here: >>> http://blog.sina.com.cn/s/blog_5f15ead20100drss.html >>> >>> ############################################################# >>> INPUT FILE OF GRAPHENE RIBBON 6 >>> Input file:graphene.rx.in >>> &CONTROL >>> calculation = 'relax' , >>> restart_mode = ?? >>> outdir = ?? >>> pseudo_dir = ?? >>> etot_conv_thr = 1.0e-4 , >>> forc_conv_thr = 1.0e-3 , >>> tstress = .true. , >>> tprnfor = .true. , >>> / >>> &SYSTEM >>> ibrav = 8, >>> celldm(1) = 4.67689278, >>> celldm(2) = 8.623989813, >>> celldm(3) = 4.048794087, >>> nat = 12, >>> ntyp = 2,// the largest ntype=10 >>> ecutwfc = 60.D0 , >>> ecutrho = 500.D0 , >>> nosym = .false. , >>> nbnd = 36, >>> nelec = 48, >>> occupations = 'smearing' , >>> degauss = 0.02 , >>> smearing = 'gaussian' , >>> nspin = 2 , >>> starting_magnetization(1) = 1.0, >>> starting_magnetization(2) = -0.5, >>> / >>> &ELECTRONS >>> conv_thr = 1.D-6 , >>> mixing_mode = 'plain' , >>> mixing_beta = 0.7D0 , >>> diagonalization = 'david' , >>> diago_david_ndim = 8, >>> / >>> &IONS >>> ion_dynamics = 'damp' , >>> pot_extrapolation = 'second_order' , >>> wfc_extrapolation = 'second_order' , >>> / >>> ATOMIC_SPECIES >>> C1 12.00000 C.pbe-rrkjus.UPF >>> C2 12.00000 C.pbe-rrkjus.UPF >>> ATOMIC_POSITIONS crystal >>> C1 0.000000000 0.236465542 0.000000000 >>> C2 0.500000000 0.265456486 0.000000000 >>> C1 0.500000000 0.334092417 0.000000000 >>> C2 0.000000000 0.366772814 0.000000000 >>> C1 0.000000000 0.433673757 0.000000000 >>> C2 0.500000000 0.466640035 0.000000000 >>> C1 0.500000000 0.533360168 0.000000000 >>> C2 0.000000000 0.566326232 0.000000000 >>> C1 0.000000000 0.633227130 0.000000000 >>> C2 0.500000000 0.665907475 0.000000000 >>> C1 0.500000000 0.734543349 0.000000000 >>> C2 0.000000000 0.763534596 0.000000000 >>> K_POINTS automatic >>> 13 1 1 0 0 0 >>> >>> >>> >>> >>> >>> On Tue, May 3, 2011 at 5:18 AM, swapnil chandratre < >>> swapnil.chandratre at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> I am new to Espresso, I am trying to work with Graphene Nanoribbon(1-d), >>>> though I am spending individual time on understanding how to use the >>>> software and implement conditions accordingly, can anyone provide a sample >>>> input file for a GNR? >>>> >>>> -- >>>> Regards, >>>> Swapnil Chandratre >>>> Graduate Student >>>> Dept. of Mechanical Engineering, >>>> University of Houston, >>>> Houston, TX >>>> (M)-713-294-9546 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> Regards, >> Swapnil Chandratre >> Graduate Student >> Dept. of Mechanical Engineering, >> University of Houston, >> Houston, TX >> (M)-713-294-9546 >> >> _______________________________________________ >> 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110502/c6bfe678/attachment.htm From lmartinsamos at gmail.com Tue May 3 08:13:38 2011 From: lmartinsamos at gmail.com (Layla Martin-Samos) Date: Tue, 3 May 2011 08:13:38 +0200 Subject: [Pw_forum] neb.x with intermediate images In-Reply-To: References: Message-ID: Dear Patricia, the parser that generates the input files for "pw" does not recognize INTERMEDIATE_IMAGE 1. Independetly of the number of intermediate images that you have, you have to write just INTERMEDIATE_IMAGE. cheers Layla 2011/5/3 Patricia Alejandra Paredes-Olivera > yes, you are wright, but it is not the wrong positions the reason of the > error. I had an error pasting the coordenates in the mail!! > Patricia. > > > On Mon, May 2, 2011 at 7:33 PM, Arles V. Gil Rebaza wrote: > >> If you look in your input file, the intermediate atomic position are >> wrong. Is impossible put 3 atoms in the same xyz position. >> >> INTERMEDIATE_IMAGE 1 >> ATOMIC_POSITIONS {bohr} >> H 0.0000000000 0.0000000000 0.0000000000 >> H 0.0000000000 0.0000000000 0.0000000000 >> H 0.0000000000 0.0000000000 0.0000000000 >> >> Best. >> >> PhD std. Arles V. Gil Rebaza >> Instituto de F?sica La Plata >> La Plata - Argentina >> >> >> >> 2011/5/2 Patricia Alejandra Paredes-Olivera > > >> >>> When I run neb.x with intermediate images I get a message of error: >>> >>> forrtl: severe (24): end-of-file during read, unit 99, file >>> /home/patricia/neb/prueba.in >>> Image PC Routine Line >>> Source >>> neb.x 000000000097F7DD Unknown Unknown >>> Unknown >>> neb.x 000000000097E2E5 Unknown Unknown >>> Unknown >>> neb.x 0000000000914D29 Unknown Unknown >>> Unknown >>> neb.x 00000000008AA1CA Unknown Unknown >>> Unknown >>> neb.x 00000000008A99C0 Unknown Unknown >>> Unknown >>> neb.x 00000000008D5970 Unknown Unknown >>> Unknown >>> neb.x 0000000000455233 path_gen_inputs_ 164 >>> path_gen_inputs.f90 >>> neb.x 0000000000436DD4 MAIN__ 89 >>> neb.f90 >>> neb.x 0000000000436C22 Unknown Unknown >>> Unknown >>> libc.so.6 0000003F51A1D974 Unknown Unknown >>> Unknown >>> neb.x 0000000000436B49 Unknown Unknown >>> Unknown >>> >>> The input file is the one provided with the example17 with 1 intermediate >>> image: >>> >>> BEGIN >>> BEGIN_PATH_INPUT >>> &PATH >>> restart_mode = 'from_scratch' >>> string_method = 'neb', >>> nstep_path = 20, >>> ds = 2.D0, >>> opt_scheme = "broyden", >>> num_of_images = 3, >>> k_max = 0.3D0, >>> k_min = 0.2D0, >>> CI_scheme = "auto", >>> path_thr = 0.1D0, >>> / >>> END_PATH_INPUT >>> BEGIN_ENGINE_INPUT >>> &CONTROL >>> prefix = "prueba" >>> outdir = "/tmp", >>> pseudo_dir = "/home/patricia/Programas/pwscf/pseudo", >>> / >>> &SYSTEM >>> ibrav = 0, >>> celldm(1) = 1.D0, >>> nat = 3, >>> ntyp = 1, >>> ecutwfc = 20.0D0, >>> ecutrho = 100.0D0, >>> occupations = "smearing", >>> degauss = 0.03D0, >>> / >>> &ELECTRONS >>> conv_thr = 1.D-8, >>> mixing_beta = 0.3D0, >>> / >>> &IONS >>> pot_extrapolation = "second_order", >>> wfc_extrapolation = "second_order", >>> / >>> ATOMIC_SPECIES >>> H 1.00794 C.pbe-rrkjus.UPF >>> BEGIN_POSITIONS >>> FIRST_IMAGE >>> ATOMIC_POSITIONS {bohr} >>> H -2.4165936061 0.0000000000 0.0000000000 >>> H 0.0000000000 0.0000000000 0.0000000000 >>> H 0.8243346657 0.0000000000 0.0000000000 >>> INTERMEDIATE_IMAGE 1 >>> ATOMIC_POSITIONS {bohr} >>> H 0.0000000000 0.0000000000 0.0000000000 >>> H 0.0000000000 0.0000000000 0.0000000000 >>> H 0.0000000000 0.0000000000 0.0000000000 >>> LAST_IMAGE >>> ATOMIC_POSITIONS {bohr} >>> H -0.8243346657 0.0000000000 0.0000000000 >>> H 0.0000000000 0.0000000000 0.0000000000 >>> H 2.4165936061 0.0000000000 0.0000000000 >>> END_POSITIONS >>> K_POINTS { gamma } >>> CELL_PARAMETERS { cubic } >>> 12.00000 0.00000 0.00000 >>> 0.00000 5.00000 0.00000 >>> 0.00000 0.00000 5.00000 >>> END_ENGINE_INPUT >>> END >>> >>> Thanks! >>> >>> Patricia Paredes-Olivera >>> INFIQC >>> Universidad Nacional de C?rdoba - Argentina. >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> ###---------> Arles V. <---------### >> >> _______________________________________________ >> 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/b506fa3d/attachment-0001.htm From mahmud at science.upm.edu.my Tue May 3 12:37:39 2011 From: mahmud at science.upm.edu.my (Dr. Mahmudur Rahman) Date: Tue, 3 May 2011 18:37:39 +0800 Subject: [Pw_forum] Need help to run on windows using cygwin Message-ID: <61afecebf655a3755593ad5310da8209.squirrel@science.upm.edu.my> Dear user, I have just downloaded quantum espresso and cygwin (as i am using windows 7). But I do not understand how to run the example. I read the user guide; still cannot make out. Best regards, Mahmud From giovanni.cantele at spin.cnr.it Tue May 3 13:12:28 2011 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Tue, 3 May 2011 13:12:28 +0200 Subject: [Pw_forum] Need help to run on windows using cygwin In-Reply-To: <61afecebf655a3755593ad5310da8209.squirrel@science.upm.edu.my> References: <61afecebf655a3755593ad5310da8209.squirrel@science.upm.edu.my> Message-ID: <43EDD80C-8925-4C7F-9720-A9CCBCA83177@spin.cnr.it> On May 3, 2011, at 12:37 PM, Dr. Mahmudur Rahman wrote: > Dear user, > I have just downloaded quantum espresso and cygwin (as i am using windows > 7). But I do not understand how to run the example. I read the user guide; > still cannot make out. > Best regards, > Mahmud > how to run examples is explained here: http://www.quantum-espresso.org/user_guide/node13.html But from your message it is not clear why you didn't manage to run. Did you get some error message? Was your installation successful (namely, did you build working executable? have a look to the Quantum-ESPRESSO/espresso-x.y.z/bin directory)? If so, you need to set some environment variables under cygwin according to what explained in the above link: BIN_DIR: directory where executables reside PSEUDO_DIR: directory where pseudopotential files reside TMP_DIR: directory to be used as temporary storage area On the side, although you should be able to easily install and make running Quantum-ESPRESSO under cygwin + Windows, I would strongly suggest to try (if you have time) the much better, faster, friendly, totally free, beautifully looking Linux operating system. You can download a live CD (just to try before installing it) from www.ubuntu.com. Giovanni -- **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/3fce4c3e/attachment.htm From padmaja_patnaik at yahoo.co.uk Tue May 3 14:17:31 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Tue, 3 May 2011 13:17:31 +0100 (BST) Subject: [Pw_forum] Imposing opposite spins Message-ID: <521957.84265.qm@web28506.mail.ukl.yahoo.com> Hi All I want to do calculations on a supercell where I am adding two impurity atoms of the same kind at two different places. I want to make sure that these two atoms are in opposite spins. how can I format the input file to achieve this condition. And also if somebody knows any software which can plot the atomic structure along with the spins direction then please let me know. Thanking you 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/20110503/70249ee7/attachment.htm From arvifis at gmail.com Tue May 3 15:14:48 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Tue, 3 May 2011 10:14:48 -0300 Subject: [Pw_forum] Imposing opposite spins In-Reply-To: <521957.84265.qm@web28506.mail.ukl.yahoo.com> References: <521957.84265.qm@web28506.mail.ukl.yahoo.com> Message-ID: Hi Padmaja, you need write in the input file the next variables: &system starting_magnetization(1) = 0.00 starting_magnetization(2) = 0.00 starting_magnetization(3) = 0.00 -.... starting_magnetization(i) = 1.00, starting_magnetization(j) = -1.00, where "i" and "j" is the number of the two impurity atoms, although in different spin direccion. If the other atoms in your supercell aren't magnetics, just write 0.0. Furthermore, you have to write twice the pseudopotential belonging to the impurity. For example: ATOMIC_SPECIES ...... ........ Fe1 55.845 Fe.pbe-paw_kj.UPF Fe2 55.845 Fe.pbe-paw_kj.UPF Best. Arles V. Gil Rebaza Instituto de F?sica de La Plata La Plata - Argentina 2011/5/3 Padmaja Patnaik > Hi All > > I want to do calculations on a supercell where I am adding two impurity > atoms of the same kind at two different places. I want to make sure that > these two atoms are in opposite spins. how can I format the input file to > achieve this condition. And also if somebody knows any software which can > plot the atomic structure along with the spins direction then please let me > know. > > Thanking you 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 > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/eff65291/attachment.htm From jdburton1 at gmail.com Tue May 3 17:36:15 2011 From: jdburton1 at gmail.com (J. D. Burton) Date: Tue, 3 May 2011 10:36:15 -0500 Subject: [Pw_forum] using wf_collect only for a few bands Message-ID: <052e01cc09a7$d7ad50b0$8707f210$@gmail.com> Dear All, Is there a way to use the 'wf_collect' to save wavefunctions ONLY for a few bands at each k-point, say +/- 1eV around the Fermi energy? I am trying to plot k-resolved LDOS on a fine k-grid to image the Fermi surface of a 2-D heterostructure, but saving ALL the wavefunctions takes way too much disk space and my cluster administrator starts barking at me. I've looked in the code and I might be able to figure out how to do it in a very ad hoc way, but I'm wondering if anyone has a quicker solution. Cheers, J. D. ************************************ J. D. Burton, Ph.D. jdburton1 at gmail.com Research Assistant Professor University of Nebraska Lincoln Physics and Astronomy Office Ph. (402) 472 2499 Mobile Ph. (402) 419 9918 310A Jorgensen Hall CV: http://tinyurl.com/2avltsc ************************************ "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/5b26ad0e/attachment.htm From izaakw89 at yahoo.com Tue May 3 18:54:14 2011 From: izaakw89 at yahoo.com (Izaak Williamson) Date: Tue, 3 May 2011 09:54:14 -0700 (PDT) Subject: [Pw_forum] Cohesive Energy of N2 molecule In-Reply-To: References: Message-ID: <974606.12674.qm@web43416.mail.sp1.yahoo.com> Dear all, I am trying to calculate the cohesive energy of the N2 molecule using the attached input file (relax.in) and am getting a value of -16.57 eV. I use DFT with GGA and the pseudo-potential N.pbe-rrkjus.UPF. Other work [Fuchs et. al., Phys. Rev. B 65, (2002)245212] has performed similar calculations and obtained values ~10.5 eV. They even list an experimental value of 9.76 eV. Why is my value so much higher? Is there anything in my input file that could be giving inaccurate results? Is it my pseudo-potential that is causing this problem? 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/20110503/9e728584/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: relax.in Type: application/octet-stream Size: 662 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110503/9e728584/attachment-0001.obj From faccin.giovani at gmail.com Tue May 3 19:06:10 2011 From: faccin.giovani at gmail.com (Giovani Faccin) Date: Tue, 3 May 2011 13:06:10 -0400 Subject: [Pw_forum] Cohesive Energy of N2 molecule In-Reply-To: <974606.12674.qm@web43416.mail.sp1.yahoo.com> References: <974606.12674.qm@web43416.mail.sp1.yahoo.com> Message-ID: Dear Izaak, Looking at your input file, a few things to try out came to mind: 1 - Did you try to integrate using more k points? Experiment with, say, 3x3x3 K points and see if anything changes. 2 - Try the calculation with ecutrho = 360, see if anything changes. Hope it might help. Giovani M. Faccin UFMS - Brazil 2011/5/3 Izaak Williamson > Dear all, > > I am trying to calculate the cohesive energy of the N2 molecule using the > attached input file (relax.in) and am getting a value of -16.57 eV. I use > DFT with GGA and the pseudo-potential N.pbe-rrkjus.UPF. Other work [Fuchs > et. al., Phys. Rev. B 65, (2002)245212] has performed similar calculations > and obtained values ~10.5 eV. They even list an experimental value of 9.76 > eV. Why is my value so much higher? Is there anything in my input file that > could be giving inaccurate results? Is it my pseudo-potential that is > causing this problem? > > 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 > > -- Giovani -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/3f45835a/attachment.htm From amin.torabi at gmail.com Tue May 3 19:07:39 2011 From: amin.torabi at gmail.com (Amin Torabi) Date: Tue, 3 May 2011 13:07:39 -0400 Subject: [Pw_forum] Atomic-positions VS nat, ntyp Message-ID: Hi all, As far as I can understand, the Atomic-Position input card, which is mandatory, specifies the type and coordinates of each atom in the unit cell. Then, my question is why we need to specify the number of atoms, number of type of atoms and even celldm in the system input card? Thanks in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/407adec9/attachment.htm From giannozz at democritos.it Tue May 3 19:35:46 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 3 May 2011 19:35:46 +0200 Subject: [Pw_forum] Cohesive Energy of N2 molecule In-Reply-To: References: <974606.12674.qm@web43416.mail.sp1.yahoo.com> Message-ID: <3B1883DB-E3D7-4BCC-B8EA-75BA0F913BED@democritos.it> On May 3, 2011, at 19:06 , Giovani Faccin wrote: > 1 - Did you try to integrate using more k points? not a good idea: for a molecule in a supercell, Gamma is the correct choice. In my experience, a large percentage of "I don't get the cohesive energy right" problems are due to a bad choice of atomic energies 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 May 3 19:37:34 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 3 May 2011 19:37:34 +0200 Subject: [Pw_forum] Atomic-positions VS nat, ntyp In-Reply-To: References: Message-ID: On May 3, 2011, at 19:07 , Amin Torabi wrote: > the Atomic-Position input card, which is mandatory, specifies > the type and coordinates of each atom in the unit cell. Then, > my question is why we need to specify the number of atoms, > number of type of atoms and even celldm in the system input card? celldm specifies the unit cell: a piece of information that is not contained in atomic_positions card. The number of atoms and the number of species could in principle be deduced from the contents of the atomic_positions card. This would however require a sizable amount of programming and introduce a number of undesirable complications into the code. There is a compromise to be struck between ease of use by ordinary users and ease of maintainance by developers. 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 May 3 19:33:34 2011 From: elbuesta at icqmail.com (elbuesta at icqmail.com) Date: Tue, 03 May 2011 13:33:34 -0400 Subject: [Pw_forum] Cohesive Energy of N2 molecule In-Reply-To: <974606.12674.qm@web43416.mail.sp1.yahoo.com> References: <974606.12674.qm@web43416.mail.sp1.yahoo.com> Message-ID: <8CDD7CF5CD560E6-990-430A@webmail-d087.sysops.aol.com> Dear Izaak Williamson, I believe the most important thing to be included is the magnetisation for the isolated N atom, something I am not sure if you included it or not. Attached you will find your input slightly changed for the N2 molecule and the N atom. The cohesive energy obtained with this input was 10eV. I hope it helps! Fabio Negreiros IPCF - CNR Pisa, Italy -----Original Message----- From: Izaak Williamson To: pw_forum at pwscf.org Sent: Tue, May 3, 2011 6:54 pm Subject: [Pw_forum] Cohesive Energy of N2 molecule Dear all, I am trying to calculate the cohesive energy of the N2 molecule using the attached input file (relax.in) and am getting a value of -16.57 eV. I use DFT with GGA and the pseudo-potential N.pbe-rrkjus.UPF. Other work [Fuchs et. al., Phys. Rev. B 65, (2002)245212] has performed similar calculations and obtained values ~10.5 eV. They even list an experimental value of 9.76 eV. Why is my value so much higher? Is there anything in my input file that could be giving inaccurate results? Is it my pseudo-potential that is causing this problem? 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/20110503/b30e387f/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: N.in Type: application/octet-stream Size: 629 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110503/b30e387f/attachment-0004.obj -------------- next part -------------- A non-text attachment was scrubbed... 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Name: N2.out Type: application/octet-stream Size: 35792 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110503/b30e387f/attachment-0007.obj From davide.ceresoli at materials.ox.ac.uk Tue May 3 19:39:54 2011 From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli) Date: Tue, 03 May 2011 18:39:54 +0100 Subject: [Pw_forum] Cohesive Energy of N2 molecule In-Reply-To: <974606.12674.qm@web43416.mail.sp1.yahoo.com> References: <974606.12674.qm@web43416.mail.sp1.yahoo.com> Message-ID: <4DC03DEA.2070408@materials.ox.ac.uk> On 05/03/2011 05:54 PM, Izaak Williamson wrote: > Dear all, > > I am trying to calculate the cohesive energy of the N2 molecule using the > attached input file (relax.in ) and am getting a value of > -16.57 eV. I use DFT with GGA and the pseudo-potential N.pbe-rrkjus.UPF. Other > work [Fuchs et. al., Phys. Rev. B 65, (2002)245212] has performed similar > calculations and obtained values ~10.5 eV. They even list an experimental value > of 9.76 eV. Why is my value so much higher? Is there anything in my input file > that could be giving inaccurate results? Is it my pseudo-potential that is > causing this problem? > > Thanks for any help. Dear Izaak, how much do you get for an isolated N atom, spin polarized, same cell, same pseudo, same cutoffs? In an old output file I've got: -39.7039435178 Ry for N2 at equilibrium and -19.48996768 Ry for the N atom. Therefore: -0.724 Ry = -9.85 eV (N.pbe-rrkjus.UPF) Davide From abmus007 at gmail.com Tue May 3 19:46:51 2011 From: abmus007 at gmail.com (Abolore Musari) Date: Tue, 3 May 2011 12:46:51 -0500 Subject: [Pw_forum] k-points for band structure for monoclinic system In-Reply-To: References: Message-ID: Dear Sir, I am presently working on band structure for a monoclinic system and I dont know how to get special points (x,y,z) for my k-point card Sir, I tried generating this using xcrysden but really dont know those points to choose as my special points(x,y,z) for my kpoint card Pls I need ur assistance on k-points for calculating band structure for a monoclinic system. Thanks Musari Abolore Dept Of Physics University of Agriculture Abeokuta Nigeria -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/ad7bd87c/attachment.htm From masoudnahali at gmail.com Tue May 3 19:56:01 2011 From: masoudnahali at gmail.com (Masoud Nahali) Date: Tue, 3 May 2011 22:26:01 +0430 Subject: [Pw_forum] Cohesive Energy of N2 molecule Message-ID: > > Izaak Williamson wrote on Tue, 3 May 2011 09:54:14 -0700 > > I am trying to calculate the cohesive energy of the N2 molecule using the > attached input file (relax.in) and am getting a value of -16.57 eV. I use > DFT > with GGA and the pseudo-potential N.pbe-rrkjus.UPF. Other work [Fuchs et. > al., > Phys. Rev. B 65, (2002)245212] has performed similar calculations and > obtained > values ~10.5 eV. They even list an experimental value of 9.76 eV. Why is my > value so much higher? Is there anything in my input file that could be > giving > inaccurate results? Is it my pseudo-potential that is causing this problem? > > 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/20110503/9e728584/attachment.htm > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: relax.in > Type: application/octet-stream > Size: 662 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20110503/9e728584/attachment.obj > Dear Izaak Did you considered symmetry for energy calculation of atomic nitrogen or not ? As you know the electronic configuration of atomic nitrogen is 1s[2] 2s[2] 2px[1] 2py[1] 2pz[1] and seems symmetric. In some quantum mechanical codes when one calculates the energy of this system without considering symmetry may get wrong answer since the system may go to a non-symmetric status like 1s[2] 2s[2] 2px[2] 2py[1]. Please calculate the energy with and without symmetry and compare them. Another important issue is that did you considered polarization of spin (with defining a proper starting magnetization value for nitrogen) in your calculations ? It can cause a significant change in the energy since your system includes unpaired electrons. Let us know the changes after considering the above issues. I hope it helps. Best Wishes Masoud -------------- Masoud Nahali, Sharif University of Technology > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/aa8d1a4d/attachment.htm From degironc at sissa.it Tue May 3 22:46:28 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 03 May 2011 22:46:28 +0200 Subject: [Pw_forum] Cohesive Energy of N2 molecule In-Reply-To: <974606.12674.qm@web43416.mail.sp1.yahoo.com> References: <974606.12674.qm@web43416.mail.sp1.yahoo.com> Message-ID: <4DC069A4.9070704@sissa.it> Nitrogen atom is magnetic while the molecule is not. are you taking in consideration this fact in your calculations ? stefano On 05/03/2011 06:54 PM, Izaak Williamson wrote: > Dear all, > > I am trying to calculate the cohesive energy of the N2 molecule using the > attached input file (relax.in) and am getting a value of -16.57 eV. I use DFT > with GGA and the pseudo-potential N.pbe-rrkjus.UPF. Other work [Fuchs et. al., > Phys. Rev. B 65, (2002)245212] has performed similar calculations and obtained > values ~10.5 eV. They even list an experimental value of 9.76 eV. Why is my > value so much higher? Is there anything in my input file that could be giving > inaccurate results? Is it my pseudo-potential that is causing this problem? > > Thanks for any help. > > > > _______________________________________________ > 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/20110503/dca05912/attachment.htm From degironc at sissa.it Tue May 3 22:48:52 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 03 May 2011 22:48:52 +0200 Subject: [Pw_forum] Atomic-positions VS nat, ntyp In-Reply-To: References: Message-ID: <4DC06A34.4000706@sissa.it> because the code reads one line for every atom... how many lines ? nat stefano On 05/03/2011 07:07 PM, Amin Torabi wrote: > Hi all, > > As far as I can understand, the Atomic-Position input card, which is > mandatory, specifies the type and coordinates of each atom in the unit cell. > Then, my question is why we need to specify the number of atoms, number of > type of atoms and even celldm in the system input card? > > Thanks in advance > > > > _______________________________________________ > 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/20110503/919d0bf6/attachment.htm From swapnil.chandratre at gmail.com Tue May 3 23:31:56 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Tue, 3 May 2011 16:31:56 -0500 Subject: [Pw_forum] Graphene Nanoribbon In-Reply-To: References: Message-ID: Hi, I am sending you the file I have prepared for graphene nanoribbon, could you please comment on it. On Mon, May 2, 2011 at 11:10 PM, swapnil chandratre < swapnil.chandratre at gmail.com> wrote: > Hi, > > I know how to get the H passivated graphene structure, > and regarding semi conducting property, can you help getting started by > hinting at some literature. > > > On Mon, May 2, 2011 at 10:20 PM, xirainbow wrote: > >> Dear Swapnil Chandratre: >> >> Thank you for your quick response, but is it not required to satisfy the >>> dangling bonds with h2 passivation (as I see just the C atoms here). >>> >> You have to add H by yourself. >> Do not you know how to add atoms? >> >> >>> The other query I had is Graphene is Semi Metallic, it can show semi >>> conducting properties if designed in ArmChair configuration with proper >>> geometry, is there any specific thing to keep in mind if I want to explore >>> that aspect. >>> >> I think you should know how to explore semi metallic property of two >> dimensional graphene, before dealing with nanoribbon. If you don't know the >> origin of semi-metallic graphene, you would not know how to explore it in >> nanoribbon. >> >> >>> >>> >>> On Mon, May 2, 2011 at 9:54 PM, xirainbow wrote: >>> >>>> Dear Swapnil Chandratre: >>>> The following is my input file for graphenen ribbon6 for QE4.0. >>>> You can find more information at here: >>>> http://blog.sina.com.cn/s/blog_5f15ead20100drss.html >>>> >>>> ############################################################# >>>> INPUT FILE OF GRAPHENE RIBBON 6 >>>> Input file:graphene.rx.in >>>> &CONTROL >>>> calculation = 'relax' , >>>> restart_mode = ?? >>>> outdir = ?? >>>> pseudo_dir = ?? >>>> etot_conv_thr = 1.0e-4 , >>>> forc_conv_thr = 1.0e-3 , >>>> tstress = .true. , >>>> tprnfor = .true. , >>>> / >>>> &SYSTEM >>>> ibrav = 8, >>>> celldm(1) = 4.67689278, >>>> celldm(2) = 8.623989813, >>>> celldm(3) = 4.048794087, >>>> nat = 12, >>>> ntyp = 2,// the largest ntype=10 >>>> ecutwfc = 60.D0 , >>>> ecutrho = 500.D0 , >>>> nosym = .false. , >>>> nbnd = 36, >>>> nelec = 48, >>>> occupations = 'smearing' , >>>> degauss = 0.02 , >>>> smearing = 'gaussian' , >>>> nspin = 2 , >>>> starting_magnetization(1) = 1.0, >>>> starting_magnetization(2) = -0.5, >>>> / >>>> &ELECTRONS >>>> conv_thr = 1.D-6 , >>>> mixing_mode = 'plain' , >>>> mixing_beta = 0.7D0 , >>>> diagonalization = 'david' , >>>> diago_david_ndim = 8, >>>> / >>>> &IONS >>>> ion_dynamics = 'damp' , >>>> pot_extrapolation = 'second_order' , >>>> wfc_extrapolation = 'second_order' , >>>> / >>>> ATOMIC_SPECIES >>>> C1 12.00000 C.pbe-rrkjus.UPF >>>> C2 12.00000 C.pbe-rrkjus.UPF >>>> ATOMIC_POSITIONS crystal >>>> C1 0.000000000 0.236465542 0.000000000 >>>> C2 0.500000000 0.265456486 0.000000000 >>>> C1 0.500000000 0.334092417 0.000000000 >>>> C2 0.000000000 0.366772814 0.000000000 >>>> C1 0.000000000 0.433673757 0.000000000 >>>> C2 0.500000000 0.466640035 0.000000000 >>>> C1 0.500000000 0.533360168 0.000000000 >>>> C2 0.000000000 0.566326232 0.000000000 >>>> C1 0.000000000 0.633227130 0.000000000 >>>> C2 0.500000000 0.665907475 0.000000000 >>>> C1 0.500000000 0.734543349 0.000000000 >>>> C2 0.000000000 0.763534596 0.000000000 >>>> K_POINTS automatic >>>> 13 1 1 0 0 0 >>>> >>>> >>>> >>>> >>>> >>>> On Tue, May 3, 2011 at 5:18 AM, swapnil chandratre < >>>> swapnil.chandratre at gmail.com> wrote: >>>> >>>>> Hi, >>>>> >>>>> I am new to Espresso, I am trying to work with Graphene >>>>> Nanoribbon(1-d), though I am spending individual time on understanding how >>>>> to use the software and implement conditions accordingly, can anyone provide >>>>> a sample input file for a GNR? >>>>> >>>>> -- >>>>> Regards, >>>>> Swapnil Chandratre >>>>> Graduate Student >>>>> Dept. of Mechanical Engineering, >>>>> University of Houston, >>>>> Houston, TX >>>>> (M)-713-294-9546 >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>> >>> >>> -- >>> Regards, >>> Swapnil Chandratre >>> Graduate Student >>> Dept. of Mechanical Engineering, >>> University of Houston, >>> Houston, TX >>> (M)-713-294-9546 >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/e6bd040f/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: graphene.in Type: application/octet-stream Size: 4048 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110503/e6bd040f/attachment-0001.obj From swapnil.chandratre at gmail.com Tue May 3 23:33:19 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Tue, 3 May 2011 16:33:19 -0500 Subject: [Pw_forum] Graphene Nanoribbon In-Reply-To: References: Message-ID: Hi, the input file is &control calculation = 'relax' restart_mode = 'from_scratch' pseudo_dir = '/home/s/schandratre/Espresso/pseudo' outdir = '/home/s/schandratre/Espresso/swapnil' / &system ibrav = 8 A=21.000000 B=22.000000 C=10.000000 nat=96 ntyp=2 ecutwfc=70.0 ecutrho = 600.0 occupations = 'smearing' degauss=0.02 smearing = 'guassian' / &electrons conv_thr = 1.0d-6, mixing_beta=0.01, / &ions ion_dynamics='damp' pot_extrapolation='second_order' wfc_extrapolation='second_order' trust_radius_ini=0.20D0 ATOMIC_SPECIES C 12.0107 C.pbe-rrkjus.UPF H 1.00794 H.pbe-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C 2.841720 5.953494 5.000000 C 3.552150 7.183995 5.000000 C 1.420860 5.953494 5.000000 C 2.841720 8.414496 5.000000 C 3.552150 9.644997 5.000000 C 0.710430 7.183995 5.000000 C 1.420860 8.414496 5.000000 C 2.841720 10.87550 5.000000 C 3.552150 12.10600 5.000000 C 0.710430 9.644997 5.000000 C 1.420860 10.87550 5.000000 C 2.841720 13.33650 5.000000 C 3.552150 14.56700 5.000000 C 0.710430 12.10600 5.000000 C 1.420860 13.33650 5.000000 C 0.710430 14.56700 5.000000 H 3.392220 5.000000 5.000000 H 0.870360 5.000000 5.000000 H 3.001650 15.52049 5.000000 H 1.260930 15.52049 5.000000 C 7.104300 5.953494 5.000000 C 7.814730 7.183995 5.000000 C 5.683440 5.953494 5.000000 C 7.104300 8.414496 5.000000 C 4.973010 7.183995 5.000000 C 5.683440 8.414496 5.000000 C 7.104300 10.87550 5.000000 C 7.814730 12.10600 5.000000 C 4.973010 9.644997 5.000000 C 5.683440 10.87550 5.000000 C 7.104300 13.33650 5.000000 C 7.814730 14.56700 5.000000 C 12.10600 4.973010 5.000000 C 5.683440 13.33650 5.000000 C 4.973010 14.56700 5.000000 H 7.654800 5.000000 5.000000 H 5.132940 5.000000 5.000000 H 7.264230 15.52049 5.000000 H 5.523510 15.52049 5.000000 C 11.36688 5.953494 5.000000 C 12.07731 7.183995 5.000000 C 9.946020 5.953494 5.000000 C 11.36688 8.414496 5.000000 C 12.07731 9.644997 5.000000 C 9.235590 7.183995 5.000000 C 11.36688 10.87550 5.000000 C 12.07731 12.10600 5.000000 C 11.36688 13.33650 5.000000 C 12.07731 14.56700 5.000000 C 9.235590 12.10600 5.000000 C 9.946020 13.33650 5.000000 C 9.235590 14.56700 5.000000 H 11.91738 5.000000 5.000000 H 9.395520 5.000000 5.000000 H 11.52681 15.52049 5.000000 H 9.786090 15.52049 5.000000 C 15.62946 5.953494 5.000000 C 16.33989 7.183995 5.000000 C 14.20860 5.953494 5.000000 C 15.62946 8.414496 5.000000 C 16.33989 9.644997 5.000000 C 13.49817 7.183995 5.000000 C 14.20860 8.414496 5.000000 C 15.62946 10.87550 5.000000 C 16.33989 12.10600 5.000000 C 13.49817 9.644997 5.000000 C 14.20860 10.87550 5.000000 C 15.62946 13.33650 5.000000 C 16.33989 14.56700 5.000000 C 13.49817 12.10600 5.000000 C 14.20860 13.33650 5.000000 C 13.49817 14.56700 5.000000 H 16.17996 5.000000 5.000000 H 13.65810 5.000000 5.000000 H 15.78939 15.52049 5.000000 H 14.04867 15.52049 5.000000 C 19.89204 5.953494 5.000000 C 20.60247 7.183995 5.000000 C 18.47118 5.953494 5.000000 C 19.89204 8.414496 5.000000 C 20.60247 9.644997 5.000000 C 17.76075 7.183995 5.000000 C 18.47118 8.414496 5.000000 C 19.89204 10.87550 5.000000 C 20.60247 12.10600 5.000000 C 17.76075 9.644997 5.000000 C 18.47118 10.87550 5.000000 C 19.89204 13.33650 5.000000 C 20.60247 14.56700 5.000000 C 17.76075 12.10600 5.000000 C 18.47118 13.33650 5.000000 C 17.76075 14.56700 5.000000 H 20.44254 5.000000 5.000000 H 17.92068 5.000000 5.000000 H 20.05197 15.52049 5.000000 H 18.31125 15.52049 5.000000 K_POINTS {automatic} 50 1 1 0 0 0 On Tue, May 3, 2011 at 4:31 PM, swapnil chandratre < swapnil.chandratre at gmail.com> wrote: > Hi, > > I am sending you the file I have prepared for graphene nanoribbon, could > you please comment on it. > > > On Mon, May 2, 2011 at 11:10 PM, swapnil chandratre < > swapnil.chandratre at gmail.com> wrote: > >> Hi, >> >> I know how to get the H passivated graphene structure, >> and regarding semi conducting property, can you help getting started by >> hinting at some literature. >> >> >> On Mon, May 2, 2011 at 10:20 PM, xirainbow wrote: >> >>> Dear Swapnil Chandratre: >>> >>> Thank you for your quick response, but is it not required to satisfy the >>>> dangling bonds with h2 passivation (as I see just the C atoms here). >>>> >>> You have to add H by yourself. >>> Do not you know how to add atoms? >>> >>> >>>> The other query I had is Graphene is Semi Metallic, it can show semi >>>> conducting properties if designed in ArmChair configuration with proper >>>> geometry, is there any specific thing to keep in mind if I want to explore >>>> that aspect. >>>> >>> I think you should know how to explore semi metallic property of two >>> dimensional graphene, before dealing with nanoribbon. If you don't know the >>> origin of semi-metallic graphene, you would not know how to explore it in >>> nanoribbon. >>> >>> >>>> >>>> >>>> On Mon, May 2, 2011 at 9:54 PM, xirainbow wrote: >>>> >>>>> Dear Swapnil Chandratre: >>>>> The following is my input file for graphenen ribbon6 for QE4.0. >>>>> You can find more information at here: >>>>> http://blog.sina.com.cn/s/blog_5f15ead20100drss.html >>>>> >>>>> ############################################################# >>>>> INPUT FILE OF GRAPHENE RIBBON 6 >>>>> Input file:graphene.rx.in >>>>> &CONTROL >>>>> calculation = 'relax' , >>>>> restart_mode = ?? >>>>> outdir = ?? >>>>> pseudo_dir = ?? >>>>> etot_conv_thr = 1.0e-4 , >>>>> forc_conv_thr = 1.0e-3 , >>>>> tstress = .true. , >>>>> tprnfor = .true. , >>>>> / >>>>> &SYSTEM >>>>> ibrav = 8, >>>>> celldm(1) = 4.67689278, >>>>> celldm(2) = 8.623989813, >>>>> celldm(3) = 4.048794087, >>>>> nat = 12, >>>>> ntyp = 2,// the largest ntype=10 >>>>> ecutwfc = 60.D0 , >>>>> ecutrho = 500.D0 , >>>>> nosym = .false. , >>>>> nbnd = 36, >>>>> nelec = 48, >>>>> occupations = 'smearing' , >>>>> degauss = 0.02 , >>>>> smearing = 'gaussian' , >>>>> nspin = 2 , >>>>> starting_magnetization(1) = 1.0, >>>>> starting_magnetization(2) = -0.5, >>>>> / >>>>> &ELECTRONS >>>>> conv_thr = 1.D-6 , >>>>> mixing_mode = 'plain' , >>>>> mixing_beta = 0.7D0 , >>>>> diagonalization = 'david' , >>>>> diago_david_ndim = 8, >>>>> / >>>>> &IONS >>>>> ion_dynamics = 'damp' , >>>>> pot_extrapolation = 'second_order' , >>>>> wfc_extrapolation = 'second_order' , >>>>> / >>>>> ATOMIC_SPECIES >>>>> C1 12.00000 C.pbe-rrkjus.UPF >>>>> C2 12.00000 C.pbe-rrkjus.UPF >>>>> ATOMIC_POSITIONS crystal >>>>> C1 0.000000000 0.236465542 0.000000000 >>>>> C2 0.500000000 0.265456486 0.000000000 >>>>> C1 0.500000000 0.334092417 0.000000000 >>>>> C2 0.000000000 0.366772814 0.000000000 >>>>> C1 0.000000000 0.433673757 0.000000000 >>>>> C2 0.500000000 0.466640035 0.000000000 >>>>> C1 0.500000000 0.533360168 0.000000000 >>>>> C2 0.000000000 0.566326232 0.000000000 >>>>> C1 0.000000000 0.633227130 0.000000000 >>>>> C2 0.500000000 0.665907475 0.000000000 >>>>> C1 0.500000000 0.734543349 0.000000000 >>>>> C2 0.000000000 0.763534596 0.000000000 >>>>> K_POINTS automatic >>>>> 13 1 1 0 0 0 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, May 3, 2011 at 5:18 AM, swapnil chandratre < >>>>> swapnil.chandratre at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I am new to Espresso, I am trying to work with Graphene >>>>>> Nanoribbon(1-d), though I am spending individual time on understanding how >>>>>> to use the software and implement conditions accordingly, can anyone provide >>>>>> a sample input file for a GNR? >>>>>> >>>>>> -- >>>>>> Regards, >>>>>> Swapnil Chandratre >>>>>> Graduate Student >>>>>> Dept. of Mechanical Engineering, >>>>>> University of Houston, >>>>>> Houston, TX >>>>>> (M)-713-294-9546 >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> _______________________________________________ >>>>> Pw_forum mailing list >>>>> Pw_forum at pwscf.org >>>>> http://www.democritos.it/mailman/listinfo/pw_forum >>>>> >>>>> >>>> >>>> >>>> -- >>>> Regards, >>>> Swapnil Chandratre >>>> Graduate Student >>>> Dept. of Mechanical Engineering, >>>> University of Houston, >>>> Houston, TX >>>> (M)-713-294-9546 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> Regards, >> Swapnil Chandratre >> Graduate Student >> Dept. of Mechanical Engineering, >> University of Houston, >> Houston, TX >> (M)-713-294-9546 >> > > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/3e24e143/attachment-0001.htm From s.m.rezaeisani at gmail.com Wed May 4 08:55:52 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Wed, 4 May 2011 11:25:52 +0430 Subject: [Pw_forum] k-point In-Reply-To: References: Message-ID: Dear Musari Have a look at http://www.cryst.ehu.es/cryst/get_kvec.html HTH On Tue, Apr 26, 2011 at 12:54 PM, Abolore Musari wrote: > Dear QE User, > I am having a problem as regard (k-point) > I am working on monoclinic system, and am using xcrysden to get my k-point > and my question is how do I know the special points (k-points) to select > > from the Brillion zone in the xcrysden k path selection? > > Thanks in anticipation of your favourable assistance > > Musari Abolore > Dept Of Physics > University of Agriculture, Abeokuta > Nigeria > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ========================================== Seyed Mojtaba Rezaei Sani Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel Lab: +98 311 391 3731 Fax Office: +98 311 391 3746 s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110504/cf9cee3f/attachment.htm From yhho at pub.iams.sinica.edu.tw Wed May 4 09:33:21 2011 From: yhho at pub.iams.sinica.edu.tw (yhho) Date: Wed, 4 May 2011 15:33:21 +0800 Subject: [Pw_forum] Hello, I have some problemof QE. Message-ID: <001601cc0a2d$8bc2fe80$61706d8c@mychatd6d7d1f2> Hello, Because I want to calculate my molecule by cp.x, I build the input file as espresso-4.0.3/example/example29. But I got many error massages like this: from system_checkin : error # 1 nelup out of range I think that's coused by my wrong setting of nelup in input file. But although I tried to change the value of nelup, there's still the same error when I run cp.x The version I used QE is 4.0.3. Here's my input file. Please give me some suggestions about nelup setting. Thank you very much. &CONTROL calculation = 'cp', restart_mode = 'from_scratch', nstep = 5, iprint = 10, isave = 10, tstress = .TRUE., tprnfor = .TRUE., dt = 10.0d0, prefix = 'Glu43', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &SYSTEM ibrav =0, celldm(1) = 1.0D0, nat =41, ntyp =6, ecutwfc = 30, ecutrho = 300.0, occupations ='smearing', smearing='fd', degauss =0.02, nr1b=20,nr2b=20,nr3b=20 nspin=2, nelup=6, neldw=1, / &ELECTRONS emass = 1000.d0, emass_cutoff = 4.d0, orthogonalization = 'Gram-Schmidt', startingwfc = 'random', ampre = 0.02, n_inner = 8, tcg = .true., passop=0.3, maxiter = 250, conv_thr=1.d-6 / ion_dynamics = 'damp', ion_damping = 0., ion_positions = 'from_input', greasp=1.0, ion_radius(1) = 0.8d0, ion_temperature = 'not_controlled', / ATOMIC_SPECIES C 12.01 C.pbe-van_ak.UPF N 14.01 N.pbe-van_ak.UPF Fe 55.85 Fe.pbe-sp-van_ak.UPF Cl 35.45 Cl.pbe-n-van.UPF O 16.00 O.pbe-van_ak.UPF H 1.008 H.pbe-van_ak.UPF ATOMIC_POSITIONS (crystal) Fe 4.1641719 -0.5471554 -0.5471554 Cl 4.5964120 -0.9816182 -1.5908458 C 0.0000000 0.0000000 0.0000000 C 1.2973805 0.0000000 -0.3758962 C 1.2525726 -0.0289989 1.8170181 C 2.1350316 -4.1256236 2.1865112 C 2.9221888 -3.0442425 2.4078019 C 2.8226321 -3.3447077 0.2413133 C 6.2923254 -0.8182676 2.5823989 C 5.2510634 -0.2023719 3.4131521 C 5.5088329 0.0750602 4.8865937 C 4.3333907 0.8379462 5.5071409 C 4.5779602 1.2229945 6.9527704 N 0.0000000 0.0000000 1.3847892 N 2.0542695 0.0002705 0.7687871 N 2.1102671 -4.3058679 0.8117062 N 3.3274628 -2.5693481 1.1859156 O 7.3914426 -1.1172282 3.0850061 O 6.0627468 -0.9981431 1.3551644 O 4.1575035 0.0273619 2.9063284 O 3.6274812 1.7187097 7.6151903 O 5.6844234 0.9906742 7.4543204 O 6.3046402 -3.3176420 -0.4637370 O 4.8477761 1.5314745 0.3194472 H -0.8142000 0.0187705 1.9653079 H 1.6667575 0.0001924 -1.3801718 H 1.5611887 -0.0697114 2.8404880 H 1.6328039 -5.0405899 0.3297794 H 3.1807154 -2.6355708 3.3623162 H 2.9657556 -3.2174549 -0.8109516 H 5.5447595 -0.8771014 5.3743575 H 6.3541964 0.7303920 4.9296487 H 3.5103975 0.1546553 5.5181216 H 4.2582631 1.7576717 4.9649696 H 5.4053363 -3.2956001 -0.7980536 H 6.3150255 -3.0172862 0.4481679 H 3.9484722 1.5535164 -0.0148694 H 4.8581614 1.8318303 1.2313521 H -0.8951512 0.0338588 -0.5859376 H 1.6443833 -4.7879056 2.8685623 H 2.8399482 1.1827425 7.4958090 CELL_PARAMETERS {cubic} 20.000 0.0000 0.0000 0.0000 20.000 0.0000 0.0000 0.0000 20.000 Best regards, YHHo, IAMS in Taiwan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110504/c13e1834/attachment.htm From giannozz at democritos.it Wed May 4 11:16:36 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 4 May 2011 11:16:36 +0200 Subject: [Pw_forum] Hello, I have some problemof QE. In-Reply-To: <001601cc0a2d$8bc2fe80$61706d8c@mychatd6d7d1f2> References: <001601cc0a2d$8bc2fe80$61706d8c@mychatd6d7d1f2> Message-ID: On May 4, 2011, at 9:33 , yhho wrote: > nat =41, > nelup=6, > neldw=1, 41 atoms with 7 electrons in total? --- 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 crma at sissa.it Wed May 4 11:20:38 2011 From: crma at sissa.it (Changru Ma) Date: Wed, 4 May 2011 11:20:38 +0200 Subject: [Pw_forum] Hello, I have some problemof QE. In-Reply-To: <001601cc0a2d$8bc2fe80$61706d8c@mychatd6d7d1f2> References: <001601cc0a2d$8bc2fe80$61706d8c@mychatd6d7d1f2> Message-ID: <10474BEA-9004-475E-A23F-505B6F7CEFEF@sissa.it> Dear YHHo, nelup and neldw are number of spin-up and spin-down electrons, respectively. The sum must yield nelec that must also be specified explicitly in this case. I also have a look at your molecule with XCrysden, are you sure it is a molecule? The new release, v.4.3, of the Quantum ESPRESSO distribution is available for download. I suggest you to use the newest version. Next time please specify your question explicitly in the subject of the mail. Best wishes, Changru On 4 May, 2011, at 09:33, yhho wrote: > Hello, > Because I want to calculate my molecule by cp.x, I build the input file as espresso-4.0.3/example/example29. > But I got many error massages like this: > > from system_checkin : error # 1 > nelup out of range > I think that's coused by my wrong setting of nelup in input file. > But although I tried to change the value of nelup, there's still the same error when I run cp.x > > The version I used QE is 4.0.3. > > Here's my input file. > Please give me some suggestions about nelup setting. Thank you very much. > > &CONTROL > calculation = 'cp', > restart_mode = 'from_scratch', > nstep = 5, > iprint = 10, > isave = 10, > tstress = .TRUE., > tprnfor = .TRUE., > dt = 10.0d0, > prefix = 'Glu43', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > > / > > &SYSTEM > ibrav =0, > celldm(1) = 1.0D0, > nat =41, > ntyp =6, > ecutwfc = 30, > ecutrho = 300.0, > occupations ='smearing', > smearing='fd', > degauss =0.02, > nr1b=20,nr2b=20,nr3b=20 > nspin=2, > nelup=6, > neldw=1, > / > &ELECTRONS > emass = 1000.d0, > emass_cutoff = 4.d0, > orthogonalization = 'Gram-Schmidt', > startingwfc = 'random', > ampre = 0.02, > n_inner = 8, > tcg = .true., > passop=0.3, > maxiter = 250, > conv_thr=1.d-6 > / > ion_dynamics = 'damp', > ion_damping = 0., > ion_positions = 'from_input', > greasp=1.0, > ion_radius(1) = 0.8d0, > ion_temperature = 'not_controlled', > / > > ATOMIC_SPECIES > C 12.01 C.pbe-van_ak.UPF > N 14.01 N.pbe-van_ak.UPF > Fe 55.85 Fe.pbe-sp-van_ak.UPF > Cl 35.45 Cl.pbe-n-van.UPF > O 16.00 O.pbe-van_ak.UPF > H 1.008 H.pbe-van_ak.UPF > ATOMIC_POSITIONS (crystal) > Fe 4.1641719 -0.5471554 -0.5471554 > Cl 4.5964120 -0.9816182 -1.5908458 > C 0.0000000 0.0000000 0.0000000 > C 1.2973805 0.0000000 -0.3758962 > C 1.2525726 -0.0289989 1.8170181 > C 2.1350316 -4.1256236 2.1865112 > C 2.9221888 -3.0442425 2.4078019 > C 2.8226321 -3.3447077 0.2413133 > C 6.2923254 -0.8182676 2.5823989 > C 5.2510634 -0.2023719 3.4131521 > C 5.5088329 0.0750602 4.8865937 > C 4.3333907 0.8379462 5.5071409 > C 4.5779602 1.2229945 6.9527704 > N 0.0000000 0.0000000 1.3847892 > N 2.0542695 0.0002705 0.7687871 > N 2.1102671 -4.3058679 0.8117062 > N 3.3274628 -2.5693481 1.1859156 > O 7.3914426 -1.1172282 3.0850061 > O 6.0627468 -0.9981431 1.3551644 > O 4.1575035 0.0273619 2.9063284 > O 3.6274812 1.7187097 7.6151903 > O 5.6844234 0.9906742 7.4543204 > O 6.3046402 -3.3176420 -0.4637370 > O 4.8477761 1.5314745 0.3194472 > H -0.8142000 0.0187705 1.9653079 > H 1.6667575 0.0001924 -1.3801718 > H 1.5611887 -0.0697114 2.8404880 > H 1.6328039 -5.0405899 0.3297794 > H 3.1807154 -2.6355708 3.3623162 > H 2.9657556 -3.2174549 -0.8109516 > H 5.5447595 -0.8771014 5.3743575 > H 6.3541964 0.7303920 4.9296487 > H 3.5103975 0.1546553 5.5181216 > H 4.2582631 1.7576717 4.9649696 > H 5.4053363 -3.2956001 -0.7980536 > H 6.3150255 -3.0172862 0.4481679 > H 3.9484722 1.5535164 -0.0148694 > H 4.8581614 1.8318303 1.2313521 > H -0.8951512 0.0338588 -0.5859376 > H 1.6443833 -4.7879056 2.8685623 > H 2.8399482 1.1827425 7.4958090 > > CELL_PARAMETERS {cubic} > 20.000 0.0000 0.0000 > 0.0000 20.000 0.0000 > 0.0000 0.0000 20.000 > > > Best regards, > YHHo, IAMS in Taiwan > > > > _______________________________________________ > 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: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma --- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110504/39e2faa6/attachment.htm From giovanni.cantele at spin.cnr.it Wed May 4 11:24:23 2011 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Wed, 4 May 2011 11:24:23 +0200 Subject: [Pw_forum] Hello, I have some problemof QE. In-Reply-To: <001601cc0a2d$8bc2fe80$61706d8c@mychatd6d7d1f2> References: <001601cc0a2d$8bc2fe80$61706d8c@mychatd6d7d1f2> Message-ID: <4B38E89D-6E3B-4AB2-83BA-34F201854AB1@spin.cnr.it> On May 4, 2011, at 9:33 AM, yhho wrote: > Hello, > Because I want to calculate my molecule by cp.x, I build the input file as espresso-4.0.3/example/example29. > But I got many error massages like this: > > from system_checkin : error # 1 > nelup out of range > I think that's coused by my wrong setting of nelup in input file. > But although I tried to change the value of nelup, there's still the same error when I run cp.x > > The version I used QE is 4.0.3. > > Here's my input file. > Please give me some suggestions about nelup setting. Thank you very much. > > &CONTROL > calculation = 'cp', > restart_mode = 'from_scratch', > nstep = 5, > iprint = 10, > isave = 10, > tstress = .TRUE., > tprnfor = .TRUE., > dt = 10.0d0, > prefix = 'Glu43', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > > / > > &SYSTEM > ibrav =0, > celldm(1) = 1.0D0, > nat =41, > ntyp =6, > ecutwfc = 30, > ecutrho = 300.0, > occupations ='smearing', > smearing='fd', > degauss =0.02, > nr1b=20,nr2b=20,nr3b=20 > nspin=2, > nelup=6, > neldw=1, > / > &ELECTRONS > emass = 1000.d0, > emass_cutoff = 4.d0, > orthogonalization = 'Gram-Schmidt', > startingwfc = 'random', > ampre = 0.02, > n_inner = 8, > tcg = .true., > passop=0.3, > maxiter = 250, > conv_thr=1.d-6 > / > ion_dynamics = 'damp', > ion_damping = 0., > ion_positions = 'from_input', > greasp=1.0, > ion_radius(1) = 0.8d0, > ion_temperature = 'not_controlled', > / > > ATOMIC_SPECIES > C 12.01 C.pbe-van_ak.UPF > N 14.01 N.pbe-van_ak.UPF > Fe 55.85 Fe.pbe-sp-van_ak.UPF > Cl 35.45 Cl.pbe-n-van.UPF > O 16.00 O.pbe-van_ak.UPF > H 1.008 H.pbe-van_ak.UPF > ATOMIC_POSITIONS (crystal) > Fe 4.1641719 -0.5471554 -0.5471554 > Cl 4.5964120 -0.9816182 -1.5908458 > C 0.0000000 0.0000000 0.0000000 > C 1.2973805 0.0000000 -0.3758962 > C 1.2525726 -0.0289989 1.8170181 > C 2.1350316 -4.1256236 2.1865112 > C 2.9221888 -3.0442425 2.4078019 > C 2.8226321 -3.3447077 0.2413133 > C 6.2923254 -0.8182676 2.5823989 > C 5.2510634 -0.2023719 3.4131521 > C 5.5088329 0.0750602 4.8865937 > C 4.3333907 0.8379462 5.5071409 > C 4.5779602 1.2229945 6.9527704 > N 0.0000000 0.0000000 1.3847892 > N 2.0542695 0.0002705 0.7687871 > N 2.1102671 -4.3058679 0.8117062 > N 3.3274628 -2.5693481 1.1859156 > O 7.3914426 -1.1172282 3.0850061 > O 6.0627468 -0.9981431 1.3551644 > O 4.1575035 0.0273619 2.9063284 > O 3.6274812 1.7187097 7.6151903 > O 5.6844234 0.9906742 7.4543204 > O 6.3046402 -3.3176420 -0.4637370 > O 4.8477761 1.5314745 0.3194472 > H -0.8142000 0.0187705 1.9653079 > H 1.6667575 0.0001924 -1.3801718 > H 1.5611887 -0.0697114 2.8404880 > H 1.6328039 -5.0405899 0.3297794 > H 3.1807154 -2.6355708 3.3623162 > H 2.9657556 -3.2174549 -0.8109516 > H 5.5447595 -0.8771014 5.3743575 > H 6.3541964 0.7303920 4.9296487 > H 3.5103975 0.1546553 5.5181216 > H 4.2582631 1.7576717 4.9649696 > H 5.4053363 -3.2956001 -0.7980536 > H 6.3150255 -3.0172862 0.4481679 > H 3.9484722 1.5535164 -0.0148694 > H 4.8581614 1.8318303 1.2313521 > H -0.8951512 0.0338588 -0.5859376 > H 1.6443833 -4.7879056 2.8685623 > H 2.8399482 1.1827425 7.4958090 > > CELL_PARAMETERS {cubic} > 20.000 0.0000 0.0000 > 0.0000 20.000 0.0000 > 0.0000 0.0000 20.000 > > > Best regards, > YHHo, IAMS in Taiwan > > I never used this variable, but from expresso-4.0.5/INPUT_PW.txt I read: Variables: nelup, neldw Type: REAL Description: number of spin-up and spin-down electrons, respectively Note that this fixes the final value of the magnetization. The sum must yield nelec that must also be specified explicitly in this case. Not valid for spin-unpolarized or noncollinear calculations, only for LSDA. Obsolescent: use multiplicity or tot_magnetization instead. Now, according to the above statement: i) you must specify nelec as well ii) nelup+neldw=nelec iii) this variables are obsolescent Because nat=41, it is quite unlikely that you want to make a run in which nelup+neldw=6+1=7 electrons!!! Giovanni -- **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110504/6bc3a32f/attachment-0001.htm From ma at nano.ku.dk Wed May 4 14:26:08 2011 From: ma at nano.ku.dk (Martin Andersson) Date: Wed, 04 May 2011 14:26:08 +0200 Subject: [Pw_forum] cohesive energy of water/ice Message-ID: <4DC145E0.5000004@nano.ku.dk> Hi, I have been calculating the cohesive energy of amorphous ice as well as ice/water layers on mineral surfaces with the PBE functional. I get a cohesive energy for water in amorphous ice (144 waters in a ~16x16x16 ? box) compared to water in a 20x20x20 ? box that is 1.08 eV for ultrasoft pseudopotentials (35 Ry cutoff) (the rrkjus ones from the library) and 0.98 for PAW (50 Ry cutoff) from the AtomPAW library. This is significantly different from other studies in literature, who find around 0.7 for PBE and PW91. I have no idea on why results differ so much, so any suggestions are welcome... Input files below I have used QE 4.2.1 for the calculations. Cheers, Martin Andersson University of Copenhagen Water molecule: &control calculation='relax', restart_mode='from_scratch', prefix='water', pseudo_dir = '/nanogeo/martinpa/espresso-4.1.2/pseudo/', outdir='/nanogeo/martinpa/scratch/', nstep = 500, / &system ibrav = 0, celldm(1)= 1.889726 nat= 3, ntyp= 2, ecutwfc = 25.0 ecutrho=250.0 / &electrons tqr=.true. electron_maxstep=300 mixing_beta = 0.7 conv_thr = 1.0d-8 / &ions ion_dynamics='bfgs' / ATOMIC_SPECIES O 15.999 O.pbe-rrkjus.UPF H 1.008 H.pbe-rrkjus.UPF CELL_PARAMETERS (alat) 20.0 0.0 0.0 0.0 20.0 0.0 0.0 0.0 20.0 ATOMIC_POSITIONS (angstrom) O 1.645835061 6.664706853 -3.065877101 H 1.954195796 5.741969275 -3.013292036 H 0.781969143 6.612323872 -3.513830863 K_POINTS gamma Water/ice box: &control calculation='vc-relax', restart_mode='from_scratch', prefix='water_box_pbe', pseudo_dir = '/nanogeo/martinpa/espresso-4.1.2/pseudo/', outdir='/nanogeo/martinpa/scratch/', nstep=800, / &system ibrav = 0, celldm(1)= 30.12, nat= 432, ntyp= 2, ecutwfc = 35.0 ecutrho=350.0 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / &ions ion_dynamics='bfgs' / &cell / ATOMIC_SPECIES O 15.999 O.pbe-rrkjus.UPF H 1.008 H.pbe-rrkjus.UPF CELL_PARAMETERS (alat) 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 ATOMIC_POSITIONS (angstrom) O 1.55044873 5.96202627 2.60180606 H 2.30308679 5.44140199 2.15448925 H 1.55186146 6.84277348 2.18469312 O 2.75527999 5.56261328 6.64391086 H 1.87802894 5.74881675 6.16708492 H 3.31325372 6.34758540 6.41134505 O 3.22309324 1.89168472 3.88961021 H 2.61702065 1.91739789 3.09551241 H 4.01467966 2.45594481 3.70306054 O 4.48506446 6.01381737 3.59607144 H 4.79562362 5.08661359 3.73169343 H 4.50977887 6.46474361 4.46567132 O 1.77303326 2.94790120 5.91805891 H 2.28673590 2.58580777 5.13755687 H 2.24855288 3.77512959 6.16942302 O 4.65676934 1.48321243 -0.13520423 H 4.99010076 0.81319922 0.52324992 H 5.43290580 1.98525495 -0.48533141 O 5.55987706 7.38184199 1.58481400 H 6.17984242 7.90892302 2.16733020 H 5.04800775 6.83909417 2.26677052 O 7.55291198 4.15102828 2.12039216 H 7.17902221 4.52972041 1.27124584 O 6.64425738 3.28381066 6.37285202 H 6.54501798 4.14569728 6.85517739 O 6.73402518 5.59786432 7.92002821 H 7.45748780 6.05233245 7.44773838 O 5.64728834 3.38272560 3.83732221 H 6.35185771 3.76626449 3.22325132 H 6.01549713 3.41619082 4.77312319 O 1.15580367 0.92342575 7.55891408 H 1.53237453 1.65148284 6.98102430 H 0.33603244 0.65613748 7.07671820 O 3.26481409 4.60201028 1.14248028 H 3.02908883 4.92798766 0.21902371 H 3.26715096 3.62696286 1.09066105 O 7.02500419 0.98616684 3.28860775 H 7.88449133 1.32460100 2.87488044 H 6.45468737 1.79129421 3.42040737 O 0.60992588 5.84690827 5.20692515 H 1.01132581 5.91122975 4.30224404 H 0.01367240 6.64131284 5.32349168 H 8.18675121 4.87891083 2.40805975 H 7.61653933 3.18720306 6.22068038 H 6.27629400 6.31178391 8.47864853 O 4.21779588 -0.04576478 5.74403801 H 3.80089925 0.51885747 5.04242315 H 4.30451597 0.56430788 6.55434731 O 7.05170266 0.00823077 5.76312401 H 7.15868948 0.44849492 4.86434702 H 6.06873956 -0.11926391 5.81861878 O 1.26480260 2.00201448 1.97180356 H 1.17489828 1.54585860 1.06336687 H 0.77449155 2.87361598 1.89046099 O 9.55044873 5.96202627 2.60180606 H 10.30308679 5.44140199 2.15448925 H 9.55186146 6.84277348 2.18469312 O 10.75527999 5.56261328 6.64391086 H 9.87802894 5.74881675 6.16708492 H 11.31325372 6.34758540 6.41134505 O 11.22309324 1.89168472 3.88961021 H 10.61702065 1.91739789 3.09551241 H 12.01467966 2.45594481 3.70306054 O 12.48506446 6.01381737 3.59607144 H 12.79562362 5.08661359 3.73169343 H 12.50977887 6.46474361 4.46567132 O 9.77303326 2.94790120 5.91805891 H 10.28673590 2.58580777 5.13755687 H 10.24855288 3.77512959 6.16942302 O 12.65676934 1.48321243 -0.13520423 H 12.99010076 0.81319922 0.52324992 H 13.43290580 1.98525495 -0.48533141 O 13.55987706 7.38184199 1.58481400 H 14.17984242 7.90892302 2.16733020 H 13.04800775 6.83909417 2.26677052 O 15.55291198 4.15102828 2.12039216 H 15.17902221 4.52972041 1.27124584 O 14.64425738 3.28381066 6.37285202 H 14.54501798 4.14569728 6.85517739 O 14.73402518 5.59786432 7.92002821 H 15.45748780 6.05233245 7.44773838 O 13.64728834 3.38272560 3.83732221 H 14.35185771 3.76626449 3.22325132 H 14.01549713 3.41619082 4.77312319 O 9.15580367 0.92342575 7.55891408 H 9.53237453 1.65148284 6.98102430 H 8.33603244 0.65613748 7.07671820 O 11.26481409 4.60201028 1.14248028 H 11.02908883 4.92798766 0.21902371 H 11.26715096 3.62696286 1.09066105 O 15.02500419 0.98616684 3.28860775 H 15.88449133 1.32460100 2.87488044 H 14.45468737 1.79129421 3.42040737 O 8.60992588 5.84690827 5.20692515 H 9.01132581 5.91122975 4.30224404 H 8.01367240 6.64131284 5.32349168 H 16.18675121 4.87891083 2.40805975 H 15.61653933 3.18720306 6.22068038 H 14.27629400 6.31178391 8.47864853 O 12.21779588 -0.04576478 5.74403801 H 11.80089925 0.51885747 5.04242315 H 12.30451597 0.56430788 6.55434731 O 15.05170266 0.00823077 5.76312401 H 15.15868948 0.44849492 4.86434702 H 14.06873956 -0.11926391 5.81861878 O 9.26480260 2.00201448 1.97180356 H 9.17489828 1.54585860 1.06336687 H 8.77449155 2.87361598 1.89046099 O 1.55044873 13.96202627 2.60180606 H 2.30308679 13.44140199 2.15448925 H 1.55186146 14.84277348 2.18469312 O 2.75527999 13.56261328 6.64391086 H 1.87802894 13.74881675 6.16708492 H 3.31325372 14.34758540 6.41134505 O 3.22309324 9.89168472 3.88961021 H 2.61702065 9.91739789 3.09551241 H 4.01467966 10.45594481 3.70306054 O 4.48506446 14.01381737 3.59607144 H 4.79562362 13.08661359 3.73169343 H 4.50977887 14.46474361 4.46567132 O 1.77303326 10.94790120 5.91805891 H 2.28673590 10.58580777 5.13755687 H 2.24855288 11.77512959 6.16942302 O 4.65676934 9.48321243 -0.13520423 H 4.99010076 8.81319922 0.52324992 H 5.43290580 9.98525495 -0.48533141 O 5.55987706 15.38184199 1.58481400 H 6.17984242 15.90892302 2.16733020 H 5.04800775 14.83909417 2.26677052 O 7.55291198 12.15102828 2.12039216 H 7.17902221 12.52972041 1.27124584 O 6.64425738 11.28381066 6.37285202 H 6.54501798 12.14569728 6.85517739 O 6.73402518 13.59786432 7.92002821 H 7.45748780 14.05233245 7.44773838 O 5.64728834 11.38272560 3.83732221 H 6.35185771 11.76626449 3.22325132 H 6.01549713 11.41619082 4.77312319 O 1.15580367 8.92342575 7.55891408 H 1.53237453 9.65148284 6.98102430 H 0.33603244 8.65613748 7.07671820 O 3.26481409 12.60201028 1.14248028 H 3.02908883 12.92798766 0.21902371 H 3.26715096 11.62696286 1.09066105 O 7.02500419 8.98616684 3.28860775 H 7.88449133 9.32460100 2.87488044 H 6.45468737 9.79129421 3.42040737 O 0.60992588 13.84690827 5.20692515 H 1.01132581 13.91122975 4.30224404 H 0.01367240 14.64131284 5.32349168 H 8.18675121 12.87891083 2.40805975 H 7.61653933 11.18720306 6.22068038 H 6.27629400 14.31178391 8.47864853 O 4.21779588 7.95423522 5.74403801 H 3.80089925 8.51885747 5.04242315 H 4.30451597 8.56430788 6.55434731 O 7.05170266 8.00823077 5.76312401 H 7.15868948 8.44849492 4.86434702 H 6.06873956 7.88073609 5.81861878 O 1.26480260 10.00201448 1.97180356 H 1.17489828 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10.60180606 H 2.30308679 13.44140199 10.15448925 H 1.55186146 14.84277348 10.18469312 O 2.75527999 13.56261328 14.64391086 H 1.87802894 13.74881675 14.16708492 H 3.31325372 14.34758540 14.41134505 O 3.22309324 9.89168472 11.88961021 H 2.61702065 9.91739789 11.09551241 H 4.01467966 10.45594481 11.70306054 O 4.48506446 14.01381737 11.59607144 H 4.79562362 13.08661359 11.73169343 H 4.50977887 14.46474361 12.46567132 O 1.77303326 10.94790120 13.91805891 H 2.28673590 10.58580777 13.13755687 H 2.24855288 11.77512959 14.16942302 O 4.65676934 9.48321243 7.86479577 H 4.99010076 8.81319922 8.52324992 H 5.43290580 9.98525495 7.51466859 O 5.55987706 15.38184199 9.58481400 H 6.17984242 15.90892302 10.16733020 H 5.04800775 14.83909417 10.26677052 O 7.55291198 12.15102828 10.12039216 H 7.17902221 12.52972041 9.27124584 O 6.64425738 11.28381066 14.37285202 H 6.54501798 12.14569728 14.85517739 O 6.73402518 13.59786432 15.92002821 H 7.45748780 14.05233245 15.44773838 O 5.64728834 11.38272560 11.83732221 H 6.35185771 11.76626449 11.22325132 H 6.01549713 11.41619082 12.77312319 O 1.15580367 8.92342575 15.55891408 H 1.53237453 9.65148284 14.98102430 H 0.33603244 8.65613748 15.07671820 O 3.26481409 12.60201028 9.14248028 H 3.02908883 12.92798766 8.21902371 H 3.26715096 11.62696286 9.09066105 O 7.02500419 8.98616684 11.28860775 H 7.88449133 9.32460100 10.87488044 H 6.45468737 9.79129421 11.42040737 O 0.60992588 13.84690827 13.20692515 H 1.01132581 13.91122975 12.30224404 H 0.01367240 14.64131284 13.32349168 H 8.18675121 12.87891083 10.40805975 H 7.61653933 11.18720306 14.22068038 H 6.27629400 14.31178391 16.47864853 O 4.21779588 7.95423522 13.74403801 H 3.80089925 8.51885747 13.04242315 H 4.30451597 8.56430788 14.55434731 O 7.05170266 8.00823077 13.76312401 H 7.15868948 8.44849492 12.86434702 H 6.06873956 7.88073609 13.81861878 O 1.26480260 10.00201448 9.97180356 H 1.17489828 9.54585860 9.06336687 H 0.77449155 10.87361598 9.89046099 O 9.55044873 13.96202627 10.60180606 H 10.30308679 13.44140199 10.15448925 H 9.55186146 14.84277348 10.18469312 O 10.75527999 13.56261328 14.64391086 H 9.87802894 13.74881675 14.16708492 H 11.31325372 14.34758540 14.41134505 O 11.22309324 9.89168472 11.88961021 H 10.61702065 9.91739789 11.09551241 H 12.01467966 10.45594481 11.70306054 O 12.48506446 14.01381737 11.59607144 H 12.79562362 13.08661359 11.73169343 H 12.50977887 14.46474361 12.46567132 O 9.77303326 10.94790120 13.91805891 H 10.28673590 10.58580777 13.13755687 H 10.24855288 11.77512959 14.16942302 O 12.65676934 9.48321243 7.86479577 H 12.99010076 8.81319922 8.52324992 H 13.43290580 9.98525495 7.51466859 O 13.55987706 15.38184199 9.58481400 H 14.17984242 15.90892302 10.16733020 H 13.04800775 14.83909417 10.26677052 O 15.55291198 12.15102828 10.12039216 H 15.17902221 12.52972041 9.27124584 O 14.64425738 11.28381066 14.37285202 H 14.54501798 12.14569728 14.85517739 O 14.73402518 13.59786432 15.92002821 H 15.45748780 14.05233245 15.44773838 O 13.64728834 11.38272560 11.83732221 H 14.35185771 11.76626449 11.22325132 H 14.01549713 11.41619082 12.77312319 O 9.15580367 8.92342575 15.55891408 H 9.53237453 9.65148284 14.98102430 H 8.33603244 8.65613748 15.07671820 O 11.26481409 12.60201028 9.14248028 H 11.02908883 12.92798766 8.21902371 H 11.26715096 11.62696286 9.09066105 O 15.02500419 8.98616684 11.28860775 H 15.88449133 9.32460100 10.87488044 H 14.45468737 9.79129421 11.42040737 O 8.60992588 13.84690827 13.20692515 H 9.01132581 13.91122975 12.30224404 H 8.01367240 14.64131284 13.32349168 H 16.18675121 12.87891083 10.40805975 H 15.61653933 11.18720306 14.22068038 H 14.27629400 14.31178391 16.47864853 O 12.21779588 7.95423522 13.74403801 H 11.80089925 8.51885747 13.04242315 H 12.30451597 8.56430788 14.55434731 O 15.05170266 8.00823077 13.76312401 H 15.15868948 8.44849492 12.86434702 H 14.06873956 7.88073609 13.81861878 O 9.26480260 10.00201448 9.97180356 H 9.17489828 9.54585860 9.06336687 H 8.77449155 10.87361598 9.89046099 K_POINTS gamma -------------- next part 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URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110504/eb9dba50/attachment-0001.htm From kucukben at sissa.it Wed May 4 14:39:12 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Wed, 04 May 2011 14:39:12 +0200 Subject: [Pw_forum] cohesive energy of water/ice In-Reply-To: <4DC145E0.5000004@nano.ku.dk> References: <4DC145E0.5000004@nano.ku.dk> Message-ID: <20110504143912.sodjitv5z408coww@webmail.sissa.it> Hi Martin, Just a quick note, when calculating isolated molecules, set nosym = .true. not to use any symmetry, set some form of assume_isolated for polar molecules to account for periodic image corrections. i dont know if these would affect your results but this is the correct way of accounting for an isolated system in a periodic code. Also, definitely important: compare things in the same level of accuracy: ecutwfc, ecutrho etc. should correspond to the same level of expansion in plane waves both in water molecule and amorphous ice/water complex..keep them the same. hope this helps emine kucukbenli, phd student, sissa, italy Quoting Martin Andersson : > Hi, > > I have been calculating the cohesive energy of amorphous ice as well > as ice/water layers on mineral surfaces with the PBE functional. I > get a cohesive energy for water in amorphous ice (144 waters in a > ~16x16x16 ? box) compared to water in a 20x20x20 ? box that is 1.08 > eV for ultrasoft pseudopotentials (35 Ry cutoff) (the rrkjus ones > from the library) and 0.98 for PAW (50 Ry cutoff) from the AtomPAW > library. This is significantly different from other studies in > literature, who find around 0.7 for PBE and PW91. I have no idea on > why results differ so much, so any suggestions are welcome... Input > files below > > I have used QE 4.2.1 for the calculations. > > Cheers, > Martin Andersson > University of Copenhagen > > Water molecule: > &control > calculation='relax', > restart_mode='from_scratch', > prefix='water', > pseudo_dir = '/nanogeo/martinpa/espresso-4.1.2/pseudo/', > outdir='/nanogeo/martinpa/scratch/', > nstep = 500, > > > > / > &system > ibrav = 0, celldm(1)= 1.889726 > nat= 3, > ntyp= 2, > ecutwfc = 25.0 > ecutrho=250.0 > > > / > &electrons > tqr=.true. > electron_maxstep=300 > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > &ions > ion_dynamics='bfgs' > / > > ATOMIC_SPECIES > O 15.999 O.pbe-rrkjus.UPF > H 1.008 H.pbe-rrkjus.UPF > > CELL_PARAMETERS (alat) > 20.0 0.0 0.0 > 0.0 20.0 0.0 > 0.0 0.0 20.0 > ATOMIC_POSITIONS (angstrom) > O 1.645835061 6.664706853 -3.065877101 > H 1.954195796 5.741969275 -3.013292036 > H 0.781969143 6.612323872 -3.513830863 > K_POINTS gamma > > > Water/ice box: > > &control > calculation='vc-relax', > restart_mode='from_scratch', > prefix='water_box_pbe', > pseudo_dir = '/nanogeo/martinpa/espresso-4.1.2/pseudo/', > outdir='/nanogeo/martinpa/scratch/', > nstep=800, > / > &system > ibrav = 0, celldm(1)= 30.12, > nat= 432, > ntyp= 2, > ecutwfc = 35.0 > ecutrho=350.0 > > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-8 > / > &ions > ion_dynamics='bfgs' > / > &cell > / > ATOMIC_SPECIES > O 15.999 O.pbe-rrkjus.UPF > H 1.008 H.pbe-rrkjus.UPF > CELL_PARAMETERS (alat) > 1.0 0.0 0.0 > 0.0 1.0 0.0 > 0.0 0.0 1.0 > ATOMIC_POSITIONS (angstrom) > O 1.55044873 5.96202627 2.60180606 > H 2.30308679 5.44140199 2.15448925 > H 1.55186146 6.84277348 2.18469312 > O 2.75527999 5.56261328 6.64391086 > H 1.87802894 5.74881675 6.16708492 > H 3.31325372 6.34758540 6.41134505 > O 3.22309324 1.89168472 3.88961021 > H 2.61702065 1.91739789 3.09551241 > H 4.01467966 2.45594481 3.70306054 > O 4.48506446 6.01381737 3.59607144 > H 4.79562362 5.08661359 3.73169343 > H 4.50977887 6.46474361 4.46567132 > O 1.77303326 2.94790120 5.91805891 > H 2.28673590 2.58580777 5.13755687 > H 2.24855288 3.77512959 6.16942302 > O 4.65676934 1.48321243 -0.13520423 > H 4.99010076 0.81319922 0.52324992 > H 5.43290580 1.98525495 -0.48533141 > O 5.55987706 7.38184199 1.58481400 > H 6.17984242 7.90892302 2.16733020 > H 5.04800775 6.83909417 2.26677052 > O 7.55291198 4.15102828 2.12039216 > H 7.17902221 4.52972041 1.27124584 > O 6.64425738 3.28381066 6.37285202 > H 6.54501798 4.14569728 6.85517739 > O 6.73402518 5.59786432 7.92002821 > H 7.45748780 6.05233245 7.44773838 > O 5.64728834 3.38272560 3.83732221 > H 6.35185771 3.76626449 3.22325132 > H 6.01549713 3.41619082 4.77312319 > O 1.15580367 0.92342575 7.55891408 > H 1.53237453 1.65148284 6.98102430 > H 0.33603244 0.65613748 7.07671820 > O 3.26481409 4.60201028 1.14248028 > H 3.02908883 4.92798766 0.21902371 > H 3.26715096 3.62696286 1.09066105 > O 7.02500419 0.98616684 3.28860775 > H 7.88449133 1.32460100 2.87488044 > H 6.45468737 1.79129421 3.42040737 > O 0.60992588 5.84690827 5.20692515 > H 1.01132581 5.91122975 4.30224404 > H 0.01367240 6.64131284 5.32349168 > H 8.18675121 4.87891083 2.40805975 > H 7.61653933 3.18720306 6.22068038 > H 6.27629400 6.31178391 8.47864853 > O 4.21779588 -0.04576478 5.74403801 > H 3.80089925 0.51885747 5.04242315 > H 4.30451597 0.56430788 6.55434731 > O 7.05170266 0.00823077 5.76312401 > H 7.15868948 0.44849492 4.86434702 > H 6.06873956 -0.11926391 5.81861878 > O 1.26480260 2.00201448 1.97180356 > H 1.17489828 1.54585860 1.06336687 > H 0.77449155 2.87361598 1.89046099 > O 9.55044873 5.96202627 2.60180606 > H 10.30308679 5.44140199 2.15448925 > H 9.55186146 6.84277348 2.18469312 > O 10.75527999 5.56261328 6.64391086 > H 9.87802894 5.74881675 6.16708492 > H 11.31325372 6.34758540 6.41134505 > O 11.22309324 1.89168472 3.88961021 > H 10.61702065 1.91739789 3.09551241 > H 12.01467966 2.45594481 3.70306054 > O 12.48506446 6.01381737 3.59607144 > H 12.79562362 5.08661359 3.73169343 > H 12.50977887 6.46474361 4.46567132 > O 9.77303326 2.94790120 5.91805891 > H 10.28673590 2.58580777 5.13755687 > H 10.24855288 3.77512959 6.16942302 > O 12.65676934 1.48321243 -0.13520423 > H 12.99010076 0.81319922 0.52324992 > H 13.43290580 1.98525495 -0.48533141 > O 13.55987706 7.38184199 1.58481400 > H 14.17984242 7.90892302 2.16733020 > H 13.04800775 6.83909417 2.26677052 > O 15.55291198 4.15102828 2.12039216 > H 15.17902221 4.52972041 1.27124584 > O 14.64425738 3.28381066 6.37285202 > H 14.54501798 4.14569728 6.85517739 > O 14.73402518 5.59786432 7.92002821 > H 15.45748780 6.05233245 7.44773838 > O 13.64728834 3.38272560 3.83732221 > H 14.35185771 3.76626449 3.22325132 > H 14.01549713 3.41619082 4.77312319 > O 9.15580367 0.92342575 7.55891408 > H 9.53237453 1.65148284 6.98102430 > H 8.33603244 0.65613748 7.07671820 > O 11.26481409 4.60201028 1.14248028 > H 11.02908883 4.92798766 0.21902371 > H 11.26715096 3.62696286 1.09066105 > O 15.02500419 0.98616684 3.28860775 > H 15.88449133 1.32460100 2.87488044 > H 14.45468737 1.79129421 3.42040737 > O 8.60992588 5.84690827 5.20692515 > H 9.01132581 5.91122975 4.30224404 > H 8.01367240 6.64131284 5.32349168 > H 16.18675121 4.87891083 2.40805975 > H 15.61653933 3.18720306 6.22068038 > H 14.27629400 6.31178391 8.47864853 > O 12.21779588 -0.04576478 5.74403801 > H 11.80089925 0.51885747 5.04242315 > H 12.30451597 0.56430788 6.55434731 > O 15.05170266 0.00823077 5.76312401 > H 15.15868948 0.44849492 4.86434702 > H 14.06873956 -0.11926391 5.81861878 > O 9.26480260 2.00201448 1.97180356 > H 9.17489828 1.54585860 1.06336687 > H 8.77449155 2.87361598 1.89046099 > O 1.55044873 13.96202627 2.60180606 > H 2.30308679 13.44140199 2.15448925 > H 1.55186146 14.84277348 2.18469312 > O 2.75527999 13.56261328 6.64391086 > H 1.87802894 13.74881675 6.16708492 > H 3.31325372 14.34758540 6.41134505 > O 3.22309324 9.89168472 3.88961021 > H 2.61702065 9.91739789 3.09551241 > H 4.01467966 10.45594481 3.70306054 > O 4.48506446 14.01381737 3.59607144 > H 4.79562362 13.08661359 3.73169343 > H 4.50977887 14.46474361 4.46567132 > O 1.77303326 10.94790120 5.91805891 > H 2.28673590 10.58580777 5.13755687 > H 2.24855288 11.77512959 6.16942302 > O 4.65676934 9.48321243 -0.13520423 > H 4.99010076 8.81319922 0.52324992 > H 5.43290580 9.98525495 -0.48533141 > O 5.55987706 15.38184199 1.58481400 > H 6.17984242 15.90892302 2.16733020 > H 5.04800775 14.83909417 2.26677052 > O 7.55291198 12.15102828 2.12039216 > H 7.17902221 12.52972041 1.27124584 > O 6.64425738 11.28381066 6.37285202 > H 6.54501798 12.14569728 6.85517739 > O 6.73402518 13.59786432 7.92002821 > H 7.45748780 14.05233245 7.44773838 > O 5.64728834 11.38272560 3.83732221 > H 6.35185771 11.76626449 3.22325132 > H 6.01549713 11.41619082 4.77312319 > O 1.15580367 8.92342575 7.55891408 > H 1.53237453 9.65148284 6.98102430 > H 0.33603244 8.65613748 7.07671820 > O 3.26481409 12.60201028 1.14248028 > H 3.02908883 12.92798766 0.21902371 > H 3.26715096 11.62696286 1.09066105 > O 7.02500419 8.98616684 3.28860775 > H 7.88449133 9.32460100 2.87488044 > H 6.45468737 9.79129421 3.42040737 > O 0.60992588 13.84690827 5.20692515 > H 1.01132581 13.91122975 4.30224404 > H 0.01367240 14.64131284 5.32349168 > H 8.18675121 12.87891083 2.40805975 > H 7.61653933 11.18720306 6.22068038 > H 6.27629400 14.31178391 8.47864853 > O 4.21779588 7.95423522 5.74403801 > H 3.80089925 8.51885747 5.04242315 > H 4.30451597 8.56430788 6.55434731 > O 7.05170266 8.00823077 5.76312401 > H 7.15868948 8.44849492 4.86434702 > H 6.06873956 7.88073609 5.81861878 > O 1.26480260 10.00201448 1.97180356 > H 1.17489828 9.54585860 1.06336687 > H 0.77449155 10.87361598 1.89046099 > O 9.55044873 13.96202627 2.60180606 > H 10.30308679 13.44140199 2.15448925 > H 9.55186146 14.84277348 2.18469312 > O 10.75527999 13.56261328 6.64391086 > H 9.87802894 13.74881675 6.16708492 > H 11.31325372 14.34758540 6.41134505 > O 11.22309324 9.89168472 3.88961021 > H 10.61702065 9.91739789 3.09551241 > H 12.01467966 10.45594481 3.70306054 > O 12.48506446 14.01381737 3.59607144 > H 12.79562362 13.08661359 3.73169343 > H 12.50977887 14.46474361 4.46567132 > O 9.77303326 10.94790120 5.91805891 > H 10.28673590 10.58580777 5.13755687 > H 10.24855288 11.77512959 6.16942302 > O 12.65676934 9.48321243 -0.13520423 > H 12.99010076 8.81319922 0.52324992 > H 13.43290580 9.98525495 -0.48533141 > O 13.55987706 15.38184199 1.58481400 > H 14.17984242 15.90892302 2.16733020 > H 13.04800775 14.83909417 2.26677052 > O 15.55291198 12.15102828 2.12039216 > H 15.17902221 12.52972041 1.27124584 > O 14.64425738 11.28381066 6.37285202 > H 14.54501798 12.14569728 6.85517739 > O 14.73402518 13.59786432 7.92002821 > H 15.45748780 14.05233245 7.44773838 > O 13.64728834 11.38272560 3.83732221 > H 14.35185771 11.76626449 3.22325132 > H 14.01549713 11.41619082 4.77312319 > O 9.15580367 8.92342575 7.55891408 > H 9.53237453 9.65148284 6.98102430 > H 8.33603244 8.65613748 7.07671820 > O 11.26481409 12.60201028 1.14248028 > H 11.02908883 12.92798766 0.21902371 > H 11.26715096 11.62696286 1.09066105 > O 15.02500419 8.98616684 3.28860775 > H 15.88449133 9.32460100 2.87488044 > H 14.45468737 9.79129421 3.42040737 > O 8.60992588 13.84690827 5.20692515 > H 9.01132581 13.91122975 4.30224404 > H 8.01367240 14.64131284 5.32349168 > H 16.18675121 12.87891083 2.40805975 > H 15.61653933 11.18720306 6.22068038 > H 14.27629400 14.31178391 8.47864853 > O 12.21779588 7.95423522 5.74403801 > H 11.80089925 8.51885747 5.04242315 > H 12.30451597 8.56430788 6.55434731 > O 15.05170266 8.00823077 5.76312401 > H 15.15868948 8.44849492 4.86434702 > H 14.06873956 7.88073609 5.81861878 > O 9.26480260 10.00201448 1.97180356 > H 9.17489828 9.54585860 1.06336687 > H 8.77449155 10.87361598 1.89046099 > O 1.55044873 5.96202627 10.60180606 > H 2.30308679 5.44140199 10.15448925 > H 1.55186146 6.84277348 10.18469312 > O 2.75527999 5.56261328 14.64391086 > H 1.87802894 5.74881675 14.16708492 > H 3.31325372 6.34758540 14.41134505 > O 3.22309324 1.89168472 11.88961021 > H 2.61702065 1.91739789 11.09551241 > H 4.01467966 2.45594481 11.70306054 > O 4.48506446 6.01381737 11.59607144 > H 4.79562362 5.08661359 11.73169343 > H 4.50977887 6.46474361 12.46567132 > O 1.77303326 2.94790120 13.91805891 > H 2.28673590 2.58580777 13.13755687 > H 2.24855288 3.77512959 14.16942302 > O 4.65676934 1.48321243 7.86479577 > H 4.99010076 0.81319922 8.52324992 > H 5.43290580 1.98525495 7.51466859 > O 5.55987706 7.38184199 9.58481400 > H 6.17984242 7.90892302 10.16733020 > H 5.04800775 6.83909417 10.26677052 > O 7.55291198 4.15102828 10.12039216 > H 7.17902221 4.52972041 9.27124584 > O 6.64425738 3.28381066 14.37285202 > H 6.54501798 4.14569728 14.85517739 > O 6.73402518 5.59786432 15.92002821 > H 7.45748780 6.05233245 15.44773838 > O 5.64728834 3.38272560 11.83732221 > H 6.35185771 3.76626449 11.22325132 > H 6.01549713 3.41619082 12.77312319 > O 1.15580367 0.92342575 15.55891408 > H 1.53237453 1.65148284 14.98102430 > H 0.33603244 0.65613748 15.07671820 > O 3.26481409 4.60201028 9.14248028 > H 3.02908883 4.92798766 8.21902371 > H 3.26715096 3.62696286 9.09066105 > O 7.02500419 0.98616684 11.28860775 > H 7.88449133 1.32460100 10.87488044 > H 6.45468737 1.79129421 11.42040737 > O 0.60992588 5.84690827 13.20692515 > H 1.01132581 5.91122975 12.30224404 > H 0.01367240 6.64131284 13.32349168 > H 8.18675121 4.87891083 10.40805975 > H 7.61653933 3.18720306 14.22068038 > H 6.27629400 6.31178391 16.47864853 > O 4.21779588 -0.04576478 13.74403801 > H 3.80089925 0.51885747 13.04242315 > H 4.30451597 0.56430788 14.55434731 > O 7.05170266 0.00823077 13.76312401 > H 7.15868948 0.44849492 12.86434702 > H 6.06873956 -0.11926391 13.81861878 > O 1.26480260 2.00201448 9.97180356 > H 1.17489828 1.54585860 9.06336687 > H 0.77449155 2.87361598 9.89046099 > O 9.55044873 5.96202627 10.60180606 > H 10.30308679 5.44140199 10.15448925 > H 9.55186146 6.84277348 10.18469312 > O 10.75527999 5.56261328 14.64391086 > H 9.87802894 5.74881675 14.16708492 > H 11.31325372 6.34758540 14.41134505 > O 11.22309324 1.89168472 11.88961021 > H 10.61702065 1.91739789 11.09551241 > H 12.01467966 2.45594481 11.70306054 > O 12.48506446 6.01381737 11.59607144 > H 12.79562362 5.08661359 11.73169343 > H 12.50977887 6.46474361 12.46567132 > O 9.77303326 2.94790120 13.91805891 > H 10.28673590 2.58580777 13.13755687 > H 10.24855288 3.77512959 14.16942302 > O 12.65676934 1.48321243 7.86479577 > H 12.99010076 0.81319922 8.52324992 > H 13.43290580 1.98525495 7.51466859 > O 13.55987706 7.38184199 9.58481400 > H 14.17984242 7.90892302 10.16733020 > H 13.04800775 6.83909417 10.26677052 > O 15.55291198 4.15102828 10.12039216 > H 15.17902221 4.52972041 9.27124584 > O 14.64425738 3.28381066 14.37285202 > H 14.54501798 4.14569728 14.85517739 > O 14.73402518 5.59786432 15.92002821 > H 15.45748780 6.05233245 15.44773838 > O 13.64728834 3.38272560 11.83732221 > H 14.35185771 3.76626449 11.22325132 > H 14.01549713 3.41619082 12.77312319 > O 9.15580367 0.92342575 15.55891408 > H 9.53237453 1.65148284 14.98102430 > H 8.33603244 0.65613748 15.07671820 > O 11.26481409 4.60201028 9.14248028 > H 11.02908883 4.92798766 8.21902371 > H 11.26715096 3.62696286 9.09066105 > O 15.02500419 0.98616684 11.28860775 > H 15.88449133 1.32460100 10.87488044 > H 14.45468737 1.79129421 11.42040737 > O 8.60992588 5.84690827 13.20692515 > H 9.01132581 5.91122975 12.30224404 > H 8.01367240 6.64131284 13.32349168 > H 16.18675121 4.87891083 10.40805975 > H 15.61653933 3.18720306 14.22068038 > H 14.27629400 6.31178391 16.47864853 > O 12.21779588 -0.04576478 13.74403801 > H 11.80089925 0.51885747 13.04242315 > H 12.30451597 0.56430788 14.55434731 > O 15.05170266 0.00823077 13.76312401 > H 15.15868948 0.44849492 12.86434702 > H 14.06873956 -0.11926391 13.81861878 > O 9.26480260 2.00201448 9.97180356 > H 9.17489828 1.54585860 9.06336687 > H 8.77449155 2.87361598 9.89046099 > O 1.55044873 13.96202627 10.60180606 > H 2.30308679 13.44140199 10.15448925 > H 1.55186146 14.84277348 10.18469312 > O 2.75527999 13.56261328 14.64391086 > H 1.87802894 13.74881675 14.16708492 > H 3.31325372 14.34758540 14.41134505 > O 3.22309324 9.89168472 11.88961021 > H 2.61702065 9.91739789 11.09551241 > H 4.01467966 10.45594481 11.70306054 > O 4.48506446 14.01381737 11.59607144 > H 4.79562362 13.08661359 11.73169343 > H 4.50977887 14.46474361 12.46567132 > O 1.77303326 10.94790120 13.91805891 > H 2.28673590 10.58580777 13.13755687 > H 2.24855288 11.77512959 14.16942302 > O 4.65676934 9.48321243 7.86479577 > H 4.99010076 8.81319922 8.52324992 > H 5.43290580 9.98525495 7.51466859 > O 5.55987706 15.38184199 9.58481400 > H 6.17984242 15.90892302 10.16733020 > H 5.04800775 14.83909417 10.26677052 > O 7.55291198 12.15102828 10.12039216 > H 7.17902221 12.52972041 9.27124584 > O 6.64425738 11.28381066 14.37285202 > H 6.54501798 12.14569728 14.85517739 > O 6.73402518 13.59786432 15.92002821 > H 7.45748780 14.05233245 15.44773838 > O 5.64728834 11.38272560 11.83732221 > H 6.35185771 11.76626449 11.22325132 > H 6.01549713 11.41619082 12.77312319 > O 1.15580367 8.92342575 15.55891408 > H 1.53237453 9.65148284 14.98102430 > H 0.33603244 8.65613748 15.07671820 > O 3.26481409 12.60201028 9.14248028 > H 3.02908883 12.92798766 8.21902371 > H 3.26715096 11.62696286 9.09066105 > O 7.02500419 8.98616684 11.28860775 > H 7.88449133 9.32460100 10.87488044 > H 6.45468737 9.79129421 11.42040737 > O 0.60992588 13.84690827 13.20692515 > H 1.01132581 13.91122975 12.30224404 > H 0.01367240 14.64131284 13.32349168 > H 8.18675121 12.87891083 10.40805975 > H 7.61653933 11.18720306 14.22068038 > H 6.27629400 14.31178391 16.47864853 > O 4.21779588 7.95423522 13.74403801 > H 3.80089925 8.51885747 13.04242315 > H 4.30451597 8.56430788 14.55434731 > O 7.05170266 8.00823077 13.76312401 > H 7.15868948 8.44849492 12.86434702 > H 6.06873956 7.88073609 13.81861878 > O 1.26480260 10.00201448 9.97180356 > H 1.17489828 9.54585860 9.06336687 > H 0.77449155 10.87361598 9.89046099 > O 9.55044873 13.96202627 10.60180606 > H 10.30308679 13.44140199 10.15448925 > H 9.55186146 14.84277348 10.18469312 > O 10.75527999 13.56261328 14.64391086 > H 9.87802894 13.74881675 14.16708492 > H 11.31325372 14.34758540 14.41134505 > O 11.22309324 9.89168472 11.88961021 > H 10.61702065 9.91739789 11.09551241 > H 12.01467966 10.45594481 11.70306054 > O 12.48506446 14.01381737 11.59607144 > H 12.79562362 13.08661359 11.73169343 > H 12.50977887 14.46474361 12.46567132 > O 9.77303326 10.94790120 13.91805891 > H 10.28673590 10.58580777 13.13755687 > H 10.24855288 11.77512959 14.16942302 > O 12.65676934 9.48321243 7.86479577 > H 12.99010076 8.81319922 8.52324992 > H 13.43290580 9.98525495 7.51466859 > O 13.55987706 15.38184199 9.58481400 > H 14.17984242 15.90892302 10.16733020 > H 13.04800775 14.83909417 10.26677052 > O 15.55291198 12.15102828 10.12039216 > H 15.17902221 12.52972041 9.27124584 > O 14.64425738 11.28381066 14.37285202 > H 14.54501798 12.14569728 14.85517739 > O 14.73402518 13.59786432 15.92002821 > H 15.45748780 14.05233245 15.44773838 > O 13.64728834 11.38272560 11.83732221 > H 14.35185771 11.76626449 11.22325132 > H 14.01549713 11.41619082 12.77312319 > O 9.15580367 8.92342575 15.55891408 > H 9.53237453 9.65148284 14.98102430 > H 8.33603244 8.65613748 15.07671820 > O 11.26481409 12.60201028 9.14248028 > H 11.02908883 12.92798766 8.21902371 > H 11.26715096 11.62696286 9.09066105 > O 15.02500419 8.98616684 11.28860775 > H 15.88449133 9.32460100 10.87488044 > H 14.45468737 9.79129421 11.42040737 > O 8.60992588 13.84690827 13.20692515 > H 9.01132581 13.91122975 12.30224404 > H 8.01367240 14.64131284 13.32349168 > H 16.18675121 12.87891083 10.40805975 > H 15.61653933 11.18720306 14.22068038 > H 14.27629400 14.31178391 16.47864853 > O 12.21779588 7.95423522 13.74403801 > H 11.80089925 8.51885747 13.04242315 > H 12.30451597 8.56430788 14.55434731 > O 15.05170266 8.00823077 13.76312401 > H 15.15868948 8.44849492 12.86434702 > H 14.06873956 7.88073609 13.81861878 > O 9.26480260 10.00201448 9.97180356 > H 9.17489828 9.54585860 9.06336687 > H 8.77449155 10.87361598 9.89046099 > K_POINTS gamma ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From ma at nano.ku.dk Wed May 4 14:44:58 2011 From: ma at nano.ku.dk (Martin Andersson) Date: Wed, 04 May 2011 14:44:58 +0200 Subject: [Pw_forum] cohesive energy of water/ice In-Reply-To: <20110504143912.sodjitv5z408coww@webmail.sissa.it> References: <4DC145E0.5000004@nano.ku.dk> <20110504143912.sodjitv5z408coww@webmail.sissa.it> Message-ID: <4DC14A4A.4090801@nano.ku.dk> Yes, I did use the same cutoff (35 and 350) of course. I just managed to copy and paste the wrong input file for isolated water... I will see if the the nosym and assume_isolated makes a difference. Cheers, Martin Andersson University of copenhagen On 5/4/2011 2:39 PM, Emine Kucukbenli wrote: > Hi Martin, > Just a quick note, > when calculating isolated molecules, set nosym = .true. not to use any > symmetry, set some form of assume_isolated for polar molecules to > account for periodic image corrections. i dont know if these would > affect your results but this is the correct way of accounting for an > isolated system in a periodic code. > > Also, definitely important: > compare things in the same level of accuracy: ecutwfc, ecutrho etc. > should correspond to the same level of expansion in plane waves both > in water molecule and amorphous ice/water complex..keep them the same. > > hope this helps > emine kucukbenli, phd student, sissa, italy > > Quoting Martin Andersson: > >> Hi, >> >> I have been calculating the cohesive energy of amorphous ice as well >> as ice/water layers on mineral surfaces with the PBE functional. I >> get a cohesive energy for water in amorphous ice (144 waters in a >> ~16x16x16 ? box) compared to water in a 20x20x20 ? box that is 1.08 >> eV for ultrasoft pseudopotentials (35 Ry cutoff) (the rrkjus ones >> from the library) and 0.98 for PAW (50 Ry cutoff) from the AtomPAW >> library. This is significantly different from other studies in >> literature, who find around 0.7 for PBE and PW91. I have no idea on >> why results differ so much, so any suggestions are welcome... Input >> files below >> >> I have used QE 4.2.1 for the calculations. >> >> Cheers, >> Martin Andersson >> University of Copenhagen >> >> Water molecule: >> &control >> calculation='relax', >> restart_mode='from_scratch', >> prefix='water', >> pseudo_dir = '/nanogeo/martinpa/espresso-4.1.2/pseudo/', >> outdir='/nanogeo/martinpa/scratch/', >> nstep = 500, >> >> >> >> / >> &system >> ibrav = 0, celldm(1)= 1.889726 >> nat= 3, >> ntyp= 2, >> ecutwfc = 25.0 >> ecutrho=250.0 >> >> >> / >> &electrons >> tqr=.true. >> electron_maxstep=300 >> mixing_beta = 0.7 >> conv_thr = 1.0d-8 >> / >> &ions >> ion_dynamics='bfgs' >> / >> >> ATOMIC_SPECIES >> O 15.999 O.pbe-rrkjus.UPF >> H 1.008 H.pbe-rrkjus.UPF >> >> CELL_PARAMETERS (alat) >> 20.0 0.0 0.0 >> 0.0 20.0 0.0 >> 0.0 0.0 20.0 >> ATOMIC_POSITIONS (angstrom) >> O 1.645835061 6.664706853 -3.065877101 >> H 1.954195796 5.741969275 -3.013292036 >> H 0.781969143 6.612323872 -3.513830863 >> K_POINTS gamma >> >> >> Water/ice box: >> >> &control >> calculation='vc-relax', >> restart_mode='from_scratch', >> prefix='water_box_pbe', >> pseudo_dir = '/nanogeo/martinpa/espresso-4.1.2/pseudo/', >> outdir='/nanogeo/martinpa/scratch/', >> nstep=800, >> / >> &system >> ibrav = 0, celldm(1)= 30.12, >> nat= 432, >> ntyp= 2, >> ecutwfc = 35.0 >> ecutrho=350.0 >> >> / >> &electrons >> mixing_beta = 0.7 >> conv_thr = 1.0d-8 >> / >> &ions >> ion_dynamics='bfgs' >> / >> &cell >> / >> ATOMIC_SPECIES >> O 15.999 O.pbe-rrkjus.UPF >> H 1.008 H.pbe-rrkjus.UPF >> CELL_PARAMETERS (alat) >> 1.0 0.0 0.0 >> 0.0 1.0 0.0 >> 0.0 0.0 1.0 >> ATOMIC_POSITIONS (angstrom) >> O 1.55044873 5.96202627 2.60180606 >> H 2.30308679 5.44140199 2.15448925 >> H 1.55186146 6.84277348 2.18469312 >> O 2.75527999 5.56261328 6.64391086 >> H 1.87802894 5.74881675 6.16708492 >> H 3.31325372 6.34758540 6.41134505 >> O 3.22309324 1.89168472 3.88961021 >> H 2.61702065 1.91739789 3.09551241 >> H 4.01467966 2.45594481 3.70306054 >> O 4.48506446 6.01381737 3.59607144 >> H 4.79562362 5.08661359 3.73169343 >> H 4.50977887 6.46474361 4.46567132 >> O 1.77303326 2.94790120 5.91805891 >> H 2.28673590 2.58580777 5.13755687 >> H 2.24855288 3.77512959 6.16942302 >> O 4.65676934 1.48321243 -0.13520423 >> H 4.99010076 0.81319922 0.52324992 >> H 5.43290580 1.98525495 -0.48533141 >> O 5.55987706 7.38184199 1.58481400 >> H 6.17984242 7.90892302 2.16733020 >> H 5.04800775 6.83909417 2.26677052 >> O 7.55291198 4.15102828 2.12039216 >> H 7.17902221 4.52972041 1.27124584 >> O 6.64425738 3.28381066 6.37285202 >> H 6.54501798 4.14569728 6.85517739 >> O 6.73402518 5.59786432 7.92002821 >> H 7.45748780 6.05233245 7.44773838 >> O 5.64728834 3.38272560 3.83732221 >> H 6.35185771 3.76626449 3.22325132 >> H 6.01549713 3.41619082 4.77312319 >> O 1.15580367 0.92342575 7.55891408 >> H 1.53237453 1.65148284 6.98102430 >> H 0.33603244 0.65613748 7.07671820 >> O 3.26481409 4.60201028 1.14248028 >> H 3.02908883 4.92798766 0.21902371 >> H 3.26715096 3.62696286 1.09066105 >> O 7.02500419 0.98616684 3.28860775 >> H 7.88449133 1.32460100 2.87488044 >> H 6.45468737 1.79129421 3.42040737 >> O 0.60992588 5.84690827 5.20692515 >> H 1.01132581 5.91122975 4.30224404 >> H 0.01367240 6.64131284 5.32349168 >> H 8.18675121 4.87891083 2.40805975 >> H 7.61653933 3.18720306 6.22068038 >> H 6.27629400 6.31178391 8.47864853 >> O 4.21779588 -0.04576478 5.74403801 >> H 3.80089925 0.51885747 5.04242315 >> H 4.30451597 0.56430788 6.55434731 >> O 7.05170266 0.00823077 5.76312401 >> H 7.15868948 0.44849492 4.86434702 >> H 6.06873956 -0.11926391 5.81861878 >> O 1.26480260 2.00201448 1.97180356 >> H 1.17489828 1.54585860 1.06336687 >> H 0.77449155 2.87361598 1.89046099 >> O 9.55044873 5.96202627 2.60180606 >> H 10.30308679 5.44140199 2.15448925 >> H 9.55186146 6.84277348 2.18469312 >> O 10.75527999 5.56261328 6.64391086 >> H 9.87802894 5.74881675 6.16708492 >> H 11.31325372 6.34758540 6.41134505 >> O 11.22309324 1.89168472 3.88961021 >> H 10.61702065 1.91739789 3.09551241 >> H 12.01467966 2.45594481 3.70306054 >> O 12.48506446 6.01381737 3.59607144 >> H 12.79562362 5.08661359 3.73169343 >> H 12.50977887 6.46474361 4.46567132 >> O 9.77303326 2.94790120 5.91805891 >> H 10.28673590 2.58580777 5.13755687 >> H 10.24855288 3.77512959 6.16942302 >> O 12.65676934 1.48321243 -0.13520423 >> H 12.99010076 0.81319922 0.52324992 >> H 13.43290580 1.98525495 -0.48533141 >> O 13.55987706 7.38184199 1.58481400 >> H 14.17984242 7.90892302 2.16733020 >> H 13.04800775 6.83909417 2.26677052 >> O 15.55291198 4.15102828 2.12039216 >> H 15.17902221 4.52972041 1.27124584 >> O 14.64425738 3.28381066 6.37285202 >> H 14.54501798 4.14569728 6.85517739 >> O 14.73402518 5.59786432 7.92002821 >> H 15.45748780 6.05233245 7.44773838 >> O 13.64728834 3.38272560 3.83732221 >> H 14.35185771 3.76626449 3.22325132 >> H 14.01549713 3.41619082 4.77312319 >> O 9.15580367 0.92342575 7.55891408 >> H 9.53237453 1.65148284 6.98102430 >> H 8.33603244 0.65613748 7.07671820 >> O 11.26481409 4.60201028 1.14248028 >> H 11.02908883 4.92798766 0.21902371 >> H 11.26715096 3.62696286 1.09066105 >> O 15.02500419 0.98616684 3.28860775 >> H 15.88449133 1.32460100 2.87488044 >> H 14.45468737 1.79129421 3.42040737 >> O 8.60992588 5.84690827 5.20692515 >> H 9.01132581 5.91122975 4.30224404 >> H 8.01367240 6.64131284 5.32349168 >> H 16.18675121 4.87891083 2.40805975 >> H 15.61653933 3.18720306 6.22068038 >> H 14.27629400 6.31178391 8.47864853 >> O 12.21779588 -0.04576478 5.74403801 >> H 11.80089925 0.51885747 5.04242315 >> H 12.30451597 0.56430788 6.55434731 >> O 15.05170266 0.00823077 5.76312401 >> H 15.15868948 0.44849492 4.86434702 >> H 14.06873956 -0.11926391 5.81861878 >> O 9.26480260 2.00201448 1.97180356 >> H 9.17489828 1.54585860 1.06336687 >> H 8.77449155 2.87361598 1.89046099 >> O 1.55044873 13.96202627 2.60180606 >> H 2.30308679 13.44140199 2.15448925 >> H 1.55186146 14.84277348 2.18469312 >> O 2.75527999 13.56261328 6.64391086 >> H 1.87802894 13.74881675 6.16708492 >> H 3.31325372 14.34758540 6.41134505 >> O 3.22309324 9.89168472 3.88961021 >> H 2.61702065 9.91739789 3.09551241 >> H 4.01467966 10.45594481 3.70306054 >> O 4.48506446 14.01381737 3.59607144 >> H 4.79562362 13.08661359 3.73169343 >> H 4.50977887 14.46474361 4.46567132 >> O 1.77303326 10.94790120 5.91805891 >> H 2.28673590 10.58580777 5.13755687 >> H 2.24855288 11.77512959 6.16942302 >> O 4.65676934 9.48321243 -0.13520423 >> H 4.99010076 8.81319922 0.52324992 >> H 5.43290580 9.98525495 -0.48533141 >> O 5.55987706 15.38184199 1.58481400 >> H 6.17984242 15.90892302 2.16733020 >> H 5.04800775 14.83909417 2.26677052 >> O 7.55291198 12.15102828 2.12039216 >> H 7.17902221 12.52972041 1.27124584 >> O 6.64425738 11.28381066 6.37285202 >> H 6.54501798 12.14569728 6.85517739 >> O 6.73402518 13.59786432 7.92002821 >> H 7.45748780 14.05233245 7.44773838 >> O 5.64728834 11.38272560 3.83732221 >> H 6.35185771 11.76626449 3.22325132 >> H 6.01549713 11.41619082 4.77312319 >> O 1.15580367 8.92342575 7.55891408 >> H 1.53237453 9.65148284 6.98102430 >> H 0.33603244 8.65613748 7.07671820 >> O 3.26481409 12.60201028 1.14248028 >> H 3.02908883 12.92798766 0.21902371 >> H 3.26715096 11.62696286 1.09066105 >> O 7.02500419 8.98616684 3.28860775 >> H 7.88449133 9.32460100 2.87488044 >> H 6.45468737 9.79129421 3.42040737 >> O 0.60992588 13.84690827 5.20692515 >> H 1.01132581 13.91122975 4.30224404 >> H 0.01367240 14.64131284 5.32349168 >> H 8.18675121 12.87891083 2.40805975 >> H 7.61653933 11.18720306 6.22068038 >> H 6.27629400 14.31178391 8.47864853 >> O 4.21779588 7.95423522 5.74403801 >> H 3.80089925 8.51885747 5.04242315 >> H 4.30451597 8.56430788 6.55434731 >> O 7.05170266 8.00823077 5.76312401 >> H 7.15868948 8.44849492 4.86434702 >> H 6.06873956 7.88073609 5.81861878 >> O 1.26480260 10.00201448 1.97180356 >> H 1.17489828 9.54585860 1.06336687 >> H 0.77449155 10.87361598 1.89046099 >> O 9.55044873 13.96202627 2.60180606 >> H 10.30308679 13.44140199 2.15448925 >> H 9.55186146 14.84277348 2.18469312 >> O 10.75527999 13.56261328 6.64391086 >> H 9.87802894 13.74881675 6.16708492 >> H 11.31325372 14.34758540 6.41134505 >> O 11.22309324 9.89168472 3.88961021 >> H 10.61702065 9.91739789 3.09551241 >> H 12.01467966 10.45594481 3.70306054 >> O 12.48506446 14.01381737 3.59607144 >> H 12.79562362 13.08661359 3.73169343 >> H 12.50977887 14.46474361 4.46567132 >> O 9.77303326 10.94790120 5.91805891 >> H 10.28673590 10.58580777 5.13755687 >> H 10.24855288 11.77512959 6.16942302 >> O 12.65676934 9.48321243 -0.13520423 >> H 12.99010076 8.81319922 0.52324992 >> H 13.43290580 9.98525495 -0.48533141 >> O 13.55987706 15.38184199 1.58481400 >> H 14.17984242 15.90892302 2.16733020 >> H 13.04800775 14.83909417 2.26677052 >> O 15.55291198 12.15102828 2.12039216 >> H 15.17902221 12.52972041 1.27124584 >> O 14.64425738 11.28381066 6.37285202 >> H 14.54501798 12.14569728 6.85517739 >> O 14.73402518 13.59786432 7.92002821 >> H 15.45748780 14.05233245 7.44773838 >> O 13.64728834 11.38272560 3.83732221 >> H 14.35185771 11.76626449 3.22325132 >> H 14.01549713 11.41619082 4.77312319 >> O 9.15580367 8.92342575 7.55891408 >> H 9.53237453 9.65148284 6.98102430 >> H 8.33603244 8.65613748 7.07671820 >> O 11.26481409 12.60201028 1.14248028 >> H 11.02908883 12.92798766 0.21902371 >> H 11.26715096 11.62696286 1.09066105 >> O 15.02500419 8.98616684 3.28860775 >> H 15.88449133 9.32460100 2.87488044 >> H 14.45468737 9.79129421 3.42040737 >> O 8.60992588 13.84690827 5.20692515 >> H 9.01132581 13.91122975 4.30224404 >> H 8.01367240 14.64131284 5.32349168 >> H 16.18675121 12.87891083 2.40805975 >> H 15.61653933 11.18720306 6.22068038 >> H 14.27629400 14.31178391 8.47864853 >> O 12.21779588 7.95423522 5.74403801 >> H 11.80089925 8.51885747 5.04242315 >> H 12.30451597 8.56430788 6.55434731 >> O 15.05170266 8.00823077 5.76312401 >> H 15.15868948 8.44849492 4.86434702 >> H 14.06873956 7.88073609 5.81861878 >> O 9.26480260 10.00201448 1.97180356 >> H 9.17489828 9.54585860 1.06336687 >> H 8.77449155 10.87361598 1.89046099 >> O 1.55044873 5.96202627 10.60180606 >> H 2.30308679 5.44140199 10.15448925 >> H 1.55186146 6.84277348 10.18469312 >> O 2.75527999 5.56261328 14.64391086 >> H 1.87802894 5.74881675 14.16708492 >> H 3.31325372 6.34758540 14.41134505 >> O 3.22309324 1.89168472 11.88961021 >> H 2.61702065 1.91739789 11.09551241 >> H 4.01467966 2.45594481 11.70306054 >> O 4.48506446 6.01381737 11.59607144 >> H 4.79562362 5.08661359 11.73169343 >> H 4.50977887 6.46474361 12.46567132 >> O 1.77303326 2.94790120 13.91805891 >> H 2.28673590 2.58580777 13.13755687 >> H 2.24855288 3.77512959 14.16942302 >> O 4.65676934 1.48321243 7.86479577 >> H 4.99010076 0.81319922 8.52324992 >> H 5.43290580 1.98525495 7.51466859 >> O 5.55987706 7.38184199 9.58481400 >> H 6.17984242 7.90892302 10.16733020 >> H 5.04800775 6.83909417 10.26677052 >> O 7.55291198 4.15102828 10.12039216 >> H 7.17902221 4.52972041 9.27124584 >> O 6.64425738 3.28381066 14.37285202 >> H 6.54501798 4.14569728 14.85517739 >> O 6.73402518 5.59786432 15.92002821 >> H 7.45748780 6.05233245 15.44773838 >> O 5.64728834 3.38272560 11.83732221 >> H 6.35185771 3.76626449 11.22325132 >> H 6.01549713 3.41619082 12.77312319 >> O 1.15580367 0.92342575 15.55891408 >> H 1.53237453 1.65148284 14.98102430 >> H 0.33603244 0.65613748 15.07671820 >> O 3.26481409 4.60201028 9.14248028 >> H 3.02908883 4.92798766 8.21902371 >> H 3.26715096 3.62696286 9.09066105 >> O 7.02500419 0.98616684 11.28860775 >> H 7.88449133 1.32460100 10.87488044 >> H 6.45468737 1.79129421 11.42040737 >> O 0.60992588 5.84690827 13.20692515 >> H 1.01132581 5.91122975 12.30224404 >> H 0.01367240 6.64131284 13.32349168 >> H 8.18675121 4.87891083 10.40805975 >> H 7.61653933 3.18720306 14.22068038 >> H 6.27629400 6.31178391 16.47864853 >> O 4.21779588 -0.04576478 13.74403801 >> H 3.80089925 0.51885747 13.04242315 >> H 4.30451597 0.56430788 14.55434731 >> O 7.05170266 0.00823077 13.76312401 >> H 7.15868948 0.44849492 12.86434702 >> H 6.06873956 -0.11926391 13.81861878 >> O 1.26480260 2.00201448 9.97180356 >> H 1.17489828 1.54585860 9.06336687 >> H 0.77449155 2.87361598 9.89046099 >> O 9.55044873 5.96202627 10.60180606 >> H 10.30308679 5.44140199 10.15448925 >> H 9.55186146 6.84277348 10.18469312 >> O 10.75527999 5.56261328 14.64391086 >> H 9.87802894 5.74881675 14.16708492 >> H 11.31325372 6.34758540 14.41134505 >> O 11.22309324 1.89168472 11.88961021 >> H 10.61702065 1.91739789 11.09551241 >> H 12.01467966 2.45594481 11.70306054 >> O 12.48506446 6.01381737 11.59607144 >> H 12.79562362 5.08661359 11.73169343 >> H 12.50977887 6.46474361 12.46567132 >> O 9.77303326 2.94790120 13.91805891 >> H 10.28673590 2.58580777 13.13755687 >> H 10.24855288 3.77512959 14.16942302 >> O 12.65676934 1.48321243 7.86479577 >> H 12.99010076 0.81319922 8.52324992 >> H 13.43290580 1.98525495 7.51466859 >> O 13.55987706 7.38184199 9.58481400 >> H 14.17984242 7.90892302 10.16733020 >> H 13.04800775 6.83909417 10.26677052 >> O 15.55291198 4.15102828 10.12039216 >> H 15.17902221 4.52972041 9.27124584 >> O 14.64425738 3.28381066 14.37285202 >> H 14.54501798 4.14569728 14.85517739 >> O 14.73402518 5.59786432 15.92002821 >> H 15.45748780 6.05233245 15.44773838 >> O 13.64728834 3.38272560 11.83732221 >> H 14.35185771 3.76626449 11.22325132 >> H 14.01549713 3.41619082 12.77312319 >> O 9.15580367 0.92342575 15.55891408 >> H 9.53237453 1.65148284 14.98102430 >> H 8.33603244 0.65613748 15.07671820 >> O 11.26481409 4.60201028 9.14248028 >> H 11.02908883 4.92798766 8.21902371 >> H 11.26715096 3.62696286 9.09066105 >> O 15.02500419 0.98616684 11.28860775 >> H 15.88449133 1.32460100 10.87488044 >> H 14.45468737 1.79129421 11.42040737 >> O 8.60992588 5.84690827 13.20692515 >> H 9.01132581 5.91122975 12.30224404 >> H 8.01367240 6.64131284 13.32349168 >> H 16.18675121 4.87891083 10.40805975 >> H 15.61653933 3.18720306 14.22068038 >> H 14.27629400 6.31178391 16.47864853 >> O 12.21779588 -0.04576478 13.74403801 >> H 11.80089925 0.51885747 13.04242315 >> H 12.30451597 0.56430788 14.55434731 >> O 15.05170266 0.00823077 13.76312401 >> H 15.15868948 0.44849492 12.86434702 >> H 14.06873956 -0.11926391 13.81861878 >> O 9.26480260 2.00201448 9.97180356 >> H 9.17489828 1.54585860 9.06336687 >> H 8.77449155 2.87361598 9.89046099 >> O 1.55044873 13.96202627 10.60180606 >> H 2.30308679 13.44140199 10.15448925 >> H 1.55186146 14.84277348 10.18469312 >> O 2.75527999 13.56261328 14.64391086 >> H 1.87802894 13.74881675 14.16708492 >> H 3.31325372 14.34758540 14.41134505 >> O 3.22309324 9.89168472 11.88961021 >> H 2.61702065 9.91739789 11.09551241 >> H 4.01467966 10.45594481 11.70306054 >> O 4.48506446 14.01381737 11.59607144 >> H 4.79562362 13.08661359 11.73169343 >> H 4.50977887 14.46474361 12.46567132 >> O 1.77303326 10.94790120 13.91805891 >> H 2.28673590 10.58580777 13.13755687 >> H 2.24855288 11.77512959 14.16942302 >> O 4.65676934 9.48321243 7.86479577 >> H 4.99010076 8.81319922 8.52324992 >> H 5.43290580 9.98525495 7.51466859 >> O 5.55987706 15.38184199 9.58481400 >> H 6.17984242 15.90892302 10.16733020 >> H 5.04800775 14.83909417 10.26677052 >> O 7.55291198 12.15102828 10.12039216 >> H 7.17902221 12.52972041 9.27124584 >> O 6.64425738 11.28381066 14.37285202 >> H 6.54501798 12.14569728 14.85517739 >> O 6.73402518 13.59786432 15.92002821 >> H 7.45748780 14.05233245 15.44773838 >> O 5.64728834 11.38272560 11.83732221 >> H 6.35185771 11.76626449 11.22325132 >> H 6.01549713 11.41619082 12.77312319 >> O 1.15580367 8.92342575 15.55891408 >> H 1.53237453 9.65148284 14.98102430 >> H 0.33603244 8.65613748 15.07671820 >> O 3.26481409 12.60201028 9.14248028 >> H 3.02908883 12.92798766 8.21902371 >> H 3.26715096 11.62696286 9.09066105 >> O 7.02500419 8.98616684 11.28860775 >> H 7.88449133 9.32460100 10.87488044 >> H 6.45468737 9.79129421 11.42040737 >> O 0.60992588 13.84690827 13.20692515 >> H 1.01132581 13.91122975 12.30224404 >> H 0.01367240 14.64131284 13.32349168 >> H 8.18675121 12.87891083 10.40805975 >> H 7.61653933 11.18720306 14.22068038 >> H 6.27629400 14.31178391 16.47864853 >> O 4.21779588 7.95423522 13.74403801 >> H 3.80089925 8.51885747 13.04242315 >> H 4.30451597 8.56430788 14.55434731 >> O 7.05170266 8.00823077 13.76312401 >> H 7.15868948 8.44849492 12.86434702 >> H 6.06873956 7.88073609 13.81861878 >> O 1.26480260 10.00201448 9.97180356 >> H 1.17489828 9.54585860 9.06336687 >> H 0.77449155 10.87361598 9.89046099 >> O 9.55044873 13.96202627 10.60180606 >> H 10.30308679 13.44140199 10.15448925 >> H 9.55186146 14.84277348 10.18469312 >> O 10.75527999 13.56261328 14.64391086 >> H 9.87802894 13.74881675 14.16708492 >> H 11.31325372 14.34758540 14.41134505 >> O 11.22309324 9.89168472 11.88961021 >> H 10.61702065 9.91739789 11.09551241 >> H 12.01467966 10.45594481 11.70306054 >> O 12.48506446 14.01381737 11.59607144 >> H 12.79562362 13.08661359 11.73169343 >> H 12.50977887 14.46474361 12.46567132 >> O 9.77303326 10.94790120 13.91805891 >> H 10.28673590 10.58580777 13.13755687 >> H 10.24855288 11.77512959 14.16942302 >> O 12.65676934 9.48321243 7.86479577 >> H 12.99010076 8.81319922 8.52324992 >> H 13.43290580 9.98525495 7.51466859 >> O 13.55987706 15.38184199 9.58481400 >> H 14.17984242 15.90892302 10.16733020 >> H 13.04800775 14.83909417 10.26677052 >> O 15.55291198 12.15102828 10.12039216 >> H 15.17902221 12.52972041 9.27124584 >> O 14.64425738 11.28381066 14.37285202 >> H 14.54501798 12.14569728 14.85517739 >> O 14.73402518 13.59786432 15.92002821 >> H 15.45748780 14.05233245 15.44773838 >> O 13.64728834 11.38272560 11.83732221 >> H 14.35185771 11.76626449 11.22325132 >> H 14.01549713 11.41619082 12.77312319 >> O 9.15580367 8.92342575 15.55891408 >> H 9.53237453 9.65148284 14.98102430 >> H 8.33603244 8.65613748 15.07671820 >> O 11.26481409 12.60201028 9.14248028 >> H 11.02908883 12.92798766 8.21902371 >> H 11.26715096 11.62696286 9.09066105 >> O 15.02500419 8.98616684 11.28860775 >> H 15.88449133 9.32460100 10.87488044 >> H 14.45468737 9.79129421 11.42040737 >> O 8.60992588 13.84690827 13.20692515 >> H 9.01132581 13.91122975 12.30224404 >> H 8.01367240 14.64131284 13.32349168 >> H 16.18675121 12.87891083 10.40805975 >> H 15.61653933 11.18720306 14.22068038 >> H 14.27629400 14.31178391 16.47864853 >> O 12.21779588 7.95423522 13.74403801 >> H 11.80089925 8.51885747 13.04242315 >> H 12.30451597 8.56430788 14.55434731 >> O 15.05170266 8.00823077 13.76312401 >> H 15.15868948 8.44849492 12.86434702 >> H 14.06873956 7.88073609 13.81861878 >> O 9.26480260 10.00201448 9.97180356 >> H 9.17489828 9.54585860 9.06336687 >> H 8.77449155 10.87361598 9.89046099 >> K_POINTS gamma > > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From juanlopez415 at gmail.com Wed May 4 14:46:43 2011 From: juanlopez415 at gmail.com (Juan Manuel Lopez) Date: Wed, 4 May 2011 08:46:43 -0400 Subject: [Pw_forum] cohesive energy of water/ice In-Reply-To: <4DC14A4A.4090801@nano.ku.dk> References: <4DC145E0.5000004@nano.ku.dk> <20110504143912.sodjitv5z408coww@webmail.sissa.it> <4DC14A4A.4090801@nano.ku.dk> Message-ID: Hi Martin, Try to put it in the same box-dimensions too (volumen). On Wed, May 4, 2011 at 8:44 AM, Martin Andersson wrote: > Yes, > > I did use the same cutoff (35 and 350) of course. I just managed to copy > and paste the wrong input file for isolated water... I will see if the > the nosym and assume_isolated makes a difference. > > Cheers, > Martin Andersson > University of copenhagen > > > > > On 5/4/2011 2:39 PM, Emine Kucukbenli wrote: > > Hi Martin, > > Just a quick note, > > when calculating isolated molecules, set nosym = .true. not to use any > > symmetry, set some form of assume_isolated for polar molecules to > > account for periodic image corrections. i dont know if these would > > affect your results but this is the correct way of accounting for an > > isolated system in a periodic code. > > > > Also, definitely important: > > compare things in the same level of accuracy: ecutwfc, ecutrho etc. > > should correspond to the same level of expansion in plane waves both > > in water molecule and amorphous ice/water complex..keep them the same. > > > > hope this helps > > emine kucukbenli, phd student, sissa, italy > > > > Quoting Martin Andersson: > > > >> Hi, > >> > >> I have been calculating the cohesive energy of amorphous ice as well > >> as ice/water layers on mineral surfaces with the PBE functional. I > >> get a cohesive energy for water in amorphous ice (144 waters in a > >> ~16x16x16 ? box) compared to water in a 20x20x20 ? box that is 1.08 > >> eV for ultrasoft pseudopotentials (35 Ry cutoff) (the rrkjus ones > >> from the library) and 0.98 for PAW (50 Ry cutoff) from the AtomPAW > >> library. This is significantly different from other studies in > >> literature, who find around 0.7 for PBE and PW91. I have no idea on > >> why results differ so much, so any suggestions are welcome... Input > >> files below > >> > >> I have used QE 4.2.1 for the calculations. > >> > >> Cheers, > >> Martin Andersson > >> University of Copenhagen > >> > >> Water molecule: > >> &control > >> calculation='relax', > >> restart_mode='from_scratch', > >> prefix='water', > >> pseudo_dir = '/nanogeo/martinpa/espresso-4.1.2/pseudo/', > >> outdir='/nanogeo/martinpa/scratch/', > >> nstep = 500, > >> > >> > >> > >> / > >> &system > >> ibrav = 0, celldm(1)= 1.889726 > >> nat= 3, > >> ntyp= 2, > >> ecutwfc = 25.0 > >> ecutrho=250.0 > >> > >> > >> / > >> &electrons > >> tqr=.true. > >> electron_maxstep=300 > >> mixing_beta = 0.7 > >> conv_thr = 1.0d-8 > >> / > >> &ions > >> ion_dynamics='bfgs' > >> / > >> > >> ATOMIC_SPECIES > >> O 15.999 O.pbe-rrkjus.UPF > >> H 1.008 H.pbe-rrkjus.UPF > >> > >> CELL_PARAMETERS (alat) > >> 20.0 0.0 0.0 > >> 0.0 20.0 0.0 > >> 0.0 0.0 20.0 > >> ATOMIC_POSITIONS (angstrom) > >> O 1.645835061 6.664706853 -3.065877101 > >> H 1.954195796 5.741969275 -3.013292036 > >> H 0.781969143 6.612323872 -3.513830863 > >> K_POINTS gamma > >> > >> > >> Water/ice box: > >> > >> &control > >> calculation='vc-relax', > >> restart_mode='from_scratch', > >> prefix='water_box_pbe', > >> pseudo_dir = '/nanogeo/martinpa/espresso-4.1.2/pseudo/', > >> outdir='/nanogeo/martinpa/scratch/', > >> nstep=800, > >> / > >> &system > >> ibrav = 0, celldm(1)= 30.12, > >> nat= 432, > >> ntyp= 2, > >> ecutwfc = 35.0 > >> ecutrho=350.0 > >> > >> / > >> &electrons > >> mixing_beta = 0.7 > >> conv_thr = 1.0d-8 > >> / > >> &ions > >> ion_dynamics='bfgs' > >> / > >> &cell > >> / > >> ATOMIC_SPECIES > >> O 15.999 O.pbe-rrkjus.UPF > >> H 1.008 H.pbe-rrkjus.UPF > >> CELL_PARAMETERS (alat) > >> 1.0 0.0 0.0 > >> 0.0 1.0 0.0 > >> 0.0 0.0 1.0 > >> ATOMIC_POSITIONS (angstrom) > >> O 1.55044873 5.96202627 2.60180606 > >> H 2.30308679 5.44140199 2.15448925 > >> H 1.55186146 6.84277348 2.18469312 > >> O 2.75527999 5.56261328 6.64391086 > >> H 1.87802894 5.74881675 6.16708492 > >> H 3.31325372 6.34758540 6.41134505 > >> O 3.22309324 1.89168472 3.88961021 > >> H 2.61702065 1.91739789 3.09551241 > >> H 4.01467966 2.45594481 3.70306054 > >> O 4.48506446 6.01381737 3.59607144 > >> H 4.79562362 5.08661359 3.73169343 > >> H 4.50977887 6.46474361 4.46567132 > >> O 1.77303326 2.94790120 5.91805891 > >> H 2.28673590 2.58580777 5.13755687 > >> H 2.24855288 3.77512959 6.16942302 > >> O 4.65676934 1.48321243 -0.13520423 > >> H 4.99010076 0.81319922 0.52324992 > >> H 5.43290580 1.98525495 -0.48533141 > >> O 5.55987706 7.38184199 1.58481400 > >> H 6.17984242 7.90892302 2.16733020 > >> H 5.04800775 6.83909417 2.26677052 > >> O 7.55291198 4.15102828 2.12039216 > >> H 7.17902221 4.52972041 1.27124584 > >> O 6.64425738 3.28381066 6.37285202 > >> H 6.54501798 4.14569728 6.85517739 > >> O 6.73402518 5.59786432 7.92002821 > >> H 7.45748780 6.05233245 7.44773838 > >> O 5.64728834 3.38272560 3.83732221 > >> H 6.35185771 3.76626449 3.22325132 > >> H 6.01549713 3.41619082 4.77312319 > >> O 1.15580367 0.92342575 7.55891408 > >> H 1.53237453 1.65148284 6.98102430 > >> H 0.33603244 0.65613748 7.07671820 > >> O 3.26481409 4.60201028 1.14248028 > >> H 3.02908883 4.92798766 0.21902371 > >> H 3.26715096 3.62696286 1.09066105 > >> O 7.02500419 0.98616684 3.28860775 > >> H 7.88449133 1.32460100 2.87488044 > >> H 6.45468737 1.79129421 3.42040737 > >> O 0.60992588 5.84690827 5.20692515 > >> H 1.01132581 5.91122975 4.30224404 > >> H 0.01367240 6.64131284 5.32349168 > >> H 8.18675121 4.87891083 2.40805975 > >> H 7.61653933 3.18720306 6.22068038 > >> H 6.27629400 6.31178391 8.47864853 > >> O 4.21779588 -0.04576478 5.74403801 > >> H 3.80089925 0.51885747 5.04242315 > >> H 4.30451597 0.56430788 6.55434731 > >> O 7.05170266 0.00823077 5.76312401 > >> H 7.15868948 0.44849492 4.86434702 > >> H 6.06873956 -0.11926391 5.81861878 > >> O 1.26480260 2.00201448 1.97180356 > >> H 1.17489828 1.54585860 1.06336687 > >> H 0.77449155 2.87361598 1.89046099 > >> O 9.55044873 5.96202627 2.60180606 > >> H 10.30308679 5.44140199 2.15448925 > >> H 9.55186146 6.84277348 2.18469312 > >> O 10.75527999 5.56261328 6.64391086 > >> H 9.87802894 5.74881675 6.16708492 > >> H 11.31325372 6.34758540 6.41134505 > >> O 11.22309324 1.89168472 3.88961021 > >> H 10.61702065 1.91739789 3.09551241 > >> H 12.01467966 2.45594481 3.70306054 > >> O 12.48506446 6.01381737 3.59607144 > >> H 12.79562362 5.08661359 3.73169343 > >> H 12.50977887 6.46474361 4.46567132 > >> O 9.77303326 2.94790120 5.91805891 > >> H 10.28673590 2.58580777 5.13755687 > >> H 10.24855288 3.77512959 6.16942302 > >> O 12.65676934 1.48321243 -0.13520423 > >> H 12.99010076 0.81319922 0.52324992 > >> H 13.43290580 1.98525495 -0.48533141 > >> O 13.55987706 7.38184199 1.58481400 > >> H 14.17984242 7.90892302 2.16733020 > >> H 13.04800775 6.83909417 2.26677052 > >> O 15.55291198 4.15102828 2.12039216 > >> H 15.17902221 4.52972041 1.27124584 > >> O 14.64425738 3.28381066 6.37285202 > >> H 14.54501798 4.14569728 6.85517739 > >> O 14.73402518 5.59786432 7.92002821 > >> H 15.45748780 6.05233245 7.44773838 > >> O 13.64728834 3.38272560 3.83732221 > >> H 14.35185771 3.76626449 3.22325132 > >> H 14.01549713 3.41619082 4.77312319 > >> O 9.15580367 0.92342575 7.55891408 > >> H 9.53237453 1.65148284 6.98102430 > >> H 8.33603244 0.65613748 7.07671820 > >> O 11.26481409 4.60201028 1.14248028 > >> H 11.02908883 4.92798766 0.21902371 > >> H 11.26715096 3.62696286 1.09066105 > >> O 15.02500419 0.98616684 3.28860775 > >> H 15.88449133 1.32460100 2.87488044 > >> H 14.45468737 1.79129421 3.42040737 > >> O 8.60992588 5.84690827 5.20692515 > >> H 9.01132581 5.91122975 4.30224404 > >> H 8.01367240 6.64131284 5.32349168 > >> H 16.18675121 4.87891083 2.40805975 > >> H 15.61653933 3.18720306 6.22068038 > >> H 14.27629400 6.31178391 8.47864853 > >> O 12.21779588 -0.04576478 5.74403801 > >> H 11.80089925 0.51885747 5.04242315 > >> H 12.30451597 0.56430788 6.55434731 > >> O 15.05170266 0.00823077 5.76312401 > >> H 15.15868948 0.44849492 4.86434702 > >> H 14.06873956 -0.11926391 5.81861878 > >> O 9.26480260 2.00201448 1.97180356 > >> H 9.17489828 1.54585860 1.06336687 > >> H 8.77449155 2.87361598 1.89046099 > >> O 1.55044873 13.96202627 2.60180606 > >> H 2.30308679 13.44140199 2.15448925 > >> H 1.55186146 14.84277348 2.18469312 > >> O 2.75527999 13.56261328 6.64391086 > >> H 1.87802894 13.74881675 6.16708492 > >> H 3.31325372 14.34758540 6.41134505 > >> O 3.22309324 9.89168472 3.88961021 > >> H 2.61702065 9.91739789 3.09551241 > >> H 4.01467966 10.45594481 3.70306054 > >> O 4.48506446 14.01381737 3.59607144 > >> H 4.79562362 13.08661359 3.73169343 > >> H 4.50977887 14.46474361 4.46567132 > >> O 1.77303326 10.94790120 5.91805891 > >> H 2.28673590 10.58580777 5.13755687 > >> H 2.24855288 11.77512959 6.16942302 > >> O 4.65676934 9.48321243 -0.13520423 > >> H 4.99010076 8.81319922 0.52324992 > >> H 5.43290580 9.98525495 -0.48533141 > >> O 5.55987706 15.38184199 1.58481400 > >> H 6.17984242 15.90892302 2.16733020 > >> H 5.04800775 14.83909417 2.26677052 > >> O 7.55291198 12.15102828 2.12039216 > >> H 7.17902221 12.52972041 1.27124584 > >> O 6.64425738 11.28381066 6.37285202 > >> H 6.54501798 12.14569728 6.85517739 > >> O 6.73402518 13.59786432 7.92002821 > >> H 7.45748780 14.05233245 7.44773838 > >> O 5.64728834 11.38272560 3.83732221 > >> H 6.35185771 11.76626449 3.22325132 > >> H 6.01549713 11.41619082 4.77312319 > >> O 1.15580367 8.92342575 7.55891408 > >> H 1.53237453 9.65148284 6.98102430 > >> H 0.33603244 8.65613748 7.07671820 > >> O 3.26481409 12.60201028 1.14248028 > >> H 3.02908883 12.92798766 0.21902371 > >> H 3.26715096 11.62696286 1.09066105 > >> O 7.02500419 8.98616684 3.28860775 > >> H 7.88449133 9.32460100 2.87488044 > >> H 6.45468737 9.79129421 3.42040737 > >> O 0.60992588 13.84690827 5.20692515 > >> H 1.01132581 13.91122975 4.30224404 > >> H 0.01367240 14.64131284 5.32349168 > >> H 8.18675121 12.87891083 2.40805975 > >> H 7.61653933 11.18720306 6.22068038 > >> H 6.27629400 14.31178391 8.47864853 > >> O 4.21779588 7.95423522 5.74403801 > >> H 3.80089925 8.51885747 5.04242315 > >> H 4.30451597 8.56430788 6.55434731 > >> O 7.05170266 8.00823077 5.76312401 > >> H 7.15868948 8.44849492 4.86434702 > >> H 6.06873956 7.88073609 5.81861878 > >> O 1.26480260 10.00201448 1.97180356 > >> H 1.17489828 9.54585860 1.06336687 > >> H 0.77449155 10.87361598 1.89046099 > >> O 9.55044873 13.96202627 2.60180606 > >> H 10.30308679 13.44140199 2.15448925 > >> H 9.55186146 14.84277348 2.18469312 > >> O 10.75527999 13.56261328 6.64391086 > >> H 9.87802894 13.74881675 6.16708492 > >> H 11.31325372 14.34758540 6.41134505 > >> O 11.22309324 9.89168472 3.88961021 > >> H 10.61702065 9.91739789 3.09551241 > >> H 12.01467966 10.45594481 3.70306054 > >> O 12.48506446 14.01381737 3.59607144 > >> H 12.79562362 13.08661359 3.73169343 > >> H 12.50977887 14.46474361 4.46567132 > >> O 9.77303326 10.94790120 5.91805891 > >> H 10.28673590 10.58580777 5.13755687 > >> H 10.24855288 11.77512959 6.16942302 > >> O 12.65676934 9.48321243 -0.13520423 > >> H 12.99010076 8.81319922 0.52324992 > >> H 13.43290580 9.98525495 -0.48533141 > >> O 13.55987706 15.38184199 1.58481400 > >> H 14.17984242 15.90892302 2.16733020 > >> H 13.04800775 14.83909417 2.26677052 > >> O 15.55291198 12.15102828 2.12039216 > >> H 15.17902221 12.52972041 1.27124584 > >> O 14.64425738 11.28381066 6.37285202 > >> H 14.54501798 12.14569728 6.85517739 > >> O 14.73402518 13.59786432 7.92002821 > >> H 15.45748780 14.05233245 7.44773838 > >> O 13.64728834 11.38272560 3.83732221 > >> H 14.35185771 11.76626449 3.22325132 > >> H 14.01549713 11.41619082 4.77312319 > >> O 9.15580367 8.92342575 7.55891408 > >> H 9.53237453 9.65148284 6.98102430 > >> H 8.33603244 8.65613748 7.07671820 > >> O 11.26481409 12.60201028 1.14248028 > >> H 11.02908883 12.92798766 0.21902371 > >> H 11.26715096 11.62696286 1.09066105 > >> O 15.02500419 8.98616684 3.28860775 > >> H 15.88449133 9.32460100 2.87488044 > >> H 14.45468737 9.79129421 3.42040737 > >> O 8.60992588 13.84690827 5.20692515 > >> H 9.01132581 13.91122975 4.30224404 > >> H 8.01367240 14.64131284 5.32349168 > >> H 16.18675121 12.87891083 2.40805975 > >> H 15.61653933 11.18720306 6.22068038 > >> H 14.27629400 14.31178391 8.47864853 > >> O 12.21779588 7.95423522 5.74403801 > >> H 11.80089925 8.51885747 5.04242315 > >> H 12.30451597 8.56430788 6.55434731 > >> O 15.05170266 8.00823077 5.76312401 > >> H 15.15868948 8.44849492 4.86434702 > >> H 14.06873956 7.88073609 5.81861878 > >> O 9.26480260 10.00201448 1.97180356 > >> H 9.17489828 9.54585860 1.06336687 > >> H 8.77449155 10.87361598 1.89046099 > >> O 1.55044873 5.96202627 10.60180606 > >> H 2.30308679 5.44140199 10.15448925 > >> H 1.55186146 6.84277348 10.18469312 > >> O 2.75527999 5.56261328 14.64391086 > >> H 1.87802894 5.74881675 14.16708492 > >> H 3.31325372 6.34758540 14.41134505 > >> O 3.22309324 1.89168472 11.88961021 > >> H 2.61702065 1.91739789 11.09551241 > >> H 4.01467966 2.45594481 11.70306054 > >> O 4.48506446 6.01381737 11.59607144 > >> H 4.79562362 5.08661359 11.73169343 > >> H 4.50977887 6.46474361 12.46567132 > >> O 1.77303326 2.94790120 13.91805891 > >> H 2.28673590 2.58580777 13.13755687 > >> H 2.24855288 3.77512959 14.16942302 > >> O 4.65676934 1.48321243 7.86479577 > >> H 4.99010076 0.81319922 8.52324992 > >> H 5.43290580 1.98525495 7.51466859 > >> O 5.55987706 7.38184199 9.58481400 > >> H 6.17984242 7.90892302 10.16733020 > >> H 5.04800775 6.83909417 10.26677052 > >> O 7.55291198 4.15102828 10.12039216 > >> H 7.17902221 4.52972041 9.27124584 > >> O 6.64425738 3.28381066 14.37285202 > >> H 6.54501798 4.14569728 14.85517739 > >> O 6.73402518 5.59786432 15.92002821 > >> H 7.45748780 6.05233245 15.44773838 > >> O 5.64728834 3.38272560 11.83732221 > >> H 6.35185771 3.76626449 11.22325132 > >> H 6.01549713 3.41619082 12.77312319 > >> O 1.15580367 0.92342575 15.55891408 > >> H 1.53237453 1.65148284 14.98102430 > >> H 0.33603244 0.65613748 15.07671820 > >> O 3.26481409 4.60201028 9.14248028 > >> H 3.02908883 4.92798766 8.21902371 > >> H 3.26715096 3.62696286 9.09066105 > >> O 7.02500419 0.98616684 11.28860775 > >> H 7.88449133 1.32460100 10.87488044 > >> H 6.45468737 1.79129421 11.42040737 > >> O 0.60992588 5.84690827 13.20692515 > >> H 1.01132581 5.91122975 12.30224404 > >> H 0.01367240 6.64131284 13.32349168 > >> H 8.18675121 4.87891083 10.40805975 > >> H 7.61653933 3.18720306 14.22068038 > >> H 6.27629400 6.31178391 16.47864853 > >> O 4.21779588 -0.04576478 13.74403801 > >> H 3.80089925 0.51885747 13.04242315 > >> H 4.30451597 0.56430788 14.55434731 > >> O 7.05170266 0.00823077 13.76312401 > >> H 7.15868948 0.44849492 12.86434702 > >> H 6.06873956 -0.11926391 13.81861878 > >> O 1.26480260 2.00201448 9.97180356 > >> H 1.17489828 1.54585860 9.06336687 > >> H 0.77449155 2.87361598 9.89046099 > >> O 9.55044873 5.96202627 10.60180606 > >> H 10.30308679 5.44140199 10.15448925 > >> H 9.55186146 6.84277348 10.18469312 > >> O 10.75527999 5.56261328 14.64391086 > >> H 9.87802894 5.74881675 14.16708492 > >> H 11.31325372 6.34758540 14.41134505 > >> O 11.22309324 1.89168472 11.88961021 > >> H 10.61702065 1.91739789 11.09551241 > >> H 12.01467966 2.45594481 11.70306054 > >> O 12.48506446 6.01381737 11.59607144 > >> H 12.79562362 5.08661359 11.73169343 > >> H 12.50977887 6.46474361 12.46567132 > >> O 9.77303326 2.94790120 13.91805891 > >> H 10.28673590 2.58580777 13.13755687 > >> H 10.24855288 3.77512959 14.16942302 > >> O 12.65676934 1.48321243 7.86479577 > >> H 12.99010076 0.81319922 8.52324992 > >> H 13.43290580 1.98525495 7.51466859 > >> O 13.55987706 7.38184199 9.58481400 > >> H 14.17984242 7.90892302 10.16733020 > >> H 13.04800775 6.83909417 10.26677052 > >> O 15.55291198 4.15102828 10.12039216 > >> H 15.17902221 4.52972041 9.27124584 > >> O 14.64425738 3.28381066 14.37285202 > >> H 14.54501798 4.14569728 14.85517739 > >> O 14.73402518 5.59786432 15.92002821 > >> H 15.45748780 6.05233245 15.44773838 > >> O 13.64728834 3.38272560 11.83732221 > >> H 14.35185771 3.76626449 11.22325132 > >> H 14.01549713 3.41619082 12.77312319 > >> O 9.15580367 0.92342575 15.55891408 > >> H 9.53237453 1.65148284 14.98102430 > >> H 8.33603244 0.65613748 15.07671820 > >> O 11.26481409 4.60201028 9.14248028 > >> H 11.02908883 4.92798766 8.21902371 > >> H 11.26715096 3.62696286 9.09066105 > >> O 15.02500419 0.98616684 11.28860775 > >> H 15.88449133 1.32460100 10.87488044 > >> H 14.45468737 1.79129421 11.42040737 > >> O 8.60992588 5.84690827 13.20692515 > >> H 9.01132581 5.91122975 12.30224404 > >> H 8.01367240 6.64131284 13.32349168 > >> H 16.18675121 4.87891083 10.40805975 > >> H 15.61653933 3.18720306 14.22068038 > >> H 14.27629400 6.31178391 16.47864853 > >> O 12.21779588 -0.04576478 13.74403801 > >> H 11.80089925 0.51885747 13.04242315 > >> H 12.30451597 0.56430788 14.55434731 > >> O 15.05170266 0.00823077 13.76312401 > >> H 15.15868948 0.44849492 12.86434702 > >> H 14.06873956 -0.11926391 13.81861878 > >> O 9.26480260 2.00201448 9.97180356 > >> H 9.17489828 1.54585860 9.06336687 > >> H 8.77449155 2.87361598 9.89046099 > >> O 1.55044873 13.96202627 10.60180606 > >> H 2.30308679 13.44140199 10.15448925 > >> H 1.55186146 14.84277348 10.18469312 > >> O 2.75527999 13.56261328 14.64391086 > >> H 1.87802894 13.74881675 14.16708492 > >> H 3.31325372 14.34758540 14.41134505 > >> O 3.22309324 9.89168472 11.88961021 > >> H 2.61702065 9.91739789 11.09551241 > >> H 4.01467966 10.45594481 11.70306054 > >> O 4.48506446 14.01381737 11.59607144 > >> H 4.79562362 13.08661359 11.73169343 > >> H 4.50977887 14.46474361 12.46567132 > >> O 1.77303326 10.94790120 13.91805891 > >> H 2.28673590 10.58580777 13.13755687 > >> H 2.24855288 11.77512959 14.16942302 > >> O 4.65676934 9.48321243 7.86479577 > >> H 4.99010076 8.81319922 8.52324992 > >> H 5.43290580 9.98525495 7.51466859 > >> O 5.55987706 15.38184199 9.58481400 > >> H 6.17984242 15.90892302 10.16733020 > >> H 5.04800775 14.83909417 10.26677052 > >> O 7.55291198 12.15102828 10.12039216 > >> H 7.17902221 12.52972041 9.27124584 > >> O 6.64425738 11.28381066 14.37285202 > >> H 6.54501798 12.14569728 14.85517739 > >> O 6.73402518 13.59786432 15.92002821 > >> H 7.45748780 14.05233245 15.44773838 > >> O 5.64728834 11.38272560 11.83732221 > >> H 6.35185771 11.76626449 11.22325132 > >> H 6.01549713 11.41619082 12.77312319 > >> O 1.15580367 8.92342575 15.55891408 > >> H 1.53237453 9.65148284 14.98102430 > >> H 0.33603244 8.65613748 15.07671820 > >> O 3.26481409 12.60201028 9.14248028 > >> H 3.02908883 12.92798766 8.21902371 > >> H 3.26715096 11.62696286 9.09066105 > >> O 7.02500419 8.98616684 11.28860775 > >> H 7.88449133 9.32460100 10.87488044 > >> H 6.45468737 9.79129421 11.42040737 > >> O 0.60992588 13.84690827 13.20692515 > >> H 1.01132581 13.91122975 12.30224404 > >> H 0.01367240 14.64131284 13.32349168 > >> H 8.18675121 12.87891083 10.40805975 > >> H 7.61653933 11.18720306 14.22068038 > >> H 6.27629400 14.31178391 16.47864853 > >> O 4.21779588 7.95423522 13.74403801 > >> H 3.80089925 8.51885747 13.04242315 > >> H 4.30451597 8.56430788 14.55434731 > >> O 7.05170266 8.00823077 13.76312401 > >> H 7.15868948 8.44849492 12.86434702 > >> H 6.06873956 7.88073609 13.81861878 > >> O 1.26480260 10.00201448 9.97180356 > >> H 1.17489828 9.54585860 9.06336687 > >> H 0.77449155 10.87361598 9.89046099 > >> O 9.55044873 13.96202627 10.60180606 > >> H 10.30308679 13.44140199 10.15448925 > >> H 9.55186146 14.84277348 10.18469312 > >> O 10.75527999 13.56261328 14.64391086 > >> H 9.87802894 13.74881675 14.16708492 > >> H 11.31325372 14.34758540 14.41134505 > >> O 11.22309324 9.89168472 11.88961021 > >> H 10.61702065 9.91739789 11.09551241 > >> H 12.01467966 10.45594481 11.70306054 > >> O 12.48506446 14.01381737 11.59607144 > >> H 12.79562362 13.08661359 11.73169343 > >> H 12.50977887 14.46474361 12.46567132 > >> O 9.77303326 10.94790120 13.91805891 > >> H 10.28673590 10.58580777 13.13755687 > >> H 10.24855288 11.77512959 14.16942302 > >> O 12.65676934 9.48321243 7.86479577 > >> H 12.99010076 8.81319922 8.52324992 > >> H 13.43290580 9.98525495 7.51466859 > >> O 13.55987706 15.38184199 9.58481400 > >> H 14.17984242 15.90892302 10.16733020 > >> H 13.04800775 14.83909417 10.26677052 > >> O 15.55291198 12.15102828 10.12039216 > >> H 15.17902221 12.52972041 9.27124584 > >> O 14.64425738 11.28381066 14.37285202 > >> H 14.54501798 12.14569728 14.85517739 > >> O 14.73402518 13.59786432 15.92002821 > >> H 15.45748780 14.05233245 15.44773838 > >> O 13.64728834 11.38272560 11.83732221 > >> H 14.35185771 11.76626449 11.22325132 > >> H 14.01549713 11.41619082 12.77312319 > >> O 9.15580367 8.92342575 15.55891408 > >> H 9.53237453 9.65148284 14.98102430 > >> H 8.33603244 8.65613748 15.07671820 > >> O 11.26481409 12.60201028 9.14248028 > >> H 11.02908883 12.92798766 8.21902371 > >> H 11.26715096 11.62696286 9.09066105 > >> O 15.02500419 8.98616684 11.28860775 > >> H 15.88449133 9.32460100 10.87488044 > >> H 14.45468737 9.79129421 11.42040737 > >> O 8.60992588 13.84690827 13.20692515 > >> H 9.01132581 13.91122975 12.30224404 > >> H 8.01367240 14.64131284 13.32349168 > >> H 16.18675121 12.87891083 10.40805975 > >> H 15.61653933 11.18720306 14.22068038 > >> H 14.27629400 14.31178391 16.47864853 > >> O 12.21779588 7.95423522 13.74403801 > >> H 11.80089925 8.51885747 13.04242315 > >> H 12.30451597 8.56430788 14.55434731 > >> O 15.05170266 8.00823077 13.76312401 > >> H 15.15868948 8.44849492 12.86434702 > >> H 14.06873956 7.88073609 13.81861878 > >> O 9.26480260 10.00201448 9.97180356 > >> H 9.17489828 9.54585860 9.06336687 > >> H 8.77449155 10.87361598 9.89046099 > >> K_POINTS gamma > > > > > > > > > > ---------------------------------------------------------------- > > SISSA Webmail https://webmail.sissa.it/ > > Powered by Horde http://www.horde.org/ > > > > > > _______________________________________________ > > 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 > -- Best regards, -------------------------------------- Juan M. Lopez Encarnacion -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110504/2342e368/attachment-0001.htm From kucukben at sissa.it Wed May 4 14:48:35 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Wed, 04 May 2011 14:48:35 +0200 Subject: [Pw_forum] cohesive energy of water/ice In-Reply-To: <20110504143912.sodjitv5z408coww@webmail.sissa.it> References: <4DC145E0.5000004@nano.ku.dk> <20110504143912.sodjitv5z408coww@webmail.sissa.it> Message-ID: <20110504144835.kb4gyreu0c4wgko8@webmail.sissa.it> Replying to the mailing list without trimming long inline attachments is not a good idea. Sorry. Hope this can serve as a reminder for future. emine kucukbenli, phd student, sissa, italy Quoting Emine Kucukbenli : > Hi Martin, > Just a quick note, .... ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From padmaja_patnaik at yahoo.co.uk Wed May 4 15:32:44 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Wed, 4 May 2011 14:32:44 +0100 (BST) Subject: [Pw_forum] Magnetization Message-ID: <679093.45105.qm@web28505.mail.ukl.yahoo.com> Dear All In the scf calculations the output file gives the total and absolute magnetization. As per my knowledge magnetization is defined as the total magnetic moment of the cell divided? by the volume of the cell. When I look into the code I couldn't see this formula for calculating magnetization. What I observe is the rho_up - rho_down is the magnetization. Then this should be treated as magnetic moment of the cell not the magnetization. I shall be thankful if anybody can please explain this. 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/20110504/d99e4974/attachment.htm From giovanni.cantele at spin.cnr.it Wed May 4 15:37:43 2011 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Wed, 4 May 2011 15:37:43 +0200 Subject: [Pw_forum] Magnetization In-Reply-To: <679093.45105.qm@web28505.mail.ukl.yahoo.com> References: <679093.45105.qm@web28505.mail.ukl.yahoo.com> Message-ID: <6FD84E6A-9883-4E6D-97E4-DA72CFB287EC@spin.cnr.it> On May 4, 2011, at 3:32 PM, Padmaja Patnaik wrote: > Dear All > > In the scf calculations the output file gives the total and absolute magnetization. As per my knowledge magnetization is defined as the total magnetic moment of the cell divided by the volume of the cell. When I look into the code I couldn't see this formula for calculating magnetization. What I observe is the rho_up - rho_down is the magnetization. Then this should be treated as magnetic moment of the cell not the magnetization. I shall be thankful if anybody can please explain this. > > 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 I think this has been explained several times in the forum. Indeed, a FAQ has been added to the online Quantum-ESPRESSO guide: http://www.quantum-espresso.org/user_guide/node64.html#SECTION000137030000000000000 Giovanni -- **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110504/75ed12dd/attachment.htm From ma at nano.ku.dk Wed May 4 15:57:35 2011 From: ma at nano.ku.dk (Martin Andersson) Date: Wed, 04 May 2011 15:57:35 +0200 Subject: [Pw_forum] cohesive energy of water/ice In-Reply-To: <20110504144835.kb4gyreu0c4wgko8@webmail.sissa.it> References: <4DC145E0.5000004@nano.ku.dk> <20110504143912.sodjitv5z408coww@webmail.sissa.it> <20110504144835.kb4gyreu0c4wgko8@webmail.sissa.it> Message-ID: <4DC15B4F.9060601@nano.ku.dk> Hi again, There is at most 0.01 eV cohesive energy difference when changing the box size or using nosym and assume_isolated='mp' or 'mt'. This has also been my experinece from other neutral molecules that a large box by itself provides reliable gas phase reference energies. Any other suggestions? I have tried both ultrasoft pseudopotentials and PAW, both of which have been checked for plane wave convergence, so I am really at a loss. Could the literature calculations with VASP really be so wrong? I feel it is more likely that I have made some mistake... Cheers, Martin Andersson University of Copenhagen From Matthieu.Verstraete at ulg.ac.be Wed May 4 18:52:00 2011 From: Matthieu.Verstraete at ulg.ac.be (matthieu verstraete) Date: Wed, 4 May 2011 18:52:00 +0200 Subject: [Pw_forum] phonons in parallel in 4.3 Message-ID: Hello everyone, I have been having trouble calculating phonons in 4.3. On a central-disk machine things work fine, but for a distributed cluster with local scratch disks the phonon temp files are not spread correctly over the nodes. Apparently only the mother node has the correct files written (including all instances on that node). Has anyone encountered this, and has it been fixed in the development version? Is there some input variable I am ignoring? The same input files were working for qe 4.2.1 Thanks Matthieu -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Prof. Matthieu Verstraete Universite de Li?ge Institut de Physique, Bat. B5, 3/7 All?e du 6 aout, 17 B- 4000 Sart Tilman, Li?ge Belgium Associate member European Theoretical Spectroscopy Facility (ETSF http://www.etsf.eu) Phone : +32 4 366 90 17 Fax?? : +32 4 366 36 29 Mail : matthieu.verstraete at ulg.ac.be ? ? ? ? ? matthieu.jean.verstraete at gmail.com From giannozz at democritos.it Wed May 4 22:18:19 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 4 May 2011 22:18:19 +0200 Subject: [Pw_forum] phonons in parallel in 4.3 In-Reply-To: References: Message-ID: On May 4, 2011, at 18:52 , matthieu verstraete wrote: > I have been having trouble calculating phonons in 4.3. On a > central-disk machine things work fine, but for a distributed cluster > with local scratch disks the phonon temp files are not spread > correctly over the nodes. Apparently only the mother node has the > correct files written (including all instances on that node). Has > anyone encountered this and has it been fixed in the development > version? none of the above. Please file a bug on qe-forge: http://qe-forge.org/tracker/?atid=133&group_id=10&func=browse Note however that it is becoming increasingly difficult to support parallel machines without a parallel file systems. Such a case is a never-ending source of trouble to an already too complex I/O. If there is an easy fix, it might be found quickly; otherwise, no warranty > Is there some input variable I am ignoring? I don't think so 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 nandan.tandon at gmail.com Wed May 4 22:40:23 2011 From: nandan.tandon at gmail.com (Nandan Tandon) Date: Wed, 4 May 2011 16:40:23 -0400 Subject: [Pw_forum] electron-phonon interaction in semiconductor Message-ID: Hello, I want to calculate electron-phonon coupling in semiconductors and am looking for suitable examples/tutorial in pwscf. Although the userguide says that it can only be done for metals, i found an email in the forum which said that it can also work for semiconductors. Any help would be appreciated. Regards, Nandan. -- *********************************************************************************************** Nandan Tandon Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA ************************************************************************************************* From germaneau at gucas.ac.cn Thu May 5 16:14:26 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 05 May 2011 10:14:26 -0400 Subject: [Pw_forum] grid of spacing k-vectors Message-ID: <4DC2B0C2.8080203@gucas.ac.cn> Dear all, I'm wondering whether it's possible to generate k-vectors for the Brillouin sampling using a grid of spacing instead of a number of vectors. Thank you, ?ric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /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/20110505/9d024df1/attachment.htm From ttduyle at gmail.com Thu May 5 04:37:18 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 4 May 2011 22:37:18 -0400 Subject: [Pw_forum] grid of spacing k-vectors In-Reply-To: <4DC2B0C2.8080203@gucas.ac.cn> References: <4DC2B0C2.8080203@gucas.ac.cn> Message-ID: If you can not find the equivalent mesh for a specific spacing, you just need to list all special k-points with their weight. And yes, you can always generate anything you want. A small, simple code will help you to do the job. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Thu, May 5, 2011 at 10:14 AM, Eric Germaneau wrote: > Dear all, > > I'm wondering whether it's possible to generate k-vectors for the Brillouin > sampling using > a grid of spacing instead of a number of vectors. > Thank you, > > ????? ? ? ? ? ? ? ? ? ? ? ?ric. > > -- > Be the change you wish to see in the world > ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > 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 > > From mcmahonj at illinois.edu Thu May 5 05:57:56 2011 From: mcmahonj at illinois.edu (Jeffrey M. McMahon) Date: Wed, 4 May 2011 22:57:56 -0500 Subject: [Pw_forum] electron-phonon interaction in QE 4.3 Message-ID: Dear All, I am having an issue calculating the electron-phonon interaction in QE 4.3. I do not know if this is due to a bug or my build of QE (most likely the latter). After compiling, when I test the program example 07 stops with an error in al.elph.out: electron-phonon interaction ... %%%%%% from efermig : error # 1 internal error, cannot bracket Ef %%%%%% It is not just example 07, but any electron-phonon calculation. All other tests and examples performed fine during testing. I tried compiling QE with Intel compilers (version 10.1, I believe) as well as GNU compilers, first version 4.3 and now 4.5-19.1, but the problem occurs in all cases. I also tried using BLAS and LAPACK as provided by the Intel MKL as well as the internal versions, and also FFTW3 and whatever is provided internally (and various combinations of the aforementioned). I did not experience any issues with QE 4.2.1 when compiled the exact same way. Any suggestions would be appreciated. Thanks in advance. Jeffrey M. McMahon The Institute for Condensed Matter Theory Department of Physics University of Illinois at Urbana-Champaign Urbana, IL 61801-3080 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110504/7447a425/attachment.htm From germaneau at gucas.ac.cn Thu May 5 18:51:30 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 05 May 2011 12:51:30 -0400 Subject: [Pw_forum] grid of spacing k-vectors In-Reply-To: <504562361.05685@test1.gucas.ac.cn> References: <4DC2B0C2.8080203@gucas.ac.cn> <504562361.05685@test1.gucas.ac.cn> Message-ID: <4DC2D592.2020309@gucas.ac.cn> Hey Duy Le, Thank for your reply. Actually I have the reciprocal vectors but don't know a how to sample the 1st Brillouin zone with. Well, to me it's not that straightforward but if you have a small, simple code that can do that I would appreciate to get it. Yours, ?ric. On 05/04/2011 10:37 PM, Duy Le wrote: > If you can not find the equivalent mesh for a specific spacing, you > just need to list all special k-points with their weight. > > And yes, you can always generate anything you want. A small, simple > code will help you to do the job. > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > > On Thu, May 5, 2011 at 10:14 AM, Eric Germaneau wrote: >> Dear all, >> >> I'm wondering whether it's possible to generate k-vectors for the Brillouin >> sampling using >> a grid of spacing instead of a number of vectors. >> Thank you, >> >> ?ric. >> >> -- >> Be the change you wish to see in the world >> ? Mahatma Gandhi ? >> >> Dr. ?ric Germaneau >> >> College of Physical Sciences >> Graduate University of Chinese Academy of Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> >> 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 >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /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/20110505/946c6afa/attachment.htm From sclauzer at sissa.it Thu May 5 10:01:52 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 5 May 2011 10:01:52 +0200 Subject: [Pw_forum] grid of spacing k-vectors In-Reply-To: <4DC2B0C2.8080203@gucas.ac.cn> References: <4DC2B0C2.8080203@gucas.ac.cn> Message-ID: Dear ?ric, I would say that, for a uniformly spaced grid of k-points, specifying the number of k-points is equivalent to specify the grid spacing (along each basis vector of the reciprocal space independently). Since you know the direct lattice vectors, then you can get the length of the reciprocal lattice vectors, which is the only thing missing. Gabriele Il giorno 05/mag/2011, alle ore 16.14, Eric Germaneau ha scritto: > Dear all, > > I'm wondering whether it's possible to generate k-vectors for the Brillouin sampling using > a grid of spacing instead of a number of vectors. > Thank you, > > ?ric. > > -- > Be the change you wish to see in the world > ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > 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 ? 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/20110505/355c888c/attachment.htm From germaneau at gucas.ac.cn Thu May 5 10:01:59 2011 From: germaneau at gucas.ac.cn (germaneau) Date: Thu, 05 May 2011 16:01:59 +0800 Subject: [Pw_forum] grid of spacing k-vectors Message-ID: Dear Gabriele, I have calculated the reciprocal lattice vectors. I don't get why you said that is the only thing missing. I have to select k-vectors from the 1st Brillouin zone only, and that's what I can't figure out. Thank you, Eric. ------------------ ???? ------------------ >From: Gabriele Sclauzero >Reply-To: PWSCF Forum >To: PWSCF Forum >Subject: Re: [Pw_forum] grid of spacing k-vectors >Date: Thu, 5 May 2011 10:01:52 +0200 > Dear ric, I would say that, for a uniformly spaced grid of k-points, specifying the number of k-points is equivalent to specify the grid spacing (along each basis vector of the reciprocal space independently). Since you know the direct lattice vectors, then you can get the length of the reciprocal lattice vectors, which is the only thing missing. Gabriele Il giorno 05/mag/2011, alle ore 16.14, Eric Germaneau ha scritto: Dear all, I'm wondering whether it's possible to generate k-vectors for the Brillouin sampling using a grid of spacing instead of a number of vectors. Thank you, ric. -- Be the change you wish to see in the world ? Mahatma Gandhi ? Dr. ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China 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 ? 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/20110505/1931ceac/attachment.htm From giannozz at democritos.it Thu May 5 10:37:32 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 5 May 2011 10:37:32 +0200 Subject: [Pw_forum] electron-phonon interaction in QE 4.3 In-Reply-To: References: Message-ID: <79B921C3-3073-4D96-BD25-7ADBC5D42964@democritos.it> On May 5, 2011, at 5:57 , Jeffrey M. McMahon wrote: > from efermig : error # 1 > internal error, cannot bracket Ef there is something wrong in the electron-phonon code. That code is actually obsolete (there are much better alternatives) but of course it has to work until it is there. It will be fixed as soon as possible. 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 sclauzer at sissa.it Thu May 5 10:50:09 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 5 May 2011 10:50:09 +0200 Subject: [Pw_forum] grid of spacing k-vectors In-Reply-To: References: Message-ID: You can sample the BZ choosing an appropriate set of k-points inside a primitive cell of the reciprocal lattice. The simplest one, using crystal coordinates, is just a cube of side 1 with a corner in the origin. Then, along each side of the cube you can chose a different grid spacing, which should be inversely proportional to the length (in cartesian metrics) of the corresponding crystal vector, in order to perform an optimal sampling (at least, in my opinion). Then you can bring all k-points back to the 1st BZ, reduce them to an irreducible set using symmetry, and transform them to cartesian coordinates, if you want. Perhaps there are other better ways to sample the BZ, but this is the simplest I have in mind and it should be the one used in PWscf (see PW/kpoint_grid.f90). HTH GS Il giorno 05/mag/2011, alle ore 10.01, germaneau ha scritto: > > Dear Gabriele, > > I have calculated the reciprocal lattice vectors. > > I don't get why you said that is the only thing missing. > > I have to select k-vectors from the 1st Brillouin zone only, and that's what I can't figure out. > > Thank you, > > Eric. > > > > > > ------------------ ???? ------------------ > >From: Gabriele Sclauzero > >Reply-To: PWSCF Forum > >To: PWSCF Forum > >Subject: Re: [Pw_forum] grid of spacing k-vectors > >Date: Thu, 5 May 2011 10:01:52 +0200 > > > > Dear ric, > > I would say that, for a uniformly spaced grid of k-points, specifying the number of k-points is equivalent to specify the grid spacing (along each basis vector of the reciprocal space independently). Since you know the direct lattice vectors, then you can get the length of the reciprocal lattice vectors, which is the only thing missing. > > > Gabriele > > > Il giorno 05/mag/2011, alle ore 16.14, Eric Germaneau ha scritto: > >> Dear all, >> >> I'm wondering whether it's possible to generate k-vectors for the Brillouin sampling using >> a grid of spacing instead of a number of vectors. >> Thank you, >> >> ric. >> >> -- >> Be the change you wish to see in the world >> ? Mahatma Gandhi ? >> >> Dr. ric Germaneau >> >> College of Physical Sciences >> Graduate University of Chinese Academy of Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> >> 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 > > > ? 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/20110505/9a62985e/attachment.htm From mahmud at science.upm.edu.my Thu May 5 12:47:57 2011 From: mahmud at science.upm.edu.my (Dr. Mahmudur Rahman) Date: Thu, 5 May 2011 18:47:57 +0800 Subject: [Pw_forum] Need help to install quantum espresso Message-ID: Dear Users, I have installed Ubuntu linux and would like to install quantum espresso. I followed the user guide but could not succeed. Anybody can help me? Regards, Mahmud From mahmud at science.upm.edu.my Thu May 5 12:56:18 2011 From: mahmud at science.upm.edu.my (Dr. Mahmudur Rahman) Date: Thu, 5 May 2011 18:56:18 +0800 Subject: [Pw_forum] Pw_forum Digest, Vol 47, Issue 8 Message-ID: <4c6f604840143ccd9755ed9ca92e1853.squirrel@science.upm.edu.my> Dear Giovanni, Thank you very much for your advice. Mahmud > 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. Need help to run on windows using cygwin (Dr. Mahmudur Rahman) 2. Re: Need help to run on windows using cygwin (Giovanni Cantele) 3. Imposing opposite spins (Padmaja Patnaik) > 4. Re: Imposing opposite spins (Arles V. Gil Rebaza) > 5. using wf_collect only for a few bands (J. D. Burton) > 6. Cohesive Energy of N2 molecule (Izaak Williamson) > ---------------------------------------------------------------------- Message: 1 > Date: Tue, 3 May 2011 18:37:39 +0800 > From: "Dr. Mahmudur Rahman" > Subject: [Pw_forum] Need help to run on windows using cygwin > To: pw_forum at pwscf.org > Message-ID: > <61afecebf655a3755593ad5310da8209.squirrel at science.upm.edu.my> > Content-Type: text/plain;charset=iso-8859-1 > Dear user, > I have just downloaded quantum espresso and cygwin (as i am using windows > 7). But I do not understand how to run the example. I read the user guide; > still cannot make out. > Best regards, > Mahmud > ------------------------------ > Message: 2 > Date: Tue, 3 May 2011 13:12:28 +0200 > From: Giovanni Cantele > Subject: Re: [Pw_forum] Need help to run on windows using cygwin To: PWSCF Forum > Message-ID: <43EDD80C-8925-4C7F-9720-A9CCBCA83177 at spin.cnr.it> > Content-Type: text/plain; charset="us-ascii" > On May 3, 2011, at 12:37 PM, Dr. Mahmudur Rahman wrote: >> Dear user, >> I have just downloaded quantum espresso and cygwin (as i am using windows >> 7). But I do not understand how to run the example. I read the user guide; >> still cannot make out. >> Best regards, >> Mahmud > how to run examples is explained here: > http://www.quantum-espresso.org/user_guide/node13.html > But from your message it is not clear why you didn't manage to run. Did you get some error message? > Was your installation successful (namely, did you build working > executable? have a look to the > Quantum-ESPRESSO/espresso-x.y.z/bin directory)? If so, you need to set some environment variables > under cygwin according to what explained in the above link: > BIN_DIR: directory where executables reside > PSEUDO_DIR: directory where pseudopotential files reside > TMP_DIR: directory to be used as temporary storage area > On the side, although you should be able to easily install and make running Quantum-ESPRESSO > under cygwin + Windows, I would strongly suggest to try (if you have time) > the much better, faster, friendly, > totally free, beautifully looking Linux operating system. You can download > a live CD (just to try before installing it) > from www.ubuntu.com. > Giovanni > -- > **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it Giovanni Cantele, PhD > CNR-SPIN and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario M. S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 - Fax: +39 081 676346 > Skype contact: giocan74 > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.na.infn.it/~cantele > http://www.nanomat.unina.it > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110503/3fce4c3e/attachment-0001.htm ------------------------------ > Message: 3 > Date: Tue, 3 May 2011 13:17:31 +0100 (BST) > From: Padmaja Patnaik > Subject: [Pw_forum] Imposing opposite spins > To: pw_forum at pwscf.org > Message-ID: <521957.84265.qm at web28506.mail.ukl.yahoo.com> > Content-Type: text/plain; charset="utf-8" > Hi All > I want to do calculations on a supercell where I am adding two impurity atoms of the same kind at two different places. I want to make sure that these two atoms are in opposite spins. how can I format the input file to > achieve this condition. And also if somebody knows any software which can > plot the atomic structure along with the spins direction then please let me know. > Thanking you 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/20110503/70249ee7/attachment-0001.htm ------------------------------ > Message: 4 > Date: Tue, 3 May 2011 10:14:48 -0300 > From: "Arles V. Gil Rebaza" > Subject: Re: [Pw_forum] Imposing opposite spins > To: PWSCF Forum > Message-ID: Content-Type: text/plain; charset="iso-8859-1" > Hi Padmaja, you need write in the input file the next variables: &system > starting_magnetization(1) = 0.00 > starting_magnetization(2) = 0.00 > starting_magnetization(3) = 0.00 > -.... > starting_magnetization(i) = 1.00, > starting_magnetization(j) = -1.00, > where "i" and "j" is the number of the two impurity atoms, although in different spin direccion. If the other atoms in your supercell aren't magnetics, just write 0.0. Furthermore, you have to write twice the pseudopotential belonging to the impurity. For example: > ATOMIC_SPECIES > ...... > ........ > Fe1 55.845 Fe.pbe-paw_kj.UPF > Fe2 55.845 Fe.pbe-paw_kj.UPF > Best. > Arles V. Gil Rebaza > Instituto de F?sica de La Plata > La Plata - Argentina > 2011/5/3 Padmaja Patnaik >> Hi All >> I want to do calculations on a supercell where I am adding two impurity atoms of the same kind at two different places. I want to make sure that >> these two atoms are in opposite spins. how can I format the input file to >> achieve this condition. And also if somebody knows any software which can >> plot the atomic structure along with the spins direction then please let >> me >> know. >> Thanking you 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 > -- > ###---------> Arles V. <---------### > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110503/eff65291/attachment-0001.htm ------------------------------ > Message: 5 > Date: Tue, 3 May 2011 10:36:15 -0500 > From: "J. D. Burton" > Subject: [Pw_forum] using wf_collect only for a few bands > To: > Message-ID: <052e01cc09a7$d7ad50b0$8707f210$@gmail.com> > Content-Type: text/plain; charset="us-ascii" > Dear All, > Is there a way to use the 'wf_collect' to save wavefunctions ONLY for a few > bands at each k-point, say +/- 1eV around the Fermi energy? I am trying to > plot k-resolved LDOS on a fine k-grid to image the Fermi surface of a 2-D > heterostructure, but saving ALL the wavefunctions takes way too much disk > space and my cluster administrator starts barking at me. > I've looked in the code and I might be able to figure out how to do it in > a > very ad hoc way, but I'm wondering if anyone has a quicker solution. Cheers, > J. D. > ************************************ > J. D. Burton, Ph.D. > jdburton1 at gmail.com > Research Assistant Professor > University of Nebraska Lincoln > Physics and Astronomy > Office Ph. (402) 472 2499 > Mobile Ph. (402) 419 9918 > 310A Jorgensen Hall > CV: http://tinyurl.com/2avltsc > ************************************ > "The job of a scientist is to generate wrong ideas as fast as possible." -- Murray Gell-Mann > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110503/5b26ad0e/attachment-0001.htm ------------------------------ > Message: 6 > Date: Tue, 3 May 2011 09:54:14 -0700 (PDT) > From: Izaak Williamson > Subject: [Pw_forum] Cohesive Energy of N2 molecule > To: pw_forum at pwscf.org > Message-ID: <974606.12674.qm at web43416.mail.sp1.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > Dear all, > I am trying to calculate the cohesive energy of the N2 molecule using the > attached input file (relax.in) and am getting a value of -16.57 eV. I use > DFT > with GGA and the pseudo-potential N.pbe-rrkjus.UPF. Other work [Fuchs et. > al., > Phys. Rev. B 65, (2002)245212] has performed similar calculations and obtained > values ~10.5 eV. They even list an experimental value of 9.76 eV. Why is my > value so much higher? Is there anything in my input file that could be giving > inaccurate results? Is it my pseudo-potential that is causing this problem? > 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/20110503/9e728584/attachment.htm -------------- next part -------------- > A non-text attachment was scrubbed... > Name: relax.in > Type: application/octet-stream > Size: 662 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20110503/9e728584/attachment.obj ------------------------------ > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > End of Pw_forum Digest, Vol 47, Issue 8 > *************************************** -- Dr. Mahmudur Rahman Senior Lecturer Department of Physics Faculty of Science University Putra Malaysia 43400 UPM Serdang Selangor MALAYSIA Tel:+60-3-8946-6683 Mobile Phone:+60-173369047 Fax:+60-3-8945-4454 Email:mahmud at science.upm.edu.my From kangbugy at lycos.co.kr Thu May 5 15:36:13 2011 From: kangbugy at lycos.co.kr (=?UTF-8?B?a2FuZ2J1Z3lAbHljb3MuY28ua3I=?=) Date: Thu, 05 May 2011 22:36:13 +0900 Subject: [Pw_forum] =?utf-8?q?band_of_LDA+U_=26_SOC?= Message-ID: <3de2d697c0ac167496184469a12a2a4d$5c6718fe@pcmail3.nate.com> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110505/6a122af5/attachment.htm From parishok at gmail.com Thu May 5 15:59:05 2011 From: parishok at gmail.com (pari shok) Date: Thu, 5 May 2011 09:59:05 -0400 Subject: [Pw_forum] smearing Message-ID: Dear All, Hi. Is there a limit that all smearings converge? For instance, is it possible to say that in very small degauss, all smearings give the same result? Thank you for your help. P Shok -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110505/89a61063/attachment.htm From nkxirainbow at gmail.com Thu May 5 16:47:36 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 5 May 2011 22:47:36 +0800 Subject: [Pw_forum] smearing In-Reply-To: References: Message-ID: Dear P Shok: Is there a limit that all smearings converge? For instance, is it possible > to say that in very small degauss, all smearings give the same result? > I think so. You can find some example at here: http://blog.sina.com.cn/s/blog_5f15ead20100d1ki.html However, keep in mind: small degauss must be used with large k-mesh. Thank you for your help. > P Shok > > _______________________________________________ > 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/20110505/d9b3f0d9/attachment.htm From nandan.tandon at gmail.com Thu May 5 16:49:04 2011 From: nandan.tandon at gmail.com (Nandan Tandon) Date: Thu, 5 May 2011 10:49:04 -0400 Subject: [Pw_forum] electron-phonon interaction in QE 4.3 In-Reply-To: <79B921C3-3073-4D96-BD25-7ADBC5D42964@democritos.it> References: <79B921C3-3073-4D96-BD25-7ADBC5D42964@democritos.it> Message-ID: Hello, Could you please elaborate on the "better alternatives". I want to calculate electron phonon coupling in semiconductors. Regards, Nandan. On Thu, May 5, 2011 at 4:37 AM, Paolo Giannozzi wrote: > > On May 5, 2011, at 5:57 , Jeffrey M. McMahon wrote: > >> ? ? ?from efermig : error # ? ? ? ? 1 >> ? ? ?internal error, cannot bracket Ef > > there is something wrong in the electron-phonon code. That code > is actually obsolete (there are much better alternatives) but of > course it has to work until it is there. It will be fixed as soon as > possible. > > 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 > -- *********************************************************************************************** Nandan Tandon Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA ************************************************************************************************* From ivan.girotto at ichec.ie Thu May 5 18:11:27 2011 From: ivan.girotto at ichec.ie (Ivan Girotto) Date: Thu, 05 May 2011 17:11:27 +0100 Subject: [Pw_forum] First PWscf GPU-enabled beta-release Message-ID: <4DC2CC2F.2040608@ichec.ie> Dear QE users & developers, We are happy to announce that the first beta GPU-enabled release of Quantum ESPRESSO (QE) has been committed today in the official repository. You can download the new version of the code using the following command: $ svn checkout svn://scm.qe-forge.org/scmrepos/svn/q-e/branches/espresso-PRACE The Irish Centre for High-End Computing (ICHEC, www.ichec.ie ) has been mainly responsible for extending the QE suite to enhance calculations on NVIDIA GPUs. The porting activity has been supported within the PRACE 1st Implementation Phase project. It is currently carried out through the Sub-task "Accelerator", led by ICHEC, within the Work-Package "Programming Techniques for High-Performance Applications" in collaboration with CINECA. The porting activity is concerned mainly with the PWscf package. But ICHEC and the Irish QE user community are interested in exploring any other initiatives which come forward from QE users or developers interested in porting on GPGPU architecture any of the QE suite related codes. We have successfully accelerated the linear algebra part of the QE suite using a library called phiGEMM, some explicit computational kernels (newd, addusdense, vloc_psi) and the 3D FFT for the single CPU/GPU version. Both linear algebra (matrix multiplication) and the FFT accelerated version make use of CUDA libraries. The porting is mainly based on wrappers that permit the use of libraries for accelerators. The distributed 3D FFT version is still in progress, since this porting requires important changes of the current structure of the code and data distribution. While running the parallel and distributed multi-GPUs version it still uses the original 3D FFT implementations. The phiGEMM library is distributed as an independent open-source external package together with the Quantum ESPRESSO suite. It aims to perform matrix multiplication ([SDZ]GEMM) taking advantage of the underlying BLAS kernel functions on both CPU and NVIDIA CUDA-based GPU, mixing and overlapping computation between the host (CPU) and the accelerator (GPU). Whatever code makes intensive use of GEMM it can derive a significant advantage linking this library when running on a CPU/GPU hybrid system. Even if the 3D FFT is accelerated only for a single CPU process (not when using MPI), other parts are already enabled to take advantage of a distributed parallel hybrid system. All of this allows PWscf to potentially use distributed message-passing parallelization (MPI) plus multi-threading (OpenMP) plus accelerators (NVIDIA GPUs) all together and produce good performance enhancement using the latest version of NVIDIA GPUs (high performance double precision is needed). This porting activity is still in progress, especially the parallel 3D FFT component that represents a bottleneck for large calculations. We have been testing this beta release using some small/medium benchmarks used in the DEISA official bench-suite and several GPU hardware (Tesla and Fermi architectures). Special thanks goes to both E4 Computer Engineering and CEA for providing access to hybrid GPU systems with differing configurations to those available at ICHEC. We look forward with interest to receiving any suggestions for improvement, feedback or request for collaboration by anyone who is interested to try and validate PWscf CUDA version on different platforms using different scientific cases.For additional information please contact qe-gpu at ichec.ie or replay at this mail. We'll be shortly available a dedicated forum q-e-gpgpu at qe-forge.org . Please use this list for bug report and any other issue related to the use of the PWscf GPU version. Although compilation of the GPU implementation is fairly straight-forward, we kindly suggest that users carefully read the README.GPU that is included. The intrinsic characteristics of hybrid multi- and many-core systems require careful consideration to best exploit the available computing power. Any and all suggestions are welcome and will be very much appreciated. Ivan Girotto & Filippo Spiga --- ICHEC GPU developer team The Tower - 7th floor Trinity Technology& Enterprise Campus Grand Canal Quay - Dublin 2 - Ireland +353-1-5241608 (ph) / +353-1-7645845 (fax) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110505/8af10ede/attachment-0001.htm From vitruss at gmail.com Thu May 5 18:24:53 2011 From: vitruss at gmail.com (Vit) Date: Thu, 5 May 2011 23:24:53 +0700 Subject: [Pw_forum] First PWscf GPU-enabled beta-release In-Reply-To: <4DC2CC2F.2040608@ichec.ie> References: <4DC2CC2F.2040608@ichec.ie> Message-ID: <201105052324.54165.vitruss@gmail.com> Dear Ivan, Can you please proveide any benchmarks and comparison of Hybrid CPU/GPU vs pure CPU computation? With best regards, Victor. Ivan Girotto Thursday 05 May 2011 > Dear QE users & developers, > > We are happy to announce that the first beta GPU-enabled release of > Quantum ESPRESSO (QE) has been committed today in the official repository. > > You can download the new version of the code using the following command: > > $ svn checkout > svn://scm.qe-forge.org/scmrepos/svn/q-e/branches/espresso-PRACE > > The Irish Centre for High-End Computing (ICHEC, www.ichec.ie > ) has been mainly responsible for extending the QE > suite to enhance calculations on NVIDIA GPUs. The porting activity has > been supported within the PRACE 1st Implementation Phase project. It is > currently carried out through the Sub-task "Accelerator", led by ICHEC, > within the Work-Package "Programming Techniques for High-Performance > Applications" in collaboration with CINECA. > > The porting activity is concerned mainly with the PWscf package. But > ICHEC and the Irish QE user community are interested in exploring any > other initiatives which come forward from QE users or developers > interested in porting on GPGPU architecture any of the QE suite related > codes. > > We have successfully accelerated the linear algebra part of the QE suite > using a library called phiGEMM, some explicit computational kernels > (newd, addusdense, vloc_psi) and the 3D FFT for the single CPU/GPU > version. Both linear algebra (matrix multiplication) and the FFT > accelerated version make use of CUDA libraries. The porting is mainly > based on wrappers that permit the use of libraries for accelerators. The > distributed 3D FFT version is still in progress, since this porting > requires important changes of the current structure of the code and data > distribution. While running the parallel and distributed multi-GPUs > version it still uses the original 3D FFT implementations. > > The phiGEMM library is distributed as an independent open-source > external package together with the Quantum ESPRESSO suite. It aims to > perform matrix multiplication ([SDZ]GEMM) taking advantage of the > underlying BLAS kernel functions on both CPU and NVIDIA CUDA-based GPU, > mixing and overlapping computation between the host (CPU) and the > accelerator (GPU). Whatever code makes intensive use of GEMM it can > derive a significant advantage linking this library when running on a > CPU/GPU hybrid system. > > Even if the 3D FFT is accelerated only for a single CPU process (not > when using MPI), other parts are already enabled to take advantage of a > distributed parallel hybrid system. All of this allows PWscf to > potentially use distributed message-passing parallelization (MPI) plus > multi-threading (OpenMP) plus accelerators (NVIDIA GPUs) all together > and produce good performance enhancement using the latest version of > NVIDIA GPUs (high performance double precision is needed). This porting > activity is still in progress, especially the parallel 3D FFT component > that represents a bottleneck for large calculations. We have been > testing this beta release using some small/medium benchmarks used in the > DEISA official bench-suite and several GPU hardware (Tesla and Fermi > architectures). Special thanks goes to both E4 Computer Engineering and > CEA for providing access to hybrid GPU systems with differing > configurations to those available at ICHEC. > > We look forward with interest to receiving any suggestions for > improvement, feedback or request for collaboration by anyone who is > interested to try and validate PWscf CUDA version on different platforms > using different scientific cases.For additional information please > contact qe-gpu at ichec.ie or replay at this mail. We'll be shortly > available a dedicated forum q-e-gpgpu at qe-forge.org > . Please use this list for bug > report and any other issue related to the use of the PWscf GPU version. > > Although compilation of the GPU implementation is fairly > straight-forward, we kindly suggest that users carefully read the > README.GPU that is included. The intrinsic characteristics of hybrid > multi- and many-core systems require careful consideration to best > exploit the available computing power. > > Any and all suggestions are welcome and will be very much appreciated. > > Ivan Girotto & Filippo Spiga > > --- > > ICHEC GPU developer team > > The Tower - 7th floor > Trinity Technology& Enterprise Campus > Grand Canal Quay - Dublin 2 - Ireland > > +353-1-5241608 (ph) / +353-1-7645845 (fax) From vitruss at gmail.com Thu May 5 18:26:59 2011 From: vitruss at gmail.com (Vit) Date: Thu, 5 May 2011 23:26:59 +0700 Subject: [Pw_forum] Need help to install quantum espresso In-Reply-To: References: Message-ID: <201105052326.59676.vitruss@gmail.com> Dear Dr. Rahmar! I can help. If you can provide me with ssh access to your Ubuntu installation. Or you can specify the problem here (or in private email) to solve it. With best regards, Koroteev Victor "Dr. Mahmudur Rahman" Thursday 05 May 2011 > Dear Users, > I have installed Ubuntu linux and would like to install quantum espresso. > I followed the user guide but could not succeed. Anybody can help me? > > Regards, > > Mahmud > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From ivan.girotto at ichec.ie Thu May 5 19:01:39 2011 From: ivan.girotto at ichec.ie (Ivan Girotto) Date: Thu, 05 May 2011 18:01:39 +0100 Subject: [Pw_forum] First PWscf GPU-enabled beta-release In-Reply-To: <201105052324.54165.vitruss@gmail.com> References: <4DC2CC2F.2040608@ichec.ie> <201105052324.54165.vitruss@gmail.com> Message-ID: <4DC2D7F3.9010903@ichec.ie> Hi Victor, benchmark and results will be presented at next ISC2011 . We have an agreement with NVIDIA as they want show our work on PWscf code through a poster at their booth. Benchmarks need to be put together and analyzed before to be presented. Then with the close deadline we'll bring number of upgrade in these days. You can however download the code and test it your own updating frequently your source directory keeping it aligned with the SVN repository. I will personally send you some number on your personal address mail early next week in excel format since you looked particularly interested. Please, let's move the discussion about PWscf GPU version on the dedicated lists. We don't want spam pw_forum's member that are not interested at this topic. Best regards, Ivan Girotto On 05/05/2011 17:24, Vit wrote: > Dear Ivan, > Can you please proveide any benchmarks and comparison of Hybrid CPU/GPU vs > pure CPU computation? > With best regards, > Victor. > > Ivan Girotto > Thursday 05 May 2011 >> Dear QE users& developers, >> >> We are happy to announce that the first beta GPU-enabled release of >> Quantum ESPRESSO (QE) has been committed today in the official repository. >> >> You can download the new version of the code using the following command: >> >> $ svn checkout >> svn://scm.qe-forge.org/scmrepos/svn/q-e/branches/espresso-PRACE >> >> The Irish Centre for High-End Computing (ICHEC, www.ichec.ie >> ) has been mainly responsible for extending the QE >> suite to enhance calculations on NVIDIA GPUs. The porting activity has >> been supported within the PRACE 1st Implementation Phase project. It is >> currently carried out through the Sub-task "Accelerator", led by ICHEC, >> within the Work-Package "Programming Techniques for High-Performance >> Applications" in collaboration with CINECA. >> >> The porting activity is concerned mainly with the PWscf package. But >> ICHEC and the Irish QE user community are interested in exploring any >> other initiatives which come forward from QE users or developers >> interested in porting on GPGPU architecture any of the QE suite related >> codes. >> >> We have successfully accelerated the linear algebra part of the QE suite >> using a library called phiGEMM, some explicit computational kernels >> (newd, addusdense, vloc_psi) and the 3D FFT for the single CPU/GPU >> version. Both linear algebra (matrix multiplication) and the FFT >> accelerated version make use of CUDA libraries. The porting is mainly >> based on wrappers that permit the use of libraries for accelerators. The >> distributed 3D FFT version is still in progress, since this porting >> requires important changes of the current structure of the code and data >> distribution. While running the parallel and distributed multi-GPUs >> version it still uses the original 3D FFT implementations. >> >> The phiGEMM library is distributed as an independent open-source >> external package together with the Quantum ESPRESSO suite. It aims to >> perform matrix multiplication ([SDZ]GEMM) taking advantage of the >> underlying BLAS kernel functions on both CPU and NVIDIA CUDA-based GPU, >> mixing and overlapping computation between the host (CPU) and the >> accelerator (GPU). Whatever code makes intensive use of GEMM it can >> derive a significant advantage linking this library when running on a >> CPU/GPU hybrid system. >> >> Even if the 3D FFT is accelerated only for a single CPU process (not >> when using MPI), other parts are already enabled to take advantage of a >> distributed parallel hybrid system. All of this allows PWscf to >> potentially use distributed message-passing parallelization (MPI) plus >> multi-threading (OpenMP) plus accelerators (NVIDIA GPUs) all together >> and produce good performance enhancement using the latest version of >> NVIDIA GPUs (high performance double precision is needed). This porting >> activity is still in progress, especially the parallel 3D FFT component >> that represents a bottleneck for large calculations. We have been >> testing this beta release using some small/medium benchmarks used in the >> DEISA official bench-suite and several GPU hardware (Tesla and Fermi >> architectures). Special thanks goes to both E4 Computer Engineering and >> CEA for providing access to hybrid GPU systems with differing >> configurations to those available at ICHEC. >> >> We look forward with interest to receiving any suggestions for >> improvement, feedback or request for collaboration by anyone who is >> interested to try and validate PWscf CUDA version on different platforms >> using different scientific cases.For additional information please >> contact qe-gpu at ichec.ie or replay at this mail. We'll be shortly >> available a dedicated forum q-e-gpgpu at qe-forge.org >> . Please use this list for bug >> report and any other issue related to the use of the PWscf GPU version. >> >> Although compilation of the GPU implementation is fairly >> straight-forward, we kindly suggest that users carefully read the >> README.GPU that is included. The intrinsic characteristics of hybrid >> multi- and many-core systems require careful consideration to best >> exploit the available computing power. >> >> Any and all suggestions are welcome and will be very much appreciated. >> >> Ivan Girotto& Filippo Spiga >> >> --- >> >> ICHEC GPU developer team >> >> The Tower - 7th floor >> Trinity Technology& Enterprise Campus >> Grand Canal Quay - Dublin 2 - Ireland >> >> +353-1-5241608 (ph) / +353-1-7645845 (fax) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- 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/20110505/d6fa2904/attachment.htm From giannozz at democritos.it Thu May 5 19:55:18 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 5 May 2011 19:55:18 +0200 Subject: [Pw_forum] electron-phonon interaction in QE 4.3 In-Reply-To: References: <79B921C3-3073-4D96-BD25-7ADBC5D42964@democritos.it> Message-ID: <29F7F223-578A-4C50-8EB7-AD3D9784B7A0@democritos.it> On May 5, 2011, at 16:49 , Nandan Tandon wrote: > Could you please elaborate on the "better alternatives". see http://epw.org.uk/, and an alternative implementation: http://prb.aps.org/abstract/PRB/v82/i16/e165111 > I want to calculate electron phonon coupling in semiconductors. QE calculates electron-phonon coupling in metals only 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 nandan.tandon at gmail.com Thu May 5 20:02:41 2011 From: nandan.tandon at gmail.com (Nandan Tandon) Date: Thu, 5 May 2011 14:02:41 -0400 Subject: [Pw_forum] electron-phonon interaction in QE 4.3 In-Reply-To: <29F7F223-578A-4C50-8EB7-AD3D9784B7A0@democritos.it> References: <79B921C3-3073-4D96-BD25-7ADBC5D42964@democritos.it> <29F7F223-578A-4C50-8EB7-AD3D9784B7A0@democritos.it> Message-ID: Thank you. I will look at these. Nandan. On Thu, May 5, 2011 at 1:55 PM, Paolo Giannozzi wrote: > > On May 5, 2011, at 16:49 , Nandan Tandon wrote: > >> Could you please elaborate on the "better alternatives". > > see http://epw.org.uk/, and an alternative implementation: > http://prb.aps.org/abstract/PRB/v82/i16/e165111 > >> I want to calculate electron phonon coupling in semiconductors. > > QE calculates electron-phonon coupling in metals only > > 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 > -- *********************************************************************************************** Nandan Tandon Department of Physics, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA ************************************************************************************************* From giannozz at democritos.it Thu May 5 20:48:41 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 5 May 2011 20:48:41 +0200 Subject: [Pw_forum] using wf_collect only for a few bands In-Reply-To: <052e01cc09a7$d7ad50b0$8707f210$@gmail.com> References: <052e01cc09a7$d7ad50b0$8707f210$@gmail.com> Message-ID: <5B6DB19F-B0BE-4EAA-96A3-324E3CD5C042@democritos.it> On May 3, 2011, at 17:36 , J. D. Burton wrote: > Is there a way to use the ?wf_collect? to save wavefunctions ONLY > for a few bands at each k-point, say +/- 1eV around the Fermi energy? > nothing ready to use, I think 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 mahmud at science.upm.edu.my Fri May 6 04:37:17 2011 From: mahmud at science.upm.edu.my (Dr. Mahmudur Rahman) Date: Fri, 6 May 2011 10:37:17 +0800 Subject: [Pw_forum] Pw_forum Digest, Vol 47, Issue 22 Message-ID: <402f409594fcfd14f3d5eb8d7da3c8be.squirrel@science.upm.edu.my> Dear Victor, Thanks. When i type the command ./configure after i move to folder where quantum espresso is installed, i get the following message: /home/mahmud/Documents/quanesp/espresso-4.3a mahmud at mahmud-ubuntu:~/Documents/quanesp/espresso-4.3a$ ./configure bash: ./configure: Permission denied mahmud at mahmud-ubuntu:~/Documents/quanesp/espresso-4.3a$ sudo ./configure sudo: ./configure: command not found Need help! Mahmud > 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: First PWscf GPU-enabled beta-release (Vit) > 2. Re: Need help to install quantum espresso (Vit) > 3. Re: First PWscf GPU-enabled beta-release (Ivan Girotto) > 4. Re: electron-phonon interaction in QE 4.3 (Paolo Giannozzi) 5. Re: electron-phonon interaction in QE 4.3 (Nandan Tandon) > 6. Re: using wf_collect only for a few bands (Paolo Giannozzi) > ---------------------------------------------------------------------- Message: 1 > Date: Thu, 5 May 2011 23:24:53 +0700 > From: Vit > Subject: Re: [Pw_forum] First PWscf GPU-enabled beta-release > To: PWSCF Forum > Message-ID: <201105052324.54165.vitruss at gmail.com> > Content-Type: Text/Plain; charset="utf-8" > Dear Ivan, > Can you please proveide any benchmarks and comparison of Hybrid CPU/GPU vs > pure CPU computation? > With best regards, > Victor. > Ivan Girotto > Thursday 05 May 2011 >> Dear QE users & developers, >> We are happy to announce that the first beta GPU-enabled release of Quantum ESPRESSO (QE) has been committed today in the official >> repository. >> You can download the new version of the code using the following command: >> $ svn checkout >> svn://scm.qe-forge.org/scmrepos/svn/q-e/branches/espresso-PRACE The Irish Centre for High-End Computing (ICHEC, www.ichec.ie >> ) has been mainly responsible for extending the QE suite to enhance calculations on NVIDIA GPUs. The porting activity has been supported within the PRACE 1st Implementation Phase project. It is currently carried out through the Sub-task "Accelerator", led by ICHEC, within the Work-Package "Programming Techniques for High-Performance Applications" in collaboration with CINECA. >> The porting activity is concerned mainly with the PWscf package. But ICHEC and the Irish QE user community are interested in exploring any other initiatives which come forward from QE users or developers interested in porting on GPGPU architecture any of the QE suite related codes. >> We have successfully accelerated the linear algebra part of the QE suite >> using a library called phiGEMM, some explicit computational kernels (newd, addusdense, vloc_psi) and the 3D FFT for the single CPU/GPU version. Both linear algebra (matrix multiplication) and the FFT accelerated version make use of CUDA libraries. The porting is mainly based on wrappers that permit the use of libraries for accelerators. The >> distributed 3D FFT version is still in progress, since this porting requires important changes of the current structure of the code and data >> distribution. While running the parallel and distributed multi-GPUs version it still uses the original 3D FFT implementations. >> The phiGEMM library is distributed as an independent open-source external package together with the Quantum ESPRESSO suite. It aims to perform matrix multiplication ([SDZ]GEMM) taking advantage of the underlying BLAS kernel functions on both CPU and NVIDIA CUDA-based GPU, mixing and overlapping computation between the host (CPU) and the accelerator (GPU). Whatever code makes intensive use of GEMM it can derive a significant advantage linking this library when running on a CPU/GPU hybrid system. >> Even if the 3D FFT is accelerated only for a single CPU process (not when using MPI), other parts are already enabled to take advantage of a distributed parallel hybrid system. All of this allows PWscf to potentially use distributed message-passing parallelization (MPI) plus multi-threading (OpenMP) plus accelerators (NVIDIA GPUs) all together and produce good performance enhancement using the latest version of NVIDIA GPUs (high performance double precision is needed). This porting activity is still in progress, especially the parallel 3D FFT component that represents a bottleneck for large calculations. We have been testing this beta release using some small/medium benchmarks used in the >> DEISA official bench-suite and several GPU hardware (Tesla and Fermi architectures). Special thanks goes to both E4 Computer Engineering and CEA for providing access to hybrid GPU systems with differing >> configurations to those available at ICHEC. >> We look forward with interest to receiving any suggestions for >> improvement, feedback or request for collaboration by anyone who is interested to try and validate PWscf CUDA version on different platforms >> using different scientific cases.For additional information please contact qe-gpu at ichec.ie or replay at this mail. We'll be shortly available a dedicated forum q-e-gpgpu at qe-forge.org >> . Please use this list for bug report and any other issue related to the use of the PWscf GPU version. Although compilation of the GPU implementation is fairly >> straight-forward, we kindly suggest that users carefully read the README.GPU that is included. The intrinsic characteristics of hybrid multi- and many-core systems require careful consideration to best exploit the available computing power. >> Any and all suggestions are welcome and will be very much appreciated. Ivan Girotto & Filippo Spiga >> --- >> ICHEC GPU developer team >> The Tower - 7th floor >> Trinity Technology& Enterprise Campus >> Grand Canal Quay - Dublin 2 - Ireland >> +353-1-5241608 (ph) / +353-1-7645845 (fax) > ------------------------------ > Message: 2 > Date: Thu, 5 May 2011 23:26:59 +0700 > From: Vit > Subject: Re: [Pw_forum] Need help to install quantum espresso > To: PWSCF Forum > Message-ID: <201105052326.59676.vitruss at gmail.com> > Content-Type: Text/Plain; charset="utf-8" > Dear Dr. Rahmar! > I can help. If you can provide me with ssh access to your Ubuntu installation. > Or you can specify the problem here (or in private email) to solve it. With best regards, > Koroteev Victor > "Dr. Mahmudur Rahman" > Thursday 05 May 2011 >> Dear Users, >> I have installed Ubuntu linux and would like to install quantum espresso. >> I followed the user guide but could not succeed. Anybody can help me? Regards, >> Mahmud >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > ------------------------------ > Message: 3 > Date: Thu, 05 May 2011 18:01:39 +0100 > From: Ivan Girotto > Subject: Re: [Pw_forum] First PWscf GPU-enabled beta-release > To: PWSCF Forum > Message-ID: <4DC2D7F3.9010903 at ichec.ie> > Content-Type: text/plain; charset="iso-8859-1" > Hi Victor, > benchmark and results will be presented at next ISC2011 > . > We have an agreement with NVIDIA as they want show our work on PWscf code through a poster at their booth. > Benchmarks need to be put together and analyzed before to be presented. Then with the close deadline we'll bring number of upgrade in these days. > You can however download the code and test it your own updating > frequently your source directory keeping it aligned with the SVN repository. > I will personally send you some number on your personal address mail early next week in excel format since you looked particularly interested. > Please, let's move the discussion about PWscf GPU version on the dedicated lists. We don't want spam pw_forum's member that are not interested at this topic. > Best regards, > Ivan Girotto > On 05/05/2011 17:24, Vit wrote: >> Dear Ivan, >> Can you please proveide any benchmarks and comparison of Hybrid CPU/GPU vs >> pure CPU computation? >> With best regards, >> Victor. >> Ivan Girotto >> Thursday 05 May 2011 >>> Dear QE users& developers, >>> We are happy to announce that the first beta GPU-enabled release of Quantum ESPRESSO (QE) has been committed today in the official repository. >>> You can download the new version of the code using the following command: >>> $ svn checkout >>> svn://scm.qe-forge.org/scmrepos/svn/q-e/branches/espresso-PRACE The Irish Centre for High-End Computing (ICHEC, www.ichec.ie >>> ) has been mainly responsible for extending the QE >>> suite to enhance calculations on NVIDIA GPUs. The porting activity has been supported within the PRACE 1st Implementation Phase project. It is >>> currently carried out through the Sub-task "Accelerator", led by ICHEC, >>> within the Work-Package "Programming Techniques for High-Performance Applications" in collaboration with CINECA. >>> The porting activity is concerned mainly with the PWscf package. But ICHEC and the Irish QE user community are interested in exploring any other initiatives which come forward from QE users or developers interested in porting on GPGPU architecture any of the QE suite related >>> codes. >>> We have successfully accelerated the linear algebra part of the QE suite >>> using a library called phiGEMM, some explicit computational kernels (newd, addusdense, vloc_psi) and the 3D FFT for the single CPU/GPU version. Both linear algebra (matrix multiplication) and the FFT accelerated version make use of CUDA libraries. The porting is mainly based on wrappers that permit the use of libraries for accelerators. The >>> distributed 3D FFT version is still in progress, since this porting requires important changes of the current structure of the code and data >>> distribution. While running the parallel and distributed multi-GPUs version it still uses the original 3D FFT implementations. >>> The phiGEMM library is distributed as an independent open-source external package together with the Quantum ESPRESSO suite. It aims to perform matrix multiplication ([SDZ]GEMM) taking advantage of the underlying BLAS kernel functions on both CPU and NVIDIA CUDA-based GPU, >>> mixing and overlapping computation between the host (CPU) and the accelerator (GPU). Whatever code makes intensive use of GEMM it can derive a significant advantage linking this library when running on a CPU/GPU hybrid system. >>> Even if the 3D FFT is accelerated only for a single CPU process (not when using MPI), other parts are already enabled to take advantage of a >>> distributed parallel hybrid system. All of this allows PWscf to potentially use distributed message-passing parallelization (MPI) plus multi-threading (OpenMP) plus accelerators (NVIDIA GPUs) all together and produce good performance enhancement using the latest version of NVIDIA GPUs (high performance double precision is needed). This porting >>> activity is still in progress, especially the parallel 3D FFT component >>> that represents a bottleneck for large calculations. We have been testing this beta release using some small/medium benchmarks used in the >>> DEISA official bench-suite and several GPU hardware (Tesla and Fermi architectures). Special thanks goes to both E4 Computer Engineering and >>> CEA for providing access to hybrid GPU systems with differing >>> configurations to those available at ICHEC. >>> We look forward with interest to receiving any suggestions for improvement, feedback or request for collaboration by anyone who is interested to try and validate PWscf CUDA version on different platforms >>> using different scientific cases.For additional information please contact qe-gpu at ichec.ie or replay at this mail. We'll be shortly available a dedicated forum q-e-gpgpu at qe-forge.org >>> . Please use this list for bug report and any other issue related to the use of the PWscf GPU version. >>> Although compilation of the GPU implementation is fairly >>> straight-forward, we kindly suggest that users carefully read the README.GPU that is included. The intrinsic characteristics of hybrid multi- and many-core systems require careful consideration to best exploit the available computing power. >>> Any and all suggestions are welcome and will be very much appreciated. Ivan Girotto& Filippo Spiga >>> --- >>> ICHEC GPU developer team >>> The Tower - 7th floor >>> Trinity Technology& Enterprise Campus >>> Grand Canal Quay - Dublin 2 - Ireland >>> +353-1-5241608 (ph) / +353-1-7645845 (fax) >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > -- > 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/20110505/d6fa2904/attachment-0001.htm ------------------------------ > Message: 4 > Date: Thu, 5 May 2011 19:55:18 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] electron-phonon interaction in QE 4.3 > To: PWSCF Forum > Message-ID: <29F7F223-578A-4C50-8EB7-AD3D9784B7A0 at democritos.it> Content-Type: text/plain; charset=US-ASCII; format=flowed > On May 5, 2011, at 16:49 , Nandan Tandon wrote: >> Could you please elaborate on the "better alternatives". > see http://epw.org.uk/, and an alternative implementation: > http://prb.aps.org/abstract/PRB/v82/i16/e165111 >> I want to calculate electron phonon coupling in semiconductors. > QE calculates electron-phonon coupling in metals only > 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: 5 > Date: Thu, 5 May 2011 14:02:41 -0400 > From: Nandan Tandon > Subject: Re: [Pw_forum] electron-phonon interaction in QE 4.3 > To: PWSCF Forum > Message-ID: Content-Type: text/plain; charset=ISO-8859-1 > Thank you. I will look at these. > Nandan. > On Thu, May 5, 2011 at 1:55 PM, Paolo Giannozzi wrote: >> On May 5, 2011, at 16:49 , Nandan Tandon wrote: >>> Could you please elaborate on the "better alternatives". >> see http://epw.org.uk/, and an alternative implementation: >> http://prb.aps.org/abstract/PRB/v82/i16/e165111 >>> I want to calculate electron phonon coupling in semiconductors. >> QE calculates electron-phonon coupling in metals only >> 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 > -- > *********************************************************************************************** Nandan Tandon > Department of Physics, > Worcester Polytechnic Institute, > 100 Institute Road, > Worcester, MA > ************************************************************************************************* ------------------------------ > Message: 6 > Date: Thu, 5 May 2011 20:48:41 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] using wf_collect only for a few bands > To: PWSCF Forum > Message-ID: <5B6DB19F-B0BE-4EAA-96A3-324E3CD5C042 at democritos.it> Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; > format=flowed > On May 3, 2011, at 17:36 , J. D. Burton wrote: >> Is there a way to use the ?wf_collect? to save wavefunctions ONLY for a few bands at each k-point, say +/- 1eV around the Fermi energy? > nothing ready to use, I think > 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 > End of Pw_forum Digest, Vol 47, Issue 22 > **************************************** -- Dr. Mahmudur Rahman Senior Lecturer Department of Physics Faculty of Science University Putra Malaysia 43400 UPM Serdang Selangor MALAYSIA Tel:+60-3-8946-6683 Mobile Phone:+60-173369047 Fax:+60-3-8945-4454 Email:mahmud at science.upm.edu.my From dalcorso at sissa.it Fri May 6 08:58:16 2011 From: dalcorso at sissa.it (Andrea Dal Corso) Date: Fri, 06 May 2011 08:58:16 +0200 Subject: [Pw_forum] electron-phonon interaction in QE 4.3 In-Reply-To: References: Message-ID: <1304665096.18540.1.camel@ulisse.cm.sissa.it> Thank you for reporting this. There is a problem when the electron phonon is compiled in serial (without the flag __PARA). I commited the fix on the cvs version. You can take the routine PH/elphon.f90 and recompile. Andrea On Wed, 2011-05-04 at 22:57 -0500, Jeffrey M. McMahon wrote: > Dear All, > > > I am having an issue calculating the electron-phonon interaction in QE > 4.3. I do not know if this is due to a bug or my build of QE (most > likely the latter). After compiling, when I test the program example > 07 stops with an error in al.elph.out: > > electron-phonon interaction ... > > %%%%%% > from efermig : error # 1 > internal error, cannot bracket Ef > %%%%%% > > It is not just example 07, but any electron-phonon calculation. All > other tests and examples performed fine during testing. I tried > compiling QE with Intel compilers (version 10.1, I believe) as well as > GNU compilers, first version 4.3 and now 4.5-19.1, but the problem > occurs in all cases. I also tried using BLAS and LAPACK as provided by > the Intel MKL as well as the internal versions, and also FFTW3 and > whatever is provided internally (and various combinations of the > aforementioned). I did not experience any issues with QE 4.2.1 when > compiled the exact same way. > > Any suggestions would be appreciated. Thanks in advance. > > Jeffrey M. McMahon > > > The Institute for Condensed Matter Theory > Department of Physics > University of Illinois at Urbana-Champaign > Urbana, IL 61801-3080 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Andrea Dal Corso Tel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it From giannozz at democritos.it Fri May 6 09:14:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 06 May 2011 09:14:07 +0200 Subject: [Pw_forum] electron-phonon interaction in QE 4.3 In-Reply-To: <1304665096.18540.1.camel@ulisse.cm.sissa.it> References: <1304665096.18540.1.camel@ulisse.cm.sissa.it> Message-ID: <1304666047.19206.2.camel@fe12lx.fisica.uniud.it> On Fri, 2011-05-06 at 08:58 +0200, Andrea Dal Corso wrote: > I commited the fix on the cvs version. actually, svn: http://qe-forge.org/scm/browser.php?group_id=10, rev. 7754. (the link on the QE web site still points to the old repository) P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From agkvashnin at gmail.com Fri May 6 11:20:36 2011 From: agkvashnin at gmail.com (Alexander G. Kvashnin) Date: Fri, 6 May 2011 13:20:36 +0400 Subject: [Pw_forum] The question about difference between diamond and graphite Message-ID: Dear PWSCF community In my study I got a problem which I can't solve by myself, unfortunately. I hope you can give me some tips where I made a mistake. I have to to investigate the energy difference between graphite and diamond, but I can't get trusted result.First of all, I used LDA PP (PZ), I tested it by subsequently increasing of energy cutoff (from 30 Ry to 120 Ry) as well as increasing of k-points mesh (4x4x1 for graphite, 4x4x4 for diamond; 6x6x2 for graphite, 6x6x6 for diamond; 8x8x3 for graphite, 8x8x8 for diamond; 10x10x4 for graphite, 10x10x10 for diamond). I got the difference between energies of diamond and graphite and tried to understand it trend (please, see attached figure). As you can see from the figure difference between energy diamond and graphite is almost zero so I can't say with confidence what structure is more favorable. This result different from other theoretical and experimental studies, therefore it seems that I did something wrong... My result: ~ 0.001?0.001 eV/atom _______________________________________________ | Energy difference (eV/atom) | Method | Reference | | 0.03 |Experiment | PRB29_6996 | | 0.01 | LDA-PP | PRB29_6996 | | 0.04 | LDA-PP | PRB54_14994| ----------------------------------------------------------------------------------- Input files for diamond and graphite are attached to the letter. -- Sincerely yours *Alexander G. Kvashnin* -------------------------------------------------------------------------------------------------------------------------------- First year of master degree study Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia ================================================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/a1b4ce06/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: input_diamond.opt Type: application/octet-stream Size: 1047 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110506/a1b4ce06/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: input_graphite.opt Type: application/octet-stream Size: 1113 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110506/a1b4ce06/attachment-0001.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: Energy_difference.GIF Type: image/gif Size: 10172 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110506/a1b4ce06/attachment.gif From mashiatalaaii at gmail.com Fri May 6 12:22:59 2011 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Fri, 6 May 2011 06:22:59 -0400 Subject: [Pw_forum] the unit of DOS Message-ID: Hello, what is the unit of DOS? Should I divide the DOS that QE provides to the volume of slab? Thank you Alaaii -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/3d3c98c7/attachment.htm From giovanni.cantele at spin.cnr.it Fri May 6 12:27:31 2011 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Fri, 6 May 2011 12:27:31 +0200 Subject: [Pw_forum] the unit of DOS In-Reply-To: References: Message-ID: On May 6, 2011, at 12:22 PM, mashiat alaaii wrote: > Hello, > what is the unit of DOS? > Should I divide the DOS that QE provides to the volume of slab? > Thank you > Alaaii > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum 1/eV (the DOS integral up to the Fermi energy gives the number of electrons) Giovanni -- **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it From rameshchitumalla at gmail.com Fri May 6 12:35:06 2011 From: rameshchitumalla at gmail.com (Ramesh Kumar) Date: Fri, 6 May 2011 16:05:06 +0530 Subject: [Pw_forum] the unit of DOS In-Reply-To: References: Message-ID: Dear Mashiat alaaii, DOS is a number and I feel it doesn't have any unit. On Fri, May 6, 2011 at 3:52 PM, mashiat alaaii wrote: > Hello, > what is the unit of DOS? > Should I divide the DOS that QE provides to the volume of slab? > Thank you > Alaaii > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -* * *CH. Ramesh Kumar Research Scholar, Computational Chemistry Lab, Indian Institute of Chemical Technology(IICT),* *Tarnaka, ** Hyderabad. * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/f232c74f/attachment-0001.htm From songsong19840614 at gmail.com Fri May 6 12:50:16 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Fri, 6 May 2011 18:50:16 +0800 Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? Message-ID: My pwscf is used in calculating Si phonon dispersion.The trend of picture in most special Symmetry is right.But the only K-X is wrong.I use Xcrysden to get K-point. I found most paper is dash line in 'K' point.So what is mean? Please anyone could tell me! Thanks! The attachment is my picture and reference paper. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/406d1e3a/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Sipwscf.jpg Type: image/jpeg Size: 80454 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110506/406d1e3a/attachment-0002.jpg -------------- next part -------------- A non-text attachment was scrubbed... Name: Sipaper.jpg Type: image/jpeg Size: 33282 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110506/406d1e3a/attachment-0003.jpg From rameshchitumalla at gmail.com Fri May 6 12:59:38 2011 From: rameshchitumalla at gmail.com (Ramesh Kumar) Date: Fri, 6 May 2011 16:29:38 +0530 Subject: [Pw_forum] the unit of DOS In-Reply-To: References: Message-ID: Dear Mashiat alaaii, Sorry for previous posting. The unit is 1/Energy.Volume i.e., Energy-1Volume-1 On Fri, May 6, 2011 at 4:05 PM, Ramesh Kumar wrote: > Dear Mashiat alaaii, > > DOS is a number and I feel it doesn't have any unit. > > On Fri, May 6, 2011 at 3:52 PM, mashiat alaaii wrote: > >> Hello, >> what is the unit of DOS? >> Should I divide the DOS that QE provides to the volume of slab? >> Thank you >> Alaaii >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -* > > * > *CH. Ramesh Kumar > Research Scholar, > Computational Chemistry Lab, > Indian Institute of Chemical Technology(IICT),* > *Tarnaka, ** > Hyderabad. > * > > -- *With Best Regards: * *CH. Ramesh Kumar Senior Research Fellow, Computational Chemistry Lab, Indian Institute of Chemical Technology(IICT),* *Tarnaka, ** Hyderabad. * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/965b9363/attachment.htm From giovanni.cantele at spin.cnr.it Fri May 6 13:05:55 2011 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Fri, 6 May 2011 13:05:55 +0200 Subject: [Pw_forum] the unit of DOS In-Reply-To: References: Message-ID: <63CBE223-64C6-4067-92A4-AC14EFCAE5FF@spin.cnr.it> From Doc/INPUT_DOS.txt :::: Notes ::: Output The total DOS (states/eV plotted vs E in eV) is written to file "fildos" So there is no volume in the units, I guess!!! Giovanni On May 6, 2011, at 12:59 PM, Ramesh Kumar wrote: > Dear Mashiat alaaii, > > > Sorry for previous posting. > > The unit is 1/Energy.Volume i.e., Energy?1Volume?1 > > On Fri, May 6, 2011 at 4:05 PM, Ramesh Kumar wrote: > Dear Mashiat alaaii, > > DOS is a number and I feel it doesn't have any unit. > > On Fri, May 6, 2011 at 3:52 PM, mashiat alaaii wrote: > Hello, > what is the unit of DOS? > Should I divide the DOS that QE provides to the volume of slab? > Thank you > Alaaii > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > - > > CH. Ramesh Kumar > Research Scholar, > Computational Chemistry Lab, > Indian Institute of Chemical Technology(IICT), > Tarnaka, Hyderabad. > > > > > -- > With Best Regards: > > CH. Ramesh Kumar > Senior Research Fellow, > Computational Chemistry Lab, > Indian Institute of Chemical Technology(IICT), > Tarnaka, Hyderabad. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/38afd983/attachment.htm From eyvaz_isaev at yahoo.com Fri May 6 13:51:26 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 6 May 2011 04:51:26 -0700 (PDT) Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? In-Reply-To: References: Message-ID: <345129.85014.qm@web65710.mail.ac4.yahoo.com> Hi, First of all I would recommend the use of PlotPhon utility to plot phonon dispersion relations. For this one you have to have calculated interatomic force constants matrix (*.fc) file. Regarding your particular question: you should choose K(0.75,0.75,0), then from the K point go to the X point (1, 1, 0) which is equivalent to the X(1,0,0) point. Then from the X(1,0,0) to the Gamma (0,0,0) point. Dashed line just means that we can continue in this direction to match phonons at the X point (i.e. it is an intermediate point from the Gamma to the X point) . Please also provide your affiliation. Bests, Eyvaz ------------------------------------------------------------------- Prof. Eyvaz Isaev, Department of Physics, Chemistry, and Biology (IFM), Linkoping University, Sweden Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at yahoo.com ________________________________ From: lucking-pine To: Pw_forum at pwscf.org Sent: Fri, May 6, 2011 2:50:16 PM Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? My pwscf is used in calculating Si phonon dispersion.The trend of picture in most special Symmetry is right.But the only K-X is wrong.I use Xcrysden to get K-point. I found most paper is dash line in 'K' point.So what is mean? Please anyone could tell me! Thanks! The attachment is my picture and reference paper. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/81b8148d/attachment.htm From giannozz at democritos.it Fri May 6 13:57:49 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 06 May 2011 13:57:49 +0200 Subject: [Pw_forum] Pw_forum Digest, Vol 47, Issue 22 In-Reply-To: <402f409594fcfd14f3d5eb8d7da3c8be.squirrel@science.upm.edu.my> References: <402f409594fcfd14f3d5eb8d7da3c8be.squirrel@science.upm.edu.my> Message-ID: <1304683069.19206.40.camel@fe12lx.fisica.uniud.it> On Fri, 2011-05-06 at 10:37 +0800, Dr. Mahmudur Rahman wrote: > Need help! you need to learn some basics of Unix. Please do not reply to a digest: see http://www.quantum-espresso.org/wiki/index.php/Pw_users P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From iurii.timrov at polytechnique.edu Fri May 6 14:12:23 2011 From: iurii.timrov at polytechnique.edu (Iurii TIMROV) Date: Fri, 6 May 2011 14:12:23 +0200 Subject: [Pw_forum] the unit of DOS In-Reply-To: <63CBE223-64C6-4067-92A4-AC14EFCAE5FF@spin.cnr.it> References: <63CBE223-64C6-4067-92A4-AC14EFCAE5FF@spin.cnr.it> Message-ID: <581015e49e39f8fc7ce8efee034b9fd3.squirrel@theory.polytechnique.fr> Dear All, I would also like to clarify for myself the units of DOS. By definition, the DOS reads: DOS(E) = \sum_n \int delta(E - E_n(k_x,k_y,k_z)) dk_x dk_y dk_z / (4 \pi^3), where \delta is the Dirac delta function, k_x,k_y,k_z are the 3 components of the wave vector, n is the band index, E is the energy (Ref. Ashcroft and Mermin). According to this equation the unit of DOS is 1/(Energy*length^3). Is the following statement correct?: "The Density of States of a system is the number of states per interval of energy -in the unit cell volume-". Could somebody comment on this? Is there a mistake in the above thinking? Thanks! Best, Iurii Iurii TIMROV Doctorant (PhD student) Laboratoire des Solides Irradies Ecole Polytechnique F-91128 Palaiseau +33 1 69 33 45 08 timrov at theory.polytechnique.fr > From Doc/INPUT_DOS.txt > > :::: Notes > > > ::: Output > > The total DOS (states/eV plotted vs E in eV) is written to file > "fildos" > > > So there is no volume in the units, I guess!!! > > Giovanni > > > > On May 6, 2011, at 12:59 PM, Ramesh Kumar wrote: > >> Dear Mashiat alaaii, >> >> >> Sorry for previous posting. >> >> The unit is 1/Energy.Volume i.e., Energy???1Volume???1 >> >> On Fri, May 6, 2011 at 4:05 PM, Ramesh Kumar >> wrote: >> Dear Mashiat alaaii, >> >> DOS is a number and I feel it doesn't have any unit. >> >> On Fri, May 6, 2011 at 3:52 PM, mashiat alaaii >> wrote: >> Hello, >> what is the unit of DOS? >> Should I divide the DOS that QE provides to the volume of slab? >> Thank you >> Alaaii >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> - >> >> CH. Ramesh Kumar >> Research Scholar, >> Computational Chemistry Lab, >> Indian Institute of Chemical Technology(IICT), >> Tarnaka, Hyderabad. >> >> >> >> >> -- >> With Best Regards: >> >> CH. Ramesh Kumar >> Senior Research Fellow, >> Computational Chemistry Lab, >> Indian Institute of Chemical Technology(IICT), >> Tarnaka, Hyderabad. >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > > **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it > > Giovanni Cantele, PhD > CNR-SPIN and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario M. S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 - Fax: +39 081 676346 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.na.infn.it/~cantele > http://www.nanomat.unina.it > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > Iurii TIMROV Doctorant (PhD student) Laboratoire des Solides Irradies Ecole Polytechnique F-91128 Palaiseau +33 1 69 33 45 08 timrov at theory.polytechnique.fr From tfcao at theory.issp.ac.cn Fri May 6 14:35:14 2011 From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=) Date: Fri, 06 May 2011 20:35:14 +0800 Subject: [Pw_forum] =?utf-8?q?STM__images_____=27tfcao=27?= Message-ID: <20110506123514.1306.qmail@ms.hfcas.ac.cn> Dear QE users: I do the calculation of graphene with three Hydrogens absorbed on it .And I want to ask if it is possible to give the STM images of the three Hydrogens . If any one has done the similar things .Can you give me an example . Thank you . -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/2b98157f/attachment.htm From giovanni.cantele at spin.cnr.it Fri May 6 15:19:31 2011 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Fri, 6 May 2011 15:19:31 +0200 Subject: [Pw_forum] the unit of DOS In-Reply-To: <581015e49e39f8fc7ce8efee034b9fd3.squirrel@theory.polytechnique.fr> References: <63CBE223-64C6-4067-92A4-AC14EFCAE5FF@spin.cnr.it> <581015e49e39f8fc7ce8efee034b9fd3.squirrel@theory.polytechnique.fr> Message-ID: <2D6806F2-6254-4D4D-A508-061A44952C45@spin.cnr.it> On May 6, 2011, at 2:12 PM, Iurii TIMROV wrote: > I would also like to clarify for myself the units of DOS. By definition, > the DOS reads: > > DOS(E) = \sum_n \int delta(E - E_n(k_x,k_y,k_z)) dk_x dk_y dk_z / (4 \pi^3), > > where \delta is the Dirac delta function, k_x,k_y,k_z are the 3 components > of the wave vector, n is the band index, E is the energy (Ref. Ashcroft > and Mermin). According to this equation the unit of DOS is > 1/(Energy*length^3). > > Is the following statement correct?: > "The Density of States of a system is the number of states per interval of > energy -in the unit cell volume-". > > Could somebody comment on this? Is there a mistake in the above thinking? I would say that the correct statement is (of course it is just a matter of definition!): The Density of States per unit volume of a system is the number of states per interval of energy -in the unit cell volume- There is just a volume factor difference between the two definitions. Usually: DOS(E) dE = number of energy levels in the energy range from E and E+dE and according to this definition \int_E0^E1 DOS(E) dE = total number of states between E0 and E1 (adimensional). This is what the dos.x executable included in Quantum-ESPRESSO computes. According to the above definition: DOS(E) = \sum_n \int delta(E - E_n(k_x,k_y,k_z)) dk_x dk_y dk_z *V / (4 \pi^3) If you carefully read the chapter 8 of Ashcroft-Mermin, it says: "....one can define a density of levels per unit volume (or "density of levels" for short)....." and Eq. (8.57) (provided we're looking to the same edition!) is exactly the definition you gave (so, "per-unit-of-volume" definition). Giovanni -- **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it From nkxirainbow at gmail.com Fri May 6 15:27:48 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 6 May 2011 21:27:48 +0800 Subject: [Pw_forum] the unit of DOS In-Reply-To: References: Message-ID: I am sure the unit of DOS is states/eV/(unit cell) The unit of pdos is * states/eV/atom* On Fri, May 6, 2011 at 6:22 PM, mashiat alaaii wrote: > Hello, > what is the unit of DOS? > Should I divide the DOS that QE provides to the volume of slab? > Thank you > Alaaii > > _______________________________________________ > 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/20110506/9ed83b03/attachment.htm From iurii.timrov at polytechnique.edu Fri May 6 15:39:07 2011 From: iurii.timrov at polytechnique.edu (Iurii TIMROV) Date: Fri, 6 May 2011 15:39:07 +0200 Subject: [Pw_forum] the unit of DOS In-Reply-To: <2D6806F2-6254-4D4D-A508-061A44952C45@spin.cnr.it> References: <63CBE223-64C6-4067-92A4-AC14EFCAE5FF@spin.cnr.it> <581015e49e39f8fc7ce8efee034b9fd3.squirrel@theory.polytechnique.fr> <2D6806F2-6254-4D4D-A508-061A44952C45@spin.cnr.it> Message-ID: Thank you, Giovanni! Best regards, Iurii Iurii TIMROV Doctorant (PhD student) Laboratoire des Solides Irradies Ecole Polytechnique F-91128 Palaiseau +33 1 69 33 45 08 timrov at theory.polytechnique.fr > > On May 6, 2011, at 2:12 PM, Iurii TIMROV wrote: > >> I would also like to clarify for myself the units of DOS. By definition, >> the DOS reads: >> >> DOS(E) = \sum_n \int delta(E - E_n(k_x,k_y,k_z)) dk_x dk_y dk_z / (4 >> \pi^3), >> >> where \delta is the Dirac delta function, k_x,k_y,k_z are the 3 >> components >> of the wave vector, n is the band index, E is the energy (Ref. Ashcroft >> and Mermin). According to this equation the unit of DOS is >> 1/(Energy*length^3). >> >> Is the following statement correct?: >> "The Density of States of a system is the number of states per interval >> of >> energy -in the unit cell volume-". >> >> Could somebody comment on this? Is there a mistake in the above >> thinking? > > I would say that the correct statement is (of course it is just a matter > of definition!): > > The Density of States per unit volume of a system is the number of states > per interval of > energy -in the unit cell volume- > > > There is just a volume factor difference between the two definitions. > > Usually: > DOS(E) dE = number of energy levels in the energy range from E and E+dE > > and according to this definition > \int_E0^E1 DOS(E) dE = total number of states between E0 and E1 > (adimensional). > > This is what the dos.x executable included in Quantum-ESPRESSO computes. > > According to the above definition: > > DOS(E) = \sum_n \int delta(E - E_n(k_x,k_y,k_z)) dk_x dk_y dk_z *V / (4 > \pi^3) > > If you carefully read the chapter 8 of Ashcroft-Mermin, it says: > "....one can define a density of levels per unit volume (or "density of > levels" for short)....." > and Eq. (8.57) (provided we're looking to the same edition!) is exactly > the definition you gave > (so, "per-unit-of-volume" definition). > > Giovanni > > -- > > **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it > > Giovanni Cantele, PhD > CNR-SPIN and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario M. S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 - Fax: +39 081 676346 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.na.infn.it/~cantele > http://www.nanomat.unina.it > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From parishok at gmail.com Fri May 6 21:49:02 2011 From: parishok at gmail.com (pari shok) Date: Fri, 6 May 2011 15:49:02 -0400 Subject: [Pw_forum] making a supercell Message-ID: Hello, I am using QE (obviously) and xcrysden. I am making the supercells just by: - making the unit cell - using xcrysden to modify the small cell by doubling it in different directions - finding the atom positions one by one - making supecell by entering those atomic positions into a new lattice to give exactly the thing that I made with xcrysden. I was wondering whether there is a simple way to double the unit cell in different directions. Thank you P Shok -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/4a25c557/attachment.htm From lars.matthes at uni-jena.de Fri May 6 22:43:09 2011 From: lars.matthes at uni-jena.de (Lars Matthes) Date: Fri, 6 May 2011 22:43:09 +0200 Subject: [Pw_forum] making a supercell In-Reply-To: References: Message-ID: Hello, with xcrysden you can also save the supercell as .xsf structure (File > Save XSF structure). Within the saved file you can find the positions of all atoms (I found them below the line 'BRILLOUIN-ZONE-CONVCELL_END'). The first column includes the number of the element and, therefore, needs some modification before you can use it in QE. But much easier than what you did up to now, isn't it?! Ciao Lars 2011/5/6 pari shok > Hello, > I am using QE (obviously) and xcrysden. > I am making the supercells just by: > > - making the unit cell > - using xcrysden to modify the small cell by doubling it in different > directions > - finding the atom positions one by one > - making supecell by entering those atomic positions into a new lattice > to give exactly the thing that I made with xcrysden. > > I was wondering whether there is a simple way to double the unit cell in > different directions. > Thank you > P Shok > > _______________________________________________ > 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 Universit? degli Studi di Roma Tor Vergata Dipartimento di Fisica Teorie di Fisica della materia via della Ricerca Scientifica 1 00133 Rome Italy -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110506/6ca08657/attachment.htm From jenaparadies at googlemail.com Fri May 6 23:25:17 2011 From: jenaparadies at googlemail.com (Lars Matthes) Date: Fri, 6 May 2011 23:25:17 +0200 Subject: [Pw_forum] making a supercell In-Reply-To: References: Message-ID: Hello, with xcrysden you can also save the supercell as .xsf structure (File > Save XSF structure). Within the saved file you can find the positions of all atoms (I found them below the line 'BRILLOUIN-ZONE-CONVCELL_END'). The first column includes the number of the element and, therefore, needs some modification before you can use it in QE. But much easier than what you did up to now, isn't it?! Ciao Lars 2011/5/6 pari shok > Hello, > I am using QE (obviously) and xcrysden. > I am making the supercells just by: > > - making the unit cell > - using xcrysden to modify the small cell by doubling it in different > directions > - finding the atom positions one by one > - making supecell by entering those atomic positions into a new lattice > to give exactly the thing that I made with xcrysden. > > I was wondering whether there is a simple way to double the unit cell in > different directions. > Thank you > P Shok > > _______________________________________________ > 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/20110506/925ae513/attachment-0001.htm From padmaja_patnaik at yahoo.co.uk Sat May 7 20:45:42 2011 From: padmaja_patnaik at yahoo.co.uk (Padmaja Patnaik) Date: Sat, 7 May 2011 19:45:42 +0100 (BST) Subject: [Pw_forum] Doubt in band plot Message-ID: <812918.68921.qm@web28516.mail.ukl.yahoo.com> Hi All I am plotting band structure for cubic SiC. Got good shape when compared. SiC has an indirect band gap. Next I tried to plot the band structure of cubic SIC with a supercell. I have expanded the lattice constant by twice in all direction and generated supercell with Phonon code. Now the band plot of this supercell shows direct band gap. how is this possible? It is expected that even if the supercell should produce the same band plot. Please suggets. 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/20110507/7ec458d2/attachment.htm From w2agz at w2agz.com Sat May 7 20:30:40 2011 From: w2agz at w2agz.com (W2AGZ) Date: Sat, 7 May 2011 11:30:40 -0700 Subject: [Pw_forum] Problem with pseudopotential Message-ID: <014101cc0ce4$df65cf90$9e316eb0$@w2agz.com> Just a wild suggestion...try the PP (attached) I constructed to better model the valence of Cu in HTSC layered copper oxide peroskites...and also change the orbital configuration of Cu in tabd.f90 to occ_loc = 9.d0. Like I said...a wild suggestion. -Paul -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Nicola Marzari Sent: Wednesday, March 30, 2011 2:29 PM To: PWSCF Forum Subject: Re: [Pw_forum] Problem with pseudopotential Dear Izaak, it seems that in Cu.pbe-d-rrkjus.UPF the average electrostatic potential inside the slab (i.e. the average over one layer of the planar average) would be higher than the vacuum level, so on electrostatic considerations a test charge would want to run away. So, I'm very baffled. Any one else has some suggestion? The two input files do look identical. The fermi energy that you print is the one given by the slab calculation (not really a good choice, unless you have a thick slab) or is given by calculating in bulk cu the position of the fermi energy with respect to the layer-average of the planar avarage, and then using that info in the slab calculation to position the fermi energy of the bulk, and obtain the work function? Last - a 14% is the last of the worries - LDA and GGA seem to be all over the place (have a look at the paper I had cited). nicola On 3/30/11 4:53 PM, Izaak Williamson wrote: > First of all, thank you so much for your replies. > > One more question: in the pbedrrkjus plot, there are maxima at the > location of each atomic layer whereas the pbevanak plot has minima. > What would cause this? Is it a problem? > > > Both the calculations were done using exactly the same parameters but > different pseudopotentials. I get the following values for workfunctions. > Cu.pbe-d-rrkjus.UPF ---> 3.956405463 eV Cu.pbe-n-van_ak.UPF ---> > 4.042282570 eV Experimental value ---> 4.59 eV > > I know that DFT-GGA calculations can underestimate the workfunctions > of metal surfaces, but are these acceptable values (almost a 14% error)? > > Thank you again for all your help. > > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University -- ---------------------------------------------------------------------- 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 _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- A non-text attachment was scrubbed... Name: Cu.pz-3d9_4s2-rrkjus.UPF Type: application/octet-stream Size: 180660 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110507/40007286/attachment-0001.obj From w2agz at w2agz.com Sat May 7 20:29:42 2011 From: w2agz at w2agz.com (W2AGZ) Date: Sat, 7 May 2011 11:29:42 -0700 Subject: [Pw_forum] electron-phonon interaction in QE 4.3 Message-ID: <013f01cc0ce4$bd233620$3769a260$@w2agz.com> Paolo, can the QE 4.3 e-p suite handle "spin" yet, e.g., LDA+U? -Paul -----Original Message----- From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Thursday, May 05, 2011 10:55 AM To: PWSCF Forum Subject: Re: [Pw_forum] electron-phonon interaction in QE 4.3 On May 5, 2011, at 16:49 , Nandan Tandon wrote: > Could you please elaborate on the "better alternatives". see http://epw.org.uk/, and an alternative implementation: http://prb.aps.org/abstract/PRB/v82/i16/e165111 > I want to calculate electron phonon coupling in semiconductors. QE calculates electron-phonon coupling in metals only 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 nkxirainbow at gmail.com Sun May 8 04:25:54 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Sun, 8 May 2011 10:25:54 +0800 Subject: [Pw_forum] Doubt in band plot In-Reply-To: <812918.68921.qm@web28516.mail.ukl.yahoo.com> References: <812918.68921.qm@web28516.mail.ukl.yahoo.com> Message-ID: Dear Padmaja Patnaik: I am plotting band structure for cubic SiC. Got good shape when compared. > SiC has an indirect band gap. Next I tried to plot the band structure of > cubic SIC with a supercell. I have expanded the lattice constant by twice in > all direction and generated supercell with Phonon code. Now the band plot of > this supercell shows direct band gap. how is this possible? It is expected > that even if the supercell should produce the same band plot. When you expand the lattice constant, the Brillouin Zone will be folded. Therefore, the indirect gap may turn into direct gap. If you plot the dos, the primitive cell and supercell will give the same shape, but the bands are different. Please suggets. > > 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 > > -- ____________________________________ 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/20110508/41c2a5e3/attachment.htm From mayankaditya at gmail.com Sun May 8 15:07:11 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Sun, 8 May 2011 18:37:11 +0530 Subject: [Pw_forum] Phonon frequency of Body centred cubic strucure Message-ID: Dear PWSCF User's, I am doing phonon calculation of a material having 40 atoms in the unit cell and BCC structure. The phonon frequncy which should be degenerate are not coming out exactly degenerate, like transverse acoustic mode along 100 direction having frequency 0.44579 and 0.54478 Thz while they should have equal frequency. what should be the error which I made kindly suggest me. thanks in Advance. Mayank gupta BARC From merlin.meheut at lmtg.obs-mip.fr Sun May 8 16:11:36 2011 From: merlin.meheut at lmtg.obs-mip.fr (Merlin Meheut) Date: Sun, 08 May 2011 16:11:36 +0200 Subject: [Pw_forum] Phonon frequency of Body centred cubic strucure In-Reply-To: References: Message-ID: <4DC6A498.8060403@lmtg.obs-mip.fr> Dear Mayank, My opinion is that your problem comes from a symetry problem with the FFT grid: the FFT grid your system has chosen may not be compatible with the symetry of your crystal (which is apparently very symetric). If this is the case, yous hould have warnings about symetry operations not taken into account in the preamble of your scf output. The solution is to define by hand your fft grid using the nr1, nr2, nr3 parameters (choose them larger than those chosen by the program but with different dividers so as to comply with the symetry of your system). Another solution usually proposed is to increase the ecut_rho, but I prefer the first one. Hope this helps, Merlin mayank gupta a ?crit : > Dear PWSCF User's, > > I am doing phonon calculation of a material having 40 atoms in the > unit cell and BCC structure. The phonon frequncy which should be > degenerate are not coming out exactly degenerate, like transverse > acoustic mode along 100 direction having frequency 0.44579 and > 0.54478 Thz while they should have equal frequency. what should be the > error which I made kindly suggest me. thanks in Advance. > > > > > > Mayank gupta > BARC > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From swapnil.chandratre at gmail.com Mon May 9 05:36:30 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Sun, 8 May 2011 22:36:30 -0500 Subject: [Pw_forum] Relaxed Graphene Nanoribbon Message-ID: Hi, I have prepared an input file for a porous graphene nanoribbon, can anyone please comment if there are any errors with the file. &control calculation = 'relax' restart_mode = 'from_scratch' pseudo_dir = '/home/s/schandratre/Espresso/pseudo' outdir = '/home/s/schandratre/Espresso/run' / &system ibrav = 0 nat=96 ntyp=2 ecutwfc=80.0 ecutrho = 600.0 occupations = 'smearing' degauss=0.02 smearing = 'gaussian', / &electrons conv_thr = 1.0d-6, mixing_beta=0.3, / &ions ion_dynamics='damp' pot_extrapolation='second_order' wfc_extrapolation='second_order' / ATOMIC_SPECIES C 12.0000 C.pz-rrkjus.UPF H 1.00000 H.pz-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C 2.841720 5.953494 5.000000 C 3.552150 7.183995 5.000000 C 1.420860 5.953494 5.000000 C 2.841720 8.414496 5.000000 C 3.552150 9.644997 5.000000 C 0.710430 7.183995 5.000000 C 1.420860 8.414496 5.000000 C 2.841720 10.87550 5.000000 C 3.552150 12.10600 5.000000 C 0.710430 9.644997 5.000000 C 1.420860 10.87550 5.000000 C 2.841720 13.33650 5.000000 C 3.552150 14.56700 5.000000 C 0.710430 12.10600 5.000000 C 1.420860 13.33650 5.000000 C 0.710430 14.56700 5.000000 H 3.392220 5.000000 5.000000 H 0.870360 5.000000 5.000000 H 3.001650 15.52049 5.000000 H 1.260930 15.52049 5.000000 C 7.104300 5.953494 5.000000 C 7.814730 7.183995 5.000000 C 5.683440 5.953494 5.000000 C 7.104300 8.414496 5.000000 C 4.973010 7.183995 5.000000 C 5.683440 8.414496 5.000000 C 7.104300 10.87550 5.000000 C 7.814730 12.10600 5.000000 C 4.973010 9.644997 5.000000 C 5.683440 10.87550 5.000000 C 7.104300 13.33650 5.000000 C 7.814730 14.56700 5.000000 C 4.973010 12.10600 5.000000 C 5.683440 13.33650 5.000000 C 4.973010 14.56700 5.000000 H 7.654800 5.000000 5.000000 H 5.132940 5.000000 5.000000 H 7.264230 15.52049 5.000000 H 5.523510 15.52049 5.000000 C 11.36688 5.953494 5.000000 C 12.07731 7.183995 5.000000 C 9.946020 5.953494 5.000000 C 11.36688 8.414496 5.000000 C 12.07731 9.644997 5.000000 C 9.235590 7.183995 5.000000 C 11.36688 10.87550 5.000000 C 12.07731 12.10600 5.000000 C 11.36688 13.33650 5.000000 C 12.07731 14.56700 5.000000 C 9.235590 12.10600 5.000000 C 9.946020 13.33650 5.000000 C 9.235590 14.56700 5.000000 H 11.91738 5.000000 5.000000 H 9.395520 5.000000 5.000000 H 11.52681 15.52049 5.000000 H 9.786090 15.52049 5.000000 C 15.62946 5.953494 5.000000 C 16.33989 7.183995 5.000000 C 14.20860 5.953494 5.000000 C 15.62946 8.414496 5.000000 C 16.33989 9.644997 5.000000 C 13.49817 7.183995 5.000000 C 14.20860 8.414496 5.000000 C 15.62946 10.87550 5.000000 C 16.33989 12.10600 5.000000 C 13.49817 9.644997 5.000000 C 14.20860 10.87550 5.000000 C 15.62946 13.33650 5.000000 C 16.33989 14.56700 5.000000 C 13.49817 12.10600 5.000000 C 14.20860 13.33650 5.000000 C 13.49817 14.56700 5.000000 H 16.17996 5.000000 5.000000 H 13.65810 5.000000 5.000000 H 15.78939 15.52049 5.000000 H 14.04867 15.52049 5.000000 C 19.89204 5.953494 5.000000 C 20.60247 7.183995 5.000000 C 18.47118 5.953494 5.000000 C 19.89204 8.414496 5.000000 C 20.60247 9.644997 5.000000 C 17.76075 7.183995 5.000000 C 18.47118 8.414496 5.000000 C 19.89204 10.87550 5.000000 C 20.60247 12.10600 5.000000 C 17.76075 9.644997 5.000000 C 18.47118 10.87550 5.000000 C 19.89204 13.33650 5.000000 C 20.60247 14.56700 5.000000 C 17.76075 12.10600 5.000000 C 18.47118 13.33650 5.000000 C 17.76075 14.56700 5.000000 H 20.44254 5.000000 5.000000 H 17.92068 5.000000 5.000000 H 20.05197 15.52049 5.000000 H 18.31125 15.52049 5.000000 CELL_PARAMETERS 19.200000 0.000000 0.000000 0.0000000 21.90350 0.000000 0.0000000 0.000000 10.00000 K_POINTS {automatic} 25 1 1 0 0 0 -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110508/071c2c5c/attachment.htm From kirtinandan07 at gmail.com Mon May 9 07:15:27 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Mon, 9 May 2011 10:45:27 +0530 Subject: [Pw_forum] charge density Message-ID: Hi I am studying the effect of alloying on a supercell with 40 atoms. I am replacing one Ni with different alloying elements. To get the charge density should i relax the system and the perform the scf or simple scf will give the effect of alloying. Thanks in advance. vicky singh research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110509/0f5d51ed/attachment.htm From giannozz at democritos.it Mon May 9 08:53:11 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 09 May 2011 08:53:11 +0200 Subject: [Pw_forum] electron-phonon interaction in QE 4.3 In-Reply-To: <013f01cc0ce4$bd233620$3769a260$@w2agz.com> References: <013f01cc0ce4$bd233620$3769a260$@w2agz.com> Message-ID: <1304923991.27255.0.camel@fe12lx.fisica.uniud.it> On Sat, 2011-05-07 at 11:29 -0700, W2AGZ wrote: > Paolo, can the QE 4.3 e-p suite handle "spin" yet, e.g., LDA+U? I don't think so P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From nkxirainbow at gmail.com Mon May 9 11:17:33 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Mon, 9 May 2011 17:17:33 +0800 Subject: [Pw_forum] charge density In-Reply-To: References: Message-ID: Dear vicky singh: > I am studying the effect of alloying on a supercell with 40 atoms. I am > replacing one Ni with different alloying elements. To get the charge density > should i relax the system and the perform the scf or simple scf will give > the effect of alloying. > I do not think there is simple answer. It depends on what you are interested and the computer power. You could find how other people do it in published papers. > vicky singh > research student > Bangalore > > _______________________________________________ > 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/20110509/0c6878c3/attachment.htm From mayankaditya at gmail.com Mon May 9 11:44:44 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Mon, 9 May 2011 15:14:44 +0530 Subject: [Pw_forum] Phonon frequency of Body centred cubic strucure Message-ID: Thanks Dr Merlin for your guidance. one more thing i want to ask you that How much I should increase FFT mesh, default value is (120 120 120) and in output file I am getting the warning like negative rho (up, down): 0.691E+00 0.000E+00 I have chosen 10 times ecutrho that of ecut. Thanks Mayank Gupta BARC From masoudnahali at gmail.com Mon May 9 12:53:28 2011 From: masoudnahali at gmail.com (Masoud Nahali) Date: Mon, 9 May 2011 15:23:28 +0430 Subject: [Pw_forum] charge density Message-ID: On Mon, May 9, 2011 at 12:29 PM, vicky singh wrote: > > > Hi > > I am studying the effect of alloying on a supercell with 40 atoms. I am > replacing one Ni with different alloying elements. To get the charge > density > should i relax the system and the perform the scf or simple scf will give > the effect of alloying. > > Thanks in advance. > > vicky singh > research student > Bangalore > Dear Vicky Atoms with different sizes have different strain effects in your system and certainly their electronic states aren't same. So if I were you I do a relax calculation. Also, if you want to decrease the cost of your calculations, sometimes it may be good to fix the positions of some side atoms. I hope it helps. Best Wishes Masoud -------------- Masoud Nahali, Sharif University of Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110509/8923e111/attachment.htm From giovanni.cantele at spin.cnr.it Mon May 9 15:00:06 2011 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Mon, 9 May 2011 15:00:06 +0200 Subject: [Pw_forum] Relaxed Graphene Nanoribbon In-Reply-To: References: Message-ID: <42A538DB-6378-48A1-A6CC-528BF0005A2C@spin.cnr.it> On May 9, 2011, at 5:36 AM, swapnil chandratre wrote: > Hi, I have prepared an input file for a porous graphene nanoribbon, can anyone please comment if there are any errors with the file. it is always a good idea to open the input file using XCrysDen (or any other visualization software with a working Quantum-ESPRESSO interface), because this often helps in pointing out "structural" (cell paramenters and/or atomic positions) issues (see below). > ecutwfc=80.0 > ecutrho = 600.0 ..... > C 12.0000 C.pz-rrkjus.UPF > H 1.00000 H.pz-rrkjus.UPF > because your pseudos are ultrasoft a 80 Ry cutoff is likely very huge, you can reach convergence with much lower values, I think. Concerning the structural part, there is a problem for sure. > CELL_PARAMETERS > 19.200000 0.000000 0.000000 > 0.0000000 21.90350 0.000000 > 0.0000000 0.000000 10.00000 you chose an orthorombic unit cell with axis lengths of about 10, 11.4 and 5,0 Angstrom, respectively. But if you look at the atomic positions, you can easily see that: > C 0.710430 9.644997 5.000000 > H 20.44254 5.000000 5.000000 the x coordinates of these two atoms differ by 20.4 - 0.7 = 19.7 A which is less than your unit cell size along the x axis. The mistake probably originates from the fact that if you DO NOT specify celldm(1), the units of coordinates within the CELL_PARAMETERS card is a.u., namely, Bohr. I guess that you want to specify those units in Angstrom, indeed, the structure looks much better (with a hole that is what you mean with "porous") if you set celldm(1)=1.889727 (inverse of Bohr). Anyway, orthorombic cells are much easier specified by setting ibrav=8 and then a, b, c as axis lengths in Angstrom (see Doc/INPUT_PW.txt). Even after correctly specifying axis length units there is still a problem with the above atoms, because the 19.7 A difference of x coordinates is still larger than the 19.2 Angstrom a-axis. So, either the atomic positions are wrong, or the cell size was incorrectly computed. Giovanni -- **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110509/7d765035/attachment.htm From larikamonu at gmail.com Mon May 9 15:57:33 2011 From: larikamonu at gmail.com (mousumi uk) Date: Mon, 9 May 2011 16:57:33 +0300 Subject: [Pw_forum] Relaxed Graphene Nanoribbon In-Reply-To: References: Message-ID: Your unit cell is wrong.... visualize your structure in xcrysden and correct the CELL_PARAMETERS. Best regards, Mousumi On Mon, May 9, 2011 at 6:36 AM, swapnil chandratre < swapnil.chandratre at gmail.com> wrote: > Hi, > > I have prepared an input file for a porous graphene nanoribbon, can anyone > please comment if there are any errors with the file. > > &control > calculation = 'relax' > restart_mode = 'from_scratch' > pseudo_dir = '/home/s/schandratre/Espresso/pseudo' > outdir = '/home/s/schandratre/Espresso/run' > > / > &system > > ibrav = 0 > nat=96 > ntyp=2 > ecutwfc=80.0 > ecutrho = 600.0 > occupations = 'smearing' > degauss=0.02 > smearing = 'gaussian', > / > &electrons > conv_thr = 1.0d-6, > mixing_beta=0.3, > / > &ions > ion_dynamics='damp' > pot_extrapolation='second_order' > wfc_extrapolation='second_order' > / > > ATOMIC_SPECIES > C 12.0000 C.pz-rrkjus.UPF > H 1.00000 H.pz-rrkjus.UPF > > ATOMIC_POSITIONS {angstrom} > C 2.841720 5.953494 5.000000 > C 3.552150 7.183995 5.000000 > C 1.420860 5.953494 5.000000 > C 2.841720 8.414496 5.000000 > C 3.552150 9.644997 5.000000 > C 0.710430 7.183995 5.000000 > C 1.420860 8.414496 5.000000 > C 2.841720 10.87550 5.000000 > C 3.552150 12.10600 5.000000 > C 0.710430 9.644997 5.000000 > C 1.420860 10.87550 5.000000 > C 2.841720 13.33650 5.000000 > C 3.552150 14.56700 5.000000 > C 0.710430 12.10600 5.000000 > C 1.420860 13.33650 5.000000 > C 0.710430 14.56700 5.000000 > H 3.392220 5.000000 5.000000 > H 0.870360 5.000000 5.000000 > H 3.001650 15.52049 5.000000 > H 1.260930 15.52049 5.000000 > C 7.104300 5.953494 5.000000 > C 7.814730 7.183995 5.000000 > C 5.683440 5.953494 5.000000 > C 7.104300 8.414496 5.000000 > C 4.973010 7.183995 5.000000 > C 5.683440 8.414496 5.000000 > C 7.104300 10.87550 5.000000 > C 7.814730 12.10600 5.000000 > C 4.973010 9.644997 5.000000 > C 5.683440 10.87550 5.000000 > C 7.104300 13.33650 5.000000 > C 7.814730 14.56700 5.000000 > C 4.973010 12.10600 5.000000 > C 5.683440 13.33650 5.000000 > C 4.973010 14.56700 5.000000 > H 7.654800 5.000000 5.000000 > H 5.132940 5.000000 5.000000 > H 7.264230 15.52049 5.000000 > H 5.523510 15.52049 5.000000 > C 11.36688 5.953494 5.000000 > C 12.07731 7.183995 5.000000 > C 9.946020 5.953494 5.000000 > C 11.36688 8.414496 5.000000 > C 12.07731 9.644997 5.000000 > C 9.235590 7.183995 5.000000 > C 11.36688 10.87550 5.000000 > C 12.07731 12.10600 5.000000 > C 11.36688 13.33650 5.000000 > C 12.07731 14.56700 5.000000 > C 9.235590 12.10600 5.000000 > C 9.946020 13.33650 5.000000 > C 9.235590 14.56700 5.000000 > H 11.91738 5.000000 5.000000 > H 9.395520 5.000000 5.000000 > H 11.52681 15.52049 5.000000 > H 9.786090 15.52049 5.000000 > C 15.62946 5.953494 5.000000 > C 16.33989 7.183995 5.000000 > C 14.20860 5.953494 5.000000 > C 15.62946 8.414496 5.000000 > C 16.33989 9.644997 5.000000 > C 13.49817 7.183995 5.000000 > C 14.20860 8.414496 5.000000 > C 15.62946 10.87550 5.000000 > C 16.33989 12.10600 5.000000 > C 13.49817 9.644997 5.000000 > C 14.20860 10.87550 5.000000 > C 15.62946 13.33650 5.000000 > C 16.33989 14.56700 5.000000 > C 13.49817 12.10600 5.000000 > C 14.20860 13.33650 5.000000 > C 13.49817 14.56700 5.000000 > H 16.17996 5.000000 5.000000 > H 13.65810 5.000000 5.000000 > H 15.78939 15.52049 5.000000 > H 14.04867 15.52049 5.000000 > C 19.89204 5.953494 5.000000 > C 20.60247 7.183995 5.000000 > C 18.47118 5.953494 5.000000 > C 19.89204 8.414496 5.000000 > C 20.60247 9.644997 5.000000 > C 17.76075 7.183995 5.000000 > C 18.47118 8.414496 5.000000 > C 19.89204 10.87550 5.000000 > C 20.60247 12.10600 5.000000 > C 17.76075 9.644997 5.000000 > C 18.47118 10.87550 5.000000 > C 19.89204 13.33650 5.000000 > C 20.60247 14.56700 5.000000 > C 17.76075 12.10600 5.000000 > C 18.47118 13.33650 5.000000 > C 17.76075 14.56700 5.000000 > H 20.44254 5.000000 5.000000 > H 17.92068 5.000000 5.000000 > H 20.05197 15.52049 5.000000 > H 18.31125 15.52049 5.000000 > > CELL_PARAMETERS > 19.200000 0.000000 0.000000 > 0.0000000 21.90350 0.000000 > 0.0000000 0.000000 10.00000 > > K_POINTS {automatic} > 25 1 1 0 0 0 > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > > _______________________________________________ > 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/20110509/bb55455c/attachment-0001.htm From arvifis at gmail.com Mon May 9 16:44:24 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 9 May 2011 11:44:24 -0300 Subject: [Pw_forum] Relaxed Graphene Nanoribbon In-Reply-To: References: Message-ID: Your unit cell vectors are wrong, because many atoms positions are out the unit cell..!! futhermore, why do you put 25 1 1 k-points...?? remember that the reciprocal space is inversely proportional to real space....!!! Best. PhD std. Arles V. Gil Rebaza Instituto de F?sica de La Plata La Plata-Argentina 2011/5/9 mousumi uk > Your unit cell is wrong.... visualize your structure in xcrysden and > correct the CELL_PARAMETERS. > > Best regards, > Mousumi > > On Mon, May 9, 2011 at 6:36 AM, swapnil chandratre < > swapnil.chandratre at gmail.com> wrote: > >> Hi, >> >> I have prepared an input file for a porous graphene nanoribbon, can anyone >> please comment if there are any errors with the file. >> >> &control >> calculation = 'relax' >> restart_mode = 'from_scratch' >> pseudo_dir = '/home/s/schandratre/Espresso/pseudo' >> outdir = '/home/s/schandratre/Espresso/run' >> >> / >> &system >> >> ibrav = 0 >> nat=96 >> ntyp=2 >> ecutwfc=80.0 >> ecutrho = 600.0 >> occupations = 'smearing' >> degauss=0.02 >> smearing = 'gaussian', >> / >> &electrons >> conv_thr = 1.0d-6, >> mixing_beta=0.3, >> / >> &ions >> ion_dynamics='damp' >> pot_extrapolation='second_order' >> wfc_extrapolation='second_order' >> / >> >> ATOMIC_SPECIES >> C 12.0000 C.pz-rrkjus.UPF >> H 1.00000 H.pz-rrkjus.UPF >> >> ATOMIC_POSITIONS {angstrom} >> C 2.841720 5.953494 5.000000 >> C 3.552150 7.183995 5.000000 >> C 1.420860 5.953494 5.000000 >> C 2.841720 8.414496 5.000000 >> C 3.552150 9.644997 5.000000 >> C 0.710430 7.183995 5.000000 >> C 1.420860 8.414496 5.000000 >> C 2.841720 10.87550 5.000000 >> C 3.552150 12.10600 5.000000 >> C 0.710430 9.644997 5.000000 >> C 1.420860 10.87550 5.000000 >> C 2.841720 13.33650 5.000000 >> C 3.552150 14.56700 5.000000 >> C 0.710430 12.10600 5.000000 >> C 1.420860 13.33650 5.000000 >> C 0.710430 14.56700 5.000000 >> H 3.392220 5.000000 5.000000 >> H 0.870360 5.000000 5.000000 >> H 3.001650 15.52049 5.000000 >> H 1.260930 15.52049 5.000000 >> C 7.104300 5.953494 5.000000 >> C 7.814730 7.183995 5.000000 >> C 5.683440 5.953494 5.000000 >> C 7.104300 8.414496 5.000000 >> C 4.973010 7.183995 5.000000 >> C 5.683440 8.414496 5.000000 >> C 7.104300 10.87550 5.000000 >> C 7.814730 12.10600 5.000000 >> C 4.973010 9.644997 5.000000 >> C 5.683440 10.87550 5.000000 >> C 7.104300 13.33650 5.000000 >> C 7.814730 14.56700 5.000000 >> C 4.973010 12.10600 5.000000 >> C 5.683440 13.33650 5.000000 >> C 4.973010 14.56700 5.000000 >> H 7.654800 5.000000 5.000000 >> H 5.132940 5.000000 5.000000 >> H 7.264230 15.52049 5.000000 >> H 5.523510 15.52049 5.000000 >> C 11.36688 5.953494 5.000000 >> C 12.07731 7.183995 5.000000 >> C 9.946020 5.953494 5.000000 >> C 11.36688 8.414496 5.000000 >> C 12.07731 9.644997 5.000000 >> C 9.235590 7.183995 5.000000 >> C 11.36688 10.87550 5.000000 >> C 12.07731 12.10600 5.000000 >> C 11.36688 13.33650 5.000000 >> C 12.07731 14.56700 5.000000 >> C 9.235590 12.10600 5.000000 >> C 9.946020 13.33650 5.000000 >> C 9.235590 14.56700 5.000000 >> H 11.91738 5.000000 5.000000 >> H 9.395520 5.000000 5.000000 >> H 11.52681 15.52049 5.000000 >> H 9.786090 15.52049 5.000000 >> C 15.62946 5.953494 5.000000 >> C 16.33989 7.183995 5.000000 >> C 14.20860 5.953494 5.000000 >> C 15.62946 8.414496 5.000000 >> C 16.33989 9.644997 5.000000 >> C 13.49817 7.183995 5.000000 >> C 14.20860 8.414496 5.000000 >> C 15.62946 10.87550 5.000000 >> C 16.33989 12.10600 5.000000 >> C 13.49817 9.644997 5.000000 >> C 14.20860 10.87550 5.000000 >> C 15.62946 13.33650 5.000000 >> C 16.33989 14.56700 5.000000 >> C 13.49817 12.10600 5.000000 >> C 14.20860 13.33650 5.000000 >> C 13.49817 14.56700 5.000000 >> H 16.17996 5.000000 5.000000 >> H 13.65810 5.000000 5.000000 >> H 15.78939 15.52049 5.000000 >> H 14.04867 15.52049 5.000000 >> C 19.89204 5.953494 5.000000 >> C 20.60247 7.183995 5.000000 >> C 18.47118 5.953494 5.000000 >> C 19.89204 8.414496 5.000000 >> C 20.60247 9.644997 5.000000 >> C 17.76075 7.183995 5.000000 >> C 18.47118 8.414496 5.000000 >> C 19.89204 10.87550 5.000000 >> C 20.60247 12.10600 5.000000 >> C 17.76075 9.644997 5.000000 >> C 18.47118 10.87550 5.000000 >> C 19.89204 13.33650 5.000000 >> C 20.60247 14.56700 5.000000 >> C 17.76075 12.10600 5.000000 >> C 18.47118 13.33650 5.000000 >> C 17.76075 14.56700 5.000000 >> H 20.44254 5.000000 5.000000 >> H 17.92068 5.000000 5.000000 >> H 20.05197 15.52049 5.000000 >> H 18.31125 15.52049 5.000000 >> >> CELL_PARAMETERS >> 19.200000 0.000000 0.000000 >> 0.0000000 21.90350 0.000000 >> 0.0000000 0.000000 10.00000 >> >> K_POINTS {automatic} >> 25 1 1 0 0 0 >> >> >> -- >> Regards, >> Swapnil Chandratre >> Graduate Student >> Dept. of Mechanical Engineering, >> University of Houston, >> Houston, TX >> (M)-713-294-9546 >> >> _______________________________________________ >> 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 > > -- ###---------> Arles V. <---------### -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110509/1cc2961b/attachment.htm From swapnil.chandratre at gmail.com Mon May 9 19:33:53 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 9 May 2011 12:33:53 -0500 Subject: [Pw_forum] Relaxed Graphene Nanoribbon In-Reply-To: References: Message-ID: Hello, Thank you all for your responses, I was using a software to generate the geometry of ribbon, it gave me the data regarding the *unit cell *dimensions so I just transfered the data from there. And when I visualized it there, it seemed to be perfect, I am trying to install XCrysden so that I can avoid such issues again. Arles, can you shed some knowledge on how to go for the k points, as it is 1d,I assume 100 k points may be sufficient to give reasonable idea, I just randomly selected 25 as a starting point, and can anyone suggest any reading material or approach towards defining the cut off energies and K points. Thank you. On Mon, May 9, 2011 at 9:44 AM, Arles V. Gil Rebaza wrote: > Your unit cell vectors are wrong, because many atoms positions are out the > unit cell..!! futhermore, why do you put 25 1 1 k-points...?? remember that > the reciprocal space is inversely proportional to real space....!!! > > Best. > > PhD std. Arles V. Gil Rebaza > Instituto de F?sica de La Plata > La Plata-Argentina > > > 2011/5/9 mousumi uk > >> Your unit cell is wrong.... visualize your structure in xcrysden and >> correct the CELL_PARAMETERS. >> >> Best regards, >> Mousumi >> >> On Mon, May 9, 2011 at 6:36 AM, swapnil chandratre < >> swapnil.chandratre at gmail.com> wrote: >> >>> Hi, >>> >>> I have prepared an input file for a porous graphene nanoribbon, can >>> anyone please comment if there are any errors with the file. >>> >>> &control >>> calculation = 'relax' >>> restart_mode = 'from_scratch' >>> pseudo_dir = '/home/s/schandratre/Espresso/pseudo' >>> outdir = '/home/s/schandratre/Espresso/run' >>> >>> / >>> &system >>> >>> ibrav = 0 >>> nat=96 >>> ntyp=2 >>> ecutwfc=80.0 >>> ecutrho = 600.0 >>> occupations = 'smearing' >>> degauss=0.02 >>> smearing = 'gaussian', >>> / >>> &electrons >>> conv_thr = 1.0d-6, >>> mixing_beta=0.3, >>> / >>> &ions >>> ion_dynamics='damp' >>> pot_extrapolation='second_order' >>> wfc_extrapolation='second_order' >>> / >>> >>> ATOMIC_SPECIES >>> C 12.0000 C.pz-rrkjus.UPF >>> H 1.00000 H.pz-rrkjus.UPF >>> >>> ATOMIC_POSITIONS {angstrom} >>> C 2.841720 5.953494 5.000000 >>> C 3.552150 7.183995 5.000000 >>> C 1.420860 5.953494 5.000000 >>> C 2.841720 8.414496 5.000000 >>> C 3.552150 9.644997 5.000000 >>> C 0.710430 7.183995 5.000000 >>> C 1.420860 8.414496 5.000000 >>> C 2.841720 10.87550 5.000000 >>> C 3.552150 12.10600 5.000000 >>> C 0.710430 9.644997 5.000000 >>> C 1.420860 10.87550 5.000000 >>> C 2.841720 13.33650 5.000000 >>> C 3.552150 14.56700 5.000000 >>> C 0.710430 12.10600 5.000000 >>> C 1.420860 13.33650 5.000000 >>> C 0.710430 14.56700 5.000000 >>> H 3.392220 5.000000 5.000000 >>> H 0.870360 5.000000 5.000000 >>> H 3.001650 15.52049 5.000000 >>> H 1.260930 15.52049 5.000000 >>> C 7.104300 5.953494 5.000000 >>> C 7.814730 7.183995 5.000000 >>> C 5.683440 5.953494 5.000000 >>> C 7.104300 8.414496 5.000000 >>> C 4.973010 7.183995 5.000000 >>> C 5.683440 8.414496 5.000000 >>> C 7.104300 10.87550 5.000000 >>> C 7.814730 12.10600 5.000000 >>> C 4.973010 9.644997 5.000000 >>> C 5.683440 10.87550 5.000000 >>> C 7.104300 13.33650 5.000000 >>> C 7.814730 14.56700 5.000000 >>> C 4.973010 12.10600 5.000000 >>> C 5.683440 13.33650 5.000000 >>> C 4.973010 14.56700 5.000000 >>> H 7.654800 5.000000 5.000000 >>> H 5.132940 5.000000 5.000000 >>> H 7.264230 15.52049 5.000000 >>> H 5.523510 15.52049 5.000000 >>> C 11.36688 5.953494 5.000000 >>> C 12.07731 7.183995 5.000000 >>> C 9.946020 5.953494 5.000000 >>> C 11.36688 8.414496 5.000000 >>> C 12.07731 9.644997 5.000000 >>> C 9.235590 7.183995 5.000000 >>> C 11.36688 10.87550 5.000000 >>> C 12.07731 12.10600 5.000000 >>> C 11.36688 13.33650 5.000000 >>> C 12.07731 14.56700 5.000000 >>> C 9.235590 12.10600 5.000000 >>> C 9.946020 13.33650 5.000000 >>> C 9.235590 14.56700 5.000000 >>> H 11.91738 5.000000 5.000000 >>> H 9.395520 5.000000 5.000000 >>> H 11.52681 15.52049 5.000000 >>> H 9.786090 15.52049 5.000000 >>> C 15.62946 5.953494 5.000000 >>> C 16.33989 7.183995 5.000000 >>> C 14.20860 5.953494 5.000000 >>> C 15.62946 8.414496 5.000000 >>> C 16.33989 9.644997 5.000000 >>> C 13.49817 7.183995 5.000000 >>> C 14.20860 8.414496 5.000000 >>> C 15.62946 10.87550 5.000000 >>> C 16.33989 12.10600 5.000000 >>> C 13.49817 9.644997 5.000000 >>> C 14.20860 10.87550 5.000000 >>> C 15.62946 13.33650 5.000000 >>> C 16.33989 14.56700 5.000000 >>> C 13.49817 12.10600 5.000000 >>> C 14.20860 13.33650 5.000000 >>> C 13.49817 14.56700 5.000000 >>> H 16.17996 5.000000 5.000000 >>> H 13.65810 5.000000 5.000000 >>> H 15.78939 15.52049 5.000000 >>> H 14.04867 15.52049 5.000000 >>> C 19.89204 5.953494 5.000000 >>> C 20.60247 7.183995 5.000000 >>> C 18.47118 5.953494 5.000000 >>> C 19.89204 8.414496 5.000000 >>> C 20.60247 9.644997 5.000000 >>> C 17.76075 7.183995 5.000000 >>> C 18.47118 8.414496 5.000000 >>> C 19.89204 10.87550 5.000000 >>> C 20.60247 12.10600 5.000000 >>> C 17.76075 9.644997 5.000000 >>> C 18.47118 10.87550 5.000000 >>> C 19.89204 13.33650 5.000000 >>> C 20.60247 14.56700 5.000000 >>> C 17.76075 12.10600 5.000000 >>> C 18.47118 13.33650 5.000000 >>> C 17.76075 14.56700 5.000000 >>> H 20.44254 5.000000 5.000000 >>> H 17.92068 5.000000 5.000000 >>> H 20.05197 15.52049 5.000000 >>> H 18.31125 15.52049 5.000000 >>> >>> CELL_PARAMETERS >>> 19.200000 0.000000 0.000000 >>> 0.0000000 21.90350 0.000000 >>> 0.0000000 0.000000 10.00000 >>> >>> K_POINTS {automatic} >>> 25 1 1 0 0 0 >>> >>> >>> -- >>> Regards, >>> Swapnil Chandratre >>> Graduate Student >>> Dept. of Mechanical Engineering, >>> University of Houston, >>> Houston, TX >>> (M)-713-294-9546 >>> >>> _______________________________________________ >>> 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 >> >> > > > -- > ###---------> Arles V. <---------### > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110509/65b25733/attachment-0001.htm From swapnil.chandratre at gmail.com Mon May 9 21:13:18 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 9 May 2011 14:13:18 -0500 Subject: [Pw_forum] Error Installing XCrysden Message-ID: Hi, I am trying to install XCrysden 1.5.23, i receive the error, ./xcrysden: line 224: /home/...../bin/xcrys: No such file or directorym what could be wrong. I am installing it on Windows64 bit -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110509/1add8156/attachment.htm From kirtinandan07 at gmail.com Mon May 9 21:14:53 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Tue, 10 May 2011 00:44:53 +0530 Subject: [Pw_forum] charge density In-Reply-To: References: Message-ID: Thanks for your advice. On Mon, May 9, 2011 at 4:23 PM, Masoud Nahali wrote: > > > On Mon, May 9, 2011 at 12:29 PM, vicky singh wrote: > >> >> >> Hi >> >> >> I am studying the effect of alloying on a supercell with 40 atoms. I am >> replacing one Ni with different alloying elements. To get the charge >> density >> should i relax the system and the perform the scf or simple scf will give >> the effect of alloying. >> >> Thanks in advance. >> >> >> vicky singh >> research student >> Bangalore >> > > Dear Vicky > > Atoms with different sizes have different strain effects in your system and > certainly their electronic states aren't same. So if I were you I do a relax > calculation. Also, if you want to decrease the cost of your calculations, > sometimes it may be good to fix the positions of some side atoms. I hope it > helps. > > Best Wishes > > Masoud > > -------------- > Masoud Nahali, Sharif University of Technology > > _______________________________________________ > 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/20110510/08e63f27/attachment.htm From trambui at u.boisestate.edu Tue May 10 00:45:35 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Mon, 9 May 2011 16:45:35 -0600 Subject: [Pw_forum] problems with variables in US pseudopotential generation Message-ID: Dear Everyone, In the pseudopotential generation input file, under &inputp, I need to fill in the data for rcut (matching radius for norm-conserving) and rcutus (matching radius for Ultra soft PP). I have looked at some examples, and most of the time the rcut & rcutus are the same. So i'm just wondering how one would have different rcut& rcutus? 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/20110509/c3fc6c74/attachment.htm From arvifis at gmail.com Tue May 10 03:03:05 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Mon, 9 May 2011 22:03:05 -0300 Subject: [Pw_forum] Relaxed Graphene Nanoribbon In-Reply-To: References: Message-ID: About the relationship between the reciprocal and real spaces, you can find in some book of Solid State, authors like Ashcroft or Kittel. In order to select the number of k-points you need to do convergence of the total energy (or your observable) respect the number of k-points...!!! The same criteria to select the optimal value of cut-off energy and perhaps also for the length of the third vector (z direction) because you should consider the periodicity of QE. Best. PhD std. Arles V. Gil Rebaza Instituto de F?sica de La Plata La Plata-Argentina 2011/5/9 swapnil chandratre > Hello, > > > Thank you all for your responses, I was using a software to generate the > geometry of ribbon, it gave me the data regarding the *unit cell *dimensions > so I just transfered the data from there. And when I visualized it there, it > seemed to be perfect, I am trying to install XCrysden so that I can avoid > such issues again. > > Arles, can you shed some knowledge on how to go for the k points, as it is > 1d,I assume 100 k points may be sufficient to give reasonable idea, I just > randomly selected 25 as a starting point, and can anyone suggest any reading > material or approach towards defining the cut off energies and K points. > > Thank you. > > On Mon, May 9, 2011 at 9:44 AM, Arles V. Gil Rebaza wrote: > >> Your unit cell vectors are wrong, because many atoms positions are out the >> unit cell..!! futhermore, why do you put 25 1 1 k-points...?? remember that >> the reciprocal space is inversely proportional to real space....!!! >> >> Best. >> >> PhD std. Arles V. Gil Rebaza >> Instituto de F?sica de La Plata >> La Plata-Argentina >> >> >> 2011/5/9 mousumi uk >> >>> Your unit cell is wrong.... visualize your structure in xcrysden and >>> correct the CELL_PARAMETERS. >>> >>> Best regards, >>> Mousumi >>> >>> On Mon, May 9, 2011 at 6:36 AM, swapnil chandratre < >>> swapnil.chandratre at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> I have prepared an input file for a porous graphene nanoribbon, can >>>> anyone please comment if there are any errors with the file. >>>> >>>> &control >>>> calculation = 'relax' >>>> restart_mode = 'from_scratch' >>>> pseudo_dir = '/home/s/schandratre/Espresso/pseudo' >>>> outdir = '/home/s/schandratre/Espresso/run' >>>> >>>> / >>>> &system >>>> >>>> ibrav = 0 >>>> nat=96 >>>> ntyp=2 >>>> ecutwfc=80.0 >>>> ecutrho = 600.0 >>>> occupations = 'smearing' >>>> degauss=0.02 >>>> smearing = 'gaussian', >>>> / >>>> &electrons >>>> conv_thr = 1.0d-6, >>>> mixing_beta=0.3, >>>> / >>>> &ions >>>> ion_dynamics='damp' >>>> pot_extrapolation='second_order' >>>> wfc_extrapolation='second_order' >>>> / >>>> >>>> ATOMIC_SPECIES >>>> C 12.0000 C.pz-rrkjus.UPF >>>> H 1.00000 H.pz-rrkjus.UPF >>>> >>>> ATOMIC_POSITIONS {angstrom} >>>> C 2.841720 5.953494 5.000000 >>>> C 3.552150 7.183995 5.000000 >>>> C 1.420860 5.953494 5.000000 >>>> C 2.841720 8.414496 5.000000 >>>> C 3.552150 9.644997 5.000000 >>>> C 0.710430 7.183995 5.000000 >>>> C 1.420860 8.414496 5.000000 >>>> C 2.841720 10.87550 5.000000 >>>> C 3.552150 12.10600 5.000000 >>>> C 0.710430 9.644997 5.000000 >>>> C 1.420860 10.87550 5.000000 >>>> C 2.841720 13.33650 5.000000 >>>> C 3.552150 14.56700 5.000000 >>>> C 0.710430 12.10600 5.000000 >>>> C 1.420860 13.33650 5.000000 >>>> C 0.710430 14.56700 5.000000 >>>> H 3.392220 5.000000 5.000000 >>>> H 0.870360 5.000000 5.000000 >>>> H 3.001650 15.52049 5.000000 >>>> H 1.260930 15.52049 5.000000 >>>> C 7.104300 5.953494 5.000000 >>>> C 7.814730 7.183995 5.000000 >>>> C 5.683440 5.953494 5.000000 >>>> C 7.104300 8.414496 5.000000 >>>> C 4.973010 7.183995 5.000000 >>>> C 5.683440 8.414496 5.000000 >>>> C 7.104300 10.87550 5.000000 >>>> C 7.814730 12.10600 5.000000 >>>> C 4.973010 9.644997 5.000000 >>>> C 5.683440 10.87550 5.000000 >>>> C 7.104300 13.33650 5.000000 >>>> C 7.814730 14.56700 5.000000 >>>> C 4.973010 12.10600 5.000000 >>>> C 5.683440 13.33650 5.000000 >>>> C 4.973010 14.56700 5.000000 >>>> H 7.654800 5.000000 5.000000 >>>> H 5.132940 5.000000 5.000000 >>>> H 7.264230 15.52049 5.000000 >>>> H 5.523510 15.52049 5.000000 >>>> C 11.36688 5.953494 5.000000 >>>> C 12.07731 7.183995 5.000000 >>>> C 9.946020 5.953494 5.000000 >>>> C 11.36688 8.414496 5.000000 >>>> C 12.07731 9.644997 5.000000 >>>> C 9.235590 7.183995 5.000000 >>>> C 11.36688 10.87550 5.000000 >>>> C 12.07731 12.10600 5.000000 >>>> C 11.36688 13.33650 5.000000 >>>> C 12.07731 14.56700 5.000000 >>>> C 9.235590 12.10600 5.000000 >>>> C 9.946020 13.33650 5.000000 >>>> C 9.235590 14.56700 5.000000 >>>> H 11.91738 5.000000 5.000000 >>>> H 9.395520 5.000000 5.000000 >>>> H 11.52681 15.52049 5.000000 >>>> H 9.786090 15.52049 5.000000 >>>> C 15.62946 5.953494 5.000000 >>>> C 16.33989 7.183995 5.000000 >>>> C 14.20860 5.953494 5.000000 >>>> C 15.62946 8.414496 5.000000 >>>> C 16.33989 9.644997 5.000000 >>>> C 13.49817 7.183995 5.000000 >>>> C 14.20860 8.414496 5.000000 >>>> C 15.62946 10.87550 5.000000 >>>> C 16.33989 12.10600 5.000000 >>>> C 13.49817 9.644997 5.000000 >>>> C 14.20860 10.87550 5.000000 >>>> C 15.62946 13.33650 5.000000 >>>> C 16.33989 14.56700 5.000000 >>>> C 13.49817 12.10600 5.000000 >>>> C 14.20860 13.33650 5.000000 >>>> C 13.49817 14.56700 5.000000 >>>> H 16.17996 5.000000 5.000000 >>>> H 13.65810 5.000000 5.000000 >>>> H 15.78939 15.52049 5.000000 >>>> H 14.04867 15.52049 5.000000 >>>> C 19.89204 5.953494 5.000000 >>>> C 20.60247 7.183995 5.000000 >>>> C 18.47118 5.953494 5.000000 >>>> C 19.89204 8.414496 5.000000 >>>> C 20.60247 9.644997 5.000000 >>>> C 17.76075 7.183995 5.000000 >>>> C 18.47118 8.414496 5.000000 >>>> C 19.89204 10.87550 5.000000 >>>> C 20.60247 12.10600 5.000000 >>>> C 17.76075 9.644997 5.000000 >>>> C 18.47118 10.87550 5.000000 >>>> C 19.89204 13.33650 5.000000 >>>> C 20.60247 14.56700 5.000000 >>>> C 17.76075 12.10600 5.000000 >>>> C 18.47118 13.33650 5.000000 >>>> C 17.76075 14.56700 5.000000 >>>> H 20.44254 5.000000 5.000000 >>>> H 17.92068 5.000000 5.000000 >>>> H 20.05197 15.52049 5.000000 >>>> H 18.31125 15.52049 5.000000 >>>> >>>> CELL_PARAMETERS >>>> 19.200000 0.000000 0.000000 >>>> 0.0000000 21.90350 0.000000 >>>> 0.0000000 0.000000 10.00000 >>>> >>>> K_POINTS {automatic} >>>> 25 1 1 0 0 0 >>>> >>>> >>>> -- >>>> Regards, >>>> Swapnil Chandratre >>>> Graduate Student >>>> Dept. of Mechanical Engineering, >>>> University of Houston, >>>> Houston, TX >>>> (M)-713-294-9546 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> >> -- >> ###---------> Arles V. <---------### >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > > _______________________________________________ > 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/20110509/d882d4b8/attachment-0001.htm From kucukben at sissa.it Tue May 10 09:46:49 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Tue, 10 May 2011 09:46:49 +0200 Subject: [Pw_forum] problems with variables in US pseudopotential generation In-Reply-To: References: Message-ID: <20110510094649.a7p090fhsssg4ks8@webmail.sissa.it> Dear Tram, rcut and rcutus are kept the same for norm conserving angular momentum channels (all channels in norm conserving pseudos or local channels in ultrasoft/paw) . There are many other working examples for US/PAW in pslibrary project. Try downloading from : http://qe-forge.org/projects/pslibrary/ cheers emine kucukbenli, phd student, sissa, italy Quoting Tram Bui : > I have looked at some examples, > and most of the time the rcut & rcutus are the same. So i'm just > wondering how one would have different rcut& rcutus? > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From lorenzo.paulatto at impmc.upmc.fr Tue May 10 09:51:23 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 10 May 2011 09:51:23 +0200 Subject: [Pw_forum] problems with variables in US pseudopotential generation In-Reply-To: References: Message-ID: In data 10 maggio 2011 alle ore 00:45:35, Tram Bui ha scritto: > Dear Everyone, > In the pseudopotential generation input file, under &inputp, I > need to fill in the data for rcut (matching radius for norm-conserving) > and > rcutus (matching radius for Ultra soft PP). I have looked at some > examples, and most of the time the rcut & rcutus are the same. So i'm > just > wondering how one would have different rcut& rcutus? Dear Tram Bui, for norm-conserving pseudopotentials they are indeed the same. For ultrasoft pseudopotentials the set of rcut defines a very hard norm-conserving pseudo on top of which the ultrasoft one is build, but further pseudizing at rcutus. As a consequence, rcut determine the hardness of the augmentation charge, while rcutus is linked to the hardness of the pseudo wavefunctions. Unfortunately the presence of ghost states often gives you little choice for rcut and rcutus. As of chosing them, if you do not have a similar element to take inspiration, start with a reasonable norm-conserving single-projector pseudopotential and make it harder until 4*ecutwfc is the ecutrho you wish to use. Then double the number of projectors and change it to ultrasoft; keep increasing rcutus up from rcut until you reach a reasonable hardness. This procedure is difficult to apply for configurations with semicore in valence. 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 suza.rri at gmail.com Tue May 10 10:35:23 2011 From: suza.rri at gmail.com (Suza W) Date: Tue, 10 May 2011 10:35:23 +0200 Subject: [Pw_forum] SVN versus CVS Message-ID: Dear QE Community, I was able to download the CVS Version from the qe-forge site earlier. Now that link is replaced by SVN. Are both of the versions updated each night, in parallel ? Now which one of the above two should be configured and make installed for the most recent change ? And how ? Simple "./configure" and "make all" do not work directly as before. Could any one please explain me the way to install the latest version ? Thank you, Suza W -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110510/7700ba42/attachment.htm From faride.he64 at gmail.com Tue May 10 10:45:50 2011 From: faride.he64 at gmail.com (faride heydari) Date: Tue, 10 May 2011 12:15:50 +0330 Subject: [Pw_forum] optimizing of celldm(1) and celldm(3) Message-ID: Hi I'm studying on single-walled carbon nanotube , that it's bravia lattice is hegzagonal, how to optimize celldm(1) and celldm(3) ?can i optimize them Simultaneous? Best Wishes -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110510/260920c1/attachment.htm From giannozz at democritos.it Tue May 10 10:59:53 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 10 May 2011 10:59:53 +0200 Subject: [Pw_forum] SVN versus CVS In-Reply-To: References: Message-ID: <1305017993.31206.4.camel@fe12lx.fisica.uniud.it> On Tue, 2011-05-10 at 10:35 +0200, Suza W wrote: > I was able to download the CVS Version from the qe-forge site earlier. > Now that link is replaced by SVN. Are both versions updated each > night, in parallel ? development work goes on ONLY on the svn version. The cvs repository is no longer updated. The daily *.tar.gz file is not available right now. There will be a 4.3.1 version soon. > Simple "./configure" and "make all" do not work directly as before. they do P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From tone.kokalj at ijs.si Tue May 10 17:07:56 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 10 May 2011 17:07:56 +0200 Subject: [Pw_forum] Error Installing XCrysden In-Reply-To: References: Message-ID: <1305040076.2614.38.camel@catalyst.ijs.si> On Mon, 2011-05-09 at 14:13 -0500, swapnil chandratre wrote: > Hi, > > > I am trying to install XCrysden 1.5.23, i receive the error, > > > ./xcrysden: line 224: /home/...../bin/xcrys: No such file or > directorym > what could be wrong. Please address next time such questions to xcrysden mailing list. There are two possibilities: (1) you downloaded the source package and you didn't compile it, so the file $$$/bin/xcrys is not there (2) you downloaded the binary package, and mis-defined the XCRYSDEN_TOPDIR variable (note that from 1.5.* on the XCRYSDEN_TOPDIR is not required anymore, hence you may unset it) 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 songsong19840614 at gmail.com Wed May 11 03:34:10 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Wed, 11 May 2011 09:34:10 +0800 Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? In-Reply-To: <345129.85014.qm@web65710.mail.ac4.yahoo.com> References: <345129.85014.qm@web65710.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz Isaev: Thank you for your advice.My k-point is chosen by Xcrysden.such as: G 0.0000000000 0.0000000000 0.0000000000 K -0.7500000000 -0.3750000000 -0.3750000000 X -0.5000000000 0.0000000000 -0.5000000000 G 0.0000000000 0.0000000000 0.0000000000 L - 0.5000000000 -0.5000000000 -0.5000000000 X 0.0000000000 -0.5000000000 -0.5000000000 W -0.2500000000 -0.5000000000 -0.7500000000 L -0.5000000000 -0.5000000000 -0.5000000000 and I try to use your advice through using 3 type of attempt. 1.only chang K,Xpoint of K-G path to K(0.75,0.75,0), X point (1, 1, 0) 2.all k point multipy 2 times. such as: G 0.0000000000 0.0000000000 0.0000000000 K -1.5000000000 -0.7500000000 -0.7500000000 X -1.0000000000 0.0000000000 -1.0000000000 G 0.0000000000 0.0000000000 0.0000000000 L - 1.0000000000 -1.0000000000 -1.0000000000 X 0.0000000000 -1.0000000000 -1.0000000000 W -0.5000000000 -1.0000000000 -1.5000000000 L -1.0000000000 -1.0000000000 -1.0000000000 3.only K,Xpoint of K-G path multiply 2 times. such as G 0.0000000000 0.0000000000 0.0000000000 K -1.5000000000 -0.7500000000 -0.7500000000 X -1.0000000000 0.0000000000 -1.0000000000 G 0.0000000000 0.0000000000 0.0000000000 L - 0.5000000000 -0.5000000000 -0.5000000000 X 0.0000000000 -0.5000000000 -0.5000000000 W -0.2500000000 -0.5000000000 -0.7500000000 L -0.5000000000 -0.5000000000 -0.5000000000 However,all this attempts yield wrong picture. So,this must be something I didn't understand correctly.Would you tell me where is my fault ? 2011/5/6 Eyvaz Isaev > Hi, > > First of all I would recommend the use of PlotPhon utility to plot phonon > dispersion relations. For this one you have to have calculated interatomic > force constants matrix (*.fc) file. > > Regarding your particular question: you should choose K(0.75,0.75,0), then > from the K point go to the X point (1, 1, 0) which is equivalent to > the X(1,0,0) point. Then from the X(1,0,0) to the Gamma (0,0,0) point. > Dashed line just means that we can continue in this direction to match > phonons at the X point (i.e. it is an intermediate point from the Gamma to > the X point) . > > Please also provide your affiliation. > > Bests, > Eyvaz > > ------------------------------------------------------------------- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > ------------------------------ > *From:* lucking-pine > *To:* Pw_forum at pwscf.org > *Sent:* Fri, May 6, 2011 2:50:16 PM > *Subject:* [Pw_forum] why K-X point of phonon dispersion is wrong? > > My pwscf is used in calculating Si phonon dispersion.The trend of picture > in > > most special Symmetry is right.But the only K-X is wrong.I use Xcrysden to > > get K-point. > I found most paper is dash line in 'K' point.So what is mean? Please anyone > > > could tell me! Thanks! > The attachment is my picture and reference paper. > > _______________________________________________ > 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/20110511/e5857d84/attachment.htm From kirtinandan07 at gmail.com Wed May 11 06:44:54 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Wed, 11 May 2011 10:14:54 +0530 Subject: [Pw_forum] charge density In-Reply-To: References: Message-ID: I am very new to analyse the charge density plot. Now I am plottting the charge density for the supersell by relaxing the structure and then performing scf and then pp.x and without relaxing i.e scf and pp.x. with the results what should i be careful about for both the case. How should i decide the correct approach. I tried to look for any paper but what i could get just mention the charge density plot. can anybody plese help. On Tue, May 10, 2011 at 12:44 AM, vicky singh wrote: > Thanks for your advice. > > > On Mon, May 9, 2011 at 4:23 PM, Masoud Nahali wrote: > >> >> >> On Mon, May 9, 2011 at 12:29 PM, vicky singh wrote: >> >>> >>> >>> Hi >>> >>> >>> I am studying the effect of alloying on a supercell with 40 atoms. I am >>> replacing one Ni with different alloying elements. To get the charge >>> density >>> should i relax the system and the perform the scf or simple scf will give >>> the effect of alloying. >>> >>> Thanks in advance. >>> >>> >>> vicky singh >>> research student >>> Bangalore >>> >> >> Dear Vicky >> >> Atoms with different sizes have different strain effects in your system >> and certainly their electronic states aren't same. So if I were you I do a >> relax calculation. Also, if you want to decrease the cost of your >> calculations, sometimes it may be good to fix the positions of some side >> atoms. I hope it helps. >> >> Best Wishes >> >> Masoud >> >> -------------- >> Masoud Nahali, Sharif University of Technology >> >> _______________________________________________ >> 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/20110511/385e3828/attachment-0001.htm From mayankaditya at gmail.com Wed May 11 11:45:12 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Wed, 11 May 2011 15:15:12 +0530 Subject: [Pw_forum] error during vc-relax Message-ID: Dear Pwscf users I am trying to relax my hexagonal structure, while during the relaxation processes i got the error message "From scale_h: error# not enough space allocated for radial FFT try restarting with larger supercell factor" Thanks -- Mayank BARC From mayankaditya at gmail.com Wed May 11 11:48:13 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Wed, 11 May 2011 15:18:13 +0530 Subject: [Pw_forum] Negative phonon frequency Message-ID: Hi Dear User's I am trying to calculate the phonon frequency of SrFeO compund, but I got negative frequancies at gamma also at other Q points, while I have chossen very high cutoff (ecut=100Ry and ecut_rho=1000), while experimentally the structure is stable at room temperature even up to very low temperature. what could be the possible reason for such negative frequecies. -- Mayank BHABHA ATOMIC RESEARCH CENTER MUMBAI Office: ?022-25595606 Home: 9920397437/9869834437 From mayankaditya at gmail.com Wed May 11 11:52:10 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Wed, 11 May 2011 15:22:10 +0530 Subject: [Pw_forum] warning in SCF run Message-ID: Hi I am calculating the total energy of ZrO2, I am getting warning "Negative rho up down= 0.695E00 0.00" I have choosen 20 times ecut_rho that of ecut. does this affect our results or we can ignore this. Thanks -- Mayank BARC From sclauzer at sissa.it Wed May 11 11:58:45 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 11 May 2011 11:58:45 +0200 Subject: [Pw_forum] The question about difference between diamond and graphite In-Reply-To: References: Message-ID: <5A6D09FC-67F4-487B-AB7B-A78E23AF65A4@sissa.it> How different are your optimized structural parameters from those reported in the literature? Looking at your input file, I would suggest to test convergence with degauss, maybe 0.05 (Rydberg!) is too large. Also try shifted k-points meshes, they should give faster convergence. HTH GS Il giorno 06/mag/2011, alle ore 11.20, Alexander G. Kvashnin ha scritto: > Dear PWSCF community > > In my study I got a problem which I can't solve by myself, > unfortunately. I hope you can give me some tips where I made a > mistake. I have to to investigate the energy difference between > graphite and diamond, but I can't get trusted result.First of all, I > used LDA PP (PZ), I tested it by subsequently increasing of energy > cutoff (from 30 Ry to 120 Ry) as well as increasing of k-points mesh > (4x4x1 for graphite, 4x4x4 for diamond; 6x6x2 for graphite, 6x6x6 for diamond; > 8x8x3 for graphite, 8x8x8 for diamond; 10x10x4 for graphite, 10x10x10 for diamond). > I got the difference between energies of diamond and graphite and tried to understand it > trend (please, see attached figure). As you can see from the figure > difference between energy diamond and graphite is almost zero so I > can't say with confidence what structure is more favorable. > This result different from other theoretical and experimental > studies, therefore it seems that I did something wrong... > > My result: ~ 0.001?0.001 eV/atom > > _______________________________________________ > > | Energy difference (eV/atom) | Method | Reference | > | 0.03 |Experiment | PRB29_6996 | > | 0.01 | LDA-PP | PRB29_6996 | > | 0.04 | LDA-PP | PRB54_14994| > ----------------------------------------------------------------------------------- > > Input files for diamond and graphite are attached to the letter. > > > -- > Sincerely yours > Alexander G. Kvashnin > -------------------------------------------------------------------------------------------------------------------------------- > First year of master degree study > Moscow Institute of Physics and Technology http://mipt.ru/ > 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia > > Junior research scientist > Technological Institute for Superhard > and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ > 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia > ================================================================ > > _______________________________________________ > 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/20110511/b74aaf67/attachment.htm From sclauzer at sissa.it Wed May 11 12:06:12 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 11 May 2011 12:06:12 +0200 Subject: [Pw_forum] The question about difference between diamond and graphite In-Reply-To: <5A6D09FC-67F4-487B-AB7B-A78E23AF65A4@sissa.it> References: <5A6D09FC-67F4-487B-AB7B-A78E23AF65A4@sissa.it> Message-ID: <5B91C1FC-0C2F-4E65-BFF0-39AD40C59B82@sissa.it> Il giorno 11/mag/2011, alle ore 11.58, Gabriele Sclauzero ha scritto: > > How different are your optimized structural parameters from those reported in the literature? > Looking at your input file, I would suggest to test convergence with degauss, maybe 0.05 (Rydberg!) is too large. Moreover smearing is not needed for diamond, since it has a large band gap, while graphene could also be converged without smearing or with a very small spread. > Also try shifted k-points meshes, they should give faster convergence. > > HTH > > GS > > > Il giorno 06/mag/2011, alle ore 11.20, Alexander G. Kvashnin ha scritto: > >> Dear PWSCF community >> >> In my study I got a problem which I can't solve by myself, >> unfortunately. I hope you can give me some tips where I made a >> mistake. I have to to investigate the energy difference between >> graphite and diamond, but I can't get trusted result.First of all, I >> used LDA PP (PZ), I tested it by subsequently increasing of energy >> cutoff (from 30 Ry to 120 Ry) as well as increasing of k-points mesh >> (4x4x1 for graphite, 4x4x4 for diamond; 6x6x2 for graphite, 6x6x6 for diamond; >> 8x8x3 for graphite, 8x8x8 for diamond; 10x10x4 for graphite, 10x10x10 for diamond). >> I got the difference between energies of diamond and graphite and tried to understand it >> trend (please, see attached figure). As you can see from the figure >> difference between energy diamond and graphite is almost zero so I >> can't say with confidence what structure is more favorable. >> This result different from other theoretical and experimental >> studies, therefore it seems that I did something wrong... >> >> My result: ~ 0.001?0.001 eV/atom >> >> _______________________________________________ >> >> | Energy difference (eV/atom) | Method | Reference | >> | 0.03 |Experiment | PRB29_6996 | >> | 0.01 | LDA-PP | PRB29_6996 | >> | 0.04 | LDA-PP | PRB54_14994| >> ----------------------------------------------------------------------------------- >> >> Input files for diamond and graphite are attached to the letter. >> >> >> -- >> Sincerely yours >> Alexander G. Kvashnin >> -------------------------------------------------------------------------------------------------------------------------------- >> First year of master degree study >> Moscow Institute of Physics and Technology http://mipt.ru/ >> 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia >> >> Junior research scientist >> Technological Institute for Superhard >> and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ >> 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia >> ================================================================ >> >> _______________________________________________ >> 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/20110511/ce68efb1/attachment-0001.htm From martins at if.uff.br Wed May 11 12:46:36 2011 From: martins at if.uff.br (martins at if.uff.br) Date: Wed, 11 May 2011 07:46:36 -0300 Subject: [Pw_forum] The question about difference between diamond and graphite Message-ID: <20110511074636.10200umugj9hml1o@webmail.if.uff.br> Dear Alexander, Unfortunately, I can't find your attached figure. Anyway, I'd like to make a comment. First, my question is: What did you compare? The total energies of diamond and graphite? If so, in my guess this procedure is wrong: you have to compare the formation energy of both compounds. For the diamond, the formation energy, E_for, would be: E_for = E_tot(diamond) - 2*E_tot(single C atom, isolated) In the above expression, I'm assuming that for the diamond calculation you used a 2-atom unitary cell. Again, FOR ME make sense only the comparison between the formation energies. If you did this, disregard my comment (but in you e-mail you mentioned "energy difference".) Cheers, Adriano ---------------------------------------- Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense - Brazil ---------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From sks.jnc at gmail.com Wed May 11 13:20:06 2011 From: sks.jnc at gmail.com (S. K. S.) Date: Wed, 11 May 2011 13:20:06 +0200 Subject: [Pw_forum] matdyn.x Message-ID: Dear All, I find a bit strange results when using matdyn.x to perform the interpolation in order to get a complete phonon dispersion plot. In case of my system, at Gamma point, ph.x prints out two noticeably distinguishable triply degenerate phonon modes of frequency values as follows : -18.9595 -18.9595 -18.9595 -11.8835 -11.8835 -11.8835 However, after using "matdyn.x" the above phonons become like : -18.6356 -18.6356 -18.6356 -18.6096 -18.6096 -18.6096 This looks quite strange to me. As far as I understand, the phonon interpolation should not change the frequency values at Gamma point or any other high-symmetry point (suppose X in my case) which have been already computed by the QE_phonon code. Interpolation means, it should only generate more frequencies in between Gamma and X point, not changing the frequency values in the exact Gamma and X point, which have been already printed by the ph.x run. Looking forward to your comments. Thanking you and with my best regards, Saha S. K. R&D Assistant, JNCASR Bangalore -560064 From degironc at sissa.it Wed May 11 14:13:09 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 11 May 2011 14:13:09 +0200 Subject: [Pw_forum] matdyn.x In-Reply-To: References: Message-ID: <4DCA7D55.80309@sissa.it> are you imposing acoustic sum rule ? this change slightly the frequencies . isn't strange that your frequencies are all negative (imaginary) ? is your system stable ? stefano 05/11/2011 01:20 PM, S. K. S. wrote: > Dear All, > > I find a bit strange results when using matdyn.x to perform the > interpolation in order > to get a complete phonon dispersion plot. > > In case of my system, at Gamma point, ph.x prints out two noticeably > distinguishable triply degenerate phonon modes of frequency values as follows : > > -18.9595 -18.9595 -18.9595 -11.8835 -11.8835 -11.8835 > > However, after using "matdyn.x" the above phonons become like : > > -18.6356 -18.6356 -18.6356 -18.6096 -18.6096 -18.6096 > > This looks quite strange to me. As far as I understand, the phonon > interpolation should > not change the frequency values at Gamma point or any other > high-symmetry point > (suppose X in my case) which have been already computed by the > QE_phonon code. Interpolation means, it should only generate more > frequencies in between > Gamma and X point, not changing the frequency values in the exact > Gamma and X point, which have been already printed by the ph.x run. > > Looking forward to your comments. > > Thanking you and with my best regards, > > Saha S. K. > R&D Assistant, > JNCASR > Bangalore -560064 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sks.jnc at gmail.com Wed May 11 14:35:20 2011 From: sks.jnc at gmail.com (S. K. S.) Date: Wed, 11 May 2011 14:35:20 +0200 Subject: [Pw_forum] matdyn.x In-Reply-To: <4DCA7D55.80309@sissa.it> References: <4DCA7D55.80309@sissa.it> Message-ID: Dear Stefano, Thanks a lot for your quick reply. Yes, both set of the frequencies are obtained after imposing ASR. All of frequencies are not negative. Two of the modes among total 5 modes (triply generate) are negative, which are not very unusual in a BaTiO3-type cubic perovskite. regards, Saha S. K. On 5/11/11, Stefano de Gironcoli wrote: > are you imposing acoustic sum rule ? this change slightly the frequencies . > isn't strange that your frequencies are all negative (imaginary) ? > is your system stable ? > stefano > From ttduyle at gmail.com Wed May 11 16:25:38 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 11 May 2011 10:25:38 -0400 Subject: [Pw_forum] Negative phonon frequency In-Reply-To: References: Message-ID: Did you optimize WELL the structure of SrFeO? -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Wed, May 11, 2011 at 5:48 AM, mayank gupta wrote: > Hi Dear User's > > > I am trying to calculate the phonon frequency of SrFeO compund, but I > got negative frequancies at gamma also at other Q points, while I have > chossen very high cutoff (ecut=100Ry and ecut_rho=1000), while > experimentally the structure is stable at room temperature even up to > very low temperature. what could be the possible reason for such > negative frequecies. > > -- > Mayank > > BHABHA ATOMIC RESEARCH CENTER > MUMBAI > Office: ?022-25595606 > Home: 9920397437/9869834437 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From swapnil.chandratre at gmail.com Wed May 11 21:18:25 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Wed, 11 May 2011 14:18:25 -0500 Subject: [Pw_forum] Error Installing XCrysden In-Reply-To: <1305040076.2614.38.camel@catalyst.ijs.si> References: <1305040076.2614.38.camel@catalyst.ijs.si> Message-ID: Hi, I think the error is the first one, can you help me compile it better? On Tue, May 10, 2011 at 10:07 AM, Tone Kokalj wrote: > On Mon, 2011-05-09 at 14:13 -0500, swapnil chandratre wrote: > > Hi, > > > > > > I am trying to install XCrysden 1.5.23, i receive the error, > > > > > > ./xcrysden: line 224: /home/...../bin/xcrys: No such file or > > directorym > > what could be wrong. > > Please address next time such questions to xcrysden mailing list. > > There are two possibilities: > > (1) you downloaded the source package and you didn't compile it, so the > file $$$/bin/xcrys is not there > > (2) you downloaded the binary package, and mis-defined the > XCRYSDEN_TOPDIR variable (note that from 1.5.* on the XCRYSDEN_TOPDIR is > not required anymore, hence you may unset it) > > Regards, Tone > > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110511/7c09e20a/attachment.htm From swapnil.chandratre at gmail.com Wed May 11 23:20:40 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Wed, 11 May 2011 16:20:40 -0500 Subject: [Pw_forum] Strained Graphene Nanoribbon Message-ID: Hi, I have prepared input file for strained Graphene Nanoribbon, I am to get it relaxed. But I receive the following error: *from davcio : error # 10error while writing to file* * * I am using an orthorombic supercell with periodicity of the ribbon in z direction. I have tried to make sure the error is not because of some negligence in setting the output directory. I believe I need to input celldm() with proper values, being new to QE, i am trying to install XCrysden as well to figure out that part, but I was wondering if anyone can suggest the error in the file or possibly suggest the values of celldm that I should used. The input file is &control calculation = 'relax' restart_mode = 'from_scratch' pseudo_dir = '/home/s/schandratre/Espresso/pseudo' outdir = '/home/s/schandratre/Espresso/strained74' / &system ibrav = 8 a = 10.000000 b = 27.903500 c = 17.391306 nat=128 ntyp=2 ecutwfc=50.0 ecutrho = 450.0 occupations = 'smearing' degauss=0.02 smearing = 'gaussian', / &electrons conv_thr = 1.0d-6, mixing_beta=0.3, / &ions ion_dynamics='damp' pot_extrapolation='second_order' wfc_extrapolation='second_order' / ATOMIC_SPECIES C 12.0000 C.pz-rrkjus.UPF H 1.00000 H.pz-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C 5.000000e+00 5.953494e+00 2.898550e+00 C 5.000000e+00 7.183995e+00 3.623188e+00 C 5.000000e+00 5.953494e+00 1.449275e+00 C 5.000000e+00 8.414496e+00 2.898550e+00 C 5.000000e+00 9.644997e+00 3.623188e+00 C 5.000000e+00 7.183995e+00 7.246375e-01 C 5.000000e+00 8.414496e+00 1.449275e+00 C 5.000000e+00 1.087550e+01 2.898550e+00 C 5.000000e+00 1.210600e+01 3.623188e+00 C 5.000000e+00 9.644997e+00 7.246375e-01 C 5.000000e+00 1.087550e+01 1.449275e+00 C 5.000000e+00 1.333650e+01 2.898550e+00 C 5.000000e+00 1.456700e+01 3.623188e+00 C 5.000000e+00 1.210600e+01 7.246375e-01 C 5.000000e+00 1.333650e+01 1.449275e+00 C 5.000000e+00 1.579750e+01 2.898550e+00 C 5.000000e+00 1.702800e+01 3.623188e+00 C 5.000000e+00 1.456700e+01 7.246375e-01 C 5.000000e+00 1.579750e+01 1.449275e+00 C 5.000000e+00 1.825850e+01 2.898550e+00 C 5.000000e+00 1.948900e+01 3.623188e+00 C 5.000000e+00 1.702800e+01 7.246375e-01 C 5.000000e+00 1.825850e+01 1.449275e+00 C 5.000000e+00 2.071950e+01 2.898550e+00 C 5.000000e+00 2.195001e+01 3.623188e+00 C 5.000000e+00 1.948900e+01 7.246375e-01 C 5.000000e+00 2.071950e+01 1.449275e+00 C 5.000000e+00 2.195001e+01 7.246375e-01 H 5.000000e+00 5.000000e+00 3.460059e+00 H 5.000000e+00 5.000000e+00 8.877659e-01 H 5.000000e+00 2.290350e+01 3.061678e+00 H 5.000000e+00 2.290350e+01 1.286147e+00 C 5.000000e+00 5.953494e+00 7.246375e+00 C 5.000000e+00 7.183995e+00 7.971013e+00 C 5.000000e+00 5.953494e+00 5.797100e+00 C 5.000000e+00 8.414496e+00 7.246375e+00 C 5.000000e+00 9.644997e+00 7.971013e+00 C 5.000000e+00 7.183995e+00 5.072463e+00 C 5.000000e+00 8.414496e+00 5.797100e+00 C 5.000000e+00 1.087550e+01 7.246375e+00 C 5.000000e+00 1.210600e+01 7.971013e+00 C 5.000000e+00 9.644997e+00 5.072463e+00 C 5.000000e+00 1.087550e+01 5.797100e+00 C 5.000000e+00 1.333650e+01 7.246375e+00 C 5.000000e+00 1.456700e+01 7.971013e+00 C 5.000000e+00 1.210600e+01 5.072463e+00 C 5.000000e+00 1.333650e+01 5.797100e+00 C 5.000000e+00 1.579750e+01 7.246375e+00 C 5.000000e+00 1.702800e+01 7.971013e+00 C 5.000000e+00 1.456700e+01 5.072463e+00 C 5.000000e+00 1.579750e+01 5.797100e+00 C 5.000000e+00 1.825850e+01 7.246375e+00 C 5.000000e+00 1.948900e+01 7.971013e+00 C 5.000000e+00 1.702800e+01 5.072463e+00 C 5.000000e+00 1.825850e+01 5.797100e+00 C 5.000000e+00 2.071950e+01 7.246375e+00 C 5.000000e+00 2.195001e+01 7.971013e+00 C 5.000000e+00 1.948900e+01 5.072463e+00 C 5.000000e+00 2.071950e+01 5.797100e+00 C 5.000000e+00 2.195001e+01 5.072463e+00 H 5.000000e+00 5.000000e+00 7.807884e+00 H 5.000000e+00 5.000000e+00 5.235591e+00 H 5.000000e+00 2.290350e+01 7.409503e+00 H 5.000000e+00 2.290350e+01 5.633972e+00 C 5.000000e+00 5.953494e+00 1.159420e+01 C 5.000000e+00 7.183995e+00 1.231884e+01 C 5.000000e+00 5.953494e+00 1.014493e+01 C 5.000000e+00 8.414496e+00 1.159420e+01 C 5.000000e+00 9.644997e+00 1.231884e+01 C 5.000000e+00 7.183995e+00 9.420288e+00 C 5.000000e+00 8.414496e+00 1.014493e+01 C 5.000000e+00 1.087550e+01 1.159420e+01 C 5.000000e+00 1.210600e+01 1.231884e+01 C 5.000000e+00 9.644997e+00 9.420288e+00 C 5.000000e+00 1.087550e+01 1.014493e+01 C 5.000000e+00 1.333650e+01 1.159420e+01 C 5.000000e+00 1.456700e+01 1.231884e+01 C 5.000000e+00 1.210600e+01 9.420288e+00 C 5.000000e+00 1.333650e+01 1.014493e+01 C 5.000000e+00 1.579750e+01 1.159420e+01 C 5.000000e+00 1.702800e+01 1.231884e+01 C 5.000000e+00 1.456700e+01 9.420288e+00 C 5.000000e+00 1.579750e+01 1.014493e+01 C 5.000000e+00 1.825850e+01 1.159420e+01 C 5.000000e+00 1.948900e+01 1.231884e+01 C 5.000000e+00 1.702800e+01 9.420288e+00 C 5.000000e+00 1.825850e+01 1.014493e+01 C 5.000000e+00 2.071950e+01 1.159420e+01 C 5.000000e+00 2.195001e+01 1.231884e+01 C 5.000000e+00 1.948900e+01 9.420288e+00 C 5.000000e+00 2.071950e+01 1.014493e+01 C 5.000000e+00 2.195001e+01 9.420288e+00 H 5.000000e+00 5.000000e+00 1.215571e+01 H 5.000000e+00 5.000000e+00 9.583416e+00 H 5.000000e+00 2.290350e+01 1.175733e+01 H 5.000000e+00 2.290350e+01 9.981797e+00 C 5.000000e+00 5.953494e+00 1.594203e+01 C 5.000000e+00 7.183995e+00 1.666666e+01 C 5.000000e+00 5.953494e+00 1.449275e+01 C 5.000000e+00 8.414496e+00 1.594203e+01 C 5.000000e+00 9.644997e+00 1.666666e+01 C 5.000000e+00 7.183995e+00 1.376811e+01 C 5.000000e+00 8.414496e+00 1.449275e+01 C 5.000000e+00 1.087550e+01 1.594203e+01 C 5.000000e+00 1.210600e+01 1.666666e+01 C 5.000000e+00 9.644997e+00 1.376811e+01 C 5.000000e+00 1.087550e+01 1.449275e+01 C 5.000000e+00 1.333650e+01 1.594203e+01 C 5.000000e+00 1.456700e+01 1.666666e+01 C 5.000000e+00 1.210600e+01 1.376811e+01 C 5.000000e+00 1.333650e+01 1.449275e+01 C 5.000000e+00 1.579750e+01 1.594203e+01 C 5.000000e+00 1.702800e+01 1.666666e+01 C 5.000000e+00 1.456700e+01 1.376811e+01 C 5.000000e+00 1.579750e+01 1.449275e+01 C 5.000000e+00 1.825850e+01 1.594203e+01 C 5.000000e+00 1.948900e+01 1.666666e+01 C 5.000000e+00 1.702800e+01 1.376811e+01 C 5.000000e+00 1.825850e+01 1.449275e+01 C 5.000000e+00 2.071950e+01 1.594203e+01 C 5.000000e+00 2.195001e+01 1.666666e+01 C 5.000000e+00 1.948900e+01 1.376811e+01 C 5.000000e+00 2.071950e+01 1.449275e+01 C 5.000000e+00 2.195001e+01 1.376811e+01 H 5.000000e+00 5.000000e+00 1.650353e+01 H 5.000000e+00 5.000000e+00 1.393124e+01 H 5.000000e+00 2.290350e+01 1.610515e+01 H 5.000000e+00 2.290350e+01 1.432962e+01 K_POINTS {automatic} 1 1 100 0 0 0 -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110511/16c52133/attachment-0001.htm From taoohee at gmail.com Thu May 12 03:18:14 2011 From: taoohee at gmail.com (=?utf-8?B?dGFvb2hlZQ==?=) Date: Thu, 12 May 2011 09:18:14 +0800 Subject: [Pw_forum] =?utf-8?q?Can_pwscf_calculate_the_structure_of_charged?= =?utf-8?q?_slab_=3F?= Message-ID: <201105120918099726071@gmail.com> Dear pwscf users, I wonder if pwscf is capable of calculating the equilibrium structure of charged system, e.g., charged 2D slab. As I know VASP is unable to calculate the energe of charged slab, what about pwscf? Thanks! 2011-05-12 taoohee ???? swapnil chandratre ????? 2011-05-12 05:20:52 ???? PWSCF Forum ??? ??? [Pw_forum] Strained Graphene Nanoribbon Hi, I have prepared input file for strained Graphene Nanoribbon, I am to get it relaxed. But I receive the following error: from davcio : error # 10error while writing to file I am using an orthorombic supercell with periodicity of the ribbon in z direction. I have tried to make sure the error is not because of some negligence in setting the output directory. I believe I need to input celldm() with proper values, being new to QE, i am trying to install XCrysden as well to figure out that part, but I was wondering if anyone can suggest the error in the file or possibly suggest the values of celldm that I should used. The input file is &control calculation = 'relax' restart_mode = 'from_scratch' pseudo_dir = '/home/s/schandratre/Espresso/pseudo' outdir = '/home/s/schandratre/Espresso/strained74' / &system ibrav = 8 a = 10.000000 b = 27.903500 c = 17.391306 nat=128 ntyp=2 ecutwfc=50.0 ecutrho = 450.0 occupations = 'smearing' degauss=0.02 smearing = 'gaussian', / &electrons conv_thr = 1.0d-6, mixing_beta=0.3, / &ions ion_dynamics='damp' pot_extrapolation='second_order' wfc_extrapolation='second_order' / ATOMIC_SPECIES C 12.0000 C.pz-rrkjus.UPF H 1.00000 H.pz-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C 5.000000e+00 5.953494e+00 2.898550e+00 C 5.000000e+00 7.183995e+00 3.623188e+00 C 5.000000e+00 5.953494e+00 1.449275e+00 C 5.000000e+00 8.414496e+00 2.898550e+00 C 5.000000e+00 9.644997e+00 3.623188e+00 C 5.000000e+00 7.183995e+00 7.246375e-01 C 5.000000e+00 8.414496e+00 1.449275e+00 C 5.000000e+00 1.087550e+01 2.898550e+00 C 5.000000e+00 1.210600e+01 3.623188e+00 C 5.000000e+00 9.644997e+00 7.246375e-01 C 5.000000e+00 1.087550e+01 1.449275e+00 C 5.000000e+00 1.333650e+01 2.898550e+00 C 5.000000e+00 1.456700e+01 3.623188e+00 C 5.000000e+00 1.210600e+01 7.246375e-01 C 5.000000e+00 1.333650e+01 1.449275e+00 C 5.000000e+00 1.579750e+01 2.898550e+00 C 5.000000e+00 1.702800e+01 3.623188e+00 C 5.000000e+00 1.456700e+01 7.246375e-01 C 5.000000e+00 1.579750e+01 1.449275e+00 C 5.000000e+00 1.825850e+01 2.898550e+00 C 5.000000e+00 1.948900e+01 3.623188e+00 C 5.000000e+00 1.702800e+01 7.246375e-01 C 5.000000e+00 1.825850e+01 1.449275e+00 C 5.000000e+00 2.071950e+01 2.898550e+00 C 5.000000e+00 2.195001e+01 3.623188e+00 C 5.000000e+00 1.948900e+01 7.246375e-01 C 5.000000e+00 2.071950e+01 1.449275e+00 C 5.000000e+00 2.195001e+01 7.246375e-01 H 5.000000e+00 5.000000e+00 3.460059e+00 H 5.000000e+00 5.000000e+00 8.877659e-01 H 5.000000e+00 2.290350e+01 3.061678e+00 H 5.000000e+00 2.290350e+01 1.286147e+00 C 5.000000e+00 5.953494e+00 7.246375e+00 C 5.000000e+00 7.183995e+00 7.971013e+00 C 5.000000e+00 5.953494e+00 5.797100e+00 C 5.000000e+00 8.414496e+00 7.246375e+00 C 5.000000e+00 9.644997e+00 7.971013e+00 C 5.000000e+00 7.183995e+00 5.072463e+00 C 5.000000e+00 8.414496e+00 5.797100e+00 C 5.000000e+00 1.087550e+01 7.246375e+00 C 5.000000e+00 1.210600e+01 7.971013e+00 C 5.000000e+00 9.644997e+00 5.072463e+00 C 5.000000e+00 1.087550e+01 5.797100e+00 C 5.000000e+00 1.333650e+01 7.246375e+00 C 5.000000e+00 1.456700e+01 7.971013e+00 C 5.000000e+00 1.210600e+01 5.072463e+00 C 5.000000e+00 1.333650e+01 5.797100e+00 C 5.000000e+00 1.579750e+01 7.246375e+00 C 5.000000e+00 1.702800e+01 7.971013e+00 C 5.000000e+00 1.456700e+01 5.072463e+00 C 5.000000e+00 1.579750e+01 5.797100e+00 C 5.000000e+00 1.825850e+01 7.246375e+00 C 5.000000e+00 1.948900e+01 7.971013e+00 C 5.000000e+00 1.702800e+01 5.072463e+00 C 5.000000e+00 1.825850e+01 5.797100e+00 C 5.000000e+00 2.071950e+01 7.246375e+00 C 5.000000e+00 2.195001e+01 7.971013e+00 C 5.000000e+00 1.948900e+01 5.072463e+00 C 5.000000e+00 2.071950e+01 5.797100e+00 C 5.000000e+00 2.195001e+01 5.072463e+00 H 5.000000e+00 5.000000e+00 7.807884e+00 H 5.000000e+00 5.000000e+00 5.235591e+00 H 5.000000e+00 2.290350e+01 7.409503e+00 H 5.000000e+00 2.290350e+01 5.633972e+00 C 5.000000e+00 5.953494e+00 1.159420e+01 C 5.000000e+00 7.183995e+00 1.231884e+01 C 5.000000e+00 5.953494e+00 1.014493e+01 C 5.000000e+00 8.414496e+00 1.159420e+01 C 5.000000e+00 9.644997e+00 1.231884e+01 C 5.000000e+00 7.183995e+00 9.420288e+00 C 5.000000e+00 8.414496e+00 1.014493e+01 C 5.000000e+00 1.087550e+01 1.159420e+01 C 5.000000e+00 1.210600e+01 1.231884e+01 C 5.000000e+00 9.644997e+00 9.420288e+00 C 5.000000e+00 1.087550e+01 1.014493e+01 C 5.000000e+00 1.333650e+01 1.159420e+01 C 5.000000e+00 1.456700e+01 1.231884e+01 C 5.000000e+00 1.210600e+01 9.420288e+00 C 5.000000e+00 1.333650e+01 1.014493e+01 C 5.000000e+00 1.579750e+01 1.159420e+01 C 5.000000e+00 1.702800e+01 1.231884e+01 C 5.000000e+00 1.456700e+01 9.420288e+00 C 5.000000e+00 1.579750e+01 1.014493e+01 C 5.000000e+00 1.825850e+01 1.159420e+01 C 5.000000e+00 1.948900e+01 1.231884e+01 C 5.000000e+00 1.702800e+01 9.420288e+00 C 5.000000e+00 1.825850e+01 1.014493e+01 C 5.000000e+00 2.071950e+01 1.159420e+01 C 5.000000e+00 2.195001e+01 1.231884e+01 C 5.000000e+00 1.948900e+01 9.420288e+00 C 5.000000e+00 2.071950e+01 1.014493e+01 C 5.000000e+00 2.195001e+01 9.420288e+00 H 5.000000e+00 5.000000e+00 1.215571e+01 H 5.000000e+00 5.000000e+00 9.583416e+00 H 5.000000e+00 2.290350e+01 1.175733e+01 H 5.000000e+00 2.290350e+01 9.981797e+00 C 5.000000e+00 5.953494e+00 1.594203e+01 C 5.000000e+00 7.183995e+00 1.666666e+01 C 5.000000e+00 5.953494e+00 1.449275e+01 C 5.000000e+00 8.414496e+00 1.594203e+01 C 5.000000e+00 9.644997e+00 1.666666e+01 C 5.000000e+00 7.183995e+00 1.376811e+01 C 5.000000e+00 8.414496e+00 1.449275e+01 C 5.000000e+00 1.087550e+01 1.594203e+01 C 5.000000e+00 1.210600e+01 1.666666e+01 C 5.000000e+00 9.644997e+00 1.376811e+01 C 5.000000e+00 1.087550e+01 1.449275e+01 C 5.000000e+00 1.333650e+01 1.594203e+01 C 5.000000e+00 1.456700e+01 1.666666e+01 C 5.000000e+00 1.210600e+01 1.376811e+01 C 5.000000e+00 1.333650e+01 1.449275e+01 C 5.000000e+00 1.579750e+01 1.594203e+01 C 5.000000e+00 1.702800e+01 1.666666e+01 C 5.000000e+00 1.456700e+01 1.376811e+01 C 5.000000e+00 1.579750e+01 1.449275e+01 C 5.000000e+00 1.825850e+01 1.594203e+01 C 5.000000e+00 1.948900e+01 1.666666e+01 C 5.000000e+00 1.702800e+01 1.376811e+01 C 5.000000e+00 1.825850e+01 1.449275e+01 C 5.000000e+00 2.071950e+01 1.594203e+01 C 5.000000e+00 2.195001e+01 1.666666e+01 C 5.000000e+00 1.948900e+01 1.376811e+01 C 5.000000e+00 2.071950e+01 1.449275e+01 C 5.000000e+00 2.195001e+01 1.376811e+01 H 5.000000e+00 5.000000e+00 1.650353e+01 H 5.000000e+00 5.000000e+00 1.393124e+01 H 5.000000e+00 2.290350e+01 1.610515e+01 H 5.000000e+00 2.290350e+01 1.432962e+01 K_POINTS {automatic} 1 1 100 0 0 0 -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/80d88f8f/attachment-0001.htm From tanycimr at gmail.com Thu May 12 04:37:18 2011 From: tanycimr at gmail.com (=?Big5?B?zuu0xqbB?=) Date: Thu, 12 May 2011 10:37:18 +0800 Subject: [Pw_forum] CELL PARAMETERS Message-ID: Dear all i want to get the CELL PARAMETERS after optimization . i input celldm(1)=9.562 celldm(4)=0.5269558 .and the result of vc-relax is CELL_PARAMETERS (alat= 9.56200000) 0.474658417 -0.274044165 0.810068437 0.000000000 0.548088330 0.810068437 -0.474658417 -0.274044165 0.810068437 i wonder why the celldm(1) is still the same . thanks in advance tanyci nankai university tianjin china -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/2514c9a5/attachment.htm From nkxirainbow at gmail.com Thu May 12 05:36:06 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Thu, 12 May 2011 11:36:06 +0800 Subject: [Pw_forum] Can pwscf calculate the structure of charged slab ? In-Reply-To: <201105120918099726071@gmail.com> References: <201105120918099726071@gmail.com> Message-ID: Dear Swapnil: Dear pwscf users, > I wonder if pwscf is capable of calculating the equilibrium structure of > charged system, e.g., charged 2D slab. As I know VASP is unable to calculate > the energe of charged slab, what about pwscf? > I beg to differ. As far as I know, both vasp ans QE can deal with charged system. If you searched "charged pwscf" or "charged vasp", you will get a lot of helpful results. > Thanks! > > 2011-05-12 > ------------------------------ > taoohee > > 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/20110512/b68d1c09/attachment.htm From mayankaditya at gmail.com Thu May 12 06:55:31 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Thu, 12 May 2011 10:25:31 +0530 Subject: [Pw_forum] Warning in PW.x run Message-ID: Dear All I have to post this question again since I didn't get any answer on web. In my SCF out file I got warning "negative rho (up, down): 0.715E+00 0.000E+00" I have also check this wth increase the ecut_rho value but the numerical value in the warning message is same. I would like to know this is the problem of pseodo potential, It can affect the results like phonon frequencies etc. Thanks -- Mayank BARC From raamesh123 at rediffmail.com Thu May 12 07:07:17 2011 From: raamesh123 at rediffmail.com (ramesh kumar) Date: 12 May 2011 05:07:17 -0000 Subject: [Pw_forum] =?utf-8?q?_Error_Installing_XCrysden?= In-Reply-To: Message-ID: <1305148817.S.44512.29009.F.H.TnB3X2ZvcnVtLXJlcXVlc3RAcHdzY2Yub3JnAFB3X2ZvcnVtIERpZ2VzdCwgVm9sIDQ3LCBJc3N1ZSAzNw__.f6-144-198.old.1305176823.46208@webmail.rediffmail.com> Dear Swapnil Compilation is simple....if your system has tcl/tk libraries..... Yesterday i got this message from prof. Kokalj "Let me know how this xcrysden version works. Make sure you install the following cygwin packages: * bash * bc * coreutils * gawk * grep * gzip * ImageMagick * less * more * opengl * tcltk Regards, Tone" I followed it ....working fine... just give ./xcConfigure.sh that will do the job with regards ramesh 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/20110512/1519d87f/attachment.htm From sclauzer at sissa.it Thu May 12 09:17:17 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 12 May 2011 09:17:17 +0200 Subject: [Pw_forum] Warning in PW.x run In-Reply-To: References: Message-ID: Dear Mayank, Does this happen at the beginning or at the end of the SCF loop? How may electrons do you have in your system. Please provide more details. Have you searched on the forum archives for similar posts? GS Il giorno 12/mag/2011, alle ore 06.55, mayank gupta ha scritto: > Dear All > > > I have to post this question again since I didn't get any answer on > web. In my SCF out file I got warning "negative rho (up, down): > 0.715E+00 0.000E+00" > I have also check this wth increase the ecut_rho value but the > numerical value in the warning message is same. I would like to know > this is the problem of pseodo potential, It can affect the results > like phonon frequencies etc. > > > Thanks > -- > Mayank > BARC > _______________________________________________ > 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/20110512/e85675c0/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Thu May 12 11:27:10 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Thu, 12 May 2011 11:27:10 +0200 Subject: [Pw_forum] Can pwscf calculate the structure of charged slab ? In-Reply-To: References: <201105120918099726071@gmail.com> Message-ID: <201105121127.10650.giuseppe.mattioli@mlib.ism.cnr.it> A different matter is perhaps to obtain meaningful energy differences between neutral and charged supercells, e.g., in the case of Dscf-like calculations. At variance with real-space (i.e. Hartree-Fock on gaussian basis set) calculations, you need nontrivial tricks to align the potential... dunno if this can help Giuseppe On Thursday 12 May 2011 05:36:06 xirainbow wrote: > Dear Swapnil: > > Dear pwscf users, > > > I wonder if pwscf is capable of calculating the equilibrium structure of > > charged system, e.g., charged 2D slab. As I know VASP is unable to > > calculate the energe of charged slab, what about pwscf? > > I beg to differ. > As far as I know, both vasp ans QE can deal with charged system. > If you searched "charged pwscf" or "charged vasp", you will get a lot of > helpful results. > > > Thanks! > > > > 2011-05-12 > > ------------------------------ > > taoohee > > > > > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From sks.jnc at gmail.com Thu May 12 11:28:14 2011 From: sks.jnc at gmail.com (S. K. S.) Date: Thu, 12 May 2011 11:28:14 +0200 Subject: [Pw_forum] Problem in paralization with QE4.3 Message-ID: Dear All, Has anybody implemented "wfcdir" option in the QE_ph code as like QE_pw code ? The exactly same job which was running okay in the older version of QE (4.2) is not running in the newest version of QE (4.3). Here is the error : Calculation of q = 0.0000000 0.0000000 0.0000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from diropn : error # 21 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from diropn : error # 21 error opening pbmno.bar error opening pbmno.bar %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from diropn : error # 21 error opening pbmno.bar %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from diropn : error # 21 error opening pbmno.bar %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... stopping ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from diropn : error # 21 error opening pbmno.bar %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD with errorcode 0. 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. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun has exited due to process rank 5 with PID 4397 on Looking forward to your comments. Thanking you and with my best regards, Saha S. K. R&D Assistant JNCASR Bangalore - 560064 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/37aa1739/attachment.htm From giannozz at democritos.it Thu May 12 13:01:24 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 May 2011 13:01:24 +0200 Subject: [Pw_forum] CELL PARAMETERS In-Reply-To: References: Message-ID: <585FFEC7-C1AE-4F7E-94D2-9BA5FBA2391D@democritos.it> On May 12, 2011, at 4:37 , ??? wrote: > i wonder why the celldm(1) is still the same . because the important output is the new unit cell, described by the primitive vectors. Vectors are written in units of celldm(1) only in order to produce an output format that looks like the input one. One may always redefine celldm(1) in such a way that it is the length of one of the primitive vectors ( a typical definition of lattice parameters "a") 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 May 12 13:04:33 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 May 2011 13:04:33 +0200 Subject: [Pw_forum] Problem in paralization with QE4.3 In-Reply-To: References: Message-ID: On May 12, 2011, at 11:28 , S. K. S. wrote: > Has anybody implemented "wfcdir" option in the QE_ph code as like > QE_pw > code ? The exactly same job which was running okay in the older > version > of QE (4.2) is not running in the newest version of QE (4.3). this might be the same problem as here: http://www.democritos.it/pipermail/pw_forum/2011-May/020382.html My answer is still valid: http://www.democritos.it/pipermail/pw_forum/2011-May/020383.html 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 mohnish.iitk at gmail.com Thu May 12 13:06:46 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Thu, 12 May 2011 16:36:46 +0530 Subject: [Pw_forum] Negative phonon frequency In-Reply-To: References: Message-ID: Dear Mayank! There is no need to use this much high cutoff. First of all see proper convergence with k-points grids. Then "conv_thr" should be less than 10^-12. Before doing phonon calculation do vc-relax with high accuracy. And if you get very small negative value then you can ignore it.. On Wed, May 11, 2011 at 3:18 PM, mayank gupta wrote: > Hi Dear User's > > > I am trying to calculate the phonon frequency of SrFeO compund, but I > got negative frequancies at gamma also at other Q points, while I have > chossen very high cutoff (ecut=100Ry and ecut_rho=1000), while > experimentally the structure is stable at room temperature even up to > very low temperature. what could be the possible reason for such > negative frequecies. > > -- > Mayank > > BHABHA ATOMIC RESEARCH CENTER > MUMBAI > Office: 022-25595606 > Home: 9920397437/9869834437 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/592fd3f4/attachment.htm From hicpalm at gmail.com Thu May 12 13:47:38 2011 From: hicpalm at gmail.com (hichem bouderba) Date: Thu, 12 May 2011 14:47:38 +0300 Subject: [Pw_forum] UPF PAW with Atompaw Message-ID: Hi, I have a PAW generated with Atompaw and when used with pw.x the code stops at : Parallel version (MPI), running on 1 processors 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... With the following error : ######################################################################################################################## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_attr (iotk_attr.spp:439) # CVS Revision: 1.21 # Attribute size does not match attr= size=1 ######################################################################################################################## here is the atompaw input ( just an example to reproduce the error): Ge 32 GGA-PBE 4 4 3 0 0 0 4 1 2 0 0 0 c c c v c c v v 2 2.25 y 0.5 n y 3 n y 0.6 n vanderbilt 3 2 2.25 2.25 2.25 2.25 2.25 2.25 3 default 0 this is Ge dataset with 3d electrons in the valence. if I keep the 3d electrons in the core the error disappears. the atompaw input is: Ge 32 GGA-PBE 4 4 3 0 0 0 4 1 2 0 0 0 c c c v c c v c 1 2.25 y 0.5 n y 3 n vanderbilt 3 2 2.25 2.25 2.25 2.25 3 default 0 it seems that there is a problem at the level of the data translation to the UPF format in the atompaw code. thank you for your help. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/a7a29e57/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Thu May 12 14:13:25 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 12 May 2011 14:13:25 +0200 Subject: [Pw_forum] UPF PAW with Atompaw In-Reply-To: References: Message-ID: On Thu, 12 May 2011 13:47:38 +0200, hichem bouderba wrote: > I have a PAW generated with Atompaw and when used with pw.x the code > stops > at : [...] Dear Hichem, they both work perfectly here with Quantum-ESPRESSO ~4.2 compiled with G95 4.0.3 and atompaw compiled with gfortan 4.1.2. 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?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From hicpalm at gmail.com Thu May 12 14:55:54 2011 From: hicpalm at gmail.com (hichem bouderba) Date: Thu, 12 May 2011 15:55:54 +0300 Subject: [Pw_forum] UPF PAW with Atompaw In-Reply-To: References: Message-ID: Hi lorenzo, I am using QE 4.3 and Atompaw both with openmpi and ifort 2011. I will try with QE 4.2. thank you lorenzo. regards On Thu, May 12, 2011 at 3:13 PM, Lorenzo Paulatto < Lorenzo.Paulatto at impmc.upmc.fr> wrote: > On Thu, 12 May 2011 13:47:38 +0200, hichem bouderba > wrote: > > I have a PAW generated with Atompaw and when used with pw.x the code > > stops > > at : [...] > > > Dear Hichem, > they both work perfectly here with Quantum-ESPRESSO ~4.2 compiled with G95 > 4.0.3 and atompaw compiled with gfortan 4.1.2. > > 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?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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/525813a2/attachment-0001.htm From giannozz at democritos.it Thu May 12 15:16:41 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 May 2011 15:16:41 +0200 Subject: [Pw_forum] Strained Graphene Nanoribbon In-Reply-To: References: Message-ID: On May 11, 2011, at 23:20 , swapnil chandratre wrote: > I have tried to make sure the error is not because of some > negligence in setting the output directory. then try to make sure that you have enough disk space: your job is quite large 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 zhaohscas at yahoo.com.cn Fri May 13 03:17:24 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Thu, 12 May 2011 21:17:24 -0400 Subject: [Pw_forum] Script for MP grid sampling test. Message-ID: <4DCC86A4.1020808@yahoo.com.cn> Hi all, I want to write a specific script for MP grid sampling test for a specific system. Basically, the idea is as follows: 1- Determine a initial MP grid, say: 4 4 4. 2- increase the divisions along each directions according to a step, say: 1 1 1, In this way, we will have a series of MP grids: 4 4 4, 5 5 5, ... Then, compute the total energy for each MP grid and determine the ultimate MP grid I should used. My issues are: 1- Does this method make sense? 2- About the initial MP grid and the increasing step, could someone please give me some hints on the guidelines to choosing them for a specific system? Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/4d68f55c/attachment.htm From swapnil.chandratre at gmail.com Thu May 12 15:49:48 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Thu, 12 May 2011 08:49:48 -0500 Subject: [Pw_forum] Strained Graphene Nanoribbon In-Reply-To: References: Message-ID: Thank you Dr. Giannozzi I just wanted to know if there is no error with the script, if the only problem is with disk space, then it is little less concerning. Thank you for taking time to answer such questions. On Thu, May 12, 2011 at 8:16 AM, Paolo Giannozzi wrote: > > On May 11, 2011, at 23:20 , swapnil chandratre wrote: > > > I have tried to make sure the error is not because of some > > negligence in setting the output directory. > > then try to make sure that you have enough disk space: > your job is quite large > > 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 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/808092af/attachment.htm From giannozz at democritos.it Thu May 12 16:03:51 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 May 2011 16:03:51 +0200 Subject: [Pw_forum] Strained Graphene Nanoribbon In-Reply-To: References: Message-ID: On May 12, 2011, at 15:49 , swapnil chandratre wrote: > I just wanted to know if there is no error with the script I don't know if there is an error in the script. I just tried to run it on a PC, it starts but it is definitely too large for a single CPU. Since the code writes > 800Mb Kohn-Sham wavefunctions for each of the 100 k-points, insufficient disk space looks like a promising explanation 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 swapnil.chandratre at gmail.com Thu May 12 16:07:51 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Thu, 12 May 2011 09:07:51 -0500 Subject: [Pw_forum] Strained Graphene Nanoribbon In-Reply-To: References: Message-ID: Hi, Thank you for sparing time on this, I will try to get it resolved sooner. Any suggestions are heartily welcomed. On Thu, May 12, 2011 at 9:03 AM, Paolo Giannozzi wrote: > > On May 12, 2011, at 15:49 , swapnil chandratre wrote: > > > I just wanted to know if there is no error with the script > > I don't know if there is an error in the script. I just tried to > run it on a PC, it starts but it is definitely too large for a > single CPU. Since the code writes > 800Mb Kohn-Sham > wavefunctions for each of the 100 k-points, insufficient disk > space looks like a promising explanation > > 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 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/56250b1f/attachment.htm From mayankaditya at gmail.com Thu May 12 16:09:05 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Thu, 12 May 2011 19:39:05 +0530 Subject: [Pw_forum] WARNING :: NEGATIVE RHO UP DOWN Message-ID: Thanks Dr. Gabriele Sclauzero for your interest. yes this warning has started from the beginning till end of the calculation. there are 320 electrons in the system. Here I have post my input file. &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='yo', pseudo_dir = '/home/usr1305/rmittal/pseudo/', outdir='/scratch/rmittal/' / &system ibrav= 3 , celldm(1)=20.05 , nat= 40 , ntyp=3, ecutwfc= 45.00000000 ecutrho= 450.00000000 / &electrons / ATOMIC_SPECIES Y1 88.905 Y.pbe-nsp-van.UPF Y2 88.905 Y.pbe-nsp-van.UPF O 15.99 O.pbe-van_ak.UPF ATOMIC_POSITIONS Y1 0.250000000 0.250000000 0.250000000 0 0 0 Y1 0.250000000 0.750000000 0.750000000 0 0 0 Y1 0.750000000 0.750000000 0.250000000 0 0 0 Y1 0.750000000 0.250000000 0.750000000 0 0 0 Y2 0.967120139 0.000000000 0.250000000 1 0 0 Y2 0.532879861 0.000000000 0.750000000 1 0 0 Y2 0.250000000 0.967119689 0.000000000 0 1 0 Y2 0.750000000 0.532880311 0.000000000 0 1 0 Y2 0.000000000 0.250000000 0.967124172 0 0 1 Y2 0.000000000 0.750000000 0.532877560 0 0 1 Y2 0.032860071 0.000000000 0.750000000 1 0 0 Y2 0.467139929 0.000000000 0.250000000 1 0 0 Y2 0.750000000 0.032860701 0.000000000 0 1 0 Y2 0.250000000 0.467139299 0.000000000 0 1 0 Y2 0.000000000 0.750000000 0.032861271 0 0 1 Y2 0.000000000 0.250000000 0.467115482 0 0 1 O 0.390998425 0.152138160 0.379958450 O 0.109001575 0.847861840 0.879958450 O 0.608997854 0.652141038 0.120029038 O 0.891002146 0.347858962 0.620029038 O 0.379957996 0.390999728 0.152138112 O 0.879956876 0.108999421 0.847864349 O 0.120042004 0.609000272 0.652138112 O 0.620043124 0.891000579 0.347864349 O 0.152142612 0.379962145 0.390987420 O 0.847862406 0.879957655 0.108999866 O 0.652137594 0.120042345 0.608999866 O 0.347857388 0.620037855 0.890987420 O 0.609006964 0.847866491 0.620024431 O 0.890993036 0.152133509 0.120024431 O 0.390991503 0.347868409 0.879975343 O 0.109008497 0.652131591 0.379975343 O 0.620024777 0.609009267 0.847856632 O 0.120025492 0.890990961 0.152132316 O 0.879975223 0.390990733 0.347856632 O 0.379974508 0.109009039 0.652132316 O 0.847868047 0.620023883 0.609007996 O 0.152132724 0.120024779 0.890989530 O 0.347867276 0.879975221 0.390989530 O 0.652131953 0.379976117 0.109007996 K_POINTS automatic 4 4 4 1 1 1 -- Mayank BARC From giannozz at democritos.it Thu May 12 16:21:21 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 May 2011 16:21:21 +0200 Subject: [Pw_forum] WARNING :: NEGATIVE RHO UP DOWN In-Reply-To: References: Message-ID: <70982876-80E2-42B4-AFF6-98A5A07E0951@democritos.it> On May 12, 2011, at 16:09 , mayank gupta wrote: > yes this warning has started from the beginning till end of the > calculation. there are 320 electrons in the system. and ultrasoft PP's, and not of the simplest kind (Y) . Negative charges are sometimes a consequence of non-positiveness of the augmentation charges, arising in their pseudization. It is better not to have them but they shouldn't be a big problem 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 arvifis at gmail.com Thu May 12 17:11:45 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Thu, 12 May 2011 12:11:45 -0300 Subject: [Pw_forum] Strained Graphene Nanoribbon In-Reply-To: References: Message-ID: Why do you choose 1 1 100 k-points.... this is an insane desicion....!!!!!! PhD std. Arles V. Gil Rebaza Instituto de F?sica de La Plata La Plata - Argentina 2011/5/12 swapnil chandratre > Hi, > > Thank you for sparing time on this, I will try to get it resolved sooner. > Any suggestions are heartily welcomed. > > > On Thu, May 12, 2011 at 9:03 AM, Paolo Giannozzi wrote: > >> >> On May 12, 2011, at 15:49 , swapnil chandratre wrote: >> >> > I just wanted to know if there is no error with the script >> >> I don't know if there is an error in the script. I just tried to >> run it on a PC, it starts but it is definitely too large for a >> single CPU. Since the code writes > 800Mb Kohn-Sham >> wavefunctions for each of the 100 k-points, insufficient disk >> space looks like a promising explanation >> >> 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 >> > > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > > _______________________________________________ > 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/20110512/787e3f60/attachment-0001.htm From swapnil.chandratre at gmail.com Thu May 12 17:16:50 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Thu, 12 May 2011 10:16:50 -0500 Subject: [Pw_forum] Strained Graphene Nanoribbon In-Reply-To: References: Message-ID: Hi Arles, Sorry, I realized the same, the reason I chose 1 1 100 was, I was using another quantum software and the forum there had displayed results with having the k points as 100, so to be in better position to be able to compare with their result I chose 100, but as you have pointed out and I learned myself, the decision was indeed insane. I am still trying to learn how specifically can one decide on k points, do you have any suggestion on k points for my input file, On Thu, May 12, 2011 at 10:11 AM, Arles V. Gil Rebaza wrote: > Why do you choose 1 1 100 k-points.... this is an insane > desicion....!!!!!! > > PhD std. Arles V. Gil Rebaza > Instituto de F?sica de La Plata > La Plata - Argentina > > > > > > 2011/5/12 swapnil chandratre > >> Hi, >> >> Thank you for sparing time on this, I will try to get it resolved sooner. >> Any suggestions are heartily welcomed. >> >> >> On Thu, May 12, 2011 at 9:03 AM, Paolo Giannozzi wrote: >> >>> >>> On May 12, 2011, at 15:49 , swapnil chandratre wrote: >>> >>> > I just wanted to know if there is no error with the script >>> >>> I don't know if there is an error in the script. I just tried to >>> run it on a PC, it starts but it is definitely too large for a >>> single CPU. Since the code writes > 800Mb Kohn-Sham >>> wavefunctions for each of the 100 k-points, insufficient disk >>> space looks like a promising explanation >>> >>> 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 >>> >> >> >> >> -- >> Regards, >> Swapnil Chandratre >> Graduate Student >> Dept. of Mechanical Engineering, >> University of Houston, >> Houston, TX >> (M)-713-294-9546 >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > ###---------> Arles V. <---------### > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/7b4f0bb1/attachment.htm From amin.torabi at gmail.com Thu May 12 17:24:43 2011 From: amin.torabi at gmail.com (Amin Torabi) Date: Thu, 12 May 2011 11:24:43 -0400 Subject: [Pw_forum] 12 Beryllium atoms in the unit cell Message-ID: Dear all, I have some problems in understanding the input file on page 27 of the following tutorial: http://www.ichec.ie/education_training/qe_workshop/material/02/tutorial_io.pdf My questions are: 1. According to Ashcroft & Mermin (p.77), Beryllium is a Hexagonal Closed Packed crystal with c/a=1.56(A). Now, why do we have celldm(3)=16.0 in this tutorial? 2. Why do we have 12 atoms in the unit cell? Can anyone give me a reference or a plain explanation on this unit cell? Thanks in advance! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/da94aa18/attachment.htm From degironc at sissa.it Thu May 12 17:28:42 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 12 May 2011 17:28:42 +0200 Subject: [Pw_forum] 12 Beryllium atoms in the unit cell In-Reply-To: References: Message-ID: <4DCBFCAA.7020606@sissa.it> it'a (0001) surface calculation with 12 layer + vacuum stefano de Gironcoli On 05/12/2011 05:24 PM, Amin Torabi wrote: > Dear all, > > I have some problems in understanding the input file on page 27 of the > following tutorial: > http://www.ichec.ie/education_training/qe_workshop/material/02/tutorial_io.pdf > > My questions are: > > 1. According to Ashcroft& Mermin (p.77), Beryllium is a Hexagonal Closed > Packed crystal with c/a=1.56(A). Now, why do we have celldm(3)=16.0 in this > tutorial? > > 2. Why do we have 12 atoms in the unit cell? Can anyone give me a reference > or a plain explanation on this unit cell? > > > Thanks in advance! > > > > _______________________________________________ > 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/20110512/255b0871/attachment.htm From rfaccio at fq.edu.uy Thu May 12 17:32:24 2011 From: rfaccio at fq.edu.uy (Ricardo Faccio) Date: Thu, 12 May 2011 12:32:24 -0300 (UYT) Subject: [Pw_forum] Strained Graphene Nanoribbon In-Reply-To: References: Message-ID: <2a4729dbbeb56bf149afdb73e9165a2c.squirrel@webmail.fq.edu.uy> Hi The number of k points is always chosen in terms of convergence of some physical property, this is the final decision. Dependent of the metallic nature of your case, you may choose high or lower number of k-points. In the case of codes with not so efficient methods for Brillouin Zone integration, e.g. SIESTA, you need to use a considerable amount of k-points in order to reach convergence. But in QE, you can get the best choice, going step by step, increase little by little, the number of k-pints, until reaching convergence. Certainly, you will get a number considerably lower than 100. Additionally, H-saturated zigzag nanoribbons are insulators - antiferromagnets, so maybe you will need few kpoints. Regards Ricardo > Hi Arles, > > Sorry, I realized the same, the reason I chose 1 1 100 was, I was using > another quantum software and the forum there had displayed results with > having the k points as 100, so to be in better position to be able to > compare with their result I chose 100, but as you have pointed out and I > learned myself, the decision was indeed insane. I am still trying to learn > how specifically can one decide on k points, do you have any suggestion on > k > points for my input file, > > On Thu, May 12, 2011 at 10:11 AM, Arles V. Gil Rebaza > wrote: > >> Why do you choose 1 1 100 k-points.... this is an insane >> desicion....!!!!!! >> >> PhD std. Arles V. Gil Rebaza >> Instituto de F?sica de La Plata >> La Plata - Argentina >> >> >> >> >> >> 2011/5/12 swapnil chandratre >> >>> Hi, >>> >>> Thank you for sparing time on this, I will try to get it resolved >>> sooner. >>> Any suggestions are heartily welcomed. >>> >>> >>> On Thu, May 12, 2011 at 9:03 AM, Paolo Giannozzi >>> wrote: >>> >>>> >>>> On May 12, 2011, at 15:49 , swapnil chandratre wrote: >>>> >>>> > I just wanted to know if there is no error with the script >>>> >>>> I don't know if there is an error in the script. I just tried to >>>> run it on a PC, it starts but it is definitely too large for a >>>> single CPU. Since the code writes > 800Mb Kohn-Sham >>>> wavefunctions for each of the 100 k-points, insufficient disk >>>> space looks like a promising explanation >>>> >>>> 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 >>>> >>> >>> >>> >>> -- >>> Regards, >>> Swapnil Chandratre >>> Graduate Student >>> Dept. of Mechanical Engineering, >>> University of Houston, >>> Houston, TX >>> (M)-713-294-9546 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >> >> >> -- >> ###---------> Arles V. <---------### >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ------------------------------------------------- Dr. Ricardo Faccio Prof. Adjunto de F?sica Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA Facultad de Qu?mica, Universidad de la Rep?blica Av. Gral. Flores 2124, C.C. 1157 C.P. 11800, Montevideo, Uruguay. E-mail: rfaccio at fq.edu.uy Phone: 598 2 924 98 59 598 2 929 06 48 Fax: 598 2 9241906 Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm From mayankaditya at gmail.com Thu May 12 17:43:30 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Thu, 12 May 2011 21:13:30 +0530 Subject: [Pw_forum] non degenerate phonon frequency for cubic crystal along 1 0 0 Message-ID: Thanks Dear Prof. Paolo Giannozzi, one more thing regarding the same calculation . The phonon frequency for cubic crystal should have degenerate along [1 0 0] for TA modes, But i got different frequency. I have calculate the same with larger value of ecut_rho as well as with higher FFT mesh and still they are non degenerate. -- Mayank From arvifis at gmail.com Thu May 12 18:07:07 2011 From: arvifis at gmail.com (Arles V. Gil Rebaza) Date: Thu, 12 May 2011 13:07:07 -0300 Subject: [Pw_forum] Strained Graphene Nanoribbon In-Reply-To: <2a4729dbbeb56bf149afdb73e9165a2c.squirrel@webmail.fq.edu.uy> References: <2a4729dbbeb56bf149afdb73e9165a2c.squirrel@webmail.fq.edu.uy> Message-ID: I agree with Ricardo, you need a convergence of total energy (or the property you want to analyze)... this comment I told you by email some day ago....!!! PhD std. Arles V. Gil Rebaza Instituto de F?sica de La Plata La Plata - Argentina 2011/5/12 Ricardo Faccio > Hi > The number of k points is always chosen in terms of convergence of some > physical property, this is the final decision. Dependent of the metallic > nature of your case, you may choose high or lower number of k-points. > In the case of codes with not so efficient methods for Brillouin Zone > integration, e.g. SIESTA, you need to use a considerable amount of > k-points in order to reach convergence. > But in QE, you can get the best choice, going step by step, increase > little by little, the number of k-pints, until reaching convergence. > Certainly, you will get a number considerably lower than 100. > Additionally, H-saturated zigzag nanoribbons are insulators - > antiferromagnets, so maybe you will need few kpoints. > Regards > Ricardo > > > Hi Arles, > > > > Sorry, I realized the same, the reason I chose 1 1 100 was, I was using > > another quantum software and the forum there had displayed results with > > having the k points as 100, so to be in better position to be able to > > compare with their result I chose 100, but as you have pointed out and I > > learned myself, the decision was indeed insane. I am still trying to > learn > > how specifically can one decide on k points, do you have any suggestion > on > > k > > points for my input file, > > > > On Thu, May 12, 2011 at 10:11 AM, Arles V. Gil Rebaza > > wrote: > > > >> Why do you choose 1 1 100 k-points.... this is an insane > >> desicion....!!!!!! > >> > >> PhD std. Arles V. Gil Rebaza > >> Instituto de F?sica de La Plata > >> La Plata - Argentina > >> > >> > >> > >> > >> > >> 2011/5/12 swapnil chandratre > >> > >>> Hi, > >>> > >>> Thank you for sparing time on this, I will try to get it resolved > >>> sooner. > >>> Any suggestions are heartily welcomed. > >>> > >>> > >>> On Thu, May 12, 2011 at 9:03 AM, Paolo Giannozzi > >>> wrote: > >>> > >>>> > >>>> On May 12, 2011, at 15:49 , swapnil chandratre wrote: > >>>> > >>>> > I just wanted to know if there is no error with the script > >>>> > >>>> I don't know if there is an error in the script. I just tried to > >>>> run it on a PC, it starts but it is definitely too large for a > >>>> single CPU. Since the code writes > 800Mb Kohn-Sham > >>>> wavefunctions for each of the 100 k-points, insufficient disk > >>>> space looks like a promising explanation > >>>> > >>>> 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 > >>>> > >>> > >>> > >>> > >>> -- > >>> Regards, > >>> Swapnil Chandratre > >>> Graduate Student > >>> Dept. of Mechanical Engineering, > >>> University of Houston, > >>> Houston, TX > >>> (M)-713-294-9546 > >>> > >>> _______________________________________________ > >>> Pw_forum mailing list > >>> Pw_forum at pwscf.org > >>> http://www.democritos.it/mailman/listinfo/pw_forum > >>> > >>> > >> > >> > >> -- > >> ###---------> Arles V. <---------### > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > >> > > > > > > -- > > Regards, > > Swapnil Chandratre > > Graduate Student > > Dept. of Mechanical Engineering, > > University of Houston, > > Houston, TX > > (M)-713-294-9546 > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ------------------------------------------------- > Dr. Ricardo Faccio > Prof. Adjunto de F?sica > Mail: Cryssmat-Lab., C?tedra de F?sica, DETEMA > Facultad de Qu?mica, Universidad de la Rep?blica > Av. Gral. Flores 2124, C.C. 1157 > C.P. 11800, Montevideo, Uruguay. > E-mail: rfaccio at fq.edu.uy > Phone: 598 2 924 98 59 > 598 2 929 06 48 > Fax: 598 2 9241906 > Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > > > _______________________________________________ > 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/20110512/0c35e02a/attachment-0001.htm From hicpalm at gmail.com Thu May 12 20:32:22 2011 From: hicpalm at gmail.com (hichem bouderba) Date: Thu, 12 May 2011 21:32:22 +0300 Subject: [Pw_forum] UPF PAW with Atompaw In-Reply-To: References: Message-ID: Hi lorenzo, I tried QE 4.2.1 with gfortran 4.3.3 and openmpi 1.4.3; atompaw with gfortran but I still have the same error. Any suggestion ! where should I look ? thanks. On Thu, May 12, 2011 at 3:13 PM, Lorenzo Paulatto < Lorenzo.Paulatto at impmc.upmc.fr> wrote: > On Thu, 12 May 2011 13:47:38 +0200, hichem bouderba > wrote: > > I have a PAW generated with Atompaw and when used with pw.x the code > > stops > > at : [...] > > > Dear Hichem, > they both work perfectly here with Quantum-ESPRESSO ~4.2 compiled with G95 > 4.0.3 and atompaw compiled with gfortan 4.1.2. > > 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?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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/196600bc/attachment.htm From giannozz at democritos.it Thu May 12 22:25:52 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 May 2011 22:25:52 +0200 Subject: [Pw_forum] UPF PAW with Atompaw In-Reply-To: References: Message-ID: <536A9CD6-D351-4946-9A3D-EA49773D7E23@democritos.it> On May 12, 2011, at 20:32 , hichem bouderba wrote: > Any suggestion ! where should I look ? since you mentioned that Ge with semicore in valence does not work while Ge with semicore in core works, you should look for some tag that differs between the two files, or some tag that looks weird in the first file. If you do not locate the problem, put some print statements into Modules/read_upf_v2.f90, routine read_upf_v2. Note that if there is something not correct in the file format, you should contact the developers of atomPAW. Please sign your posts with your affiliation 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 May 12 22:38:18 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 12 May 2011 22:38:18 +0200 Subject: [Pw_forum] non degenerate phonon frequency for cubic crystal along 1 0 0 In-Reply-To: References: Message-ID: <70596BDF-4C84-4573-9BB4-0AA4F18254EF@democritos.it> On May 12, 2011, at 17:43 , mayank gupta wrote: > The phonon frequency for cubic crystal should have degenerate > along [1 0 0] for TA modes, But i got different frequency. I have > calculate the same with larger value of ecut_rho as well as with > higher FFT mesh and still they are non degenerate. symmetry doesn't change with the cutoff. You may want to try a tighter convergence criterion (tr2_ph) 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 hicpalm at gmail.com Thu May 12 22:50:21 2011 From: hicpalm at gmail.com (hichem bouderba) Date: Thu, 12 May 2011 23:50:21 +0300 Subject: [Pw_forum] UPF PAW with Atompaw In-Reply-To: <536A9CD6-D351-4946-9A3D-EA49773D7E23@democritos.it> References: <536A9CD6-D351-4946-9A3D-EA49773D7E23@democritos.it> Message-ID: Thank you professor, I will follow your hints. note that I have also tried with G95 with AtomPAW and QE 4.1.2 (serial version) without success. thanks On Thu, May 12, 2011 at 11:25 PM, Paolo Giannozzi wrote: > > On May 12, 2011, at 20:32 , hichem bouderba wrote: > > > Any suggestion ! where should I look ? > > since you mentioned that Ge with semicore in valence > does not work while Ge with semicore in core works, > you should look for some tag that differs between > the two files, or some tag that looks weird in the first > file. If you do not locate the problem, put some print > statements into Modules/read_upf_v2.f90, routine > read_upf_v2. Note that if there is something not > correct in the file format, you should contact the > developers of atomPAW. > > Please sign your posts with your affiliation > > 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 > -- Mr. Hichem Bouderba d?partement de physique Universit? de Batna Alg?rie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/e95da123/attachment.htm From degironc at sissa.it Fri May 13 08:43:39 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 13 May 2011 08:43:39 +0200 Subject: [Pw_forum] non degenerate phonon frequency for cubic crystal along 1 0 0 In-Reply-To: <70596BDF-4C84-4573-9BB4-0AA4F18254EF@democritos.it> References: <70596BDF-4C84-4573-9BB4-0AA4F18254EF@democritos.it> Message-ID: <4DCCD31B.8040106@sissa.it> Does the scf calculation find the expected symmetry ? then I'm surprised that the dynamical matrix does not show it. Does the structure look as it should when visualized with xcrysden ? Are you providing the atomic coordinates with enough digits ? stefano - Stefano de Gironcoli - SISSA and DEMOCRITOS On 05/12/2011 10:38 PM, Paolo Giannozzi wrote: > On May 12, 2011, at 17:43 , mayank gupta wrote: > >> The phonon frequency for cubic crystal should have degenerate >> along [1 0 0] for TA modes, But i got different frequency. I have >> calculate the same with larger value of ecut_rho as well as with >> higher FFT mesh and still they are non degenerate. > symmetry doesn't change with the cutoff. You may want to try > a tighter convergence criterion (tr2_ph) > > 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 Lorenzo.Paulatto at impmc.upmc.fr Fri May 13 12:30:58 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 13 May 2011 12:30:58 +0200 Subject: [Pw_forum] UPF PAW with Atompaw In-Reply-To: References: <536A9CD6-D351-4946-9A3D-EA49773D7E23@democritos.it> Message-ID: On Thu, 12 May 2011 22:50:21 +0200, hichem bouderba wrote: > note that I have also tried with G95 with AtomPAW and QE 4.1.2 (serial > version) without success. > thanks Could you please provide some more useful data? like the make.sys file you have used to compile QE, and maybe a gzipped copy of the generated pseudopotential files (you can send them in private if the mailing list does not accept large attachments). 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?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From hicpalm at gmail.com Fri May 13 12:46:24 2011 From: hicpalm at gmail.com (hichem bouderba) Date: Fri, 13 May 2011 13:46:24 +0300 Subject: [Pw_forum] UPF PAW with Atompaw In-Reply-To: References: <536A9CD6-D351-4946-9A3D-EA49773D7E23@democritos.it> Message-ID: as soon as possible. On Fri, May 13, 2011 at 1:30 PM, Lorenzo Paulatto < Lorenzo.Paulatto at impmc.upmc.fr> wrote: > On Thu, 12 May 2011 22:50:21 +0200, hichem bouderba > wrote: > > note that I have also tried with G95 with AtomPAW and QE 4.1.2 (serial > > version) without success. > > thanks > > Could you please provide some more useful data? like the make.sys file you > have used to compile QE, and maybe a gzipped copy of the generated > pseudopotential files (you can send them in private if the mailing list > does not accept large attachments). > > 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?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 > -- Mr. Hichem Bouderba d?partement de physique Universit? de Batna Alg?rie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110513/5f0648f7/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Fri May 13 14:06:21 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 13 May 2011 14:06:21 +0200 Subject: [Pw_forum] UPF PAW with Atompaw In-Reply-To: References: <536A9CD6-D351-4946-9A3D-EA49773D7E23@democritos.it> Message-ID: I report here for future reference that there is a small bug in the atompaw version bundled with abinit: orbital occupation >= 10 are miswritten in the UPF file. The bug is already fixed in the most recent stand-alone version of atompaw (3.0.1.1) available from http://www.wfu.edu/~natalie/papers/pwpaw/man.html. -- 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?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From hicpalm at gmail.com Fri May 13 16:00:11 2011 From: hicpalm at gmail.com (hichem bouderba) Date: Fri, 13 May 2011 17:00:11 +0300 Subject: [Pw_forum] UPF PAW with Atompaw In-Reply-To: References: <536A9CD6-D351-4946-9A3D-EA49773D7E23@democritos.it> Message-ID: Thank you all ! On Fri, May 13, 2011 at 3:06 PM, Lorenzo Paulatto < Lorenzo.Paulatto at impmc.upmc.fr> wrote: > > I report here for future reference that there is a small bug in the > atompaw version bundled with abinit: orbital occupation >= 10 are > miswritten in the UPF file. The bug is already fixed in the most recent > stand-alone version of atompaw (3.0.1.1) available from > http://www.wfu.edu/~natalie/papers/pwpaw/man.html. > > > -- > 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?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 > -- Mr. Hichem Bouderba d?partement de physique Universit? de Batna Alg?rie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110513/daf1c71e/attachment.htm From martins at if.uff.br Fri May 13 21:09:43 2011 From: martins at if.uff.br (martins at if.uff.br) Date: Fri, 13 May 2011 16:09:43 -0300 Subject: [Pw_forum] Problem with PP codes Message-ID: <20110513160943.126654mwsrd8gg6v@webmail.if.uff.br> Dear all, I'm having a problem related with the postprocessing codes. When I try to run the example 05, the following message appears: structure...######################################################## # 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 ##################################################################### what should I do for fixing this problem? I appreciate any help. Thanks in advance, 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 giannozz at democritos.it Fri May 13 22:19:09 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 13 May 2011 22:19:09 +0200 Subject: [Pw_forum] Problem with PP codes In-Reply-To: <20110513160943.126654mwsrd8gg6v@webmail.if.uff.br> References: <20110513160943.126654mwsrd8gg6v@webmail.if.uff.br> Message-ID: On May 13, 2011, at 21:09 , martins at if.uff.br wrote: > I'm having a problem related with the postprocessing codes. no, you are having a problem with your compiler. Many compilers miscompile iotk. 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 eyvaz_isaev at yahoo.com Fri May 13 22:33:52 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Fri, 13 May 2011 13:33:52 -0700 (PDT) Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? In-Reply-To: References: <345129.85014.qm@web65710.mail.ac4.yahoo.com> Message-ID: <123551.52373.qm@web65706.mail.ac4.yahoo.com> Hi, XCryDen gives you q-points coordinates with respect to basis vectors. But X(1,1,0) and K(3/4,3/4,0) are in Cartesian and in units of 2*\pi/a. If I am not wrong, matdyn.x uses (at least, always I used) q-points in Cartesian, so, you have to transform these points to Cartesian. Or see a text book (H.Jones The Theory of Brillouin zones and electronic states in crystals, or J. Callaway Energy band Theory, or whatever you like) to find them in Cartesian. Bests, Eyvaz. ________________________________ From: lucking-pine To: PWSCF Forum Sent: Wed, May 11, 2011 5:34:10 AM Subject: Re: [Pw_forum] why K-X point of phonon dispersion is wrong? Dear Eyvaz Isaev: Thank you for your advice.My k-point is chosen by Xcrysden.such as: G 0.0000000000 0.0000000000 0.0000000000 K -0.7500000000 -0.3750000000 -0.3750000000 X -0.5000000000 0.0000000000 -0.5000000000 G 0.0000000000 0.0000000000 0.0000000000 L - 0.5000000000 -0.5000000000 -0.5000000000 X 0.0000000000 -0.5000000000 -0.5000000000 W -0.2500000000 -0.5000000000 -0.7500000000 L -0.5000000000 -0.5000000000 -0.5000000000 and I try to use your advice through using 3 type of attempt. 1.only chang K,Xpoint of K-G path to K(0.75,0.75,0), X point (1, 1, 0) 2.all k point multipy 2 times. such as: G 0.0000000000 0.0000000000 0.0000000000 K -1.5000000000 -0.7500000000 -0.7500000000 X -1.0000000000 0.0000000000 -1.0000000000 G 0.0000000000 0.0000000000 0.0000000000 L - 1.0000000000 -1.0000000000 -1.0000000000 X 0.0000000000 -1.0000000000 -1.0000000000 W -0.5000000000 -1.0000000000 -1.5000000000 L -1.0000000000 -1.0000000000 -1.0000000000 3.only K,Xpoint of K-G path multiply 2 times. such as G 0.0000000000 0.0000000000 0.0000000000 K -1.5000000000 -0.7500000000 -0.7500000000 X -1.0000000000 0.0000000000 -1.0000000000 G 0.0000000000 0.0000000000 0.0000000000 L - 0.5000000000 -0.5000000000 -0.5000000000 X 0.0000000000 -0.5000000000 -0.5000000000 W -0.2500000000 -0.5000000000 -0.7500000000 L -0.5000000000 -0.5000000000 -0.5000000000 However,all this attempts yield wrong picture. So,this must be something I didn't understand correctly.Would you tell me where is my fault ? 2011/5/6 Eyvaz Isaev Hi, > >First of all I would recommend the use of PlotPhon utility to plot phonon >dispersion relations. For this one you have to have calculated interatomic force >constants matrix (*.fc) file. > >Regarding your particular question: you should choose K(0.75,0.75,0), then from >the K point go to the X point (1, 1, 0) which is equivalent to > >the X(1,0,0) point. Then from the X(1,0,0) to the Gamma (0,0,0) point. >Dashed line just means that we can continue in this direction to match phonons >at the X point (i.e. it is an intermediate point from the Gamma to the X point) >. > >Please also provide your affiliation. > >Bests, >Eyvaz > > >------------------------------------------------------------------- >Prof. Eyvaz Isaev, >Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >Sweden > >Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >Russia, > >isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > > > ________________________________ From: lucking-pine >To: Pw_forum at pwscf.org >Sent: Fri, May 6, 2011 2:50:16 PM >Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? > > > >My pwscf is used in calculating Si phonon dispersion.The trend of picture in >most special Symmetry is right.But the only K-X is wrong.I use Xcrysden to >get K-point. >I found most paper is dash line in 'K' point.So what is mean? Please anyone >could tell me! Thanks! >The attachment is my picture and reference paper. >_______________________________________________ >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/20110513/418e656a/attachment-0001.htm From songsong19840614 at gmail.com Sat May 14 03:04:44 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Sat, 14 May 2011 09:04:44 +0800 Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? In-Reply-To: <123551.52373.qm@web65706.mail.ac4.yahoo.com> References: <345129.85014.qm@web65710.mail.ac4.yahoo.com> <123551.52373.qm@web65706.mail.ac4.yahoo.com> Message-ID: Dear Eyvaz Isaev: Hi,Thanks for your help.I will read these books you Recommended. And I want to ask that I use these k-points into ,and then the will auto-transform the k-point into Cartesian and units of 2*\pi/a,and I use these output k-point in .I always get k-point in this way.Is there something wrong? Bests, Pine. 2011/5/14 Eyvaz Isaev > Hi, > > XCryDen gives you q-points coordinates with respect to basis vectors. > But X(1,1,0) and K(3/4,3/4,0) are in Cartesian and in units of 2*\pi/a. > > If I am not wrong, matdyn.x uses (at least, always I used) q-points in > Cartesian, so, you have to transform these points to Cartesian. > Or see a text book (H.Jones The Theory of Brillouin zones and electronic > states in crystals, or J. Callaway Energy band Theory, or > whatever you like) to find them in Cartesian. > > > Bests, > Eyvaz. > > ------------------------------ > *From:* lucking-pine > *To:* PWSCF Forum > *Sent:* Wed, May 11, 2011 5:34:10 AM > *Subject:* Re: [Pw_forum] why K-X point of phonon dispersion is wrong? > > Dear Eyvaz Isaev: > Thank you for your advice.My k-point is chosen by Xcrysden.such as: > G 0.0000000000 0.0000000000 0.0000000000 > K -0.7500000000 -0.3750000000 -0.3750000000 > X -0.5000000000 0.0000000000 -0.5000000000 > G 0.0000000000 0.0000000000 0.0000000000 > L - 0.5000000000 -0.5000000000 -0.5000000000 > X 0.0000000000 -0.5000000000 -0.5000000000 > W -0.2500000000 -0.5000000000 -0.7500000000 > L -0.5000000000 -0.5000000000 -0.5000000000 > > and I try to use your advice through using 3 type of attempt. > 1.only chang K,Xpoint of K-G path to K(0.75,0.75,0), X point (1, 1, 0) > 2.all k point multipy 2 times. > such as: > > G 0.0000000000 0.0000000000 0.0000000000 > K -1.5000000000 -0.7500000000 -0.7500000000 > X -1.0000000000 0.0000000000 -1.0000000000 > G 0.0000000000 0.0000000000 0.0000000000 > L - 1.0000000000 -1.0000000000 -1.0000000000 > X 0.0000000000 -1.0000000000 -1.0000000000 > W -0.5000000000 -1.0000000000 -1.5000000000 > L -1.0000000000 -1.0000000000 -1.0000000000 > > 3.only K,Xpoint of K-G path multiply 2 times. > such as > > G 0.0000000000 0.0000000000 0.0000000000 > K -1.5000000000 -0.7500000000 -0.7500000000 > X -1.0000000000 0.0000000000 -1.0000000000 > G 0.0000000000 0.0000000000 0.0000000000 > L - 0.5000000000 -0.5000000000 -0.5000000000 > X 0.0000000000 -0.5000000000 -0.5000000000 > W -0.2500000000 -0.5000000000 -0.7500000000 > L -0.5000000000 -0.5000000000 -0.5000000000 > > However,all this attempts yield wrong picture. So,this must be something I > didn't understand correctly.Would you tell me where is my fault ? > 2011/5/6 Eyvaz Isaev > >> Hi, >> >> First of all I would recommend the use of PlotPhon utility to plot phonon >> dispersion relations. For this one you have to have calculated interatomic >> force constants matrix (*.fc) file. >> >> Regarding your particular question: you should choose K(0.75,0.75,0), then >> from the K point go to the X point (1, 1, 0) which is equivalent to >> the X(1,0,0) point. Then from the X(1,0,0) to the Gamma (0,0,0) point. >> Dashed line just means that we can continue in this direction to match >> phonons at the X point (i.e. it is an intermediate point from the Gamma to >> the X point) . >> >> Please also provide your affiliation. >> >> Bests, >> Eyvaz >> >> ------------------------------------------------------------------- >> Prof. Eyvaz Isaev, >> Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >> Sweden >> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >> Russia, >> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> ------------------------------ >> *From:* lucking-pine >> *To:* Pw_forum at pwscf.org >> *Sent:* Fri, May 6, 2011 2:50:16 PM >> *Subject:* [Pw_forum] why K-X point of phonon dispersion is wrong? >> >> My pwscf is used in calculating Si phonon dispersion.The trend of picture >> in >> >> most special Symmetry is right.But the only K-X is wrong.I use Xcrysden to >> >> >> get K-point. >> I found most paper is dash line in 'K' point.So what is mean? Please >> anyone >> >> could tell me! Thanks! >> The attachment is my picture and reference paper. >> >> _______________________________________________ >> 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110514/9e4da2fc/attachment.htm From kirtinandan07 at gmail.com Sun May 15 06:59:08 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Sun, 15 May 2011 10:29:08 +0530 Subject: [Pw_forum] charge density In-Reply-To: References: Message-ID: Hi can anybody please suggest me. I am studying a system of Ni with 40 atoms and then i am replacing one Ni with any other alloying elements. I want to the charge density plot. I have got the charge density by two methods. 1) substituted the alloying element and performed scf through pw.x, and pp.x 2) relax the structure and then performed scf through pw.x, and pp.x. what difference should i try to figure out which will suggest the right method. Thanks in advance vicky singh On Wed, May 11, 2011 at 10:14 AM, vicky singh wrote: > I am very new to analyse the charge density plot. Now I am plottting the > charge density for the supersell by relaxing the structure and then > performing scf and then pp.x and without relaxing i.e scf and pp.x. with the > results what should i be careful about for both the case. How should i > decide the correct approach. I tried to look for any paper but what i could > get just mention the charge density plot. can anybody plese help. > > > On Tue, May 10, 2011 at 12:44 AM, vicky singh wrote: > >> Thanks for your advice. >> >> >> On Mon, May 9, 2011 at 4:23 PM, Masoud Nahali wrote: >> >>> >>> >>> On Mon, May 9, 2011 at 12:29 PM, vicky singh wrote: >>> >>>> >>>> >>>> Hi >>>> >>>> >>>> I am studying the effect of alloying on a supercell with 40 atoms. I am >>>> replacing one Ni with different alloying elements. To get the charge >>>> density >>>> should i relax the system and the perform the scf or simple scf will >>>> give >>>> the effect of alloying. >>>> >>>> Thanks in advance. >>>> >>>> >>>> vicky singh >>>> research student >>>> Bangalore >>>> >>> >>> Dear Vicky >>> >>> Atoms with different sizes have different strain effects in your system >>> and certainly their electronic states aren't same. So if I were you I do a >>> relax calculation. Also, if you want to decrease the cost of your >>> calculations, sometimes it may be good to fix the positions of some side >>> atoms. I hope it helps. >>> >>> Best Wishes >>> >>> Masoud >>> >>> -------------- >>> Masoud Nahali, Sharif University of Technology >>> >>> _______________________________________________ >>> 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/20110515/9cccab99/attachment.htm From kirtinandan07 at gmail.com Sun May 15 07:20:39 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Sun, 15 May 2011 10:50:39 +0530 Subject: [Pw_forum] error in post procesing with temp file Message-ID: Hi I am ploting charge density. since my system size is big i am performing scf cycle on another system and performing pp.x and plotrho.x on my system. but theis is giving error ############## # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_open_read (iotk_files.spp:487) # CVS Revision: 1.20 # unit file=./temp/Nickel.save/./K00001/eigenval.xml binary=F iostat=2 # ERROR IN: iotk_scan_begin (iotk_scan.spp:137) # CVS Revision: 1.23 ############### Thanks in advance. Vicky singh Research Student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110515/4c1c7b17/attachment.htm From masoudnahali at gmail.com Sun May 15 11:38:25 2011 From: masoudnahali at gmail.com (Masoud Nahali) Date: Sun, 15 May 2011 14:08:25 +0430 Subject: [Pw_forum] charge density Message-ID: Dear Vicky As I know, a new structure should be relaxed so then you can use the relaxed structure as input for post-processing process like calculating charge density. I hope it helps. Best Wishes Masoud -------------- Masoud Nahali, Sharif University of Technology On Sun, May 15, 2011 at 12:10 PM, vicky singh wrote: > > > Hi > > can anybody please suggest me. I am studying a system of Ni with 40 atoms > and then i am replacing one Ni with any other alloying elements. I want to > the charge density plot. I have got the charge density by two methods. > 1) substituted the alloying element and performed scf through pw.x, and > pp.x > 2) relax the structure and then performed scf through pw.x, and pp.x. > > what difference should i try to figure out which will suggest the right > method. > > Thanks in advance > vicky singh > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110515/3bdf970b/attachment.htm From eyvaz_isaev at yahoo.com Sun May 15 20:45:37 2011 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 15 May 2011 11:45:37 -0700 (PDT) Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? In-Reply-To: References: <345129.85014.qm@web65710.mail.ac4.yahoo.com> <123551.52373.qm@web65706.mail.ac4.yahoo.com> Message-ID: <497191.52372.qm@web65710.mail.ac4.yahoo.com> Hi, The way you used to generate q-points is somewhat unusual, but seems to be correct. Try also PlotPhon utility in your QE suite. Bests, Eyvaz. ________________________________ From: lucking-pine To: PWSCF Forum Sent: Sat, May 14, 2011 5:04:44 AM Subject: Re: [Pw_forum] why K-X point of phonon dispersion is wrong? Dear Eyvaz Isaev: Hi,Thanks for your help.I will read these books you Recommended. And I want to ask that I use these k-points into ,and then the will auto-transform the k-point into Cartesian and units of 2*\pi/a,and I use these output k-point in .I always get k-point in this way.Is there something wrong? Bests, Pine. 2011/5/14 Eyvaz Isaev Hi, > >XCryDen gives you q-points coordinates with respect to basis vectors. >But X(1,1,0) and K(3/4,3/4,0) are in Cartesian and in units of 2*\pi/a. > >If I am not wrong, matdyn.x uses (at least, always I used) q-points in >Cartesian, so, you have to transform these points to Cartesian. >Or see a text book (H.Jones The Theory of Brillouin zones and electronic states >in crystals, or J. Callaway Energy band Theory, or > >whatever you like) to find them in Cartesian. > > >Bests, >Eyvaz. > > > > ________________________________ From: lucking-pine >To: PWSCF Forum >Sent: Wed, May 11, 2011 5:34:10 AM >Subject: Re: [Pw_forum] why K-X point of phonon dispersion is wrong? > > > >Dear Eyvaz Isaev: >Thank you for your advice.My k-point is chosen by Xcrysden.such as: >G 0.0000000000 0.0000000000 0.0000000000 >K -0.7500000000 -0.3750000000 -0.3750000000 >X -0.5000000000 0.0000000000 -0.5000000000 >G 0.0000000000 0.0000000000 0.0000000000 >L - 0.5000000000 -0.5000000000 -0.5000000000 >X 0.0000000000 -0.5000000000 -0.5000000000 >W -0.2500000000 -0.5000000000 -0.7500000000 >L -0.5000000000 -0.5000000000 -0.5000000000 > >and I try to use your advice through using 3 type of attempt. >1.only chang K,Xpoint of K-G path to K(0.75,0.75,0), X point (1, 1, 0) >2.all k point multipy 2 times. > such as: > >G 0.0000000000 0.0000000000 0.0000000000 >K -1.5000000000 -0.7500000000 -0.7500000000 >X -1.0000000000 0.0000000000 -1.0000000000 >G 0.0000000000 0.0000000000 0.0000000000 >L - 1.0000000000 -1.0000000000 -1.0000000000 >X 0.0000000000 -1.0000000000 -1.0000000000 >W -0.5000000000 -1.0000000000 -1.5000000000 >L -1.0000000000 -1.0000000000 -1.0000000000 > >3.only K,Xpoint of K-G path multiply 2 times. > such as > >G 0.0000000000 0.0000000000 0.0000000000 >K -1.5000000000 -0.7500000000 -0.7500000000 >X -1.0000000000 0.0000000000 -1.0000000000 >G 0.0000000000 0.0000000000 0.0000000000 >L - 0.5000000000 -0.5000000000 -0.5000000000 >X 0.0000000000 -0.5000000000 -0.5000000000 >W -0.2500000000 -0.5000000000 -0.7500000000 >L -0.5000000000 -0.5000000000 -0.5000000000 > >However,all this attempts yield wrong picture. So,this must be something I >didn't understand correctly.Would you tell me where is my fault ? >2011/5/6 Eyvaz Isaev > >Hi, >> >>First of all I would recommend the use of PlotPhon utility to plot phonon >>dispersion relations. For this one you have to have calculated interatomic force >>constants matrix (*.fc) file. >> >>Regarding your particular question: you should choose K(0.75,0.75,0), then from >>the K point go to the X point (1, 1, 0) which is equivalent to >> >>the X(1,0,0) point. Then from the X(1,0,0) to the Gamma (0,0,0) point. >>Dashed line just means that we can continue in this direction to match phonons >>at the X point (i.e. it is an intermediate point from the Gamma to the X point) >>. >> >>Please also provide your affiliation. >> >>Bests, >>Eyvaz >> >> >>------------------------------------------------------------------- >>Prof. Eyvaz Isaev, >>Department of Physics, Chemistry, and Biology (IFM), Linkoping University, >>Sweden >> >>Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >>Russia, >> >>isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >> >> >> >> >> ________________________________ From: lucking-pine >>To: Pw_forum at pwscf.org >>Sent: Fri, May 6, 2011 2:50:16 PM >>Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? >> >> >> >>My pwscf is used in calculating Si phonon dispersion.The trend of picture in >>most special Symmetry is right.But the only K-X is wrong.I use Xcrysden to >>get K-point. >>I found most paper is dash line in 'K' point.So what is mean? Please anyone >>could tell me! Thanks! >>The attachment is my picture and reference paper. >>_______________________________________________ >>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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110515/b3d5292e/attachment.htm From swapnil.chandratre at gmail.com Mon May 16 01:31:20 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Sun, 15 May 2011 18:31:20 -0500 Subject: [Pw_forum] Graphene Nanoribbon Message-ID: Hi, Has anyone worked with Espresso to explore semi conducting properties on a Graphene Nanoribbon ( armchair configuration with specific geometry). Can anyone point to some articles to the same. -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110515/9cf36f51/attachment.htm From tanycimr at gmail.com Mon May 16 03:47:07 2011 From: tanycimr at gmail.com (=?Big5?B?zuu0xqbB?=) Date: Mon, 16 May 2011 09:47:07 +0800 Subject: [Pw_forum] CELL PARAMETERS In-Reply-To: <585FFEC7-C1AE-4F7E-94D2-9BA5FBA2391D@democritos.it> References: <585FFEC7-C1AE-4F7E-94D2-9BA5FBA2391D@democritos.it> Message-ID: Dear Giannozzi thanks a lot . the explanation gives me a lot of help . while if i want to get the outcome of the optimization,like the new lattice parameters "a" , what should i do . 2011/5/12 Paolo Giannozzi > > On May 12, 2011, at 4:37 , ??? wrote: > > > i wonder why the celldm(1) is still the same . > > because the important output is the new unit cell, > described by the primitive vectors. Vectors are written > in units of celldm(1) only in order to produce an output > format that looks like the input one. One may always > redefine celldm(1) in such a way that it is the length > of one of the primitive vectors ( a typical definition of > lattice parameters "a") > > 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/20110516/faa899d3/attachment-0001.htm From mayankaditya at gmail.com Mon May 16 06:58:06 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Mon, 16 May 2011 10:28:06 +0530 Subject: [Pw_forum] relaxation doesn't keep the Wyckoff relation between related atoms. Message-ID: Dear PWscf User's I have relaxed my structure but the relaxed atomic positions are not related by wycoff relations, their third decimal places has been changed. While in some atoms even second decimal places changed. Is their any thing by which I can relax the structure while keeping symmetry constrains. Thanks -- Mayank BARC, India From giannozz at democritos.it Mon May 16 08:21:21 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 16 May 2011 08:21:21 +0200 Subject: [Pw_forum] relaxation doesn't keep the Wyckoff relation between related atoms. In-Reply-To: References: Message-ID: <62EBE3CF-C87D-4109-A4D7-9E5F29D08D7B@democritos.it> On May 16, 2011, at 6:58 , mayank gupta wrote: > I have relaxed my structure but the relaxed atomic positions are not > related by wycoff relations, their third decimal places has been > changed. While in some atoms even second decimal places changed. Is > their any thing by which I can relax the structure while keeping > symmetry constrains. structural optimization with the BGFS algorithm keeps the 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 May 16 08:23:12 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 16 May 2011 08:23:12 +0200 Subject: [Pw_forum] CELL PARAMETERS In-Reply-To: References: <585FFEC7-C1AE-4F7E-94D2-9BA5FBA2391D@democritos.it> Message-ID: <545621A8-A738-464A-B767-3122EE389C5D@democritos.it> On May 16, 2011, at 3:47 , ??? wrote: > while if i want to get the outcome of the optimization, > like the new lattice parameters "a" , what should i do . you haven't read or understood what follows, have you? > One may always redefine celldm(1) in such a way that > it is the length of one of the primitive vectors ( a typical > definition of lattice parameters "a") 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 mayankaditya at gmail.com Mon May 16 10:13:16 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Mon, 16 May 2011 13:43:16 +0530 Subject: [Pw_forum] relaxation doesn't keep the Wyckoff relation Message-ID: Dear Prof. Paolo Giannozzi. I didn't use any option under &IONS section. I think default value is BGFS and it will take ions dynamics BGFS. Here I have paste my input file as well as relaxed output cordinates. &control calculation='relax' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='zrpo', pseudo_dir = '/home/mayank/pseudo/', outdir='/home/mayank/tmp/' / &system ibrav= 1 , celldm(1)= 16.010104949, nat= 40 , ntyp=3, ecutwfc= 70.00000000 ecutrho= 700.00000000 / &electrons / &ions / ATOMIC_SPECIES Zr 91.220 Zr.pbe-nsp-van.UPF P 30.974 P.pbe-n-van.UPF O 15.99 O.pbe-van_bm.UPF ATOMIC_POSITIONS Zr 0.000 0.000 0.000 0 0 0 Zr 0.500 0.000 0.500 0 0 0 Zr 0.000 0.500 0.500 0 0 0 Zr 0.500 0.500 0.000 0 0 0 P 0.394 0.394 0.394 P 0.106 0.606 0.894 P 0.606 0.894 0.106 P 0.894 0.106 0.606 P 0.606 0.606 0.606 P 0.894 0.394 0.106 P 0.394 0.106 0.894 P 0.106 0.894 0.394 O 0.414 0.225 0.422 O 0.060 0.775 0.922 O 0.560 0.725 0.078 O 0.940 0.275 0.578 O 0.422 0.440 0.225 O 0.922 0.060 0.775 O 0.078 0.560 0.725 O 0.578 0.940 0.275 O 0.225 0.422 0.440 O 0.775 0.922 0.060 O 0.725 0.078 0.560 O 0.275 0.578 0.940 O 0.560 0.775 0.578 O 0.954 0.225 0.078 O 0.440 0.275 0.922 O 0.060 0.725 0.422 O 0.578 0.560 0.775 O 0.078 0.940 0.225 O 0.922 0.440 0.275 O 0.422 0.060 0.725 O 0.775 0.578 0.560 O 0.225 0.078 0.940 O 0.275 0.922 0.440 O 0.725 0.422 0.060 O 0.500 0.500 0.500 0 0 0 O 0.000 0.500 0.000 0 0 0 O 0.500 0.000 0.000 0 0 0 O 0.000 0.000 0.500 0 0 0 K_points automatic 4 4 4 and the relaxed coordinates are ATOMIC_POSITIONS (alat) Zr 0.000000000 0.000000000 0.000000000 0 0 0 Zr 0.500000000 0.000000000 0.500000000 0 0 0 Zr 0.000000000 0.500000000 0.500000000 0 0 0 Zr 0.500000000 0.500000000 0.000000000 0 0 0 P 0.391857268 0.392064642 0.391869812 P 0.108159780 0.608089918 0.891944457 P 0.608173455 0.892037444 0.108232425 P 0.891894536 0.108240826 0.607953432 P 0.608106767 0.608235980 0.608186839 P 0.891823536 0.391730527 0.108066685 P 0.391900833 0.108036823 0.891673415 P 0.107930859 0.891662145 0.391879684 O 0.441424235 0.221808060 0.420471370 O 0.056447185 0.778022501 0.918854352 O 0.557323160 0.721800712 0.081415061 O 0.944723954 0.277868578 0.581150485 O 0.420730674 0.442130481 0.221875693 O 0.917884807 0.056486948 0.778066344 O 0.081550763 0.556493649 0.721933617 O 0.580496558 0.944075752 0.277901661 O 0.221667693 0.420935097 0.441546171 O 0.778165180 0.919401673 0.057056756 O 0.722083994 0.081973620 0.555369103 O 0.278036017 0.581104155 0.944016800 O 0.556970404 0.778151286 0.580707585 O 0.944397061 0.221983576 0.081527676 O 0.442718982 0.278177928 0.918825189 O 0.054648677 0.722258439 0.418630605 O 0.580356873 0.556916837 0.778075064 O 0.081820871 0.943540689 0.221792680 O 0.917822100 0.443701212 0.278058184 O 0.419873617 0.056315774 0.721998244 O 0.778018630 0.580712132 0.557179718 O 0.221773748 0.080560759 0.942344343 O 0.277891614 0.917739359 0.444058133 O 0.722170011 0.418050765 0.055181416 O 0.500000000 0.500000000 0.500000000 0 0 0 O 0.000000000 0.500000000 0.000000000 0 0 0 O 0.500000000 0.000000000 0.000000000 0 0 0 O 0.000000000 0.000000000 0.500000000 0 0 0 End final coordinates -- Mayank BHABHA ATOMIC RESEARCH CENTER MUMBAI Office: ?022-25595606 Home: 9920397437/9869834437 From degironc at sissa.it Mon May 16 10:44:56 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 16 May 2011 10:44:56 +0200 Subject: [Pw_forum] relaxation doesn't keep the Wyckoff relation In-Reply-To: References: Message-ID: <4DD0E408.2010704@sissa.it> Does BFGS stops saying it lost some symmetry ? If not the algorithm is not having problems with symmetry. Does BFGS recongnize al symmetry you think it should ? If not check your coordinates. stefano de Gironcoli SISSA and DEMOCRITOS On 05/16/2011 10:13 AM, mayank gupta wrote: > Dear Prof. Paolo Giannozzi. > > I didn't use any option under&IONS section. I think default value is > BGFS and it will take ions dynamics BGFS. Here I have paste my input > file as well as relaxed output cordinates. > > &control > calculation='relax' > restart_mode='from_scratch', > tstress = .true. > tprnfor = .true. > prefix='zrpo', > pseudo_dir = '/home/mayank/pseudo/', > outdir='/home/mayank/tmp/' > / > &system > ibrav= 1 , celldm(1)= 16.010104949, nat= 40 , > ntyp=3, > ecutwfc= 70.00000000 > ecutrho= 700.00000000 > > > > / > &electrons > / > &ions > > / > ATOMIC_SPECIES > Zr 91.220 Zr.pbe-nsp-van.UPF > P 30.974 P.pbe-n-van.UPF > O 15.99 O.pbe-van_bm.UPF > ATOMIC_POSITIONS > Zr 0.000 0.000 0.000 0 0 0 > Zr 0.500 0.000 0.500 0 0 0 > Zr 0.000 0.500 0.500 0 0 0 > Zr 0.500 0.500 0.000 0 0 0 > P 0.394 0.394 0.394 > P 0.106 0.606 0.894 > P 0.606 0.894 0.106 > P 0.894 0.106 0.606 > P 0.606 0.606 0.606 > P 0.894 0.394 0.106 > P 0.394 0.106 0.894 > P 0.106 0.894 0.394 > O 0.414 0.225 0.422 > O 0.060 0.775 0.922 > O 0.560 0.725 0.078 > O 0.940 0.275 0.578 > O 0.422 0.440 0.225 > O 0.922 0.060 0.775 > O 0.078 0.560 0.725 > O 0.578 0.940 0.275 > O 0.225 0.422 0.440 > O 0.775 0.922 0.060 > O 0.725 0.078 0.560 > O 0.275 0.578 0.940 > O 0.560 0.775 0.578 > O 0.954 0.225 0.078 > O 0.440 0.275 0.922 > O 0.060 0.725 0.422 > O 0.578 0.560 0.775 > O 0.078 0.940 0.225 > O 0.922 0.440 0.275 > O 0.422 0.060 0.725 > O 0.775 0.578 0.560 > O 0.225 0.078 0.940 > O 0.275 0.922 0.440 > O 0.725 0.422 0.060 > O 0.500 0.500 0.500 0 0 0 > O 0.000 0.500 0.000 0 0 0 > O 0.500 0.000 0.000 0 0 0 > O 0.000 0.000 0.500 0 0 0 > K_points automatic > 4 4 4 > > > and the relaxed coordinates are > > > ATOMIC_POSITIONS (alat) > Zr 0.000000000 0.000000000 0.000000000 0 0 0 > Zr 0.500000000 0.000000000 0.500000000 0 0 0 > Zr 0.000000000 0.500000000 0.500000000 0 0 0 > Zr 0.500000000 0.500000000 0.000000000 0 0 0 > P 0.391857268 0.392064642 0.391869812 > P 0.108159780 0.608089918 0.891944457 > P 0.608173455 0.892037444 0.108232425 > P 0.891894536 0.108240826 0.607953432 > P 0.608106767 0.608235980 0.608186839 > P 0.891823536 0.391730527 0.108066685 > P 0.391900833 0.108036823 0.891673415 > P 0.107930859 0.891662145 0.391879684 > O 0.441424235 0.221808060 0.420471370 > O 0.056447185 0.778022501 0.918854352 > O 0.557323160 0.721800712 0.081415061 > O 0.944723954 0.277868578 0.581150485 > O 0.420730674 0.442130481 0.221875693 > O 0.917884807 0.056486948 0.778066344 > O 0.081550763 0.556493649 0.721933617 > O 0.580496558 0.944075752 0.277901661 > O 0.221667693 0.420935097 0.441546171 > O 0.778165180 0.919401673 0.057056756 > O 0.722083994 0.081973620 0.555369103 > O 0.278036017 0.581104155 0.944016800 > O 0.556970404 0.778151286 0.580707585 > O 0.944397061 0.221983576 0.081527676 > O 0.442718982 0.278177928 0.918825189 > O 0.054648677 0.722258439 0.418630605 > O 0.580356873 0.556916837 0.778075064 > O 0.081820871 0.943540689 0.221792680 > O 0.917822100 0.443701212 0.278058184 > O 0.419873617 0.056315774 0.721998244 > O 0.778018630 0.580712132 0.557179718 > O 0.221773748 0.080560759 0.942344343 > O 0.277891614 0.917739359 0.444058133 > O 0.722170011 0.418050765 0.055181416 > O 0.500000000 0.500000000 0.500000000 0 0 0 > O 0.000000000 0.500000000 0.000000000 0 0 0 > O 0.500000000 0.000000000 0.000000000 0 0 0 > O 0.000000000 0.000000000 0.500000000 0 0 0 > End final coordinates From degironc at sissa.it Mon May 16 10:51:23 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 16 May 2011 10:51:23 +0200 Subject: [Pw_forum] relaxation doesn't keep the Wyckoff relation In-Reply-To: References: Message-ID: <4DD0E58B.2000005@sissa.it> dear Mayank On 05/16/2011 10:13 AM, mayank gupta wrote: > O 0.414 0.225 0.422 are you sure of this one ? shouldn't rather be something like O 0.440 0.225 0.422 ? stefano From swapnil.chandratre at gmail.com Mon May 16 11:17:06 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 16 May 2011 04:17:06 -0500 Subject: [Pw_forum] Relaxation Simulation Message-ID: Hi, I am trying to relax graphene ribbon, the set up runs for long time and I notice Self-consistent Calculation iteration # 1 ecut= 60.00 Ry beta=0.30 Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged c_bands: 1 eigenvalues not converged ethr = 1.00E-06, avg # of iterations = 18.8 I think there is error somewhere due to which takes time for it to converge, could anyone suggest what parameters would affect this. -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110516/a65d499a/attachment.htm From CJH085 at bham.ac.uk Mon May 16 12:17:33 2011 From: CJH085 at bham.ac.uk (Christopher Heard) Date: Mon, 16 May 2011 11:17:33 +0100 Subject: [Pw_forum] Relaxation giving negative relative coordinates. Message-ID: <4406F1904F879A4D9FE86E310EA6634102136F5A784E@mbx5.adf.bham.ac.uk> Hello, I am running QE for a small atomic cluster, in a single cubic unit cell, with the 'relax' keyword, just a simple local minimisation. The atomic coordinates are fractional coordinates of the unit cell, but the problem is that the output gives some negative values. I'm new to QE, so perhaps this is easily explained (if so, sorry), but it seems strange that the simulation would converge, and how does the code know what positions/energies negative values correspond to? ----------------------------------------------------------------------------------------------------------------- INPUT &CONTROL calculation = "relax", prefix = "pwscf", pseudo_dir = ".", outdir = ".", etot_conv_thr= 1.D-3, forc_conv_thr= 1.D-2, nstep = 200, / &SYSTEM ibrav = 0, nat = 4, ntyp = 2, ecutwfc = 20.D0, occupations = "smearing", smearing = "mp", degauss = 0.6, / &ELECTRONS electron_maxstep = 100, conv_thr = 1.D-6, mixing_beta = 0.3, / &IONS / CELL_PARAMETERS cubic 6.70 0.00 0.00 0.00 6.70 0.00 0.00 0.00 6.70 ATOMIC_SPECIES Cu 63.55 Cu.pbe-d-rrkjus.upf Ag 107.80 Ag.pbe-d-rrkjus.upf ATOMIC_POSITIONS {crystal} Cu 3.352950000000000E-002 0.231848250000000 0.909548000000000 Cu 0.385636250000000 0.891478500000000 9.939174999999999E-002 Cu 0.205962500000000 0.843170750000000 0.568072500000000 Ag 0.109203000000000 5.366124999999999E-002 5.051524999999999E-002 K_POINTS {Gamma} ----------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------- SAMPLE OF FINAL OUTPUT the Fermi energy is 19.5731 ev ! total energy = -336.07301310 Ry Harris-Foulkes estimate = -336.07301304 Ry estimated scf accuracy < 2.4E-09 Ry The total energy is the sum of the following terms: one-electron contribution = -15.71264533 Ry hartree contribution = 65.46190146 Ry xc contribution = -55.48851306 Ry ewald contribution = -330.01856694 Ry - averaged Fock potential = 0.00000000 Ry + Fock energy = 0.00000000 Ry smearing contrib. (-TS) = -0.31518923 Ry convergence has been achieved in 6 iterations Forces acting on atoms (Ry/au): atom 1 type 1 force = -0.00120005 -0.00208895 -0.00171136 atom 2 type 1 force = -0.00716149 -0.00098208 0.00204276 atom 3 type 1 force = 0.00892231 0.00566633 0.00154815 atom 4 type 2 force = -0.00056077 -0.00259530 -0.00187956 Total force = 0.013779 Total SCF correction = 0.000064 bfgs converged in 41 scf cycles and 30 bfgs steps (criteria: energy < 0.10E-02, force < 0.10E-01) End of BFGS Geometry Optimization Final energy = -336.0730131033 Ry Begin final coordinates ATOMIC_POSITIONS (crystal) Cu -0.050437709 0.504314433 0.629069336 Cu 0.445520384 0.504573287 0.216995562 Cu 0.419644090 1.004288078 0.669422976 Ag -0.080395515 0.006982952 0.112039626 End final coordinates ----------------------------------------------------------------------------------------------------------------- Many thanks, Chris From degironc at sissa.it Mon May 16 13:14:06 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 16 May 2011 13:14:06 +0200 Subject: [Pw_forum] Relaxation Simulation In-Reply-To: References: Message-ID: <4DD106FE.9000609@sissa.it> check your structure. stefano On 05/16/2011 11:17 AM, swapnil chandratre wrote: > Hi, > > I am trying to relax graphene ribbon, the set up runs for long time and I > notice > > Self-consistent Calculation > > iteration # 1 ecut= 60.00 Ry beta=0.30 > Davidson diagonalization with overlap > c_bands: 1 eigenvalues not converged > c_bands: 1 eigenvalues not converged > c_bands: 1 eigenvalues not converged > c_bands: 1 eigenvalues not converged > ethr = 1.00E-06, avg # of iterations = 18.8 > > I think there is error somewhere due to which takes time for it to converge, > could anyone suggest what parameters would affect this. > > > > _______________________________________________ > 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/20110516/026c08db/attachment-0001.htm From degironc at sissa.it Mon May 16 13:13:02 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 16 May 2011 13:13:02 +0200 Subject: [Pw_forum] Relaxation giving negative relative coordinates. In-Reply-To: <4406F1904F879A4D9FE86E310EA6634102136F5A784E@mbx5.adf.bham.ac.uk> References: <4406F1904F879A4D9FE86E310EA6634102136F5A784E@mbx5.adf.bham.ac.uk> Message-ID: <4DD106BE.3040704@sissa.it> there is nothing strange in negative positions anyway the system is periodic so you can remap them on the positive axes if you like, stefano On 05/16/2011 12:17 PM, Christopher Heard wrote: > Hello, > > I am running QE for a small atomic cluster, in a single cubic unit cell, with the 'relax' keyword, just a simple local minimisation. > The atomic coordinates are fractional coordinates of the unit cell, but the problem is that the output gives some negative values. > I'm new to QE, so perhaps this is easily explained (if so, sorry), but it seems strange that the simulation would converge, and how does the code know what positions/energies negative values correspond to? > > ----------------------------------------------------------------------------------------------------------------- > INPUT > &CONTROL > calculation = "relax", > prefix = "pwscf", > pseudo_dir = ".", > outdir = ".", > etot_conv_thr= 1.D-3, > forc_conv_thr= 1.D-2, > nstep = 200, > / > &SYSTEM > ibrav = 0, > nat = 4, > ntyp = 2, > ecutwfc = 20.D0, > occupations = "smearing", > smearing = "mp", > degauss = 0.6, > / > &ELECTRONS > electron_maxstep = 100, > conv_thr = 1.D-6, > mixing_beta = 0.3, > / > &IONS > / > CELL_PARAMETERS cubic > 6.70 0.00 0.00 > 0.00 6.70 0.00 > 0.00 0.00 6.70 > ATOMIC_SPECIES > Cu 63.55 Cu.pbe-d-rrkjus.upf > Ag 107.80 Ag.pbe-d-rrkjus.upf > ATOMIC_POSITIONS {crystal} > Cu 3.352950000000000E-002 0.231848250000000 0.909548000000000 > Cu 0.385636250000000 0.891478500000000 9.939174999999999E-002 > Cu 0.205962500000000 0.843170750000000 0.568072500000000 > Ag 0.109203000000000 5.366124999999999E-002 5.051524999999999E-002 > K_POINTS {Gamma} > ----------------------------------------------------------------------------------------------------------------- > > > ----------------------------------------------------------------------------------------------------------------- > SAMPLE OF FINAL OUTPUT > > the Fermi energy is 19.5731 ev > > ! total energy = -336.07301310 Ry > Harris-Foulkes estimate = -336.07301304 Ry > estimated scf accuracy< 2.4E-09 Ry > > The total energy is the sum of the following terms: > > one-electron contribution = -15.71264533 Ry > hartree contribution = 65.46190146 Ry > xc contribution = -55.48851306 Ry > ewald contribution = -330.01856694 Ry > - averaged Fock potential = 0.00000000 Ry > + Fock energy = 0.00000000 Ry > smearing contrib. (-TS) = -0.31518923 Ry > > convergence has been achieved in 6 iterations > > Forces acting on atoms (Ry/au): > > atom 1 type 1 force = -0.00120005 -0.00208895 -0.00171136 > atom 2 type 1 force = -0.00716149 -0.00098208 0.00204276 > atom 3 type 1 force = 0.00892231 0.00566633 0.00154815 > atom 4 type 2 force = -0.00056077 -0.00259530 -0.00187956 > > Total force = 0.013779 Total SCF correction = 0.000064 > > bfgs converged in 41 scf cycles and 30 bfgs steps > (criteria: energy< 0.10E-02, force< 0.10E-01) > > End of BFGS Geometry Optimization > > Final energy = -336.0730131033 Ry > Begin final coordinates > > ATOMIC_POSITIONS (crystal) > Cu -0.050437709 0.504314433 0.629069336 > Cu 0.445520384 0.504573287 0.216995562 > Cu 0.419644090 1.004288078 0.669422976 > Ag -0.080395515 0.006982952 0.112039626 > End final coordinates > > ----------------------------------------------------------------------------------------------------------------- > > > Many thanks, > Chris > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From CJH085 at bham.ac.uk Mon May 16 14:38:32 2011 From: CJH085 at bham.ac.uk (Christopher Heard) Date: Mon, 16 May 2011 13:38:32 +0100 Subject: [Pw_forum] Relaxation giving negative relative coordinates. / Chris Heard Message-ID: <4406F1904F879A4D9FE86E310EA6634102136F5A7852@mbx5.adf.bham.ac.uk> Dear Stefano, thanks for the answer. I will do that. Cheers, Chris ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of Stefano de Gironcoli [degironc at sissa.it] Sent: 16 May 2011 12:13 To: PWSCF Forum Subject: Re: [Pw_forum] Relaxation giving negative relative coordinates. there is nothing strange in negative positions anyway the system is periodic so you can remap them on the positive axes if you like, stefano On 05/16/2011 12:17 PM, Christopher Heard wrote: > Hello, > > I am running QE for a small atomic cluster, in a single cubic unit cell, with the 'relax' keyword, just a simple local minimisation. > The atomic coordinates are fractional coordinates of the unit cell, but the problem is that the output gives some negative values. > I'm new to QE, so perhaps this is easily explained (if so, sorry), but it seems strange that the simulation would converge, and how does the code know what positions/energies negative values correspond to? > > ----------------------------------------------------------------------------------------------------------------- > INPUT > &CONTROL > calculation = "relax", > prefix = "pwscf", > pseudo_dir = ".", > outdir = ".", > etot_conv_thr= 1.D-3, > forc_conv_thr= 1.D-2, > nstep = 200, > / > &SYSTEM > ibrav = 0, > nat = 4, > ntyp = 2, > ecutwfc = 20.D0, > occupations = "smearing", > smearing = "mp", > degauss = 0.6, > / > &ELECTRONS > electron_maxstep = 100, > conv_thr = 1.D-6, > mixing_beta = 0.3, > / > &IONS > / > CELL_PARAMETERS cubic > 6.70 0.00 0.00 > 0.00 6.70 0.00 > 0.00 0.00 6.70 > ATOMIC_SPECIES > Cu 63.55 Cu.pbe-d-rrkjus.upf > Ag 107.80 Ag.pbe-d-rrkjus.upf > ATOMIC_POSITIONS {crystal} > Cu 3.352950000000000E-002 0.231848250000000 0.909548000000000 > Cu 0.385636250000000 0.891478500000000 9.939174999999999E-002 > Cu 0.205962500000000 0.843170750000000 0.568072500000000 > Ag 0.109203000000000 5.366124999999999E-002 5.051524999999999E-002 > K_POINTS {Gamma} > ----------------------------------------------------------------------------------------------------------------- > > > ----------------------------------------------------------------------------------------------------------------- > SAMPLE OF FINAL OUTPUT > > the Fermi energy is 19.5731 ev > > ! total energy = -336.07301310 Ry > Harris-Foulkes estimate = -336.07301304 Ry > estimated scf accuracy< 2.4E-09 Ry > > The total energy is the sum of the following terms: > > one-electron contribution = -15.71264533 Ry > hartree contribution = 65.46190146 Ry > xc contribution = -55.48851306 Ry > ewald contribution = -330.01856694 Ry > - averaged Fock potential = 0.00000000 Ry > + Fock energy = 0.00000000 Ry > smearing contrib. (-TS) = -0.31518923 Ry > > convergence has been achieved in 6 iterations > > Forces acting on atoms (Ry/au): > > atom 1 type 1 force = -0.00120005 -0.00208895 -0.00171136 > atom 2 type 1 force = -0.00716149 -0.00098208 0.00204276 > atom 3 type 1 force = 0.00892231 0.00566633 0.00154815 > atom 4 type 2 force = -0.00056077 -0.00259530 -0.00187956 > > Total force = 0.013779 Total SCF correction = 0.000064 > > bfgs converged in 41 scf cycles and 30 bfgs steps > (criteria: energy< 0.10E-02, force< 0.10E-01) > > End of BFGS Geometry Optimization > > Final energy = -336.0730131033 Ry > Begin final coordinates > > ATOMIC_POSITIONS (crystal) > Cu -0.050437709 0.504314433 0.629069336 > Cu 0.445520384 0.504573287 0.216995562 > Cu 0.419644090 1.004288078 0.669422976 > Ag -0.080395515 0.006982952 0.112039626 > End final coordinates > > ----------------------------------------------------------------------------------------------------------------- > > > Many thanks, > Chris > _______________________________________________ > 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 From songsong19840614 at gmail.com Mon May 16 14:53:52 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Mon, 16 May 2011 20:53:52 +0800 Subject: [Pw_forum] why K-X point of phonon dispersion is wrong? In-Reply-To: <497191.52372.qm@web65710.mail.ac4.yahoo.com> References: <345129.85014.qm@web65710.mail.ac4.yahoo.com> <123551.52373.qm@web65706.mail.ac4.yahoo.com> <497191.52372.qm@web65710.mail.ac4.yahoo.com> Message-ID: Hi, I also want to learn PlotPhon.This is a new tool since version4.2.I hope it can solve this problem. Bests. Pine. 2011/5/16 Eyvaz Isaev > Hi, > > The way you used to generate q-points is somewhat unusual, but seems to be > correct. > > Try also PlotPhon utility in your QE suite. > > Bests, > Eyvaz. > > ------------------------------ > *From:* lucking-pine > *To:* PWSCF Forum > *Sent:* Sat, May 14, 2011 5:04:44 AM > > *Subject:* Re: [Pw_forum] why K-X point of phonon dispersion is wrong? > > Dear Eyvaz Isaev: > Hi,Thanks for your help.I will read these books you Recommended. > And I want to ask that I use these k-points into ,and then the > will auto-transform the k-point into Cartesian and units of > 2*\pi/a,and I use these output k-point in .I always get > k-point in this way.Is there something wrong? > > Bests, > Pine. > > 2011/5/14 Eyvaz Isaev > >> Hi, >> >> XCryDen gives you q-points coordinates with respect to basis vectors. >> But X(1,1,0) and K(3/4,3/4,0) are in Cartesian and in units of 2*\pi/a. >> >> If I am not wrong, matdyn.x uses (at least, always I used) q-points in >> Cartesian, so, you have to transform these points to Cartesian. >> Or see a text book (H.Jones The Theory of Brillouin zones and electronic >> states in crystals, or J. Callaway Energy band Theory, or >> whatever you like) to find them in Cartesian. >> >> >> Bests, >> Eyvaz. >> >> ------------------------------ >> *From:* lucking-pine >> *To:* PWSCF Forum >> *Sent:* Wed, May 11, 2011 5:34:10 AM >> *Subject:* Re: [Pw_forum] why K-X point of phonon dispersion is wrong? >> >> Dear Eyvaz Isaev: >> Thank you for your advice.My k-point is chosen by Xcrysden.such as: >> G 0.0000000000 0.0000000000 0.0000000000 >> K -0.7500000000 -0.3750000000 -0.3750000000 >> X -0.5000000000 0.0000000000 -0.5000000000 >> G 0.0000000000 0.0000000000 0.0000000000 >> L - 0.5000000000 -0.5000000000 -0.5000000000 >> X 0.0000000000 -0.5000000000 -0.5000000000 >> W -0.2500000000 -0.5000000000 -0.7500000000 >> L -0.5000000000 -0.5000000000 -0.5000000000 >> >> and I try to use your advice through using 3 type of attempt. >> 1.only chang K,Xpoint of K-G path to K(0.75,0.75,0), X point (1, 1, 0) >> 2.all k point multipy 2 times. >> such as: >> >> G 0.0000000000 0.0000000000 0.0000000000 >> K -1.5000000000 -0.7500000000 -0.7500000000 >> X -1.0000000000 0.0000000000 -1.0000000000 >> G 0.0000000000 0.0000000000 0.0000000000 >> L - 1.0000000000 -1.0000000000 -1.0000000000 >> X 0.0000000000 -1.0000000000 -1.0000000000 >> W -0.5000000000 -1.0000000000 -1.5000000000 >> L -1.0000000000 -1.0000000000 -1.0000000000 >> >> 3.only K,Xpoint of K-G path multiply 2 times. >> such as >> >> G 0.0000000000 0.0000000000 0.0000000000 >> K -1.5000000000 -0.7500000000 -0.7500000000 >> X -1.0000000000 0.0000000000 -1.0000000000 >> G 0.0000000000 0.0000000000 0.0000000000 >> L - 0.5000000000 -0.5000000000 -0.5000000000 >> X 0.0000000000 -0.5000000000 -0.5000000000 >> W -0.2500000000 -0.5000000000 -0.7500000000 >> L -0.5000000000 -0.5000000000 -0.5000000000 >> >> However,all this attempts yield wrong picture. So,this must be something I >> didn't understand correctly.Would you tell me where is my fault ? >> 2011/5/6 Eyvaz Isaev >> >>> Hi, >>> >>> First of all I would recommend the use of PlotPhon utility to plot >>> phonon dispersion relations. For this one you have to have calculated >>> interatomic force constants matrix (*.fc) file. >>> >>> Regarding your particular question: you should choose K(0.75,0.75,0), >>> then from the K point go to the X point (1, 1, 0) which is equivalent to >>> the X(1,0,0) point. Then from the X(1,0,0) to the Gamma (0,0,0) point. >>> Dashed line just means that we can continue in this direction to match >>> phonons at the X point (i.e. it is an intermediate point from the Gamma to >>> the X point) . >>> >>> Please also provide your affiliation. >>> >>> Bests, >>> Eyvaz >>> >>> ------------------------------------------------------------------- >>> Prof. Eyvaz Isaev, >>> Department of Physics, Chemistry, and Biology (IFM), Linkoping >>> University, Sweden >>> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, >>> Russia, >>> isaev at ifm.liu.se, eyvaz_isaev at yahoo.com >>> >>> >>> ------------------------------ >>> *From:* lucking-pine >>> *To:* Pw_forum at pwscf.org >>> *Sent:* Fri, May 6, 2011 2:50:16 PM >>> *Subject:* [Pw_forum] why K-X point of phonon dispersion is wrong? >>> >>> My pwscf is used in calculating Si phonon dispersion.The trend of picture >>> in >>> >>> most special Symmetry is right.But the only K-X is wrong.I use Xcrysden >>> to >>> >>> get K-point. >>> I found most paper is dash line in 'K' point.So what is mean? Please >>> anyone >>> >>> could tell me! Thanks! >>> The attachment is my picture and reference paper. >>> >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > 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/20110516/cadda810/attachment-0001.htm From mashiatalaaii at gmail.com Mon May 16 20:46:12 2011 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Mon, 16 May 2011 14:46:12 -0400 Subject: [Pw_forum] LDOS on x-y direction, perpendicular to z Message-ID: Dear All, Is there a way to find the LDOS of different planes (with different thicknesses) on x-y direction, perpendicular to z? Thank you for your help. M Alaaii -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110516/2d485f0b/attachment.htm From Ari.P.Seitsonen at iki.fi Mon May 16 21:39:46 2011 From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen) Date: Mon, 16 May 2011 21:39:46 +0200 (CEST) Subject: [Pw_forum] Graphene Nanoribbon In-Reply-To: References: Message-ID: Dear Swapnil Chandratre, We recently published some studies on graphene nanoribbons terminated with hydrogen, oxygen, and (dissociated) water and ammonia; there are manymanymany other studies as well, but here the citations to our works (Wassmann et alia): * Structure, stability, edge states and aromaticity of graphene ribbons Tobias Wassmann, Ari P Seitsonen, A Marco Saitta, Michele Lazzeri and Francesco Mauri, Physical Review Letters 101 096402 (2008); http://dx.doi.org/10.1103/PhysRevLett.101.096402 * Clar's Theory, ?-Electron Distribution, and Geometry of Graphene Nanoribbons Tobias Wassmann, Ari Paavo Seitsonen, A Marco Saitta, Michele Lazzeri and Francesco Mauri, Journal of the American Chemical Society 132 3440-3451 (2010); http://dx.doi.org/10.1021/ja909234y * Structure and stability of graphene nanoribbons in oxygen, carbon dioxide, water and ammonia Ari P Seitsonen, A Marco Saitta, Tobias Wassmann, Michele Lazzeri and Francesco Mauri, Physical Review B 82 (2010) 115425; http://dx.doi.org/10.1103/PhysRevB.82.115425 Greetings from Lund/Sweden, 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 Sun, 15 May 2011, swapnil chandratre wrote: > Hi, > Has anyone worked with Espresso to explore semi conducting properties on a Graphene Nanoribbon ( armchair configuration with specific > geometry). Can anyone point to some articles to the same.? > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > > From swapnil.chandratre at gmail.com Mon May 16 22:03:02 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 16 May 2011 15:03:02 -0500 Subject: [Pw_forum] Graphene Nanoribbon In-Reply-To: References: Message-ID: Hi, Thank you Ari, I will go through the articles. 2011/5/16 Ari P Seitsonen > > Dear Swapnil Chandratre, > > We recently published some studies on graphene nanoribbons terminated with > hydrogen, oxygen, and (dissociated) water and ammonia; there are > manymanymany other studies as well, but here the citations to our works > (Wassmann et alia): > > * Structure, stability, edge states and aromaticity of graphene ribbons > Tobias Wassmann, Ari P Seitsonen, A Marco Saitta, Michele Lazzeri and > Francesco Mauri, Physical Review Letters 101 096402 (2008); > http://dx.doi.org/10.1103/PhysRevLett.101.096402 > > * Clar's Theory, ?-Electron Distribution, and Geometry of Graphene > Nanoribbons Tobias Wassmann, Ari Paavo Seitsonen, A Marco Saitta, Michele > Lazzeri and Francesco Mauri, Journal of the American Chemical Society 132 > 3440-3451 (2010); http://dx.doi.org/10.1021/ja909234y > > * Structure and stability of graphene nanoribbons in oxygen, carbon > dioxide, water and ammonia Ari P Seitsonen, A Marco Saitta, Tobias Wassmann, > Michele Lazzeri and Francesco Mauri, Physical Review B 82 (2010) 115425; > http://dx.doi.org/10.1103/PhysRevB.82.115425 > > Greetings from Lund/Sweden, > > 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 Sun, 15 May 2011, swapnil chandratre wrote: > > Hi, >> Has anyone worked with Espresso to explore semi conducting properties on a >> Graphene Nanoribbon ( armchair configuration with specific >> geometry). Can anyone point to some articles to the same. >> >> -- >> Regards, >> Swapnil Chandratre >> Graduate Student >> Dept. of Mechanical Engineering, >> University of Houston, >> Houston, TX >> (M)-713-294-9546 >> >> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110516/5f2b3e4d/attachment.htm From gm030212 at gmail.com Tue May 17 09:57:29 2011 From: gm030212 at gmail.com (Fen Hong) Date: Tue, 17 May 2011 16:57:29 +0900 Subject: [Pw_forum] transition state doesn't converge Message-ID: Dear all. I am trying to use CI to search transition state. The initial and final state 's structure are very different and there is no intermediate between them. The transition state is easily got by Gaussian program with very small imaginary frequency. I tried two ways. 1 Use initial and final state and large/small num_of_images 2 use initial and final state, and an intermediate ( from Gaussian ts searching result) Both of the ways can not successfully find the TS, The TS searching calculation does not converge. Does there anyone have experience to solve this kind of problems? Thank you very much. Yours, Gao Min -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110517/014391d0/attachment.htm From giovanni.cantele at spin.cnr.it Tue May 17 12:21:09 2011 From: giovanni.cantele at spin.cnr.it (Giovanni Cantele) Date: Tue, 17 May 2011 12:21:09 +0200 Subject: [Pw_forum] Graphene Nanoribbon In-Reply-To: <4DD1A97E.9080200@materials.ox.ac.uk> References: <4DD1A97E.9080200@materials.ox.ac.uk> Message-ID: Dear Swapnil Chandratre, let me also add this reference that you might find of interest: * Spin Channels in Functionalized Graphene Nanoribbons Author(s): Cantele, G; Lee, YS; Ninno, D; Marzari, N NANO LETTERS Volume: 9 Issue: 10 Pages: 3425-3429 Published: 2009 There are also some recently appeared review papers, among the many: * Properties of graphene: a theoretical perspective D.S.L. Abergela, V. Apalkov, J. Berashevich, K. Ziegler and Tapash Chakraborty Advances in Physics Vol. 59, No. 4, July?August 2010, 261?482 * Electronic states of graphene nanoribbons and analytical solutions Katsunori Wakabayashi, Ken-ichi Sasaki1, Takeshi Nakanishi and Toshiaki Enoki Sci. Technol. Adv. Mater. 11 (2010) 054504 (18pp) doi:10.1088/1468-6996/11/5/054504 Giovanni > Dear Swapnil Chandratre, > > We recently published some studies on graphene nanoribbons > terminated with hydrogen, oxygen, and (dissociated) water and ammonia; > there are manymanymany other studies as well, but here the citations to > our works (Wassmann et alia): > > * Structure, stability, edge states and aromaticity of graphene ribbons > Tobias Wassmann, Ari P Seitsonen, A Marco Saitta, Michele Lazzeri and > Francesco Mauri, Physical Review Letters 101 096402 (2008); > http://dx.doi.org/10.1103/PhysRevLett.101.096402 > > * Clar's Theory, ?-Electron Distribution, and Geometry of Graphene > Nanoribbons Tobias Wassmann, Ari Paavo Seitsonen, A Marco Saitta, Michele > Lazzeri and Francesco Mauri, Journal of the American Chemical Society 132 > 3440-3451 (2010); http://dx.doi.org/10.1021/ja909234y > > * Structure and stability of graphene nanoribbons in oxygen, carbon > dioxide, water and ammonia Ari P Seitsonen, A Marco Saitta, Tobias > Wassmann, Michele Lazzeri and Francesco Mauri, Physical Review B 82 (2010) > 115425; http://dx.doi.org/10.1103/PhysRevB.82.115425 > > Greetings from Lund/Sweden, > > apsi > > >> Hi, >> Has anyone worked with Espresso to explore semi conducting properties on a Graphene Nanoribbon ( armchair configuration with specific >> geometry). Can anyone point to some articles to the same. >> >> -- >> Regards, >> Swapnil Chandratre >> Graduate Student >> Dept. of Mechanical Engineering, >> University of Houston, >> Houston, TX >> (M)-713-294-9546 -- **** PLEASE NOTICE THE NEW E-MAIL ADDRESS: giovanni.cantele at spin.cnr.it Giovanni Cantele, PhD CNR-SPIN and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario M. S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 - Fax: +39 081 676346 Skype contact: giocan74 ResearcherID: http://www.researcherid.com/rid/A-1951-2009 Web page: http://people.na.infn.it/~cantele http://www.nanomat.unina.it From fratesi at mater.unimib.it Tue May 17 12:30:43 2011 From: fratesi at mater.unimib.it (Guido Fratesi) Date: Tue, 17 May 2011 12:30:43 +0200 (CEST) Subject: [Pw_forum] LDOS on x-y direction, perpendicular to z In-Reply-To: References: Message-ID: Dear Alaaii, it can be done by using projwfc.x Have a look to examples/example16/README (task number 7) with volumes in the near-surface region. You can define volumes which span the full unit cell in x-y directions by setting irmin=1 and irmax to the number of points in the FFT grid. Notice that: Augmentation contributions are currently not included to the DOS in boxes If you are partitioning charge inside a crystal, using the atom-projected DOS might be a better option. HTH Guido On Mon, 16 May 2011, mashiat alaaii wrote: > Dear All, > Is there a way to find the LDOS of different planes (with different > thicknesses) on x-y direction, perpendicular to z? > Thank you for your help. > M Alaaii > -- Guido Fratesi Dipartimento di Scienza dei Materiali Universita` degli Studi di Milano-Bicocca via Cozzi 53, 20125 Milano, Italy From martins at if.uff.br Tue May 17 14:04:58 2011 From: martins at if.uff.br (martins at if.uff.br) Date: Tue, 17 May 2011 09:04:58 -0300 Subject: [Pw_forum] EE namelist Message-ID: <20110517090458.14052xb276svj2wa@webmail.if.uff.br> Dear users, I'm interested in running the PW program for simulating an isolated system. I know that I have to set the assume_isolated variable to 'dcc', for example. In this case, I have to supply an extra namelist (&EE), but in the user manual and in the wiki of the espresso code has not anything about this. Is there any reference for this namelist? An example? I appreciate any help. Regards, Adriano ------------------------------------ Adriano de Souza Martins Professor Adjunto III Departamento de F?sica - ICEx Polo Universit?rio de Volta Redonda Universidade Federal Fluminense - Brazil ------------------------------------ ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From oliviero at MIT.EDU Tue May 17 15:09:18 2011 From: oliviero at MIT.EDU (Oliviero Andreussi) Date: Tue, 17 May 2011 14:09:18 +0100 Subject: [Pw_forum] EE namelist In-Reply-To: <20110517090458.14052xb276svj2wa@webmail.if.uff.br> References: <20110517090458.14052xb276svj2wa@webmail.if.uff.br> Message-ID: <4DD2737E.8010204@mit.edu> Dear Adriano, As far as I know the dcc correction has been disabled in the last version of the code. The author is reimplementing it, I am not sure when it will be available again. You can use other approaches for isolated systems, if you are only interested in the energy correction, makov-payne is an alternative, just specify assume_isolated = 'makov-payne' in the &SYSTEM namelist. Otherwise I think there are other correction schemes for periodic boundaries implemented, try to have a look at the assume_isolated keyword. Best, Oliviero Andreussi Postdoctoral Associate, DMSE-MIT, 77 Massachusetts Ave, Cambridge, MA, 02139, USA On 17/05/11 13:04, martins at if.uff.br wrote: > Dear users, > > I'm interested in running the PW program for simulating an isolated > system. I know that I have to set the assume_isolated variable to > 'dcc', for example. In this case, I have to supply an extra namelist > (&EE), but in the user manual and in the wiki of the espresso code has > not anything about this. Is there any reference for this namelist? An > example? > > I appreciate any help. Regards, > > Adriano > > > ------------------------------------ > Adriano de Souza Martins > Professor Adjunto III > Departamento de F?sica - ICEx > Polo Universit?rio de Volta Redonda > Universidade Federal Fluminense - Brazil > ------------------------------------ > > ---------------------------------------------------------------- > 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 From m.g.p.krishna at chem.leidenuniv.nl Tue May 17 16:22:44 2011 From: m.g.p.krishna at chem.leidenuniv.nl (m.g.p.krishna at chem.leidenuniv.nl) Date: Tue, 17 May 2011 16:22:44 +0200 Subject: [Pw_forum] vc-relax with nspin=2 . Crashin Message-ID: <20110517162244.167524pv6gp725ro@webmail.chem.leidenuniv.nl> Dear List, I am trying a bond-length optimization of a simple graphene layer using QE v4.3. It works fine when I use nspin=1 but crashes when I switch to nspin=2. I already tried with different optmizers (CG and BFGS) and file collection methods ('random'...) together. But still the error persists. Please see also the input file. The error messages are: (using mpirun -np 128 ~/krishna/MyBin/espresso-4.3/bin/pw.x -npool 8 < test.spur.in > test.spur.out &): ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Writing output data file grapheneSpU.save NEW-OLD atomic charge density approx. for the potential forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source libopen-pal.so.0 00002B2FA6EA1BD0 Unknown Unknown Unknown libopen-pal.so.0 00002B2FA6EA05A5 Unknown Unknown Unknown libmpi.so.0 00002B2FA663F0BF Unknown Unknown Unknown libmpi.so.0 00002B2FA664054D Unknown Unknown Unknown libmpi.so.0 00002B2FA663EA56 Unknown Unknown Unknown libmpi.so.0 00002B2FA6630D10 Unknown Unknown Unknown libmpi.so.0 00002B2FA66312FB Unknown Unknown Unknown libmpi.so.0 00002B2FA66739BD Unknown Unknown Unknown libmpi_f77.so.0 00002B2FA63E500D Unknown Unknown Unknown pw.x 00000000006B03F1 mp_mp_mp_comm_spl 214 mp.f90 pw.x 0000000000464FAC paw_onecenter_mp_ 114 paw_onecenter.f90 pw.x 000000000050804C extrapolate_charg 435 update_pot.f90 pw.x 0000000000503634 update_pot_ 206 update_pot.f90 pw.x 000000000043DADB hinit1_ 34 hinit1.f90 pw.x 0000000000433BE9 MAIN__ 203 pwscf.f90 pw.x 000000000043388C Unknown Unknown Unknown libc.so.6 00000032ED61D974 Unknown Unknown Unknown pw.x 0000000000433799 Unknown Unknown Unknown ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I guess some fishy thing is there in IO w.r.t. spin. Does any one has Idea about it? Although It is a simple bond-length optimization test, later this need to be changed to some other system for a real production work. Thanks in advance, cheers Krishna Mohan G. P. Centre for Superfunctional Materials POSTECH S. Korea ===================================================================== &CONTROL calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = './' , pseudo_dir = '/home01/a202kks/krishna/myPSP' , prefix = 'grapheneSpU' , tprnfor = .true. , wf_collect=.true., etot_conv_thr=1.0E-4, forc_conv_thr=1.0E-3, / &SYSTEM ibrav = 0, celldm(1) = 1., nat = 2, ntyp = 1, ecutwfc = 30 , ecutrho = 250 , nbnd = 16, nosym = .true., tot_charge = 0.000000, nspin = 2, starting_magnetization(1) = 1, starting_magnetization(2) = 1, occupations = 'smearing', smearing = 'gauss', degauss = 0.02, / &ELECTRONS conv_thr = 1.E-4 , mixing_mode = 'plain' , mixing_beta = 0.3 , diagonalization = 'cg' , startingwfc='file', startingpot='file', / &IONS ion_dynamics='damp', wfc_extrapolation='second_order', wfc_extrapolation='second_order', / &CELL cell_dynamics = 'damp-pr' , cell_factor=3, cell_dofree='all', / CELL_PARAMETERS Hexagonal 4.025116724967956 2.323902182969979 0.000000000000000 4.025116724967956 -2.323902182969979 0.000000000000000 0.000000000000000 0.000000000000000 15.000000000000000 ATOMIC_SPECIES C 12.0107 C.pbe-paw_kj.UPF ATOMIC_POSITIONS angstrom C 1.420000000000000 0.000000000000000 0.000000000000000 C 2.840000000000000 0.000000000000000 0.000000000000000 K_POINTS automatic 8 8 1 1 1 1 From giannozz at democritos.it Tue May 17 17:13:02 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Tue, 17 May 2011 17:13:02 +0200 Subject: [Pw_forum] vc-relax with nspin=2 . Crashin In-Reply-To: <20110517162244.167524pv6gp725ro@webmail.chem.leidenuniv.nl> References: <20110517162244.167524pv6gp725ro@webmail.chem.leidenuniv.nl> Message-ID: <1305645182.7101.68.camel@fe12lx.fisica.uniud.it> On Tue, 2011-05-17 at 16:22 +0200, m.g.p.krishna at chem.leidenuniv.nl > forrtl: severe (174): SIGSEGV, segmentation fault occurred > calculation = 'vc-relax' , not sure it is your case, but there is a rather serious and nasty bug in variable-cell optimization in some cases. Tru to replace PW/scale_h.f90 with the attached version P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy -------------- next part -------------- A non-text attachment was scrubbed... Name: scale_h.f90 Type: text/x-fortran Size: 2671 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110517/3f4ad9ff/attachment.bin From willykohn at gmail.com Tue May 17 18:05:43 2011 From: willykohn at gmail.com (willy kohn) Date: Tue, 17 May 2011 12:05:43 -0400 Subject: [Pw_forum] How to restart md calculation using pw.x Message-ID: Dear Pwscf Users: I'm trying to use the "md" option in the pw.x to do some Born-Oppenheimer molecular dynamics calculation, but found that there is no way to restart the md calculation from the last configuration (including both positions and velocities) of atoms in a properly finished running. I'm wondering if there is a simple solution for that. Best, Will student of Gatech From crma at sissa.it Tue May 17 18:15:05 2011 From: crma at sissa.it (Changru Ma) Date: Tue, 17 May 2011 18:15:05 +0200 Subject: [Pw_forum] How to restart md calculation using pw.x In-Reply-To: References: Message-ID: <903F032B-A232-4866-9002-73705B49A71E@sissa.it> Dear Will, You can just simply set restart_mode = 'restart', in CONTROL namelist. With the same "prefix" and "outdir", atomic positions are read from directory $outdir/$prefix.save, which is the last configuration in the previous calculation. Best wishes, Changru On 17 May, 2011, at 18:05, willy kohn wrote: > Dear Pwscf Users: > > I'm trying to use the "md" option in the pw.x to do some > Born-Oppenheimer molecular dynamics calculation, but found that there > is no way to restart the md calculation from the last configuration > (including both positions and velocities) of atoms in a properly > finished running. I'm wondering if there is a simple solution for > that. > > Best, > > Will > > student of Gatech > _______________________________________________ > 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: +39 040 375 8713 (Elettra) +39 040 378 7870 (SISSA) http://www.sissa.it/~crma --- From willykohn at gmail.com Tue May 17 19:38:22 2011 From: willykohn at gmail.com (willy kohn) Date: Tue, 17 May 2011 13:38:22 -0400 Subject: [Pw_forum] How to restart md calculation using pw.x In-Reply-To: <903F032B-A232-4866-9002-73705B49A71E@sissa.it> References: <903F032B-A232-4866-9002-73705B49A71E@sissa.it> Message-ID: Dear Changru: Thanks a lot for the reply. I have tried this way but found the information of velocities got lost. All the best, Wei On Tue, May 17, 2011 at 12:15 PM, Changru Ma wrote: > Dear Will, > > You can just simply set > > ? ?restart_mode = 'restart', > > in CONTROL namelist. With the same "prefix" and "outdir", atomic positions are read from directory $outdir/$prefix.save, which is the last configuration in the previous calculation. > > Best wishes, > Changru > > On 17 May, 2011, at 18:05, willy kohn wrote: > >> Dear Pwscf Users: >> >> I'm trying to use the "md" option in the pw.x to do some >> Born-Oppenheimer molecular dynamics calculation, but found that there >> is no way to restart the md calculation from the last configuration >> (including both positions and velocities) of atoms in a properly >> finished running. I'm wondering if there is a simple solution for >> that. >> >> Best, >> >> Will >> >> student of Gatech >> _______________________________________________ >> 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: +39 040 375 8713 (Elettra) > ? ? ?+39 040 378 7870 (SISSA) > http://www.sissa.it/~crma > --- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From trambui at u.boisestate.edu Tue May 17 23:37:44 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Tue, 17 May 2011 15:37:44 -0600 Subject: [Pw_forum] Generating the Cs ultrasoft PP Message-ID: Dear Everyone, I've been tryign to generate an US PP for cesium. And I have built various input files ( as in the attachment is one of them), after running PP generation I do the plot for matching AE and pseudo wave functions and logarithmic derivative ( I also enclosed the plots in the files). The wave function matching seem correct but the ld ones do not match. I have tried with different rcut and rcutus values for each valence states but the results turned out to be similar to the one in the files. And I have been able to find anyone that have generated the US PP for Cs but norm-conserving PP. Would you give me some insights on what I might have done wrong in my input file ? and is it possible to generate the US PP for cesium? Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -------------- next part -------------- An HTML attachment was scrubbed... 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Name: gnuplot.pdf Type: application/pdf Size: 43129 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110517/402ee226/attachment-0003.pdf From nicola.marzari at materials.ox.ac.uk Tue May 17 23:40:42 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Tue, 17 May 2011 22:40:42 +0100 Subject: [Pw_forum] Generating the Cs ultrasoft PP In-Reply-To: References: Message-ID: <4DD2EB5A.2050904@materials.ox.ac.uk> first question is - do you really need an ultrasoft ? Cs might be quite soft, and if used with other harder elements, you might not really benefit much (a part from added trasnferability of US PP). PP generation is an ultra-worthy task, but you need to dedicate a substantial effort if you want to get mmeaningful results. nicola On 5/17/11 10:37 PM, Tram Bui wrote: > > Dear Everyone, > I've been tryign to generate an US PP for cesium. And I have built > various input files ( as in the attachment is one of them), after > running PP generation I do the plot for matching AE and pseudo wave > functions and logarithmic derivative ( I also enclosed the plots in the > files). The wave function matching seem correct but the ld ones do not > match. I have tried with different rcut and rcutus values for each > valence states but the results turned out to be similar to the one in > the files. And I have been able to find anyone that have generated the > US PP for Cs but norm-conserving PP. Would you give me some insights on > what I might have done wrong in my input file ? and is it possible to > generate the US PP for cesium? > > Regards, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > -- ---------------------------------------------------------------------- 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 kucukben at sissa.it Wed May 18 02:43:00 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Wed, 18 May 2011 02:43:00 +0200 Subject: [Pw_forum] Generating the Cs ultrasoft PP In-Reply-To: References: Message-ID: <20110518024300.42e8u1ufy8wsow4g@webmail.sissa.it> Dear Tram, first, try adding more channels: (as the warnings in the output of ld1.x have been asking you to) 6S 1 0 1.00 0.00 4.20 4.50 > add another s 6P 2 1 0.00 0.00 6.10 6.10 > add another p if you want to have different rcut and rcutus. 5D 3 2 0.00 0.00 3.00 3.00 try other local channels, try tm=.true. to use Troullier-Martins pseudization, try the ionized version like in the pseudo database, try adding 5s and 5p as two other channels, change rcuts, energies and trytrytry. it might be of help if you find the generation file of the NC pseudo in the database, try asking the author. have fun, emine kucukbenli, phd student, sissa, italy ps:you probably need non linear core correction with this pp. pps:are cesium orbitals really that huge to use 6au for rcut? ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From m.g.p.krishna at chem.leidenuniv.nl Wed May 18 03:58:29 2011 From: m.g.p.krishna at chem.leidenuniv.nl (m.g.p.krishna at chem.leidenuniv.nl) Date: Wed, 18 May 2011 03:58:29 +0200 Subject: [Pw_forum] vc-relax with nspin=2 . Crashin Message-ID: <20110518035829.12236foce5mzkfr9@webmail.chem.leidenuniv.nl> Dear Paolo Thanks a lot, I recompiled it with that file and it works, (may more tests is needed, though) with best regards Krishna From giannozz at democritos.it Wed May 18 09:51:24 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 18 May 2011 09:51:24 +0200 Subject: [Pw_forum] How to restart md calculation using pw.x In-Reply-To: References: <903F032B-A232-4866-9002-73705B49A71E@sissa.it> Message-ID: <0A2AC16C-CFBB-4CBA-A4B3-B591BFC9922A@democritos.it> On May 17, 2011, at 19:38 , willy kohn wrote: > Thanks a lot for the reply. I have tried this way but found the > information of velocities got lost. it is a known limitation of the current implementation 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 samolyuk at gmail.com Wed May 18 16:25:34 2011 From: samolyuk at gmail.com (German Samolyuk) Date: Wed, 18 May 2011 10:25:34 -0400 Subject: [Pw_forum] pwscf: energy convergence of noncollinear with spin-orbit calculations Message-ID: Dear qe users, I'm trying to calculate total energy of artificial FCC PtFe compound with magnetic moment (MM) along z- and x-directionsi (MAE). In order to supress oscillation of moment direction I used for MM||z calculation input instructions constrained_magnetization = 'total direction' , fixed_magnetization(1) = 0.0, fixed_magnetization(2) = 0.0, fixed_magnetization(3) = 1.0, However I can not reach total energy convergence and it looks like I still have direction oscillation of MM. What can be done to resolve this problem? Thank you in advance. The complete input file for MM||z is and energy accuracy output file are attached. German Samolyuk, ORNL, USA -------------- next part -------------- A non-text attachment was scrubbed... Name: ptfe.pw.in Type: application/octet-stream Size: 1571 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110518/bc3ab60c/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: accu.out Type: application/octet-stream Size: 2384 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110518/bc3ab60c/attachment-0001.obj From sks.jnc at gmail.com Wed May 18 23:38:24 2011 From: sks.jnc at gmail.com (S. K. S.) Date: Wed, 18 May 2011 23:38:24 +0200 Subject: [Pw_forum] LDA PZ USPP for Mg Message-ID: Dear All, Would someone like to share a PZ-LDA USPP for Mg ? regards, Saha SK stewart at cnf.cornell.eduwrote: > Hi all, > > I was wondering if anyone had a reliable ultrasoft > pseudopotential for Mg in > the local density approximation. The periodic table > on the PWscf site has > only norm-conserving and a GGA ultrasoft. > > Thanks, Hi Derek, I can try generate it. My US GGA pseudopotential for Mg works quite well. It will take few days, hopefully, including tests. Bests, Eyvaz. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110518/30742ec4/attachment.htm From germaneau at gucas.ac.cn Thu May 19 12:20:48 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Thu, 19 May 2011 06:20:48 -0400 Subject: [Pw_forum] How to restart md calculation using pw.x In-Reply-To: <505704280.22405@test1.gucas.ac.cn> References: <903F032B-A232-4866-9002-73705B49A71E@sissa.it> <505704280.22405@test1.gucas.ac.cn> Message-ID: <4DD4EF00.8060203@gucas.ac.cn> Why not write a script to do that? It should not be difficult. Good luck, ?ric. On 05/18/2011 03:51 AM, Paolo Giannozzi wrote: > On May 17, 2011, at 19:38 , willy kohn wrote: > >> Thanks a lot for the reply. I have tried this way but found the >> information of velocities got lost. > it is a known limitation of the current implementation > > 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 > -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /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/20110519/721870ac/attachment.htm From willykohn at gmail.com Thu May 19 08:11:22 2011 From: willykohn at gmail.com (willy kohn) Date: Thu, 19 May 2011 02:11:22 -0400 Subject: [Pw_forum] How to restart md calculation using pw.x In-Reply-To: <0A2AC16C-CFBB-4CBA-A4B3-B591BFC9922A@democritos.it> References: <903F032B-A232-4866-9002-73705B49A71E@sissa.it> <0A2AC16C-CFBB-4CBA-A4B3-B591BFC9922A@democritos.it> Message-ID: Dear Paolo: I'm just wondering why it has not been implemented yet. Are there any serious conflicts with the other functions of the present implementation? Best, Wei On Wed, May 18, 2011 at 3:51 AM, Paolo Giannozzi wrote: > > On May 17, 2011, at 19:38 , willy kohn wrote: > >> Thanks a lot for the reply. I have tried this way but found the >> information of velocities got lost. > > it is a known limitation of the current implementation > > 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 mayankaditya at gmail.com Thu May 19 09:03:17 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Thu, 19 May 2011 12:33:17 +0530 Subject: [Pw_forum] relaxed structure Message-ID: Hi Dear PWSCF Users I have relaxed structure using variable cell relaxation method (vc- relax) and got the relax cell parameter and atomic cordinates corresponds to total force=0.0004 Ry/A and pressure=0.25 Kbar. I have used the relaxed parameter for my scf calculations but after scf run the pressure become -3 Kbar and force is 0.163 Ry/A. kindly suggest the possible errors. Thanks -- Mayank BARC Mumbai INDIA From giannozz at democritos.it Thu May 19 10:11:38 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 19 May 2011 10:11:38 +0200 Subject: [Pw_forum] How to restart md calculation using pw.x In-Reply-To: References: <903F032B-A232-4866-9002-73705B49A71E@sissa.it> <0A2AC16C-CFBB-4CBA-A4B3-B591BFC9922A@democritos.it> Message-ID: On May 19, 2011, at 8:11 , willy kohn wrote: > I'm just wondering why it has not been implemented yet. for the usual reason: nobody among those who need it has - time - knowledge - good will - any combination of the above to implement it. Actually I am not even sure that it is not implemented. I just remember that there was something strange happening at each restart. It would be useful to have a detailed report of what exactly is the problem and under which circumstances and on which version of the code. > Are there any serious conflicts with the other functions of the > present implementation? not that I know. 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 May 19 10:25:04 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Thu, 19 May 2011 10:25:04 +0200 Subject: [Pw_forum] relaxed structure In-Reply-To: References: Message-ID: <06A028A7-A5D4-4BAC-8FD5-6A04AB146B44@democritos.it> On May 19, 2011, at 9:03 , mayank gupta wrote: > I have relaxed structure using variable cell relaxation method (vc- > relax) and got the relax cell parameter and atomic cordinates > corresponds to total force=0.0004 Ry/A and pressure=0.25 Kbar. I have > used the relaxed parameter for my scf calculations but after scf run > the pressure become -3 Kbar and force is 0.163 Ry/A. kindly suggest > the possible errors. there is no error, as explained an infinite number of 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 max.n.popov at gmail.com Thu May 19 10:29:49 2011 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Thu, 19 May 2011 10:29:49 +0200 Subject: [Pw_forum] relaxed structure In-Reply-To: <06A028A7-A5D4-4BAC-8FD5-6A04AB146B44@democritos.it> References: <06A028A7-A5D4-4BAC-8FD5-6A04AB146B44@democritos.it> Message-ID: Dear Mayank, what version of QE do you use? -- > 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/20110519/3ae69981/attachment.htm From njuwangda at gmail.com Thu May 19 14:59:37 2011 From: njuwangda at gmail.com (da wang) Date: Thu, 19 May 2011 20:59:37 +0800 Subject: [Pw_forum] mixing pseudopotentials using virtual.x Message-ID: Dear all: I have met a problem when I used virtual.x to mix pseudopotentials of O and F (http://www.quantum-espresso.org/pseudo/1.3/UPF/O.pbe-van_ak.UPF, http://www.quantum-espresso.org/pseudo/1.3/UPF/F.pbe-n-van.UPF) it says: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from Virtual : error # 1 different nqf are not implemented (yet) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I want to know how to do it correctly? Thanks in advance. From germaneau at gucas.ac.cn Fri May 20 12:22:34 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Fri, 20 May 2011 06:22:34 -0400 Subject: [Pw_forum] relaxed structure In-Reply-To: <505787777.23051@test1.gucas.ac.cn> References: <505787777.23051@test1.gucas.ac.cn> Message-ID: <4DD640EA.3040108@gucas.ac.cn> The 1.43 release performs a scf calculation of the optimized structure and the end of the run. You'd better check your results with it. Best, ?ric. On 05/19/2011 03:03 AM, mayank gupta wrote: > Hi Dear PWSCF Users > > I have relaxed structure using variable cell relaxation method (vc- > relax) and got the relax cell parameter and atomic cordinates > corresponds to total force=0.0004 Ry/A and pressure=0.25 Kbar. I have > used the relaxed parameter for my scf calculations but after scf run > the pressure become -3 Kbar and force is 0.163 Ry/A. kindly suggest > the possible errors. > > Thanks -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /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/20110520/d2e8c717/attachment.htm From trambui at u.boisestate.edu Fri May 20 00:34:40 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Thu, 19 May 2011 16:34:40 -0600 Subject: [Pw_forum] Error message from scf calculation Message-ID: Dear QE users, I'm trying to run a simple calculation for bulk cesium's total energy. and I have got an error message saying that "charge is wrong: smearing is needed". Would you please give me some information on how to solve this error? I have enclosed the input file here, in case you would like to take a look at it. Thank you very much, 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/20110519/353707b4/attachment.htm From kucukben at sissa.it Fri May 20 01:20:50 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Fri, 20 May 2011 01:20:50 +0200 Subject: [Pw_forum] mixing pseudopotentials using virtual.x In-Reply-To: References: Message-ID: <20110520012050.dhnwqsodc0cssoko@webmail.sissa.it> Dear user, Not an expert on the issue, but from what i see, these pseudopotentials are generated using Vanderbilts's code, where you can use some taylor expansion to pseudize the augmentation charge and i guess nqf stands for how many terms in the expansion are hold. Apparently the pseudopotentials you are using use different numbers of nqf (6 and 8) and quoting the error message "(mixing of?) different nqf are not implemented (yet) " The "yet" at the end gives some hope though.Let's hear from the developers. In the meanwhile you can use some ld1 generated pseudopotentials, where this expansion is not supported as far as i know... or try to find/generate ones with the same number of nqf obviously.. Please sign your posts with your name and affiliation. cheers, emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From zhaohscas at yahoo.com.cn Fri May 20 13:46:50 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Fri, 20 May 2011 07:46:50 -0400 Subject: [Pw_forum] Is it possiable to do MP grid test based on grid density within pwscf? Message-ID: <4DD654AA.4070601@yahoo.com.cn> Hi all, For some DFT codes, say, CASTEP, we can do the MP grid test based on grid density (see http://www.tcm.phy.cam.ac.uk/castep/Geom_Opt/node6.html for detail) : A second way of requesting a Monkhurst-Pack grid is to specify a minimum grid density. ----------------- KPOINTS_MP_SPACING $ R$ [units] Where $ R$ is the maximum distance between any two k-points in the grid. The default [units] of the k-point spacing are ?$ ^{-1}$. --------------------- Considering that this method is more benefit for MP grid test by using a shell script, I want to know is there similar technique(s) fulfilled within pwscf? Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From bipulrr at gmail.com Fri May 20 07:00:45 2011 From: bipulrr at gmail.com (Bipul Rakshit) Date: Fri, 20 May 2011 10:30:45 +0530 Subject: [Pw_forum] Phonons with constrained Magnetisation & espresso-4.3 Message-ID: Dear PWSCF users, Recently i am doing phonon calculation in LaMnO3 using constrained magnetisation. The earlier versions 4.1.1 gives an error message that "phonons with constrained magnetisation is not yet implimented". But there is no such error message in espresso-4.3. So just want to know the success of calculating the LO-TO splitting correctly with constrained magnetisation using espresso-4.3, with these type of perovskites compounds. A part of my input is as follows &SYSTEM ibrav = 8, celldm(1) = 10.9920312470, celldm(2) = 1.3605399684, celldm(3) = 0.996021, nat = 20, ntyp = 4 , ecutwfc = 30, ecutrho = 310, nspin =2, starting_magnetization(1)=0.0, starting_magnetization(2)=1.0, starting_magnetization(3)=-1.0, starting_magnetization(4)=0.0, tot_magnetization=0.0, occupations='fixed' / -- Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India From giannozz at democritos.it Fri May 20 08:06:48 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 20 May 2011 08:06:48 +0200 Subject: [Pw_forum] Error message from scf calculation In-Reply-To: References: Message-ID: <9321C8E6-434C-4B1F-9792-C9BB9BD3E6E5@democritos.it> On May 20, 2011, at 24:34 , Tram Bui wrote: > "charge is wrong: smearing is needed". Would you please > give me some information on how to solve this error? use smearing > I have enclosed the input file here > really? 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 CJH085 at bham.ac.uk Fri May 20 14:02:37 2011 From: CJH085 at bham.ac.uk (Christopher Heard) Date: Fri, 20 May 2011 13:02:37 +0100 Subject: [Pw_forum] vc-relax - negative and non-zero cell parameters Message-ID: <4406F1904F879A4D9FE86E310EA6634102136F5A7862@mbx5.adf.bham.ac.uk> Hi, I have a question regarding vc-relaxation in relative coordinates. If I input a cubic lattice and allow the program to relax the cell parameters, and print as relative coordinates of the original cell parameters (alat), I dont understand how off diagonal terms can be non-zero (what is 0 x 0.9 if not 0?) or how negative values have physical meaning. Perhaps I am not understanding the method by which the calculation is made, but I couldn't get any understanding from the INPUT_PW.txt file or the manual, so I am asking the list. Cheers, Chris ======================================================== INPUT FILE &CONTROL calculation = "vc-relax", prefix = "QETEST", pseudo_dir = " /home/heard/pseudo ", outdir = ".", nstep = 10, / &SYSTEM ibrav = 0, nat = 3, ntyp = 2, ecutwfc = 20.D0, occupations = 'smearing' smearing = 'mp' degauss = 0.06 / &ELECTRONS electron_maxstep = 1000, conv_thr = 1.D-6, mixing_beta = 0.3D0, / &IONS / &CELL cell_dynamics = 'bfgs', / CELL_PARAMETERS cubic 30.23 0.0 0.0 0.0 30.23 0.0 0.0 0.0 30.23 ATOMIC_SPECIES Cu 63.5 Cu.pbe-d-rrkjus.upf Ag 107.9 Ag.pbe-d-rrkjus.upf ATOMIC_POSITIONS {crystal} Cu 0.9110342051985 0.5412603911172 0.9652262133233 Cu 0.3046428810907 0.3592799679414 0.0488897975312 Ag 0.868139803195 0.7597487846068 0.8302658063157 K_POINTS {Gamma} ====================================================== START OF OUTPUT FILE bravais-lattice index = 0 lattice parameter (a_0) = 30.2300 a.u. unit-cell volume = 27625.7732 (a.u.)^3 number of atoms/cell = 3 number of atomic types = 2 number of electrons = 33.00 number of Kohn-Sham states= 21 kinetic-energy cutoff = 20.0000 Ry charge density cutoff = 80.0000 Ry convergence threshold = 1.0E-06 mixing beta = 0.3000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) EXX-fraction = 0.00 nstep = 10 celldm(1)= 30.230000 celldm(2)= 0.000000 celldm(3)= 0.000000 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( 0.000000 1.000000 0.000000 ) a(3) = ( 0.000000 0.000000 1.000000 ) =========================================================== OUTPUT COORDINATES new unit-cell volume = 27844.52160 a.u.^3 ( 4126.13235 Ang^3 ) CELL_PARAMETERS (alat= 30.23000000) 1.003485881 0.000341145 -0.000166335 0.000341140 1.002476151 0.000847099 -0.000166325 0.000846982 1.001936910 ATOMIC_POSITIONS (crystal) Cu 0.911117504 0.540084682 0.965438693 Cu 0.305212112 0.357448827 0.044305096 Ag 0.867487274 0.762755634 0.834638028 =========================================================== From max.n.popov at gmail.com Fri May 20 14:25:37 2011 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Fri, 20 May 2011 14:25:37 +0200 Subject: [Pw_forum] vc-relax - negative and non-zero cell parameters In-Reply-To: <4406F1904F879A4D9FE86E310EA6634102136F5A7862@mbx5.adf.bham.ac.uk> References: <4406F1904F879A4D9FE86E310EA6634102136F5A7862@mbx5.adf.bham.ac.uk> Message-ID: Dear Christopher, 1) the structure, in the input you provided, looks weird to me. Are you sure it is really what you intend to simulate? 2) The vc-relaxation process with symmetry conservation is driven by crystal symmetry. That is to say: cubic unit cell does not necessary mean cubic symmetry. Coming back to your structure, by visual inspection one can see that it does not possess cubic symmetry (it is P1, most probably). Therefore off-diagonal terms of Bravais matrix evolved during cell-shape relaxation. Best regards, Maxim. 2011/5/20 Christopher Heard > Hi, > I have a question regarding vc-relaxation in relative coordinates. > If I input a cubic lattice and allow the program to relax the cell > parameters, and print as relative coordinates of the original cell > parameters (alat), I dont understand how off diagonal terms can be non-zero > (what is 0 x 0.9 if not 0?) or how negative values have physical meaning. > > Perhaps I am not understanding the method by which the calculation is made, > but I couldn't get any understanding from the INPUT_PW.txt file or the > manual, so I am asking the list. > > Cheers, > Chris > > > ======================================================== > INPUT FILE > > &CONTROL > calculation = "vc-relax", > prefix = "QETEST", > pseudo_dir = " /home/heard/pseudo ", > outdir = ".", > nstep = 10, > / > &SYSTEM > ibrav = 0, > nat = 3, > ntyp = 2, > ecutwfc = 20.D0, > occupations = 'smearing' > smearing = 'mp' > degauss = 0.06 > / > &ELECTRONS > electron_maxstep = 1000, > conv_thr = 1.D-6, > mixing_beta = 0.3D0, > / > &IONS > / > &CELL > cell_dynamics = 'bfgs', > / > CELL_PARAMETERS cubic > 30.23 0.0 0.0 > 0.0 30.23 0.0 > 0.0 0.0 30.23 > ATOMIC_SPECIES > Cu 63.5 Cu.pbe-d-rrkjus.upf > Ag 107.9 Ag.pbe-d-rrkjus.upf > > ATOMIC_POSITIONS {crystal} > > Cu 0.9110342051985 0.5412603911172 0.9652262133233 > Cu 0.3046428810907 0.3592799679414 0.0488897975312 > Ag 0.868139803195 0.7597487846068 0.8302658063157 > K_POINTS {Gamma} > > > ====================================================== > START OF OUTPUT FILE > > bravais-lattice index = 0 > lattice parameter (a_0) = 30.2300 a.u. > unit-cell volume = 27625.7732 (a.u.)^3 > number of atoms/cell = 3 > number of atomic types = 2 > number of electrons = 33.00 > number of Kohn-Sham states= 21 > kinetic-energy cutoff = 20.0000 Ry > charge density cutoff = 80.0000 Ry > convergence threshold = 1.0E-06 > mixing beta = 0.3000 > number of iterations used = 8 plain mixing > Exchange-correlation = SLA PW PBE PBE (1434) > EXX-fraction = 0.00 > nstep = 10 > > > celldm(1)= 30.230000 celldm(2)= 0.000000 celldm(3)= 0.000000 > celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 1.000000 0.000000 0.000000 ) > a(2) = ( 0.000000 1.000000 0.000000 ) > a(3) = ( 0.000000 0.000000 1.000000 ) > > =========================================================== > OUTPUT COORDINATES > > new unit-cell volume = 27844.52160 a.u.^3 ( 4126.13235 Ang^3 ) > > CELL_PARAMETERS (alat= 30.23000000) > 1.003485881 0.000341145 -0.000166335 > 0.000341140 1.002476151 0.000847099 > -0.000166325 0.000846982 1.001936910 > > ATOMIC_POSITIONS (crystal) > Cu 0.911117504 0.540084682 0.965438693 > Cu 0.305212112 0.357448827 0.044305096 > Ag 0.867487274 0.762755634 0.834638028 > =========================================================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- 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/20110520/49feed11/attachment.htm From giannozz at democritos.it Fri May 20 14:42:21 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 20 May 2011 14:42:21 +0200 Subject: [Pw_forum] Is it possiable to do MP grid test based on grid density within pwscf? In-Reply-To: <4DD654AA.4070601@yahoo.com.cn> References: <4DD654AA.4070601@yahoo.com.cn> Message-ID: <1305895341.1293.0.camel@fe12lx.fisica.uniud.it> On Fri, 2011-05-20 at 07:46 -0400, Hongsheng Zhao wrote: > A second way of requesting a Monkhurst-Pack grid is to specify a minimum > grid density.[..] is there similar technique(s) fulfilled within pwscf? no -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From CJH085 at bham.ac.uk Fri May 20 15:02:40 2011 From: CJH085 at bham.ac.uk (Christopher Heard) Date: Fri, 20 May 2011 14:02:40 +0100 Subject: [Pw_forum] ?spam? Re: vc-relax - negative and non-zero cell parameters In-Reply-To: References: <4406F1904F879A4D9FE86E310EA6634102136F5A7862@mbx5.adf.bham.ac.uk>, Message-ID: <4406F1904F879A4D9FE86E310EA6634102136F5A7863@mbx5.adf.bham.ac.uk> Dear Maxim, The structure is chosen at random, as I simply wish to test the vc-relax procedure, so I don't expect it to have a particular symmetry, although in general, I am dealing with clusters of low symmetry anyway. My problem is that it makes no sense to me that off diagonal elements can be non-zero, when they are relative. How can one have a value 0.000341145 x 0 (in the case of element (1,2))? This, I do not understand. Furthermore, what would a negative relative parameter mean? I suspect I am misinterpreting the meaning of these alat cell parameter matrices, but I'm not sure how. Chris ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of ?????? ????? [max.n.popov at gmail.com] Sent: 20 May 2011 13:25 To: PWSCF Forum Subject: ?spam? Re: [Pw_forum] vc-relax - negative and non-zero cell parameters Dear Christopher, 1) the structure, in the input you provided, looks weird to me. Are you sure it is really what you intend to simulate? 2) The vc-relaxation process with symmetry conservation is driven by crystal symmetry. That is to say: cubic unit cell does not necessary mean cubic symmetry. Coming back to your structure, by visual inspection one can see that it does not possess cubic symmetry (it is P1, most probably). Therefore off-diagonal terms of Bravais matrix evolved during cell-shape relaxation. Best regards, Maxim. 2011/5/20 Christopher Heard > Hi, I have a question regarding vc-relaxation in relative coordinates. If I input a cubic lattice and allow the program to relax the cell parameters, and print as relative coordinates of the original cell parameters (alat), I dont understand how off diagonal terms can be non-zero (what is 0 x 0.9 if not 0?) or how negative values have physical meaning. Perhaps I am not understanding the method by which the calculation is made, but I couldn't get any understanding from the INPUT_PW.txt file or the manual, so I am asking the list. Cheers, Chris ======================================================== INPUT FILE &CONTROL calculation = "vc-relax", prefix = "QETEST", pseudo_dir = " /home/heard/pseudo ", outdir = ".", nstep = 10, / &SYSTEM ibrav = 0, nat = 3, ntyp = 2, ecutwfc = 20.D0, occupations = 'smearing' smearing = 'mp' degauss = 0.06 / &ELECTRONS electron_maxstep = 1000, conv_thr = 1.D-6, mixing_beta = 0.3D0, / &IONS / &CELL cell_dynamics = 'bfgs', / CELL_PARAMETERS cubic 30.23 0.0 0.0 0.0 30.23 0.0 0.0 0.0 30.23 ATOMIC_SPECIES Cu 63.5 Cu.pbe-d-rrkjus.upf Ag 107.9 Ag.pbe-d-rrkjus.upf ATOMIC_POSITIONS {crystal} Cu 0.9110342051985 0.5412603911172 0.9652262133233 Cu 0.3046428810907 0.3592799679414 0.0488897975312 Ag 0.868139803195 0.7597487846068 0.8302658063157 K_POINTS {Gamma} ====================================================== START OF OUTPUT FILE bravais-lattice index = 0 lattice parameter (a_0) = 30.2300 a.u. unit-cell volume = 27625.7732 (a.u.)^3 number of atoms/cell = 3 number of atomic types = 2 number of electrons = 33.00 number of Kohn-Sham states= 21 kinetic-energy cutoff = 20.0000 Ry charge density cutoff = 80.0000 Ry convergence threshold = 1.0E-06 mixing beta = 0.3000 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBE PBE (1434) EXX-fraction = 0.00 nstep = 10 celldm(1)= 30.230000 celldm(2)= 0.000000 celldm(3)= 0.000000 celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.000000 0.000000 0.000000 ) a(2) = ( 0.000000 1.000000 0.000000 ) a(3) = ( 0.000000 0.000000 1.000000 ) =========================================================== OUTPUT COORDINATES new unit-cell volume = 27844.52160 a.u.^3 ( 4126.13235 Ang^3 ) CELL_PARAMETERS (alat= 30.23000000) 1.003485881 0.000341145 -0.000166335 0.000341140 1.002476151 0.000847099 -0.000166325 0.000846982 1.001936910 ATOMIC_POSITIONS (crystal) Cu 0.911117504 0.540084682 0.965438693 Cu 0.305212112 0.357448827 0.044305096 Ag 0.867487274 0.762755634 0.834638028 =========================================================== _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Best regards, Max Popov Ph.D. student Materials center Leoben (MCL), Leoben, Austria. From giannozz at democritos.it Fri May 20 15:19:07 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 20 May 2011 15:19:07 +0200 Subject: [Pw_forum] vc-relax - negative and non-zero cell parameters In-Reply-To: <4406F1904F879A4D9FE86E310EA6634102136F5A7863@mbx5.adf.bham.ac.uk> References: <4406F1904F879A4D9FE86E310EA6634102136F5A7862@mbx5.adf.bham.ac.uk> , <4406F1904F879A4D9FE86E310EA6634102136F5A7863@mbx5.adf.bham.ac.uk> Message-ID: <1305897547.1293.3.camel@fe12lx.fisica.uniud.it> On Fri, 2011-05-20 at 14:02 +0100, Christopher Heard wrote: > My problem is that it makes no sense to me that off diagonal elements can be non-zero, when they are relative. > CELL_PARAMETERS (alat= 30.23000000) > 1.003485881 0.000341145 -0.000166335 > 0.000341140 1.002476151 0.000847099 > -0.000166325 0.000846982 1.001936910 lattice vector 1 : (1.003485881 0.000341145 -0.000166335)*alat lattice vector 2 : (0.000341140 1.002476151 0.000847099)*alat lattice vector 3 : (-0.000166325 0.000846982 1.001936910)*alat Where is the problem? -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From max.n.popov at gmail.com Fri May 20 15:22:25 2011 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Fri, 20 May 2011 15:22:25 +0200 Subject: [Pw_forum] ?spam? Re: vc-relax - negative and non-zero cell parameters In-Reply-To: <4406F1904F879A4D9FE86E310EA6634102136F5A7863@mbx5.adf.bham.ac.uk> References: <4406F1904F879A4D9FE86E310EA6634102136F5A7862@mbx5.adf.bham.ac.uk> <4406F1904F879A4D9FE86E310EA6634102136F5A7863@mbx5.adf.bham.ac.uk> Message-ID: Dear Christopher, The structure is chosen at random, as I simply wish to test the vc-relax > procedure, so I don't expect it to have a particular symmetry, although in > general, I am dealing with clusters of low symmetry anyway. > > If you are dealing with clusters, then there is no utility of vc-relax for you. > My problem is that it makes no sense to me that off diagonal elements can > be non-zero, when they are relative. How can one have a value 0.000341145 x > 0 (in the case of element (1,2))? This, I do not understand. > > Furthermore, what would a negative relative parameter mean? > I suspect I am misinterpreting the meaning of these alat cell parameter > matrices, but I'm not sure how. > The matrix, you see in the output, is Bravais matrix, i.e. a matrix, where the cartesian coordinates of a unit cell vectors are packed in rows. The notation: CELL_PARAMETERS (alat= 30.23000000) 1.003485881 0.000341145 -0.000166335 0.000341140 1.002476151 0.000847099 -0.000166325 0.000846982 1.001936910 means that Bravais matrix is: { 1.003485881 0.000341145 -0.000166335 } { 0.000341140 1.002476151 0.000847099 } times alat = { -0.000166325 0.000846982 1.001936910 } { 30.3354 0.0103 -0.0050 } { 0.0103 30.3049 0.0256 } { -0.0050 0.0256 30.2886 } Hope, it helps. -- 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/20110520/d51dc599/attachment-0001.htm From CJH085 at bham.ac.uk Fri May 20 16:01:01 2011 From: CJH085 at bham.ac.uk (Christopher Heard) Date: Fri, 20 May 2011 15:01:01 +0100 Subject: [Pw_forum] vc-relax - negative and non-zero cell parameters In-Reply-To: <1305897547.1293.3.camel@fe12lx.fisica.uniud.it> References: <4406F1904F879A4D9FE86E310EA6634102136F5A7862@mbx5.adf.bham.ac.uk> , <4406F1904F879A4D9FE86E310EA6634102136F5A7863@mbx5.adf.bham.ac.uk>, <1305897547.1293.3.camel@fe12lx.fisica.uniud.it> Message-ID: <4406F1904F879A4D9FE86E310EA6634102136F5A7864@mbx5.adf.bham.ac.uk> You are of course right, there is none. I see now, Thanks, Chris ________________________________________ From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi [giannozz at democritos.it] Sent: 20 May 2011 14:19 To: PWSCF Forum Subject: Re: [Pw_forum] vc-relax - negative and non-zero cell parameters On Fri, 2011-05-20 at 14:02 +0100, Christopher Heard wrote: > My problem is that it makes no sense to me that off diagonal elements can be non-zero, when they are relative. > CELL_PARAMETERS (alat= 30.23000000) > 1.003485881 0.000341145 -0.000166335 > 0.000341140 1.002476151 0.000847099 > -0.000166325 0.000846982 1.001936910 lattice vector 1 : (1.003485881 0.000341145 -0.000166335)*alat lattice vector 2 : (0.000341140 1.002476151 0.000847099)*alat lattice vector 3 : (-0.000166325 0.000846982 1.001936910)*alat Where is the problem? -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From trambui at u.boisestate.edu Fri May 20 22:40:27 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Fri, 20 May 2011 14:40:27 -0600 Subject: [Pw_forum] Error message from scf calculation In-Reply-To: <9321C8E6-434C-4B1F-9792-C9BB9BD3E6E5@democritos.it> References: <9321C8E6-434C-4B1F-9792-C9BB9BD3E6E5@democritos.it> Message-ID: I'm so sorry I forgot the file:) here it is. And I have added the variables of : occupations='smearing', and degauss=0.01. And the calculation ran fine. It gave me a total energy value for Cs of 0.01301261 Ry. does it seem trustable? Thank you very much, Tram On Fri, May 20, 2011 at 12:06 AM, Paolo Giannozzi wrote: > > On May 20, 2011, at 24:34 , Tram Bui wrote: > > > "charge is wrong: smearing is needed". Would you please > > give me some information on how to solve this error? > > use smearing > > > I have enclosed the input file here > > > > > really? > > 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 > -- 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/20110520/12060535/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: cs1.in Type: application/octet-stream Size: 509 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110520/12060535/attachment.obj From ttduyle at gmail.com Fri May 20 23:02:58 2011 From: ttduyle at gmail.com (Duy Le) Date: Fri, 20 May 2011 17:02:58 -0400 Subject: [Pw_forum] Error message from scf calculation In-Reply-To: References: <9321C8E6-434C-4B1F-9792-C9BB9BD3E6E5@democritos.it> Message-ID: I believe that you have asked us about the calculation for an isolated atom sometimes ago. It was about C. You should have done the same approach. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Fri, May 20, 2011 at 4:40 PM, Tram Bui wrote: > I'm so sorry I forgot the file:) here it is. And I have added the variables > of : occupations='smearing', and degauss=0.01. And the calculation ran fine. > It gave me a total energy value for Cs of 0.01301261 Ry. does it seem > trustable? > > Thank you very much, > Tram > > On Fri, May 20, 2011 at 12:06 AM, Paolo Giannozzi > wrote: >> >> On May 20, 2011, at 24:34 , Tram Bui wrote: >> >> > "charge is wrong: smearing is needed". Would you please >> > give me some information on how to solve this error? >> >> use smearing >> >> > I have enclosed the input file here >> >> > >> >> really? >> >> 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 > > > > -- > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From ttduyle at gmail.com Fri May 20 23:09:11 2011 From: ttduyle at gmail.com (Duy Le) Date: Fri, 20 May 2011 17:09:11 -0400 Subject: [Pw_forum] Error message from scf calculation In-Reply-To: References: <9321C8E6-434C-4B1F-9792-C9BB9BD3E6E5@democritos.it> Message-ID: Sorry, I answer wrong question. Please ignore my previous email. For your calculation, it is hard to tell because we don't know the reference for the calculated total energy. On top of that, it should not be POSITIVE. You should optimize the lattice parameter for Cs and then calculate its cohesive energy. You can compare the cohesive energy with experimental or other theoretical data. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Fri, May 20, 2011 at 5:02 PM, Duy Le wrote: > I believe that you have asked us about the calculation for an > isolated atom sometimes ago. It was about C. You should have done the > same approach. > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > > > On Fri, May 20, 2011 at 4:40 PM, Tram Bui wrote: >> I'm so sorry I forgot the file:) here it is. And I have added the variables >> of : occupations='smearing', and degauss=0.01. And the calculation ran fine. >> It gave me a total energy value for Cs of 0.01301261 Ry. does it seem >> trustable? >> >> Thank you very much, >> Tram >> >> On Fri, May 20, 2011 at 12:06 AM, Paolo Giannozzi >> wrote: >>> >>> On May 20, 2011, at 24:34 , Tram Bui wrote: >>> >>> > "charge is wrong: smearing is needed". Would you please >>> > give me some information on how to solve this error? >>> >>> use smearing >>> >>> > I have enclosed the input file here >>> >>> > >>> >>> really? >>> >>> 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 >> >> >> >> -- >> Tram Bui >> >> M.S. Materials Science & Engineering >> trambui at u.boisestate.edu >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > From degironc at sissa.it Fri May 20 23:28:42 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 20 May 2011 23:28:42 +0200 Subject: [Pw_forum] ?spam? Re: vc-relax - negative and non-zero cell parameters In-Reply-To: <4406F1904F879A4D9FE86E310EA6634102136F5A7863@mbx5.adf.bham.ac.uk> References: <4406F1904F879A4D9FE86E310EA6634102136F5A7862@mbx5.adf.bham.ac.uk>, <4406F1904F879A4D9FE86E310EA6634102136F5A7863@mbx5.adf.bham.ac.uk> Message-ID: <4DD6DD0A.8050702@sissa.it> Dear Christopher On 05/20/2011 03:02 PM, Christopher Heard wrote: > Dear Maxim, > > The structure is chosen at random, as I simply wish to test the vc-relax procedure, so I don't expect it to have a particular symmetry, although in general, I am dealing with clusters of low symmetry anyway. > > My problem is that it makes no sense to me that off diagonal elements can be non-zero, when they are relative. How can one have a value 0.000341145 x 0 (in the case of element (1,2))? This, I do not understand. > I don't understand what you don't understand... cell parameters are just the three fundamental lattice vectors defining the Bravais lattice. why should it be a problem to have a vector with a negative component ? stefano - Stefano de Gironcoli, SISSA and DEMOCRITOS > Furthermore, what would a negative relative parameter mean? > I suspect I am misinterpreting the meaning of these alat cell parameter matrices, but I'm not sure how. > > > Chris > > > ________________________________________ > From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of ?????? ????? [max.n.popov at gmail.com] > Sent: 20 May 2011 13:25 > To: PWSCF Forum > Subject: ?spam? Re: [Pw_forum] vc-relax - negative and non-zero cell parameters > > Dear Christopher, > > 1) the structure, in the input you provided, looks weird to me. Are you sure it is really what you intend to simulate? > 2) The vc-relaxation process with symmetry conservation is driven by crystal symmetry. That is to say: cubic unit > cell does not necessary mean cubic symmetry. Coming back to your structure, by visual inspection one can see > that it does not possess cubic symmetry (it is P1, most probably). Therefore off-diagonal terms of Bravais matrix > evolved during cell-shape relaxation. > > Best regards, > Maxim. > > 2011/5/20 Christopher Heard> > Hi, > I have a question regarding vc-relaxation in relative coordinates. > If I input a cubic lattice and allow the program to relax the cell parameters, and print as relative coordinates of the original cell parameters (alat), I dont understand how off diagonal terms can be non-zero (what is 0 x 0.9 if not 0?) or how negative values have physical meaning. > > Perhaps I am not understanding the method by which the calculation is made, but I couldn't get any understanding from the INPUT_PW.txt file or the manual, so I am asking the list. > > Cheers, > Chris > > > ======================================================== > INPUT FILE > > &CONTROL > calculation = "vc-relax", > prefix = "QETEST", > pseudo_dir = " /home/heard/pseudo ", > outdir = ".", > nstep = 10, > / > &SYSTEM > ibrav = 0, > nat = 3, > ntyp = 2, > ecutwfc = 20.D0, > occupations = 'smearing' > smearing = 'mp' > degauss = 0.06 > / > &ELECTRONS > electron_maxstep = 1000, > conv_thr = 1.D-6, > mixing_beta = 0.3D0, > / > &IONS > / > &CELL > cell_dynamics = 'bfgs', > / > CELL_PARAMETERS cubic > 30.23 0.0 0.0 > 0.0 30.23 0.0 > 0.0 0.0 30.23 > ATOMIC_SPECIES > Cu 63.5 Cu.pbe-d-rrkjus.upf > Ag 107.9 Ag.pbe-d-rrkjus.upf > > ATOMIC_POSITIONS {crystal} > > Cu 0.9110342051985 0.5412603911172 0.9652262133233 > Cu 0.3046428810907 0.3592799679414 0.0488897975312 > Ag 0.868139803195 0.7597487846068 0.8302658063157 > K_POINTS {Gamma} > > > ====================================================== > START OF OUTPUT FILE > > bravais-lattice index = 0 > lattice parameter (a_0) = 30.2300 a.u. > unit-cell volume = 27625.7732 (a.u.)^3 > number of atoms/cell = 3 > number of atomic types = 2 > number of electrons = 33.00 > number of Kohn-Sham states= 21 > kinetic-energy cutoff = 20.0000 Ry > charge density cutoff = 80.0000 Ry > convergence threshold = 1.0E-06 > mixing beta = 0.3000 > number of iterations used = 8 plain mixing > Exchange-correlation = SLA PW PBE PBE (1434) > EXX-fraction = 0.00 > nstep = 10 > > > celldm(1)= 30.230000 celldm(2)= 0.000000 celldm(3)= 0.000000 > celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000 > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 1.000000 0.000000 0.000000 ) > a(2) = ( 0.000000 1.000000 0.000000 ) > a(3) = ( 0.000000 0.000000 1.000000 ) > > =========================================================== > OUTPUT COORDINATES > > new unit-cell volume = 27844.52160 a.u.^3 ( 4126.13235 Ang^3 ) > > CELL_PARAMETERS (alat= 30.23000000) > 1.003485881 0.000341145 -0.000166335 > 0.000341140 1.002476151 0.000847099 > -0.000166325 0.000846982 1.001936910 > > ATOMIC_POSITIONS (crystal) > Cu 0.911117504 0.540084682 0.965438693 > Cu 0.305212112 0.357448827 0.044305096 > Ag 0.867487274 0.762755634 0.834638028 > =========================================================== > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > Best regards, Max Popov > Ph.D. student > Materials center Leoben (MCL), Leoben, Austria. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From sd.wang000 at gmail.com Sat May 21 10:16:44 2011 From: sd.wang000 at gmail.com (S. D. Wang) Date: Sat, 21 May 2011 16:16:44 +0800 Subject: [Pw_forum] GPU-enabled Message-ID: Dear all: Waht does the GPU-enabled mean? -- S. D. Wang * * *???* * * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110521/181793c6/attachment.htm From tavana.ali at gmail.com Sat May 21 11:04:25 2011 From: tavana.ali at gmail.com (Ali Tavana) Date: Sat, 21 May 2011 13:34:25 +0430 Subject: [Pw_forum] GPU-enabled In-Reply-To: References: Message-ID: Or, How is it possible to compile the QE on GPUs? (any reference to a detailed tutorial?) Ali Tavana 2011/5/21 S. D. Wang > Dear all: > Waht does the GPU-enabled mean? > > -- > S. D. Wang > * > * > *???* > * > * > > > _______________________________________________ > 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/20110521/bca7fb95/attachment.htm From bipulrr at gmail.com Sat May 21 12:03:28 2011 From: bipulrr at gmail.com (Bipul Rakshit) Date: Sat, 21 May 2011 15:33:28 +0530 Subject: [Pw_forum] Nodes Hang bcoz of High IO's Message-ID: Dear PWSCF users, I am faceing an unusual error while running espresso. I am running espresso in parallel clusters. And while running espresso for few days, it make the nodes hang. My system administrator saying that its bcoz of high IO's generated by espresso. I do use the options like 'wf_collect'=.false. and disk_io=low etc. but still the problem occurs. Some of my cluster information is as follows The home is on NFS and we r using, intel ifort and mkl libraries and openmpi. The processors memory is 24 GB and we have 27 nodes. (8 processors/node) Intel(R) Xeon(R) CPU E5530 @ 2.40GHz Please tell me if u require more information and also tell me the possible solution. -- Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India From davide.ceresoli at materials.ox.ac.uk Sat May 21 12:14:29 2011 From: davide.ceresoli at materials.ox.ac.uk (Davide Ceresoli) Date: Sat, 21 May 2011 11:14:29 +0100 Subject: [Pw_forum] GPU-enabled In-Reply-To: References: Message-ID: <4DD79085.9010505@materials.ox.ac.uk> Dear Ali and Wang, if you search the pw-forum archives, you will find that on May 5th, the "First PWscf GPU-enabled beta-release" has been announced and that there is a mailing list dedicated to this project. Best, Davide On 05/21/2011 10:04 AM, Ali Tavana wrote: > Or, How is it possible to compile the QE on GPUs? > (any reference to a detailed tutorial?) > > > Ali Tavana > > > 2011/5/21 S. D. Wang > > > Dear all: > Waht does the GPU-enabled mean? > > -- > S. D. Wang > * > * > *???* > * > * > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at democritos.it Sat May 21 20:13:00 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 21 May 2011 20:13:00 +0200 Subject: [Pw_forum] Nodes Hang bcoz of High IO's In-Reply-To: References: Message-ID: On May 21, 2011, at 12:03 , Bipul Rakshit wrote: > My system administrator saying that its bcoz of high IO's > generated by espresso. http://www.quantum-espresso.org/user_guide/ node18.html#SECTION00043100000000000000 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 sd.wang000 at gmail.com Sun May 22 05:57:45 2011 From: sd.wang000 at gmail.com (S. D. Wang) Date: Sun, 22 May 2011 11:57:45 +0800 Subject: [Pw_forum] G-vectors Message-ID: Dear developers: In scf.out file, it has 'G cutoff = 122.3770 ( 89195 G-vectors) FFT grid: ( 24, 40,216)' , I want to kown the relation of cutoff and G-vectors. How can I understand the 122.3770 and 89195? -- S. D. Wang * * *???* * * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110522/f2e12ede/attachment.htm From degironc at sissa.it Sun May 22 11:24:44 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 22 May 2011 11:24:44 +0200 Subject: [Pw_forum] G-vectors In-Reply-To: References: Message-ID: <4DD8D65C.7040200@sissa.it> On 05/22/2011 05:57 AM, S. D. Wang wrote: > Dear developers: > In scf.out file, it has 'G cutoff = 122.3770 ( 89195 G-vectors) FFT > grid: ( 24, 40,216)' , I want to kown the relation of cutoff and G-vectors. > How can I understand the 122.3770 and 89195 G = b1*n1+b2*n2+b3*n3: where b1,b2,b3 are fundamental lattice vectors of the reciprocal lattice. All G such that G^2 < Ecut_rho are included in the G vector list. G cutoff is just Ecut_rho in unit of (2pi/a)^2 (or maybe the sqrt of it). The number of G in the cutoff sphere is in your case 89195. the FFT grid dimensions are set in such a way that the sphere is contained in it. FFT grid contains 24*40*216= 207360 which is about twice the number of G in the list. It is the expected ratio as the volume between a sphere and the cube containing it is pi/6 stefano > > _______________________________________________ > 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/20110522/d65790b3/attachment.htm From s.m.rezaeisani at gmail.com Sun May 22 13:27:02 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Sun, 22 May 2011 15:57:02 +0430 Subject: [Pw_forum] q-points unit Message-ID: Dear all I have a simple question. All q-points in phonon calculations are with respect to reciprocal primitive vectors, aren't they? Best regards -- ========================================== Seyed Mojtaba Rezaei Sani Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel Lab: +98 311 391 3731 s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110522/4742bc0e/attachment.htm From degironc at sissa.it Sun May 22 14:07:53 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 22 May 2011 14:07:53 +0200 Subject: [Pw_forum] q-points unit In-Reply-To: References: Message-ID: <4DD8FC99.8020002@sissa.it> if given explicitly they are in Cartesian coordinates in unit of 2pi/a If chosen by the ldisp=.true. flag they are given as fractions of reciprocal lattice vectors stefano - Stefano de Gironcoli - SISSA and DEMOCRITOS On 05/22/2011 01:27 PM, Seyed Mojtaba Rezaei Sani wrote: > Dear all > > I have a simple question. All q-points in phonon calculations are with > respect to reciprocal primitive vectors, aren't they? > > Best regards > > > _______________________________________________ > 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/20110522/d0aed2fa/attachment.htm From s.m.rezaeisani at gmail.com Sun May 22 15:38:03 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Sun, 22 May 2011 18:08:03 +0430 Subject: [Pw_forum] q-points unit In-Reply-To: <4DD8FC99.8020002@sissa.it> References: <4DD8FC99.8020002@sissa.it> Message-ID: Dear Stefano Thanks, but which one: reciprocal primitive or conventional vectors? On Sun, May 22, 2011 at 4:37 PM, Stefano de Gironcoli wrote: > if given explicitly they are in Cartesian coordinates in unit of 2pi/a > If chosen by the ldisp=.true. flag they are given as fractions of > reciprocal lattice vectors > > stefano > - > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > On 05/22/2011 01:27 PM, Seyed Mojtaba Rezaei Sani wrote: > > Dear all > > I have a simple question. All q-points in phonon calculations are with > respect to reciprocal primitive vectors, aren't they? > > Best regards > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > 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/20110522/32bf19b7/attachment.htm From degironc at sissa.it Sun May 22 16:50:41 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 22 May 2011 16:50:41 +0200 Subject: [Pw_forum] q-points unit In-Reply-To: References: <4DD8FC99.8020002@sissa.it> Message-ID: <4DD922C1.1000007@sissa.it> The only ones that the code knows... those given in the output of scf calculation with pw. stefano On 05/22/2011 03:38 PM, Seyed Mojtaba Rezaei Sani wrote: > Dear Stefano > > Thanks, but which one: reciprocal primitive or conventional vectors? > > > On Sun, May 22, 2011 at 4:37 PM, Stefano de Gironcoliwrote: > >> if given explicitly they are in Cartesian coordinates in unit of 2pi/a >> If chosen by the ldisp=.true. flag they are given as fractions of >> reciprocal lattice vectors >> >> stefano >> - >> Stefano de Gironcoli - SISSA and DEMOCRITOS >> >> >> On 05/22/2011 01:27 PM, Seyed Mojtaba Rezaei Sani wrote: >> >> Dear all >> >> I have a simple question. All q-points in phonon calculations are with >> respect to reciprocal primitive vectors, aren't they? >> >> Best regards >> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> _______________________________________________ >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110522/e9368a7f/attachment.htm From s.m.rezaeisani at gmail.com Sun May 22 17:21:50 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Sun, 22 May 2011 19:51:50 +0430 Subject: [Pw_forum] q-points unit In-Reply-To: <4DD922C1.1000007@sissa.it> References: <4DD8FC99.8020002@sissa.it> <4DD922C1.1000007@sissa.it> Message-ID: Pardon me but I can't find any clue about this matter in any of output files. No where has mentioned with respect to which reciprocal vectors q-points are. I wanna make a supercell and need to be sure about. On Sun, May 22, 2011 at 7:20 PM, Stefano de Gironcoli wrote: > The only ones that the code knows... those given in the output of scf > calculation with pw. > > stefano > > > On 05/22/2011 03:38 PM, Seyed Mojtaba Rezaei Sani wrote: > > Dear Stefano > > Thanks, but which one: reciprocal primitive or conventional vectors? > > > On Sun, May 22, 2011 at 4:37 PM, Stefano de Gironcoli wrote: > > > if given explicitly they are in Cartesian coordinates in unit of 2pi/a > If chosen by the ldisp=.true. flag they are given as fractions of > reciprocal lattice vectors > > stefano > - > Stefano de Gironcoli - SISSA and DEMOCRITOS > > > On 05/22/2011 01:27 PM, Seyed Mojtaba Rezaei Sani wrote: > > Dear all > > I have a simple question. All q-points in phonon calculations are with > respect to reciprocal primitive vectors, aren't they? > > Best regards > > > ______________________________ > _________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > 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/20110522/1c48e43b/attachment-0001.htm From giannozz at democritos.it Sun May 22 17:39:09 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 22 May 2011 17:39:09 +0200 Subject: [Pw_forum] q-points unit In-Reply-To: References: <4DD8FC99.8020002@sissa.it> <4DD922C1.1000007@sissa.it> Message-ID: <7649E2AA-BCDF-482D-AD82-56A7C6FDE348@democritos.it> On May 22, 2011, at 17:21 , Seyed Mojtaba Rezaei Sani wrote: > Pardon me but I can't find any clue about this matter in any of > output files. the three vectors generating the reciprocal lattice are reprinted on output. QE does not use "conventional" cells, only "primitive" cells. 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 s.m.rezaeisani at gmail.com Sun May 22 18:45:48 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Sun, 22 May 2011 21:15:48 +0430 Subject: [Pw_forum] q-points unit In-Reply-To: <7649E2AA-BCDF-482D-AD82-56A7C6FDE348@democritos.it> References: <4DD8FC99.8020002@sissa.it> <4DD922C1.1000007@sissa.it> <7649E2AA-BCDF-482D-AD82-56A7C6FDE348@democritos.it> Message-ID: Dear Paolo Thanks for your finishing. On Sun, May 22, 2011 at 8:09 PM, Paolo Giannozzi wrote: > > On May 22, 2011, at 17:21 , Seyed Mojtaba Rezaei Sani wrote: > > > Pardon me but I can't find any clue about this matter in any of > > output files. > > the three vectors generating the reciprocal lattice are reprinted on > output. > QE does not use "conventional" cells, only "primitive" cells. > > 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/20110522/a1908ceb/attachment.htm From swapnil.chandratre at gmail.com Mon May 23 05:27:38 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Sun, 22 May 2011 22:27:38 -0500 Subject: [Pw_forum] Error computing berry phase Message-ID: Hi I receive the following error when I perform the nscf calculation after completing the scf calculation... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from potinit : error # 1 starting and expected charges differ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I read in the forum that this may be due to inconsistent charge calculation from scf as compared to what nscf does, can anyone suggest what steps should be taken to overcome this ? -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110522/5a12b539/attachment.htm From bali.6666 at gmail.com Mon May 23 15:59:29 2011 From: bali.6666 at gmail.com (drbaliram lone) Date: Mon, 23 May 2011 06:59:29 -0700 Subject: [Pw_forum] =?utf-8?q?I_added_you_as_a_friend_on_Quepasa=2Ecom?= Message-ID: <20110523135929.33506479621.4.4.0.0.me@CHA-ME-001> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110523/d148c1d3/attachment.htm From bali.6666 at gmail.com Mon May 23 16:35:26 2011 From: bali.6666 at gmail.com (drbaliram lone) Date: Mon, 23 May 2011 07:35:26 -0700 Subject: [Pw_forum] =?utf-8?q?I_added_you_as_a_friend_on_Quepasa=2Ecom?= Message-ID: <20110523143526.33537555911.4.9.0.0.me@CHA-ME-002> An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110523/bffaa8db/attachment.htm From giannozz at democritos.it Mon May 23 19:53:21 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 23 May 2011 19:53:21 +0200 Subject: [Pw_forum] Error computing berry phase In-Reply-To: References: Message-ID: On May 23, 2011, at 5:27 , swapnil chandratre wrote: > I receive the following error when I perform the nscf > calculation after completing the scf calculation... look at example10, compare with your data. Consider that berry's phase calculations are allowed only in insulators. 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 swapnil.chandratre at gmail.com Mon May 23 20:15:27 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 23 May 2011 13:15:27 -0500 Subject: [Pw_forum] Error computing berry phase In-Reply-To: References: Message-ID: Hi, Does it mean that I cant work with the berry phase in case I have semiconducting stucture ? On Mon, May 23, 2011 at 12:53 PM, Paolo Giannozzi wrote: > > On May 23, 2011, at 5:27 , swapnil chandratre wrote: > > > I receive the following error when I perform the nscf > > calculation after completing the scf calculation... > > look at example10, compare with your data. Consider > that berry's phase calculations are allowed only in > insulators. > > 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 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110523/30e8dd94/attachment.htm From giannozz at democritos.it Mon May 23 20:58:43 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 23 May 2011 20:58:43 +0200 Subject: [Pw_forum] Error computing berry phase In-Reply-To: References: Message-ID: On May 23, 2011, at 20:15 , swapnil chandratre wrote: > Does it mean that I cant work with the berry phase in case > I have semiconducting stucture ? as far as semiconductors are treated as insulators, you can 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 swapnil.chandratre at gmail.com Mon May 23 21:04:19 2011 From: swapnil.chandratre at gmail.com (swapnil chandratre) Date: Mon, 23 May 2011 14:04:19 -0500 Subject: [Pw_forum] Error computing berry phase In-Reply-To: References: Message-ID: Hi Paolo, Thank you for the reply, just to confirm my set up, can you emphasize on what I should focus (in scf and nscf) to see, that I have defined semi conductors as insulators. I checked on the band gap of the structure, it shows an opening and hence semi conducting property. On Mon, May 23, 2011 at 1:58 PM, Paolo Giannozzi wrote: > > On May 23, 2011, at 20:15 , swapnil chandratre wrote: > > > Does it mean that I cant work with the berry phase in case > > I have semiconducting stucture ? > > as far as semiconductors are treated as insulators, you can > > 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 > -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110523/fa7eaf97/attachment.htm From s.m.rezaeisani at gmail.com Tue May 24 07:44:02 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Tue, 24 May 2011 10:14:02 +0430 Subject: [Pw_forum] constrained cell optimization In-Reply-To: <4D8418E0.2020808@gucas.ac.cn> References: <4D83954F.3090005@gucas.ac.cn> <500433372.15826@test1.gucas.ac.cn> <4D8418E0.2020808@gucas.ac.cn> Message-ID: Dear Eric May be variable-cell optimization has broken the starting symmetry of the cell. did you set cell dynamics='damp-w' ? On Sat, Mar 19, 2011 at 6:15 AM, Eric Germaneau wrote: > I'm sorry I had to provide more details. > I use the last version (4.2.1). > I set ibrav=4, calculation='vc-relax' and cell_dofree = 'x' (I also tried > xy). > The program crash with the following message: > > * from checkallsym : error # 2 > not orthogonal operation* > > What I'd like to do is to optimized the lattice parameter "a" and keep "c" > constant. > Thanks, > > Eric. > > > > On 03/18/2011 03:30 AM, Paolo Giannozzi wrote: > > On Mar 18, 2011, at 18:24 , Eric Germaneau wrote: > > > I tried to set "cell_dofree" but the program complains. > > which version of which code complains how when you > set cell_dofree to 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 > > > > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > -- > * Be the change you wish to see in the world > * ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > * Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. * > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ========================================== Seyed Mojtaba Rezaei Sani Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel Lab: +98 311 391 3731 s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110524/bdf721c3/attachment-0001.htm From germaneau at gucas.ac.cn Tue May 24 19:52:29 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Tue, 24 May 2011 13:52:29 -0400 Subject: [Pw_forum] constrained cell optimization In-Reply-To: <506214974.04431@test1.gucas.ac.cn> References: <4D83954F.3090005@gucas.ac.cn> <500433372.15826@test1.gucas.ac.cn> <4D8418E0.2020808@gucas.ac.cn> <506214974.04431@test1.gucas.ac.cn> Message-ID: <4DDBF05D.4020904@gucas.ac.cn> Dear Seyed Mojtaba Rezaei Sani, Thank you for your reply. No I did not set cell dynamics='damp-w' But I figure that cell_dofree corresponds to the Cartesian axis and not to the cell. So it may not work. Anyway, I solved this issue by calculating energy of structures with different lattice parameters. Thanks again, Best, ?ric. On 05/24/2011 01:44 AM, Seyed Mojtaba Rezaei Sani wrote: > Dear Eric > > May be variable-cell optimization has broken the starting symmetry of > the cell. did you set cell dynamics='damp-w' ? > > On Sat, Mar 19, 2011 at 6:15 AM, Eric Germaneau > wrote: > > I'm sorry I had to provide more details. > I use the last version (4.2.1). > I set ibrav=4, calculation='vc-relax' and cell_dofree = 'x' (I > also tried xy). > The program crash with the following message: > > / from checkallsym : error # 2 > not orthogonal operation/ > > What I'd like to do is to optimized the lattice parameter "a" and > keep "c" constant. > Thanks, > > Eric. > > > > On 03/18/2011 03:30 AM, Paolo Giannozzi wrote: >> On Mar 18, 2011, at 18:24 , Eric Germaneau wrote: >> >>> I tried to set "cell_dofree" but the program complains. >> which version of which code complains how when you >> set cell_dofree to 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 >> _______________________________________________ Pw_forum mailing >> list Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > /Be the change you wish to see in the world > / ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > /Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. / > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ========================================== > Seyed Mojtaba Rezaei Sani > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology > 84156-83111 Isfahan, Iran > Tel Lab: +98 311 391 3731 > s.rezaeisani at ph.iut.ac.ir > =========================================== > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /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/20110524/6a057ada/attachment.htm From s.m.rezaeisani at gmail.com Tue May 24 08:05:12 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Tue, 24 May 2011 10:35:12 +0430 Subject: [Pw_forum] "Not orthogonal operation" error in vc-relax optimization Message-ID: Dear all My vc-relax opt, although I set cell dynamics='damp-w',ends with this error : > from checkallsym : error # 2 > not orthogonal operation Is there any suggestion for solving that? (If anyone thinks about using nonsymmetric cell, I will send my input file and will be grateful to learn how it can be) Thanks -- ========================================== Seyed Mojtaba Rezaei Sani Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel Lab: +98 311 391 3731 s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110524/29cdbe0a/attachment.htm From mohnish.iitk at gmail.com Tue May 24 12:12:39 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 24 May 2011 15:42:39 +0530 Subject: [Pw_forum] "Not orthogonal operation" error in vc-relax optimization In-Reply-To: References: Message-ID: Dear Seyed! The relaxation of cell is breaking the symmetry, this error message shows that. For example, if you use surface unit cell as hexagonal and try to relax the 'x' and 'y' direction of the cell, then it will give the error message because the cell vector is not orthogonal and the direction of relaxation of your cell is is independent in 'x' and 'y' direction. So if you want to get to rid of this error message then the direction of relaxation should be in the direction of unit cell vector. The relaxation process should not break the symmetry of the system. Hope it helps. Feel free to ask further if you have any doubts. On Tue, May 24, 2011 at 11:35 AM, Seyed Mojtaba Rezaei Sani < s.m.rezaeisani at gmail.com> wrote: > Dear all > > My vc-relax opt, although I set cell dynamics='damp-w',ends with this > error : > > > from checkallsym : error # 2 > > not orthogonal operation > > Is there any suggestion for solving that? > (If anyone thinks about using nonsymmetric cell, I will send my input file > and will be grateful to learn how it can be) > > Thanks > -- > ========================================== > Seyed Mojtaba Rezaei Sani > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology > 84156-83111 Isfahan, Iran > Tel Lab: +98 311 391 3731 > s.rezaeisani at ph.iut.ac.ir > =========================================== > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110524/28694cc7/attachment.htm From physics.skgupta at gmail.com Tue May 24 14:10:30 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Tue, 24 May 2011 17:40:30 +0530 Subject: [Pw_forum] Yb pseudo Message-ID: Dear Sir I am trying to calculate Yb pseudo using ld1.x implemented in pwscf, where my input file is: &input iswitch=3, rlderiv=2.1, eminld=-15.0, emaxld=20.0, deld=0.01d0, nld=3, rel=0, zed=70.0, config="[Xe] 4f14 6s2 5d-1" dft='PBE', / &inputp lloc=3, pseudotype=1, file_pseudopw='Yb.trial.UPF', zval=16.0, / 3 4F 4 3 14.0 0.00 2.4000 2.4000 5D 3 2 0.00 -0.10 2.4000 2.4000 6S 1 0 2.00 0.00 2.4000 2.4000 after this, I got output, which is: Program LD1 v.4.2.1 starts on 24May2011 at 17:37:27 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 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from ld1_setup : error # 3 mismatch between lloc and l of the wavefunction chosen for local potential %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ~ Please suggest, where I am wrong Thanking You. Best Regards Sanjeev Gupta Dept. of Physics, Bhavnagar University Bhavnagar-Gujarat ~ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110524/93006104/attachment.htm From sclauzer at sissa.it Tue May 24 15:31:54 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 24 May 2011 15:31:54 +0200 Subject: [Pw_forum] Yb pseudo In-Reply-To: References: Message-ID: <4E59F6BD-C854-418B-AC40-ADA6F70AB6A0@sissa.it> The wavefunction used to build the local channel (in your case the 4f, because you set lloc=3), MUST be listed as the last one (i.e. after the 5D and &S in your input). Please take some time to read the documentation in Doc/INPUT_LD1 HTH GS Il giorno 24/mag/2011, alle ore 14.10, Sanjeev Gupta ha scritto: > Dear Sir > > I am trying to calculate Yb pseudo using ld1.x implemented in pwscf, where my input file is: > > &input > iswitch=3, > > rlderiv=2.1, > eminld=-15.0, > emaxld=20.0, > deld=0.01d0, > nld=3, > > rel=0, > zed=70.0, > config="[Xe] 4f14 6s2 5d-1" > dft='PBE', > / > &inputp > lloc=3, > pseudotype=1, > file_pseudopw='Yb.trial.UPF', > zval=16.0, > / > 3 > 4F 4 3 14.0 0.00 2.4000 2.4000 > 5D 3 2 0.00 -0.10 2.4000 2.4000 > 6S 1 0 2.00 0.00 2.4000 2.4000 > > > after this, I got output, which is: > > Program LD1 v.4.2.1 starts on 24May2011 at 17:37:27 > > 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 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from ld1_setup : error # 3 > mismatch between lloc and l of the wavefunction chosen for local potential > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > ~ > > Please suggest, where I am wrong > Thanking You. > > Best Regards > Sanjeev Gupta > Dept. of Physics, > Bhavnagar University > Bhavnagar-Gujarat > ~ > _______________________________________________ > 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/20110524/420485a6/attachment.htm From amin.torabi at gmail.com Tue May 24 22:03:59 2011 From: amin.torabi at gmail.com (Amin Torabi) Date: Tue, 24 May 2011 16:03:59 -0400 Subject: [Pw_forum] box size in example03 Message-ID: Hi all, ../examples/example03/README says that "The molecule is put in a cubic box of side 12 bohr" My questions are: 1. how did you chose it to be 12? I tried different numbers and noticed that the total energy depends on this value. 2. Is it not a calculation on an isolated molecule? cause for an isolated molecule, it should not be important what the size of the box is. Thanks in advance Amin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110524/ed61fa5c/attachment.htm From ttduyle at gmail.com Tue May 24 22:14:10 2011 From: ttduyle at gmail.com (Duy Le) Date: Tue, 24 May 2011 16:14:10 -0400 Subject: [Pw_forum] box size in example03 In-Reply-To: References: Message-ID: On Tue, May 24, 2011 at 4:03 PM, Amin Torabi wrote: > Hi all, > ../examples/example03/README says that "The molecule is put in a cubic box > of side 12 bohr" > My questions are: > > how did you chose it to be 12? I tried different numbers and noticed that > the total energy depends on this value. Indeed. Energy_of_system=Energy_of_molecule+Interaction_energy_with_neighboring_molecules. Different box sizes yield different Interaction energies. > Is it not a calculation on an isolated molecule? cause for an isolated > molecule, it should not be important what the size of the box is. No, it is not. It is a calculation of bunch of molecules. By changing box size, you change the interaction between those molecules. Eventually, those interactions are almost negligible, you'll get isolated molecules. > -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" From degironc at sissa.it Wed May 25 00:19:03 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 25 May 2011 00:19:03 +0200 Subject: [Pw_forum] box size in example03 In-Reply-To: References: Message-ID: <4DDC2ED7.70407@sissa.it> this is an example, meant to demonstrate the principle and to be fast, not to be accurate. serious calculations require testing convergence w.r.t. computational parameters. 12 au is not converged. stefano - Stefano de Gironcoli - SISSA and DEMOCRITOS On 05/24/2011 10:03 PM, Amin Torabi wrote: > Hi all, > > ../examples/example03/README says that "The molecule is put in a cubic box > of side 12 bohr" > > My questions are: > > 1. how did you chose it to be 12? I tried different numbers and noticed > that the total energy depends on this value. > 2. Is it not a calculation on an isolated molecule? cause for an isolated > molecule, it should not be important what the size of the box is. > > > Thanks in advance > > Amin > > > > _______________________________________________ > 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/20110525/4023add8/attachment-0001.htm From zhaohscas at yahoo.com.cn Wed May 25 18:49:18 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Wed, 25 May 2011 12:49:18 -0400 Subject: [Pw_forum] Single point energy calculation within PWSCF. Message-ID: <4DDD330E.4090506@yahoo.com.cn> Hi all, I've learned that the single point energy calculation should be the most appropriate method for any type of convergence testings (whether that be k-point, cutoff, fine grid or cell size). I want to know if there are keywords/flags within PWSCF for single point energy calculation? Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From kirtinandan07 at gmail.com Wed May 25 06:55:10 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Wed, 25 May 2011 10:25:10 +0530 Subject: [Pw_forum] installing QE Message-ID: Hi I have recently got a new system with i5 processor. Since it has 4 processor how can i install QE such that i can run parallel processing. Documentation says just to use ./configure and make to be done for compiling. will these command when run will consider the system configuration and install parallel version. Thanks for suggestion in advance. Vicky singh research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110525/330e7006/attachment.htm From germaneau at gucas.ac.cn Wed May 25 19:12:36 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Wed, 25 May 2011 13:12:36 -0400 Subject: [Pw_forum] installing QE In-Reply-To: <506298369.00495@test1.gucas.ac.cn> References: <506298369.00495@test1.gucas.ac.cn> Message-ID: <4DDD3884.6010005@gucas.ac.cn> Hey Vicky, if mpich (for instance) is installed, it will automatically detect it. Then you will have to do mpiexec -n 4 path_to_qe_exec < input_file > out_file in order to use the 4 cores. Note that this is well documented in the examples. The other solution is to build QE with OpenMP, but I have not really tried. Well, the only one tentative I did was unsuccessful. Hope it helps, ?ric. On 05/25/2011 12:55 AM, vicky singh wrote: > Hi > I have recently got a new system with i5 processor. Since it has 4 > processor how can i install QE such that i can run parallel > processing. Documentation says just to use ./configure and make to be > done for compiling. will these command when run will consider the > system configuration and install parallel version. > > Thanks for suggestion in advance. > > Vicky singh > research student > Bangalore > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /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/20110525/9ccfe6e7/attachment.htm From mohnish.iitk at gmail.com Wed May 25 07:15:05 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 25 May 2011 10:45:05 +0530 Subject: [Pw_forum] Single point energy calculation within PWSCF. In-Reply-To: <4DDD330E.4090506@yahoo.com.cn> References: <4DDD330E.4090506@yahoo.com.cn> Message-ID: Dear Hongsheng! The flag is "calculation" = 'scf' for single point energy calculation. But I will suggest you if you want to test the convergence for structure then you must relax the atomic position as well as cell volume, because the single point energy calculation will not relax the stress and forces. So for bulk structures "calculation = 'vc-relax' is the way to test the convergence with respect to energy, because that will release the stress and forces in the system. I hope it helps. Feel free to ask any doubt further. On Wed, May 25, 2011 at 10:19 PM, Hongsheng Zhao wrote: > Hi all, > > I've learned that the single point energy calculation should be the > most appropriate method for any type of convergence testings (whether > that be k-point, cutoff, fine grid or cell size). I want to know if > there are keywords/flags within PWSCF for single point energy calculation? > > Regards. > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110525/a0046eb3/attachment.htm From kirtinandan07 at gmail.com Wed May 25 08:27:46 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Wed, 25 May 2011 11:57:46 +0530 Subject: [Pw_forum] installing QE In-Reply-To: <4DDD3884.6010005@gucas.ac.cn> References: <506298369.00495@test1.gucas.ac.cn> <4DDD3884.6010005@gucas.ac.cn> Message-ID: Dear Eric Thanks a lot for your suggestion. Can you let me know that if mpich is not there can it be installed. vicky singh On Wed, May 25, 2011 at 10:42 PM, Eric Germaneau wrote: > Hey Vicky, > > if mpich (for instance) is installed, it will automatically detect it. > Then you will have to do > > mpiexec -n 4 path_to_qe_exec < input_file > out_file > > in order to use the 4 cores. > Note that this is well documented in the examples. > > The other solution is to build QE with OpenMP, but I have not really > tried. > Well, the only one tentative I did was unsuccessful. > > Hope it helps, > > ?ric. > > > On 05/25/2011 12:55 AM, vicky singh wrote: > > Hi > I have recently got a new system with i5 processor. Since it has 4 > processor how can i install QE such that i can run parallel processing. > Documentation says just to use ./configure and make to be done for > compiling. will these command when run will consider the system > configuration and install parallel version. > > Thanks for suggestion in advance. > > Vicky singh > research student > Bangalore > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > -- > * Be the change you wish to see in the world > * ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > * 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/20110525/57a5aca7/attachment.htm From germaneau at gucas.ac.cn Wed May 25 20:44:23 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Wed, 25 May 2011 14:44:23 -0400 Subject: [Pw_forum] installing QE In-Reply-To: <506303976.02641@test1.gucas.ac.cn> References: <506298369.00495@test1.gucas.ac.cn> <4DDD3884.6010005@gucas.ac.cn> <506303976.02641@test1.gucas.ac.cn> Message-ID: <4DDD4E07.90600@gucas.ac.cn> Well, just take a look here or here . I built it long time ago, I remember that was not difficult. Check whether there is mpich2 or open-mpi package for your distro. Remember that you have OpenMP on your machine .... ?ric. On 05/25/2011 02:27 AM, vicky singh wrote: > Dear Eric > Thanks a lot for your suggestion. Can you let me know that if mpich is > not there can it be installed. > > vicky singh > > On Wed, May 25, 2011 at 10:42 PM, Eric Germaneau > > wrote: > > Hey Vicky, > > if mpich (for instance) is installed, it will automatically detect it. > Then you will have to do > > mpiexec -n 4 path_to_qe_exec < input_file > out_file > > in order to use the 4 cores. > Note that this is well documented in the examples. > > The other solution is to build QE with OpenMP, but I have not > really tried. > Well, the only one tentative I did was unsuccessful. > > Hope it helps, > > ?ric. > > > On 05/25/2011 12:55 AM, vicky singh wrote: >> Hi >> I have recently got a new system with i5 processor. Since it has >> 4 processor how can i install QE such that i can run parallel >> processing. Documentation says just to use ./configure and make >> to be done for compiling. will these command when run will >> consider the system configuration and install parallel version. >> >> Thanks for suggestion in advance. >> >> Vicky singh >> research student >> Bangalore >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > /Be the change you wish to see in the world > / ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > /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 > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- /Be the change you wish to see in the world / ? Mahatma Gandhi ? Dr. ?ric Germaneau College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China /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/20110525/2e4b2732/attachment-0001.htm From Michael at ihpc.a-star.edu.sg Wed May 25 06:59:13 2011 From: Michael at ihpc.a-star.edu.sg (Michael Sullivan) Date: Wed, 25 May 2011 12:59:13 +0800 Subject: [Pw_forum] Single point energy calculation within PWSCF. In-Reply-To: <4DDD330E.4090506@yahoo.com.cn> References: <4DDD330E.4090506@yahoo.com.cn> Message-ID: Hongsheng: It's just calculation='scf' in &CONTROL http://www.quantum-espresso.org/input-syntax/INPUT_PW.html#id2933659 Mike michael at ihpc.a-star.edu.sg http://www.sullivan.sg/ On 26-May-2011, at 12:49 AM, Hongsheng Zhao wrote: > Hi all, > > I've learned that the single point energy calculation should be the > most appropriate method for any type of convergence testings (whether > that be k-point, cutoff, fine grid or cell size). I want to know if > there are keywords/flags within PWSCF for single point energy calculation? > > Regards. > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China "1991-2011 - Creating Growth, Enhancing Lives. Commemorating A*STAR's 20 Years of Science, Technology and Research in Singapore." IHPC Values :: Impact :: Honesty :: Performance :: Co-operation This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. From physics.skgupta at gmail.com Wed May 25 09:38:21 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Wed, 25 May 2011 13:08:21 +0530 Subject: [Pw_forum] installing QE In-Reply-To: <4DDD4E07.90600@gucas.ac.cn> References: <506298369.00495@test1.gucas.ac.cn> <4DDD3884.6010005@gucas.ac.cn> <506303976.02641@test1.gucas.ac.cn> <4DDD4E07.90600@gucas.ac.cn> Message-ID: Dear Vicky Go in download package manager and just "type" there "mpich" , it will find the required files, which you install. It is very easy now. Thanks to developer for hard effort to make it easy. After installation of mpich, then you configure as you said before in mail. it will work fine. Best Sanjeev Dept. of Phys. Bhavnagar University On Thu, May 26, 2011 at 12:14 AM, Eric Germaneau wrote: > Well, just take a look hereor > here . > I built it long time ago, I remember that was not difficult. > Check whether there is mpich2 or open-mpi package for your distro. > Remember that you have OpenMP on your machine .... > > ?ric. > > > > On 05/25/2011 02:27 AM, vicky singh wrote: > > Dear Eric > Thanks a lot for your suggestion. Can you let me know that if mpich is not > there can it be installed. > > vicky singh > > On Wed, May 25, 2011 at 10:42 PM, Eric Germaneau wrote: > >> Hey Vicky, >> >> if mpich (for instance) is installed, it will automatically detect it. >> Then you will have to do >> >> mpiexec -n 4 path_to_qe_exec < input_file > out_file >> >> in order to use the 4 cores. >> Note that this is well documented in the examples. >> >> The other solution is to build QE with OpenMP, but I have not really >> tried. >> Well, the only one tentative I did was unsuccessful. >> >> Hope it helps, >> >> ?ric. >> >> >> On 05/25/2011 12:55 AM, vicky singh wrote: >> >> Hi >> I have recently got a new system with i5 processor. Since it has 4 >> processor how can i install QE such that i can run parallel processing. >> Documentation says just to use ./configure and make to be done for >> compiling. will these command when run will consider the system >> configuration and install parallel version. >> >> Thanks for suggestion in advance. >> >> Vicky singh >> research student >> Bangalore >> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> -- >> * Be the change you wish to see in the world >> * ? Mahatma Gandhi ? >> >> Dr. ?ric Germaneau >> >> College of Physical Sciences >> Graduate University of Chinese Academy of Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> >> * 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 >> >> > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > -- > * Be the change you wish to see in the world > * ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of Chinese Academy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > * 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/20110525/61eb0e4a/attachment.htm From kirtinandan07 at gmail.com Wed May 25 11:08:53 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Wed, 25 May 2011 14:38:53 +0530 Subject: [Pw_forum] installing QE In-Reply-To: References: <506298369.00495@test1.gucas.ac.cn> <4DDD3884.6010005@gucas.ac.cn> <506303976.02641@test1.gucas.ac.cn> <4DDD4E07.90600@gucas.ac.cn> Message-ID: Thanks a lot. On Wed, May 25, 2011 at 1:08 PM, Sanjeev Gupta wrote: > Dear Vicky > > Go in download package manager and just "type" there "mpich" , it will find > the required files, which you install. It is very easy now. Thanks to > developer for hard effort to make it easy. After installation of mpich, then > you configure as you said before in mail. it will work fine. > > > Best > Sanjeev > Dept. of Phys. > Bhavnagar University > > > > > On Thu, May 26, 2011 at 12:14 AM, Eric Germaneau wrote: > >> Well, just take a look hereor >> here . >> I built it long time ago, I remember that was not difficult. >> Check whether there is mpich2 or open-mpi package for your distro. >> Remember that you have OpenMP on your machine .... >> >> ?ric. >> >> >> >> On 05/25/2011 02:27 AM, vicky singh wrote: >> >> Dear Eric >> Thanks a lot for your suggestion. Can you let me know that if mpich is not >> there can it be installed. >> >> vicky singh >> >> On Wed, May 25, 2011 at 10:42 PM, Eric Germaneau wrote: >> >>> Hey Vicky, >>> >>> if mpich (for instance) is installed, it will automatically detect it. >>> Then you will have to do >>> >>> mpiexec -n 4 path_to_qe_exec < input_file > out_file >>> >>> in order to use the 4 cores. >>> Note that this is well documented in the examples. >>> >>> The other solution is to build QE with OpenMP, but I have not really >>> tried. >>> Well, the only one tentative I did was unsuccessful. >>> >>> Hope it helps, >>> >>> ?ric. >>> >>> >>> On 05/25/2011 12:55 AM, vicky singh wrote: >>> >>> Hi >>> I have recently got a new system with i5 processor. Since it has 4 >>> processor how can i install QE such that i can run parallel processing. >>> Documentation says just to use ./configure and make to be done for >>> compiling. will these command when run will consider the system >>> configuration and install parallel version. >>> >>> Thanks for suggestion in advance. >>> >>> Vicky singh >>> research student >>> Bangalore >>> >>> >>> _______________________________________________ >>> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> -- >>> * Be the change you wish to see in the world >>> * ? Mahatma Gandhi ? >>> >>> Dr. ?ric Germaneau >>> >>> College of Physical Sciences >>> Graduate University of Chinese Academy of Sciences >>> Yuquan Road 19A >>> Beijing 100049 >>> China >>> >>> * 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 >>> >>> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> -- >> * Be the change you wish to see in the world >> * ? Mahatma Gandhi ? >> >> Dr. ?ric Germaneau >> >> College of Physical Sciences >> Graduate University of Chinese Academy of Sciences >> Yuquan Road 19A >> Beijing 100049 >> China >> >> * 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 >> >> > > _______________________________________________ > 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/20110525/d077b401/attachment.htm From mirnezhad.mm at gmail.com Wed May 25 15:07:14 2011 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Wed, 25 May 2011 06:07:14 -0700 Subject: [Pw_forum] K point in matdyn.x Message-ID: Dear All, I want to calculate the phonon dispersion-relation with matdyn.x. What is the unit of q-points in this code (tpiba, crystal, tpiba-b, crystal-b)?? Best Regards, Mahdi Mirnezhad, Guilan University, Rasht, Iran. From mohnish.iitk at gmail.com Wed May 25 15:16:20 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Wed, 25 May 2011 18:46:20 +0530 Subject: [Pw_forum] K point in matdyn.x In-Reply-To: References: Message-ID: Dear Mahdi, Your answer lies here: http://www.democritos.it/pipermail/pw_forum/2011-May/020576.html On Wed, May 25, 2011 at 6:37 PM, Mahdi Mirnezhad wrote: > Dear All, > I want to calculate the phonon dispersion-relation with matdyn.x. What > is the unit of q-points in this code (tpiba, crystal, tpiba-b, > crystal-b)?? > Best Regards, > > Mahdi Mirnezhad, > Guilan University, Rasht, Iran. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110525/a860cf95/attachment.htm From mirnezhad.mm at gmail.com Wed May 25 15:24:17 2011 From: mirnezhad.mm at gmail.com (Mahdi Mirnezhad) Date: Wed, 25 May 2011 06:24:17 -0700 Subject: [Pw_forum] K point in matdyn.x In-Reply-To: References: Message-ID: Dear mohnish, Thanks in advance for your help. On 5/25/11, mohnish pandey wrote: > Dear Mahdi, > Your answer lies here: > http://www.democritos.it/pipermail/pw_forum/2011-May/020576.html > > On Wed, May 25, 2011 at 6:37 PM, Mahdi Mirnezhad > wrote: > >> Dear All, >> I want to calculate the phonon dispersion-relation with matdyn.x. What >> is the unit of q-points in this code (tpiba, crystal, tpiba-b, >> crystal-b)?? >> Best Regards, >> >> Mahdi Mirnezhad, >> Guilan University, Rasht, Iran. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > From zhaohscas at yahoo.com.cn Thu May 26 04:25:05 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Wed, 25 May 2011 22:25:05 -0400 Subject: [Pw_forum] Single point energy calculation within PWSCF. In-Reply-To: References: <4DDD330E.4090506@yahoo.com.cn> Message-ID: <4DDDBA01.8060804@yahoo.com.cn> On 05/25/2011 01:15 AM, mohnish pandey wrote: > Dear Hongsheng! > The flag is "calculation" = 'scf' for single point energy > calculation. But I will suggest you if you want to test the > convergence for structure then you must relax the atomic position as > well as cell volume, because the single point energy calculation will > not relax the stress and forces. So for bulk structures "calculation = > 'vc-relax' is the way to test the convergence with respect to energy, > because that will release the stress and forces in the system. I hope > it helps. Feel free to ask any doubt further. 1- What do you mean by saying "for bulk structures", do you mean 3D, other than 2D/1D/0D case? If so, what should I use for the non-bulk structures, in this case, if I want to determine the convergence for structure, the single point calculation is enough? 2- If I can run a series of single-point energy calculations w.r.t different cut-off energies, k-point samplings, fine grids, cell size, and etc. Then look for when the energies, forces and stresses are all converged adequately. In this way, I'll achieve the same aim as 'vc-relax' done for me, am I right? I mean, if the energy, forces and stresses are all accurately converged based on a series of single-point energy calculations, then the final structure will also be accurate. Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From degliesposti at bo.imm.cnr.it Wed May 25 11:37:21 2011 From: degliesposti at bo.imm.cnr.it (Cristian Degli Esposti Boschi) Date: Wed, 25 May 2011 11:37:21 +0200 Subject: [Pw_forum] Minor problem in tests and cptests scripts for QE 4.3 Message-ID: <4DDCCDD1.1060207@bo.imm.cnr.it> Dear users, I've just installed Quantum Espresso 4.3 and performed the tests and cptests. However (contrarily to what written in the comments within the scripts), in order to get them work I had to define the environment variables TMP_DIR and PSEUDO_DIR within the scripts check-pw.x.j and check-cp.x.j because they are not defined in each input file. Am I missing something or is it a minor problem with the scripts? Thanks for your time, Cristian Degli Esposti Boschi CNR-IMM, Sezione di Bologna, via Gobetti, 101, 40129, Bologna, Italia tel. ++39 051 6399152, fax ++39 051 6399216 degliesposti -AT- bo.imm.cnr.it From giannozz at democritos.it Wed May 25 17:51:17 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 25 May 2011 17:51:17 +0200 Subject: [Pw_forum] Minor problem in tests and cptests scripts for QE 4.3 In-Reply-To: <4DDCCDD1.1060207@bo.imm.cnr.it> References: <4DDCCDD1.1060207@bo.imm.cnr.it> Message-ID: <5C3F751F-77A8-464C-86E4-3E8F04F63455@democritos.it> On May 25, 2011, at 11:37 , Cristian Degli Esposti Boschi wrote: > Am I missing something or is it a minor problem with the scripts? or maybe your are using some weird machine that does not honor "getenv". One such machine I known is IBM BG. PS: post from the same e-mail you used to register or else your messages will not go through 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 ttduyle at gmail.com Wed May 25 17:56:39 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 25 May 2011 11:56:39 -0400 Subject: [Pw_forum] Minor problem in tests and cptests scripts for QE 4.3 In-Reply-To: <5C3F751F-77A8-464C-86E4-3E8F04F63455@democritos.it> References: <4DDCCDD1.1060207@bo.imm.cnr.it> <5C3F751F-77A8-464C-86E4-3E8F04F63455@democritos.it> Message-ID: On Wed, May 25, 2011 at 11:51 AM, Paolo Giannozzi wrote: > > On May 25, 2011, at 11:37 , Cristian Degli Esposti Boschi wrote: > >> Am I missing something or is it a minor problem with the scripts? > > or maybe your are using some weird machine that does not > honor "getenv". One such machine I known is IBM BG. > But it is weird. QE does not take TMP_DIR or PSEUDO_DIR -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" > PS: post from the same e-mail you used to register or else > your messages will not go through > > > 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 giannozz at democritos.it Wed May 25 17:59:02 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 25 May 2011 17:59:02 +0200 Subject: [Pw_forum] Minor problem in tests and cptests scripts for QE 4.3 In-Reply-To: References: <4DDCCDD1.1060207@bo.imm.cnr.it> <5C3F751F-77A8-464C-86E4-3E8F04F63455@democritos.it> Message-ID: On May 25, 2011, at 17:56 , Duy Le wrote: > But it is weird. QE does not take TMP_DIR or PSEUDO_DIR it uses ESPRESSO_PSEUDO and ESPRESSO_TMPDIR, if defined and not overridden by input variables 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 ttduyle at gmail.com Wed May 25 18:07:52 2011 From: ttduyle at gmail.com (Duy Le) Date: Wed, 25 May 2011 12:07:52 -0400 Subject: [Pw_forum] Minor problem in tests and cptests scripts for QE 4.3 In-Reply-To: References: <4DDCCDD1.1060207@bo.imm.cnr.it> <5C3F751F-77A8-464C-86E4-3E8F04F63455@democritos.it> Message-ID: On Wed, May 25, 2011 at 11:59 AM, Paolo Giannozzi wrote: > > On May 25, 2011, at 17:56 , Duy Le wrote: > >> But it is weird. QE does not take TMP_DIR or PSEUDO_DIR > > it uses ESPRESSO_PSEUDO and ESPRESSO_TMPDIR, if > defined and not overridden by input variables > Right. I meant Cristian's claim (of using two new ENV. variables) and your answer (about weird machine) are not compatible. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" > 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 giannozz at democritos.it Wed May 25 19:23:34 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Wed, 25 May 2011 19:23:34 +0200 Subject: [Pw_forum] Quantum Espresso v.4.3.1 Message-ID: <981B781E-62E0-466A-8976-7744086AE436@democritos.it> Version 4.3.1 of the Quantum ESPRESSO distribution is available for download from the website http://www.quantum-espresso.org and http://www.qe-forge.org. This release fixes several bugs and contains the following improvements over version 4.3: * Effective Screening Medium (Otani and Sugino PRB 73 115407 (2006) * CP: faster implementation of LDA+U * A new, improved version of GIPAW is available as a separate package, that can be downloaded from http://qe-forge.org/frs/?group_id=37 For a list of bug fixes, see file Doc/release-notes. Note that the source repository has been moved to svn; the GPU- enabled beta release of PWscf is available as a svn branch, that can be downloaded using: svn checkout svn://scm.qe-forge.org/scmrepos/svn/q-e/branches/ espresso-PRACE Everybody who is using the Quantum ESPRESSO distribution is encouraged to upgrade and to report problems to the mailing list. The Quantum ESPRESSO group --- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy --- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From s.m.rezaeisani at gmail.com Wed May 25 20:27:37 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Wed, 25 May 2011 22:57:37 +0430 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation Message-ID: Dear all I have chosen a grid of 6*6*6 q-points for phonon frequencies calculation. Code selected 16 points but calculations are done just for 9 points. I don't know why. Any suggestion? Thanks -- ========================================== Seyed Mojtaba Rezaei Sani Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel Lab: +98 311 391 3731 s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110525/fec131fd/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Wed May 25 20:31:56 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 25 May 2011 20:31:56 +0200 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation In-Reply-To: References: Message-ID: In data 25 maggio 2011 alle ore 20:27:37, Seyed Mojtaba Rezaei Sani ha scritto: > I don't know why. Any suggestion? Dear Seyed, please provide more detail if you want a serious response. 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 kucukben at sissa.it Wed May 25 20:53:54 2011 From: kucukben at sissa.it (Emine Kucukbenli) Date: Wed, 25 May 2011 20:53:54 +0200 Subject: [Pw_forum] Single point energy calculation within PWSCF. In-Reply-To: <4DDDBA01.8060804@yahoo.com.cn> References: <4DDD330E.4090506@yahoo.com.cn> <4DDDBA01.8060804@yahoo.com.cn> Message-ID: <20110525205354.bae5zalli4g04kk4@webmail.sissa.it> Dear Hongsheng Zhao > 2- If I can run a series of single-point energy calculations w.r.t > different cut-off energies, k-point samplings, fine grids, cell size, > and etc. Then look for when the energies, forces and stresses are all > converged adequately. In this way, I'll achieve the same aim as > 'vc-relax' done for me, am I right? I mean, if the energy, forces and > stresses are all accurately converged based on a series of single-point > energy calculations, then the final structure will also be accurate. I was thinking that you were trying to optimize the calculation parameters however with this post I am lost.I will give a generic answer: Before starting to work on a system, you need to optimize the calculation parameters, much like an experimentalist optimizing their machine set up before an experiment. You need to make sure that what you will get, once you do the desired calculation, (like a desired experiment) would be sensible data. This is a preparation scheme _before_ the actual calculations. In this preparation process, you need to check the convergence of energy, and/or forces, pressure etc, basically whatever interests you, or whatever the interested property is sensitive to. And by convergence, I mean convergence with respect to calculation parameters: ecutwfc/rho ; kpoints ; smearing for metals; box size for isolated systems, convergence thresholds etc ..again, whatever is relevant. Once you know the optimum values for these parameters, you can do some applications: One of them might be finding the equilibrium lattice parameter. If so, now you can run a "vc-relax" calculation to get the zero pressure structure.. Hope this made any sense and didnt confuse you even more. cheers, emine kucukbenli, phd student, sissa, italy ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From s.m.rezaeisani at gmail.com Wed May 25 21:02:57 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Wed, 25 May 2011 23:32:57 +0430 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation In-Reply-To: References: Message-ID: Dear Lorenzo In *.dyn0, as a ph.x output file, 16 points have been selected from my 6*6*6 chosen grid. But I get just *.dyn1-9. On the other word calculations are done just for 9 q-points. If any more details are needed, please notify me. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110525/cfb75ac6/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Wed May 25 21:10:36 2011 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 25 May 2011 21:10:36 +0200 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation In-Reply-To: References: Message-ID: In data 25 maggio 2011 alle ore 21:02:57, Seyed Mojtaba Rezaei Sani ha scritto: > In *.dyn0, as a ph.x output file, 16 points have been selected from my > 6*6*6 > chosen grid. But I get just *.dyn1-9. On the other word calculations are > done just for 9 q-points. If any more details are needed, please notify > me. Dear Seyed, it could be anything, from you not just finding the files to crash in the code or a time limit in your computing hardware. Keep in mind that nobody in this forum knows what is going on in you computer. You MUST provide at the very least the input and output of your job, otherwise we can only guess. As a side note: asking a good question takes a lot of time, often more times that it takes to give a good answer. If it takes you only 30 seconds to write your email it is very unlikely to contain any good question. 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 trambui at u.boisestate.edu Thu May 26 01:00:45 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Wed, 25 May 2011 17:00:45 -0600 Subject: [Pw_forum] Pseudo-potential testing Message-ID: Dear Paul, In the file that I have attached here (Paul's note on PP generation), under section 3.10: checking for transferability, you have mentioned about the:"The error on total energy di?erences between PP and AE results gives a feeling on how good the PP is." Do you mean the difference in AE and PP eigenvalues? because I saw the Etot and Etotps are huge difference but their eigenvalue (e, Ry) are closed. Dear QE users, I'm trying to test the Cs' US PP with reference configuration of :[Xe] 6s1 5d0 6p0. To test the PP, I'm using these five configuration (just by guessing): configts(1)= '6s1 6p0 5d0' configts(2)= '6s0.5 6p0.5 5d0' configts(3)= '6s0.5 6p0 5d0.5' configts(4)= '6s0 6p1 5d0' configts(5)= '6s0 6p0 5d1' My questions are: - how to choose the configurations for PP testing based on the reference one? is there a strategy or some sort? - how many configurations are enough for the test? Thank you very much, 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/20110525/6a5d52b6/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: pseudo-gen.pdf Type: application/pdf Size: 140764 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20110525/6a5d52b6/attachment-0001.pdf From trambui at u.boisestate.edu Thu May 26 01:21:58 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Wed, 25 May 2011 17:21:58 -0600 Subject: [Pw_forum] Pseudo-potential testing In-Reply-To: References: Message-ID: Dear Dr. Paolo Giannozzi, I'm so sorry I got your name wrong on the last email. Please forgive my mistake. Sincerely, Tram Bui On Wed, May 25, 2011 at 5:00 PM, Tram Bui wrote: > Dear Paul, > In the file that I have attached here (Paul's note on PP > generation), under section 3.10: checking for transferability, you have > mentioned about the:"The error on total energy di?erences > between PP and AE results gives a feeling on how good the PP is." Do you > mean the difference in AE and PP eigenvalues? because I saw the Etot and > Etotps are huge difference but their eigenvalue (e, Ry) are closed. > > Dear QE users, > I'm trying to test the Cs' US PP with reference configuration of :[Xe] > 6s1 5d0 6p0. To test the PP, I'm using these five configuration (just by > guessing): > configts(1)= '6s1 6p0 5d0' > configts(2)= '6s0.5 6p0.5 5d0' > configts(3)= '6s0.5 6p0 5d0.5' > configts(4)= '6s0 6p1 5d0' > configts(5)= '6s0 6p0 5d1' > My questions are: > - how to choose the configurations for PP testing based on the reference > one? is there a strategy or some sort? > - how many configurations are enough for the test? > > Thank you very much, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > -- 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/20110525/02a8e426/attachment.htm From songsong19840614 at gmail.com Thu May 26 03:37:05 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Thu, 26 May 2011 09:37:05 +0800 Subject: [Pw_forum] PlotPhon run example failed! Message-ID: Hi, Recently,I learn PlotPhon utility.Unfortunately,I am unsuccessful. I follow the Readme from PlotPhon. I set the make.inc,sucn as: # Intel Fortran FC = ifort LD = $(FC) -static FFLAGS = -FR # g95 compiler FC = f90 LD = $(FC) FFLAGS = # gfortran compiler FC = ifort LD = $(FC) FFLAGS = . And the I run example,but all of them failed,such as: AL_SC gnuplot> set arrow nohead from 0.50000, E_min to 0.50000, E_max lw 3 ^ "plot.Thz.GNU", line 26: duplicated or contradicting arguments in set arrow ERROR: /rangecheck in --.peekstring-- Operand stack: --nostringval-- --nostringval-- (%!\n%) Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1 3 %oparray_pop --nostringval-- Dictionary stack: --dict:1120/1686(ro)(G)-- --dict:0/20(G)-- --dict:102/200(L)-- Current allocation mode is local ESP Ghostscript 815.02: Unrecoverable error, exit code 1 ############################################################################################### ############################################################################################### You have got phonon dispersion relations plotted using gnuplot ( www.gnuplot.info) Now you can edit plot.Thz.GNU in order to define E_min, E_max and Label_position more accurately to get publication-quality Postscript and PDF files. You can also redefine default parameters and add experimental data, too. I have installed gnuplot.And I edit plot.Thz.GNU,which set E_min=0, E_max=400,Label_position=-0.5(this is defult,I don't know if change it.) Please tell me how my fault is. Thanks. Best pine. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/d34463ad/attachment.htm From flux_ray12 at 163.com Thu May 26 05:58:57 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 26 May 2011 11:58:57 +0800 (CST) Subject: [Pw_forum] PlotPhon run example failed! In-Reply-To: References: Message-ID: <1ec3a174.14c0f.1302a748567.Coremail.flux_ray12@163.com> In my opinion, the error is this: set arrow nohead from 0.50000, E_min to 0.50000, E_max lw 3 I am not familiar with gnuplot, but after all, you can still plot the file "Frequency" by other software such as xmgrace or ROOT. At 2011-05-26 09:37:05?lucking-pine wrote: Hi, Recently,I learn PlotPhon utility.Unfortunately,I am unsuccessful. I follow the Readme from PlotPhon. I set the make.inc,sucn as: # Intel Fortran FC = ifort LD = $(FC) -static FFLAGS = -FR # g95 compiler FC = f90 LD = $(FC) FFLAGS = # gfortran compiler FC = ifort LD = $(FC) FFLAGS = . And the I run example,but all of them failed,such as: AL_SC gnuplot> set arrow nohead from 0.50000, E_min to 0.50000, E_max lw 3 ^ "plot.Thz.GNU", line 26: duplicated or contradicting arguments in set arrow ERROR: /rangecheck in --.peekstring-- Operand stack: --nostringval-- --nostringval-- (%!\n%) Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1 3 %oparray_pop --nostringval-- Dictionary stack: --dict:1120/1686(ro)(G)-- --dict:0/20(G)-- --dict:102/200(L)-- Current allocation mode is local ESP Ghostscript 815.02: Unrecoverable error, exit code 1 ############################################################################################### ############################################################################################### You have got phonon dispersion relations plotted using gnuplot (www.gnuplot.info) Now you can edit plot.Thz.GNU in order to define E_min, E_max and Label_position more accurately to get publication-quality Postscript and PDF files. You can also redefine default parameters and add experimental data, too. I have installed gnuplot.And I edit plot.Thz.GNU,which set E_min=0, E_max=400,Label_position=-0.5(this is defult,I don't know if change it.) Please tell me how my fault is. Thanks. Best pine. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/7bd1966e/attachment.htm From flux_ray12 at 163.com Thu May 26 05:45:29 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Thu, 26 May 2011 11:45:29 +0800 (CST) Subject: [Pw_forum] installing QE In-Reply-To: References: Message-ID: <698746fe.148a8.1302a683206.Coremail.flux_ray12@163.com> Installing OpenMPI or MPICH2 firstly, then you can compile parrallel version PWscf. When you run it with multi-cores, using mpirun -n $CoreNum pw.x -npool $PoolNum At 2011-05-25 12:55:10?"vicky singh" wrote: Hi I have recently got a new system with i5 processor. Since it has 4 processor how can i install QE such that i can run parallel processing. Documentation says just to use ./configure and make to be done for compiling. will these command when run will consider the system configuration and install parallel version. Thanks for suggestion in advance. Vicky singh research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/c48ac75b/attachment-0001.htm From s.m.rezaeisani at gmail.com Thu May 26 08:45:18 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Thu, 26 May 2011 11:15:18 +0430 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation In-Reply-To: References: Message-ID: Dear Lorenzo OK. There is no crash and my job is done completely without any time limitation termination. In output, frequencies are calculated for all 16 points, but the code write just *.dyn1-9 files, 7 q-points' *.dyn are missed. I have attached in & output and *.dyn0 files. On Wed, May 25, 2011 at 11:40 PM, Lorenzo Paulatto < lorenzo.paulatto at impmc.upmc.fr> wrote: > In data 25 maggio 2011 alle ore 21:02:57, Seyed Mojtaba Rezaei Sani > ha scritto: > > In *.dyn0, as a ph.x output file, 16 points have been selected from my > > 6*6*6 > > chosen grid. But I get just *.dyn1-9. On the other word calculations are > > done just for 9 q-points. If any more details are needed, please notify > > me. > > Dear Seyed, > it could be anything, from you not just finding the files to crash in the > code or a time limit in your computing hardware. > > Keep in mind that nobody in this forum knows what is going on in you > computer. You MUST provide at the very least the input and output of your > job, otherwise we can only guess. > > As a side note: asking a good question takes a lot of time, often more > times that it takes to give a good answer. If it takes you only 30 seconds > to write your email it is very unlikely to contain any good question. > > 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 > _______________________________________________ > 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/20110526/a2330911/attachment.htm From mayankaditya at gmail.com Thu May 26 08:56:40 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Thu, 26 May 2011 12:26:40 +0530 Subject: [Pw_forum] accuracy of calculated phonon frequency Message-ID: Hi dear all I have a query regarding the accuracy of phonon frequency. What is the order of accuracy of phonon frequency and how we can improve it. -- Mayank BARC From degironc at sissa.it Thu May 26 09:37:33 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 26 May 2011 09:37:33 +0200 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation In-Reply-To: References: Message-ID: <4DDE033D.2050501@sissa.it> On 05/26/2011 08:45 AM, Seyed Mojtaba Rezaei Sani wrote: > Dear Lorenzo > > OK. There is no crash and my job is done completely without any timen > limitation termination. In output, frequencies are calculated for all 16 > points, but the code write just *.dyn1-9 files, 7 q-points' *.dyn are > missed. I have attached in& output and *.dyn0 files. you have not. there should also be a dyn0 file ... do you have it ? what are the dates of your *.dyn* files ? stefano > On Wed, May 25, 2011 at 11:40 PM, Lorenzo Paulatto< > lorenzo.paulatto at impmc.upmc.fr> wrote: > >> In data 25 maggio 2011 alle ore 21:02:57, Seyed Mojtaba Rezaei Sani >> ha scritto: >>> In *.dyn0, as a ph.x output file, 16 points have been selected from my >>> 6*6*6 >>> chosen grid. But I get just *.dyn1-9. On the other word calculations are >>> done just for 9 q-points. If any more details are needed, please notify >>> me. >> Dear Seyed, >> it could be anything, from you not just finding the files to crash in the >> code or a time limit in your computing hardware. >> >> Keep in mind that nobody in this forum knows what is going on in you >> computer. You MUST provide at the very least the input and output of your >> job, otherwise we can only guess. >> >> As a side note: asking a good question takes a lot of time, often more >> times that it takes to give a good answer. If it takes you only 30 seconds >> to write your email it is very unlikely to contain any good question. >> >> 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 >> _______________________________________________ >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/a7503e5b/attachment.htm From sclauzer at sissa.it Thu May 26 10:16:38 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 26 May 2011 10:16:38 +0200 Subject: [Pw_forum] Pseudo-potential testing In-Reply-To: References: Message-ID: Il giorno 26/mag/2011, alle ore 01.00, Tram Bui ha scritto: > Dear Paul, > In the file that I have attached here (Paul's note on PP generation), under section 3.10: checking for transferability, you have mentioned about the:"The error on total energy di?erences > between PP and AE results gives a feeling on how good the PP is." Do you mean the difference in AE and PP eigenvalues? No, I think here Paolo "Paul" Giannozzi really meant what you understood first, but you didn't get it in the correct way. You should really compare total energy differences, which means: E_2(AE) - E_1(AE) versus E_2(PS) - E_1(PS) where 1 and 2 label two different electronic configurations, and NOT E_1(PS) versus E_1(AE) as you are probably trying to do. > because I saw the Etot and Etotps are huge difference This is often the case, given the high degree of freedom in the choice of PP parameters (especially for the local potential, I suppose). > but their eigenvalue (e, Ry) are closed. Indeed this is how it should be, since the modern PP are designed to reproduce the scattering properties of the AE atomic potential as best as possible. > > Dear QE users, > I'm trying to test the Cs' US PP with reference configuration of :[Xe] 6s1 5d0 6p0. To test the PP, I'm using these five configuration (just by guessing): > configts(1)= '6s1 6p0 5d0' > configts(2)= '6s0.5 6p0.5 5d0' > configts(3)= '6s0.5 6p0 5d0.5' > configts(4)= '6s0 6p1 5d0' > configts(5)= '6s0 6p0 5d1' > My questions are: > - how to choose the configurations for PP testing based on the reference one? is there a strategy or some sort? Use some reasonable configurations (remove or add one electron, or a fraction of it, move one or more electrons between different orbitals, ...). The choice may also be driven by the class of materials that you are going to study (e.g. ionic crystals). > - how many configurations are enough for the test? That's up to you... 5 look enough for me. Don't forget to do some testing with the solid state code (e.g. bond distance of dimers, lattice constant of simple solids...). HTH GS > > Thank you very much, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > _______________________________________________ > 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/20110526/1ce972bd/attachment.htm From yhho at pub.iams.sinica.edu.tw Thu May 26 11:15:53 2011 From: yhho at pub.iams.sinica.edu.tw (yhho) Date: Thu, 26 May 2011 17:15:53 +0800 Subject: [Pw_forum] Caculation of Graphene's phonon dispersion and pdos Message-ID: <001c01cc1b85$834c5580$61706d8c@mychatd6d7d1f2> Deae all, I'm trying to do the phonon dispersion calaulation of Graphene. Although the jobs have done sucessfully, the result are not great. I think it may be coused by the wrong setting of my q2r.in or matdyn.in. But some of terms in thoese input file are unfamiliar to me. Please give me some suggestions about setting them. Thanks. phonons of AuC &inputph tr2_ph=1.0d-14, ldisp=.true., nq1=4, nq2=4, nq3=4 amass(1)= 12.0107 prefix='AuC', outdir='./' fildyn='AuC.dyn', / &input fildyn='AuC.dyn', zasr='crystal', flfrc='AuC444.fc' / &input asr='simple', amass(1)=12.0107, flfrc='AuC444.fc', flfrq='AuC.freq' / 13 0.00000000 0.00000000 0.00000000 1 0.00000000 0.12500000 0.00000000 2 0.00000000 0.25000000 0.00000000 3 0.00000000 0.37500000 0.00000000 4 0.00000000 0.50000000 0.00000000 5 0.08333250 0.45833250 0.00000000 6 0.16666500 0.41666500 0.00000000 7 0.24999750 0.37499750 0.00000000 8 0.33333000 0.33333000 0.00000000 9 0.24999750 0.24999750 0.00000000 10 0.16666500 0.16666500 0.00000000 11 0.08333250 0.08333250 0.00000000 12 0.00000000 0.00000000 0.00000000 13 Otherwise, I have another question about the last part of matdyn.in. Does that mean the points such as gamma, M, K ,gamma? I'm not sure about that... Thanks a lot. Best regarts, Yu Han Ho -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/df07779a/attachment.htm From priyankagoud8 at gmail.com Thu May 26 12:24:35 2011 From: priyankagoud8 at gmail.com (priyanka goud) Date: Thu, 26 May 2011 15:54:35 +0530 Subject: [Pw_forum] Hybrid XC with USP Message-ID: Dear PWSCF users, I have came across an error while using hybrid XC functional as Input_dft = "PBE0" using ultrasoft psedopotentials of PBE for C,H,N,S atoms. Job terminated with an error "HYBRID XC not implemented for USPP or PAW". For the same I could able to run my job with hybrid XC functional Input_dft = "B3LYP" using norm conservative pseudopotentials. Can any one please say me can't we implement hybrid XC functional for ultrsoft pseudo potentials. -- *With Regards*, B.Priyanka, Research Scholar, Computational Chemistry, IICT,Habsiguda, India. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/eefb1cb6/attachment.htm From sclauzer at sissa.it Thu May 26 12:44:29 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 26 May 2011 12:44:29 +0200 Subject: [Pw_forum] Hybrid XC with USP In-Reply-To: References: Message-ID: Il giorno 26/mag/2011, alle ore 12.24, priyanka goud ha scritto: > Dear PWSCF users, > > I have came across an error while using hybrid XC functional as Input_dft = "PBE0" using ultrasoft psedopotentials of PBE for C,H,N,S atoms. > Job terminated with an error "HYBRID XC not implemented for USPP or PAW". > > For the same I could able to run my job with hybrid XC functional Input_dft = "B3LYP" using norm conservative pseudopotentials. norm conserving > > Can any one please say me can't we implement hybrid XC functional for ultrsoft pseudo potentials. Yes, you can implement it. Indeed you would be the most welcome if you do it! Regards, GS > > > > > -- > With Regards, > > B.Priyanka, > Research Scholar, > Computational Chemistry, > IICT,Habsiguda, > 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/20110526/d8d78544/attachment.htm From priyankagoud8 at gmail.com Thu May 26 12:54:18 2011 From: priyankagoud8 at gmail.com (priyanka goud) Date: Thu, 26 May 2011 16:24:18 +0530 Subject: [Pw_forum] Hybrid XC with USP In-Reply-To: References: Message-ID: Dear Gabriele, Thank you for your favorable reply , at the same time can you please suggest me what to be mentioned in input file to overcome the output error "HYBRID XC not implemented for USPP or PAW".. and to run it successfully. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/10d30d64/attachment-0001.htm From sclauzer at sissa.it Thu May 26 13:45:17 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 26 May 2011 13:45:17 +0200 Subject: [Pw_forum] Hybrid XC with USP In-Reply-To: References: Message-ID: Il giorno 26/mag/2011, alle ore 12.54, priyanka goud ha scritto: > Dear Gabriele, > > Thank you for your favorable reply , at the same time can you please suggest me what to be mentioned > in input file to overcome the output error "HYBRID XC not implemented for USPP or PAW".. and to run it successfully. Use norm conserving PPs instead of USPP (or PAW). You said that you've already discovered it by yourself for B3LYP (which should also be a hybrid functional, to my knowledge). Regards, 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/20110526/c6d62fbf/attachment.htm From guptasanjay.56 at gmail.com Thu May 26 14:30:04 2011 From: guptasanjay.56 at gmail.com (Sanjay D. Gupta) Date: Thu, 26 May 2011 18:00:04 +0530 Subject: [Pw_forum] very high pressure in scf Message-ID: Dear, PWSCF users, Greetings!!! Here I am facing problem of high pressure in per nitride materials. When we do scf using two different platform such as ABINIT and PWSCF, we got different pressure like abinit give nearly 20 GPa and pwscf gives 2720.7 GPa, while I am using same geometry and even same strcture. Two codes should not differ so much, so I am not clear, where i am doing mistake. From max.n.popov at gmail.com Thu May 26 14:45:07 2011 From: max.n.popov at gmail.com (=?KOI8-R?B?7cHL08nNIPDP0M/X?=) Date: Thu, 26 May 2011 14:45:07 +0200 Subject: [Pw_forum] very high pressure in scf In-Reply-To: References: Message-ID: Dear Sanjay, it is very difficult to suggest something without looking, at least, in your input files. One idea comes to my mind - are you sure that length units are the same in both abinit and qe calculations? More specific, my suspicion is that in abinit you used unit cell in Angstroems, and put the same numbers to qe input (celldm(X)). Taking into account, that celldm unit is Bohr, one can understand this discrepancy in calculated pressures: in qe the unit cell volume is almost 8(!) times smaller. Hope, this helps. Best regards, Maxim. 2011/5/26 Sanjay D. Gupta > Dear, PWSCF users, > > Greetings!!! > > Here I am facing problem of high pressure in per nitride materials. When we > do scf using two different platform such as ABINIT and PWSCF, we got > different pressure like abinit give nearly 20 GPa and pwscf gives 2720.7 > GPa, while I am using same geometry and even same strcture. Two codes should > not differ so much, so I am not clear, where i am doing mistake. > From ABINIT, it is GGA-FHI pseudo, while in pwscf it is UPF. > > Please suggest me. Thanks in advance. > > Best Regards > Sanjay D. Gupta > > > > > > > ~Best Regards > ........................................................... > Sanjay D. Gupta > Research Fellow > Department of Physics, > Bhavnagar University, Bhavnagar-364 022 > Gujarat, Mobile-9879666643 > email:guptasanjay_56 at yahoo.co.in > ........................................................... > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- 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/20110526/22a38714/attachment.htm From tkuehne at gmail.com Thu May 26 14:52:26 2011 From: tkuehne at gmail.com (=?iso-8859-1?Q?Thomas_K=FChne?=) Date: Thu, 26 May 2011 14:52:26 +0200 Subject: [Pw_forum] Postdoctoral Research Position: Ab-Initio Dynamics of Condensed Matter In-Reply-To: References: Message-ID: <80FC5CDD-4B93-4B3B-8D0E-CCAA1705EE3D@gmail.com> In the Ab-Initio Dynamics of Condensed Matter Group we are aiming to develop novel computational methods to study complex many-body systems such as liquids, biomolecules in solution and solids from first-principles. Along those lines we do have a postdoctoral research positions to offer, which consists of both method development and application. Potential candidates must have a PhD degree in Chemistry, Physics, or related discipline and a strong interest in computer simulations as well as programming. Basic experiences with Linux, numerical methods of theoretical physics/chemistry, electronic structure methods and/or molecular dynamics are required. Consideration of candidates will begin immediately until the position is filled. Questions and applications in electronic form including a cover letter and contact informations of at least two academic references should be directed to kuehne at uni-mainz.de. ============================== Thomas D. K?hne Johannes Gutenberg University Mainz Institute of Physical Chemistry and Center for Computational Sciences Staudinger Weg 9 D-55128 Mainz Germany kuehne at uni-mainz.de +49/(0)6131/39-26843 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/883d082f/attachment.htm From zhaohscas at yahoo.com.cn Fri May 27 03:57:43 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Thu, 26 May 2011 21:57:43 -0400 Subject: [Pw_forum] Single point energy calculation within PWSCF. In-Reply-To: <20110525205354.bae5zalli4g04kk4@webmail.sissa.it> References: <4DDD330E.4090506@yahoo.com.cn> <4DDDBA01.8060804@yahoo.com.cn> <20110525205354.bae5zalli4g04kk4@webmail.sissa.it> Message-ID: <4DDF0517.3070404@yahoo.com.cn> On 05/25/2011 02:53 PM, Emine Kucukbenli wrote: > I was thinking that you were trying to optimize the calculation > parameters however with this post I am lost.I will give a generic > answer: > > Before starting to work on a system, you need to optimize the > calculation parameters, much like an experimentalist optimizing their > machine set up before an experiment. > > You need to make sure that what you will get, once you do the desired > calculation, (like a desired experiment) would be sensible data. This > is a preparation scheme_before_ the actual calculations. > > In this preparation process, you need to check the convergence of > energy, and/or forces, pressure etc, basically whatever interests you, > or whatever the interested property is sensitive to. And by > convergence, I mean convergence with respect to calculation > parameters: ecutwfc/rho ; kpoints ; smearing for metals; box size for > isolated systems, convergence thresholds etc ..again, whatever is > relevant. > > Once you know the optimum values for these parameters, you can do some > applications: One of them might be finding the equilibrium lattice > parameter. If so, now you can run a "vc-relax" calculation to get the > zero pressure structure.. > > Hope this made any sense and didnt confuse you even more. > cheers, > emine kucukbenli, phd student, sissa, italy Thanks a lot for your systematic analysis ;-) Regards -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From physics.skgupta at gmail.com Thu May 26 16:13:11 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Thu, 26 May 2011 19:43:11 +0530 Subject: [Pw_forum] very high pressure in scf In-Reply-To: References: Message-ID: Dear Maxim Thank for kind reply. My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I am using the spacegroup 166 (R3(bar)M) space group with conventional unit cell rather than primitive unit cell the lattice parameter is taken as below 1. for abinit a=5.359168252 Bohr b=5.359168252 Bohr c=20.08294707 Bohr 2. for PWSCF ibrav=4, celldm(1) = 5.359168242 Bohr celldm(3) = 3.7474 Part of my input file is : PWSCF &control calculation = 'scf' prefix='FeN2', restart_mode='from_scratch', outdir='./' pseudo_dir = '/', tstress = .true. tprnfor = .true. etot_conv_thr = 1.0d-5, forc_conv_thr = 1.0d-4, / &system ibrav=4, celldm(1) = 5.359168242, celldm(3) = 3.7474 nat=9, ntyp=2, nosym =.true., ecutwfc = 20, ecutrho=200, occupations='smearing', smearing='m-p', degauss=0.001, / &electrons mixing_mode = "local-TF", mixing_beta = 0.700000, conv_thr = 1.0d-10, / ATOMIC_SPECIES Fe 55.845 Fe.pbe-sp-van.UPF N 14.0067 N.pbe-van_ak.UPF ATOMIC_POSITIONS Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 .......................................... N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 K_POINTS automatic 6 6 6 0 0 0 Best Regards Sanjay D. Gupta Research Fellow Department of Physics, Bhavnagar University, Bhavnagar-364 022 Gujarat, Mobile-9879666643 email:guptasanjay_56 at yahoo.co.in -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/a7c2fb30/attachment-0001.htm From songsong19840614 at gmail.com Thu May 26 16:17:47 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Thu, 26 May 2011 22:17:47 +0800 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation In-Reply-To: References: Message-ID: Hi? In my opinion,this may be resule from 'recover' in ph.input.Most of times,I choose recover=.ture. The ph.output is obtainde very fast,but dyn0 is often lack.So I suggest you to set recover=.false.It maybe work. Bests, Pine. 2011/5/26 Seyed Mojtaba Rezaei Sani > Dear Lorenzo > > OK. There is no crash and my job is done completely without any time > limitation termination. In output, frequencies are calculated for all 16 > points, but the code write just *.dyn1-9 files, 7 q-points' *.dyn are > missed. I have attached in & output and *.dyn0 files. > > On Wed, May 25, 2011 at 11:40 PM, Lorenzo Paulatto < > lorenzo.paulatto at impmc.upmc.fr> wrote: > >> In data 25 maggio 2011 alle ore 21:02:57, Seyed Mojtaba Rezaei Sani >> ha scritto: >> > In *.dyn0, as a ph.x output file, 16 points have been selected from my >> > 6*6*6 >> > chosen grid. But I get just *.dyn1-9. On the other word calculations are >> > done just for 9 q-points. If any more details are needed, please notify >> > me. >> >> Dear Seyed, >> it could be anything, from you not just finding the files to crash in the >> code or a time limit in your computing hardware. >> >> Keep in mind that nobody in this forum knows what is going on in you >> computer. You MUST provide at the very least the input and output of your >> job, otherwise we can only guess. >> >> As a side note: asking a good question takes a lot of time, often more >> times that it takes to give a good answer. If it takes you only 30 seconds >> to write your email it is very unlikely to contain any good question. >> >> 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 >> _______________________________________________ >> 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/88b1b0d1/attachment.htm From songsong19840614 at gmail.com Thu May 26 16:35:08 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Thu, 26 May 2011 22:35:08 +0800 Subject: [Pw_forum] Running parallel in some example of 2 cup is wrong? Message-ID: My computer is 2 cpu and 8 core of Dell. In some examples are crash. Such as:co.out of example 03 show that 'from d_&_i:error;some nodes have no k points'. And the environment_varibles of examples I set : PARA_PREFIX="mpiexec -n 8" PARA_POSTFIX="-npool 2" And how odd is when I set : PARA_PREFIX="mpiexec -n 4" PARA_POSTFIX="-npool 1" the example 03 can be work. The similar case occur also in some of other examples. Please tell what problem is????thanks. ps:my compiler is:icc11.1.075,ifort11.1.075,mpich2,pwscf 4.2.1 system is red hat enterprise linux 5 Best Pine. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/17c37e5a/attachment.htm From ttduyle at gmail.com Thu May 26 18:05:35 2011 From: ttduyle at gmail.com (Duy Le) Date: Thu, 26 May 2011 12:05:35 -0400 Subject: [Pw_forum] Running parallel in some example of 2 cup is wrong? In-Reply-To: References: Message-ID: 2011/5/26 lucking-pine : > My computer is 2 cpu and 8 core of Dell. In some examples are crash. Such > as:co.out of example 03 show that 'from d_&_i:error;some nodes have no k > points'. > And the environment_varibles of examples I set : > > PARA_PREFIX="mpiexec -n 8" > PARA_POSTFIX="-npool 2" > > And how odd is when I set : > > PARA_PREFIX="mpiexec -n 4" > PARA_POSTFIX="-npool 1" > You need understand the parallelism of QE before using it. http://www.quantum-espresso.org/user_guide/node15.html For example, it is obvious that if you have only one k-point, you can not distribute it to 2 different pools. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" > the example 03 can be work. > > The?similar case occur also in some of?other examples. > > ?Please tell what problem is????thanks. > ps:my compiler is:icc11.1.075,ifort11.1.075,mpich2,pwscf 4.2.1 > system is red hat enterprise linux 5 > > Best > Pine. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From flux_ray12 at 163.com Thu May 26 18:09:31 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 27 May 2011 00:09:31 +0800 (CST) Subject: [Pw_forum] Caculation of Graphene's phonon dispersion and pdos In-Reply-To: <001c01cc1b85$834c5580$61706d8c@mychatd6d7d1f2> References: <001c01cc1b85$834c5580$61706d8c@mychatd6d7d1f2> Message-ID: <601441a0.1e07a.1302d115e85.Coremail.flux_ray12@163.com> According to my experience, phonon calculation is very sensitive to the groud state. Therefore, a strict relax (by pw.x) is required before using ph.x, for example, higher cut-off, more k-points and smaller threshold. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-05-26 17:15:53?yhho wrote: Deae all, I'm trying to do thephonon dispersion calaulation of Graphene. Although the jobs have done sucessfully, the result are not great. I think it may be coused by the wrong setting of myq2r.in ormatdyn.in. But some of terms in thoese input file are unfamiliar to me. Please give me some suggestions about setting them. Thanks. phonons of AuC &inputph tr2_ph=1.0d-14, ldisp=.true., nq1=4, nq2=4, nq3=4 amass(1)= 12.0107 prefix='AuC', outdir='./' fildyn='AuC.dyn', / &input fildyn='AuC.dyn', zasr='crystal', flfrc='AuC444.fc' / &input asr='simple', amass(1)=12.0107, flfrc='AuC444.fc', flfrq='AuC.freq' / 13 0.00000000 0.00000000 0.00000000 1 0.00000000 0.12500000 0.00000000 2 0.00000000 0.25000000 0.00000000 3 0.00000000 0.37500000 0.00000000 4 0.00000000 0.50000000 0.00000000 5 0.08333250 0.45833250 0.00000000 6 0.16666500 0.41666500 0.00000000 7 0.24999750 0.37499750 0.00000000 8 0.33333000 0.33333000 0.00000000 9 0.24999750 0.24999750 0.00000000 10 0.16666500 0.16666500 0.00000000 11 0.08333250 0.08333250 0.00000000 12 0.00000000 0.00000000 0.00000000 13 Otherwise, I have another question about the last part of matdyn.in. Does that mean the points such as gamma, M, K ,gamma? I'm not sure about that... Thanks a lot. Best regarts, Yu Han Ho -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110527/b00c68ab/attachment.htm From flux_ray12 at 163.com Thu May 26 18:15:18 2011 From: flux_ray12 at 163.com (GAO Zhe) Date: Fri, 27 May 2011 00:15:18 +0800 (CST) Subject: [Pw_forum] Running parallel in some example of 2 cup is wrong? In-Reply-To: References: Message-ID: <1ae96464.1e0c6.1302d16ad1f.Coremail.flux_ray12@163.com> In example 03, the first step is a calculation of CO atGAMMA point. Thus, you cannot use more than one pool to run it. Why not trympiexec -n 8 pw.x -npool 1 and see how it goes? -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-05-26 22:35:08?lucking-pine wrote: My computer is 2 cpu and 8 core of Dell. In some examples are crash. Such as:co.out of example 03 show that 'from d_&_i:error;some nodes have no k points'. And the environment_varibles of examples I set : PARA_PREFIX="mpiexec -n 8" PARA_POSTFIX="-npool 2" And how odd is when I set : PARA_PREFIX="mpiexec -n 4" PARA_POSTFIX="-npool 1" the example 03 can be work. The similar case occur also in some of other examples. Please tell what problem is????thanks. ps:my compiler is:icc11.1.075,ifort11.1.075,mpich2,pwscf 4.2.1 system is red hat enterprise linux 5 Best Pine. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110527/c6a0ffcf/attachment-0001.htm From ttduyle at gmail.com Thu May 26 18:18:06 2011 From: ttduyle at gmail.com (Duy Le) Date: Thu, 26 May 2011 12:18:06 -0400 Subject: [Pw_forum] very high pressure in scf In-Reply-To: References: Message-ID: On Thu, May 26, 2011 at 10:13 AM, Sanjeev Gupta wrote: > ??? tstress = .true. > ??? ecutwfc = 20, > ??? ecutrho=200, Did you check these cutoff values? -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" From degironc at sissa.it Thu May 26 18:53:08 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 26 May 2011 18:53:08 +0200 Subject: [Pw_forum] very high pressure in scf In-Reply-To: References: Message-ID: <4DDE8574.8090504@sissa.it> with this input the Fe-N distance is some 1.2 A... I'm pretty sure it cannot be the intended structure Are you sure the system is not in crystal coordinate ? stefano On 05/26/2011 04:13 PM, Sanjeev Gupta wrote: > Dear Maxim > > Thank for kind reply. > > My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I > am using the spacegroup 166 (R3(bar)M) space group with conventional unit > cell rather than primitive unit cell the lattice parameter is taken as below > 1. for abinit > > a=5.359168252 Bohr > b=5.359168252 Bohr > c=20.08294707 Bohr > > 2. for PWSCF > > ibrav=4, > celldm(1) = 5.359168242 Bohr > celldm(3) = 3.7474 > > Part of my input file is : > > PWSCF > > &control > calculation = 'scf' > prefix='FeN2', > restart_mode='from_scratch', > outdir='./' > pseudo_dir = '/', > tstress = .true. > tprnfor = .true. > etot_conv_thr = 1.0d-5, > forc_conv_thr = 1.0d-4, > / > &system > ibrav=4, > celldm(1) = 5.359168242, > celldm(3) = 3.7474 > nat=9, > ntyp=2, > nosym =.true., > ecutwfc = 20, > ecutrho=200, > occupations='smearing', > smearing='m-p', > degauss=0.001, > / > &electrons > mixing_mode = "local-TF", > mixing_beta = 0.700000, > conv_thr = 1.0d-10, > / > ATOMIC_SPECIES > Fe 55.845 Fe.pbe-sp-van.UPF > N 14.0067 N.pbe-van_ak.UPF > ATOMIC_POSITIONS > Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 > N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 > > .......................................... > > N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 > K_POINTS automatic > 6 6 6 0 0 0 > > > Best Regards > > > Sanjay D. Gupta > Research Fellow > Department of Physics, > Bhavnagar University, Bhavnagar-364 022 > Gujarat, Mobile-9879666643 > email:guptasanjay_56 at yahoo.co.in > > > > _______________________________________________ > 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/20110526/f949df1e/attachment.htm From physics.skgupta at gmail.com Thu May 26 20:50:54 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Fri, 27 May 2011 00:20:54 +0530 Subject: [Pw_forum] very high pressure in scf In-Reply-To: <4DDE8574.8090504@sissa.it> References: <4DDE8574.8090504@sissa.it> Message-ID: Dear Sir, Thanks for reply. On Thu, May 26, 2011 at 10:23 PM, Stefano de Gironcoli wrote: > with this input the Fe-N distance is some 1.2 A... I'm pretty sure it > cannot be the intended structure > Are you sure the system is not in crystal coordinate ? > stefano > Yes, its true that while looking from xcrysden particularly the bond lengths between the Fe-N and N-N but i am very surprised why both ABINIT and PWSCF code gives such vast Difference in calculated Pressure for the identical geometry which is not cleared yet. Here the bond lenth Fe-N is ~1.24Ang. Please Suggest More. > > > On 05/26/2011 04:13 PM, Sanjeev Gupta wrote: > > Dear Maxim > > Thank for kind reply. > > My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I > am using the spacegroup 166 (R3(bar)M) space group with conventional unit > cell rather than primitive unit cell the lattice parameter is taken as below > 1. for abinit > > a=5.359168252 Bohr > b=5.359168252 Bohr > c=20.08294707 Bohr > > 2. for PWSCF > > ibrav=4, > celldm(1) = 5.359168242 Bohr > celldm(3) = 3.7474 > > Part of my input file is : > > PWSCF > > &control > calculation = 'scf' > prefix='FeN2', > restart_mode='from_scratch', > outdir='./' > pseudo_dir = '/', > tstress = .true. > tprnfor = .true. > etot_conv_thr = 1.0d-5, > forc_conv_thr = 1.0d-4, > / > &system > ibrav=4, > celldm(1) = 5.359168242, > celldm(3) = 3.7474 > nat=9, > ntyp=2, > nosym =.true., > ecutwfc = 20, > ecutrho=200, > occupations='smearing', > smearing='m-p', > degauss=0.001, > / > &electrons > mixing_mode = "local-TF", > mixing_beta = 0.700000, > conv_thr = 1.0d-10, > / > ATOMIC_SPECIES > Fe 55.845 Fe.pbe-sp-van.UPF > N 14.0067 N.pbe-van_ak.UPF > ATOMIC_POSITIONS > Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 > N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 > > .......................................... > > N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 > K_POINTS automatic > 6 6 6 0 0 0 > > > Best Regards > > > Sanjay D. Gupta > Research Fellow > Department of Physics, > Bhavnagar University, Bhavnagar-364 022 > Gujarat, Mobile-9879666643email:guptasanjay_56 at yahoo.co.in > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > 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/20110527/d9794a84/attachment.htm From elie.moujaes at hotmail.co.uk Thu May 26 20:47:32 2011 From: elie.moujaes at hotmail.co.uk (Elie Moujaes) Date: Thu, 26 May 2011 19:47:32 +0100 Subject: [Pw_forum] c_bands : eigenvalues not converged Message-ID: Dear All, I am still running a band structure calculation on a 72 Carbon atom system but it is taking a bit too long and till now the results are: negative rho (up, down) = 0.0406, 0 Band Structure Calculation: Davidson Diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 2 eigenvalues not converged c_bands: 1 eigenvalue not converged and is still running for like 6 days. The system is very similar to graphene and its DOS should be similar. I gathered that there might be something wrong with my input..Please can anyone help me on that? The input is: control prefix='GBdensity', calculation='bands', restart_mode='from_scratch', pseudo_dir = '/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo/', outdir='/exp/home/caiapo/emoujaes/espresso/espresso-4.1.3/pseudo', / &system ibrav= 0, celldm(1) =1.889725989, nat=72, ntyp= 1, ecutwfc =32.0, ecutrho = 160.D0, nosym=.true.,occupations='smearing', smearing='mp', degauss=0.01 / &electrons conv_thr=1.D-4, mixing_beta=0.1D0, / CELL_PARAMETERS (alat) 29.416600000 0.000000000 0.000000000 0.000000000 6.609900000 0.000000000 0.000000000 0.000000000 33.000000000 ATOMIC_SPECIES C 12.0107 C.pz-rrjus.UPF ATOMIC_POSITIONS (angstrom) C -17.267939 -5.262892 -0.000002 C -17.658134 -3.893047 -0.000002 C -16.648186 -2.892145 0.000000 C -16.979016 -1.481403 -0.000001 C -15.822497 -7.188651 0.000003 C -15.974769 -5.758011 0.000001 C -14.931838 -4.783788 -0.000002 C -15.260133 -3.372206 -0.000003 C -14.164353 -2.443247 -0.000001 C -14.448789 -1.038033 0.000001 C -13.357280 -6.694629 -0.000003 C -13.589274 -5.266428 -0.000006 C -12.507820 -4.324210 -0.000003 C -12.797007 -2.912572 -0.000003 C -11.713425 -1.967554 0.000002 C -11.996028 -0.554049 0.000001 C -10.908497 -6.218111 -0.000001 C -11.153648 -4.798395 0.000000 C -10.348701 -2.439065 0.000002 C -10.066097 -3.852576 -0.000001 C -9.265132 -1.494029 -0.000001 C -9.554319 -0.082394 0.000000 C -8.472857 -5.750083 -0.000002 C -8.704854 -4.321888 0.000001 C -7.613348 -3.368592 0.000001 C -7.897799 -1.963373 -0.000003 C -6.802030 -1.034415 0.000000 C -7.130288 0.377174 -0.000002 C -6.239632 -3.827864 -0.000001 C -6.087349 -5.258489 0.000002 C -5.083140 -2.925203 0.000000 C -5.413953 -1.514463 0.000000 C -4.403993 -0.513566 0.000002 C -4.794134 0.856288 0.000002 C -3.676893 -4.887701 -0.000001 C -3.676919 -3.479951 -0.000003 C -2.270708 -2.925222 -0.000002 C -2.949816 -0.513582 -0.000002 C -1.939871 -1.514481 0.000001 .... ..... ..... K_POINTS crystal_b 5 0.00000 0.00000 0.00000 12 0.00000 0.50000 0.00000 12 0.50000 0.02160 0.00000 12 0.38540 0.50000 0.00000 12 0.00000 0.00000 0.00000 12 Regards Elie Moujaes University of Nottingham Nottingham NG7 2RD UK -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/f0fa5036/attachment-0001.htm From mashiatalaaii at gmail.com Thu May 26 21:37:52 2011 From: mashiatalaaii at gmail.com (mashiat alaaii) Date: Thu, 26 May 2011 15:37:52 -0400 Subject: [Pw_forum] is there a way to find the edge of conduction band from fermi level? Message-ID: Hello. I was wondering whether there is a way to guess what the edge of conduction band is by the Fermi level that the software provides. As you know for a new structure, it is very difficult to see where the conduction band starts. I appreciate your help as always. Yours M Alaaii. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/fcdce7bb/attachment.htm From degironc at sissa.it Thu May 26 21:46:42 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Thu, 26 May 2011 21:46:42 +0200 Subject: [Pw_forum] very high pressure in scf In-Reply-To: References: <4DDE8574.8090504@sissa.it> Message-ID: <4DDEAE22.9000800@sissa.it> I think the two structures are not the same, or some of the parameters have non equivalent values. stefano On 05/26/2011 08:50 PM, Sanjeev Gupta wrote: > Dear Sir, > Thanks for reply. > > > On Thu, May 26, 2011 at 10:23 PM, Stefano de Gironcoliwrote: > >> with this input the Fe-N distance is some 1.2 A... I'm pretty sure it >> cannot be the intended structure >> Are you sure the system is not in crystal coordinate ? >> stefano >> > Yes, its true that while looking from xcrysden particularly the bond > lengths between the Fe-N and N-N but i am very surprised why both ABINIT > and PWSCF code gives such vast Difference in calculated Pressure for the > identical geometry which is not cleared yet. Here the bond lenth Fe-N is > ~1.24Ang. > Please Suggest More. > > > >> On 05/26/2011 04:13 PM, Sanjeev Gupta wrote: >> >> Dear Maxim >> >> Thank for kind reply. >> >> My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I >> am using the spacegroup 166 (R3(bar)M) space group with conventional unit >> cell rather than primitive unit cell the lattice parameter is taken as below >> 1. for abinit >> >> a=5.359168252 Bohr >> b=5.359168252 Bohr >> c=20.08294707 Bohr >> >> 2. for PWSCF >> >> ibrav=4, >> celldm(1) = 5.359168242 Bohr >> celldm(3) = 3.7474 >> >> Part of my input file is : >> >> PWSCF >> >> &control >> calculation = 'scf' >> prefix='FeN2', >> restart_mode='from_scratch', >> outdir='./' >> pseudo_dir = '/', >> tstress = .true. >> tprnfor = .true. >> etot_conv_thr = 1.0d-5, >> forc_conv_thr = 1.0d-4, >> / >> &system >> ibrav=4, >> celldm(1) = 5.359168242, >> celldm(3) = 3.7474 >> nat=9, >> ntyp=2, >> nosym =.true., >> ecutwfc = 20, >> ecutrho=200, >> occupations='smearing', >> smearing='m-p', >> degauss=0.001, >> / >> &electrons >> mixing_mode = "local-TF", >> mixing_beta = 0.700000, >> conv_thr = 1.0d-10, >> / >> ATOMIC_SPECIES >> Fe 55.845 Fe.pbe-sp-van.UPF >> N 14.0067 N.pbe-van_ak.UPF >> ATOMIC_POSITIONS >> Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 >> N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 >> >> .......................................... >> >> N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 >> K_POINTS automatic >> 6 6 6 0 0 0 >> >> >> Best Regards >> >> >> Sanjay D. Gupta >> Research Fellow >> Department of Physics, >> Bhavnagar University, Bhavnagar-364 022 >> Gujarat, Mobile-9879666643email:guptasanjay_56 at yahoo.co.in >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> _______________________________________________ >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110526/bfbf5f25/attachment.htm From songsong19840614 at gmail.com Fri May 27 02:46:32 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Fri, 27 May 2011 08:46:32 +0800 Subject: [Pw_forum] Running parallel in some example of 2 cup is wrong? In-Reply-To: <1ae96464.1e0c6.1302d16ad1f.Coremail.flux_ray12@163.com> References: <1ae96464.1e0c6.1302d16ad1f.Coremail.flux_ray12@163.com> Message-ID: Hi, Thank you for Duy Le and GAO Zhe's help.I will follow your suggestion to try again. ? 2011?5?27? ??12:15?GAO Zhe ??? > In example 03, the first step is a calculation of CO at GAMMA point. > Thus, you cannot use more than one pool to run it. Why not try *mpiexec -n > 8 pw.x -npool 1* and see how it goes? > -- > GAO Zhe > CMC Lab, MSE, SNU, Seoul, S.Korea > > At 2011-05-26 22:35:08?lucking-pine wrote: > > My computer is 2 cpu and 8 core of Dell. In some examples are crash. Such > as:co.out of example 03 show that 'from d_&_i:error;some nodes have no k > points'. > And the environment_varibles of examples I set : > > PARA_PREFIX="mpiexec -n 8" > PARA_POSTFIX="-npool 2" > > And how odd is when I set : > > PARA_PREFIX="mpiexec -n 4" > PARA_POSTFIX="-npool 1" > the example 03 can be work. > > The similar case occur also in some of other examples. > > Please tell what problem is????thanks. > ps:my compiler is:icc11.1.075,ifort11.1.075,mpich2,pwscf 4.2.1 > system is red hat enterprise linux 5 > > Best > Pine. > > > > > _______________________________________________ > 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/20110527/14bbb538/attachment.htm From zhaohscas at yahoo.com.cn Fri May 27 04:20:01 2011 From: zhaohscas at yahoo.com.cn (=?utf-8?B?57qi55SfIOi1tQ==?=) Date: Fri, 27 May 2011 10:20:01 +0800 (CST) Subject: [Pw_forum] How to obtain the excition binding energy of ZnO using pwscf? Message-ID: <100426.10921.qm@web15606.mail.cnb.yahoo.com> Hi all, It is well know that ZnO has a larger excition binding energy ( about 60 meV ).? But could someone please give me some hints how to calculate this property by using pwscf? Regards. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110527/967103da/attachment.htm From bipulrr at gmail.com Fri May 27 05:13:12 2011 From: bipulrr at gmail.com (Bipul Rakshit) Date: Fri, 27 May 2011 07:43:12 +0430 Subject: [Pw_forum] LO-TO splitting Message-ID: Dear PWSCF users, is it possible/implemented in PWSCF to get lo-to splitting in case of anti-ferro magnetic insulator compounds? thx -- Bipul Rakshit Research Associate, S N Bose Centre for Basic Sciences, Salt Lake, Kolkata 700 098 India From nkxirainbow at gmail.com Fri May 27 05:35:39 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Fri, 27 May 2011 11:35:39 +0800 Subject: [Pw_forum] LO-TO splitting In-Reply-To: References: Message-ID: Dear Bipul Rakshit: As long as you can get the "effectiv charge" of AFM insulator, you can get the LO-TO splitting. However, I think it is difficult to deal with the "effective charge" of AFM insulator. Maybe this could give you some help:) http://www.democritos.it/pipermail/pw_forum/2011-January/019131.html On Fri, May 27, 2011 at 11:13 AM, Bipul Rakshit wrote: > Dear PWSCF users, > is it possible/implemented in PWSCF to get lo-to splitting in case of > anti-ferro magnetic insulator compounds? > thx > > -- > Bipul Rakshit > Research Associate, > S N Bose Centre for Basic Sciences, > Salt Lake, > Kolkata 700 098 > India > _______________________________________________ > 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/20110527/e2729155/attachment.htm From physics.skgupta at gmail.com Fri May 27 06:19:10 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Fri, 27 May 2011 09:49:10 +0530 Subject: [Pw_forum] very high pressure in scf In-Reply-To: <4DDEAE22.9000800@sissa.it> References: <4DDE8574.8090504@sissa.it> <4DDEAE22.9000800@sissa.it> Message-ID: Dear Sir, Thank you for kind reply. Here i am attaching the input file of ABINIT which gives less pressure for same structure as i have taken in PWSCF (I mentioned in my previous mail). Please look in this matter and suggest me. #********** input file from abinit code...... ndtset 1 acell 5.30 5.30 19.65615823 dilatmx 1.02 toldfe 1.0d-6 #Common data**************** ixc 11 kptopt 1 nshiftk 1 shiftk 0.0 0.0 0.5 ngkpt 6 6 6 ecut 30 ecutsm 0.5 ntime 50 iscf 7 nstep 50 nband 32 angdeg 90 90 120 spgroup 166 brvltt 0 occopt 3 tsmear 0.01 natom 9 typat 1 2 2 1 2 2 1 2 2 ntypat 2 znucl 26 7 xred -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 ........... ............ ........... 3.3333333333E-01 6.6666666667E-01 2.2599217437E-01 chkprim 0 #**************************************************************************** 1,1 Top On Fri, May 27, 2011 at 1:16 AM, Stefano de Gironcoli wrote: > I think the two structures are not the same, or some of the parameters > have non equivalent > values. > stefano > > > On 05/26/2011 08:50 PM, Sanjeev Gupta wrote: > > Dear Sir, > Thanks for reply. > > > On Thu, May 26, 2011 at 10:23 PM, Stefano de Gironcoli wrote: > > > with this input the Fe-N distance is some 1.2 A... I'm pretty sure it > cannot be the intended structure > Are you sure the system is not in crystal coordinate ? > stefano > > > Yes, its true that while looking from xcrysden particularly the bond > lengths between the Fe-N and N-N but i am very surprised why both ABINIT > and PWSCF code gives such vast Difference in calculated Pressure for the > identical geometry which is not cleared yet. Here the bond lenth Fe-N is > ~1.24Ang. > Please Suggest More. > > > > > On 05/26/2011 04:13 PM, Sanjeev Gupta wrote: > > Dear Maxim > > Thank for kind reply. > > My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I > am using the spacegroup 166 (R3(bar)M) space group with conventional unit > cell rather than primitive unit cell the lattice parameter is taken as below > 1. for abinit > > a=5.359168252 Bohr > b=5.359168252 Bohr > c=20.08294707 Bohr > > 2. for PWSCF > > ibrav=4, > celldm(1) = 5.359168242 Bohr > celldm(3) = 3.7474 > > Part of my input file is : > > PWSCF > > &control > calculation = 'scf' > prefix='FeN2', > restart_mode='from_scratch', > outdir='./' > pseudo_dir = '/', > tstress = .true. > tprnfor = .true. > etot_conv_thr = 1.0d-5, > forc_conv_thr = 1.0d-4, > / > &system > ibrav=4, > celldm(1) = 5.359168242, > celldm(3) = 3.7474 > nat=9, > ntyp=2, > nosym =.true., > ecutwfc = 20, > ecutrho=200, > occupations='smearing', > smearing='m-p', > degauss=0.001, > / > &electrons > mixing_mode = "local-TF", > mixing_beta = 0.700000, > conv_thr = 1.0d-10, > / > ATOMIC_SPECIES > Fe 55.845 Fe.pbe-sp-van.UPF > N 14.0067 N.pbe-van_ak.UPF > ATOMIC_POSITIONS > Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 > N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 > > .............................. > ............ > > N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 > K_POINTS automatic > 6 6 6 0 0 0 > > > Best Regards > > > Sanjay D. Gupta > Research Fellow > Department of Physics, > Bhavnagar University, Bhavnagar-364 022 > Gujarat, Mobile-9879666643email:guptasanjay_56 at yahoo.co.in > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > 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/20110527/19dc0e10/attachment-0001.htm From s.m.rezaeisani at gmail.com Fri May 27 08:33:56 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Fri, 27 May 2011 11:03:56 +0430 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation In-Reply-To: References: Message-ID: Dear Pine *.dyn0 exists and I had sent it before. On Thu, May 26, 2011 at 6:47 PM, lucking-pine wrote: > Hi? > In my opinion,this may be resule from 'recover' in ph.input.Most of times,I > choose recover=.ture. The ph.output is obtainde very fast,but dyn0 is often > lack.So I suggest you to set recover=.false.It maybe work. > > Bests, > Pine. > 2011/5/26 Seyed Mojtaba Rezaei Sani > >> Dear Lorenzo >> >> OK. There is no crash and my job is done completely without any time >> limitation termination. In output, frequencies are calculated for all 16 >> points, but the code write just *.dyn1-9 files, 7 q-points' *.dyn are >> missed. I have attached in & output and *.dyn0 files. >> >> On Wed, May 25, 2011 at 11:40 PM, Lorenzo Paulatto < >> lorenzo.paulatto at impmc.upmc.fr> wrote: >> >>> In data 25 maggio 2011 alle ore 21:02:57, Seyed Mojtaba Rezaei Sani >>> ha scritto: >>> > In *.dyn0, as a ph.x output file, 16 points have been selected from >>> my >>> > 6*6*6 >>> > chosen grid. But I get just *.dyn1-9. On the other word calculations >>> are >>> > done just for 9 q-points. If any more details are needed, please >>> notify >>> > me. >>> >>> Dear Seyed, >>> it could be anything, from you not just finding the files to crash in the >>> code or a time limit in your computing hardware. >>> >>> Keep in mind that nobody in this forum knows what is going on in you >>> computer. You MUST provide at the very least the input and output of your >>> job, otherwise we can only guess. >>> >>> As a side note: asking a good question takes a lot of time, often more >>> times that it takes to give a good answer. If it takes you only 30 >>> seconds >>> to write your email it is very unlikely to contain any good question. >>> >>> 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 >>> _______________________________________________ >>> 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 >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ========================================== Seyed Mojtaba Rezaei Sani Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel Lab: +98 311 391 3731 s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110527/9cd24bc8/attachment.htm From sclauzer at sissa.it Fri May 27 08:44:05 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 27 May 2011 08:44:05 +0200 Subject: [Pw_forum] very high pressure in scf In-Reply-To: References: <4DDE8574.8090504@sissa.it> <4DDEAE22.9000800@sissa.it> Message-ID: <7BD246D2-20CC-4253-BF90-3ABCA1A5663E@sissa.it> Do you know that there is a free tool converting input file from ab-init to PWscf format? You can download it from qe-forge. http://qe-forge.org/frs/?group_id=10 I've never used it, but you can give it a try to see if you get the same PWscf input. HTH GS Il giorno 27/mag/2011, alle ore 06.19, Sanjeev Gupta ha scritto: > Dear Sir, > > Thank you for kind reply. > > Here i am attaching the input file of ABINIT which gives less pressure for same structure as i have taken in PWSCF (I mentioned in my previous mail). Please look in this matter and suggest me. > > > #********** input file from abinit code...... > > ndtset 1 > acell 5.30 5.30 19.65615823 > dilatmx 1.02 > toldfe 1.0d-6 > #Common data**************** > ixc 11 > kptopt 1 > nshiftk 1 > shiftk 0.0 0.0 0.5 > ngkpt 6 6 6 > ecut 30 > ecutsm 0.5 > ntime 50 > iscf 7 > nstep 50 > nband 32 > angdeg 90 90 120 > spgroup 166 > brvltt 0 > occopt 3 > tsmear 0.01 > natom 9 > typat 1 2 2 1 2 2 1 2 2 > ntypat 2 > znucl 26 7 > xred > -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 > ........... > ............ > ........... > 3.3333333333E-01 6.6666666667E-01 2.2599217437E-01 > chkprim 0 > > > > > #**************************************************************************** > 1,1 Top > > > On Fri, May 27, 2011 at 1:16 AM, Stefano de Gironcoli wrote: > I think the two structures are not the same, or some of the parameters have non equivalent > values. > stefano > > > On 05/26/2011 08:50 PM, Sanjeev Gupta wrote: >> Dear Sir, >> Thanks for reply. >> >> >> On Thu, May 26, 2011 at 10:23 PM, Stefano de Gironcoli wrote: >> >>> with this input the Fe-N distance is some 1.2 A... I'm pretty sure it >>> cannot be the intended structure >>> Are you sure the system is not in crystal coordinate ? >>> stefano >>> >> Yes, its true that while looking from xcrysden particularly the bond >> lengths between the Fe-N and N-N but i am very surprised why both ABINIT >> and PWSCF code gives such vast Difference in calculated Pressure for the >> identical geometry which is not cleared yet. Here the bond lenth Fe-N is >> ~1.24Ang. >> Please Suggest More. >> >> >> >>> >> >>> >> >>> On 05/26/2011 04:13 PM, Sanjeev Gupta wrote: >>> >>> Dear Maxim >>> >>> Thank for kind reply. >>> >>> My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I >>> am using the spacegroup 166 (R3(bar)M) space group with conventional unit >>> cell rather than primitive unit cell the lattice parameter is taken as below >>> 1. for abinit >>> >>> a=5.359168252 Bohr >>> b=5.359168252 Bohr >>> c=20.08294707 Bohr >>> >>> 2. for PWSCF >>> >>> ibrav=4, >>> celldm(1) = 5.359168242 Bohr >>> celldm(3) = 3.7474 >>> >>> Part of my input file is : >>> >>> PWSCF >>> >>> &control >>> calculation = 'scf' >>> prefix='FeN2', >>> restart_mode='from_scratch', >>> outdir='./' >>> pseudo_dir = '/', >>> tstress = .true. >>> tprnfor = .true. >>> etot_conv_thr = 1.0d-5, >>> forc_conv_thr = 1.0d-4, >>> / >>> &system >>> ibrav=4, >>> celldm(1) = 5.359168242, >>> celldm(3) = 3.7474 >>> nat=9, >>> ntyp=2, >>> nosym =.true., >>> ecutwfc = 20, >>> ecutrho=200, >>> occupations='smearing', >>> smearing='m-p', >>> degauss=0.001, >>> / >>> &electrons >>> mixing_mode = "local-TF", >>> mixing_beta = 0.700000, >>> conv_thr = 1.0d-10, >>> / >>> ATOMIC_SPECIES >>> Fe 55.845 Fe.pbe-sp-van.UPF >>> N 14.0067 N.pbe-van_ak.UPF >>> ATOMIC_POSITIONS >>> Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 >>> N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 >>> >>> .............................. >>> ............ >>> >>> N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 >>> K_POINTS automatic >>> 6 6 6 0 0 0 >>> >>> >>> Best Regards >>> >>> >>> Sanjay D. Gupta >>> Research Fellow >>> Department of Physics, >>> Bhavnagar University, Bhavnagar-364 022 >>> Gujarat, Mobile-9879666643email:guptasanjay_56 at yahoo.co.in >>> >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> >>> >>> _______________________________________________ >>> 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 > > > _______________________________________________ > 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/20110527/242f651d/attachment.htm From zhaohscas at yahoo.com.cn Fri May 27 08:49:07 2011 From: zhaohscas at yahoo.com.cn (=?utf-8?B?57qi55SfIOi1tQ==?=) Date: Fri, 27 May 2011 14:49:07 +0800 (CST) Subject: [Pw_forum] How to obtain the binding energy ( in the unit of eV/Zn-O pair ) for Wurtsite ZnO? Message-ID: <608184.45685.qm@web15606.mail.cnb.yahoo.com> Hi all, I want to obtain the binding energy ( in the unit of eV/Zn-O pair ) for Wurtsite ZnO.? Considering that there are two different length of Zn-O bond, I cann't figure out how to calculate the binding energy in the unit ev/ZnO.? Any hints on this issue? Regards. Hongsheng. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110527/93d7ba69/attachment-0001.htm From physics.skgupta at gmail.com Fri May 27 09:11:13 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Fri, 27 May 2011 12:41:13 +0530 Subject: [Pw_forum] very high pressure in scf In-Reply-To: <7BD246D2-20CC-4253-BF90-3ABCA1A5663E@sissa.it> References: <4DDE8574.8090504@sissa.it> <4DDEAE22.9000800@sissa.it> <7BD246D2-20CC-4253-BF90-3ABCA1A5663E@sissa.it> Message-ID: Thanks Gabriele Sclauzero, I tried to do same, but when i compile QE-ABINIT, then i got one error. *gfortran: /opt/espresso-4.3/flib/error.o: No such file or directory* what is problem here. Best On Fri, May 27, 2011 at 12:14 PM, Gabriele Sclauzero wrote: > Do you know that there is a free tool converting input file from ab-init to > PWscf format? You can download it from qe-forge. > http://qe-forge.org/frs/?group_id=10 > I've never used it, but you can give it a try to see if you get the same > PWscf input. > > HTH > > GS > > > Il giorno 27/mag/2011, alle ore 06.19, Sanjeev Gupta ha scritto: > > Dear Sir, > > Thank you for kind reply. > > Here i am attaching the input file of ABINIT which gives less pressure for > same structure as i have taken in PWSCF (I mentioned in my previous mail). > Please look in this matter and suggest me. > > > #********** input file from abinit code...... > > ndtset 1 > acell 5.30 5.30 19.65615823 > dilatmx 1.02 > toldfe 1.0d-6 > #Common data**************** > ixc 11 > kptopt 1 > nshiftk 1 > shiftk 0.0 0.0 0.5 > ngkpt 6 6 6 > ecut 30 > ecutsm 0.5 > ntime 50 > iscf 7 > nstep 50 > nband 32 > angdeg 90 90 120 > spgroup 166 > brvltt 0 > occopt 3 > tsmear 0.01 > natom 9 > typat 1 2 2 1 2 2 1 2 2 > ntypat 2 > znucl 26 7 > xred > -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 > ........... > ............ > ........... > 3.3333333333E-01 6.6666666667E-01 2.2599217437E-01 > chkprim 0 > > > > > > #**************************************************************************** > > 1,1 Top > > > On Fri, May 27, 2011 at 1:16 AM, Stefano de Gironcoli wrote: > >> I think the two structures are not the same, or some of the parameters >> have non equivalent >> values. >> stefano >> >> >> On 05/26/2011 08:50 PM, Sanjeev Gupta wrote: >> >> Dear Sir, >> Thanks for reply. >> >> >> On Thu, May 26, 2011 at 10:23 PM, Stefano de Gironcoli wrote: >> >> >> with this input the Fe-N distance is some 1.2 A... I'm pretty sure it >> cannot be the intended structure >> Are you sure the system is not in crystal coordinate ? >> stefano >> >> >> Yes, its true that while looking from xcrysden particularly the bond >> lengths between the Fe-N and N-N but i am very surprised why both ABINIT >> and PWSCF code gives such vast Difference in calculated Pressure for the >> identical geometry which is not cleared yet. Here the bond lenth Fe-N is >> ~1.24Ang. >> Please Suggest More. >> >> >> >> >> On 05/26/2011 04:13 PM, Sanjeev Gupta wrote: >> >> Dear Maxim >> >> Thank for kind reply. >> >> My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I >> am using the spacegroup 166 (R3(bar)M) space group with conventional unit >> cell rather than primitive unit cell the lattice parameter is taken as below >> 1. for abinit >> >> a=5.359168252 Bohr >> b=5.359168252 Bohr >> c=20.08294707 Bohr >> >> 2. for PWSCF >> >> ibrav=4, >> celldm(1) = 5.359168242 Bohr >> celldm(3) = 3.7474 >> >> Part of my input file is : >> >> PWSCF >> >> &control >> calculation = 'scf' >> prefix='FeN2', >> restart_mode='from_scratch', >> outdir='./' >> pseudo_dir = '/', >> tstress = .true. >> tprnfor = .true. >> etot_conv_thr = 1.0d-5, >> forc_conv_thr = 1.0d-4, >> / >> &system >> ibrav=4, >> celldm(1) = 5.359168242, >> celldm(3) = 3.7474 >> nat=9, >> ntyp=2, >> nosym =.true., >> ecutwfc = 20, >> ecutrho=200, >> occupations='smearing', >> smearing='m-p', >> degauss=0.001, >> / >> &electrons >> mixing_mode = "local-TF", >> mixing_beta = 0.700000, >> conv_thr = 1.0d-10, >> / >> ATOMIC_SPECIES >> Fe 55.845 Fe.pbe-sp-van.UPF >> N 14.0067 N.pbe-van_ak.UPF >> ATOMIC_POSITIONS >> Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 >> N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 >> >> .............................. >> ............ >> >> N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 >> K_POINTS automatic >> 6 6 6 0 0 0 >> >> >> Best Regards >> >> >> Sanjay D. Gupta >> Research Fellow >> Department of Physics, >> Bhavnagar University, Bhavnagar-364 022 >> Gujarat, Mobile-9879666643email:guptasanjay_56 at yahoo.co.in >> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> _______________________________________________ >> 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* > > > _______________________________________________ > 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/20110527/eca232c5/attachment.htm From anupvthomas at gmail.com Fri May 27 09:41:19 2011 From: anupvthomas at gmail.com (ANUP THOMAS) Date: Fri, 27 May 2011 13:11:19 +0530 Subject: [Pw_forum] Dear Users Message-ID: Good Morning to all Would you please inform me, is it possible to do band strcuture calculatiuons using Hybrid Functionals (PWSCF) Look forward to hear from you. -- Regards Anup Thomas SRF 7123 Computational Chemistry Lab of I and PC Division Indian Institute of Chemical Technology Hyderabad 500007 India "Praise the Lord, all you nations; extol him, all you peoples. For great is his love toward us, and the faithfulness of the Lord endures forever. Praise the Lord" -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110527/51def36f/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Fri May 27 11:45:56 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 27 May 2011 11:45:56 +0200 Subject: [Pw_forum] How to obtain the excition binding energy of ZnO using pwscf? In-Reply-To: <100426.10921.qm@web15606.mail.cnb.yahoo.com> References: <100426.10921.qm@web15606.mail.cnb.yahoo.com> Message-ID: <201105271145.56976.giuseppe.mattioli@mlib.ism.cnr.it> You can not calculate excitonic properties by using pw.x You may have a (in-depth) look at the YAMBO or SAX post-processing codes. Please provide always your affiliation when posting. Giuseppe On Friday 27 May 2011 04:20:01 ?? ? wrote: > Hi all, > > It is well know that ZnO has a larger excition binding energy ( about 60 > meV ).? But could someone please give me some hints how to calculate this > property by using pwscf? > > Regards. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From giuseppe.mattioli at mlib.ism.cnr.it Fri May 27 11:51:33 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 27 May 2011 11:51:33 +0200 Subject: [Pw_forum] Dear Users In-Reply-To: References: Message-ID: <201105271151.33284.giuseppe.mattioli@mlib.ism.cnr.it> Dear Anup Thomas Well... yes and no. Please read carefully the README file contained in the yourQE/examples/EXX_example directory Yours Giuseppe P.S. Use meaningful subjects when posting... G. On Friday 27 May 2011 09:41:19 ANUP THOMAS wrote: > Good Morning to all > > Would you please inform me, is it possible to do band strcuture > calculatiuons using Hybrid Functionals (PWSCF) > > Look forward to hear from you. -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From baroni at sissa.it Fri May 27 11:56:22 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 27 May 2011 11:56:22 +0200 Subject: [Pw_forum] How to obtain the excition binding energy of ZnO using pwscf? In-Reply-To: <201105271145.56976.giuseppe.mattioli@mlib.ism.cnr.it> References: <100426.10921.qm@web15606.mail.cnb.yahoo.com> <201105271145.56976.giuseppe.mattioli@mlib.ism.cnr.it> Message-ID: <24DB3EEF-17E2-4739-BD03-DD13C8AC02DD@sissa.it> If I can add a comment to Giuseppe's reply, I would suggest that before asking what "a code" can or cannot calculate, one asks (oneself, in the first place) what the theory/approximations on which the code is based can or cannot calculate. If Hongsheng had done this exercise, he would have easily found the answer by himself, using the information that easily available. 1) standard dft does not give access to exciton binding energy (this is probably what Hongshen should think about and make sure to understand in the first place). 2) PWscf implements several flavors of standard dft 3) the conclusions are left to the reader as a simple exercise ;-) HTH - SB On May 27, 2011, at 11:45 AM, Giuseppe Mattioli wrote: > You can not calculate excitonic properties by using pw.x > You may have a (in-depth) look at the YAMBO or SAX post-processing codes. > Please provide always your affiliation when posting. > > Giuseppe > > > On Friday 27 May 2011 04:20:01 ?? ? wrote: >> Hi all, >> >> It is well know that ZnO has a larger excition binding energy ( about 60 >> meV ). But could someone please give me some hints how to calculate this >> property by using pwscf? >> >> Regards. > > > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: > _______________________________________________ > 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/20110527/1dfb5c9b/attachment.htm From degironc at sissa.it Fri May 27 12:00:33 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 27 May 2011 12:00:33 +0200 Subject: [Pw_forum] very high pressure in scf In-Reply-To: References: <4DDE8574.8090504@sissa.it> <4DDEAE22.9000800@sissa.it> Message-ID: <4DDF7641.4050102@sissa.it> dear Sanjeev Gupta I think you should find what is wrong with your input. my suggestion is to read the documentation of Abinit and QE and understand each variable you are setting and how they translate betwenn the codes. there used to be an input translator between the two codes that may still work although has not been used extensively (look in to qe-forge ->quantum espresso ->files ->QE-ABINIT converter) it may help to take a simpler system where you have less variable to test and the incrementally add complexity good luck stefano On 05/27/2011 06:19 AM, Sanjeev Gupta wrote: > Dear Sir, > > Thank you for kind reply. > > Here i am attaching the input file of ABINIT which gives less pressure for > same structure as i have taken in PWSCF (I mentioned in my previous mail). > Please look in this matter and suggest me. > > > #********** input file from abinit code...... > > ndtset 1 > acell 5.30 5.30 19.65615823 > dilatmx 1.02 > toldfe 1.0d-6 > #Common data**************** > ixc 11 > kptopt 1 > nshiftk 1 > shiftk 0.0 0.0 0.5 > ngkpt 6 6 6 > ecut 30 > ecutsm 0.5 > ntime 50 > iscf 7 > nstep 50 > nband 32 > angdeg 90 90 120 > spgroup 166 > brvltt 0 > occopt 3 > tsmear 0.01 > natom 9 > typat 1 2 2 1 2 2 1 2 2 > ntypat 2 > znucl 26 7 > xred > -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 > ........... > ............ > ........... > 3.3333333333E-01 6.6666666667E-01 2.2599217437E-01 > chkprim 0 > > > > > #**************************************************************************** > > 1,1 Top > > > On Fri, May 27, 2011 at 1:16 AM, Stefano de Gironcoliwrote: > >> I think the two structures are not the same, or some of the parameters >> have non equivalent >> values. >> stefano >> >> >> On 05/26/2011 08:50 PM, Sanjeev Gupta wrote: >> >> Dear Sir, >> Thanks for reply. >> >> >> On Thu, May 26, 2011 at 10:23 PM, Stefano de Gironcoli wrote: >> >> >> with this input the Fe-N distance is some 1.2 A... I'm pretty sure it >> cannot be the intended structure >> Are you sure the system is not in crystal coordinate ? >> stefano >> >> >> Yes, its true that while looking from xcrysden particularly the bond >> lengths between the Fe-N and N-N but i am very surprised why both ABINIT >> and PWSCF code gives such vast Difference in calculated Pressure for the >> identical geometry which is not cleared yet. Here the bond lenth Fe-N is >> ~1.24Ang. >> Please Suggest More. >> >> >> >> >> On 05/26/2011 04:13 PM, Sanjeev Gupta wrote: >> >> Dear Maxim >> >> Thank for kind reply. >> >> My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I >> am using the spacegroup 166 (R3(bar)M) space group with conventional unit >> cell rather than primitive unit cell the lattice parameter is taken as below >> 1. for abinit >> >> a=5.359168252 Bohr >> b=5.359168252 Bohr >> c=20.08294707 Bohr >> >> 2. for PWSCF >> >> ibrav=4, >> celldm(1) = 5.359168242 Bohr >> celldm(3) = 3.7474 >> >> Part of my input file is : >> >> PWSCF >> >> &control >> calculation = 'scf' >> prefix='FeN2', >> restart_mode='from_scratch', >> outdir='./' >> pseudo_dir = '/', >> tstress = .true. >> tprnfor = .true. >> etot_conv_thr = 1.0d-5, >> forc_conv_thr = 1.0d-4, >> / >> &system >> ibrav=4, >> celldm(1) = 5.359168242, >> celldm(3) = 3.7474 >> nat=9, >> ntyp=2, >> nosym =.true., >> ecutwfc = 20, >> ecutrho=200, >> occupations='smearing', >> smearing='m-p', >> degauss=0.001, >> / >> &electrons >> mixing_mode = "local-TF", >> mixing_beta = 0.700000, >> conv_thr = 1.0d-10, >> / >> ATOMIC_SPECIES >> Fe 55.845 Fe.pbe-sp-van.UPF >> N 14.0067 N.pbe-van_ak.UPF >> ATOMIC_POSITIONS >> Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 >> N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 >> >> .............................. >> ............ >> >> N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 >> K_POINTS automatic >> 6 6 6 0 0 0 >> >> >> Best Regards >> >> >> Sanjay D. Gupta >> Research Fellow >> Department of Physics, >> Bhavnagar University, Bhavnagar-364 022 >> Gujarat, Mobile-9879666643email:guptasanjay_56 at yahoo.co.in >> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> _______________________________________________ >> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> _______________________________________________ >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110527/0f3154d8/attachment-0001.htm From baroni at sissa.it Fri May 27 12:03:10 2011 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 27 May 2011 12:03:10 +0200 Subject: [Pw_forum] very high pressure in scf In-Reply-To: References: <4DDE8574.8090504@sissa.it> <4DDEAE22.9000800@sissa.it> <7BD246D2-20CC-4253-BF90-3ABCA1A5663E@sissa.it> Message-ID: <4ABA28F1-14E2-4AE1-BDE0-7F66C4FA1C05@sissa.it> Two problems: 1) as the compiler compiler/loader clearly states, it cannot find an object file called "error.o", which it expects to find in the flib/ directory. Compile error.f (or whatever it is called the source file for that that routine) and give it another try. 2) you are probably a bit too lazy. is it really that difficult to understand what each variable of your input file means and translate them by yourself from the abinig to the qe format? I am sure it won't take more that a few hours of work ...I can assure you that understanding what a code is doing for you is a rewarding experience ... SB On May 27, 2011, at 9:11 AM, Sanjeev Gupta wrote: > Thanks Gabriele Sclauzero, > > I tried to do same, but when i compile QE-ABINIT, then i got one error. > > gfortran: /opt/espresso-4.3/flib/error.o: No such file or directory > > what is problem here. > > Best > > > On Fri, May 27, 2011 at 12:14 PM, Gabriele Sclauzero wrote: > Do you know that there is a free tool converting input file from ab-init to PWscf format? You can download it from qe-forge. > http://qe-forge.org/frs/?group_id=10 > I've never used it, but you can give it a try to see if you get the same PWscf input. > > HTH > > GS > > > Il giorno 27/mag/2011, alle ore 06.19, Sanjeev Gupta ha scritto: > >> Dear Sir, >> >> Thank you for kind reply. >> >> Here i am attaching the input file of ABINIT which gives less pressure for same structure as i have taken in PWSCF (I mentioned in my previous mail). Please look in this matter and suggest me. >> >> >> #********** input file from abinit code...... >> >> ndtset 1 >> acell 5.30 5.30 19.65615823 >> dilatmx 1.02 >> toldfe 1.0d-6 >> #Common data**************** >> ixc 11 >> kptopt 1 >> nshiftk 1 >> shiftk 0.0 0.0 0.5 >> ngkpt 6 6 6 >> ecut 30 >> ecutsm 0.5 >> ntime 50 >> iscf 7 >> nstep 50 >> nband 32 >> angdeg 90 90 120 >> spgroup 166 >> brvltt 0 >> occopt 3 >> tsmear 0.01 >> natom 9 >> typat 1 2 2 1 2 2 1 2 2 >> ntypat 2 >> znucl 26 7 >> xred >> -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 >> ........... >> ............ >> ........... >> 3.3333333333E-01 6.6666666667E-01 2.2599217437E-01 >> chkprim 0 >> >> >> >> >> #**************************************************************************** >> 1,1 Top >> >> >> On Fri, May 27, 2011 at 1:16 AM, Stefano de Gironcoli wrote: >> I think the two structures are not the same, or some of the parameters have non equivalent >> values. >> stefano >> >> >> On 05/26/2011 08:50 PM, Sanjeev Gupta wrote: >>> Dear Sir, >>> Thanks for reply. >>> >>> >>> On Thu, May 26, 2011 at 10:23 PM, Stefano de Gironcoli wrote: >>> >>>> with this input the Fe-N distance is some 1.2 A... I'm pretty sure it >>>> cannot be the intended structure >>>> Are you sure the system is not in crystal coordinate ? >>>> stefano >>>> >>> Yes, its true that while looking from xcrysden particularly the bond >>> lengths between the Fe-N and N-N but i am very surprised why both ABINIT >>> and PWSCF code gives such vast Difference in calculated Pressure for the >>> identical geometry which is not cleared yet. Here the bond lenth Fe-N is >>> ~1.24Ang. >>> Please Suggest More. >>> >>> >>> >>>> >>> >>>> >>> >>>> On 05/26/2011 04:13 PM, Sanjeev Gupta wrote: >>>> >>>> Dear Maxim >>>> >>>> Thank for kind reply. >>>> >>>> My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I >>>> am using the spacegroup 166 (R3(bar)M) space group with conventional unit >>>> cell rather than primitive unit cell the lattice parameter is taken as below >>>> 1. for abinit >>>> >>>> a=5.359168252 Bohr >>>> b=5.359168252 Bohr >>>> c=20.08294707 Bohr >>>> >>>> 2. for PWSCF >>>> >>>> ibrav=4, >>>> celldm(1) = 5.359168242 Bohr >>>> celldm(3) = 3.7474 >>>> >>>> Part of my input file is : >>>> >>>> PWSCF >>>> >>>> &control >>>> calculation = 'scf' >>>> prefix='FeN2', >>>> restart_mode='from_scratch', >>>> outdir='./' >>>> pseudo_dir = '/', >>>> tstress = .true. >>>> tprnfor = .true. >>>> etot_conv_thr = 1.0d-5, >>>> forc_conv_thr = 1.0d-4, >>>> / >>>> &system >>>> ibrav=4, >>>> celldm(1) = 5.359168242, >>>> celldm(3) = 3.7474 >>>> nat=9, >>>> ntyp=2, >>>> nosym =.true., >>>> ecutwfc = 20, >>>> ecutrho=200, >>>> occupations='smearing', >>>> smearing='m-p', >>>> degauss=0.001, >>>> / >>>> &electrons >>>> mixing_mode = "local-TF", >>>> mixing_beta = 0.700000, >>>> conv_thr = 1.0d-10, >>>> / >>>> ATOMIC_SPECIES >>>> Fe 55.845 Fe.pbe-sp-van.UPF >>>> N 14.0067 N.pbe-van_ak.UPF >>>> ATOMIC_POSITIONS >>>> Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 >>>> N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 >>>> >>>> .............................. >>>> ............ >>>> >>>> N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 >>>> K_POINTS automatic >>>> 6 6 6 0 0 0 >>>> >>>> >>>> Best Regards >>>> >>>> >>>> Sanjay D. Gupta >>>> Research Fellow >>>> Department of Physics, >>>> Bhavnagar University, Bhavnagar-364 022 >>>> Gujarat, Mobile-9879666643email:guptasanjay_56 at yahoo.co.in >>>> >>>> >>>> _______________________________________________ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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/20110527/5edbc2bc/attachment.htm From giuseppe.mattioli at mlib.ism.cnr.it Fri May 27 12:04:22 2011 From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli) Date: Fri, 27 May 2011 12:04:22 +0200 Subject: [Pw_forum] is there a way to find the edge of conduction band from fermi level? In-Reply-To: References: Message-ID: <201105271204.23050.giuseppe.mattioli@mlib.ism.cnr.it> Dear M Alaii Please provide always your affiliation when posting. > I was wondering whether there is a way to guess what the edge of conduction > band is by the Fermi level that the software provides. It depends on the system. In the case of an insulator or semiconductor you should draw a reasonable band structure and compare with it the Ef value given by the code. You can always try to fill the bands by hand with the correct amount of electrons... In the case of insulating isolated systems (i.e., molecules) the LUMO orbital is just the first above the given Ef at gamma. In the case of metals or semimetals you should find that the Ef value crosses (one of) the bands. Of course you should also calculate a given number of unoccupied eigenstates, either by using a nbnd value greater than nelec/2, or by using some smearing scheme. Remember that enegy gaps (or HOMO-LUMO gaps) are affected by a static correlation error when using LDA or GGA approximations, so they often compare badly with optical gaps. HTH Giuseppe -- ******************************************************** - Article premier - Les hommes naissent et demeurent libres et ?gaux en droits. Les distinctions sociales ne peuvent ?tre fond?es que sur l'utilit? commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libert?, la propri?t?, la s?ret? et la r?sistance ? l'oppression. ******************************************************** ? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? ? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ? ? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ? ? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ? ? ?E-mail: From physics.skgupta at gmail.com Fri May 27 12:20:10 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Fri, 27 May 2011 15:50:10 +0530 Subject: [Pw_forum] very high pressure in scf In-Reply-To: <4ABA28F1-14E2-4AE1-BDE0-7F66C4FA1C05@sissa.it> References: <4DDE8574.8090504@sissa.it> <4DDEAE22.9000800@sissa.it> <7BD246D2-20CC-4253-BF90-3ABCA1A5663E@sissa.it> <4ABA28F1-14E2-4AE1-BDE0-7F66C4FA1C05@sissa.it> Message-ID: Dear Sir Thank for Your kind reply. I have successfully converted ABINIT to PWSCF. Herewith, I am putting my input file, here again i am getting pressure too large as compare in ABINIT. Kindly suggest me, why i am getting large pressure. &control calculation = 'scf' prefix='FeN2', restart_mode='from_scratch', outdir='./' pseudo_dir = '/home/sanjay/WORK/pseudo/', tstress = .true. tprnfor = .true. etot_conv_thr = 1.0d-5, forc_conv_thr = 1.0d-4, / &system ibrav=0, celldm(1) = 5.359168242, nat=9, ntyp=2, nosym =.true., ecutwfc = 60, occupations='smearing', smearing='fd', degauss=0.02, / &electrons mixing_beta = 0.4, conv_thr = 1.0d-10, / ATOMIC_SPECIES Fe 55.845 Fe.pbe-sp-van.UPF N 14.0067 N.pbe-van_ak.UPF CELL_PARAMETERS 5.0000000000E+00 0.0000000000E+00 0.0000000000E+00 -5.0000000000E-01 8.6602540378E-01 0.0000000000E+00 0.0000000000E+00 8.6602540378E-01 5.0000000000E+00 ATOMIC_POSITIONS {crystal} Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 N -1.8503717077E-17 -1.8503717077E-17 5.6000000000E-01 Fe 6.6666666667E-01 3.3333333333E-01 3.3333333333E-01 N 6.6666666667E-01 3.3333333333E-01 7.7333333333E-01 N 6.6666666667E-01 3.3333333333E-01 8.9333333333E-01 Fe 3.3333333333E-01 6.6666666667E-01 6.6666666667E-01 N 3.3333333333E-01 6.6666666667E-01 1.0666666667E-01 N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 K_POINTS automatic 6 6 6 0 0 0 Best On Fri, May 27, 2011 at 3:33 PM, Stefano Baroni wrote: > Two problems: > > 1) as the compiler compiler/loader clearly states, it cannot find an object > file called "error.o", which it expects to find in the flib/ directory. > Compile error.f (or whatever it is called the source file for that that > routine) and give it another try. > > 2) you are probably a bit too lazy. is it really that difficult to > understand what each variable of your input file means and translate them by > yourself from the abinig to the qe format? I am sure it won't take more that > a few hours of work ...I can assure you that understanding what a code is > doing for you is a rewarding experience ... > > SB > > On May 27, 2011, at 9:11 AM, Sanjeev Gupta wrote: > > Thanks Gabriele Sclauzero, > > I tried to do same, but when i compile QE-ABINIT, then i got one error. > > *gfortran: /opt/espresso-4.3/flib/error.o: No such file or directory* > > what is problem here. > > Best > > > On Fri, May 27, 2011 at 12:14 PM, Gabriele Sclauzero wrote: > >> Do you know that there is a free tool converting input file from ab-init >> to PWscf format? You can download it from qe-forge. >> http://qe-forge.org/frs/?group_id=10 >> I've never used it, but you can give it a try to see if you get the same >> PWscf input. >> >> HTH >> >> GS >> >> >> Il giorno 27/mag/2011, alle ore 06.19, Sanjeev Gupta ha scritto: >> >> Dear Sir, >> >> Thank you for kind reply. >> >> Here i am attaching the input file of ABINIT which gives less pressure for >> same structure as i have taken in PWSCF (I mentioned in my previous mail). >> Please look in this matter and suggest me. >> >> >> #********** input file from abinit code...... >> >> ndtset 1 >> acell 5.30 5.30 19.65615823 >> dilatmx 1.02 >> toldfe 1.0d-6 >> #Common data**************** >> ixc 11 >> kptopt 1 >> nshiftk 1 >> shiftk 0.0 0.0 0.5 >> ngkpt 6 6 6 >> ecut 30 >> ecutsm 0.5 >> ntime 50 >> iscf 7 >> nstep 50 >> nband 32 >> angdeg 90 90 120 >> spgroup 166 >> brvltt 0 >> occopt 3 >> tsmear 0.01 >> natom 9 >> typat 1 2 2 1 2 2 1 2 2 >> ntypat 2 >> znucl 26 7 >> xred >> -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 >> ........... >> ............ >> ........... >> 3.3333333333E-01 6.6666666667E-01 2.2599217437E-01 >> chkprim 0 >> >> >> >> >> >> #**************************************************************************** >> >> 1,1 Top >> >> >> On Fri, May 27, 2011 at 1:16 AM, Stefano de Gironcoli wrote: >> >>> I think the two structures are not the same, or some of the parameters >>> have non equivalent >>> values. >>> stefano >>> >>> >>> On 05/26/2011 08:50 PM, Sanjeev Gupta wrote: >>> >>> Dear Sir, >>> Thanks for reply. >>> >>> >>> On Thu, May 26, 2011 at 10:23 PM, Stefano de Gironcoli wrote: >>> >>> >>> with this input the Fe-N distance is some 1.2 A... I'm pretty sure it >>> cannot be the intended structure >>> Are you sure the system is not in crystal coordinate ? >>> stefano >>> >>> >>> Yes, its true that while looking from xcrysden particularly the bond >>> lengths between the Fe-N and N-N but i am very surprised why both ABINIT >>> and PWSCF code gives such vast Difference in calculated Pressure for the >>> identical geometry which is not cleared yet. Here the bond lenth Fe-N is >>> ~1.24Ang. >>> Please Suggest More. >>> >>> >>> >>> >>> On 05/26/2011 04:13 PM, Sanjeev Gupta wrote: >>> >>> Dear Maxim >>> >>> Thank for kind reply. >>> >>> My unit cell is as same in ABINIT as in pwscf in Bohr unit. In addition I >>> am using the spacegroup 166 (R3(bar)M) space group with conventional unit >>> cell rather than primitive unit cell the lattice parameter is taken as below >>> 1. for abinit >>> >>> a=5.359168252 Bohr >>> b=5.359168252 Bohr >>> c=20.08294707 Bohr >>> >>> 2. for PWSCF >>> >>> ibrav=4, >>> celldm(1) = 5.359168242 Bohr >>> celldm(3) = 3.7474 >>> >>> Part of my input file is : >>> >>> PWSCF >>> >>> &control >>> calculation = 'scf' >>> prefix='FeN2', >>> restart_mode='from_scratch', >>> outdir='./' >>> pseudo_dir = '/', >>> tstress = .true. >>> tprnfor = .true. >>> etot_conv_thr = 1.0d-5, >>> forc_conv_thr = 1.0d-4, >>> / >>> &system >>> ibrav=4, >>> celldm(1) = 5.359168242, >>> celldm(3) = 3.7474 >>> nat=9, >>> ntyp=2, >>> nosym =.true., >>> ecutwfc = 20, >>> ecutrho=200, >>> occupations='smearing', >>> smearing='m-p', >>> degauss=0.001, >>> / >>> &electrons >>> mixing_mode = "local-TF", >>> mixing_beta = 0.700000, >>> conv_thr = 1.0d-10, >>> / >>> ATOMIC_SPECIES >>> Fe 55.845 Fe.pbe-sp-van.UPF >>> N 14.0067 N.pbe-van_ak.UPF >>> ATOMIC_POSITIONS >>> Fe -1.8503717077E-17 -1.8503717077E-17 -1.8503717077E-17 >>> N -1.8503717077E-17 -1.8503717077E-17 4.4000000000E-01 >>> >>> .............................. >>> ............ >>> >>> N 3.3333333333E-01 6.6666666667E-01 2.2666666667E-01 >>> K_POINTS automatic >>> 6 6 6 0 0 0 >>> >>> >>> Best Regards >>> >>> >>> Sanjay D. Gupta >>> Research Fellow >>> Department of Physics, >>> Bhavnagar University, Bhavnagar-364 022 >>> Gujarat, Mobile-9879666643email:guptasanjay_56 at yahoo.co.in >>> >>> >>> _______________________________________________ >>> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> >>> >>> _______________________________________________ >>> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> _______________________________________________ >>> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> >>> _______________________________________________ >>> 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* >> >> >> _______________________________________________ >> 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 > > > > > _______________________________________________ > 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/20110527/f856414e/attachment.htm From giannozz at democritos.it Fri May 27 12:24:10 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Fri, 27 May 2011 12:24:10 +0200 Subject: [Pw_forum] very high pressure in scf In-Reply-To: References: <4DDE8574.8090504@sissa.it> <4DDEAE22.9000800@sissa.it> <7BD246D2-20CC-4253-BF90-3ABCA1A5663E@sissa.it> <4ABA28F1-14E2-4AE1-BDE0-7F66C4FA1C05@sissa.it> Message-ID: <1306491850.22550.2.camel@fe12lx.fisica.uniud.it> On Fri, 2011-05-27 at 15:50 +0530, Sanjeev Gupta wrote: > Herewith, I am putting my input file, here again i am getting pressure > too large as compare in ABINIT. > Kindly suggest me, why i am getting large pressure. do you get the same results with the same psedupotentials? You should. If you don't, you should first understand why P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From ttduyle at gmail.com Fri May 27 15:46:14 2011 From: ttduyle at gmail.com (Duy Le) Date: Fri, 27 May 2011 09:46:14 -0400 Subject: [Pw_forum] very high pressure in scf In-Reply-To: <1306491850.22550.2.camel@fe12lx.fisica.uniud.it> References: <4DDE8574.8090504@sissa.it> <4DDEAE22.9000800@sissa.it> <7BD246D2-20CC-4253-BF90-3ABCA1A5663E@sissa.it> <4ABA28F1-14E2-4AE1-BDE0-7F66C4FA1C05@sissa.it> <1306491850.22550.2.camel@fe12lx.fisica.uniud.it> Message-ID: 1. How does the pressure come out in the 2nd input? Coordinates of atoms in the first and 2nd inputs are different, hope you can see that. 2. What are these lattice parameter of the system calculated with ABINIT and QE? They are using different potential so the lattice parameters are not be the same. A few % of changing in lattice parameter (in comparison to equilibrium lattice parameter) can lead to a huge change in the pressure. -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" On Fri, May 27, 2011 at 6:24 AM, Paolo Giannozzi wrote: > On Fri, 2011-05-27 at 15:50 +0530, Sanjeev Gupta wrote: > >> Herewith, I am putting my input file, here again i am getting pressure >> too large as compare in ABINIT. >> Kindly suggest me, why i am getting large pressure. > > do you get the same results with the same psedupotentials? > You should. If you don't, you should first understand why > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From Lorenzo.Paulatto at impmc.upmc.fr Fri May 27 16:53:42 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Fri, 27 May 2011 16:53:42 +0200 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation In-Reply-To: References: Message-ID: On Fri, 27 May 2011 08:33:56 +0200, Seyed Mojtaba Rezaei Sani wrote: > *.dyn0 exists and I had sent it before. You did not send anything before. Apparently you forgot to attach the attachment. -- 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 trambui at u.boisestate.edu Fri May 27 20:05:52 2011 From: trambui at u.boisestate.edu (Tram Bui) Date: Fri, 27 May 2011 12:05:52 -0600 Subject: [Pw_forum] Pseudo-potential testing In-Reply-To: References: Message-ID: Dear Gabriele, Thank you for your respond. Just to make sure that I'm understanding your answer correctly, below is a shortcut on the output file of my PP testing: ---------------------- Testing the pseudopotential ---------------------- scalar relativistic calculation atomic number is 55.00 valence charge is 1.00 dft =PBE lsd =0 sic =0 latt =0 beta=0.20 tr2=1.0E-14 mesh =1251 r(mesh) = 101.25750 xmin = -7.00 dx = 0.01250 n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) 1 0 6S 1( 0.50) -0.17728 -0.17238 -0.00490 2 1 6P 1( 0.50) -0.07657 -0.07687 0.00030 3 2 5D 1( 0.00) -0.05580 -0.05081 -0.00499 eps = 8.5E-15 iter = 22 Etot = -15573.817276 Ry, -7786.908638 Ha, -211892.560039 eV Etotps = -0.217507 Ry, -0.108753 Ha, -2.959329 eV dEtot_ae = 0.049938 Ry dEtot_ps = 0.048795 Ry, Delta E= 0.001144 Ry Ekin = 0.080184 Ry, 0.040092 Ha, 1.090963 eV So I should look at the "De AE-PS (Ry)", which is the difference in the eigenvalues? or the "Delta E"? I assume it is the Delta E based on your respond. But am I correct? Regards, Tram On Thu, May 26, 2011 at 2:16 AM, Gabriele Sclauzero wrote: > > Il giorno 26/mag/2011, alle ore 01.00, Tram Bui ha scritto: > > Dear Paul, > In the file that I have attached here (Paul's note on PP > generation), under section 3.10: checking for transferability, you have > mentioned about the:"The error on total energy di?erences > between PP and AE results gives a feeling on how good the PP is." Do you > mean the difference in AE and PP eigenvalues? > > > No, I think here Paolo "Paul" Giannozzi really meant what you understood > first, but you didn't get it in the correct way. > You should really compare total energy differences, which means: > E_2(AE) - E_1(AE) versus E_2(PS) - E_1(PS) > where 1 and 2 label two different electronic configurations, and NOT > E_1(PS) versus E_1(AE) > as you are probably trying to do. > > because I saw the Etot and Etotps are huge difference > > > This is often the case, given the high degree of freedom in the choice of > PP parameters (especially for the local potential, I suppose). > > but their eigenvalue (e, Ry) are closed. > > > Indeed this is how it should be, since the modern PP are designed to > reproduce the scattering properties of the AE atomic potential as best as > possible. > > > Dear QE users, > I'm trying to test the Cs' US PP with reference configuration of :[Xe] > 6s1 5d0 6p0. To test the PP, I'm using these five configuration (just by > guessing): > configts(1)= '6s1 6p0 5d0' > configts(2)= '6s0.5 6p0.5 5d0' > configts(3)= '6s0.5 6p0 5d0.5' > configts(4)= '6s0 6p1 5d0' > configts(5)= '6s0 6p0 5d1' > My questions are: > - how to choose the configurations for PP testing based on the reference > one? is there a strategy or some sort? > > > Use some reasonable configurations (remove or add one electron, or a > fraction of it, move one or more electrons between different orbitals, ...). > The choice may also be driven by the class of materials that you are going > to study (e.g. ionic crystals). > > - how many configurations are enough for the test? > > > That's up to you... 5 look enough for me. Don't forget to do some testing > with the solid state code (e.g. bond distance of dimers, lattice constant of > simple solids...). > > > HTH > > > GS > > > Thank you very much, > > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > _______________________________________________ > 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 > > -- 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/20110527/d3fc2c22/attachment.htm From amin.torabi at gmail.com Fri May 27 20:26:44 2011 From: amin.torabi at gmail.com (Amin Torabi) Date: Fri, 27 May 2011 14:26:44 -0400 Subject: [Pw_forum] energy/force/stress obtained from scf versus vc-relax Message-ID: Dear all, I did a vc-relax calculation. Then, I used the cell_parameters and atomic_positions obtained at the end of vc-relax to do an scf calculation. I didn't change any other settings, like k-point or ecutoff. However, the total energy, the total force and the total stress obtained from the scf calculation are different form the values obtained at the end of the vc-relax calculation. (The vc-relax values are lower.) Why is it so? Thanks is advance. Amin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110527/8a7bb8f7/attachment.htm From antonio.msj1 at gmail.com Fri May 27 20:48:08 2011 From: antonio.msj1 at gmail.com (Antonio) Date: Fri, 27 May 2011 15:48:08 -0300 Subject: [Pw_forum] Electro-optical coefficients Message-ID: Dear QE users, Somebody knows how to calculate the electro-optical coefficients (i.e. beta) by the phonon code for the Raman calculation within PWSCF? 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 nkxirainbow at gmail.com Sat May 28 04:14:15 2011 From: nkxirainbow at gmail.com (xirainbow) Date: Sat, 28 May 2011 10:14:15 +0800 Subject: [Pw_forum] energy/force/stress obtained from scf versus vc-relax In-Reply-To: References: Message-ID: Dear Amin: On Sat, May 28, 2011 at 2:26 AM, Amin Torabi wrote: > Dear all, > > I did a vc-relax calculation. Then, I used the cell_parameters and > atomic_positions obtained at the end of vc-relax to do an scf calculation. I > didn't change any other settings, like k-point or ecutoff. > However, the total energy, the total force and the total stress obtained > from the scf calculation are different form the values obtained at the end > of the vc-relax calculation. (The vc-relax values are lower.) > Why is it so? > You are right. When you do vc-relax, the G points contained in wave-function does not change with the cell parameters(That means the energy cutoff changes when cell parameters change during vc-relax). When you do scf after vc-relax, the cell parameters of scf is different from that of vc-relax. Therefore, the G points contained in wave-function of scf differs from that of vc-relax. Usually, you should do the second vc-relax if the cell parameters change a lot. After the second vc-relax, the force/stress of scf will be close to that of second vc-relax. > > > Thanks is advance. > > Amin > > _______________________________________________ > 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/20110528/a882f756/attachment.htm From leommj at usp.br Sat May 28 05:35:49 2011 From: leommj at usp.br (Leonardo Matheus Marion Jorge) Date: Sat, 28 May 2011 00:35:49 -0300 Subject: [Pw_forum] HSE Message-ID: <75A8B230-489B-410B-A944-D42345DCA01F@usp.br> Hi, I would like to know exactly which "version" of HSE is implemented on Quantum-ESPRESSO. In the original HSE work a value for the screening parameter w is used, but on an errata another value is given. In recent publications they are usually called HSE03 (which uses w_{HF}=0.15/sqrt(2) and w_{PBE}=0.15 x 2^(1/3) ) and HSE06 (w_{HF}=w_{PBE}=0.15). Looking at the code insde funct.f90 I found "screening_parameter = 0.106", which is the value of w_{HF} used on HSE03, which induces me to think that it's this "version" that is implemented. I couldn't find though if this value is used also for w_{PBE} (which would be a mistake) or not (and w_{PBE} is corrected at a later point in calculation). Can someone give me some info? Thanks, Leonardo Jorge PhD Student Instituto de F?sica, Universidade de S?o Paulo, Brazil From member at linkedin.com Sat May 28 05:35:10 2011 From: member at linkedin.com (BAC PHUNG via LinkedIn) Date: Sat, 28 May 2011 03:35:10 +0000 (UTC) Subject: [Pw_forum] Invitation to connect on LinkedIn Message-ID: <1103979661.170758.1306553710954.JavaMail.app@ela4-bed37.prod> LinkedIn ------------ BAC PHUNG requested to add you as a connection on LinkedIn: ------------------------------------------ veronica, I'd like to add you to my professional network on LinkedIn. - BAC Accept invitation from BAC PHUNG http://www.linkedin.com/e/-iqpnjm-go80cfhj-2s/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I50390134_60/pmpxnSRJrSdvj4R5fnhv9ClRsDgZp6lQs6lzoQ5AomZIpn8_c3pvd3cNc3APc3l9bQxjrDlip4AUbPgVejgTejAOc3cLrCBxbOYWrSlI/EML_comm_afe/ View invitation from BAC PHUNG http://www.linkedin.com/e/-iqpnjm-go80cfhj-2s/XAAkmOm8d3sw5mZYSULFbcFqV9UKwx/blk/I50390134_60/0MdBYQcP4MejcMdkALqnpPbOYWrSlI/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-go80cfhj-2s/ask/inv-23/ -- (c) 2011, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110528/63e41fd7/attachment.htm From zhaohscas at yahoo.com.cn Sat May 28 20:27:08 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Sat, 28 May 2011 14:27:08 -0400 Subject: [Pw_forum] The difference between binding energy and cohesive energy. Message-ID: <4DE13E7C.3050401@yahoo.com.cn> Hi all, Does the binding energy and cohesive energy mean the same thing or not? From here: http://www.physicsforums.com/showthread.php?t=300117 I find the following explains: Binding energy - the energy gained from chemical binding, usually measured against the element in its 'pure' form, e.g. an O2 molecule for oxygen. Cohesive energy - the binding energy for the atoms of a crystal, measured against the state of neutral free atoms. But, I also read some references which regards them as same thing. Any hints? Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From mohnish.iitk at gmail.com Sat May 28 08:44:54 2011 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Sat, 28 May 2011 12:14:54 +0530 Subject: [Pw_forum] How to obtain the binding energy ( in the unit of eV/Zn-O pair ) for Wurtsite ZnO? In-Reply-To: <608184.45685.qm@web15606.mail.cnb.yahoo.com> References: <608184.45685.qm@web15606.mail.cnb.yahoo.com> Message-ID: Dear Hongsheng, All the four bonds in ZnO wurtzite are equivalent. So to calculate the binding energy you have to use the below formula : E_{binding-ZnO}=E{calculated-ZnO-wurtzite}-E_{Zn_{crystal-total}}-E_{E(1/2*O2}}. Remember that you have to do spin-polarised calculation for O2 otherwise it will give wrong answer. Binding energy definition is same as above. And cohesive energy is the difference in energy between the energy of crystal and corresponding species in isolated phases. Below are the some references. http://arxiv.org/ftp/cond-mat/papers/0610/0610002.pdf http://prb.aps.org/pdf/PRB/v70/i5/e054104 On Fri, May 27, 2011 at 12:19 PM, ?? ? wrote: > Hi all, > > I want to obtain the binding energy ( in the unit of eV/Zn-O pair ) for > Wurtsite ZnO. Considering that there are two different length of Zn-O bond, > I cann't figure out how to calculate the binding energy in the unit ev/ZnO. > Any hints on this issue? > > Regards. > Hongsheng. > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110528/083cd09e/attachment.htm From giannozz at democritos.it Sat May 28 09:31:55 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sat, 28 May 2011 09:31:55 +0200 Subject: [Pw_forum] Electro-optical coefficients In-Reply-To: References: Message-ID: <8FE08C47-AB04-4DD1-86B8-63AD567FB353@democritos.it> On May 27, 2011, at 20:48 , Antonio wrote: > Somebody knows how to calculate the electro-optical coefficients (i.e. > beta) by the phonon code for the Raman calculation within PWSCF? elop=.true. (see example15) 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 BarnardEP at ufs.ac.za Sat May 28 10:35:35 2011 From: BarnardEP at ufs.ac.za (Egbert Barnard) Date: Sat, 28 May 2011 10:35:35 +0200 Subject: [Pw_forum] NEB error: unexpected dimension in ngg Message-ID: <4DE0CFF70200009A0002FA90@gwinter.ufs.ac.za> I am performing a NEB calculation on a Fe-S system and after the calculation has run for a few hours I get the following error. task # 22 from igk_l2g_kdip : error # 1 unexpected dimension in ngg Any help solving this problem would be greatly appreciated Pieter Barnard University of the Free State South Africa _____________________________________________________________________ University of the Free State: This message and its contents are subject to a disclaimer. Please refer to http://www.ufs.ac.za/disclaimer for full details. Universiteit van die Vrystaat: Hierdie boodskap en sy inhoud is aan 'n vrywaringsklousule onderhewig. Volledige besonderhede is by http://www.ufs.ac.za/vrywaring beskikbaar. _____________________________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110528/c0d13d0f/attachment.htm From s.m.rezaeisani at gmail.com Sat May 28 12:44:05 2011 From: s.m.rezaeisani at gmail.com (Seyed Mojtaba Rezaei Sani) Date: Sat, 28 May 2011 15:14:05 +0430 Subject: [Pw_forum] Insufficient q-points be calculated by phonon calculation In-Reply-To: References: Message-ID: Dear all Thanks to all. I've run the job again and the problem has been disappeared. On Fri, May 27, 2011 at 7:38 PM, Seyed Mojtaba Rezaei Sani < s.m.rezaeisani at gmail.com> wrote: > This is the fourth time that I send the files. I guess the code does not > make *.dyn* for more than 9, i.e. two digit numbers. > > > On Fri, May 27, 2011 at 7:23 PM, Lorenzo Paulatto < > Lorenzo.Paulatto at impmc.upmc.fr> wrote: > >> On Fri, 27 May 2011 08:33:56 +0200, Seyed Mojtaba Rezaei Sani >> wrote: >> > *.dyn0 exists and I had sent it before. >> >> You did not send anything before. Apparently you forgot to attach the >> attachment. >> >> -- >> 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 >> > > > > -- > ========================================== > Seyed Mojtaba Rezaei Sani > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology > 84156-83111 Isfahan, Iran > Tel Lab: +98 311 391 3731 > s.rezaeisani at ph.iut.ac.ir > =========================================== > > -- ========================================== Seyed Mojtaba Rezaei Sani Computational Condensed Matter Research Lab Physics Department, Isfahan University of Technology 84156-83111 Isfahan, Iran Tel Lab: +98 311 391 3731 s.rezaeisani at ph.iut.ac.ir =========================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110528/2f8395e4/attachment.htm From zhaohscas at yahoo.com.cn Sun May 29 01:03:11 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Sat, 28 May 2011 19:03:11 -0400 Subject: [Pw_forum] How to obtain the binding energy ( in the unit of eV/Zn-O pair ) for Wurtsite ZnO? In-Reply-To: References: <608184.45685.qm@web15606.mail.cnb.yahoo.com> Message-ID: <4DE17F2F.90305@yahoo.com.cn> On 05/28/2011 02:44 AM, mohnish pandey wrote: > Dear Hongsheng, > All the four bonds in ZnO wurtzite are equivalent. But the four bonds have different bond lengths: the bond length parallel to c axis is different from that of the other two bonds. Why can you say are equivalent? > So to calculate the binding energy you have to use the below formula : > E_{binding-ZnO}=E{calculated-ZnO-wurtzite}-E_{Zn_{crystal-total}}-E_{E(1/2*O2}}. > Remember that you have to do spin-polarised calculation for O2 > otherwise it will give wrong answer. I've learned that this is due to O atom's open-shell configuration. Than what is the initial spin should I use for O2? Furthermore, for ZnO wurtzite, should I do spin-polarised calculation or not? > Binding energy definition is same as above. And cohesive energy is the > difference in energy between the energy of crystal and corresponding > species in isolated phases. Below are the some references. Do you mean, for the calculation of cohesive energy, I should use the big box model, then put one Zn in the big box, and O atom in another box to obtain the total energy of each isolated phases? > http://arxiv.org/ftp/cond-mat/papers/0610/0610002.pdf > http://prb.aps.org/pdf/PRB/v70/i5/e054104 Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China From bdslipun at gmail.com Sat May 28 14:08:37 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sat, 28 May 2011 17:38:37 +0530 Subject: [Pw_forum] problem on phonon Message-ID: sir i used to calculate the phonon calculation on a 4*4*4 grid in cscl phase but the unstability persists upto 500 gpa but it is the thermodyanamic stability after 140 gpa kpoints 24*24*24 what may be reseon i donot know please help me -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110528/d72e13ef/attachment.htm From physics.skgupta at gmail.com Sat May 28 14:17:11 2011 From: physics.skgupta at gmail.com (Sanjeev Gupta) Date: Sat, 28 May 2011 17:47:11 +0530 Subject: [Pw_forum] problem on phonon In-Reply-To: References: Message-ID: Dear Sahoo, Without knowing your input file, how one can judge. Please provide your input file. Further, not fully optimization may be one reason. Best SKG Dept. of Phys. Bhavnagar University Gujarat On Sat, May 28, 2011 at 5:38 PM, bhabya sahoo wrote: > sir > i used to calculate the phonon calculation on a 4*4*4 grid in cscl phase > but the unstability persists upto 500 gpa > but it is the thermodyanamic stability after 140 gpa kpoints 24*24*24 > what may be reseon i donot know > please help me > > _______________________________________________ > 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/20110528/947b2660/attachment.htm From hannu.komsa at epfl.ch Sat May 28 16:04:02 2011 From: hannu.komsa at epfl.ch (hannu.komsa at epfl.ch) Date: Sat, 28 May 2011 16:04:02 +0200 Subject: [Pw_forum] HSE In-Reply-To: References: Message-ID: <20110528160402.85315wql7s5i40cy@webmail.epfl.ch> Hi Leonardo, It is HSE06. I'm not sure where you got the value 0.15 bohr^-1 for HSE06. You can see in Krukau et al., JCP 125, 224106 (2006), that they say to use 0.11 bohr^-1 (or 0.15/sqrt(2)). (Also compare, in VASP they use 0.2 Angstrom^-1.) The same value is used for both PBE and HF parts. Shameless plug: some small details about the implementation can also be found in Komsa et al., PRB 81, 205118 (2010). Best regards, Hannu-Pekka Komsa EPFL, Switzerland > I would like to know exactly which "version" of HSE is implemented > on Quantum-ESPRESSO. > In the original HSE work a value for the screening parameter w is > used, but on an errata another value is given. > > In recent publications they are usually called HSE03 (which uses > w_{HF}=0.15/sqrt(2) and w_{PBE}=0.15 x 2^(1/3) ) and HSE06 > (w_{HF}=w_{PBE}=0.15). > > Looking at the code insde funct.f90 I found "screening_parameter = > 0.106", which is the value of w_{HF} used on HSE03, which induces me > to think that it's this "version" that is implemented. > I couldn't find though if this value is used also for w_{PBE} (which > would be a mistake) or not (and w_{PBE} is corrected at a later > point in calculation). > > Can someone give me some info? From bdslipun at gmail.com Sat May 28 17:46:40 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sat, 28 May 2011 21:16:40 +0530 Subject: [Pw_forum] problem on phonon In-Reply-To: References: Message-ID: i am using quantum espresso static calculation obeys thermdyanamic stability transition from B1 to B2 transition at 138 gpa so ihave used 24 24 24 kpoint grid for phonon in B2 phase is calculated 4 4 4 grid by linear response calculation but why the instability (negative frequency in phonon ) upto 450 gpa i have used pbe psudo potentials also the lattice constant is exact for experimental data can metastability have negative frequency so why this occures optimisation is ok other problem why free energy is not coming for unstable phase for qha code in quantum espresso replay immidiate if u have solution On Sat, May 28, 2011 at 5:38 PM, bhabya sahoo wrote: > sir > i used to calculate the phonon calculation on a 4*4*4 grid in cscl phase > but the unstability persists upto 500 gpa > but it is the thermodyanamic stability after 140 gpa kpoints 24*24*24 > what may be reseon i donot know > please help me > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110528/54fd37f5/attachment-0001.htm From degironc at sissa.it Sat May 28 18:06:23 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sat, 28 May 2011 18:06:23 +0200 Subject: [Pw_forum] problem on phonon In-Reply-To: References: Message-ID: <4DE11D7F.7010102@sissa.it> Dear Bhabya Sahoo, your very stingy use of punctuation make quite difficult (at least for me) to follow your request... Take your time and try to make you clear providing more detailed information about your system, what is your aim, what is the problem, what are the tests you have done. No one is going to spend more time in thinking about your problem than you do in explaining it. Please provide your affiliation. stefano - Stefano de Gironcoli, SISSA and DEMOCRITOS On 05/28/2011 05:46 PM, bhabya sahoo wrote: > i am using quantum espresso static calculation obeys thermdyanamic stability > transition from B1 to B2 transition at 138 gpa so ihave used 24 24 24 > kpoint grid for phonon in B2 phase is calculated 4 4 4 grid by linear > response calculation but why the instability (negative frequency in phonon ) > upto 450 gpa i have used pbe psudo potentials also the lattice constant is > exact for experimental data > can metastability have negative frequency so why this occures > optimisation is ok > other problem why free energy is not coming for unstable phase for qha code > in quantum espresso > replay immidiate if u have solution > On Sat, May 28, 2011 at 5:38 PM, bhabya sahoo wrote: > >> sir >> i used to calculate the phonon calculation on a 4*4*4 grid in cscl phase >> but the unstability persists upto 500 gpa >> but it is the thermodyanamic stability after 140 gpa kpoints 24*24*24 >> what may be reseon i donot know >> please help me >> > > > _______________________________________________ > 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/20110528/a0b31bdf/attachment.htm From lyue at gmx.net Sat May 28 18:42:45 2011 From: lyue at gmx.net (Lun Yue) Date: Sat, 28 May 2011 18:42:45 +0200 Subject: [Pw_forum] question about the convergence of eigenvalues Message-ID: <20110528164245.124420@gmx.net> Hello, dear pwscf users: I have a question about the convergence of eigenvalues. In section 11.1.0.24 of the user guide, it is mentioned that a warning of N eigenvectors not converged may signal serious trouble if it's presented in the last steps of self-consistency. (http://www.quantum-espresso.org/user_guide/node52.html#SECTION0001210240000000000000) But how about the non-scf calculations? In the bands and nscf calculations I got warning messanges as following: **example in band calculation (calculation = 'bands'): Computing kpt #: 28 c_bands: 1 eigenvalues not converged **example in nscf calculation (calculation = 'nscf'): Computing kpt #: 144 c_bands: 2 eigenvalues not converged Are they acceptable? Thank you and best regards, Lun Yue -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de From bdslipun at gmail.com Sat May 28 19:22:27 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sat, 28 May 2011 22:52:27 +0530 Subject: [Pw_forum] problem on phonon In-Reply-To: <4DE11D7F.7010102@sissa.it> References: <4DE11D7F.7010102@sissa.it> Message-ID: sir i am using quantum espresso 4.3 version i want to study the phase transition of yitrium nitride(yn) first by doing scf calculation at 0k i found a phase transition of B1 to B2 transition at 137 gpa for this i used a 14*14*14 kpoints mesh and convergence achived for scf is 10^-9 i used GGA psudo potentials of pbe type avalable in code of espresso website for y and n but when i did the calculation for phonon dispersion B2 stucter instablity (negative frequency ) in phonon spectrum continues upto 500 gpa why ? for this i used 4*4*4* mesh q points for dyanamical matrices i have incresed further but nothing results On Sat, May 28, 2011 at 9:36 PM, Stefano de Gironcoli wrote: > Dear Bhabya Sahoo, > > your very stingy use of punctuation make quite difficult (at least for > me) to follow your request... > Take your time and try to make you clear providing more detailed > information about your system, what is your aim, what is the problem, what > are the tests you have done. > No one is going to spend more time in thinking about your problem than > you do in explaining it. > > Please provide your affiliation. > > stefano > - > Stefano de Gironcoli, SISSA and DEMOCRITOS > > > On 05/28/2011 05:46 PM, bhabya sahoo wrote: > > i am using quantum espresso static calculation obeys thermdyanamic stability > transition from B1 to B2 transition at 138 gpa so ihave used 24 24 24 > kpoint grid for phonon in B2 phase is calculated 4 4 4 grid by linear > response calculation but why the instability (negative frequency in phonon ) > upto 450 gpa i have used pbe psudo potentials also the lattice constant is > exact for experimental data > can metastability have negative frequency so why this occures > optimisation is ok > other problem why free energy is not coming for unstable phase for qha code > in quantum espresso > replay immidiate if u have solution > On Sat, May 28, 2011 at 5:38 PM, bhabya sahoo wrote: > > > sir > i used to calculate the phonon calculation on a 4*4*4 grid in cscl phase > but the unstability persists upto 500 gpa > but it is the thermodyanamic stability after 140 gpa kpoints 24*24*24 > what may be reseon i donot know > please help me > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > _______________________________________________ > 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/20110528/da419bf8/attachment.htm From amin.torabi at gmail.com Sun May 29 05:51:20 2011 From: amin.torabi at gmail.com (Amin Torabi) Date: Sat, 28 May 2011 23:51:20 -0400 Subject: [Pw_forum] enthalpy in damped dynamic Message-ID: Dear all, When I use bfgs algorithm for ion_dynamics in vc-relax calculation, the enthalpy is calculated and can be found in the output file. However, it seems that no enthalpy information is provided when damped dynamics are used. Why is it so? Thanks in advance, Amin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110528/ae0ef0d3/attachment.htm From kirtinandan07 at gmail.com Sun May 29 08:53:20 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Sun, 29 May 2011 12:23:20 +0530 Subject: [Pw_forum] installing QE In-Reply-To: <698746fe.148a8.1302a683206.Coremail.flux_ray12@163.com> References: <698746fe.148a8.1302a683206.Coremail.flux_ray12@163.com> Message-ID: Dear PWSCF users Thanks for advising to install mpich. I installed mpich2 in my machine and the i ran the espresso-4.3_examples. Many programme were succesfully done but may came out with error. Foe eg. /home/Software/espresso-4.3_examples/examples/example14 : starting This example shows how to use pw.x, ph.x and d3.x to calculate the third-order expansion coefficients of the total energy of Si. executables directory: /home/Software/espresso-4.3/bin pseudo directory: /home/Software/pseudo temporary directory: ./tmp checking that needed directories and files exist... done running pw.x as: mpirun -np 4 /home/Software/espresso-4.3/bin/pw.x running ph.x as: mpirun -np 4 /home/Software/espresso-4.3/bin/ph.x running d3.x as: mpirun -np 4 /home/Software/espresso-4.3/bin/d3.x cleaning ./tmp... done running the scf calculation for Si... done running the phonon calculation for Si at Gamma...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 application called MPI_Abort(MPI_COMM_WORLD, 0) - process 3 application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 Error condition encountered during test: exit status = 15 Aborting many eg (15,18, ..) showed the same error. what can be the possible error. thanks in advance Vicky singh 2011/5/26 GAO Zhe > Installing OpenMPI or MPICH2 firstly, then you can compile parrallel > version PWscf. > When you run it with multi-cores, using mpirun -n $CoreNum pw.x -npool > $PoolNum > > > At 2011-05-25 12:55:10?"vicky singh" wrote: > > Hi > I have recently got a new system with i5 processor. Since it has 4 > processor how can i install QE such that i can run parallel processing. > Documentation says just to use ./configure and make to be done for > compiling. will these command when run will consider the system > configuration and install parallel version. > > Thanks for suggestion in advance. > > Vicky singh > research student > Bangalore > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > D -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110529/9889a128/attachment.htm From degironc at sissa.it Sun May 29 12:53:38 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 29 May 2011 12:53:38 +0200 Subject: [Pw_forum] enthalpy in damped dynamic In-Reply-To: References: Message-ID: <4DE225B2.6060307@sissa.it> On 05/29/2011 05:51 AM, Amin Torabi wrote: > Dear all, > > When I use bfgs algorithm for ion_dynamics in vc-relax calculation, the > enthalpy is calculated and can be found in the output file. However, it > seems that no enthalpy information is provided when damped dynamics are > used. Why is it so? I think that what is printed as Etot is actually Enthalpy in the case of P/=0 stefano - Stefano de Gironcoli - SISSA and DEMOCRITOS > Thanks in advance, > > > Amin > > > > _______________________________________________ > 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/20110529/c1baaa2c/attachment.htm From bdslipun at gmail.com Sun May 29 13:27:15 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 29 May 2011 16:57:15 +0530 Subject: [Pw_forum] phonon free energy Message-ID: sir i am using quantum espresso 4.3 version QHA is part of this software why the phonon free energy is not coming for unstable phases (negative frequency in phonon spectrum )but it comes when there will be all positive frequency for which i canot compare the gibbs free energy of two phases -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110529/2eab42c4/attachment.htm From degironc at sissa.it Sun May 29 13:46:26 2011 From: degironc at sissa.it (Stefano de Gironcoli) Date: Sun, 29 May 2011 13:46:26 +0200 Subject: [Pw_forum] phonon free energy In-Reply-To: References: Message-ID: <4DE23212.4080402@sissa.it> because QHA cannot be defined for unstable structures. stefano On 05/29/2011 01:27 PM, bhabya sahoo wrote: > sir > i am using quantum espresso 4.3 version > QHA is part of this software > why the phonon free energy is not coming for unstable phases (negative > frequency in phonon spectrum )but it comes when there will be all positive > frequency > for which i canot compare the gibbs free energy of two phases > > > > _______________________________________________ > 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/20110529/1af7afb9/attachment.htm From farzad_c81 at yahoo.com Sun May 29 13:52:38 2011 From: farzad_c81 at yahoo.com (Farzad Molani) Date: Sun, 29 May 2011 04:52:38 -0700 (PDT) Subject: [Pw_forum] sumpdos.x Message-ID: <28007.81522.qm@web125903.mail.ne1.yahoo.com> Hi QE users, I want to sum resalts from projwfc.x by sumpdos.x. I should say I read pwforum and examples and usergide from PWSCF site,?but I don't know how? make an input file for sumpdos.x. please help me and give an example clearly. thanks in advance. Farzad Molani, Ph.D Student, Department of Theoretical Physical Chemistry, K. N. Toosi University of Technology, Tehran, Iran. Tel.: 009891 4442 3308 Tel.: 009821 2306 4280 Fax: 009821 2285 3650 Web: http://www.chem.kntu.ac.ir/~sjalili:/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110529/60b44b90/attachment.htm From bdslipun at gmail.com Sun May 29 13:59:31 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 29 May 2011 17:29:31 +0530 Subject: [Pw_forum] problem on phonon In-Reply-To: References: Message-ID: On Sat, May 28, 2011 at 5:38 PM, bhabya sahoo wrote: > sir > i used to calculate the phonon calculation on a 4*4*4 grid in cscl phase > but the unstability persists upto 500 gpa > but it is the thermodyanamic stability after 140 gpa kpoints 24*24*24 > what may be reseon i donot know > please help me > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110529/ba5d2bd1/attachment.htm From bdslipun at gmail.com Sun May 29 13:59:47 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Sun, 29 May 2011 17:29:47 +0530 Subject: [Pw_forum] problem on phonon In-Reply-To: References: <4DE11D7F.7010102@sissa.it> Message-ID: On Sat, May 28, 2011 at 10:52 PM, bhabya sahoo wrote: > sir > i am using quantum espresso 4.3 version > i want to study the phase transition of yitrium nitride(yn) > first by doing scf calculation at 0k > i found a phase transition of B1 to B2 transition at 137 gpa for this i > used a 14*14*14 kpoints mesh and convergence achived for scf is 10^-9 > i used GGA psudo potentials of pbe type avalable in code of espresso > website for y and n > but when i did the calculation for phonon dispersion > B2 stucter instablity (negative frequency ) in phonon spectrum continues > upto 500 gpa why ? > for this i used 4*4*4* mesh q points for dyanamical matrices i have > incresed further but nothing results > > On Sat, May 28, 2011 at 9:36 PM, Stefano de Gironcoli wrote: > >> Dear Bhabya Sahoo, >> >> your very stingy use of punctuation make quite difficult (at least for >> me) to follow your request... >> Take your time and try to make you clear providing more detailed >> information about your system, what is your aim, what is the problem, what >> are the tests you have done. >> No one is going to spend more time in thinking about your problem than >> you do in explaining it. >> >> Please provide your affiliation. >> >> stefano >> - >> Stefano de Gironcoli, SISSA and DEMOCRITOS >> >> >> On 05/28/2011 05:46 PM, bhabya sahoo wrote: >> >> i am using quantum espresso static calculation obeys thermdyanamic stability >> transition from B1 to B2 transition at 138 gpa so ihave used 24 24 24 >> kpoint grid for phonon in B2 phase is calculated 4 4 4 grid by linear >> response calculation but why the instability (negative frequency in phonon ) >> upto 450 gpa i have used pbe psudo potentials also the lattice constant is >> exact for experimental data >> can metastability have negative frequency so why this occures >> optimisation is ok >> other problem why free energy is not coming for unstable phase for qha code >> in quantum espresso >> replay immidiate if u have solution >> On Sat, May 28, 2011 at 5:38 PM, bhabya sahoo wrote: >> >> >> sir >> i used to calculate the phonon calculation on a 4*4*4 grid in cscl phase >> but the unstability persists upto 500 gpa >> but it is the thermodyanamic stability after 140 gpa kpoints 24*24*24 >> what may be reseon i donot know >> please help me >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum >> >> >> >> _______________________________________________ >> 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/20110529/4ca703fd/attachment.htm From sxu2 at ncsu.edu Sun May 29 14:16:26 2011 From: sxu2 at ncsu.edu (shu xu) Date: Sun, 29 May 2011 08:16:26 -0400 Subject: [Pw_forum] sumpdos.x In-Reply-To: <28007.81522.qm@web125903.mail.ne1.yahoo.com> References: <28007.81522.qm@web125903.mail.ne1.yahoo.com> Message-ID: there is no need to make input file for sumpdos.x Use the pdos files generated by projwfc.x that you wanna sum up. e.g you wanna sum up XX.pdos.atom#1.. XX.pdos.atom#2.. ./sumdos.x XX.pdos.atom#1.. XX.pdos.atom#2.. > result On Sun, May 29, 2011 at 7:52 AM, Farzad Molani wrote: > Hi QE users, > I want to sum resalts from projwfc.x by sumpdos.x. I should say I read > pwforum and examples and usergide from PWSCF site, but I don't know how > make an input file for sumpdos.x. please help me and give an example > clearly. > thanks in advance. > > Farzad Molani, > Ph.D Student, > Department of Theoretical Physical Chemistry, > K. N. Toosi University of Technology, > Tehran, Iran. > Tel.: 009891 4442 3308 > Tel.: 009821 2306 4280 > Fax: 009821 2285 3650 > Web: http://www.chem.kntu.ac.ir/~sjalili:/ > > _______________________________________________ > 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/20110529/fffcd329/attachment-0001.htm From mayankaditya at gmail.com Sun May 29 17:25:08 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Sun, 29 May 2011 20:55:08 +0530 Subject: [Pw_forum] different born effective charges of symmetry related atom Message-ID: Hi Dear QE Users I have a doubt regarding the Born effective charges. I am doing phonon calculation of ZrP2O7 (cubic structure). The wyckoff site of Zr , P and two different kind of oxygen O1 and O2 are 4a, 8c, 24d and 4b respectively. The calculated born effective charges are same for all Zr, P and O2, while in case of O1 atoms the effective charges are different. So is it necessary to have same born effective charge for symmetry linked atom( wyckoff relation). Thanks -- Mayank P.hd. Student BHABHA ATOMIC RESEARCH CENTER MUMBAI, INDIA From giannozz at democritos.it Sun May 29 19:06:17 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Sun, 29 May 2011 19:06:17 +0200 Subject: [Pw_forum] NEB error: unexpected dimension in ngg In-Reply-To: <4DE0CFF70200009A0002FA90@gwinter.ufs.ac.za> References: <4DE0CFF70200009A0002FA90@gwinter.ufs.ac.za> Message-ID: <98079767-CDBD-4CCC-8F3B-520C38B74F96@democritos.it> On May 28, 2011, at 10:35 , Egbert Barnard wrote: > I am performing a NEB calculation on a Fe-S system and > after the calculation has run for a few hours I get the following > error. > > task # 22 > from igk_l2g_kdip : error # 1 > unexpected dimension in ngg funny: this is something that should never happen. Please provide input and output, or better, file a bug report on qe-forge 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 zhaohscas at yahoo.com.cn Mon May 30 13:49:54 2011 From: zhaohscas at yahoo.com.cn (Hongsheng Zhao) Date: Mon, 30 May 2011 07:49:54 -0400 Subject: [Pw_forum] How to obtain the binding energy ( in the unit of eV/Zn-O pair ) for Wurtsite ZnO? In-Reply-To: References: <608184.45685.qm@web15606.mail.cnb.yahoo.com> <4DE17F2F.90305@yahoo.com.cn> Message-ID: <4DE38462.2070202@yahoo.com.cn> On 05/28/2011 10:18 AM, mohnish pandey wrote: > > > On Sun, May 29, 2011 at 4:33 AM, Hongsheng Zhao > > wrote: > > On 05/28/2011 02:44 AM, mohnish pandey wrote: > > Dear Hongsheng, > All the four bonds in ZnO wurtzite are equivalent. > > But the four bonds have different bond lengths: the bond length > parallel to c axis is different from that of the other two bonds. > Why can you say are equivalent? > They have different orientation but the length are same. You can > check it by calculating the bond length using crystal convention. > Just give the coordinate in crystal-convention in Xcrysden and you > can measure it.You will get all the bonds as same. > The Xcrysden is not so intuitive for measuring the bond lengths. I use materials studio's visualizer to do this test. And find they have different bond lengths. Please see the snapshot for this from here: http://h1.ripway.com/zhaohs/ZnO-b4-bond-length.tif I also give you the corresponding cif file which I used to measure the bond lengths, just for your information. To obtain the cif file, from here: http://h1.ripway.com/zhaohs/ZnO.cif > > So to calculate the binding energy you have to use the below > formula : > E_{binding-ZnO}=E{calculated-ZnO-wurtzite}-E_{Zn_{crystal-total}}-E_{E(1/2*O2}}. > Remember that you have to do spin-polarised calculation for > O2 otherwise it will give wrong answer. > > I've learned that this is due to O atom's open-shell > configuration. Than what is the initial spin should I use for O2? > > Furthermore, for ZnO wurtzite, should I do spin-polarised > calculation or not? > > No for ZnO you dont have to. I said for O2 only. You can do both the > unpolarised and polarised calculation, and you will find the > difference in bond energy and bond length too. This is just the things that I cann't figure them out completely. Let me give more detail descriptions of my understanding and my confusion: 1- For most open-shell atoms, there are non-spherical density due to unfilled shells and a non-zero spin state, say, for O atom. In this case, if we want to obtain the atom energy via DFT calculation by using the big box model, a spin-polarised calculation should be used. 2- When the open-shell atoms combined together to form molecular, say, O to O2, then open-shell orbitals will form covalent bonds. In this case, does it mean that the open-shell atoms configurations will be changed into close-shelled configurations? If so, I think we should not do a spin-polarised calculation for O2, just a non spin-polarised calculation should be OK. 3- For the Wurtsite ZnO, the Zn atom is a closed subshell atom, but the O atom is a open subshell atom. When they combine to form Wurtsite ZnO, how we know the Wurtsite ZnO molecule should be open-shell or close-shell? 4- In one word, when we calculate the total energy for a atom/molecule, what's the criteria that determine the spin-polarised calculation should be done or not? Regards. > > > Binding energy definition is same as above. And cohesive > energy is the difference in energy between the energy of > crystal and corresponding species in isolated phases. Below > are the some references. > > Do you mean, for the calculation of cohesive energy, I should use > the big box model, then put one Zn in the big box, and O atom in > another box to obtain the total energy of each isolated phases? > Yea you have to use box model as you correctly mentioned. > > http://arxiv.org/ftp/cond-mat/papers/0610/0610002.pdf > http://prb.aps.org/pdf/PRB/v70/i5/e054104 > > > Regards. > -- > > Hongsheng Zhao> > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > > > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110530/2ba99591/attachment.htm From kirtinandan07 at gmail.com Mon May 30 07:40:57 2011 From: kirtinandan07 at gmail.com (vicky singh) Date: Mon, 30 May 2011 11:10:57 +0530 Subject: [Pw_forum] error in running the espresso-4.3 examples Message-ID: Dear PWSCF users I installed mpich2 in my machine and the i ran the espresso-4.3_examples. Many programme were succesfully done but many showed error. Foe eg. /home/Software/espresso-4.3_ examples/examples/example14 : starting This example shows how to use pw.x, ph.x and d3.x to calculate the third-order expansion coefficients of the total energy of Si. executables directory: /home/Software/espresso-4.3/bin pseudo directory: /home/Software/pseudo temporary directory: ./tmp checking that needed directories and files exist... done running pw.x as: mpirun -np 4 /home/Software/espresso-4.3/bin/pw.x running ph.x as: mpirun -np 4 /home/Software/espresso-4.3/bin/ph.x running d3.x as: mpirun -np 4 /home/Software/espresso-4.3/bin/d3.x cleaning ./tmp... done running the scf calculation for Si... done running the phonon calculation for Si at Gamma...application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 application called MPI_Abort(MPI_COMM_WORLD, 0) - process 3 application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 Error condition encountered during test: exit status = 15 Aborting many eg (15,18, ..) showed the same error. what can be the possible error. thanks in advance Vicky singh research student Bangalore -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110530/b40b09e8/attachment.htm From sclauzer at sissa.it Mon May 30 10:08:04 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 May 2011 10:08:04 +0200 Subject: [Pw_forum] Pseudo-potential testing In-Reply-To: References: Message-ID: Hello, Il giorno 27/mag/2011, alle ore 20.05, Tram Bui ha scritto: > Dear Gabriele, > Thank you for your respond. Just to make sure that I'm understanding your answer correctly, below is a shortcut on the output file of my PP testing: > > ---------------------- Testing the pseudopotential ---------------------- > > > scalar relativistic calculation > > atomic number is 55.00 valence charge is 1.00 > dft =PBE lsd =0 sic =0 latt =0 beta=0.20 tr2=1.0E-14 > mesh =1251 r(mesh) = 101.25750 xmin = -7.00 dx = 0.01250 > > n l nl e AE (Ry) e PS (Ry) De AE-PS (Ry) > 1 0 6S 1( 0.50) -0.17728 -0.17238 -0.00490 > 2 1 6P 1( 0.50) -0.07657 -0.07687 0.00030 > 3 2 5D 1( 0.00) -0.05580 -0.05081 -0.00499 > > eps = 8.5E-15 iter = 22 > > Etot = -15573.817276 Ry, -7786.908638 Ha, -211892.560039 eV > Etotps = -0.217507 Ry, -0.108753 Ha, -2.959329 eV > dEtot_ae = 0.049938 Ry > dEtot_ps = 0.048795 Ry, Delta E= 0.001144 Ry > > Ekin = 0.080184 Ry, 0.040092 Ha, 1.090963 eV > So I should look at the "De AE-PS (Ry)", which is the difference in the eigenvalues? or the "Delta E"? I assume it is the Delta E based on your respond. But am I correct? I would say that you should look at both, but what Paolo was referring to in the guide is the second thing. The Delta E looks fair to me, that's what you can expect from standard USPP. The difference in the eigenvalues seems instead a bit too large, maybe you can still improve a bit the quality of the PP. HTH GS > > Regards, > Tram > > On Thu, May 26, 2011 at 2:16 AM, Gabriele Sclauzero wrote: > > Il giorno 26/mag/2011, alle ore 01.00, Tram Bui ha scritto: > >> Dear Paul, >> In the file that I have attached here (Paul's note on PP generation), under section 3.10: checking for transferability, you have mentioned about the:"The error on total energy di?erences >> between PP and AE results gives a feeling on how good the PP is." Do you mean the difference in AE and PP eigenvalues? > > No, I think here Paolo "Paul" Giannozzi really meant what you understood first, but you didn't get it in the correct way. > You should really compare total energy differences, which means: > E_2(AE) - E_1(AE) versus E_2(PS) - E_1(PS) > where 1 and 2 label two different electronic configurations, and NOT > E_1(PS) versus E_1(AE) > as you are probably trying to do. > >> because I saw the Etot and Etotps are huge difference > > This is often the case, given the high degree of freedom in the choice of PP parameters (especially for the local potential, I suppose). > >> but their eigenvalue (e, Ry) are closed. > > Indeed this is how it should be, since the modern PP are designed to reproduce the scattering properties of the AE atomic potential as best as possible. > >> >> Dear QE users, >> I'm trying to test the Cs' US PP with reference configuration of :[Xe] 6s1 5d0 6p0. To test the PP, I'm using these five configuration (just by guessing): >> configts(1)= '6s1 6p0 5d0' >> configts(2)= '6s0.5 6p0.5 5d0' >> configts(3)= '6s0.5 6p0 5d0.5' >> configts(4)= '6s0 6p1 5d0' >> configts(5)= '6s0 6p0 5d1' >> My questions are: >> - how to choose the configurations for PP testing based on the reference one? is there a strategy or some sort? > > Use some reasonable configurations (remove or add one electron, or a fraction of it, move one or more electrons between different orbitals, ...). > The choice may also be driven by the class of materials that you are going to study (e.g. ionic crystals). > >> - how many configurations are enough for the test? > > That's up to you... 5 look enough for me. Don't forget to do some testing with the solid state code (e.g. bond distance of dimers, lattice constant of simple solids...). > > > HTH > > > GS > >> >> Thank you very much, >> >> Tram Bui >> >> M.S. Materials Science & Engineering >> trambui at u.boisestate.edu >> >> _______________________________________________ >> 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 > > > > > -- > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > _______________________________________________ > 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/20110530/1a290525/attachment.htm From sclauzer at sissa.it Mon May 30 10:13:49 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 May 2011 10:13:49 +0200 Subject: [Pw_forum] sumpdos.x In-Reply-To: <28007.81522.qm@web125903.mail.ne1.yahoo.com> References: <28007.81522.qm@web125903.mail.ne1.yahoo.com> Message-ID: [gabriele at macgurlo:~]$ sumpdos.x -h USAGE: sumpdos [-h] [-f ] [ ... ] Sum the pdos from the file specified in input and write the sum to stdout -h : write this manual -f : takes the list of pdos files from (one per line) instead of command line : the M-th pdos file Il giorno 29/mag/2011, alle ore 13.52, Farzad Molani ha scritto: > Hi QE users, > I want to sum resalts from projwfc.x by sumpdos.x. I should say I read pwforum and examples and usergide from PWSCF site, but I don't know how make an input file for sumpdos.x. please help me and give an example clearly. > thanks in advance. > > Farzad Molani, > Ph.D Student, > Department of Theoretical Physical Chemistry, > K. N. Toosi University of Technology, > Tehran, Iran. > Tel.: 009891 4442 3308 > Tel.: 009821 2306 4280 > Fax: 009821 2285 3650 > Web: http://www.chem.kntu.ac.ir/~sjalili:/ > _______________________________________________ > 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/20110530/a6137b77/attachment.htm From sclauzer at sissa.it Mon May 30 10:18:51 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 May 2011 10:18:51 +0200 Subject: [Pw_forum] question about the convergence of eigenvalues In-Reply-To: <20110528164245.124420@gmx.net> References: <20110528164245.124420@gmx.net> Message-ID: <0C3E231D-CB99-4BD6-A939-DEAB37206F1E@sissa.it> Hello, well, in my opinion it depends on what you have to do with those eigenvalues. If you include many empty bands, then probably the eigenvalues that did not converge will be at very high energies and you should not care about them if you just want to plot the DOS, for instance. HTH GS Il giorno 28/mag/2011, alle ore 18.42, Lun Yue ha scritto: > Hello, dear pwscf users: > > I have a question about the convergence of eigenvalues. > > In section 11.1.0.24 of the user guide, it is mentioned that a warning of N eigenvectors not converged may signal serious trouble if it's presented in the last steps of self-consistency. (http://www.quantum-espresso.org/user_guide/node52.html#SECTION0001210240000000000000) > > But how about the non-scf calculations? > > In the bands and nscf calculations I got warning messanges as following: > > > > **example in band calculation (calculation = 'bands'): > > Computing kpt #: 28 > c_bands: 1 eigenvalues not converged > > > **example in nscf calculation (calculation = 'nscf'): > > Computing kpt #: 144 > c_bands: 2 eigenvalues not converged > > > > Are they acceptable? > > > Thank you and best regards, > > Lun Yue > -- > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > _______________________________________________ > 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/20110530/1f58c25d/attachment-0001.htm From BarnardEP at ufs.ac.za Mon May 30 10:33:58 2011 From: BarnardEP at ufs.ac.za (Egbert Barnard) Date: Mon, 30 May 2011 10:33:58 +0200 Subject: [Pw_forum] NEB error: unexpected dimension in ngg Message-ID: <4DE372960200009A0002FB01@gwinter.ufs.ac.za> I am using Quantum espresso 4.2.1. Here is my input and output as requested, together with the error file. I will also report the bug on qe-forge. --INPUT-- &CONTROL calculation = 'neb' , prefix = 'FeS_int_fixedPos_NEB', restart_mode = 'restart' , outdir = '/home/pieter/QE/Fe/temp', nstep = 300 , / &SYSTEM ibrav = 0, celldm(1) =16.17, nat = 55, ntyp = 2, ecutwfc =28, ecutrho = $((28*12)), occupations = 'smearing', smearing = 'mp', degauss = 0.04, nspin = 2, starting_magnetization(1) = 0.4, nbnd = 522, nosym = .true. , / &ELECTRONS electron_maxstep = 400, conv_thr = 1.D-7, mixing_beta = 0.6, mixing_mode = 'local-TF', / &IONS ds = 2.D0, opt_scheme = "broyden", num_of_images = 6, k_max = 0.2D0, k_min = 0.02D0, CI_scheme = "no-CI", pot_extrapolation = "second_order", wfc_extrapolation = "second_order", path_thr = 0.05D0, / ATOMIC_SPECIES Fe 55.845 Fe.pw91-sp-van_ak.UPF S 32.066 S.pw91-van_ak.UPF ATOMIC_POSITIONS first_image Fe 0.000000000 0.000000000 0.000000000 0 0 0 Fe 0.000531265 0.000000029 0.332286163 0 0 0 Fe 0.000531298 0.000000002 0.667713812 0 0 0 Fe 0.000530993 0.332286435 0.000000040 0 0 0 Fe 0.006924478 0.325712226 0.325712056 0 0 0 Fe 0.006924535 0.325712232 0.674287944 0 0 0 Fe 0.000530966 0.667713524 0.000000020 0 0 0 Fe 0.006924580 0.674287717 0.325712072 0 0 0 Fe 0.006924606 0.674287785 0.674287909 0 0 0 Fe 0.333091770 0.000000003 -0.000000015 0 0 0 Fe 0.332786078 -0.000000027 0.332283565 0 0 0 Fe 0.332786103 -0.000000049 0.667716418 0 0 0 Fe 0.332786424 0.332283895 0.000000008 0 0 0 Fe 0.326414685 0.325710146 0.325709980 0 0 0 Fe 0.326414762 0.325710198 0.674290017 0 0 0 Fe 0.332786396 0.667716183 -0.000000031 0 0 0 Fe 0.326414766 0.674289874 0.325709977 0 0 0 Fe 0.326414794 0.674289822 0.674290010 0 0 0 Fe 0.666625086 -0.000000010 0.000000001 0 0 0 Fe 0.666657383 0.000000003 0.333435573 0 0 0 Fe 0.666657405 -0.000000032 0.666564402 0 0 0 Fe 0.666657427 0.333436077 0.000000026 0 0 0 Fe 0.666656830 0.325330605 0.325329865 1 1 1 Fe 0.666656779 0.325330599 0.674670118 1 1 1 Fe 0.666657401 0.666563931 -0.000000005 1 1 1 S 0.666586713 0.500000013 0.500000000 0 0 0 Fe 0.666656865 0.674669407 0.325329864 1 1 1 Fe 0.666656853 0.674669400 0.674670128 1 1 1 Fe 0.166611608 0.162991849 0.162991667 0 0 0 Fe 0.166672830 0.163714006 0.500000017 0 0 0 Fe 0.166611583 0.162991828 0.837008367 0 0 0 Fe 0.166672897 0.500000061 0.163713963 0 0 0 Fe 0.166691313 0.500000028 0.499999989 0 0 0 Fe 0.166672862 0.499999990 0.836286073 0 0 0 Fe 0.166611616 0.837008153 0.162991639 0 0 0 Fe 0.166672911 0.836285964 0.499999976 0 0 0 Fe 0.166611601 0.837008128 0.837008336 0 0 0 Fe 0.499525338 0.164873119 0.164872628 0 0 0 Fe 0.497480562 0.165023100 0.499999964 0 0 0 Fe 0.499525362 0.164873151 0.835127303 0 0 0 Fe 0.497480795 0.500000029 0.165022722 0 0 0 Fe 0.439284005 0.500000068 0.499999997 1 1 1 Fe 0.497480772 0.500000061 0.834977257 0 0 0 Fe 0.499525280 0.835126839 0.164872680 0 0 0 Fe 0.497480500 0.834976831 0.500000034 0 0 0 Fe 0.499525308 0.835126838 0.835127346 0 0 0 Fe 0.833739734 0.164914974 0.164914502 0 0 0 Fe 0.835847486 0.165016679 0.499999944 0 0 0 Fe 0.833739748 0.164914964 0.835085477 0 0 0 Fe 0.835847228 0.499999982 0.165016283 0 0 0 Fe 0.894070136 0.499999967 0.499999932 1 1 1 Fe 0.835847179 0.500000031 0.834983736 0 0 0 Fe 0.833739721 0.835085018 0.164914513 0 0 0 Fe 0.835847465 0.834983373 0.500000028 0 0 0 Fe 0.833739696 0.835085057 0.835085540 0 0 0 last_image Fe 0.000000000 0.000000000 0.000000000 Fe -0.000000004 0.000536556 0.332296407 Fe 0.000000012 0.000536488 0.667703675 Fe 0.000000009 0.333072059 0.000000042 Fe 0.000000013 0.332776848 0.332291179 Fe -0.000000011 0.332776770 0.667708693 Fe 0.000000009 0.666627870 0.000000013 Fe -0.000000051 0.666661963 0.333425444 Fe 0.000000083 0.666662153 0.666574548 Fe 0.332296404 0.000536583 -0.000000041 Fe 0.325683735 0.006943280 0.325683744 Fe 0.325683603 0.006943151 0.674316362 Fe 0.332291272 0.332776779 0.000000058 Fe 0.325673353 0.326386615 0.325673213 Fe 0.325673410 0.326386625 0.674326679 Fe 0.333425328 0.666662029 -0.000000054 Fe 0.325318231 0.666663793 0.325318281 Fe 0.325318167 0.666664006 0.674681741 Fe 0.667703621 0.000536574 -0.000000017 Fe 0.674316264 0.006943229 0.325683651 Fe 0.674316318 0.006943262 0.674316412 Fe 0.667708718 0.332776740 0.000000048 Fe 0.674326689 0.326386676 0.325673271 Fe 0.674326586 0.326386572 0.674326591 Fe 0.666574671 0.666662081 0.000000087 S 0.500000005 0.666584751 0.500000002 Fe 0.674681834 0.666663708 0.325318243 Fe 0.674681770 0.666663861 0.674681713 Fe 0.163024413 0.166607159 0.163024430 Fe 0.163727069 0.166662676 0.500000008 Fe 0.163024383 0.166606989 0.836975609 Fe 0.164861935 0.499496907 0.164862035 Fe 0.165000320 0.497474731 0.499999944 Fe 0.164862006 0.499497047 0.835137973 Fe 0.164906799 0.833775119 0.164906872 Fe 0.164999313 0.835864200 0.500000137 Fe 0.164906819 0.833775188 0.835093037 Fe 0.500000047 0.166662740 0.163727088 Fe 0.499999998 0.166664603 0.499999986 Fe 0.499999968 0.166662622 0.836272921 Fe 0.500000044 0.497474704 0.165000336 Fe 0.500000072 0.439226279 0.499999816 Fe 0.499999929 0.497474738 0.834999707 Fe 0.500000075 0.835864185 0.164999302 Fe 0.499999911 0.894163268 0.500000163 Fe 0.499999931 0.835864219 0.835000683 Fe 0.836975612 0.166607155 0.163024399 Fe 0.836272931 0.166662710 0.499999949 Fe 0.836975583 0.166607001 0.836975555 Fe 0.835138037 0.499496958 0.164862120 Fe 0.834999679 0.497474714 0.499999843 Fe 0.835138064 0.499497015 0.835137981 Fe 0.835093148 0.833775128 0.164906891 Fe 0.835000705 0.835864197 0.500000007 Fe 0.835093210 0.833775249 0.835093104 CELL_PARAMETERS 1.0000000000 0.00000000 0.000000000 0.000000000 1.00000000 0.000000000 0.000000000 0.00000000 1.000000000 K_POINTS {automatic} 3 3 3 0 0 0 --Output-- Program PWSCF v.4.2.1 starts on 30May2011 at 8:20: 6 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 Parallel version (MPI), running on 48 processors path-images division: nimage = 2 K-points division: npool = 2 R & G space division: proc/pool = 12 wavefunctions fft division: fft/group = 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... Message from routine iosys: pot_extrapolation='second_order' not available, using 'atomic' Message from routine iosys: wfc_extrapolation='second_order' not available, using 'atomic' reading file 'FeS_int_fixedPos_NEB.path' calculation = neb restart_mode = restart opt_scheme = broyden num_of_images = 6 nstep = 300 CI_scheme = no-CI first_last_opt = F coarse-grained phase-space = F use_freezing = F ds = 2.0000 a.u. k_max = 0.2000 a.u. k_min = 0.0200 a.u. suggested k_max = 0.1542 a.u. suggested k_min = 0.0154 a.u. path_thr = 0.0500 eV / A ------------------------------ iteration 1 ------------------------------ rank 36 in job 1 node0308.int.hpc.ufs.ac.za_40349 caused collective abort of all ranks exit status of rank 36: return code 0 --ERROR MESSAGE-- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 36 from igk_l2g_kdip : error # 1 unexpected dimension in ngg %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Thank you Pieter Barnard University of the Free State South Africa _____________________________________________________________________ University of the Free State: This message and its contents are subject to a disclaimer. Please refer to http://www.ufs.ac.za/disclaimer for full details. Universiteit van die Vrystaat: Hierdie boodskap en sy inhoud is aan 'n vrywaringsklousule onderhewig. Volledige besonderhede is by http://www.ufs.ac.za/vrywaring beskikbaar. _____________________________________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110530/9abb8dbf/attachment-0001.htm From eariel99 at gmail.com Mon May 30 17:26:23 2011 From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin) Date: Mon, 30 May 2011 11:26:23 -0400 Subject: [Pw_forum] total energy with GW Message-ID: Hi, I wish to know if the GWW code calculates total energies of the ground state, such that can be used to obtain defect formation energies or elastic constants. If not GWW, is there any code with that capability? -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110530/5cc8d06b/attachment.htm From giannozz at democritos.it Mon May 30 17:29:28 2011 From: giannozz at democritos.it (Paolo Giannozzi) Date: Mon, 30 May 2011 17:29:28 +0200 Subject: [Pw_forum] NEB error: unexpected dimension in ngg In-Reply-To: <4DE372960200009A0002FB01@gwinter.ufs.ac.za> References: <4DE372960200009A0002FB01@gwinter.ufs.ac.za> Message-ID: <1306769368.24984.65.camel@fe12lx.fisica.uniud.it> Debugging such a big job, moreover after a restart, is going to be close to impossible ... P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy From mayankaditya at gmail.com Mon May 30 19:34:40 2011 From: mayankaditya at gmail.com (mayank gupta) Date: Mon, 30 May 2011 23:04:40 +0530 Subject: [Pw_forum] Born effective Charges Message-ID: Hi dear user's Sorry about my last post. actually the born effective charges has transform according to symmetry. I didn't observe all the component of tensor, it is ok born effective charge are same for all the symmetry linked atom. Thanks -- Mayank BHABHA ATOMIC RESEARCH CENTER MUMBAI, INDIA Office: 022-25595606 Home: 9920397437 / 9869834437 From vovi47 at yahoo.com Tue May 31 03:23:46 2011 From: vovi47 at yahoo.com (Vi Vo) Date: Mon, 30 May 2011 18:23:46 -0700 (PDT) Subject: [Pw_forum] Using mixture of pseudo potential Message-ID: <707981.30870.qm@web114501.mail.gq1.yahoo.com> Dear All, In my calculation, I used a mixture of pseudo potentials, ie. norm-conserving pp (NC pp) for one element and ultrasoft pp (US pp) for another. If I don't specify ecutrho in the input, what will be the default value for ecutrho for the ultrasoft pp. I know that for NC pp, ecutrho = 4*ecutwfc, but I do not know if the same value is used for US pp. On the other hand, if I specify ecutrho = 8*ecutwfc, then does the same value apply to the NC pp. Thank you very much, Vi University of Houston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110530/eeb95881/attachment.htm From songsong19840614 at gmail.com Tue May 31 06:35:59 2011 From: songsong19840614 at gmail.com (lucking-pine) Date: Tue, 31 May 2011 12:35:59 +0800 Subject: [Pw_forum] Using mixture of pseudo potential In-Reply-To: <707981.30870.qm@web114501.mail.gq1.yahoo.com> References: <707981.30870.qm@web114501.mail.gq1.yahoo.com> Message-ID: Hi, In my way,I usually test ecutrho = X*ecutwfc using scf or relax.I look the result of total energy or enthalpy. Such as: 1.ecutwfc=47 ecutrho=400, total energy= -290.983 2.ecutwfc=47 ecutrho=380, total energy= -290.993 So,I thought '2' is better than '1'. Bests, Pine. 2011/5/31 Vi Vo > Dear All, > > In my calculation, I used a mixture of pseudo potentials, ie. > norm-conserving pp (NC pp) for one element and ultrasoft pp (US pp) for > another. If I don't specify ecutrho in the input, what will be the default > value for ecutrho for the ultrasoft pp. I know that for NC pp, ecutrho = > 4*ecutwfc, but I do not know if the same value is used for US pp. On the > other hand, if I specify ecutrho = 8*ecutwfc, then does the same value apply > to the NC pp. > > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110531/f5a1baac/attachment.htm From jiejiangnc at gmail.com Tue May 31 15:10:19 2011 From: jiejiangnc at gmail.com (Jie Jiang) Date: Tue, 31 May 2011 09:10:19 -0400 Subject: [Pw_forum] PBE0 convergence Message-ID: Dear PWscf, I get a problem in PBE0 convergence. Below is part of the input file, &CONTROL calculation = "scf", / &SYSTEM ibrav = 12, celldm(1) = 15.73981, celldm(2) = 0.62519, celldm(3) = 4.39673, celldm(4) = 0.62519, nat = 58, ntyp = 5, ecutwfc = 80.0, input_dft = 'pbe0', nqx1 = 2, nqx2 = 1, nqx3 = 1, exxdiv_treatment= 'gygi-baldereschi' ecutvcut = 0.7 x_gamma_extrapolation= .TRUE. occupations = "smearing", smearing = "methfessel-paxton", degauss = 0.01, / &ELECTRONS conv_thr = 1.D-6, mixing_beta = 0.5D0, / ATOMIC_SPECIES C 12.0107 S 32.066 H 1.00794 O 15.9994 Zn 65.409 / K_POINTS {automatic} 6 3 1 0 0 0 The output 'dexx' is est. exchange err (dexx) = 0.00059720 Ry est. exchange err (dexx) = -0.02431459 Ry est. exchange err (dexx) = -0.02596414 Ry est. exchange err (dexx) = -0.02720608 Ry est. exchange err (dexx) = -0.02821286 Ry est. exchange err (dexx) = -0.02946368 Ry est. exchange err (dexx) = -0.03148666 Ry est. exchange err (dexx) = -0.03481403 Ry est. exchange err (dexx) = -0.03964928 Ry est. exchange err (dexx) = -0.04531623 Ry and Fock energy is -177.9185854736362 -177.9185854736362 -177.8610717829301 -177.8047524875259 -177.8047524875259 -177.8356769333793 -177.8179722072562 -177.8179722072562 -177.8457748551563 -177.8216492155755 -177.8216492155755 -177.8490273372818 -177.8219932983469 -177.8219932983469 -177.8500300290520 -177.8216410368603 -177.8216410368603 -177.8505498629616 -177.8205313239625 -177.8205313239625 -177.8511288881755 -177.8187531280260 -177.8187531280260 -177.8519180436694 -177.8154548907789 -177.8154548907789 -177.8530355735678 -177.8113176980133 -177.8113176980133 -177.8542927054368 -177.8066352532881 Can you please help me in this issue. Thanks, Jie Jiang Applied Physics Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110531/9fed8521/attachment.htm From nicola.marzari at materials.ox.ac.uk Tue May 31 15:50:51 2011 From: nicola.marzari at materials.ox.ac.uk (Nicola Marzari) Date: Tue, 31 May 2011 14:50:51 +0100 Subject: [Pw_forum] FFT grid and cutoff energy. In-Reply-To: <4DE58F8F.8070005@yahoo.com.cn> References: <4DE58F8F.8070005@yahoo.com.cn> Message-ID: <4DE4F23B.3000303@materials.ox.ac.uk> On 6/1/11 2:02 AM, Hongsheng Zhao wrote: > //Hi all, > > //I've learned that, for all of the PW based DFT codes, such as, > VASP/PWscf/Abinit/CASTEP, the > FFT grid is generated based on the cutoff energy. So if we have tested > the convergence total energy vs cutoff energy, then the > FFT grid used for our calcultions should also be OK based on the > selected cutoff energy. In other words, it is unnecessary to do a > > Independent FFT grid convergence test. Am I right? > > Regards. Yes, indeed. In the old days one would use slightly coarser meshes than what prescribed, and get away with it (especially if that allowed for the FFT dimension to be a power of 2, for which typically FFT used to be much faster); nowadays noone bothers. FFTs dominate the cost of small calculations (relevant if you need to do a lot of them) and can be tricky in massively parallel calculations, but in general I wouldn't bother. The CP code in Q-E is slightly more sophisticated, and for ultrasoft pseudopotentials it uses different FFT grids to transform the softer wavefunctions, and harder charge density - not sure if other codes do the same (the technique is all described in Pasquarello 1993 PRB). nicola ---------------------------------------------------------------------- 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 ttduyle at gmail.com Tue May 31 15:51:13 2011 From: ttduyle at gmail.com (Duy Le) Date: Tue, 31 May 2011 09:51:13 -0400 Subject: [Pw_forum] FFT grid and cutoff energy. In-Reply-To: <4DE58F8F.8070005@yahoo.com.cn> References: <4DE58F8F.8070005@yahoo.com.cn> Message-ID: On Tue, May 31, 2011 at 9:02 PM, Hongsheng Zhao wrote: > Hi all, > > I've learned that, for all of the PW based DFT codes, such as, > VASP/PWscf/Abinit/CASTEP, the > FFT grid is generated based on the cutoff energy. Not really true. There is no direct relationship between FFT grid and cutoff energy (I supposed that by cutoff energy you meant Kinetic energy cutoff for the planewave expansion) FFT mesh is calculated based on the cutoff for charge density. In any code, the coder usually set a default relationship between cutoff for PW expansion and cutoff for charge density. For example, in QE, the later is 4 time larger. > So if we have tested the > convergence total energy vs cutoff energy, then the > FFT grid used for our calcultions should also be OK based on the selected > cutoff energy.? In other words, it is unnecessary to do a > > Independent FFT grid convergence test. Am I right? > It depends. If that default value is good enough, you don't have to do an additional test. The default value is good enough for PAW potential, but too small for US or NC potential. BTW, I understood that by saying "Independent FFT grid convergence test" you really meant "Independent *cutoff energy for the charge density* convergence test" -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" > Regards. > -- > > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From tfcao at theory.issp.ac.cn Tue May 31 16:24:36 2011 From: tfcao at theory.issp.ac.cn (=?utf-8?B?Q2FvIFRG?=) Date: Tue, 31 May 2011 22:24:36 +0800 Subject: [Pw_forum] =?utf-8?q?problem_with_the_pdos_calculation?= Message-ID: <20110531142436.10187.qmail@ms.hfcas.ac.cn> Dear Q.E users I want to do pdos calculation of graphene with one hydrogen absorbed on it . And the calculation run for a short time before it stopped,with the error massage as follows: Program PROJWFC v.4.2.1 starts on 30May2011 at 20:21:10 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please acknowledge Gaussian broadening (read from input): ngauss,degauss= 0 0.010000 Calling projwave .... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from davcio : error # 10 error while reading from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... "pdos.out" 25L, 1009C 1,0-1 ?? And I have done the scf and nscf calculation before the pdos calculation .My input information for pdos as follow: &inputpp prefix = 'graphene' , outdir = './tmp' , ngauss = 0 , degauss =0.005 Emax = 2.0 , Emin = -3.0 , lsym = .true. , filpdos = 'graphene.pdos' , filproj = 'graphene.proj' , / What can be the reasons? Any advice will be greatly appreciated . -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110531/71899dcb/attachment.htm From vovi47 at yahoo.com Tue May 31 19:11:48 2011 From: vovi47 at yahoo.com (Vi Vo) Date: Tue, 31 May 2011 10:11:48 -0700 (PDT) Subject: [Pw_forum] Using mixture of pseudo potential In-Reply-To: References: <707981.30870.qm@web114501.mail.gq1.yahoo.com> Message-ID: <702418.87073.qm@web114505.mail.gq1.yahoo.com> Hi Pine, Thank you. Yes, I know that I have to do different tests for ecutrho and ecutwfc, but my questions are different. I would like to know what is the default setting for ecutrho the code would assume. I restate my question as follows: If I forgot to specify the ecutrho, what default value of ecutrho would the code assume for US PP? (I guess it still uses the default ecutrho=4*ecutwfc). On the other hand, assuming I set the ecutrho=9*ecutwfc, does then the same value of ecutrho=8*ecutwfc also apply to NC PP, or does the value of ecutrho=4*ecutwfc will be used for NC PP. Thank you, Vi ________________________________ From: lucking-pine To: PWSCF Forum Sent: Mon, May 30, 2011 9:35:59 PM Subject: Re: [Pw_forum] Using mixture of pseudo potential Hi, In my way,I usually test ecutrho = X*ecutwfc using scf or relax.I look the result of total energy or enthalpy. Such as: 1.ecutwfc=47 ecutrho=400, total energy= -290.983 2.ecutwfc=47 ecutrho=380, total energy= -290.993 So,I thought '2' is better than '1'. Bests, Pine. 2011/5/31 Vi Vo Dear All, > >In my calculation, I used a mixture of pseudo potentials, ie. norm-conserving pp >(NC pp) for one element and ultrasoft pp (US pp) for another. If I don't >specify ecutrho in the input, what will be the default value for ecutrho for the >ultrasoft pp. I know that for NC pp, ecutrho = 4*ecutwfc, but I do not know if >the same value is used for US pp. On the other hand, if I specify ecutrho = >8*ecutwfc, then does the same value apply to the NC pp. > >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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110531/1bc2fffd/attachment-0001.htm From ttduyle at gmail.com Tue May 31 19:29:36 2011 From: ttduyle at gmail.com (Duy Le) Date: Tue, 31 May 2011 13:29:36 -0400 Subject: [Pw_forum] Using mixture of pseudo potential In-Reply-To: <702418.87073.qm@web114505.mail.gq1.yahoo.com> References: <707981.30870.qm@web114501.mail.gq1.yahoo.com> <702418.87073.qm@web114505.mail.gq1.yahoo.com> Message-ID: On Tue, May 31, 2011 at 1:11 PM, Vi Vo wrote: > Hi Pine, > > Thank you.? Yes, I know that I have to do different tests for ecutrho and > ecutwfc, but my questions are different. I would like to know what is the > default setting for ecutrho the code would assume. I restate my question as > follows: > > If I forgot to specify the ecutrho, what default value of? ecutrho would the > code assume for US PP?? (I guess it still uses the default > ecutrho=4*ecutwfc). > > On the other hand, assuming I set the ecutrho=9*ecutwfc, does then the same > value of ecutrho=8*ecutwfc also apply to NC PP, or does the value of > ecutrho=4*ecutwfc will be used for NC PP. If there is nothing changed, according to the QE manual, the default factor of 4 does not depend on the type of potential. Also, there is only one ecutrho in a single calculation, and it is written in the output (most of parameters can be found in the output). > > Thank you, > -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" > Vi > > > ________________________________ > From: lucking-pine > To: PWSCF Forum > Sent: Mon, May 30, 2011 9:35:59 PM > Subject: Re: [Pw_forum] Using mixture of pseudo potential > > Hi, > In my way,I usually test ecutrho = X*ecutwfc using scf?or relax.I look the > result of total energy or enthalpy. > Such as: > 1.ecutwfc=47 ecutrho=400, total energy= -290.983 > 2.ecutwfc=47 ecutrho=380, total energy= -290.993 > So,I thought '2' is better than '1'. > > Bests, > Pine. > 2011/5/31 Vi Vo >> >> Dear All, >> >> In my calculation, I used a mixture of pseudo potentials, ie. >> norm-conserving pp (NC pp)? for one element and ultrasoft pp (US pp) for >> another.? If I don't specify ecutrho in the input, what will be the default >> value for ecutrho for the ultrasoft pp.? I know that for NC pp, ecutrho = >> 4*ecutwfc, but I do not know if the same value is used for US pp.? On the >> other hand, if I specify ecutrho = 8*ecutwfc, then does the same value apply >> to the NC pp. >> >> 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 >> > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From bdslipun at gmail.com Tue May 31 19:54:56 2011 From: bdslipun at gmail.com (bhabya sahoo) Date: Tue, 31 May 2011 23:24:56 +0530 Subject: [Pw_forum] (no subject) Message-ID: i am using quantum espresso can u how to know the gibbs free energy for unstable phases by any means in the quasi harmonic approximation because i can not the phase transition with temperture and how can i add anaharmonic contribution to phonon spectrum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110531/038070e6/attachment.htm From vovi47 at yahoo.com Tue May 31 20:24:19 2011 From: vovi47 at yahoo.com (Vi Vo) Date: Tue, 31 May 2011 11:24:19 -0700 (PDT) Subject: [Pw_forum] Using mixture of pseudo potential In-Reply-To: References: <707981.30870.qm@web114501.mail.gq1.yahoo.com> <702418.87073.qm@web114505.mail.gq1.yahoo.com> Message-ID: <356260.72190.qm@web114502.mail.gq1.yahoo.com> Hi Duy, Thanks. I see it in the output, but I was not sure how the ecutrho is set for different PPs. If only one ecutrho in set in one calculation, it is not a good idea to use a mixture of PPs, since then if ecutrho is set to be N*ecutwfc, the same value is used for NC PP. Vi ________________________________ From: Duy Le To: PWSCF Forum Sent: Tue, May 31, 2011 10:29:36 AM Subject: Re: [Pw_forum] Using mixture of pseudo potential On Tue, May 31, 2011 at 1:11 PM, Vi Vo wrote: > Hi Pine, > > Thank you. Yes, I know that I have to do different tests for ecutrho and > ecutwfc, but my questions are different. I would like to know what is the > default setting for ecutrho the code would assume. I restate my question as > follows: > > If I forgot to specify the ecutrho, what default value of ecutrho would the > code assume for US PP? (I guess it still uses the default > ecutrho=4*ecutwfc). > > On the other hand, assuming I set the ecutrho=9*ecutwfc, does then the same > value of ecutrho=8*ecutwfc also apply to NC PP, or does the value of > ecutrho=4*ecutwfc will be used for NC PP. If there is nothing changed, according to the QE manual, the default factor of 4 does not depend on the type of potential. Also, there is only one ecutrho in a single calculation, and it is written in the output (most of parameters can be found in the output). > > Thank you, > -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" > Vi > > > ________________________________ > From: lucking-pine > To: PWSCF Forum > Sent: Mon, May 30, 2011 9:35:59 PM > Subject: Re: [Pw_forum] Using mixture of pseudo potential > > Hi, > In my way,I usually test ecutrho = X*ecutwfc using scf or relax.I look the > result of total energy or enthalpy. > Such as: > 1.ecutwfc=47 ecutrho=400, total energy= -290.983 > 2.ecutwfc=47 ecutrho=380, total energy= -290.993 > So,I thought '2' is better than '1'. > > Bests, > Pine. > 2011/5/31 Vi Vo >> >> Dear All, >> >> In my calculation, I used a mixture of pseudo potentials, ie. >> norm-conserving pp (NC pp) for one element and ultrasoft pp (US pp) for >> another. If I don't specify ecutrho in the input, what will be the default >> value for ecutrho for the ultrasoft pp. I know that for NC pp, ecutrho = >> 4*ecutwfc, but I do not know if the same value is used for US pp. On the >> other hand, if I specify ecutrho = 8*ecutwfc, then does the same value apply >> to the NC pp. >> >> 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 >> > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110531/b68880aa/attachment.htm From ttduyle at gmail.com Tue May 31 21:42:44 2011 From: ttduyle at gmail.com (Duy Le) Date: Tue, 31 May 2011 15:42:44 -0400 Subject: [Pw_forum] Using mixture of pseudo potential In-Reply-To: <356260.72190.qm@web114502.mail.gq1.yahoo.com> References: <707981.30870.qm@web114501.mail.gq1.yahoo.com> <702418.87073.qm@web114505.mail.gq1.yahoo.com> <356260.72190.qm@web114502.mail.gq1.yahoo.com> Message-ID: On Tue, May 31, 2011 at 2:24 PM, Vi Vo wrote: > Hi Duy, > > Thanks.? I see it in the output, but I was not sure how the ecutrho is set > for different PPs. ? If only one ecutrho in set in one calculation, it is > not a good idea to use a mixture of PPs, since then if ecutrho is set to be > N*ecutwfc, the same value is used for NC PP. > I think it is not a good idea to have 2 or more ecutrho in a single calculation because I don't know why we need to and how to implement :-) -------------------------------------------------- Duy Le PhD Student Department of Physics University of Central Florida. "Men don't need hand to do things" > Vi > ________________________________ > From: Duy Le > To: PWSCF Forum > Sent: Tue, May 31, 2011 10:29:36 AM > Subject: Re: [Pw_forum] Using mixture of pseudo potential > > On Tue, May 31, 2011 at 1:11 PM, Vi Vo wrote: >> Hi Pine, >> >> Thank you.? Yes, I know that I have to do different tests for ecutrho and >> ecutwfc, but my questions are different. I would like to know what is the >> default setting for ecutrho the code would assume. I restate my question >> as >> follows: >> >> If I forgot to specify the ecutrho, what default value of? ecutrho would >> the >> code assume for US PP?? (I guess it still uses the default >> ecutrho=4*ecutwfc). >> >> On the other hand, assuming I set the ecutrho=9*ecutwfc, does then the >> same >> value of ecutrho=8*ecutwfc also apply to NC PP, or does the value of >> ecutrho=4*ecutwfc will be used for NC PP. > > If there is nothing changed, according to the QE manual, the default > factor of 4 does not depend on the type of potential. > Also, there is only one ecutrho in a single calculation, and it is > written in the output (most of parameters can be found in the output). > > >> >> Thank you, >> > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > >> Vi >> >> >> ________________________________ >> From: lucking-pine >> To: PWSCF Forum >> Sent: Mon, May 30, 2011 9:35:59 PM >> Subject: Re: [Pw_forum] Using mixture of pseudo potential >> >> Hi, >> In my way,I usually test ecutrho = X*ecutwfc using scf?or relax.I look the >> result of total energy or enthalpy. >> Such as: >> 1.ecutwfc=47 ecutrho=400, total energy= -290.983 >> 2.ecutwfc=47 ecutrho=380, total energy= -290.993 >> So,I thought '2' is better than '1'. >> >> Bests, >> Pine. >> 2011/5/31 Vi Vo >>> >>> Dear All, >>> >>> In my calculation, I used a mixture of pseudo potentials, ie. >>> norm-conserving pp (NC pp)? for one element and ultrasoft pp (US pp) for >>> another.? If I don't specify ecutrho in the input, what will be the >>> default >>> value for ecutrho for the ultrasoft pp.? I know that for NC pp, ecutrho = >>> 4*ecutwfc, but I do not know if the same value is used for US pp.? On the >>> other hand, if I specify ecutrho = 8*ecutwfc, then does the same value >>> apply >>> to the NC pp. >>> >>> 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 >>> >> >> >> _______________________________________________ >> 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 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > >